Gene Ontology
Names
More detailed information about this field from each metasource.
Gene Ontology
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: Biontology / Bioportal
version: 2022-10-07 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/GO
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
GO
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: Biontology / Bioportal
version: 2022-10-07 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/GO
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
Gene Ontology (GO)
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:12.564649
go
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:12.564649
Names
More detailed information about this field from each metasource.
Gene Ontology
metasource: Fairsharing.orgversion: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: Biontology / Bioportal
version: 2022-10-07 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/GO
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
GO
metasource: Fairsharing.orgversion: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: Biontology / Bioportal
version: 2022-10-07 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/GO
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
Gene Ontology (GO)
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.564649
go
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.564649
Other names: GO, Gene Ontology (GO), go
Names
More detailed information about this field from each metasource.
Gene Ontology
metasource: Fairsharing.orgversion: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: Biontology / Bioportal
version: 2022-10-07 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/GO
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
GO
metasource: Fairsharing.orgversion: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: Biontology / Bioportal
version: 2022-10-07 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/GO
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
Gene Ontology (GO)
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.564649
go
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.564649
The Gene Ontology resource provides a computational representation of our current scientific knowledge about the functions of genes (or, more properly, the protein and non-coding RNA molecules produced by genes) from many different organisms, from humans to bacteria. It describes our knowledge of the biological domain with respect to three aspects: Molecular Function (molecular-level activities performed by gene products), Cellular Component (locations in cellular structures in which a gene product performs a function, Biological Process (‘biological programs’ done by multiple molecular activities, not pathway). Those are semi-disjoint - no is_a link between the 3 but other like part_of and regulates exist.
Description
More detailed information about this field from each metasource.
The Gene Ontology resource provides a computational representation of our current scientific knowledge about the functions of genes (or, more properly, the protein and non-coding RNA molecules produced by genes) from many different organisms, from humans to bacteria. It describes our knowledge of the biological domain with respect to three aspects: Molecular Function (molecular-level activities performed by gene products), Cellular Component (locations in cellular structures in which a gene product performs a function, Biological Process (‘biological programs’ done by multiple molecular activities, not pathway). Those are semi-disjoint - no is_a link between the 3 but other like part_of and regulates exist.
metasource: BiŌkeanós-Medsourcingversion: 0.0.1:2022-11-04T13:34:25.975929
The Gene Ontology (GO) is a structured vocabulary for use by the research community for the annotation of genes, gene products and sequences. The GO defines concepts/classes used to describe gene function and relationships between these concepts.
metasource: Fairsharing.orgversion: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Provides structured controlled vocabularies for the annotation of gene products with respect to their molecular function, cellular component, and biological role. The Gene Ontology consists of three Vocabularies.
metasource: Biontology / Bioportalversion: 2022-10-07 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/GO
The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two years. The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs. In addition, we describe the impacts of several collaborations to refine GO and report a 10% increase in the number of GO annotations, a 25% increase in annotated gene products, and over 9,400 new scientific articles annotated. As the project matures, we continue our efforts to review older annotations in light of newer findings, and, to maintain consistency with other ontologies. As a result, 20 000 annotations derived from experimental data were reviewed, corresponding to 2.5% of experimental GO annotations. The website (http://geneontology.org) was redesigned for quick access to documentation, downloads and tools. To maintain an accurate resource and support traceability and reproducibility, we have made available a historical archive covering the past 15 years of GO data with a consistent format and file structure for both the ontology and annotations.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
The Gene Ontology Consortium continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences. Several new relationship types have been introduced and used, along with existing relationships, to create links between and within the domains. Gene product annotation continues to increase both in the number of total annotations and in species coverage. Tools have seen major improvements in functionality, speed and usage.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.564649
Webpage:
http://geneontology.orgWebpage
More detailed information about this field from each metasource.
http://geneontology.org
metasource: BiŌkeanós-Medsourcingversion: 0.0.1:2022-11-04T13:34:25.975929
http://www.geneontology.org
metasource: Fairsharing.orgversion: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: Biontology / Bioportal
version: 2022-10-07 extracted_at: 2022-11-04T11:10:15.597147, http://bioportal.bioontology.org/ontologies/GO
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
http://www.geneontology.org/
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.564649
Licence:
Name: Creative Commons Attribution v4.0Licence name
More detailed information about this field from each metasource.
Creative Commons Attribution v4.0
metasource: BiŌkeanós-Medsourcingversion: 0.0.1:2022-11-04T13:34:25.975929
Creative Commons Attribution 4.0 International (CC BY 4.0)
metasource: Fairsharing.orgversion: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Licence URL
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http://geneontology.org/docs/go-citation-policy/
metasource: BiŌkeanós-Medsourcingversion: 0.0.1:2022-11-04T13:34:25.975929
https://creativecommons.org/licenses/by/4.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Publications:
(12)
Publications
More detailed information about this field from each metasource.
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
PMID: 10802651
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
The Gene Ontology (GO) database and informatics resource
PMID: 14681407
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
The Gene Ontology Resource: 20 years and still GOing strong
PMID: 30395331
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Gene Ontology Consortium: going forward
PMID: 25428369
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Gene Ontology annotations and resources
PMID: 23161678
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
The Gene Ontology in 2010: extensions and refinements
PMID: 19920128
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:12.564649
The Gene Ontology: enhancements for 2011
PMID: 22102568
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:12.564649
The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species
PMID: 19578431
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology
PMID: 23895341
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3037419/
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323945/
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929
https://doi.org/10.1093/nar/gkaa1113
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
PMID: 10802651
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
The Gene Ontology (GO) database and informatics resource
PMID: 14681407
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
The Gene Ontology Resource: 20 years and still GOing strong
PMID: 30395331
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Gene Ontology Consortium: going forward
PMID: 25428369
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Gene Ontology annotations and resources
PMID: 23161678
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
The Gene Ontology in 2010: extensions and refinements
PMID: 19920128
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:12.564649
The Gene Ontology: enhancements for 2011
PMID: 22102568
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:12.564649
The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species
PMID: 19578431
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology
PMID: 23895341
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3037419/
metasource: BiŌkeanós-Medsourcingversion: 0.0.1:2022-11-04T13:34:25.975929
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323945/
metasource: BiŌkeanós-Medsourcingversion: 0.0.1:2022-11-04T13:34:25.975929
https://doi.org/10.1093/nar/gkaa1113
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
PubMed citations: 9999.
9999 articles citing: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
Temporally divergent regulatory mechanisms govern neuronal diversification and maturation in the mouse and marmoset neocortex. PMID:35915179
Genome sequence and comparative analysis of fungal antagonistic strain Bacillus velezensis LJBV19. PMID:35913660
Transcriptome and Metabolome Analyses Reveal the Involvement of Multiple Pathways in Flowering Intensity in Mango. PMID:35909785
The Construction and Analysis of Infiltrating Immune Cell and ceRNA Networks in Diabetic Foot Ulcer. PMID:35909542
FLASHIda enables intelligent data acquisition for top-down proteomics to boost proteoform identification counts. PMID:35906205
Mutations in SORL1 and MTHFDL1 possibly contribute to the development of Alzheimer's disease in a multigenerational Colombian Family. PMID:35905044
Epigenetically silenced apoptosis-associated tyrosine kinase (AATK) facilitates a decreased expression of Cyclin D1 and WEE1, phosphorylates TP53 and reduces cell proliferation in a kinase-dependent manner. PMID:35902728
Dynamic Transcriptomic Profiling During Liver Development in Schizothorax Prenanti. PMID:35899028
Shared Genetics and Causality Between Decaffeinated Coffee Consumption and Neuropsychiatric Diseases: A Large-Scale Genome-Wide Cross-Trait Analysis and Mendelian Randomization Analysis. PMID:35898629
Bioinformatics Analysis Identifies Potential Ferroptosis Key Gene in Type 2 Diabetic Islet Dysfunction. PMID:35898457
Characterizing the extracellular matrix transcriptome of cervical, endometrial, and uterine cancers. PMID:35898192
Pro-Survival Factor EDEM3 Confers Therapy Resistance in Prostate Cancer. PMID:35897761
Taste 2 Receptor Is Involved in Differentiation of 3T3-L1 Preadipocytes. PMID:35897692
In silico development and experimental validation of a novel 7-gene signature based on PI3K pathway-related genes in bladder cancer. PMID:35896848
Ribosomal RNA-Depletion Provides an Efficient Method for Successful Dual RNA-Seq Expression Profiling of a Marine Sponge Holobiont. PMID:35895230
Pan-Cancer Analysis Reveals the Prognostic Potential of the THAP9/THAP9-AS1 Sense-Antisense Gene Pair in Human Cancers. PMID:35893234
Activation of Oncogenic and Immune-Response Pathways Is Linked to Disease-Specific Survival in Merkel Cell Carcinoma. PMID:35892849
Use of Autoreactive Antibodies in Blood of Patients with Pancreatic Intraductal Papillary Mucinous Neoplasms (IPMN) for Grade Distinction and Detection of Malignancy. PMID:35892825
AKT1 Transcriptomic Landscape in Breast Cancer Cells. PMID:35892586
Genome-Wide Association Analysis and Genetic Parameters for Feed Efficiency and Related Traits in Yorkshire and Duroc Pigs. PMID:35892552
An accurate prediction model of digenic interaction for estimating pathogenic gene pairs of human diseases. PMID:35891796
The Protective Effect of Edaravone on TDP-43 Plus Oxidative Stress-Induced Neurotoxicity in Neuronal Cells: Analysis of Its Neuroprotective Mechanisms Using RNA Sequencing. PMID:35890141
Characterization of Cronobacter sakazakii Strains Originating from Plant-Origin Foods Using Comparative Genomic Analyses and Zebrafish Infectivity Studies. PMID:35889115
Transcriptional Profiling of Leishmania infantum Infected Dendritic Cells: Insights into the Role of Immunometabolism in Host-Parasite Interaction. PMID:35888991
A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics. PMID:35888710
Role of PsnWRKY70 in Regulatory Network Response to Infection with Alternaria alternata (Fr.) Keissl in Populus. PMID:35886886
REDfly: An Integrated Knowledgebase for Insect Regulatory Genomics. PMID:35886794
Systematic Functional Annotation Workflow for Insects. PMID:35886762
A Narrative Literature Review of Natural Language Processing Applied to the Occupational Exposome. PMID:35886395
Identification of New Toxicity Mechanisms in Drug-Induced Liver Injury through Systems Pharmacology. PMID:35886075
Identification of Differential Expression Genes between Volume and Pressure Overloaded Hearts Based on Bioinformatics Analysis. PMID:35886059
Genomic Characterization by Whole-Exome Sequencing of Hypermobility Spectrum Disorder. PMID:35886052
Exploring the Mutational Landscape of Isolated Congenital Heart Defects: An Exome Sequencing Study Using Cardiac DNA. PMID:35885997
Genome-Wide Evolutionary Analysis of Putative Non-Specific Herbicide Resistance Genes and Compilation of Core Promoters between Monocots and Dicots. PMID:35885954
Whole Transcriptome Sequencing Reveals Drought Resistance-Related Genes in Upland Cotton. PMID:35885942
Comparative Transcriptome Profiling Reveals the Genes Involved in Storage Root Expansion in Sweetpotato (Ipomoea batatas (L.) Lam.). PMID:35885939
EGFAFS: A Novel Feature Selection Algorithm Based on Explosion Gravitation Field Algorithm. PMID:35885095
New Evidence of Tiger Subspecies Differentiation and Environmental Adaptation: Comparison of the Whole Genomes of the Amur Tiger and the South China Tiger. PMID:35883364
Gene Updater: a web tool that autocorrects and updates for Excel misidentified gene names. PMID:35882976
Transcriptomic and proteomic retinal pigment epithelium signatures of age-related macular degeneration. PMID:35882847
Aging endometrium in young women: molecular classification of endometrial aging-based markers in women younger than 35 years with recurrent implantation failure. PMID:35881273
Genome-Wide Analysis of microRNAs Identifies the Lipid Metabolism Pathway to Be a Defining Factor in Adipose Tissue From Different Sheep. PMID:35880040
Pan-cancer integrative analysis of whole-genome De novo somatic point mutations reveals 17 cancer types. PMID:35879674
Integration of probabilistic functional networks without an external Gold Standard. PMID:35879662
A supervised protein complex prediction method with network representation learning and gene ontology knowledge. PMID:35879648
Characterization of methylation patterns associated with lifestyle factors and vitamin D supplementation in a healthy elderly cohort from Southwest Sweden. PMID:35879377
Dynamic changes in O-GlcNAcylation regulate osteoclast differentiation and bone loss via nucleoporin 153. PMID:35879285
Mechanisms of Action of Semen Ziziphi spinosae in the Treatment of Tourette Syndrome. PMID:35875687
Venom composition of Trimeresurus albolabris, T. insularis, T. puniceus and T. purpureomaculatus from Indonesia. PMID:35875602
Methylated RNA Immunoprecipitation Sequencing Reveals the m6A Landscape in Oral Squamous Cell Carcinoma. PMID:35874897
The Culture Dish Surface Influences the Phenotype and Dissociation Strategy in Distinct Mouse Macrophage Populations. PMID:35874686
Protocol for establishing a protein-protein interaction network using tandem affinity purification followed by mass spectrometry in mammalian cells. PMID:35874475
Chromatin Separation Regulators Predict the Prognosis and Immune Microenvironment Estimation in Lung Adenocarcinoma. PMID:35873497
Exploration of the Mechanisms of Differential Indole Alkaloid Biosynthesis in Dedifferentiated and Cambial Meristematic Cells of Catharanthus roseus Using Transcriptome Sequencing. PMID:35873460
Unveiling Co-Infection in Cystic Fibrosis Airways: Transcriptomic Analysis of Pseudomonas aeruginosa and Staphylococcus aureus Dual-Species Biofilms. PMID:35873457
Interspecies Isobaric Labeling-Based Quantitative Proteomics Reveals Protein Changes in the Ovary of Aedes aegypti Coinfected With ZIKV and Wolbachia. PMID:35873163
orsum: a Python package for filtering and comparing enrichment analyses using a simple principle. PMID:35870894
Gene expression profiling before and after internode culture for adventitious shoot formation in ipecac. PMID:35869421
Identification of microRNAs and their target genes related to the accumulation of anthocyanin in purple potato tubers (Solanum tuberosum). PMID:35865074
Cold exposure induces lipid dynamics and thermogenesis in brown adipose tissue of goats. PMID:35864448
Heterogeneous nuclear ribonucleoprotein U (HNRNPU) safeguards the developing mouse cortex. PMID:35864088
Network Pharmacology-Based Prediction and Pharmacological Validation of Effects of Astragali Radix on Acetaminophen-Induced Liver Injury. PMID:35860733
Increased Development of Th1, Th17, and Th1.17 Cells Under T1 Polarizing Conditions in Juvenile Idiopathic Arthritis. PMID:35860254
Virofree, an Herbal Medicine-Based Formula, Interrupts the Viral Infection of Delta and Omicron Variants of SARS-CoV-2. PMID:35860023
N6-methyladenosine modulates long non-coding RNA in the developing mouse heart. PMID:35858921
Cancer-associated fibroblast-derived exosomal microRNA-20a suppresses the PTEN/PI3K-AKT pathway to promote the progression and chemoresistance of non-small cell lung cancer. PMID:35857905
Revealing the difference of α-amylase and CYP6AE76 gene between polyphagous Conogethes punctiferalis and oligophagous C. pinicolalis by multiple-omics and molecular biological technique. PMID:35854244
TMT-based proteomic analysis of liquorice root in response to drought stress. PMID:35854220
Prospective role and immunotherapeutic targets of sideroflexin protein family in lung adenocarcinoma: evidence from bioinformatics validation. PMID:35851932
Analysis on the desert adaptability of indigenous sheep in the southern edge of Taklimakan Desert. PMID:35851076
Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer's disease. PMID:35849618
From Transcriptomics, Metabolomics to Functional Studies: Extracellular ATP Induces TGF-β-Like Epithelial Mesenchymal Transition in Lung Cancer Cells. PMID:35847855
A Computational Framework to Characterize the Cancer Drug Induced Effect on Aging Using Transcriptomic Data. PMID:35847024
Identification of a Prognostic Model Based on Fatty Acid Metabolism-Related Genes of Head and Neck Squamous Cell Carcinoma. PMID:35846149
Transcriptomic Insight into Viviparous Growth in Water Lily. PMID:35845943
Excessive Sodium Intake Leads to Cardiovascular Disease by Promoting Sex-Specific Dysfunction of Murine Heart. PMID:35845798
Network pharmacology-based analysis of the effects of puerarin on sarcopenia. PMID:35845507
Ferroptosis and Autophagy-Related Genes in the Pathogenesis of Ischemic Cardiomyopathy. PMID:35845045
Single-Cell RNA Sequencing Unravels Upregulation of Immune Cell Crosstalk in Relapsed Pediatric Ependymoma. PMID:35844565
Isolation, Identification, and Investigation of Pathogenic Bacteria From Common Carp (Cyprinus carpio) Naturally Infected With Plesiomonas shigelloides. PMID:35844551
Diagnostic and Predictive Values of Ferroptosis-Related Genes in Child Sepsis. PMID:35844488
Time and phenotype-dependent transcriptome analysis in AAV-TGFβ1 and Bleomycin-induced lung fibrosis models. PMID:35842487
Protein expression profiling identifies a prognostic model for ovarian cancer. PMID:35840928
MiR-30c-1-3p targets matrix metalloproteinase 9 involved in the rupture of abdominal aortic aneurysms. PMID:35840740
Vascular Regulation by Super Enhancer-Derived LINC00607. PMID:35837599
De novo Transcriptome Analysis of Drought-Adapted Cluster Bean (Cultivar RGC-1025) Reveals the Wax Regulatory Genes Involved in Drought Resistance. PMID:35837463
Genome-Wide Dissection of the Genetic Basis for Drought Tolerance in Gossypium hirsutum L. Races. PMID:35837453
Dissecting the Genetic Structure of Maize Leaf Sheaths at Seedling Stage by Image-Based High-Throughput Phenotypic Acquisition and Characterization. PMID:35837446
A TP53 Related Immune Prognostic Model for the Prediction of Clinical Outcomes and Therapeutic Responses in Lung Adenocarcinoma. PMID:35837383
Identification and Validation of Autophagy-Related Genes in Primary Ovarian Insufficiency by Gene Expression Profile and Bioinformatic Analysis. PMID:35837294
Weighted Gene Correlation Network Analysis (WGCNA) of Arabidopsis Somatic Embryogenesis (SE) and Identification of Key Gene Modules to Uncover SE-Associated Hub Genes. PMID:35837132
Arecoline promotes proliferation and migration of human HepG2 cells through activation of the PI3K/AKT/mTOR pathway. PMID:35836300
Differential expression profile and in-silico functional analysis of long noncoding RNA and mRNA in duck embryo fibroblasts infected with duck plague virus. PMID:35836133
Comparative transcriptomics identifies candidate genes involved in the evolutionary transition from dehiscent to indehiscent fruits in Lepidium (Brassicaceae). PMID:35836106
Transcriptome analysis and phenotyping of walnut seedling roots under nitrogen stresses. PMID:35835799
Antioxidant Mechanism of Lactiplantibacillus plantarum KM1 Under H2O2 Stress by Proteomics Analysis. PMID:35832808
Comprehensive Genome-Wide Identification and Expression Profiling of Eceriferum (CER) Gene Family in Passion Fruit (Passiflora edulis) Under Fusarium kyushuense and Drought Stress Conditions. PMID:35832215
Chromosome-scale assembly and annotation of the perennial ryegrass genome. PMID:35831814
Quantitative proteomics analysis to assess protein expression levels in the ovaries of pubescent goats. PMID:35831802
Selective expression of variant surface antigens enables Plasmodium falciparum to evade immune clearance in vivo. PMID:35831417
Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery. PMID:35831314
Multi-omics profiling of collagen-induced arthritis mouse model reveals early metabolic dysregulation via SIRT1 axis. PMID:35821263
The heterogeneous pharmacological medical biochemical network PharMeBINet. PMID:35821017
Alternative splicing patterns reveal prognostic indicator in muscle-invasive bladder cancer. PMID:35820925
Spatially resolved proteomic map shows that extracellular matrix regulates epidermal growth. PMID:35817779
Proteomic characterisation of triple negative breast cancer cells following CDK4/6 inhibition. PMID:35817775
The evolutionary history of human spindle genes includes back-and-forth gene flow with Neandertals. PMID:35816093
Features and Colonization Strategies of Enterococcus faecalis in the Gut of Bombyx mori. PMID:35814682
Dengue Virus-2 Infection Affects Fecundity and Elicits Specific Transcriptional Changes in the Ovaries of Aedes aegypti Mosquitoes. PMID:35814655
Beneficial Effect of Selenium Doped Carbon Quantum Dots Supplementation on the in vitro Development Competence of Ovine Oocytes. PMID:35814612
Exosome-mediated transduction of mechanical force regulates prostate cancer migration via microRNA. PMID:35812347
Integrated Transcriptome Profiling Identifies Prognostic Hub Genes as Therapeutic Targets of Glioblastoma: Evidenced by Bioinformatics Analysis. PMID:35811900
Metabolome and transcriptome profiling reveal regulatory network and mechanism of flavonoid biosynthesis during color formation of Dioscorea cirrhosa L. PMID:35811818
Identification and Validation of Candidate Gene Module Along With Immune Cells Infiltration Patterns in Atherosclerosis Progression to Plaque Rupture via Transcriptome Analysis. PMID:35811739
Lilac (Syringa oblata) genome provides insights into its evolution and molecular mechanism of petal color change. PMID:35810211
Single-cell RNA sequencing reveals localized tumour ablation and intratumoural immunostimulant delivery potentiate T cell mediated tumour killing. PMID:35808806
Lim Domain Binding 3 (Ldb3) Identified as a Potential Marker of Cardiac Extracellular Vesicles. PMID:35806378
Genome Assembly and Analysis of the Flavonoid and Phenylpropanoid Biosynthetic Pathways in Fingerroot Ginger (Boesenbergia rotunda). PMID:35806276
Semantics of Dairy Fermented Foods: A Microbiologist's Perspective. PMID:35804753
Gene function prediction in five model eukaryotes exclusively based on gene relative location through machine learning. PMID:35803984
Upper airway gene expression shows a more robust adaptive immune response to SARS-CoV-2 in children. PMID:35803954
Lipolysis regulates major transcriptional programs in brown adipocytes. PMID:35803907
The role of toll-like receptors (TLRs) in pan-cancer. PMID:35801728
New Mutations in cls Lead to Daptomycin Resistance in a Clinical Vancomycin- and Daptomycin-Resistant Enterococcus faecium Strain. PMID:35801099
Functional Heterogeneity of the Young and Old Duplicate Genes in Tung Tree (Vernicia fordii). PMID:35800614
Identification of Potential miRNA-mRNA Regulatory Network in Denervated Muscular Atrophy by Bioinformatic Analysis. PMID:35800215
Tandem Mass Tag-based proteomics analysis reveals the vital role of inflammation in traumatic brain injury in a mouse model. PMID:35799536
Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies. PMID:35799218
Biomimetic generation of the strongest known biomaterial found in limpet tooth. PMID:35798724
RNA-Seq and Gene Ontology Analysis Reveal Differences Associated With Low R/FR-Induced Shade Responses in Cultivated Lentil and a Wild Relative. PMID:35795209
Identification of Immune-Related Gene Signature in Stanford Type A Aortic Dissection. PMID:35795203
A statistical, reference-free algorithm subsumes myriad problems in genome science and enables novel discovery. PMID:35794890
Diet and feeding pattern modulate diurnal dynamics of the ileal microbiome and transcriptome. PMID:35793637
Increased CSF-decorin predicts brain pathological changes driven by Alzheimer's Aβ amyloidosis. PMID:35787306
A Comprehensive Pan-Cancer Analysis of the Tumorigenic Role of Matrix Metallopeptidase 7 (MMP7) Across Human Cancers. PMID:35785154
Investigation of the Pharmacological Effect and Mechanism of Jinbei Oral Liquid in the Treatment of Idiopathic Pulmonary Fibrosis Using Network Pharmacology and Experimental Validation. PMID:35784749
Temporal Whole-Transcriptomic Analysis of Characterized In Vitro and Ex Vivo Primary Nasal Epithelia. PMID:35784475
Exposure of Keratinocytes to Candida Albicans in the Context of Atopic Milieu Induces Changes in the Surface Glycosylation Pattern of Small Extracellular Vesicles to Enhance Their Propensity to Interact With Inhibitory Siglec Receptors. PMID:35784319
A consensus view of the proteome of the last universal common ancestor. PMID:35784055
Integrated Metabolomics and Transcriptome Analyses Unveil Pathways Involved in Sugar Content and Rind Color of Two Sugarcane Varieties. PMID:35783968
Genome-scale phylogeography resolves the native population structure of the Asian longhorned beetle, Anoplophora glabripennis (Motschulsky). PMID:35782014
The splicing factor RBM17 drives leukemic stem cell maintenance by evading nonsense-mediated decay of pro-leukemic factors. PMID:35781533
Refining bulk segregant analyses: ontology-mediated discovery of flowering time genes in Brassica oleracea. PMID:35780674
Transcriptomic analysis of starch accumulation patterns in different glutinous sorghum seeds. PMID:35778525
Differential regulation of mRNAs and lncRNAs related to lipid metabolism in Duolang and Small Tail Han sheep. PMID:35778462
The Bioinformatic Study Uncovers Probable Critical Genes Involved in the Pathophysiology of Biliary Atresia. PMID:35774294
Identification of hub genes and regulatory networks in histologically unstable carotid atherosclerotic plaque by bioinformatics analysis. PMID:35773742
N(6)-methyladenosine methylation-regulated polo-like kinase 1 cell cycle homeostasis as a potential target of radiotherapy in pancreatic adenocarcinoma. PMID:35773310
A versatile new tool derived from a bacterial deubiquitylase to detect and purify ubiquitylated substrates and their interacting proteins. PMID:35771886
Icariside II Restores Vascular Smooth Muscle Cell Contractile Phenotype by Enhancing the Focal Adhesion Signaling Pathway in the Rat Vascular Remodeling Model. PMID:35770073
Identification of stress-related genes by co-expression network analysis based on the improved turbot genome. PMID:35768602
GREM1 is required to maintain cellular heterogeneity in pancreatic cancer. PMID:35768509
Genome sequence and pathogenicity of Vibrio vulnificus strain MCCC 1A08743 isolated from contaminated prawns. PMID:35766638
DIP2 is a unique regulator of diacylglycerol lipid homeostasis in eukaryotes. PMID:35766356
Integrated Multi-Omics Analysis Model to Identify Biomarkers Associated With Prognosis of Breast Cancer. PMID:35761863
Inferring functional communities from partially observed biological networks exploiting geometric topology and side information. PMID:35760826
DeepGOZero: improving protein function prediction from sequence and zero-shot learning based on ontology axioms. PMID:35758802
Exploring automatic inconsistency detection for literature-based gene ontology annotation. PMID:35758780
Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions. PMID:35758606
GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba. PMID:35758513
Dysregulation of Neuropeptide and Tau Peptide Signatures in Human Alzheimer's Disease Brain. PMID:35758417
Regional Downregulation of Dopamine Receptor D1 in Bilateral Dorsal Lateral Geniculate Nucleus of Monocular Form-Deprived Amblyopia Models. PMID:35757538
Full-Length Transcriptomics Reveals Complex Molecular Mechanism of Salt Tolerance in Bromus inermis L. PMID:35755679
Orrella daihaiensis sp. nov., a bacterium isolated from Daihai Lake in Inner Mongolia. PMID:35751751
A chromosome-level genome assembly of the orange wheat blossom midge, Sitodiplosis mosellana Géhin (Diptera: Cecidomyiidae) provides insights into the evolution of a detoxification system. PMID:35751604
SAPFIR: A webserver for the identification of alternative protein features. PMID:35751026
Calculating genetic risk for dysfunction in pleiotropic biological processes using whole exome sequencing data. PMID:35751013
Pathway importance by graph convolutional network and Shapley additive explanations in gene expression phenotype of diffuse large B-cell lymphoma. PMID:35749395
Bioinformatics Approach Predicts Candidate Targets for SARS-CoV-2 Infections to COPD Patients. PMID:35747501
Transcriptome and Metabolome Analysis of Upland Cotton (Gossypium hirsutum) Seed Pretreatment with MgSO4 in Response to Salinity Stress. PMID:35743952
Comprehensive RNA Expression Analysis Revealed Biological Functions of Key Gene Sets and Identified Disease-Associated Cell Types Involved in Rat Traumatic Brain Injury. PMID:35743506
Gene Expression Profiling in Abdominal Aortic Aneurysms. PMID:35743331
Dietary Long-Chain n-3 Polyunsaturated Fatty Acid Supplementation Alters Electrophysiological Properties in the Nucleus Accumbens and Emotional Behavior in Naïve and Chronically Stressed Mice. PMID:35743093
Transcriptome Analysis Reveals the Regulatory Networks of Cytokinin in Promoting Floral Feminization in Castanea henryi. PMID:35742833
Identification and Regulatory Network Analysis of Genes Related to Reproductive Performance in the Hypothalamus and Pituitary of Angus Cattle. PMID:35741727
Transcriptomics Integrated with Metabolomics Unveil Carotenoids Accumulation and Correlated Gene Regulation in White and Yellow-Fleshed Turnip (Brassica rapa ssp. rapa). PMID:35741715
The Osmoprotectant Switch of Potassium to Compatible Solutes in an Extremely Halophilic Archaea Halorubrum kocurii 2020YC7. PMID:35741701
A Quantitative Proteomic Approach Explores the Possible Mechanisms by Which the Small Molecule Stemazole Promotes the Survival of Human Neural Stem Cells. PMID:35741576
Cryopreservation of Endangered Ornamental Plants and Fruit Crops from Tropical and Subtropical Regions. PMID:35741368
Predicting prognosis and clinical features of the tumor microenvironment based on ferroptosis score in patients with breast cancer. PMID:35739315
PD-L1 blockade restores CAR T cell activity through IFN-γ-regulation of CD163+ M2 macrophages. PMID:35738799
Transcriptome analysis reveals regulation mechanism of methyl jasmonate-induced terpenes biosynthesis in Curcuma wenyujin. PMID:35737688
Transcriptomics and Metabolomics Analyses Reveal High Induction of the Phenolamide Pathway in Tomato Plants Attacked by the Leafminer Tuta absoluta. PMID:35736416
Genome Analysis of a Novel Polysaccharide-Degrading Bacterium Paenibacillus algicola and Determination of Alginate Lyases. PMID:35736191
Pan-Genomes Provide Insights into the Genetic Basis of Auricularia heimuer Domestication. PMID:35736064
Exploration of the Nurse Shark (Ginglymostoma cirratum) Plasma Immunoproteome Using High-Resolution LC-MS/MS. PMID:35734164
The chromosome-level genome for Toxicodendron vernicifluum provides crucial insights into Anacardiaceae evolution and urushiol biosynthesis. PMID:35733792
Antennal transcriptome analysis of olfactory genes and tissue expression profiling of odorant binding proteins in Semanotus bifasciatus (cerambycidae: coleoptera). PMID:35733103
Single-nucleus profiling of human dilated and hypertrophic cardiomyopathy. PMID:35732739
Integrative transcriptome-wide analysis of atopic dermatitis for drug repositioning. PMID:35729261
Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests. PMID:35727987
Systematic identification of molecular mediators of interspecies sensing in a community of two frequently coinfecting bacterial pathogens. PMID:35727825
Detecting Structural Variants and Associated Gene Presence-Absence Variation Phenomena in the Genomes of Marine Organisms. PMID:35727540
Increased expression of tribbles homolog 3 predicts poor prognosis and correlates with tumor immunity in clear cell renal cell carcinoma: a bioinformatics study. PMID:35726370
Integrated Bioinformatics Analysis for Identifying the Significant Genes as Poor Prognostic Markers in Gastric Adenocarcinoma. PMID:35726219
Deep embeddings to comprehend and visualize microbiome protein space. PMID:35725732
Human follicular mites: Ectoparasites becoming symbionts. PMID:35724423
Developing Biliary Atresia-like Model by Treating Human Liver Organoids with Polyinosinic:Polycytidylic Acid (Poly (I:C)). PMID:35723330
Integrated Analysis of Glutathione Metabolic Pathway in Pancreatic Cancer. PMID:35721499
Identification of a neural development gene expression signature in colon cancer stem cells reveals a role for EGR2 in tumorigenesis. PMID:35720265
Integrating Network Pharmacology and Experimental Validation to Explore the Key Mechanism of Gubitong Recipe in the Treatment of Osteoarthritis. PMID:35720033
A Robust Immuno-Prognostic Model of Non-Muscle-Invasive Bladder Cancer Indicates Dynamic Interaction in Tumor Immune Microenvironment Contributes to Cancer Progression. PMID:35719408
Identification of potential gene markers in gestational diabetes mellitus. PMID:35718998
Longitudinal plasma proteomic profiling of patients with non-small cell lung cancer undergoing immune checkpoint blockade. PMID:35718373
The TIP60-ATM axis regulates replication fork stability in BRCA-deficient cells. PMID:35717336
Impact of circadian time of dosing on cardiomyocyte-autonomous effects of glucocorticoids. PMID:35717025
Proteomics Reveals Long-Term Alterations in Signaling and Metabolic Pathways Following Both Myocardial Infarction and Chemically Induced Denervation. PMID:35716295
Ascorbate peroxidase-mediated in situ labelling of proteins in secreted exosomes. PMID:35716063
Protein Subcellular Localization Prediction Model Based on Graph Convolutional Network. PMID:35713780
Molecular Signatures of Response to Mecasermin in Children With Rett Syndrome. PMID:35712450
Identification of Core Genes and Screening of Potential Targets in Intervertebral Disc Degeneration Using Integrated Bioinformatics Analysis. PMID:35711934
SFARI genes and where to find them; modelling Autism Spectrum Disorder specific gene expression dysregulation with RNA-seq data. PMID:35710789
A hexa-species transcriptome atlas of mammalian embryogenesis delineates metabolic regulation across three different implantation modes. PMID:35710749
Genome-wide association study of musical beat synchronization demonstrates high polygenicity. PMID:35710621
Empowering the discovery of novel target-disease associations via machine learning approaches in the open targets platform. PMID:35710324
CaveCrawler: an interactive analysis suite for cavefish bioinformatics. PMID:35708643
Computation-Based Discovery of Potential Targets for Rheumatoid Arthritis and Related Molecular Screening and Mechanism Analysis of Traditional Chinese Medicine. PMID:35707715
An Insight Into Pentatricopeptide-Mediated Chloroplast Necrosis via microRNA395a During Rhizoctonia solani Infection. PMID:35706449
Analysis and pharmacological modulation of senescence in human epithelial stem cells. PMID:35706382
Genome-wide translation control analysis of developing human neurons. PMID:35706057
Proteome analysis of urinary biomarkers in a cigarette smoke-induced COPD rat model. PMID:35705945
Combined transcriptome and metabolome analysis of Nerium indicum L. elaborates the key pathways that are activated in response to witches' broom disease. PMID:35701735
Anticancer effects of herbal medicines in pancreatic ductal adenocarcinoma through modulation of steroid hormone response proteins. PMID:35701649
Tree House Explorer: A Novel Genome Browser for Phylogenomics. PMID:35700217
The onset of PI3K-related vascular malformations occurs during angiogenesis and is prevented by the AKT inhibitor miransertib. PMID:35695059
The fourth scientific discovery paradigm for precision medicine and healthcare: Challenges ahead. PMID:35694156
Trained Immunity in Perivascular Adipose Tissue of Abdominal Aortic Aneurysm-A Novel Concept for a Still Elusive Disease. PMID:35693946
Identification of Hub Genes in Colorectal Adenocarcinoma by Integrated Bioinformatics. PMID:35693937
Identification of Four Novel Prognostic Biomarkers and Construction of Two Nomograms in Adrenocortical Carcinoma: A Multi-Omics Data Study via Bioinformatics and Machine Learning Methods. PMID:35693556
Identification of Potential Biomarkers for Ryanodine Receptor 1 (RYR1) Mutation-Associated Myopathies Using Bioinformatics Approach. PMID:35692882
Circulating Exosomal miR-144-3p from Crohn's Disease Patients Inhibits Human Umbilical Vein Endothelial Cell Function by Targeting FN1. PMID:35692876
Screening the Potential Biomarkers of COVID-19-Related Thrombosis Through Bioinformatics Analysis. PMID:35692833
Putative Biomarkers in Tears for Diabetic Retinopathy Diagnosis. PMID:35692536
Overexpression of lncRNA-Gm2044 in spermatogonia impairs spermatogenesis in partial seminiferous tubules. PMID:35691049
Novel App knock-in mouse model shows key features of amyloid pathology and reveals profound metabolic dysregulation of microglia. PMID:35690868
Omics-based integrated analysis identified IKZF2 as a biomarker associated with lupus nephritis. PMID:35688845
Connectivity Mapping Using a Novel sv2a Loss-of-Function Zebrafish Epilepsy Model as a Powerful Strategy for Anti-epileptic Drug Discovery. PMID:35686059
Analysis of the landscape of human enhancer sequences in biological databases. PMID:35685360
Bioinformatics Analysis for Identifying Differentially Expressed MicroRNAs Derived from Plasma Exosomes Associated with Radiotherapy Resistance in Non-Small-Cell Lung Cancer. PMID:35685351
The dynamic cellular and molecular features during the development of radiation proctitis revealed by transcriptomic profiling in mice. PMID:35681125
Ptpn1 deletion protects oval cells against lipoapoptosis by favoring lipid droplet formation and dynamics. PMID:35681014
Translocating proteins compartment-specifically alter the fate of epithelial-mesenchymal transition in a compartmentalized Boolean network model. PMID:35680961
A transcriptomic atlas underlying developmental plasticity of seasonal forms of Bicyclus anynana butterflies. PMID:35679434
Effects of Lightning on Rhizosphere Soil Properties, Bacterial Communities, and Active Components of Camellia sinensis var. assamica. PMID:35677900
Interaction Between Cecal Metabolites and Liver Lipid Metabolism Pathways During Induced Molting in Laying Hens. PMID:35677092
Comparative transcriptome analysis reveals a rapid response to phosphorus deficiency in a phosphorus-efficient rice genotype. PMID:35676419
Estrogen hormone is an essential sex factor inhibiting inflammation and immune response in COVID-19. PMID:35676404
3-oxo-C12:2-HSL, quorum sensing molecule from human intestinal microbiota, inhibits pro-inflammatory pathways in immune cells via bitter taste receptors. PMID:35676403
Integrative PheWAS analysis in risk categorization of major depressive disorder and identifying their associations with genetic variants using a latent topic model approach. PMID:35676267
Neuropilin-1 is present on Foxp3+ T regulatory cell-derived small extracellular vesicles and mediates immunity against skin transplantation. PMID:35676234
Comparative genomics reveals low levels of inter- and intraspecies diversity in the causal agents of dwarf and common bunt of wheat and hint at conspecificity of Tilletia caries and T. laevis. PMID:35672841
Digital quantification of p16-positive foci in fibrotic interstitial lung disease is associated with a phenotype of idiopathic pulmonary fibrosis with reduced survival. PMID:35672770
Gene network analysis reveals candidate genes related with the hair follicle development in sheep. PMID:35672687
Comprehensive analysis of lncRNA-miRNA-mRNA networks during osteogenic differentiation of bone marrow mesenchymal stem cells. PMID:35672672
Network assisted analysis of de novo variants using protein-protein interaction information identified 46 candidate genes for congenital heart disease. PMID:35671298
HemI 2.0: an online service for heatmap illustration. PMID:35670661
In Ovo Injection of CHIR-99021 Promotes Feather Follicle Development via Modulating the Wnt Signaling Pathway and Transcriptome in Goose Embryos (Anser cygnoides). PMID:35669574
Identification of the Active Compound of Liu Wei Di Huang Wan for Treatment of Gestational Diabetes Mellitus via Network Pharmacology and Molecular Docking. PMID:35669396
Digital Cell Atlas of Mouse Uterus: From Regenerative Stage to Maturational Stage. PMID:35669188
Chromosome-Scale, Haplotype-Resolved Genome Assembly of Non-Sex-Reversal Females of Swamp Eel Using High-Fidelity Long Reads and Hi-C Data. PMID:35669182
The Development of Mechanical Allodynia in Diabetic Rats Revealed by Single-Cell RNA-Seq. PMID:35668789
Circulating microRNAs (miR-16, miR-22, miR-122) expression and early diagnosis of hepatocellular carcinoma. PMID:35666610
The impact of genetic modifiers on variation in germline mutation rates within and among human populations. PMID:35666194
Quantifying concordant genetic effects of de novo mutations on multiple disorders. PMID:35666111
Incubation of canine dermal fibroblasts with serum from dogs with atopic dermatitis activates extracellular matrix signalling and represses oxidative phosphorylation. PMID:35665445
Full-Length Transcriptional Analysis of the Same Soybean Genotype With Compatible and Incompatible Reactions to Heterodera glycines Reveals Nematode Infection Activating Plant Defense Response. PMID:35665156
Complete Genome Analysis of Highly Pathogenic Non-O1/O139 Vibrio cholerae Isolated From Macrobrachium rosenbergii Reveals Pathogenicity and Antibiotic Resistance-Related Genes. PMID:35664858
The interplay between lncRNAs, RNA-binding proteins and viral genome during SARS-CoV-2 infection reveals strong connections with regulatory events involved in RNA metabolism and immune response. PMID:35664076
Evaluating the Immune Response in Treatment-Naive Hospitalised Patients With Influenza and COVID-19. PMID:35663963
Serum miRNA Profile in Diabetic Patients With Ischemic Heart Disease as a Promising Non-Invasive Biomarker. PMID:35663309
miRNA-432 and SLC38A1 as Predictors of Hepatocellular Carcinoma Complicated with Alcoholic Steatohepatitis. PMID:35663198
Proteomic-based evidence for adult neurogenesis in birds and mammals as indicated from cerebrospinal fluid. PMID:35662184
Image analysis reveals molecularly distinct patterns of TILs in NSCLC associated with treatment outcome. PMID:35661148
De novo reconstruction of cell interaction landscapes from single-cell spatial transcriptome data with DeepLinc. PMID:35659722
Simulating the restoration of normal gene expression from different thyroid cancer stages using deep learning. PMID:35659616
Integrated proteogenomic characterization of urothelial carcinoma of the bladder. PMID:35659036
Integration of the Salmonella Typhimurium Methylome and Transcriptome Reveals That DNA Methylation and Transcriptional Regulation Are Largely Decoupled under Virulence-Related Conditions. PMID:35658533
Brain proteome profiling implicates the complement and coagulation cascade in multiple system atrophy brain pathology. PMID:35657417
Overexpression of ERCC6L correlates with poor prognosis and confers malignant phenotypes of lung adenocarcinoma. PMID:35656882
Identification of molecular pathways and protein-protein interactions in adipose tissue-derived mesenchymal stromal cells (ASCs) under physiological oxygen concentration in a diabetic rat model. PMID:35655589
Spatial Mapping of Plant N-Glycosylation Cellular Heterogeneity Inside Soybean Root Nodules Provided Insights Into Legume-Rhizobia Symbiosis. PMID:35651768
Characterisation of a nucleo-adhesome. PMID:35650196
Cross-tissue, single-cell stromal atlas identifies shared pathological fibroblast phenotypes in four chronic inflammatory diseases. PMID:35649411
RSK1 promotes mammalian axon regeneration by inducing the synthesis of regeneration-related proteins. PMID:35648763
Dynamic Transcriptome Profiling Reveals LncRNA-Centred Regulatory Networks in the Modulation of Pluripotency. PMID:35646895
Pan-Cancer Single-Cell Analysis Reveals the Core Factors and Pathway in Specific Cancer Stem Cells of Upper Gastrointestinal Cancer. PMID:35646860
Reclassification of Hepatocellular Cancer With Neural-Related Genes. PMID:35646712
Identification of a Cancer Stem Cells Signature of Head and Neck Squamous Cell Carcinoma. PMID:35646104
Identification of Context-Specific Fitness Genes Associated With Metabolic Rearrangements for Prognosis and Potential Treatment Targets for Liver Cancer. PMID:35646101
An equivalence test between features lists, based on the Sorensen-Dice index and the joint frequencies of GO term enrichment. PMID:35641928
Mapping the cardiac vascular niche in heart failure. PMID:35641541
Identification of Ferroptosis-Related Hub Genes and Their Association with Immune Infiltration in Chronic Obstructive Pulmonary Disease by Bioinformatics Analysis. PMID:35637927
Chemical reaction network knowledge graphs: the OntoRXN ontology. PMID:35637523
A tensor-based bi-random walks model for protein function prediction. PMID:35637427
Single-cell transcriptomics of adult macaque hippocampus reveals neural precursor cell populations. PMID:35637371
FAM83A antisense RNA 1 (FAM83A-AS1) silencing impairs cell proliferation and induces autophagy via MET-AMPKɑ signaling in lung adenocarcinoma. PMID:35635086
Distinct Injury Responsive Regulatory T Cells Identified by Multi-Dimensional Phenotyping. PMID:35634302
Low Dose Gamma Irradiation of Trypanosoma evansi Parasites Identifies Molecular Changes That Occur to Repair Radiation Damage and Gene Transcripts That May Be Involved in Establishing Disease in Mice Post-Irradiation. PMID:35634275
High Expression of HERV-K (HML-2) Might Stimulate Interferon in COVID-19 Patients. PMID:35632738
Flavivirus Capsid Proteins Inhibit the Interferon Response. PMID:35632712
Intense Innate Immune Responses and Severe Metabolic Disorders in Chicken Embryonic Visceral Tissues Caused by Infection with Highly Virulent Newcastle Disease Virus Compared to the Avirulent Virus: A Bioinformatics Analysis. PMID:35632651
Transcriptomics Integrated with Metabolomics Reveals 2-Methoxy-1, 4-Naphthoquinone-Based Carbon Dots Induced Molecular Shifts in Penicillium italicum. PMID:35628676
Analysis of Huntington's Disease Modifiers Using the Hyperbolic Mapping of the Protein Interaction Network. PMID:35628660
The Role of Transposable Elements of the Human Genome in Neuronal Function and Pathology. PMID:35628657
Dynamic Changes in Ascorbic Acid Content during Fruit Development and Ripening of Actinidia latifolia (an Ascorbate-Rich Fruit Crop) and the Associated Molecular Mechanisms. PMID:35628618
Epigenetic Silencing of PTEN and Epi-Transcriptional Silencing of MDM2 Underlied Progression to Secondary Acute Myeloid Leukemia in Myelodysplastic Syndrome Treated with Hypomethylating Agents. PMID:35628480
ASC-J9 Blocks Cell Proliferation and Extracellular Matrix Production of Keloid Fibroblasts through Inhibiting STAT3 Signaling. PMID:35628356
Identification and Transcriptome Analysis of Genes Related to Membrane Lipid Regulation in Sweet Sorghum under Salt Stress. PMID:35628281
Impact of Environmentally Relevant Concentrations of Bisphenol A (BPA) on the Gene Expression Profile in an In Vitro Model of the Normal Human Ovary. PMID:35628146
Inferring Potential Cancer Driving Synonymous Variants. PMID:35627162
CAPTURE of the Human U2 snRNA Genes Expands the Repertoire of Associated Factors. PMID:35625631
Comparative Proteomic Analysis Reveals the Effect of Selenoprotein W Deficiency on Oligodendrogenesis in Fear Memory. PMID:35624863
Association of a Novel DOCK2 Mutation-Related Gene Signature With Immune in Hepatocellular Carcinoma. PMID:35620462
Single-Cell RNA Sequencing Profiles Identify Important Pathophysiologic Factors in the Progression of Diabetic Nephropathy. PMID:35620059
CRISPR Library Screening in Cultured Cardiomyocytes. PMID:35618895
Novel reusable animal model for comparative evaluation of in vivo growth and protein-expression of Escherichia coli O157 strains in the bovine rumen. PMID:35617366
Bacterial Infection Induces Ultrastructural and Transcriptional Changes in the King Oyster Mushroom (Pleurotus eryngii). PMID:35616396
Investigating the Molecular Mechanism of Quercetin Protecting against Podocyte Injury to Attenuate Diabetic Nephropathy through Network Pharmacology, MicroarrayData Analysis, and Molecular Docking. PMID:35615688
Identification of Differential Genes of DNA Methylation Associated With Alzheimer's Disease Based on Integrated Bioinformatics and Its Diagnostic Significance. PMID:35615586
Proteome-wide prediction and analysis of the Cryptosporidium parvum protein-protein interaction network through integrative methods. PMID:35615014
Effects of Chang-Kang-Fang Formula on the Microbiota-Gut-Brain Axis in Rats With Irritable Bowel Syndrome. PMID:35614949
Single-molecule long-read sequencing analysis improves genome annotation and sheds new light on the transcripts and splice isoforms of Zoysia japonica. PMID:35614434
Discovery of bioactive microbial gene products in inflammatory bowel disease. PMID:35614211
An Myh11 single lysine deletion causes aortic dissection by reducing aortic structural integrity and contractility. PMID:35614093
Alcohol induced increases in sperm Histone H3 lysine 4 trimethylation correlate with increased placental CTCF occupancy and altered developmental programming. PMID:35614060
7-Methoxyisoflavone ameliorates atopic dermatitis symptoms by regulating multiple signaling pathways and reducing chemokine production. PMID:35610286
R-loop Mapping and Characterization During Drosophila Embryogenesis Reveals Developmental Plasticity in R-loop Signatures. PMID:35609632
Single-cell transcriptomics reveals lineage trajectory of human scalp hair follicle and informs mechanisms of hair graying. PMID:35606346
Exploiting plant transcriptomic databases: Resources, tools, and approaches. PMID:35605200
The Translational Landscape of SARS-CoV-2-infected Cells Reveals Suppression of Innate Immune Genes. PMID:35604092
Pollock: fishing for cell states. PMID:35603231
Blood transcriptomics identifies immune signatures indicative of infectious complications in childhood cancer patients with febrile neutropenia. PMID:35602885
RNA-seq and Network Analysis Reveal Unique Chemokine Activity Signatures in the Synovial Tissue of Patients With Rheumatoid Arthritis. PMID:35602512
CancerOmicsNet: a multi-omics network-based approach to anti-cancer drug profiling. PMID:35601606
A Four-Gene Prognostic Signature Based on the TEAD4 Differential Expression Predicts Overall Survival and Immune Microenvironment Estimation in Lung Adenocarcinoma. PMID:35600867
A Protocol for the Cryopreservation of Human Intestinal Mucosal Biopsies Compatible With Single-Cell Transcriptomics and Ex Vivo Studies. PMID:35600311
Reactive Astrocytes Derived From Human Induced Pluripotent Stem Cells Suppress Oligodendrocyte Precursor Cell Differentiation. PMID:35600072
Biotechnological Combination for Co-contaminated Soil Remediation: Focus on Tripartite "Meta-Enzymatic" Activity. PMID:35599908
Dataset of De Novo hybrid berry transcriptome profiling and characterization of Piper species (Piper nigrum and Piper longum) using Illumina and Nanopore sequencing. PMID:35599816
Combined use of specific length amplified fragment sequencing (SLAF-seq) and bulked segregant analysis (BSA) for rapid identification of genes influencing fiber content of hemp (Cannabis sativa L.). PMID:35596150
The ceRNA Crosstalk between mRNAs and lncRNAs in Diabetes Myocardial Infarction. PMID:35592708
Development of a Bile Acid-Related Gene Signature for Predicting Survival in Patients with Hepatocellular Carcinoma. PMID:35592684
Patterns of genomic divergence in sympatric and allopatric speciation of three Mihoutao (Actinidia) species. PMID:35591930
Identifying Alzheimer's genes via brain transcriptome mapping. PMID:35590321
Complete genome sequence of Pseudomonas stutzeri S116 owning bifunctional catalysis provides insights into affecting performance of microbial fuel cells. PMID:35590268
Genome mining reveals polysaccharide-degrading potential and new antimicrobial gene clusters of novel intestinal bacterium Paenibacillus jilinensis sp. nov. PMID:35590262
Oceanisphaera pacifica sp. nov., isolated from the intestine of Trichiurus japonicus. PMID:35590019
Exploration of the Potential Mechanism of the Common Differentially Expressed Genes in Psoriasis and Atopic Dermatitis. PMID:35586812
Physiological Effects and Transcriptomic Analysis of sbGnRH on the Liver in Pompano (Trachinotus ovatus). PMID:35586618
CBEA: Competitive balances for taxonomic enrichment analysis. PMID:35584140
Construction and comprehensive analysis of a lncRNA-mRNA interactive network to reveal a potential lncRNA for hepatic encephalopathy development. PMID:35583799
Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain. PMID:35581640
Identification of combined biomarkers for predicting the risk of osteoporosis using machine learning. PMID:35580864
GenePlexus: a web-server for gene discovery using network-based machine learning. PMID:35580053
Human phospho-signaling networks of SARS-CoV-2 infection are rewired by population genetic variants. PMID:35579274
Immune-Related Biomarkers Associated with Lung Metastasis from the Colorectal Cancer Microenvironment. PMID:35576491
A molecular view of amyotrophic lateral sclerosis through the lens of interaction network modules. PMID:35576218
Machine learning: its challenges and opportunities in plant system biology. PMID:35575915
Transcription elongation is finely tuned by dozens of regulatory factors. PMID:35575476
Recognition of Gonadal Development in Eriocheir sinensis Based on the Impulse of Love at First Sight. PMID:35574457
A Prognostic Gene Signature for Hepatocellular Carcinoma. PMID:35574316
CsbZIP2-miR9748-CsNPF4.4 Module Mediates High Temperature Tolerance of Cucumber Through Jasmonic Acid Pathway. PMID:35574100
Integrative clustering methods for multi-omics data. PMID:35573155
lncRNA-mRNA Expression Patterns in Invasive Pituitary Adenomas: A Microarray Analysis. PMID:35572729
Mitochondrial 1555 G>A variant as a potential risk factor for childhood glioblastoma. PMID:35571988
Identification of genes and pathways leading to poor prognosis of non-small cell lung cancer using integrated bioinformatics analysis. PMID:35571642
Genome-Wide Identification of Associations of Circulating Molecules With Spontaneous Coronary Artery Dissection and Aortic Aneurysm and Dissection. PMID:35571188
Natural selenium stress influences the changes of antibiotic resistome in seleniferous forest soils. PMID:35570296
Diagnosis of pulmonary tuberculosis via identification of core genes and pathways utilizing blood transcriptional signatures: a multicohort analysis. PMID:35568895
Chemical Diversity and Potential Target Network of Woody Peony Flower Essential Oil from Eleven Representative Cultivars (Paeonia × suffruticosa Andr.). PMID:35566179
The Mantle Transcriptome of Chamelea gallina (Mollusca: Bivalvia) and Shell Biomineralization. PMID:35565623
Identification of Genes Related to Squab Muscle Growth and Lipid Metabolism from Transcriptome Profiles of Breast Muscle and Liver in Domestic Pigeon (Columba livia). PMID:35565488
Cancer Metabolic Subtypes and Their Association with Molecular and Clinical Features. PMID:35565274
Bone Progenitors Pull the Strings on the Early Metabolic Rewiring Occurring in Prostate Cancer Cells. PMID:35565211
Transcriptome Analysis of the Cf-13-Mediated Hypersensitive Response of Tomato to Cladosporium fulvum Infection. PMID:35563232
Targeting Cell Death Mechanism Specifically in Triple Negative Breast Cancer Cell Lines. PMID:35563174
Insights into the Molecular Regulation of Lignin Content in Triploid Poplar Leaves. PMID:35562994
Proteogenomic characterization of 2002 human cancers reveals pan-cancer molecular subtypes and associated pathways. PMID:35562349
Nuclear oligo hashing improves differential analysis of single-cell RNA-seq. PMID:35562344
Design and application of a knowledge network for automatic prioritization of drug mechanisms. PMID:35561182
Annotating regulatory elements by heterogeneous network embedding. PMID:35561169
CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation. PMID:35560159
Shared genetic loci between depression and cardiometabolic traits. PMID:35560157
Identification of Potential Diagnoses Based on Immune Infiltration and Autophagy Characteristics in Major Depressive Disorder. PMID:35559009
A Community-Driven, Openly Accessible Molecular Pathway Integrating Knowledge on Malignant Pleural Mesothelioma. PMID:35558518
Genome-Wide Association Study and Genomic Selection for Proteinogenic Methionine in Soybean Seeds. PMID:35557723
Exome sequencing of hepatocellular carcinoma in lemurs identifies potential cancer drivers: A pilot study. PMID:35557512
Inositol polyphosphate multikinase physically binds to the SWI/SNF complex and modulates BRG1 occupancy in mouse embryonic stem cells. PMID:35551737
The Immunometabolic Atlas: A tool for design and interpretation of metabolomics studies in immunology. PMID:35550647
Enhancing Data Integration, Interoperability, and Reuse to Address Complex and Emerging Environmental Health Problems. PMID:35549252
An Herbal Product Alleviates Bleomycin-Induced Pulmonary Fibrosis in Mice via Regulating NF-κB/TNF-α Signaling in Macrophages. PMID:35548340
Genome-Wide Identification and Expression Profiling of KCS Gene Family in Passion Fruit (Passiflora edulis) Under Fusarium kyushuense and Drought Stress Conditions. PMID:35548275
Integrative analysis of clinical and epigenetic biomarkers of mortality. PMID:35546478
LncMIR181A1HG is a novel chromatin-bound epigenetic suppressor of early stage osteogenic lineage commitment. PMID:35546168
Degron masking outlines degronons, co-degrading functional modules in the proteome. PMID:35545699
A natural mutator allele shapes mutation spectrum variation in mice. PMID:35545679
H3K27 methylation regulates the fate of two cell lineages in male gametophytes. PMID:35543471
Text mining for identification of biological entities related to antibiotic resistant organisms. PMID:35539017
Transcriptomic and metabolomic landscape of quinoa during seed germination. PMID:35538406
Acetylome analysis of acetylation providing new insight into sclerotial generation in medicinal fungus Polyporus umbellatus. PMID:35538155
Statin therapy inhibits fatty acid synthase via dynamic protein modifications. PMID:35538051
DEPCOD: a tool to detect and visualize co-evolution of protein domains. PMID:35536332
SubcellulaRVis: a web-based tool to simplify and visualise subcellular compartment enrichment. PMID:35536291
deepSimDEF: deep neural embeddings of gene products and Gene Ontology terms for functional analysis of genes. PMID:35536192
Enrichment analysis on regulatory subspaces: A novel direction for the superior description of cellular responses to SARS-CoV-2. PMID:35533463
Profiling senescent cells in human brains reveals neurons with CDKN2D/p19 and tau neuropathology. PMID:35531351
A recent burst of gene duplications in Triticeae. PMID:35529951
Selection Signature Analyses Revealed Genes Associated With Adaptation, Production, and Reproduction in Selected Goat Breeds in Kenya. PMID:35528543
Screening of molecular targets and construction of a ceRNA network for oxaliplatin resistance in colorectal cancer. PMID:35527927
Lymph node colonization induces tumor-immune tolerance to promote distant metastasis. PMID:35525247
Whole genome sequencing and analysis of fenvalerate degrading bacteria Citrobacter freundii CD-9. PMID:35523901
A Bayesian network structure learning approach to identify genes associated with stress in spleens of chickens. PMID:35523843
Multi-omics signatures of alcohol use disorder in the dorsal and ventral striatum. PMID:35523767
Wnt11 acts on dermomyotome cells to guide epaxial myotome morphogenesis. PMID:35522214
Identification and characterization of differentially expressed miRNAs in HepG2 cells under normoxic and hypoxic conditions. PMID:35516357
Full-Length Transcriptome Sequencing Reveals Tissue-Specific Gene Expression Profile of Mangrove Clam Geloina erosa. PMID:35514334
Systematic characterization of gene function in the photosynthetic alga Chlamydomonas reinhardtii. PMID:35513725
PRD-Class Homeobox Genes in Bovine Early Embryos: Function, Evolution, and Overlapping Roles. PMID:35512670
A targeted approach to investigating immune genes of an iconic Australian marsupial. PMID:35510793
Signatures of selection in core and accessory genomes indicate different ecological drivers of diversification among Bacillus cereus clades. PMID:35510788
Mechanism of Ba Zhen Tang Delaying Skin Photoaging Based on Network Pharmacology and Molecular Docking. PMID:35510223
Methamphetamine Disturbs Gut Homeostasis and Reshapes Serum Metabolome, Inducing Neurotoxicity and Abnormal Behaviors in Mice. PMID:35509309
Two conserved amino acids differentiate the biology of high-risk and low-risk HPV E5 proteins. PMID:35509176
Gaur genome reveals expansion of sperm odorant receptors in domesticated cattle. PMID:35508966
Survival-related genes are diversified across cancers but generally enriched in cancer hallmark pathways. PMID:35508961
IMEx Databases: Displaying Molecular Interactions into a Single, Standards-Compliant Dataset. PMID:35507258
Roseococcus pinisoli sp. nov., lacking pufL and pufM bacteriochlorophyll a: synthesizing genes. PMID:35507236
High MICAL-L2 expression and its role in the prognosis of colon adenocarcinoma. PMID:35501725
Evidence of multiple genome duplication events in Mytilus evolution. PMID:35501689
Mapping the epithelial-immune cell interactome upon infection in the gut and the upper airways. PMID:35501398
Identification of HMOX1 as a Critical Ferroptosis-Related Gene in Atherosclerosis. PMID:35498043
Faster Growth Enhances Low Carbon Fuel and Chemical Production Through Gas Fermentation. PMID:35497340
A new ChEMBL dataset for the similarity-based target fishing engine FastTargetPred: Annotation of an exhaustive list of linear tetrapeptides. PMID:35496477
Identification of NFASC and CHL1 as Two Novel Hub Genes in Endometriosis Using Integrated Bioinformatic Analysis and Experimental Verification. PMID:35496348
Fluvalinate-Induced Changes in MicroRNA Expression Profile of Apis mellifera ligustica Brain Tissue. PMID:35495168
m6A-mediated modulation coupled with transcriptional regulation shapes long noncoding RNA repertoire of the cGAS-STING signaling. PMID:35495108
A collaborative semantic-based provenance management platform for reproducibility. PMID:35494870
From Beginning to End: Expanding the SERINC3 Interactome Through an in silico Analysis. PMID:35494555
Single-Cell RNA Sequencing of Metastatic Testicular Seminoma Reveals the Cellular and Molecular Characteristics of Metastatic Cell Lineage. PMID:35494058
Systematic molecular analysis of the human secretome and membrane proteome in gastrointestinal adenocarcinomas. PMID:35488454
An integrated network representation of multiple cancer-specific data for graph-based machine learning. PMID:35487924
The clinical value of miRNA-21 in cervical cancer: A comprehensive investigation based on microarray datasets. PMID:35486636
Genome annotation of Caenorhabditis briggsae by TEC-RED identifies new exons, paralogs, and conserved and novel operons. PMID:35485953
Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans. PMID:35484634
Transcriptome and metabolome analyses reveal new insights into chlorophyll, photosynthesis, metal ion and phenylpropanoids related pathways during sugarcane ratoon chlorosis. PMID:35484490
Identification of replication fork-associated proteins in Drosophila embryos and cultured cells using iPOND coupled to quantitative mass spectrometry. PMID:35484306
An Arabidopsis mutant deficient in phosphatidylinositol-4-phosphate kinases ß1 and ß2 displays altered auxin-related responses in roots. PMID:35484296
Protein N-glycosylation aberrations and glycoproteomic network alterations in osteoarthritis and osteoarthritis with type 2 diabetes. PMID:35484284
The genome of hibiscus hamabo reveals its adaptation to saline and waterlogged habitat. PMID:35480957
m6A Regulator-Mediated RNA Methylation Modification Patterns are Involved in the Pathogenesis and Immune Microenvironment of Depression. PMID:35480327
Characterization of differential gene expression of broiler chicken to thermal stress in discrete developmental stages. PMID:35479510
Molecular characterization of myotonic dystrophy fibroblast cell lines for use in small molecule screening. PMID:35479399
Integrated analysis of transcriptomic data reveals the platelet response in COVID-19 disease. PMID:35477940
Proteomic networks associated with tumor-educated macrophage polarization and cytotoxicity potentiated by heat-killed tuberculosis. PMID:35477732
LM-GVP: an extensible sequence and structure informed deep learning framework for protein property prediction. PMID:35477726
Lupus Susceptibility Loci Predispose Mice to Clonal Lymphocytic Responses and Myeloid Expansion. PMID:35477687
The interferon-inducible GTPase MxB promotes capsid disassembly and genome release of herpesviruses. PMID:35475759
Integrative analysis of TCGA data identifies miRNAs as drug-specific survival biomarkers. PMID:35474090
Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data. PMID:35473573
Differential gene expression in nasal airway epithelium from overweight or obese youth with asthma. PMID:35470932
An extraction from Trametes robiniophila Murr. (Huaier) inhibits non-small cell lung cancer proliferation via targeting to epidermal growth factor receptor. PMID:35470770
Daily running enhances molecular and physiological circadian rhythms in skeletal muscle. PMID:35470095
Deletion and tandem duplications of biosynthetic genes drive the diversity of triterpenoids in Aralia elata. PMID:35468919
Trans-cinnamaldehyde protects against phenylephrine-induced cardiomyocyte hypertrophy through the CaMKII/ERK pathway. PMID:35468773
Pseudomonas aeruginosa Initiates a Rapid and Specific Transcriptional Response during Surface Attachment. PMID:35467391
Chemical-induced gene expression ranking and its application to pancreatic cancer drug repurposing. PMID:35465231
Co-expression Mechanism Analysis of Different Tachyplesin I-Resistant Strains in Pseudomonas aeruginosa Based on Transcriptome Sequencing. PMID:35464984
A Chromosome-Level Reference Genome of Chinese Balloon Flower (Platycodon grandiflorus). PMID:35464833
A Bayesian framework to integrate multi-level genome-scale data for Autism risk gene prioritization. PMID:35459094
Biometal Dyshomeostasis in Olfactory Mucosa of Alzheimer's Disease Patients. PMID:35456941
Ovarian Transcriptomic Analysis of Ninghai Indigenous Chickens at Different Egg-Laying Periods. PMID:35456401
Treatment with Ad5-Porcine Interferon-α Attenuates Ebolavirus Disease in Pigs. PMID:35456124
Ontologies and Knowledge Graphs in Oncology Research. PMID:35454813
Proteomic Response of Bacillus subtilis Spores under High Pressure Combined with Moderate Temperature and Random Peptide Mixture LK Treatment. PMID:35454710
Sphingolipid Metabolism as a New Predictive Target Correlated with Aging and AD: A Transcriptomic Analysis. PMID:35454332
Identification of Intrinsically Disordered Proteins and Regions in a Non-Model Insect Species Ostrinia nubilalis (Hbn.). PMID:35454181
Testicular "Inherited Metabolic Memory" of Ancestral High-Fat Diet Is Associated with Sperm sncRNA Content. PMID:35453658
Coexpression reveals conserved gene programs that co-vary with cell type across kingdoms. PMID:35451481
Antifungal Effect of Copper Nanoparticles against Fusarium kuroshium, an Obligate Symbiont of Euwallacea kuroshio Ambrosia Beetle. PMID:35448578
Pan-Genomic and Transcriptomic Analyses of Marine Pseudoalteromonas agarivorans Hao 2018 Revealed Its Genomic and Metabolic Features. PMID:35447921
Transcriptional Regulation of Reproductive Diapause in the Convergent Lady Beetle, Hippodamia convergens. PMID:35447785
Impact of medication on blood transcriptome reveals off-target regulations of beta-blockers. PMID:35446883
Transcriptome Analysis of Otodectes cynotis in Different Developmental Stages. PMID:35444625
Comparative Genomics Assisted Functional Characterization of Rahnella aceris ZF458 as a Novel Plant Growth Promoting Rhizobacterium. PMID:35444623
Genomics, convergent neuroscience and progress in understanding autism spectrum disorder. PMID:35440779
Loss of vascular endothelial notch signaling promotes spontaneous formation of tertiary lymphoid structures. PMID:35440634
Inhibition of the succinyl dehydrogenase complex in acute myeloid leukemia leads to a lactate-fuelled respiratory metabolic vulnerability. PMID:35440568
Integrative analysis of mutated genes and mutational processes reveals novel mutational biomarkers in colorectal cancer. PMID:35439935
Improving ovarian cancer treatment decision using a novel risk predictive tool. PMID:35439731
Construction of a circRNA-Mediated ceRNA Network Reveals Novel Biomarkers for Aortic Dissection. PMID:35437351
Integrative analysis of key microRNA-mRNA complexes and pathways in aortic aneurysm. PMID:35433971
Up-to-Date Pathologic Classification and Molecular Characteristics of Intrahepatic Cholangiocarcinoma. PMID:35433771
Integrative Analyses of Circulating mRNA and lncRNA Expression Profile in Plasma of Lung Cancer Patients. PMID:35433477
Identification and Verification of Potential Hub Genes in Amphetamine-Type Stimulant (ATS) and Opioid Dependence by Bioinformatic Analysis. PMID:35432486
Integrative Analysis of Biomarkers and Mechanisms in Adamantinomatous Craniopharyngioma. PMID:35432485
Comparative Transcriptome Analysis Provides Insight into Spatio-Temporal Expression Characteristics and Genetic Regulatory Network in Postnatal Developing Subcutaneous and Visceral Fat of Bama Pig. PMID:35432468
The LINC00452/miR-204/CHST4 Axis Regulating Thymic Tregs Might Be Involved in the Progression of Thymoma-Associated Myasthenia Gravis. PMID:35432149
Identification and Validation of Hub Genes with Poor Prognosis in Hepatocellular Carcinoma by Integrated Bioinformatical Analysis. PMID:35431572
Autophagy Induced by BCL2-Related ceRNA Network Participates in the Occurrence of COPD. PMID:35431545
Combined Hypothesis Testing on Graphs with Applications to Gene Set Enrichment Analysis. PMID:35431372
Identification and characterization of circular RNAs in Longissimus dorsi muscle tissue from two goat breeds using RNA-Seq. PMID:35429278
Ovarian cancer immunogenicity is governed by a narrow subset of progenitor tissue-resident memory T cells. PMID:35427494
Standardized genome-wide function prediction enables comparative functional genomics: a new application area for Gene Ontologies in plants. PMID:35426911
Association of Circulating Cathepsin B Levels With Blood Pressure and Aortic Dilation. PMID:35425820
Beneficial roles of the AhR ligand FICZ on the regenerative potentials of BMSCs and primed cartilage templates. PMID:35425032
Network pharmacology-based analysis for unraveling potential cancer-related molecular targets of Egyptian propolis phytoconstituents accompanied with molecular docking and in vitro studies. PMID:35423607
Identification and Validation of Immune Cells and Hub Genes in Gastric Cancer Microenvironment. PMID:35422890
Isolation of Anaerobic Bromate-Reducing Bacteria Using Different Carbon Sources and Transcriptomic Insights From Klebsiella variicola Glu3. PMID:35422780
Bioinformatics Analysis Identified the Hub Genes, mRNA-miRNA-lncRNA Axis, and Signaling Pathways Involved in Rheumatoid Arthritis Pathogenesis. PMID:35422654
Investigating the disordered regions (MoRFs, SLiMs and LCRs) and functions of mimicry proteins/peptides in silico. PMID:35421114
Vero cells gain renal tubule markers in low-calcium and magnesium chemically defined media. PMID:35418617
Integration of Aspergillus niger transcriptomic profile with metabolic model identifies potential targets to optimise citric acid production from lignocellulosic hydrolysate. PMID:35418297
Analysis of human brain tissue derived from DBS surgery. PMID:35418104
A systematic review and functional bioinformatics analysis of genes associated with Crohn's disease identify more than 120 related genes. PMID:35418025
Progenitor potential of lung epithelial organoid cells in a transplantation model. PMID:35417699
Semantic clustering analysis of E3-ubiquitin ligases in gastrointestinal tract defines genes ontology clusters with tissue expression patterns. PMID:35413796
PTH2R is related to cell proliferation and migration in ovarian cancer: a multi-omics analysis of bioinformatics and experiments. PMID:35410353
Comparative transcriptomic analysis of two Cucumis melo var. saccharinus germplasms differing in fruit physical and chemical characteristics. PMID:35410167
Identification and New Indication of Melanin-Concentrating Hormone Receptor 1 (MCHR1) Antagonist Derived from Machine Learning and Transcriptome-Based Drug Repositioning Approaches. PMID:35409167
Environmental Phenol and Paraben Exposure Risks and Their Potential Influence on the Gene Expression Involved in the Prognosis of Prostate Cancer. PMID:35409038
Circulating Vitreous microRNA as Possible Biomarker in High Myopic Eyes with Macular Hole. PMID:35409006
Enhancement Mechanism of Stibnite Dissolution Mediated by Acidithiobacillus ferrooxidans under Extremely Acidic Condition. PMID:35408938
Machine-Learning Analysis of Serum Proteomics in Neuropathic Pain after Nerve Injury in Breast Cancer Surgery Points at Chemokine Signaling via SIRT2 Regulation. PMID:35408848
Label-Free LC-MS/MS Analysis Reveals Different Proteomic Profiles between Egg Yolks of Silky Fowl and Ordinary Chickens. PMID:35407122
Chemerin Effect on the Endometrial Proteome of the Domestic Pig during Implantation Obtained by LC-MS/MS Analysis. PMID:35406725
Osteogenic Commitment of Human Periodontal Ligament Cells Is Predetermined by Methylation, Chromatin Accessibility and Expression of Key Transcription Factors. PMID:35406691
Transcriptional CDK Inhibitors as Potential Treatment Option for Testicular Germ Cell Tumors. PMID:35406461
Integrative Analyses of Antler Cartilage Transcriptome and Proteome of Gansu Red Deer (Cervus elaphus kansuensis) at Different Growth Stages. PMID:35405922
Multifaced regulator: RNA binding proteins and their roles in hematopoiesis. PMID:35402803
Combining biomedical knowledge graphs and text to improve predictions for drug-target interactions and drug-indications. PMID:35402106
TMT labeled comparative proteomic analysis reveals spleen active immune responses during Clostridium perfringens type C infected piglet diarrhea. PMID:35402105
An engineered nano-liposome-human ACE2 decoy neutralizes SARS-CoV-2 Spike protein-induced inflammation in both murine and human macrophages. PMID:35401811
Effects of Luteinizing Hormone Releasing Hormone A2 on Gonad Development in Juvenile Amur Sturgeon, Acipenser schrenckii, Revealed by Transcriptome Profiling Analysis. PMID:35401695
A Secondary Metabolism Pathway Involved in the Production of a Putative Toxin Is Expressed at Early Stage of Monilinia laxa Infection. PMID:35401637
Integrated Metabolomic and Transcriptomic Analysis and Identification of Dammarenediol-II Synthase Involved in Saponin Biosynthesis in Gynostemma longipes. PMID:35401630
Comparative Transcriptome Profiling Analysis Reveals the Adaptive Molecular Mechanism of Yellow-Green Leaf in Rosa beggeriana 'Aurea'. PMID:35401615
Single-Cell Profiling Reveals Heterogeneity of Primary and Lymph Node Metastatic Tumors and Immune Cell Populations and Discovers Important Prognostic Significance of CCDC43 in Oral Squamous Cell Carcinoma. PMID:35401551
Preclinical Studies on Convalescent Human Immune Plasma-Derived Exosome: Omics and Antiviral Properties to SARS-CoV-2. PMID:35401544
Pangenome Analysis of the Soilborne Fungal Phytopathogen Rhizoctonia solani and Development of a Comprehensive Web Resource: RsolaniDB. PMID:35401459
Human pluripotent stem cell-derived myogenic progenitors undergo maturation to quiescent satellite cells upon engraftment. PMID:35395188
FindIT2: an R/Bioconductor package to identify influential transcription factor and targets based on multi-omics data. PMID:35392802
Acetate Degradation at Low pH by the Moderately Acidophilic Sulfate Reducer Acididesulfobacillus acetoxydans gen. nov. sp. nov. PMID:35391737
Description and genome analysis of Luteimonas viscosa sp. nov., a novel bacterium isolated from soil of a sunflower field. PMID:35391590
Predicted mouse interactome and network-based interpretation of differentially expressed genes. PMID:35390003
Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content. PMID:35388368
Hierarchical multi-label classification based on LSTM network and Bayesian decision theory for LncRNA function prediction. PMID:35388048
Engineering an enthesis-like graft for rotator cuff repair: An approach to fabricate highly biomimetic scaffold capable of zone-specifically releasing stem cell differentiation inducers. PMID:35386315
Co-Expression Network Modeling Identifies Specific Inflammation and Neurological Disease-Related Genes mRNA Modules in Mood Disorder. PMID:35386281
MDN1 Mutation Is Associated With High Tumor Mutation Burden and Unfavorable Prognosis in Breast Cancer. PMID:35386280
Nextcast: A software suite to analyse and model toxicogenomics data. PMID:35386103
Altered BAF occupancy and transcription factor dynamics in PBAF-deficient melanoma. PMID:35385731
Global evolution of the tumor microenvironment associated with progression from preinvasive invasive to invasive human lung adenocarcinoma. PMID:35385730
Genetics of osteopontin in patients with chronic kidney disease: The German Chronic Kidney Disease study. PMID:35385482
A high-quality assembly reveals genomic characteristics, phylogenetic status, and causal genes for leucism plumage of Indian peafowl. PMID:35383847
Cell environment shapes TDP-43 function with implications in neuronal and muscle disease. PMID:35383280
Genome-scale transcriptomic insights into the gene co-expression network of seed abortion in triploid Siraitia grosvenorii. PMID:35382733
Harmonizing model organism data in the Alliance of Genome Resources. PMID:35380658
MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses. PMID:35380657
JaponicusDB: rapid deployment of a model organism database for an emerging model species. PMID:35380656
MTD: a unique pipeline for host and meta-transcriptome joint and integrative analyses of RNA-seq data. PMID:35380623
Cellular and transcriptional diversity over the course of human lactation. PMID:35377806
Proteomic Response Revealed Signaling Pathways Involving in the Mechanism of Polymyxin B-Induced Melanogenesis. PMID:35377227
Differential transcriptomic landscapes of multiple organs from SARS-CoV-2 early infected rhesus macaques. PMID:35377064
d-Serine Mediates Cellular Proliferation for Kidney Remodeling. PMID:35372967
Spatial proteomics reveals subcellular reorganization in human keratinocytes exposed to UVA light. PMID:35372811
Dental EHR-infused Persona Ontologies to Enrich Dental Dialogue Interaction of Agents. PMID:35371617
Transcriptome Analysis Reveals a Gene Expression Pattern That Contributes to Sugarcane Bud Propagation Induced by Indole-3-Butyric Acid. PMID:35371161
MAG2 and MAL Regulate Vesicle Trafficking and Auxin Homeostasis With Functional Redundancy. PMID:35371137
Pituitary Gonadotropin Gene Expression During Induced Onset of Postsmolt Maturation in Male Atlantic Salmon: In Vivo and Tissue Culture Studies. PMID:35370944
Comprehensive Analysis of the Transcriptome-Wide m6A Methylation in Mouse Pachytene Spermatocytes and Round Spermatids. PMID:35368708
Parthenolide leads to proteomic differences in thyroid cancer cells and promotes apoptosis. PMID:35366876
A high-quality assembled genome and its comparative analysis decode the adaptive molecular mechanism of the number one Chinese cotton variety CRI-12. PMID:35365835
Transcriptome-wide association study for postpartum depression implicates altered B-cell activation and insulin resistance. PMID:35365803
Proteome profiling reveals changes in energy metabolism, transport and antioxidation during drought stress in Nostoc flagelliforme. PMID:35365086
Non-linear archetypal analysis of single-cell RNA-seq data by deep autoencoders. PMID:35363784
Intermittent prednisone treatment in mice promotes exercise tolerance in obesity through adiponectin. PMID:35363257
Stimulation of the hepatoportal nerve plexus with focused ultrasound restores glucose homoeostasis in diabetic mice, rats and swine. PMID:35361935
NeuroSCORE is a genome-wide omics-based model that identifies candidate disease genes of the central nervous system. PMID:35361823
Gene expression study in monocytes: evidence of inflammatory dysregulation in early-onset obsessive-compulsive disorder. PMID:35361798
Genomic heterogeneity underlies multidrug resistance in Pseudomonas aeruginosa: A population-level analysis beyond susceptibility testing. PMID:35358221
Iron-Induced Respiration Promotes Antibiotic Resistance in Actinomycete Bacteria. PMID:35357210
Species Persistence with Hybridization in Toad-Headed Lizards Driven by Divergent Selection and Low Recombination. PMID:35356979
Mass Spectrometric Behavior and Molecular Mechanisms of Fermented Deoxyanthocyanidins to Alleviate Ulcerative Colitis Based on Network Pharmacology. PMID:35356765
Whole-Genome and Transcriptome Sequencing-Based Characterization of Bacillus Cereus NR1 From Subtropical Marine Mangrove and Its Potential Role in Sulfur Metabolism. PMID:35356521
Antigen-Presenting B Cells Program the Efferent Lymph T Helper Cell Response. PMID:35355990
Tissue extracellular matrix hydrogels as alternatives to Matrigel for culturing gastrointestinal organoids. PMID:35354790
Coronavirus Host Genetics South Africa (COHG-SA) database-a variant database for gene regions associated with SARS-CoV-2 outcomes. PMID:35351987
Networks and Graphs Discovery in Metabolomics Data Analysis and Interpretation. PMID:35350714
Network Crosstalk as a Basis for Drug Repurposing. PMID:35350247
Genomic diversity and post-admixture adaptation in the Uyghurs. PMID:35350227
Evaluation of Early Biomarkers of Atherosclerosis Associated with Polychlorinated Biphenyl Exposure: An in Vitro and in Vivo Study. PMID:35349355
Genome-wide association studies of metabolites in Finnish men identify disease-relevant loci. PMID:35347128
Cerebrospinal fluid tau levels are associated with abnormal neuronal plasticity markers in Alzheimer's disease. PMID:35346299
Integrative analyses of biomarkers and pathways for heart failure. PMID:35346191
Hippocampus RNA Sequencing of Pentylenetetrazole-Kindled Rats and Upon Treatment of Novel Chemical Q808. PMID:35345815
LRP1B is a Potential Biomarker for Tumor Immunogenicity and Prognosis of HCC Patients Receiving ICI Treatment. PMID:35345553
Genome Sequence and Description of Paracoccus denitrificans Strain R-1, Isolated from Activated Sludge. PMID:35343764
Screening of Potential Key Biomarkers for Ewing Sarcoma: Evidence from Gene Array Analysis. PMID:35342299
Proteomic Identification of a Gastric Tumor ECM Signature Associated With Cancer Progression. PMID:35340765
Global DNA methylation profiles of buffalo (Bubalus bubalis) preimplantation embryos produced by handmade cloning and in vitro fertilization. PMID:35338228
De novo assembly of a fruit transcriptome set identifies AmMYB10 as a key regulator of anthocyanin biosynthesis in Aronia melanocarpa. PMID:35337270
GXP: Analyze and Plot Plant Omics Data in Web Browsers. PMID:35336631
Polyopes affinis Suppressed IFN-γ- and TNF-α-Induced Inflammation in Human Keratinocytes via Down-Regulation of the NF-κB and STAT1 Pathways. PMID:35335198
Whole-genome sequencing and gene sharing network analysis powered by machine learning identifies antibiotic resistance sharing between animals, humans and environment in livestock farming. PMID:35333870
Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro. PMID:35332340
Genomic signatures of high-altitude adaptation and chromosomal polymorphism in geladas. PMID:35332281
Stripenn detects architectural stripes from chromatin conformation data using computer vision. PMID:35332165
Parallel sequence tagging for concept recognition. PMID:35331131
In silico Analysis of Publicly Available Transcriptomics Data Identifies Putative Prognostic and Therapeutic Molecular Targets for Papillary Thyroid Carcinoma. PMID:35330879
Uncovering the Pharmacological Mechanisms of Gexia-Zhuyu Formula (GXZY) in Treating Liver Cirrhosis by an Integrative Pharmacology Strategy. PMID:35330838
Characterization of Vegetative Incompatibility in Morchella importuna and Location of the Related-Genes by Bulk Segregant Analysis. PMID:35330770
HSPB8 is a Potential Prognostic Biomarker that Correlates With Immune Cell Infiltration in Bladder Cancer. PMID:35330734
Landscape of Molecular Crosstalk Perturbation between Lung Cancer and COVID-19. PMID:35329141
High Resistance to Quinclorac in Multiple-Resistant Echinochloa colona Associated with Elevated Stress Tolerance Gene Expression and Enriched Xenobiotic Detoxification Pathway. PMID:35328069
Functional Similarities of Protein-Coding Genes in Topologically Associating Domains and Spatially-Proximate Genomic Regions. PMID:35328034
Characterization of Mitochondrial Proteome and Function in Luminal A and Basal-like Breast Cancer Subtypes Reveals Alteration in Mitochondrial Dynamics and Bioenergetics Relevant to Their Diagnosis. PMID:35327574
Functional Enrichment Analysis of Regulatory Elements. PMID:35327392
Screening Repurposed Antiviral Small Molecules as Antimycobacterial Compounds by a Lux-Based phoP Promoter-Reporter Platform. PMID:35326832
Bioinformatics Analysis and Identification of Potential Genes Associated with Pathogenesis and Prognosis of Gastric Cancer. PMID:35325407
Whole Blood Metabolite Profiles Reflect Changes in Energy Metabolism in Heart Failure. PMID:35323659
Immune Defense Mechanism of Reticulitermes chinensis Snyder (Blattodea: Isoptera) against Serratia marcescens Bizio. PMID:35323524
Outstanding prognostic value of novel ferroptosis-related genes in chemoresistance osteosarcoma patients. PMID:35322804
Identification of the TF-miRNA-mRNA co-regulatory networks involved in sepsis. PMID:35322335
Identification and Characterization of the Roles of circCASP9 in Gastric Cancer Based on a circRNA-miRNA-mRNA Regulatory Network. PMID:35320976
High-Content Screening and Computational Prediction Reveal Viral Genes That Suppress the Innate Immune Response. PMID:35319251
Incorporating regulatory interactions into gene-set analyses for GWAS data: A controlled analysis with the MAGMA tool. PMID:35316269
Spatial transcriptomic reconstruction of the mouse olfactory glomerular map suggests principles of odor processing. PMID:35314823
Transcriptional analysis of peripheral memory T cells reveals Parkinson's disease-specific gene signatures. PMID:35314697
Identification of differentially expressed genes and signaling pathways with Candida infection by bioinformatics analysis. PMID:35314002
Transcriptome Analysis Revealed a Cold Stress-Responsive Transcription Factor, PaDREB1A, in Plumbago auriculata That Can Confer Cold Tolerance in Transgenic Arabidopsis thaliana. PMID:35310656
Endophytic Bacterium Serratia plymuthica From Chinese Leek Suppressed Apple Ring Rot on Postharvest Apple Fruit. PMID:35310399
GOing Forward With the Cardiac Conduction System Using Gene Ontology. PMID:35309148
Comprehensive Transcriptome Analysis of Stem-Differentiating Xylem Upon Compression Stress in Cunninghamia Lanceolata. PMID:35309135
Small genetic variation affecting mRNA isoforms associated with marbling and meat color in beef cattle. PMID:35305194
Parvimonas micra is associated with tumour immune profiles in molecular subtypes of colorectal cancer. PMID:35301576
Transcriptogram analysis reveals relationship between viral titer and gene sets responses during Corona-virus infection. PMID:35300459
Identification of Down-Regulated ADH1C is Associated With Poor Prognosis in Colorectal Cancer Using Bioinformatics Analysis. PMID:35300114
Protocol for isolation and functional validation of label-retaining quiescent colorectal cancer stem cells from patient-derived organoids for RNA-seq. PMID:35300001
Chromosome-Scale Assembly of the Dendrobium nobile Genome Provides Insights Into the Molecular Mechanism of the Biosynthesis of the Medicinal Active Ingredient of Dendrobium. PMID:35299950
Impact of 6 month conjugated equine estrogen versus estradiol-treatment on biomarkers and enriched gene sets in healthy mammary tissue of non-human primates. PMID:35298474
A multidimensional coding architecture of the vagal interoceptive system. PMID:35296859
Targeting SOX10-deficient cells to reduce the dormant-invasive phenotype state in melanoma. PMID:35296667
Comparative Analysis of Gene Expression Profiles in the Adipose Tissue of Obese Adult Mice With Rapid Infantile Growth After Undernourishment In Utero. PMID:35295992
Decoding the Role of Astrocytes in the Entorhinal Cortex in Alzheimer's Disease Using High-Dimensional Single-Nucleus RNA Sequencing Data and Next-Generation Knowledge Discovery Methodologies: Focus on Drugs and Natural Product Remedies for Dementia. PMID:35295737
Missing Links Between Gene Function and Physiology in Genomics. PMID:35295568
Beyond AOPs: A Mechanistic Evaluation of NAMs in DART Testing. PMID:35295212
Drosophila functional screening of de novo variants in autism uncovers damaging variants and facilitates discovery of rare neurodevelopmental diseases. PMID:35294868
Identification of hub genes and pathways in bladder cancer using bioinformatics analysis. PMID:35291419
Whole genome sequencing delineates regulatory, copy number, and cryptic splice variants in early onset cardiomyopathy. PMID:35288587
EnsembleFam: towards more accurate protein family prediction in the twilight zone. PMID:35287576
Analysis of the role and mechanism of EGCG in septic cardiomyopathy based on network pharmacology. PMID:35287352
Bacterial Homologs of Progestin and AdipoQ Receptors (PAQRs) Affect Membrane Energetics Homeostasis but Not Fluidity. PMID:35285724
Chondroitin Sulfate Proteoglycans Are De Facto Cellular Receptors for Human Papillomavirus 16 under High Serum Conditions. PMID:35285688
Transcriptomic Analysis Reveal the Molecular Mechanisms of Seed Coat Development in Cucurbita pepo L. PMID:35283914
Multi-Approach Analysis Reveals Pathways of Cold Tolerance Divergence in Camellia japonica. PMID:35283896
Inhibition of miR-128 Enhances Vocal Sequence Organization in Juvenile Songbirds. PMID:35283744
The Key Genes Underlying Pathophysiology Correlation Between the Acute Myocardial Infarction and COVID-19. PMID:35282650
Cold Exposure Induces Depot-Specific Alterations in Fatty Acid Composition and Transcriptional Profile in Adipose Tissues of Pigs. PMID:35282453
Establishing a competing endogenous RNA (ceRNA)-immunoregulatory network associated with the progression of Alzheimer's disease. PMID:35282112
Network Analysis Reveals Different Cellulose Degradation Strategies Across Trichoderma harzianum Strains Associated With XYR1 and CRE1. PMID:35281818
Conserved Regulatory Pathways for Stock-Scion Healing Revealed by Comparative Analysis of Arabidopsis and Tomato Grafting Transcriptomes. PMID:35281699
Insights Into the Impact of Small RNA SprC on the Metabolism and Virulence of Staphylococcus aureus. PMID:35281456
Identification of differentially expressed and methylated genes and construction of a co-expression network in age-related macular degeneration. PMID:35280389
Circ_0001174 facilitates osteosarcoma cell proliferation, migration, and invasion by targeting the miR-186-5p/MACC1 axis. PMID:35279159
Chromosome-level genome assembly, annotation, and phylogenomics of the gooseneck barnacle Pollicipes pollicipes. PMID:35277961
Genome-wide transcript and protein analysis highlights the role of protein homeostasis in the aging mouse heart. PMID:35277432
Transcriptome characterization of Larrea tridentata and identification of genes associated with phenylpropanoid metabolic pathways. PMID:35275977
GATA4/5/6 family transcription factors are conserved determinants of cardiac versus pharyngeal mesoderm fate. PMID:35275720
Proteome Analysis of Urinary Biomarkers in a Bovine IRBP-Induced Uveitis Rat Model via Data-Independent Acquisition and Parallel Reaction Monitoring Proteomics. PMID:35274006
Pan-Cancer Analysis and Validation Reveals that D-Dimer-Related Genes are Prognostic and Downregulate CD8+ T Cells via TGF-Beta Signaling in Gastric Cancer. PMID:35274004
Integrative Analyses of Genes Associated With Otologic Disorders in Turner Syndrome. PMID:35273637
Centrosomal protein 290 is a novel prognostic indicator that modulates liver cancer cell ferroptosis via the Nrf2 pathway. PMID:35271462
Protoplast Dissociation and Transcriptome Analysis Provides Insights to Salt Stress Response in Cotton. PMID:35269989
Combined Transcriptomic and Proteomic Profiling of E. coli under Microaerobic versus Aerobic Conditions: The Multifaceted Roles of Noncoding Small RNAs and Oxygen-Dependent Sensing in Global Gene Expression Control. PMID:35269716
Comprehensive Analysis of the Effect of 20(R)-Ginsenoside Rg3 on Stroke Recovery in Rats via the Integrative miRNA-mRNA Regulatory Network. PMID:35268674
Learning Ability and Hippocampal Transcriptome Responses to Early and Later Life Environmental Complexities in Dual-Purpose Chicks. PMID:35268235
WhiB4 Is Required for the Reactivation of Persistent Infection of Mycobacterium marinum in Zebrafish. PMID:35266819
FlyBase: a guided tour of highlighted features. PMID:35266522
Yin Yang 1 regulates ITGAV and ITGB1, contributing to improved prognosis of colorectal cancer. PMID:35266011
A non-canonical tricarboxylic acid cycle underlies cellular identity. PMID:35264789
Uncovering the genetic profiles underlying the intrinsic organization of the human cerebellum. PMID:35264730
CRISPR/Cas9-Mediated Insertion of HIV Long Terminal Repeat within BACH2 Promotes Expansion of T Regulatory-like Cells. PMID:35264460
Comparative whole transcriptome analysis of Parkinson's disease focusing on the efficacy of zonisamide. PMID:35264450
A nonredundant role for T cell-derived interleukin 22 in antibacterial defense of colonic crypts. PMID:35263568
Whole genome sequence of pan drug-resistant clinical isolate of Acinetobacter baumannii ST1890. PMID:35263355
Urgent need for consistent standards in functional enrichment analysis. PMID:35263338
RNA-seq and integrated network analysis reveals the hub genes and key pathway of paclitaxel inhibition on Adriamycin resistant diffuse large B cell lymphoma cells. PMID:35263200
ImmuneData: an integrated data discovery system for immunology data repositories. PMID:35262674
Tsp-1 is involved in DNA stability through Tgf-β1 activation domain in cone photoreceptor 661 W cells. PMID:35260935
Computing microRNA-gene interaction networks in pan-cancer using miRDriver. PMID:35260634
Comparative analysis of the Mercenaria mercenaria genome provides insights into the diversity of transposable elements and immune molecules in bivalve mollusks. PMID:35260071
Identification of Potential Key Biomarkers and Immune Infiltration in Oral Lichen Planus. PMID:35256894
RNA-Seq reveals miRNA role in thermogenic regulation in brown adipose tissues of goats. PMID:35255830
A multi-network integration approach for measuring disease similarity based on ncRNA regulation and heterogeneous information. PMID:35255810
Whole-genome sequencing reveals host factors underlying critical COVID-19. PMID:35255492
Transcriptome Analysis of Plasmodium falciparum Isolates From Benin Reveals Specific Gene Expression Associated With Cerebral Malaria. PMID:35255125
Draft genome sequence of myo-inositol utilizing Aeromonas dhakensis 1P11S3 isolated from striped catfish (Pangasianodon hypopthalmus) in a local fish farm in Malaysia. PMID:35252492
Identification and Comprehensive Analysis of FREM2 Mutation as a Potential Prognostic Biomarker in Colorectal Cancer. PMID:35252356
Impact of Pals1 on Expression and Localization of Transporters Belonging to the Solute Carrier Family. PMID:35252349
Indolethylamine-N-Methyltransferase Inhibits Proliferation and Promotes Apoptosis of Human Prostate Cancer Cells: A Mechanistic Exploration. PMID:35252179
A High-Quality, Chromosome-Level Genome Provides Insights Into Determinate Flowering Time and Color of Cotton Rose (Hibiscus mutabilis). PMID:35251086
Genome and Comparative Transcriptome Dissection Provide Insights Into Molecular Mechanisms of Sclerotium Formation in Culinary-Medicinal Mushroom Pleurotus tuber-regium. PMID:35250915
Smoking Status and Type 2 Diabetes, and Cardiovascular Disease: A Comprehensive Analysis of Shared Genetic Etiology and Causal Relationship. PMID:35250867
iTRAQ Proteomic Analysis of Interactions Between 20E and Phospholipase C in Apolygus lucorum (Meyer-Dür). PMID:35250643
PM2.5 exposure during pregnancy is associated with altered placental expression of lipid metabolic genes in a US birth cohort. PMID:35248564
Plasma proteome changes linked to late phase response after inhaled allergen challenge in asthmatics. PMID:35248034
DrGA: cancer driver gene analysis in a simpler manner. PMID:35247965
Biomimetic radiosensitizers unlock radiogenetics for local interstitial radiotherapy to activate systematic immune responses and resist tumor metastasis. PMID:35246159
Human biliary epithelial cells from discarded donor livers rescue bile duct structure and function in a mouse model of biliary disease. PMID:35245467
Selective requirement for polycomb repressor complex 2 in the generation of specific hypothalamic neuronal subtypes. PMID:35245348
Immunomodulatory potential of in vivo natural killer T (NKT) activation by NKTT320 in Mauritian-origin cynomolgus macaques. PMID:35243248
Dynamic Control Balancing Cell Proliferation and Inflammation is Crucial for an Effective Immune Response to Malaria. PMID:35242812
Identification of Important Genes Involved in the Sex-Differentiation Mechanism of Oriental River Prawn, Macrobrachium nipponense, During the Gonad Differentiation and Development Period. PMID:35242165
Altered Expression of Specific MicroRNAs in Plasma of Aneurysmal Subarachnoid Hemorrhage Patients. PMID:35242102
Promoter/enhancer-based controllability of regulatory networks. PMID:35241702
Tig1 regulates proximo-distal identity during salamander limb regeneration. PMID:35241664
Upregulated YB-1 protein promotes glioblastoma growth through a YB-1/CCT4/mLST8/mTOR pathway. PMID:35239512
Benchmarking the proteomic profile of animal models of mesial temporal epilepsy. PMID:35238489
Methylation- and homologous recombination deficiency-related mutant genes predict the prognosis of lung adenocarcinoma. PMID:35238419
Modeling multi-scale data via a network of networks. PMID:35238343
Investigation of miR-21-5p Key Target Genes and Pathways in Head and Neck Squamous Cell Carcinoma Based on TCGA Database and Bioinformatics Analysis. PMID:35235474
Novel genetic basis of resistance to Bt toxin Cry1Ac in Helicoverpa zea. PMID:35234875
Detection of Prognostic Biomarkers for Hepatocellular Carcinoma through CircRNA-associated CeRNA Analysis. PMID:35233376
Landscape genomics of the streamside salamander: Implications for species management in the face of environmental change. PMID:35233244
The Glycolytic Gatekeeper PDK1 defines different metabolic states between genetically distinct subtypes of human acute myeloid leukemia. PMID:35232995
Connectomic-genetic signatures in the cerebral small vessel disease. PMID:35231560
Molecular phylogeography and species distribution modelling evidence of 'oceanic' adaptation for Actinidia eriantha with a refugium along the oceanic-continental gradient in a biodiversity hotspot. PMID:35227218
Comparative transcriptomes of three different skin sites for the Asiatic toad (Bufo gargarizans). PMID:35223212
SMRT sequencing of full-length transcriptome and gene expression analysis in two chemical types of Pogostemon cablin (Blanco) Benth. PMID:35223208
Polymerase II-Associated Factor 1 Complex-Regulated FLOWERING LOCUS C-Clade Genes Repress Flowering in Response to Chilling. PMID:35222476
Investigating the Mechanism of Unilateral Cross Incompatibility in Longan (Dimocarpus longan Lour.) Cultivars (Yiduo × Shixia). PMID:35222456
Single-Cell RNA Sequencing Identifies Intra-Graft Population Heterogeneity in Acute Heart Allograft Rejection in Mouse. PMID:35222420
Multi-Omics Profiling Specifies Involvement of Alternative Ribosomal Proteins in Response to Zinc Limitation in Mycobacterium smegmatis. PMID:35222334
Dynamic Gene Expression and Alternative Splicing Events Demonstrate Co-Regulation of Testicular Differentiation and Maturation by the Brain and Gonad in Common Carp. PMID:35222265
Single-Cell RNA Sequencing Characterizes the Molecular Heterogeneity of the Larval Zebrafish Optic Tectum. PMID:35221915
MYH10 Governs Adipocyte Function and Adipogenesis through Its Interaction with GLUT4. PMID:35216482
Transient Agarose Spot (TAS) Assay: A New Method to Investigate Cell Migration. PMID:35216230
Deciphering the Interactions of SARS-CoV-2 Proteins with Human Ion Channels Using Machine-Learning-Based Methods. PMID:35215201
Analysis of Liver Responses to Non-alcoholic Steatohepatitis by mRNA-Sequencing. PMID:35212994
Student biocuration projects as a learning environment. PMID:35211294
PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types. PMID:35208748
Application of Whole Exome Sequencing and Functional Annotations to Identify Genetic Variants Associated with Marfan Syndrome. PMID:35207686
Understanding of Waggle Dance in the Honey Bee (Apis mellifera) from the Perspective of Long Non-Coding RNA. PMID:35206685
Haplotype-Resolved Genome Analyses Reveal Genetically Distinct Nuclei within a Commercial Cultivar of Lentinula edodes. PMID:35205921
Genome-Wide Association Study Reveals Genetic Architecture and Candidate Genes for Yield and Related Traits under Terminal Drought, Combined Heat and Drought in Tropical Maize Germplasm. PMID:35205393
Genomic Analyses of the Fungus Paraconiothyrium sp. Isolated from the Chinese White Wax Scale Insect Reveals Its Symbiotic Character. PMID:35205383
Characterization of the Genomic Landscape in Cervical Cancer by Next Generation Sequencing. PMID:35205332
miRNA and lncRNA Expression Networks Modulate Cell Cycle and DNA Repair Inhibition in Senescent Prostate Cells. PMID:35205253
Unlocking the Memory Component of Alzheimer's Disease: Biological Processes and Pathways across Brain Regions. PMID:35204764
Single-Cell Sequencing Reveals an Intrinsic Heterogeneity of the Preovulatory Follicular Microenvironment. PMID:35204732
Benzaldehyde Attenuates the Fifth Stage Larval Excretory-Secretory Product of Angiostrongylus cantonensis-Induced Injury in Mouse Astrocytes via Regulation of Endoplasmic Reticulum Stress and Oxidative Stress. PMID:35204678
Phosphoproteomic Analysis of Breast Cancer-Derived Small Extracellular Vesicles Reveals Disease-Specific Phosphorylated Enzymes. PMID:35203617
Genes Involved in Immune Reinduction May Constitute Biomarkers of Response for Metastatic Melanoma Patients Treated with Targeted Therapy. PMID:35203494
Chemerin Impact on Alternative mRNA Transcription in the Porcine Luteal Cells. PMID:35203364
Stage-differentiated ensemble modeling of DNA methylation landscapes uncovers salient biomarkers and prognostic signatures in colorectal cancer progression. PMID:35202405
Molecular Details of Actinomycin D-Treated MRSA Revealed via High-Dimensional Data. PMID:35200643
Effect of Different Initial Fermentation pH on Exopolysaccharides Produced by Pseudoalteromonas agarivorans Hao 2018 and Identification of Key Genes Involved in Exopolysaccharide Synthesis via Transcriptome Analysis. PMID:35200619
Identification of Potential Immune Checkpoint Inhibitor Targets in Gliomas via Bioinformatic Analyses. PMID:35198632
Comparative transcriptome analysis provides insights into grain filling commonalities and differences between foxtail millet [Setaria italica (L.) P. Beauv.] varieties with different panicle types. PMID:35198264
Protective immune trajectories in early viral containment of non-pneumonic SARS-CoV-2 infection. PMID:35197461
Combined use of Oxford Nanopore and Illumina sequencing yields insights into soybean structural variation biology. PMID:35197050
Functional buffering via cell-specific gene expression promotes tissue homeostasis and cancer robustness. PMID:35194081
Cultivating Lentinula edodes on Substrate Containing Composted Sawdust Affects the Expression of Carbohydrate and Aromatic Amino Acid Metabolism-Related Genes. PMID:35191774
Clusterin as a serum biomarker candidate contributes to the lung fibroblasts activation in chronic obstructive pulmonary disease. PMID:35191419
Comparative proteome analysis reveals the role of negative floral regulators and defense-related genes in phytoplasma infected sesame. PMID:35190871
Physiological and transcriptome analysis reveals the differences in nitrate content between lamina and midrib of flue-cured tobacco. PMID:35190651
Modeling oxidative injury response in human kidney organoids. PMID:35189973
Proteome-defined changes in cellular pathways for decidua and trophoblast tissues associated with location and viability of early-stage pregnancy. PMID:35189928
Genomic characterization of the world's longest selection experiment in mouse reveals the complexity of polygenic traits. PMID:35189878
Genome assembly of the JD17 soybean provides a new reference genome for comparative genomics. PMID:35188189
Graph-guided Bayesian SVM with Adaptive Structured Shrinkage Prior for High-dimensional Data. PMID:35187547
Genome Sequences of Two Strains of Prototheca wickerhamii Provide Insight Into the Protothecosis Evolution. PMID:35186789
Wei2GO: weighted sequence similarity-based protein function prediction. PMID:35186498
Proteomic Analysis of the Antibacterial Effect of Improved Dian Dao San against Propionibacterium acnes. PMID:35186097
Genome-Wide Identification of Direct Targets of ZjVND7 Reveals the Putative Roles of Whole-Genome Duplication in Sour Jujube in Regulating Xylem Vessel Differentiation and Drought Tolerance. PMID:35185994
Integration of Small RNA and Transcriptome Sequencing Reveal the Roles of miR395 and ATP Sulfurylase in Developing Seeds of Chinese Kale. PMID:35185948
Analysis of Biosynthetic Gene Clusters, Secretory, and Antimicrobial Peptides Reveals Environmental Suitability of Exiguobacterium profundum PHM11. PMID:35185816
Efficient link prediction in the protein-protein interaction network using topological information in a generative adversarial network machine learning model. PMID:35183129
DVPred: a disease-specific prediction tool for variant pathogenicity classification for hearing loss. PMID:35182233
Quantitative multiplexed proteomics analysis reveals reshaping of the lysine 2-hydroxyisobutyrylome in Fusarium graminearum by tebuconazole. PMID:35180840
Evaluating the detection ability of a range of epistasis detection methods on simulated data for pure and impure epistatic models. PMID:35180244
Muscle mitochondrial remodeling by intermittent glucocorticoid drugs requires an intact circadian clock and muscle PGC1α. PMID:35179955
Hypertrophic chondrocytes serve as a reservoir for marrow-associated skeletal stem and progenitor cells, osteoblasts, and adipocytes during skeletal development. PMID:35179487
Chromosome-scale assembly and population diversity analyses provide insights into the evolution of Sapindus mukorossi. PMID:35178562
Comparative transcriptome and weighted correlation network analyses reveal candidate genes involved in chlorogenic acid biosynthesis in sweet potato. PMID:35177832
Differential Transcriptome Analysis Reveals Genes Related to Low- and High-Temperature Stress in the Fall Armyworm, Spodoptera frugiperda. PMID:35173626
Time-course RNA-seq analysis reveals stage-specific and melatonin-triggered gene expression patterns during the hair follicle growth cycle in Capra hircus. PMID:35172715
Mechanism of action of Tripterygium wilfordii for treatment of idiopathic membranous nephropathy based on network pharmacology. PMID:35172688
Zika virus disrupts gene expression in human myoblasts and myotubes: Relationship with susceptibility to infection. PMID:35171909
The m6A(m)-independent role of FTO in regulating WNT signaling pathways. PMID:35169043
Haloterrigena gelatinilytica sp. nov., a new extremely halophilic archaeon isolated from salt-lake. PMID:35166931
Zebrafish information network, the knowledgebase for Danio rerio research. PMID:35166825
Factors That Affect the Rates of Adaptive and Nonadaptive Evolution at the Gene Level in Humans and Chimpanzees. PMID:35166775
Hyaluronidase-1-mediated glycocalyx impairment underlies endothelial abnormalities in polypoidal choroidal vasculopathy. PMID:35164755
MonaGO: a novel gene ontology enrichment analysis visualisation system. PMID:35164667
Comprehensive Detoxification Mechanism Assessment of Red Imported Fire Ant (Solenopsis invicta) against Indoxacarb. PMID:35164134
A Photosensitized Singlet Oxygen (1O2) Toolbox for Bio-Organic Applications: Tailoring 1O2 Generation for DNA and Protein Labelling, Targeting and Biosensing. PMID:35164045
Insights into the Steps of Breast Cancer-Brain Metastases Development: Tumor Cell Interactions with the Blood-Brain Barrier. PMID:35163822
Cold Exposure Drives Weight Gain and Adiposity following Chronic Suppression of Brown Adipose Tissue. PMID:35163791
Pleiotropic, Unique and Shared Responses Elicited by IL-6 Family Cytokines in Human Vascular Endothelial Cells. PMID:35163371
Interactome of Arabidopsis Thaliana. PMID:35161331
Analysis of Global Gene Expression in Maize (Zea mays) Vegetative and Reproductive Tissues That Differ in Accumulation of Starch and Sucrose. PMID:35161219
Single-cell dissection of the human brain vasculature. PMID:35158371
Analysis of miRNAs Involved in Mouse Heart Injury Upon Coxsackievirus A2 Infection. PMID:35155276
Low-Level Laser Therapy Effects on Rat Blood Hemostasis Via Significant Alteration in Fibrinogen and Plasminogen Expression Level. PMID:35155144
Investigating changes of proteome in the bovine milk serum after retort processing using proteomics techniques. PMID:35154669
An Augmented High-Dimensional Graphical Lasso Method to Incorporate Prior Biological Knowledge for Global Network Learning. PMID:35154240
The Landscape of Aminoacyl-tRNA Synthetases Involved in Severe Acute Respiratory Syndrome Coronavirus 2 Infection. PMID:35153822
Gene-Interaction-Sensitive enrichment analysis in congenital heart disease. PMID:35151364
Genome-wide RNAi screen identifies novel players in human 60S subunit biogenesis including key enzymes of polyamine metabolism. PMID:35150276
Adipose-derived stem cell spheroids are superior to single-cell suspensions to improve fat autograft long-term survival. PMID:35150064
BMP4 preserves the developmental potential of mESCs through Ube2s- and Chmp4b-mediated chromosomal stability safeguarding. PMID:35147915
Data Integration Challenges for Machine Learning in Precision Medicine. PMID:35145977
Classification and Association Analysis of Gerbera (Gerbera hybrida) Flower Color Traits. PMID:35145530
Identification of recurrent genetic patterns from targeted sequencing panels with advanced data science: a case-study on sporadic and genetic neurodegenerative diseases. PMID:35144616
Micronutrient supplementation affects DNA methylation in male gonads with potential intergenerational epigenetic inheritance involving the embryonic development through glutamate receptor-associated genes. PMID:35144563
Zebrafish models of alx-linked frontonasal dysplasia reveal a role for Alx1 and Alx3 in the anterior segment and vasculature of the developing eye. PMID:35142342
Upregulation of CD14 in mesenchymal stromal cells accelerates lipopolysaccharide-induced response and enhances antibacterial properties. PMID:35141503
Genome Sequencing of Hericium coralloides by a Combination of PacBio RS II and Next-Generation Sequencing Platforms. PMID:35141329
Construction and Analysis of the lncRNA-miRNA-mRNA Network Based on Competing Endogenous RNA in Atrial Fibrillation. PMID:35141302
Metabolic labeling of secreted matrix to investigate cell-material interactions in tissue engineering and mechanobiology. PMID:35140408
Characterization of a small molecule inhibitor of disulfide reductases that induces oxidative stress and lethality in lung cancer cells. PMID:35139387
Network inference with Granger causality ensembles on single-cell transcriptomics. PMID:35139376
Deficiency of ribosomal proteins reshapes the transcriptional and translational landscape in human cells. PMID:35137207
Sperm acquire epididymis-derived proteins through epididymosomes. PMID:35137089
The genome of the Paleogene relic tree Bretschneidera sinensis: insights into trade-offs in gene family evolution, demographic history, and adaptive SNPs. PMID:35137004
Protein phase separation hotspots at the presynapse. PMID:35135293
Deciphering the etiology and role in oncogenic transformation of the CpG island methylator phenotype: a pan-cancer analysis. PMID:35134107
PRDM paralogs antagonistically balance Wnt/β-catenin activity during craniofacial chondrocyte differentiation. PMID:35132438
A High-Density Genetic Map Enables Genome Synteny and QTL Mapping of Vegetative Growth and Leaf Traits in Gardenia. PMID:35132310
Comparative population genomics in Tabebuia alliance shows evidence of adaptation in Neotropical tree species. PMID:35132209
Common DNA methylation changes in biliary tract cancers identify subtypes with different immune characteristics and clinical outcomes. PMID:35130881
Extensive age-dependent loss of antibody diversity in naturally short-lived turquoise killifish. PMID:35129436
Leaf color formation mechanisms in Alternanthera bettzickiana elucidated by metabolite and transcriptome analyses. PMID:35128619
β-catenin perturbations control differentiation programs in mouse embryonic stem cells. PMID:35128356
Identification of Key Genes and Pathways Involved in Circulating Tumor Cells in Colorectal Cancer. PMID:35127345
Shared Genetic Architecture and Causal Relationship Between Asthma and Cardiovascular Diseases: A Large-Scale Cross-Trait Analysis. PMID:35126453
GRAND: An Integrated Genome, Transcriptome Resources, and Gene Network Database for Gossypium. PMID:35126443
Identification of the Association Between Toll-Like Receptors and T-Cell Activation in Takayasu's Arteritis. PMID:35126357
Exploring the total flavones of Abelmoschus manihot against IAV-induced lung inflammation by network pharmacology. PMID:35123452
RNF2 ablation reprograms the tumor-immune microenvironment and stimulates durable NK and CD4+ T-cell-dependent antitumor immunity. PMID:35121884
Systems-based approaches to study immunometabolism. PMID:35121805
Genomic basis for skin phenotype and cold adaptation in the extinct Steller's sea cow. PMID:35119923
Dynamic effects of chronic unpredictable mild stress on the hippocampal transcriptome in rats. PMID:35119083
PANDA2: protein function prediction using graph neural networks. PMID:35118378
Field cancerization profile-based prognosis signatures lead to more robust risk evaluation in hepatocellular carcinoma. PMID:35118360
Identification of key biomarkers and potential signaling pathway associated with poor progression of gastric cancer. PMID:35117911
Identification of biomarkers in colon cancer based on bioinformatic analysis. PMID:35117850
Key genes involved in cell cycle arrest and DNA damage repair identified in anaplastic thyroid carcinoma using integrated bioinformatics analysis. PMID:35117787
Candidate genes for predicting the survival of patients with gastric cancer: a study based on The Cancer Genome Atlas (TCGA) database. PMID:35117619
Identification of adriamycin resistance genes in breast cancer based on microarray data analysis. PMID:35117349
Discovered differentially expressed lncRNA AC010973.2 can act as a diagnostic and prognostic biomarker for colon adenocarcinoma. PMID:35117237
Blockade of AXL activation overcomes acquired resistance to EGFR tyrosine kinase inhibition in non-small cell lung cancer. PMID:35116995
Construction of a prognostic risk model of colorectal adenocarcinoma through integrated analysis of RNA-binding proteins. PMID:35116519
Integrated bioinformatics analysis to identify key genes related to the prognosis of esophageal squamous cell carcinoma. PMID:35116493
KRAS, YWHAE, SP1 and MSRA as biomarkers in endometrial cancer. PMID:35116456
Identification of key genes involved in tamoxifen-resistant breast cancer using bioinformatics analysis. PMID:35116374
Transcriptome analysis of the effect of a novel human serine protease inhibitor SPINK13 on gene expression in MHCC97-H cells. PMID:35116303
Identification of Inflammation-Related Biomarker Pro-ADM for Male Patients With Gout by Comprehensive Analysis. PMID:35116032
Kinsenoside Alleviates Alcoholic Liver Injury by Reducing Oxidative Stress, Inhibiting Endoplasmic Reticulum Stress, and Regulating AMPK-Dependent Autophagy. PMID:35115920
First genome-wide association study investigating blood pressure and renal traits in domestic cats. PMID:35115544
Computational image features of immune architecture is associated with clinical benefit and survival in gynecological cancers across treatment modalities. PMID:35115363
Systems pharmacology-based drug discovery and active mechanism of natural products for coronavirus pneumonia (COVID-19): An example using flavonoids. PMID:35114443
Maladaptive functional changes in alveolar fibroblasts due to perinatal hyperoxia impair epithelial differentiation. PMID:35113810
Probabilistic Graphical Models Applied to Biological Networks. PMID:35113399
Modern Approaches for Transcriptome Analyses in Plants. PMID:35113394
Deep learning program to predict protein functions based on sequence information. PMID:35111575
Use of Transposon Directed Insertion-Site Sequencing to Probe the Antibacterial Mechanism of a Model Honey on E. coli K-12. PMID:35111142
Screening of Important Markers in Peripheral Blood Mononuclear Cells to Predict Female Osteoporosis Risk Using LASSO Regression Algorithm and SVM Method. PMID:35110962
Neuropeptidergic regulation of compulsive ethanol seeking in C. elegans. PMID:35110557
Precise gene models using long-read sequencing reveal a unique poly(A) signal in Giardia lamblia. PMID:35110372
DDX10 promotes the proliferation and metastasis of colorectal cancer cells via splicing RPL35. PMID:35109823
Deep models of integrated multiscale molecular data decipher the endothelial cell response to ionizing radiation. PMID:35106469
Two heads are better than one: current landscape of integrating QSP and machine learning : An ISoP QSP SIG white paper by the working group on the integration of quantitative systems pharmacology and machine learning. PMID:35103884
Chronic Marijuana Use Is Associated with Gene Expression Changes in BAL. PMID:35103554
An in silico analysis identifies drugs potentially modulating the cytokine storm triggered by SARS-CoV-2 infection. PMID:35102208
Universal prediction of cell-cycle position using transfer learning. PMID:35101061
De novo and comparative transcriptomic analysis explain morphological differences in Panax notoginseng taproots. PMID:35100996
Expression profiles and functions of ferroptosis-related genes in the placental tissue samples of early- and late-onset preeclampsia patients. PMID:35100981
Fission stories: using PomBase to understand Schizosaccharomyces pombe biology. PMID:35100366
Effects of abolishing Whi2 on the proteome and nitrogen catabolite repression-sensitive protein production. PMID:35100365
Endothelial Cell RNA-Seq Data: Differential Expression and Functional Enrichment Analyses to Study Phenotypic Switching. PMID:35099752
Subcellular proteomics of dopamine neurons in the mouse brain. PMID:35098924
Inter-tissue convergence of gene expression during ageing suggests age-related loss of tissue and cellular identity. PMID:35098922
Exploration of the Role of Serine Proteinase Inhibitor A3 in Alcohol Dependence Using Gene Expression Omnibus Database. PMID:35095596
Draft Genome Sequence of Oceanobacillus jordanicus Strain GSFE11, a Halotolerant Plant Growth-Promoting Bacterial Endophyte Isolated From the Jordan Valley. PMID:35095268
DisEnrich: Database of Enriched Regions in Human Dark Proteome. PMID:35094056
Mapping the invisible chromatin transactions of prophase chromosome remodeling. PMID:35090599
Making sense of the linear genome, gene function and TADs. PMID:35090532
Risk stratification of gastrointestinal stromal tumors by Nanostring gene expression profiling. PMID:35089395
Increased trunk fat is associated with altered gene expression in breast tissue of normal weight women. PMID:35087024
Simple But Efficacious Enrichment of Integral Membrane Proteins and Their Interactions for In-Depth Membrane Proteomics. PMID:35085786
From communities to protein complexes: A local community detection algorithm on PPI networks. PMID:35085263
Dynamic Functional Connectivity Alterations and Their Associated Gene Expression Pattern in Autism Spectrum Disorders. PMID:35082596
Gene and metabolite expression dependence on body mass index in human myocardium. PMID:35082386
Differential roles for DNAJ isoforms in HTT-polyQ and FUS aggregation modulation revealed by chaperone screens. PMID:35082301
Proteomic screen reveals diverse protein transport between connected neurons in the visual system. PMID:35081342
Hierarchical regulation of autophagy during adipocyte differentiation. PMID:35081114
Enhancing CDK4/6 inhibitor therapy for medulloblastoma using nanoparticle delivery and scRNA-seq-guided combination with sapanisertib. PMID:35080986
Comparison of Epidermal Gene Expression Profiles in Mice Aged 1 to 20 Months. PMID:35079219
Haploidy in somatic cells is induced by mature oocytes in mice. PMID:35079104
Characterization of the COPD alveolar niche using single-cell RNA sequencing. PMID:35078977
The role of SPI1-TYROBP-FCER1G network in oncogenesis and prognosis of osteosarcoma, and its association with immune infiltration. PMID:35078433
Graphlet eigencentralities capture novel central roles of genes in pathways. PMID:35077468
A simple guide to de novo transcriptome assembly and annotation. PMID:35076693
Proteome alterations in the aqueous humor reflect structural and functional phenotypes in patients with advanced normal-tension glaucoma. PMID:35075201
Interventional- and amputation-stage muscle proteomes in the chronically threatened ischemic limb. PMID:35073463
Evaluation of deep convolutional neural networks for in situ hybridization gene expression image representation. PMID:35073334
A simplified protocol for performing MAGMA/H-MAGMA gene set analysis utilizing high-performance computing environments. PMID:35072112
Identification of Molecular Biomarkers and Key Pathways for Esophageal Carcinoma (EsC): A Bioinformatics Approach. PMID:35071597
A comprehensive characterization of the transcriptome in enzalutamide resistance prostate cancer. PMID:35071476
Identification of key genes associated with esophageal adenocarcinoma based on bioinformatics analysis. PMID:35071405
Prediction of the Mechanisms by Which Quercetin Enhances Cisplatin Action in Cervical Cancer: A Network Pharmacology Study and Experimental Validation. PMID:35070983
Violations of proportional hazard assumption in Cox regression model of transcriptomic data in TCGA pan-cancer cohorts. PMID:35070171
Potential biomarkers of acute myocardial infarction based on co-expression network analysis. PMID:35069843
Integrative Analysis of the Metabolome and Transcriptome of a Cultivated Pepper and Its Wild Progenitor Chiltepin (Capsicum annuum L. var. glabriusculum) Revealed the Loss of Pungency During Capsicum Domestication. PMID:35069640
Aggregatimonas sangjinii gen. nov., sp. nov., a novel silver nanoparticle synthesizing bacterium belonging to the family Flavobacteriaceae. PMID:35066733
RNA-seq-based transcriptomic analysis of AHL-induced biofilm and pyocyanin inhibition in Pseudomonas aeruginosa by Lactobacillus brevis. PMID:35066679
A functional cellular framework for sex and estrous cycle-dependent gene expression and behavior. PMID:35065713
Tissue-specific multi-omics analysis of atrial fibrillation. PMID:35064145
HERV-W Envelope Triggers Abnormal Dopaminergic Neuron Process through DRD2/PP2A/AKT1/GSK3 for Schizophrenia Risk. PMID:35062349
Molecular mechanism of inhibitory effects of melatonin on prostate cancer cell proliferation, migration and invasion. PMID:35061708
Transcriptomic profiling suggests candidate molecular responses to waterlogging in cassava. PMID:35061680
Differences in peripheral immune system gene expression in frontotemporal degeneration. PMID:35060553
Identification of inflammatory response and alternative splicing in acute kidney injury and experimental verification of the involvement of RNA‑binding protein RBFOX1 in this disease. PMID:35059728
Scenes From Tick Physiology: Proteins of Sialome Talk About Their Biological Processes. PMID:35059322
A Pilot Study of Gene Expression Analysis in Peripheral Blood Mononuclear Cells in Response to a Hypocaloric Mediterranean Diet. PMID:35059043
Early-life viral infections are associated with disadvantageous immune and microbiota profiles and recurrent respiratory infections. PMID:35058634
Quantitative Proteome and Transcriptome Dynamics Analysis Reveals Iron Deficiency Response Networks and Signature in Neuronal Cells. PMID:35056799
Transcriptome Analysis of Arbuscular Mycorrhizal Casuarina glauca in Damage Mitigation of Roots on NaCl Stress. PMID:35056464
Bacillus amyloliquefaciens SN16-1-Induced Resistance System of the Tomato against Rhizoctonia solani. PMID:35055983
The Fungus Metarhizium sp. BCC 4849 Is an Effective and Safe Mycoinsecticide for the Management of Spider Mites and Other Insect Pests. PMID:35055885
Biallelic Variants in PYROXD2 Cause a Severe Infantile Metabolic Disorder Affecting Mitochondrial Function. PMID:35055180
Towards an Ideal In Cell Hybridization-Based Strategy to Discover Protein Interactomes of Selected RNA Molecules. PMID:35055128
Identification of Core Genes and Pathways in Melanoma Metastasis via Bioinformatics Analysis. PMID:35054979
Thirteen Independent Genetic Loci Associated with Preserved Processing Speed in a Study of Cognitive Resilience in 330,097 Individuals in the UK Biobank. PMID:35052462
Identification of Phosphorus Stress Related Proteins in the Seedlings of Dongxiang Wild Rice (Oryza Rufipogon Griff.) Using Label-Free Quantitative Proteomic Analysis. PMID:35052448
Single-Cell Analysis of Aneurysmal Aortic Tissue in Patients with Marfan Syndrome Reveals Dysfunctional TGF-β Signaling. PMID:35052435
Capturing SNP Association across the NK Receptor and HLA Gene Regions in Multiple Sclerosis by Targeted Penalised Regression Models. PMID:35052430
Effects of the Expression of Random Sequence Clones on Growth and Transcriptome Regulation in Escherichia coli. PMID:35052392
Meta-Analysis of Transcriptome-Wide Association Studies across 13 Brain Tissues Identified Novel Clusters of Genes Associated with Nicotine Addiction. PMID:35052378
An Integrative Sialomic Analysis Reveals Molecules From Triatoma sordida (Hemiptera: Reduviidae). PMID:35047420
Targeted gene silencing in the nervous system with CRISPR-Cas13. PMID:35044815
Chromosomal-level genome and multi-omics dataset of Pueraria lobata var. thomsonii provide new insights into legume family and the isoflavone and puerarin biosynthesis pathways. PMID:35043180
Interaction of Periplasmic Fab Production and Intracellular Redox Balance in Escherichia coli Affects Product Yield. PMID:35041397
Inflammatory activation and immune cell infiltration are main biological characteristics of SARS-CoV-2 infected myocardium. PMID:35037831
Identification of potential immunotherapy biomarkers for breast cancer by bioinformatics analysis. PMID:35037689
Identification of prognostic biomarkers in papillary renal cell carcinoma and PTTG1 may serve as a biomarker for predicting immunotherapy response. PMID:35037540
The initial expression alterations occurring to transcription factors during the formation of breast cancer: Evidence from bioinformatics. PMID:35037412
Key genes associated with prognosis and metastasis of clear cell renal cell carcinoma. PMID:35036081
Screening and Identification of Key Biomarkers in Lower Grade Glioma via Bioinformatical Analysis. PMID:35035531
Quantitative Metaproteomics and Activity-based Protein Profiling of Patient Fecal Microbiome Identifies Host and Microbial Serine-type Endopeptidase Activity Associated With Ulcerative Colitis. PMID:35033677
Core promoter mutation contributes to abnormal gene expression in bladder cancer. PMID:35033028
Transcriptome analysis of Auricularia fibrillifera fruit-body responses to drought stress and rehydration. PMID:35033026
Assigning protein function from domain-function associations using DomFun. PMID:35033002
Pathogen resistance in Sphagneticola trilobata (Singapore daisy): molecular associations and differentially expressed genes in response to disease from a widespread fungus. PMID:35031940
Comparative transcriptome analysis of the cold resistance of the sterile rice line 33S. PMID:35030196
BATF promotes group 2 innate lymphoid cell-mediated lung tissue protection during acute respiratory virus infection. PMID:35030033
Schisandrin B suppresses osteosarcoma lung metastasis in vivo by inhibiting the activation of the Wnt/β‑catenin and PI3K/Akt signaling pathways. PMID:35029287
Promising novel biomarkers and candidate small-molecule drugs for lung adenocarcinoma: Evidence from bioinformatics analysis of high-throughput data. PMID:35028418
Identification of Differentially Expressed Genes and Pathways in Human Atrial Fibrillation by Bioinformatics Analysis. PMID:35023949
GWAS and ExWAS of blood mitochondrial DNA copy number identifies 71 loci and highlights a potential causal role in dementia. PMID:35023831
The amniotic fluid proteome changes with gestational age in normal pregnancy: a cross-sectional study. PMID:35022423
Subcellular and regional localization of mRNA translation in midbrain dopamine neurons. PMID:35021090
Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. PMID:35021063
Endothelial and systemic upregulation of miR-34a-5p fine-tunes senescence in progeria. PMID:35020601
Recombinant HNP-1 Produced by Escherichia coli Triggers Bacterial Apoptosis and Exhibits Antibacterial Activity against Drug-Resistant Bacteria. PMID:35019682
Chromosome-level genome assembly of Bactrocera dorsalis reveals its adaptation and invasion mechanisms. PMID:35017661
Identification of the pivotal role of SPP1 in kidney stone disease based on multiple bioinformatics analysis. PMID:35016690
The impact of methodology on the reproducibility and rigor of DNA methylation data. PMID:35013473
RNAseq reveals extensive metabolic disruptions in the sensitive SF-295 cell line treated with schweinfurthins. PMID:35013404
Age-dependent pathogenic characteristics of SARS-CoV-2 infection in ferrets. PMID:35013229
Titanium with nanotopography attenuates the osteoclast-induced disruption of osteoblast differentiation by regulating histone methylation. PMID:35012895
Transcriptomic analysis of Pseudomonas ogarae F113 reveals the antagonistic roles of AmrZ and FleQ during rhizosphere adaption. PMID:35012704
The genome of oil-Camellia and population genomics analysis provide insights into seed oil domestication. PMID:35012630
Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients. PMID:35012625
Comprehensive analysis of expression profile and prognostic significance of interferon regulatory factors in pancreatic cancer. PMID:35012444
Potential biomarkers and signaling pathways associated with the pathogenesis of primary salivary gland carcinoma: a bioinformatics study. PMID:35012286
Altered White Matter and microRNA Expression in a Murine Model Related to Williams Syndrome Suggests That miR-34b/c Affects Brain Development via Ptpru and Dcx Modulation. PMID:35011720
TMT Quantitative Proteomics Analysis Reveals the Effects of Transport Stress on Iron Metabolism in the Liver of Chicken. PMID:35011158
Systems Biology-Derived Genetic Signatures of Mastitis in Dairy Cattle: A New Avenue for Drug Repurposing. PMID:35011134
Inhibitory Effect and Potential Mechanism of Lactobacillus plantarum YE4 against Dipeptidyl Peptidase-4. PMID:35010205
Genome-Wide Variation Analysis of Four Vegetable Soybean Cultivars Based on Re-Sequencing. PMID:35009032
IL-17 Pathway Members as Potential Biomarkers of Effective Systemic Treatment and Cardiovascular Disease in Patients with Moderate-to-Severe Psoriasis. PMID:35008981
Catalase (CAT) Gene Family in Wheat (Triticum aestivum L.): Evolution, Expression Pattern and Function Analysis. PMID:35008967
The Stroma Liquid Biopsy Panel Contains a Stromal-Epithelial Gene Signature Ratio That Is Associated with the Histologic Tumor-Stroma Ratio and Predicts Survival in Colon Cancer. PMID:35008327
Chromatin profiling reveals heterogeneity in clinical isolates of the human pathogen Aspergillus fumigatus. PMID:35007279
LPCAT1 functions as a novel prognostic molecular marker in hepatocellular carcinoma. PMID:35005115
Transcriptomic Responses of Cordyceps militaris to Salt Treatment During Cordycepins Production. PMID:35004818
Decreased miR-940 expression can predict a negative prognosis in early-stage nonsmoking female lung adenocarcinoma. PMID:35004257
Searching beyond the streetlight: Neonicotinoid exposure alters the neurogenomic state of worker honey bees. PMID:35003705
Identification of Keratinocyte Differentiation-Involved Genes for Metastatic Melanoma by Gene Expression Profiles. PMID:35003328
The In Vivo Transcriptomic Blueprint of Mycobacterium tuberculosis in the Lung. PMID:35003075
Genome Characteristics Reveal the Biocontrol Potential of Actinobacteria Isolated From Sugarcane Rhizosphere. PMID:35003029
Relationship Between KCNQ1 Polymorphism and Type 2 Diabetes Risk in Northwestern China. PMID:35002291
ADAMTS8 Expression is a Potential Prognostic Biomarker for Postoperative Metastasis in Lymph Node-Negative Early-Stage Invasive Breast Carcinoma Patients. PMID:35002288
oCEM: Automatic detection and analysis of overlapping co-expressed gene modules. PMID:34998362
Identification of an at-risk subpopulation with high immune infiltration based on the peroxisome pathway and TIM3 in colorectal cancer. PMID:34996408
Limb development genes underlie variation in human fingerprint patterns. PMID:34995520
Genomic profiling and expression analysis of the diacylglycerol kinase gene family in heterologous hexaploid wheat. PMID:34993014
Insight Into the Multiple Branches Traits of a Mutant in Larix olgensis by Morphological, Cytological, and Transcriptional Analyses. PMID:34992622
HESML: a real-time semantic measures library for the biomedical domain with a reproducible survey. PMID:34991460
The cold adaption profiles of Pseudoalteromonas shioyasakiensis D1497 from Yap trench to cope with cold. PMID:34987981
RNA profiles reveal signatures of future health and disease in pregnancy. PMID:34987224
Human Astrocytes Exhibit Tumor Microenvironment-, Age-, and Sex-Related Transcriptomic Signatures. PMID:34987109
Exploration the potential mechanism of the SIRT1 and its target gene FOXO1/PPARGC1A in uteropelvic junction obstruction. PMID:34984185
Inferring the genetic responses to acute drought stress across an ecological gradient. PMID:34983380
Interaction with mammalian enteric viruses alters outer membrane vesicle production and content by commensal bacteria. PMID:34981901
Structure-function relationships of the disease-linked A218T oxytocin receptor variant. PMID:34980886
Robust normalization and transformation techniques for constructing gene coexpression networks from RNA-seq data. PMID:34980209
Screening and analysis of RNAs associated with activated memory CD4 and CD8 T cells in liver cancer. PMID:34980144
Identification of Pueraria spp. through DNA barcoding and comparative transcriptomics. PMID:34979934
Genome-wide association studies for growth traits in broilers. PMID:34979907
Capturing the transcription factor interactome in response to sub-lethal insecticide exposure. PMID:34977825
Antigen presentation and interferon signatures in B cells driven by localized ablative cancer immunotherapy correlate with extended survival. PMID:34976205
A Novel Model of Tumor-Infiltrating B Lymphocyte Specific RNA-Binding Protein-Related Genes With Potential Prognostic Value and Therapeutic Targets in Multiple Myeloma. PMID:34976013
Metabolite and Transcriptome Profiling Analysis Revealed That Melatonin Positively Regulates Floral Scent Production in Hedychium coronarium. PMID:34975998
Preconditioning With Intermittent Hypobaric Hypoxia Attenuates Stroke Damage and Modulates Endocytosis in Residual Neurons. PMID:34975719
The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping. PMID:34971560
Establishment of Human Pluripotent Stem Cell-Derived Skin Organoids Enabled Pathophysiological Model of SARS-CoV-2 Infection. PMID:34971128
Protein Function Prediction Based on PPI Networks: Network Reconstruction vs Edge Enrichment. PMID:34970299
Ultradian rhythms of AKT phosphorylation and gene expression emerge in the absence of the circadian clock components Per1 and Per2. PMID:34968386
High Expression of CEMIP Correlates Poor Prognosis and the Tumur Microenvironment in Breast Cancer as a Promisingly Prognostic Biomarker. PMID:34966410
Network pharmacology-based strategy to investigate the active ingredients and molecular mechanisms of Scutellaria Barbata D. Don against radiation pneumonitis. PMID:34964782
Bioinformatics study on different gene expression profiles of fibroblasts and vascular endothelial cells in keloids. PMID:34964740
Bioinformatics analysis of candidate genes and potential therapeutic drugs targeting adipose tissue in obesity. PMID:34964707
Mongoliitalea daihaiensis sp. nov., isolated from Daihai Lake in Inner Mongolia. PMID:34962584
CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research. PMID:34961276
Dichotomous Responses to Chronic Fetal Hypoxia Lead to a Predetermined Aging Phenotype. PMID:34958949
Integrated Gene Expression Profiling Analysis Reveals Potential Molecular Mechanisms and Candidate Biomarkers for Early Risk Stratification and Prediction of STEMI and Post-STEMI Heart Failure Patients. PMID:34957234
Integral Analyses of Competing Endogenous RNA Mechanisms and DNA Methylation Reveal Regulatory Mechanisms in Osteosarcoma. PMID:34957096
Combined Metabolome and Transcriptome Analyses of Young, Mature, and Old Rhizome Tissues of Zingiber officinale Roscoe. PMID:34956334
Unraveling Admixture, Inbreeding, and Recent Selection Signatures in West African Indigenous Cattle Populations in Benin. PMID:34956303
Ontology-Enriched Specifications Enabling Findable, Accessible, Interoperable, and Reusable Marine Metagenomic Datasets in Cyberinfrastructure Systems. PMID:34956127
Single-Larva RNA Sequencing Identifies Markers of Copper Toxicity and Exposure in Early Mytilus californianus Larvae. PMID:34955868
Dynamic immune response characteristics of piglets infected with Actinobacillus pleuropneumoniae through omic. PMID:34952961
A Novel Four-Gene Signature as a Potential Prognostic Biomarker for Hepatocellular Carcinoma. PMID:34950206
IgA-Dominated Humoral Immune Responses Govern Patients' Outcome in Endometrial Cancer. PMID:34949671
Limited allele-specific gene expression in highly polyploid sugarcane. PMID:34949669
GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data. PMID:34949163
Human TRMT112-Methyltransferase Network Consists of Seven Partners Interacting with a Common Co-Factor. PMID:34948388
Physiological, Biochemical and Transcriptomic Analysis of the Aerial Parts (Leaf-Blade and Petiole) of Asarum sieboldii Responding to Drought Stress. PMID:34948197
Targeted Therapy Modulates the Secretome of Cancer-Associated Fibroblasts to Induce Resistance in HER2-Positive Breast Cancer. PMID:34948097
Comparative Transcriptomics and Gene Knockout Reveal Virulence Factors of Arthrinium phaeospermum in Bambusa pervariabilis × Dendrocalamopsis grandis. PMID:34946984
Longitudinal Changes in Cortical Thickness in Adolescents with Autism Spectrum Disorder and Their Association with Restricted and Repetitive Behaviors. PMID:34946972
Analysis of Serum Biochemical Indexes, Egg Quality, and Liver Transcriptome in Laying Hens Fed Diets Supplemented with Gynostemma pentaphyllum Powder. PMID:34946891
Bioinformatic Analysis Identified Hub Genes Associated with Heterocyclic Amines Induced Cytotoxicity of Peripheral Blood Mononuclear Cells. PMID:34946837
MicroRNA Analysis of Human Stroke Brain Tissue Resected during Decompressive Craniectomy/Stroke-Ectomy Surgery. PMID:34946809
In Silico Investigation of the Biological Implications of Complex DNA Damage with Emphasis in Cancer Radiotherapy through a Systems Biology Approach. PMID:34946681
Mining the Genome of Bacillus velezensis VB7 (CP047587) for MAMP Genes and Non-Ribosomal Peptide Synthetase Gene Clusters Conferring Antiviral and Antifungal Activity. PMID:34946111
Genomic and Metabolic Features of an Unexpectedly Predominant, Thermophilic, Assistant Starter Microorganism, Thermus thermophilus, in Chinese Inner Mongolian Cheese. PMID:34945513
Transcription Factors Active in the Anterior Blastema of Schmidtea mediterranea. PMID:34944426
Comparative Transcriptomic Analysis of Regenerated Skins Provides Insights into Cutaneous Air-Breathing Formation in Fish. PMID:34943209
Full-Length Transcriptome Sequencing of the Scleractinian Coral Montipora foliosa Reveals the Gene Expression Profile of Coral-Zooxanthellae Holobiont. PMID:34943189
Co-existing TP53 and ARID1A mutations promote aggressive endometrial tumorigenesis. PMID:34941867
Mechanisms underlying Clostridium pasteurianum's metabolic shift when grown with Geobacter sulfurreducens. PMID:34939136
Proteomic profiling reveals engineered chitosan nanoparticles mediated cellular crosstalk and immunomodulation for therapeutic application in apical periodontitis. PMID:34938914
Gene expression and epigenetic responses of the marine Cladoceran, Evadne nordmanni, and the copepod, Acartia clausi, to elevated CO2. PMID:34938472
Extensive mitochondrial proteome disturbance occurs during the early stages of acute myocardial ischemia. PMID:34938367
Identification and Characterization of Circular RNAs in Association With the Deposition of Intramuscular Fat in Aohan Fine-Wool Sheep. PMID:34938314
Biosafety and Proteome Profiles of Different Heat Inactivation Methods for Mycobacterium tuberculosis. PMID:34937194
Epigenome-wide three-way interaction study identifies a complex pattern between TRIM27, KIAA0226, and smoking associated with overall survival of early-stage NSCLC. PMID:34932879
Identification of starch candidate genes using SLAF-seq and BSA strategies and development of related SNP-CAPS markers in tetraploid potato. PMID:34932571
Identification of Potential Genetic Biomarkers and Target Genes of Peri-Implantitis Using Bioinformatics Tools. PMID:34931168
Comparative transcriptome and DNA methylation analysis in temperature-sensitive genic male sterile wheat BS366. PMID:34930131
5-Alpha reductase inhibitors induce a prostate luminal to club cell transition in human benign prostatic hyperplasia. PMID:34928497
Effects of Serum Metabolites on the Pancreatic Transcriptome in Acute Acalculous Cholecystitis. PMID:34925503
Dual RNA-Seq Analysis of the Interaction Between Edible Fungus Morchella sextelata and Its Pathogenic Fungus Paecilomyces penicillatus Uncovers the Candidate Defense and Pathogenic Factors. PMID:34925269
Profiles of immune cell infiltration and immune-related genes in the tumor microenvironment of osteosarcoma cancer. PMID:34922489
Recurring exposure to low humidity induces transcriptional and protein level changes in the vocal folds of rabbits. PMID:34921171
Gene prediction of aging-related diseases based on DNN and Mashup. PMID:34920719
De novo transcriptome assembly and annotation of parthenogenetic lizard Darevskia unisexualis and its parental ancestors Darevskia valentini and Darevskia raddei nairensis. PMID:34917712
A Novel Single-Cell RNA Sequencing Data Feature Extraction Method Based on Gene Function Analysis and Its Applications in Glioma Study. PMID:34917514
Plasma Cell-Free DNA Methylomics of Bipolar Disorder With and Without Rapid Cycling. PMID:34916903
Identification of a Lipid Metabolism-Associated Gene Signature Predicting Survival in Breast Cancer. PMID:34916832
Genome-wide identification of enhancers and transcription factors regulating the myogenic differentiation of bovine satellite cells. PMID:34915843
Genomic analysis of Elsinoë arachidis reveals its potential pathogenic mechanism and the biosynthesis pathway of elsinochrome toxin. PMID:34914789
Draft Genome Sequence of Bacillus pacificus KVCMST-8A-12, Isolated from a Marine Sediment Sample from the Kanyakumari Coast, India. PMID:34913714
Identification of Key Deregulated RNA-Binding Proteins in Pancreatic Cancer by Meta-Analysis and Prediction of Their Role as Modulators of Oncogenesis. PMID:34912796
Exploring Pathway-Based Group Lasso for Cancer Survival Analysis: A Special Case of Multi-Task Learning. PMID:34912376
The Edible Plant Microbiome represents a diverse genetic reservoir with functional potential in the human host. PMID:34911987
Transcriptome comparative analysis of ovarian follicles reveals the key genes and signaling pathways implicated in hen egg production. PMID:34911438
DNA methylation of ARHGAP30 is negatively associated with ARHGAP30 expression in lung adenocarcinoma, which reduces tumor immunity and is detrimental to patient survival. PMID:34910688
Potential Novel Modules and Hub Genes as Prognostic Candidates of Thyroid Cancer by Weighted Gene Co-Expression Network Analysis. PMID:34908870
Genome analysis provides insight into hyper-virulence of Streptococcus suis LSM178, a human strain with a novel sequence type 1005. PMID:34907269
Competitive endogenous RNA network and pathway-based analysis of LncRNA single-nucleotide polymorphism in myasthenia gravis. PMID:34907261
Metabolic drug survey highlights cancer cell dependencies and vulnerabilities. PMID:34907165
Long noncoding RNA GSEC promotes neutrophil inflammatory activation by supporting PFKFB3-involved glycolytic metabolism in sepsis. PMID:34907156
The importance of automation in genetic diagnosis: Lessons from analyzing an inherited retinal degeneration cohort with the Mendelian Analysis Toolkit (MATK). PMID:34906470
A novel strategy to uncover specific GO terms/phosphorylation pathways in phosphoproteomic data in Arabidopsis thaliana. PMID:34906086
Computational modelling of chromosomally clustering protein domains in bacteria. PMID:34906073
Relation Extraction of Protein Complexes from Dynamic Protein-Protein Interaction Network. PMID:34904064
The mining and construction of a knowledge base for gene-disease association in mitochondrial diseases. PMID:34903783
Longitudinal DNA methylation dynamics as a practical indicator in clinical epigenetics. PMID:34903243
Computational modeling of human-nCoV protein-protein interaction network. PMID:34902553
Pathway Enrichment Analysis of Microarray Data. PMID:34902127
Robust deep learning model for prognostic stratification of pancreatic ductal adenocarcinoma patients. PMID:34901786
RNA-seq dataset of subcutaneous adipose tissue: Transcriptional differences between obesity and healthy women. PMID:34901353
Time-Resolved Extracellular Matrix Atlas of the Developing Human Skin Dermis. PMID:34901026
Regeneration of Planarian Auricles and Reestablishment of Chemotactic Ability. PMID:34901022
Development of an Oxidative Phosphorylation-Related and Immune Microenvironment Prognostic Signature in Uterine Corpus Endometrial Carcinoma. PMID:34901000
Genome-wide association of single nucleotide polymorphism loci and candidate genes for frogeye leaf spot (Cercospora sojina) resistance in soybean. PMID:34895144
OmicsOne: associate omics data with phenotypes in one-click. PMID:34895137
Identification of novel biomarkers in breast cancer via integrated bioinformatics analysis and experimental validation. PMID:34895070
Analysis of a circRNA-, miRNA-, and mRNA-associated ceRNA network reveals potential biomarkers in preeclampsia a ceRNA network in preeclampsia. PMID:34894939
Bacteriostatic effects of high-intensity ultrasonic treatment on Bacillus subtilis vegetative cells. PMID:34894527
Comparative transcriptomics of the Djungarian hamster hypothalamus during short photoperiod acclimation and spontaneous torpor. PMID:34894101
Circular RNA circCCNT2 is upregulated in the anterior cingulate cortex of individuals with bipolar disorder. PMID:34893581
Integrated genome and tissue engineering enables screening of cancer vulnerabilities in physiologically relevant perfusable ex vivo cultures. PMID:34890975
Prediction of Hormone-Binding Proteins Based on K-mer Feature Representation and Naive Bayes. PMID:34887905
Genome-wide map of N6-methyladenosine circular RNAs identified in mice model of severe acute pancreatitis. PMID:34887647
Meta-analyses identify DNA methylation associated with kidney function and damage. PMID:34887417
Epigenome-wide association study of serum urate reveals insights into urate co-regulation and the SLC2A9 locus. PMID:34887389
The N-Acetylglucosamine Kinase from Yarrowia lipolytica Is a Moonlighting Protein. PMID:34884915
Splice-Variant Knock-Out of TGFβ Receptors Perturbates the Proteome of Ovarian Carcinoma Cells. PMID:34884451
Artificial intelligence, molecular subtyping, biomarkers, and precision oncology. PMID:34881776
Circular RNA Expression and Regulation Profiling in Testicular Tissues of Immature and Mature Wandong Cattle (Bos taurus). PMID:34880896
Barcoded reciprocal hemizygosity analysis via sequencing illuminates the complex genetic basis of yeast thermotolerance. PMID:34878132
Whole-Genome Sequencing of Acer catalpifolium Reveals Evolutionary History of Endangered Species. PMID:34878129
Identifying the temporal electrophysiological and molecular changes that contribute to TSC-associated epileptogenesis. PMID:34877936
Development and Validation of a Prognostic N6-Methyladenosine-Related Immune Gene Signature for Lung Adenocarcinoma. PMID:34876833
Integrative analysis of lung molecular signatures reveals key drivers of idiopathic pulmonary fibrosis. PMID:34876074
The effect and mechanism of Jiao-tai-wan in the treatment of diabetes mellitus with depression based on network pharmacology and experimental analysis. PMID:34875999
reString: an open-source Python software to perform automatic functional enrichment retrieval, results aggregation and data visualization. PMID:34873191
Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling. PMID:34872593
Comprehensive Analysis of the Transcriptome-Wide m6A Methylation Modification Difference in Liver Fibrosis Mice by High-Throughput m6A Sequencing. PMID:34869362
Starvation to Glucose Reprograms Development of Neurovascular Unit in Embryonic Retinal Cells. PMID:34869314
Genomics Characterization of an Engineered Corynebacterium glutamicum in Bioreactor Cultivation Under Ionic Liquid Stress. PMID:34869279
Comprehensive Transcriptomic Profiling of Murine Osteoclast Differentiation Reveals Novel Differentially Expressed Genes and LncRNAs. PMID:34868271
LIMD2 is a Prognostic and Predictive Marker in Patients With Esophageal Cancer Based on a ceRNA Network Analysis. PMID:34868263
Genome-Wide Identification of Long Non-Coding RNAs and Their Potential Functions in Poplar Growth and Phenylalanine Biosynthesis. PMID:34868243
Chromosome-Scale Reference Genome of Amphicarpaea edgeworthii: A New Resource for Amphicarpic Plants Research and Complex Flowering Pattern. PMID:34868169
Hepatectomy-Induced Alterations in Hepatic Perfusion and Function - Toward Multi-Scale Computational Modeling for a Better Prediction of Post-hepatectomy Liver Function. PMID:34867441
The Pharmacological Mechanism of Guchangzhixie Capsule Against Experimental Colitis. PMID:34867387
Quantitative Proteomic Analysis of Mouse Sciatic Nerve Reveals Post-injury Upregulation of ADP-Dependent Glucokinase Promoting Macrophage Phagocytosis. PMID:34867191
Network analytics for drug repurposing in COVID-19. PMID:34864885
VectorBase.org updates: bioinformatic resources for invertebrate vectors of human pathogens and related organisms. PMID:34864248
Statistical testing in transcriptomic-neuroimaging studies: A how-to and evaluation of methods assessing spatial and gene specificity. PMID:34862695
Identification of genes related to tipburn resistance in Chinese cabbage and preliminary exploration of its molecular mechanism. PMID:34861825
Multifaceted pathomolecular mechanism of a VWF large deletion involved in the pathogenesis of severe VWD. PMID:34861678
The chromosome-level genome provides insight into the molecular mechanism underlying the tortuous-branch phenotype of Prunus mume. PMID:34861048
Antiviral RNA interference in disease vector (Asian longhorned) ticks. PMID:34860862
Maternal immune activation downregulates schizophrenia genes in the foetal mouse brain. PMID:34859219
Expression Signatures of Long Noncoding RNAs in Left Ventricular Noncompaction. PMID:34859074
Key Markers Involved in the Anticolon Cancer Response of CD8+ T Cells through the Regulation of Cholesterol Metabolism. PMID:34858500
Comparative Transcriptome Sequencing of Taro Corm Development With a Focus on the Starch and Sucrose Metabolism Pathway. PMID:34858484
A Standardized Brain Molecular Atlas: A Resource for Systems Modeling and Simulation. PMID:34858137
Multiscale interactome analysis coupled with off-target drug predictions reveals drug repurposing candidates for human coronavirus disease. PMID:34857794
Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data. PMID:34856921
Identification of key pathways and RNAs associated with skeletal muscle atrophy after spinal cord injury. PMID:34854395
Bronchopulmonary dysplasia and wnt pathway-associated single nucleotide polymorphisms. PMID:34853430
Investigation of hub gene associated with the infection of Staphylococcus aureus via weighted gene co-expression network analysis. PMID:34852788
AD-linked R47H-TREM2 mutation induces disease-enhancing microglial states via AKT hyperactivation. PMID:34851693
DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation. PMID:34850135
The Tetragnatha kauaiensis Genome Sheds Light on the Origins of Genomic Novelty in Spiders. PMID:34849853
Distinct gene expression dynamics in germ line and somatic tissue during ovariole morphogenesis in Drosophila melanogaster. PMID:34849771
Synergistic alterations in the multilevel chromatin structure anchor dysregulated genes in small cell lung cancer. PMID:34849199
Integrative genome, transcriptome, microRNA, and degradome analysis of water dropwort (Oenanthe javanica) in response to water stress. PMID:34848704
Improvement of Astragalin on Spermatogenesis in Oligoasthenozoospermia Mouse Induced by Cyclophosphamide. PMID:34846706
Bone marrow sinusoidal endothelium controls terminal erythroid differentiation and reticulocyte maturation. PMID:34845225
Toll-Like Receptor (TLR) Signaling Enables Cyclic GMP-AMP Synthase (cGAS) Sensing of HIV-1 Infection in Macrophages. PMID:34844429
Epididymal mRNA and miRNA transcriptome analyses reveal important genes and miRNAs related to sperm motility in roosters. PMID:34844112
Testing biological network motif significance with exponential random graph models. PMID:34841042
Identification of Hub Gene GRIN1 Correlated with Histological Grade and Prognosis of Glioma by Weighted Gene Coexpression Network Analysis. PMID:34840971
Identification of copy number variation-driven molecular subtypes informative for prognosis and treatment in pancreatic adenocarcinoma of a Chinese cohort. PMID:34839264
Pathway Enrichment Analysis of Microarray Data Fom Human Penis of Diabetic and Peyronie's Patients, in Comparison With Diabetic Rat Erectile Dysfunction Models. PMID:34838480
The Aliment to Bodily Condition knowledgebase (ABCkb): a database connecting plants and human health. PMID:34838100
A multitask transfer learning framework for the prediction of virus-human protein-protein interactions. PMID:34837942
Exosomes produced by melanoma cells significantly influence the biological properties of normal and cancer-associated fibroblasts. PMID:34837514
Identification of transcriptomics biomarkers for the early prediction of the prognosis of septic shock from pneumopathies. PMID:34836493
Effects of Lingonberry (Vaccinium vitis-idaea L.) Supplementation on Hepatic Gene Expression in High-Fat Diet Fed Mice. PMID:34835949
Comparison of the Proteomes of Porcine Macrophages and a Stable Porcine Cell Line after Infection with African Swine Fever Virus. PMID:34835004
Transcriptome Analysis of Lolium temulentum Exposed to a Combination of Drought and Heat Stress. PMID:34834610
Broad Spectrum Antiviral Properties of Cardiotonic Steroids Used as Potential Therapeutics for Emerging Coronavirus Infections. PMID:34834252
The Prescription of Drug Ontology 2.0 (PDRO): More Than the Sum of Its Parts. PMID:34831777
Hundreds of LncRNAs Display Circadian Rhythmicity in Zebrafish Larvae. PMID:34831396
Identification of Impacted Pathways and Transcriptomic Markers as Potential Mediators of Pulmonary Fibrosis in Transgenic Mice Expressing Human IGFBP5. PMID:34830489
Quantitative Analysis of the Cardiac Phosphoproteome in Response to Acute β-Adrenergic Receptor Stimulation In Vivo. PMID:34830474
Phosphoproteomic Comparison of Four Eimeria tenella Life Cycle Stages. PMID:34829991
MicroRNA Sequencing Analysis in Obstructive Sleep Apnea and Depression: Anti-Oxidant and MAOA-Inhibiting Effects of miR-15b-5p and miR-92b-3p through Targeting PTGS1-NF-κB-SP1 Signaling. PMID:34829725
The Genomic and Transcriptomic Analyses of Floccularia luteovirens, a Rare Edible Fungus in the Qinghai-Tibet Plateau, Provide Insights into the Taxonomy Placement and Fruiting Body Formation. PMID:34829176
Identification, Analysis, and Confirmation of Seed Storability-Related Loci in Dongxiang Wild Rice (Oryza rufipogon Griff.). PMID:34828437
Comparative RNA-Seq Analysis Reveals Potentially Resistance-Related Genes in Response to Bacterial Canker of Tomato. PMID:34828351
Proteomics Profiling with SWATH-MS Quantitative Analysis of Changes in the Human Brain with HIV Infection Reveals a Differential Impact on the Frontal and Temporal Lobes. PMID:34827437
Transcriptome Analysis Reveals Different Responsive Patterns to Nitrogen Deficiency in Two Wheat Near-Isogenic Lines Contrasting for Nitrogen Use Efficiency. PMID:34827119
Heterogeneous recruitment abilities to RNA polymerases generate nonlinear scaling of gene expression with cell volume. PMID:34824198
Identification of miRNA-mRNA network and immune-related gene signatures in IgA nephropathy by integrated bioinformatics analysis. PMID:34823491
Automatic consistency assurance for literature-based gene ontology annotation. PMID:34823464
SMAD4 target genes are part of a transcriptional network that integrates the response to BMP and SHH signaling during early limb bud patterning. PMID:34822715
A roadmap for metagenomic enzyme discovery. PMID:34821235
A proposal for score assignment to characterize biological processes from mass spectral analysis of serum. PMID:34820522
Development of a bioinformatics platform for analysis of quantitative transcriptomics and proteomics data: the OMnalysis. PMID:34820180
Establishment and characterization of prostate organoids from treatment-naïve patients with prostate cancer. PMID:34820005
Development of a chemogenomics library for phenotypic screening. PMID:34819133
Quantitative dissection of multilocus pathogenic variation in an Egyptian infant with severe neurodevelopmental disorder resulting from multiple molecular diagnoses. PMID:34816580
Multiple regression analysis of a comprehensive transcriptomic data assembly elucidates mechanically- and biochemically-driven responses to focused ultrasound blood-brain barrier disruption. PMID:34815790
A proximity proteomics screen in three-dimensional spheroid cultures identifies novel regulators of lumen formation. PMID:34815476
p300 or CBP is required for insulin-stimulated glucose uptake in skeletal muscle and adipocytes. PMID:34813504
Inheritance of gene expression throughout fruit development in chili pepper. PMID:34811443
PQN-59 antagonizes microRNA-mediated repression during post-embryonic temporal patterning and modulates translation and stress granule formation in C. elegans. PMID:34807903
Bacteroides spp. promotes branched-chain amino acid catabolism in brown fat and inhibits obesity. PMID:34805797
Whole genome sequence data of Chromobacterium violaceum WCH4, a human pathogenic strain from Sabah, Malaysia. PMID:34805463
Integrated Strategy of UHPLC-Q-TOF-MS and Molecular Networking for Identification of Diterpenoids from Euphorbia fischeriana Steud. and Prediction of the Anti-Breast-Cancer Mechanism by the Network Pharmacological Method. PMID:34804177
Edgetic Perturbations Contribute to Phenotypic Variability in PEX26 Deficiency. PMID:34804114
Selecting Hub Genes and Predicting Target Genes of microRNAs in Tuberculosis via the Bioinformatics Analysis. PMID:34803519
Analyzing differentially expressed genes and pathways of Bex2-deficient mouse lung via RNA-Seq. PMID:34803456
Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context. PMID:34800366
Transcriptome and metabolome analysis to reveal major genes of saikosaponin biosynthesis in Bupleurum chinense. PMID:34798822
USH2A Mutation is Associated With Tumor Mutation Burden and Antitumor Immunity in Patients With Colon Adenocarcinoma. PMID:34795697
Follicular T cells are clonally and transcriptionally distinct in B cell-driven mouse autoimmune disease. PMID:34795279
Altered cell and RNA isoform diversity in aging Down syndrome brains. PMID:34795060
APOBEC Mutagenesis Inhibits Breast Cancer Growth through Induction of T cell-Mediated Antitumor Immune Responses. PMID:34795033
Construction of a single nucleotide variant score-related gene-based prognostic model in hepatocellular carcinoma: analysis of multi-independent databases and validation in vitro. PMID:34794449
Asc-Seurat: analytical single-cell Seurat-based web application. PMID:34794383
Small RNA sequencing reveals various microRNAs involved in piperine biosynthesis in black pepper (Piper nigrum L.). PMID:34794378
A genome-wide search for determinants of survival in 1926 patients with advanced colorectal cancer with follow-up in over 22,000 patients. PMID:34794066
Inferred expression regulator activities suggest genes mediating cardiometabolic genetic signals. PMID:34793442
Concurrent Evolution of Antiaging Gene Duplications and Cellular Phenotypes in Long-Lived Turtles. PMID:34792580
CircleBase: an integrated resource and analysis platform for human eccDNAs. PMID:34792166
Avian ceca are indispensable for hindgut enteric nervous system development. PMID:34792104
Nucleolar GTPase Bms1 displaces Ttf1 from RFB-sites to balance progression of rDNA transcription and replication. PMID:34791311
The disease-associated proteins Drosophila Nab2 and Ataxin-2 interact with shared RNAs and coregulate neuronal morphology. PMID:34791182
Hypothalamic Transcriptome Analysis Reveals the Crucial MicroRNAs and mRNAs Affecting Litter Size in Goats. PMID:34790713
Six mutator-derived lncRNA signature of genome instability for predicting the clinical outcome of colon cancer. PMID:34790382
The protein-protein interaction ontology: for better representing and capturing the biological context of protein interaction. PMID:34789143
Transcriptomic profiling reveals gene expression in human peripheral blood after exposure to low-dose ionizing radiation. PMID:34788452
Glutathione, carbohydrate and other metabolites of Larix olgensis A. Henry reponse to polyethylene glycol-simulated drought stress. PMID:34788320
A Superefficient Ochratoxin A Hydrolase with Promising Potential for Industrial Applications. PMID:34788069
Undervalued Pseudo-nifH Sequences in Public Databases Distort Metagenomic Insights into Biological Nitrogen Fixers. PMID:34787447
Screening of differentially expressed miRNAs during osteogenic/odontogenic differentiation of human dental pulp stem cells exposed to mechanical stress. PMID:34786047
Multidimensional Analysis of the Role of Charged Multivesicular Body Protein 7 in Pan-Cancer. PMID:34785938
Dynamic Urinary Proteome Changes in Ovalbumin-Induced Asthma Mouse Model Using Data-Independent Acquisition Proteomics. PMID:34785909
Identification of key genes involved in recovery from spinal cord injury in adult zebrafish. PMID:34782579
Hub microRNAs and genes in the development of atrial fibrillation identified by weighted gene co-expression network analysis. PMID:34781940
Transcriptomic responses to drought stress in Polygonatum kingianum tuber. PMID:34781887
The differentiation state of the Schwann cell progenitor drives phenotypic variation between two contagious cancers. PMID:34780568
Categorizing Sequences of Concern by Function To Better Assess Mechanisms of Microbial Pathogenesis. PMID:34780277
Linking Diabetes Mellitus with Alzheimer's Disease: Bioinformatics Analysis for the Potential Pathways and Characteristic Genes. PMID:34779951
Trends in biological data integration for the selection of enzymes and transcription factors related to cellulose and hemicellulose degradation in fungi. PMID:34777932
Pairwise Biological Network Alignment Based on Discrete Bat Algorithm. PMID:34777564
Trichoderma-Induced Ethylene Responsive Factor MsERF105 Mediates Defense Responses in Malus sieversii. PMID:34777407
Novel Enzymes From the Red Sea Brine Pools: Current State and Potential. PMID:34777282
Identification of KIF4A as a prognostic biomarker for esophageal squamous cell carcinoma. PMID:34775374
Computationally Reconstructed Interactome of Bradyrhizobium diazoefficiens USDA110 Reveals Novel Functional Modules and Protein Hubs for Symbiotic Nitrogen Fixation. PMID:34769335
Distinct Exosomal miRNA Profiles from BALF and Lung Tissue of COPD and IPF Patients. PMID:34769265
Cross-validation of SARS-CoV-2 responses in kidney organoids and clinical populations. PMID:34767537
Severe types of fetopathy are associated with changes in the serological proteome of diabetic mothers. PMID:34766598
Computational methods for protein localization prediction. PMID:34765098
Immune Characteristics Analysis and Transcriptional Regulation Prediction Based on Gene Signatures of Chronic Obstructive Pulmonary Disease. PMID:34764646
A data-driven framework for mapping domains of human neurobiology. PMID:34764476
Chronic pathophysiological changes in the normal brain parenchyma caused by radiotherapy accelerate glioma progression. PMID:34764346
Cigarette smoking-associated isoform switching and 3' UTR lengthening via alternative polyadenylation. PMID:34763026
Identification of discriminative gene-level and protein-level features associated with pathogenic gain-of-function and loss-of-function variants. PMID:34762822
Inhibition of the renin-angiotensin system causes concentric hypertrophy of renal arterioles in mice and humans. PMID:34762601
Tlr2/4 Double Knockout Attenuates the Degeneration of Primary Auditory Neurons: Potential Mechanisms From Transcriptomic Perspectives. PMID:34760891
Integrative analysis of Iso-Seq and RNA-seq data reveals transcriptome complexity and differentially expressed transcripts in sheep tail fat. PMID:34760406
Contextualizing Genes by Using Text-Mined Co-Occurrence Features for Cancer Gene Panel Discovery. PMID:34759963
Dietary palmitic acid promotes a prometastatic memory via Schwann cells. PMID:34759321
Integration of transcriptomics and network analysis reveals co-expressed genes in Frankliniella occidentalis larval guts that respond to tomato spotted wilt virus infection. PMID:34758725
Web-based transcriptome analysis determines a sixteen-gene signature and associated drugs on hearing loss patients: A bioinformatics approach. PMID:34758154
IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis. PMID:34755877
T2-DAG: a powerful test for differentially expressed gene pathways via graph-informed structural equation modeling. PMID:34755844
Co-evolution based machine-learning for predicting functional interactions between human genes. PMID:34753957
Network analysis reveals rare disease signatures across multiple levels of biological organization. PMID:34753928
Pyroptosis-related gene mediated modification patterns and immune cell infiltration landscapes in cutaneous melanoma to aid immunotherapy. PMID:34753832
Circ-Usp10 promotes microglial activation and induces neuronal death by targeting miRNA-152-5p/CD84. PMID:34753388
GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction. PMID:34748537
The human telomeric proteome during telomere replication. PMID:34747482
Hymenoptera Genome Database: new genomes and annotation datasets for improved go enrichment and orthologue analyses. PMID:34747465
Bacterial membrane vesicles and phages in blood after consumption of lacticaseibacillus rhamnosus JB-1. PMID:34747333
Attention to time-of-day variability improves the reproducibility of gene expression patterns in multiple sclerosis. PMID:34746708
Genome Instability and Long Noncoding RNA Reveal Biomarkers for Immunotherapy and Prognosis and Novel Competing Endogenous RNA Mechanism in Colon Adenocarcinoma. PMID:34746134
Identification of Gene-Set Signature in Early-Stage Hepatocellular Carcinoma and Relevant Immune Characteristics. PMID:34745960
A Novel Three-LncRNA Signature Predicting Tumor Recurrence in Nonfunctioning Pituitary Adenomas. PMID:34745223
Multi-Omics-Based Identification and Functional Characterization of Gh_A06G1257 Proves Its Potential Role in Drought Stress Tolerance in Gossypium hirsutum. PMID:34745180
Identification of Novel Kinase-Transcription Factor-mRNA-miRNA Regulatory Network in Nasopharyngeal Carcinoma by Bioinformatics Analysis. PMID:34744455
Phenotype-tissue expression and exploration (PTEE) resource facilitates the choice of tissue for RNA-seq-based clinical genetics studies. PMID:34743696
BCG vaccination and the risk of COVID 19: A possible correlation. PMID:34742127
The Rat Genome Database (RGD) facilitates genomic and phenotypic data integration across multiple species for biomedical research. PMID:34741192
Fibromine is a multi-omics database and mining tool for target discovery in pulmonary fibrosis. PMID:34741074
β-Glucan Induces Distinct and Protective Innate Immune Memory in Differentiated Macrophages. PMID:34740960
Cross-platform transcriptomic profiling of the response to recombinant human erythropoietin. PMID:34737331
High-dose dexamethasone injection disordered metabolism and multiple protein kinases expression in the mouse kidney. PMID:34735568
Lymphocyte activation gene-3 is associated with programmed death-ligand 1 and programmed cell death protein 1 in small cell lung cancer. PMID:34734020
Tumour DDR1 promotes collagen fibre alignment to instigate immune exclusion. PMID:34732895
Dysregulated expression levels of APH1B in peripheral blood are associated with brain atrophy and amyloid-β deposition in Alzheimer's disease. PMID:34732252
Transcriptome profiling reveals the developmental regulation of NaCl-treated Forcipomyia taiwana eggs. PMID:34732124
Patch-seq of mouse DRG neurons reveals candidate genes for specific mechanosensory functions. PMID:34731626
Genome-wide CRISPR interference screen identifies long non-coding RNA loci required for differentiation and pluripotency. PMID:34731163
Proximity labeling identifies LOTUS domain proteins that promote the formation of perinuclear germ granules in C. elegans. PMID:34730513
ParsVNN: parsimony visible neural networks for uncovering cancer-specific and drug-sensitive genes and pathways. PMID:34729476
MCDB: A comprehensive curated mitotic catastrophe database for retrieval, protein sequence alignment, and target prediction. PMID:34729303
High Expression of ERK-related RASGRF2 predicts Poor prognosis in patients with Stomach Adenocarcinoma and correlates with M2 macrophage. PMID:34729119
Proteogenomic discovery of sORF-encoded peptides associated with bacterial virulence in Yersinia pestis. PMID:34728737
Bioinformatic analysis of key pathways and genes shared between endometriosis and ovarian cancer. PMID:34727222
Structure-Aware Mycobacterium tuberculosis Functional Annotation Uncloaks Resistance, Metabolic, and Virulence Genes. PMID:34726489
Transcriptome and Exome Analyses of Hepatocellular Carcinoma Reveal Patterns to Predict Cancer Recurrence in Liver Transplant Patients. PMID:34725972
Spatially resolved transcriptomics reveals the architecture of the tumor-microenvironment interface. PMID:34725363
Nitecap: An Exploratory Circadian Analysis Web Application. PMID:34724846
Plasmodium falciparum Calcium-Dependent Protein Kinase 4 is Critical for Male Gametogenesis and Transmission to the Mosquito Vector. PMID:34724830
Single-cell analysis of arthritogenic alphavirus-infected human synovial fibroblasts links low abundance of viral RNA to induction of innate immunity and arthralgia-associated gene expression. PMID:34723780
Distinct Mitochondrial Remodeling During Mesoderm Differentiation in a Human-Based Stem Cell Model. PMID:34722525
Single-Cell RNA Sequencing in Multiple Pathologic Types of Renal Cell Carcinoma Revealed Novel Potential Tumor-Specific Markers. PMID:34722263
Differential transcriptome analysis and identification of genes related to resistance to blight in three varieties of Bambusa pervariabilis × Dendrocalamopsis grandis. PMID:34721984
lncRNA HHIP-AS1 Promotes the Osteogenic Differentiation Potential and Inhibits the Migration Ability of Periodontal Ligament Stem Cells. PMID:34721591
Agent Repurposing for the Treatment of Advanced Stage Diffuse Large B-Cell Lymphoma Based on Gene Expression and Network Perturbation Analysis. PMID:34721544
Viral Strain-Specific Activation of Pathogen-Associated Molecular Pattern-Triggered Immunity Enhances Symptom Severity in Broad Bean Wilt Virus 2 Infection. PMID:34721473
Drug Repurposing for Atopic Dermatitis by Integration of Gene Networking and Genomic Information. PMID:34721386
Integrating full-length transcriptomics and metabolomics reveals the regulatory mechanisms underlying yellow pigmentation in tree peony (Paeonia suffruticosa Andr.) flowers. PMID:34719694
EWAS Open Platform: integrated data, knowledge and toolkit for epigenome-wide association study. PMID:34718752
CompoDynamics: a comprehensive database for characterizing sequence composition dynamics. PMID:34718745
Complex Portal 2022: new curation frontiers. PMID:34718729
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. PMID:34718728
Genomics analysis of hexanoic acid exposure in Drosophila species. PMID:34718544
Maternal methionine supplementation during gestation alters alternative splicing and DNA methylation in bovine skeletal muscle. PMID:34717556
PANTHER: Making genome-scale phylogenetics accessible to all. PMID:34717010
Transcriptome Analysis of Zygophyllum xanthoxylum Adaptation Strategies to Phosphate Stress. PMID:34712251
Pathway-targeting gene matrix for Drosophila gene set enrichment analysis. PMID:34710184
Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO). PMID:34710081
p21 produces a bioactive secretome that places stressed cells under immunosurveillance. PMID:34709885
Identification of a Prognosis-Related Risk Signature for Bladder Cancer to Predict Survival and Immune Landscapes. PMID:34708131
Foundations for a Realism-Based Ontology of Protein Aggregates. PMID:34707469
Whole-exome analysis in Tunisian Imazighen and Arabs shows the impact of demography in functional variation. PMID:34702931
Comparative genomics reveals molecular mechanisms underlying health and reproduction in cryptorchid mammals. PMID:34702182
DNA crosslinking and recombination-activating genes 1/2 (RAG1/2) are required for oncogenic splicing in acute lymphoblastic leukemia. PMID:34699692
Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci. PMID:34699533
Gene Ontology curation of the blood-brain barrier to improve the analysis of Alzheimer's and other neurological diseases. PMID:34697638
Analysing the fitness cost of antibiotic resistance to identify targets for combination antimicrobials. PMID:34697460
De novo transcriptome analysis provides insights into the salt tolerance of Podocarpus macrophyllus under salinity stress. PMID:34696735
Prioritization of Diagnostic and Prognostic Biomarkers for Lupus Nephritis Based on Integrated Bioinformatics Analyses. PMID:34692653
Genomic insights into biocontrol potential of Bacillus stercoris LJBS06. PMID:34692367
Rapid phenotypic evolution with shallow genomic differentiation during early stages of high elevation adaptation in Eurasian Tree Sparrows. PMID:34692022
Optical Coherence Tomography Angiography Characteristics Serve as Retinal Vein Occlusion Therapeutic Biomarkers for Dexamethasone Intravitreal Implant. PMID:34691285
RabA2b Overexpression Alters the Plasma-Membrane Proteome and Improves Drought Tolerance in Arabidopsis. PMID:34691115
Arabidopsis MED18 Interaction With RNA Pol IV and V Subunit NRPD2a in Transcriptional Regulation of Plant Immune Responses. PMID:34691090
Type 2 Diabetes Modifies Skeletal Muscle Gene Expression Response to Gastric Bypass Surgery. PMID:34690929
The KRAS-regulated kinome identifies WEE1 and ERK coinhibition as a potential therapeutic strategy in KRAS-mutant pancreatic cancer. PMID:34688654
Transcriptome changes in maternal peripheral blood during term parturition mimic perturbations preceding spontaneous preterm birth†. PMID:34686873
Nkx3-1 and Fech genes might be switch genes involved in pituitary non-functioning adenoma invasiveness. PMID:34686726
Adaptive translational pausing is a hallmark of the cellular response to severe environmental stress. PMID:34686314
Upregulation of cathepsin L gene under mild cold conditions in young Japanese male adults. PMID:34686211
Identification of Oil Palm's Consistently Upregulated Genes during Early Infections of Ganoderma boninense via RNA-Seq Technology and Real-Time Quantitative PCR. PMID:34685835
A Candidate RNAi Screen Reveals Diverse RNA-Binding Protein Phenotypes in Drosophila Flight Muscle. PMID:34685485
A Systems Approach Dissociates Fructose-Induced Liver Triglyceride from Hypertriglyceridemia and Hyperinsulinemia in Male Mice. PMID:34684643
Microarray Analysis of Paramylon, Isolated from Euglena Gracilis EOD-1, and Its Effects on Lipid Metabolism in the Ileum and Liver in Diet-Induced Obese Mice. PMID:34684408
Evidence for Lignocellulose-Decomposing Enzymes in the Genome and Transcriptome of the Aquatic Hyphomycete Clavariopsis aquatica. PMID:34682274
Identification of Novel Endogenous Controls for qPCR Normalization in SK-BR-3 Breast Cancer Cell Line. PMID:34681026
Comparative RNA-Seq Analyses of Solenopsis japonica (Hymenoptera: Formicidae) Reveal Gene in Response to Cold Stress. PMID:34681004
Silver: Forging almost Gold Standard Datasets. PMID:34680918
Trends in the Application of "Omics" to Ecotoxicology and Stress Ecology. PMID:34680873
Are There Limits in Explainability of Prognostic Biomarkers? Scrutinizing Biological Utility of Established Signatures. PMID:34680236
Revealing Pathways Associated with Feed Efficiency and Meat Quality Traits in Slow-Growing Chickens. PMID:34679997
Hybrid Sequencing in Different Types of Goat Skeletal Muscles Reveals Genes Regulating Muscle Development and Meat Quality. PMID:34679927
Transcriptomic Analysis of Polyhexamethyleneguanidine-Induced Lung Injury in Mice after a Long-Term Recovery. PMID:34678949
IL12 integrated into the CAR exodomain converts CD8+ T cells to poly-functional NK-like cells with superior killing of antigen-loss tumors. PMID:34678512
Platelet proteome dynamics in hibernating 13-lined ground squirrels. PMID:34677084
Genome-wide distribution of 5hmC in the dental pulp of mouse molars and incisors. PMID:34676418
Development and Validation of a Prognostic Model of RNA-Binding Proteins in Colon Adenocarcinoma: A Study Based on TCGA and GEO Databases. PMID:34675667
Context-aware multi-token concept recognition of biological entities. PMID:34674631
Transcriptomic profiling of neonatal mouse granulosa cells reveals new insights into primordial follicle activation†. PMID:34673933
Identification of Key Differentially Methylated/Expressed Genes and Pathways for Ovarian Endometriosis by Bioinformatics Analysis. PMID:34671938
An Atypical Autoinflammatory Disease Due to an LRR Domain NLRP3 Mutation Enhancing Binding to NEK7. PMID:34671876
Pan-cancer analysis of pathway-based gene expression pattern at the individual level reveals biomarkers of clinical prognosis. PMID:34671755
iMPT-FDNPL: Identification of Membrane Protein Types with Functional Domains and a Natural Language Processing Approach. PMID:34671418
Reduced expression of OXPHOS and DNA damage genes is linked to protection from microvascular complications in long-term type 1 diabetes: the PROLONG study. PMID:34671071
The translatome of neuronal cell bodies, dendrites, and axons. PMID:34670838
Disrupted circadian oscillations in type 2 diabetes are linked to altered rhythmic mitochondrial metabolism in skeletal muscle. PMID:34669477
Computational repurposing of therapeutic small molecules from cancer to pulmonary hypertension. PMID:34669463
Screening of anti-chronic nonbacterial prostatitis activity of different extractions of the aerial part of Glycyrrhiza uralensis, and network pharmacology research. PMID:34667596
Investigation of the transcriptomic response in Atlantic salmon (Salmo salar) gill exposed to Paramoeba perurans during early onset of disease. PMID:34667245
Construction of a 5 immune-related lncRNA-based prognostic model of NSCLC via bioinformatics. PMID:34664861
Microarray analysis of hub genes and pathways in damaged cartilage tissues of knee. PMID:34664844
Loss of the wild-type KRAS allele promotes pancreatic cancer progression through functional activation of YAP1. PMID:34663879
Genetic and epigenetic characterization of posterior pituitary tumors. PMID:34661724
Bioinformatic and experimental analyses of key biomarkers in pancreatic cancer. PMID:34659505
Identification of Novel Biomarkers Related to Lung Squamous Cell Carcinoma Using Integrated Bioinformatics Analysis. PMID:34659450
Whole-Genome Sequencing and Genome-Wide Studies of Spiny Head Croaker (Collichthys lucidus) Reveals Potential Insights for Well-Developed Otoliths in the Family Sciaenidae. PMID:34659355
High-Quality Genome of the Medicinal Plant Strobilanthes cusia Provides Insights Into the Biosynthesis of Indole Alkaloids. PMID:34659312
Proteomics Reveals an Increase in the Abundance of Glycolytic and Ethanolic Fermentation Enzymes in Developing Sugarcane Culms During Sucrose Accumulation. PMID:34659289
Comprehensive landscape and interference of clonal haematopoiesis mutations for liquid biopsy: A Chinese pan-cancer cohort. PMID:34658138
Deep post-GWAS analysis identifies potential risk genes and risk variants for Alzheimer's disease, providing new insights into its disease mechanisms. PMID:34654853
Chromosome-scale assembly and high-density genetic map of the yellow drum, Nibea albiflora. PMID:34654820
A comparative analysis of differentially expressed mRNAs, miRNAs and circRNAs provides insights into the key genes involved in the high-altitude adaptation of yaks. PMID:34654374
Text mining-based word representations for biomedical data analysis and protein-protein interaction networks in machine learning tasks. PMID:34653224
Urinary extracellular vesicles: Assessment of pre-analytical variables and development of a quality control with focus on transcriptomic biomarker research. PMID:34651466
Network Pharmacology-Based Study of the Underlying Mechanisms of Huangqi Sijunzi Decoction for Alzheimer's Disease. PMID:34650613
GNG7 and ADCY1 as diagnostic and prognostic biomarkers for pancreatic adenocarcinoma through bioinformatic-based analyses. PMID:34650124
A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation. PMID:34649616
Downregulation of mitochondrial biogenesis by virus infection triggers antiviral responses by cyclic GMP-AMP synthase. PMID:34648591
Identification of candidate genes on the basis of SNP by time-lagged heat stress interactions for milk production traits in German Holstein cattle. PMID:34648531
Leveraging Experimental Strategies to Capture Different Dimensions of Microbial Interactions. PMID:34646243
TIGER: The gene expression regulatory variation landscape of human pancreatic islets. PMID:34644572
Clarifying the molecular mechanism of tomentosin‑induced antiproliferative and proapoptotic effects in human multiple myeloma via gene expression profile and genetic interaction network analysis. PMID:34643251
Integrated analysis of dysregulated microRNA and mRNA expression in intestinal epithelial cells following ethanol intoxication and burn injury. PMID:34642361
Neutrophil Pathways of Inflammation Characterize the Blood Transcriptomic Signature of Patients with Psoriasis and Cardiovascular Disease. PMID:34639156
Platelet-Released Growth Factors Induce Genes Involved in Extracellular Matrix Formation in Human Fibroblasts. PMID:34638874
Cilostazol Induces eNOS and TM Expression via Activation with Sirtuin 1/Krüppel-like Factor 2 Pathway in Endothelial Cells. PMID:34638626
Alterations in HLA Class I-Presented Immunopeptidome and Class I-Interactome upon Osimertinib Resistance in EGFR Mutant Lung Adenocarcinoma. PMID:34638461
Comparative genome characterization of Leptospira interrogans from mild and severe leptospirosis patients. PMID:34638178
LitCovid-AGAC: cellular and molecular level annotation data set based on COVID-19. PMID:34638170
A Polycomb domain found in committed cells impairs differentiation when introduced into PRC1 in pluripotent cells. PMID:34637753
POU class 2 homeobox associating factor 1 (POU2AF1) participates in abdominal aortic aneurysm enlargement based on integrated bioinformatics analysis. PMID:34637689
Transcriptomics Reveals the Putative Mycoparasitic Strategy of the Mushroom Entoloma abortivum on Species of the Mushroom Genus Armillaria. PMID:34636668
Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication. PMID:34635656
SCovid: single-cell atlases for exposing molecular characteristics of COVID-19 across 10 human tissues. PMID:34634820
Metabolic gene regulation by Drosophila GATA transcription factor Grain. PMID:34634038
OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis. PMID:34632381
OntoRepliCov: an Ontology-Based Approach for Modeling the SARS-CoV-2 Replication Process. PMID:34630741
Regulation of Long Non-coding RNA KCNQ1OT1 Network in Colorectal Cancer Immunity. PMID:34630508
The Biocontrol and Plant Growth-Promoting Properties of Streptomyces alfalfae XN-04 Revealed by Functional and Genomic Analysis. PMID:34630371
Effects of Bacille Calmette Guerin (BCG) vaccination during COVID-19 infection. PMID:34624759
Hepatic lysosomal acid lipase overexpression worsens hepatic inflammation in mice fed a Western diet. PMID:34624333
Clustering Spatial Transcriptomics Data. PMID:34623423
mRNA Network: Solution for Tracking Chemotherapy Insensitivity in Small-Cell Lung Cancer. PMID:34621500
A Taxon-Wise Insight Into Rock Weathering and Nitrogen Fixation Functional Profiles of Proglacial Systems. PMID:34621246
An overview of machine learning methods for monotherapy drug response prediction. PMID:34619752
Differential expression profile of gluten-specific T cells identified by single-cell RNA-seq. PMID:34618841
Phenotyping stomatal closure by thermal imaging for GWAS and TWAS of water use efficiency-related genes. PMID:34618072
Neuronal activity regulates the nuclear proteome to promote activity-dependent transcription. PMID:34617965
Construction of competing endogenous RNA interaction network as prognostic markers in metastatic melanoma. PMID:34616613
Whole Genome Sequence of Alternaria alternata, the Causal Agent of Black Spot of Kiwifruit. PMID:34616379
Identification of candidate genes from androgenic gland in Macrobrachium nipponense regulated by eyestalk ablation. PMID:34615913
Genome and transcriptome analysis to understand the role diversification of cytochrome P450 gene under excess nitrogen treatment. PMID:34615481
Host genetic factors associated with the range limit of a European hantavirus. PMID:34614264
CyanoOmicsDB: an integrated omics database for functional genomic analysis of cyanobacteria. PMID:34614159
A metric for evaluating biological information in gene sets and its application to identify co-expressed gene clusters in PBMC. PMID:34613979
An updated SYSCILIA gold standard (SCGSv2) of known ciliary genes, revealing the vast progress that has been made in the cilia research field. PMID:34613793
Estrogen Hormone Is an Essential Sex Factor Inhibiting Inflammation and Immune Response in COVID-19. PMID:34611658
Aberrantly reduced expression of miR-342-5p contributes to CCND1-associated chronic myeloid leukemia progression and imatinib resistance. PMID:34611140
Genome-wide associations for immune traits in two maternal pig lines. PMID:34610786
Proteomics changes after negative pressure wound therapy in diabetic foot ulcers. PMID:34608502
A Chinese host genetic study discovered IFNs and causality of laboratory traits on COVID-19 severity. PMID:34608450
Seed sequence polymorphism rs2168518 and allele-specific target gene regulation of hsa-miR-4513. PMID:34605899
Myogenin controls via AKAP6 non-centrosomal microtubule-organizing center formation at the nuclear envelope. PMID:34605406
Transcriptomic Analysis Reveals a Sex-Dimorphic Influence of GAT-2 on Murine Liver Function. PMID:34604287
Antigen Presenting Cells Link the Female Genital Tract Microbiome to Mucosal Inflammation, With Hormonal Contraception as an Additional Modulator of Inflammatory Signatures. PMID:34604114
Genetic Analysis of Heterosis for Yield Influencing Traits in Brassica juncea Using a Doubled Haploid Population and Its Backcross Progenies. PMID:34603351
Genome-Wide Transcriptional Changes of Rhodosporidium kratochvilovae at Low Temperature. PMID:34603256
Integrated bioinformatics analysis of core regulatory elements involved in keloid formation. PMID:34600545
Neurogenomic divergence during speciation by reinforcement of mating behaviors in chorus frogs (Pseudacris). PMID:34600496
Genome-wide phenotypic RNAi screen in the Drosophila wing: phenotypic description of functional classes. PMID:34599810
Subtype heterogeneity and epigenetic convergence in neuroendocrine prostate cancer. PMID:34599169
Spatiotemporal proteomic profiling of the pro-inflammatory response to lipopolysaccharide in the THP-1 human leukaemia cell line. PMID:34599159
Quantitative phosphoproteomics reveals GSK3A substrate network is involved in the cryodamage of sperm motility. PMID:34596222
X-Ray Causes mRNA Transcripts Change to Enhance Orai2-Mediated Ca2+ Influx in Rat Brain Microvascular Endothelial Cells. PMID:34595206
The Interactions of Small Proline-Rich Proteins with Late Cornified Envelope Proteins are Involved in the Pathogenesis of Psoriasis. PMID:34594126
In vitro CSC-derived cardiomyocytes exhibit the typical microRNA-mRNA blueprint of endogenous cardiomyocytes. PMID:34593953
Dramatic transcriptomic differences in Macaca mulatta and Macaca fascicularis with Plasmodium knowlesi infections. PMID:34593836
Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19. PMID:34592166
Interpretation of cancer mutations using a multiscale map of protein systems. PMID:34591613
Transcriptional Landscapes of Long Non-coding RNAs and Alternative Splicing in Pyricularia oryzae Revealed by RNA-Seq. PMID:34589103
Subtypes of schizophrenia identified by multi-omic measures associated with dysregulated immune function. PMID:34588622
Tanshinone IIA affects the malignant growth of Cholangiocarcinoma cells by inhibiting the PI3K-Akt-mTOR pathway. PMID:34588580
Divergent patterns of selection on metabolite levels and gene expression. PMID:34587900
Protein Aggregation Is an Early Manifestation of Phospholamban p.(Arg14del)-Related Cardiomyopathy: Development of PLN-R14del-Related Cardiomyopathy. PMID:34587756
The Euscaphis japonica genome and the evolution of malvids. PMID:34587334
Isolation, characterization, and genome assembly of Barnettozyma botsteinii sp. nov. and novel strains of Kurtzmaniella quercitrusa isolated from the intestinal tract of the termite Macrotermes bellicosus. PMID:34586397
Whole-genome assembly of Ganoderma leucocontextum (Ganodermataceae, Fungi) discovered from the Tibetan Plateau of China. PMID:34586388
The genome of the naturally evolved obesity-prone Ossabaw miniature pig. PMID:34585119
Transcriptomic profile of leg muscle during early growth and development in Haiyang yellow chicken. PMID:34584942
Identical twins carry a persistent epigenetic signature of early genome programming. PMID:34584077
Activity of the mouse Notch ligand DLL1 is sensitive to C-terminal tagging in vivo. PMID:34583743
Genome-wide association study and transcriptome of olecranon-type traits in peach (Prunus persica L.) germplasm. PMID:34583632
H3K4 di-methylation governs smooth muscle lineage identity and promotes vascular homeostasis by restraining plasticity. PMID:34582749
Integrative proteome analysis implicates aberrant RNA splicing in impaired developmental potential of aged mouse oocytes. PMID:34582091
Dynamics of TCR repertoire and T cell function in COVID-19 convalescent individuals. PMID:34580278
Wnt pathway-related three-mRNA clinical outcome signature in bladder urothelial carcinoma: computational biology and experimental analyses. PMID:34579753
Morphological, physiological, and transcriptional responses to low nitrogen stress in Populus deltoides Marsh. clones with contrasting nitrogen use efficiency. PMID:34579659
Recombinant Antigen of Type 2 Porcine Reproductive and Respiratory Syndrome Virus (PRRSV-2) Promotes M1 Repolarization of Porcine Alveolar Macrophages and Th1 Type Response. PMID:34579246
Quantitative Proteomics and Phosphoproteomics Reveal TNF-α-Mediated Protein Functions in Hepatocytes. PMID:34576943
Comprehensive Survey of Recent Drug Discovery Using Deep Learning. PMID:34576146
Identification of FadT as a Novel Quorum Quenching Enzyme for the Degradation of Diffusible Signal Factor in Cupriavidus pinatubonensis Strain HN-2. PMID:34576026
Complete Genomic Characterization and Identification of Saccharomycopsisphalluae sp. nov., a Novel Pathogen Causes Yellow Rot Disease on Phallus rubrovolvatus. PMID:34575745
Antioxidant and Antiproliferative Activity of Finasteride against Glioblastoma Cells. PMID:34575486
Identification of Long Non-Coding RNAs Involved in Porcine Fat Deposition Using Two High-Throughput Sequencing Methods. PMID:34573356
Identifying GPSM Family Members as Potential Biomarkers in Breast Cancer: A Comprehensive Bioinformatics Analysis. PMID:34572330
Distinct gene-set burden patterns underlie common generalized and focal epilepsies. PMID:34571366
scMethBank: a database for single-cell whole genome DNA methylation maps. PMID:34570235
Changes in the Gut Microbiome Contribute to the Development of Behcet's Disease via Adjuvant Effects. PMID:34568329
Profiling of MicroRNAs in Midguts of Plutella xylostella Provides Novel Insights Into the Bacillus thuringiensis Resistance. PMID:34567090
Identification of a miRNA-mRNA Regulatory Networks in Placental Tissue Associated With Tibetan High Altitude Adaptation. PMID:34567059
Viral suppressor of RNA silencing in vascular plants also interferes with the development of the bryophyte Physcomitrella patens. PMID:34564869
Integrative genomics analysis of nasal intestinal-type adenocarcinomas demonstrates the major role of CACNA1C and paves the way for a simple diagnostic tool in male woodworkers. PMID:34563241
PANNZER-A practical tool for protein function prediction. PMID:34562305
Differentially expressed genes reflect disease-induced rather than disease-causing changes in the transcriptome. PMID:34561431
Challenges and opportunities in the study of extracellular vesicles: Global institutional context and national state of the art. PMID:34559503
Transcriptome repository of North-Western Himalayan endangered medicinal herbs: a paramount approach illuminating molecular perspective of phytoactive molecules and secondary metabolism. PMID:34557965
Transcriptomic Analysis of Short/Branched-Chain Acyl-Coenzyme a Dehydrogenase Knocked Out bMECs Revealed Its Regulatory Effect on Lipid Metabolism. PMID:34557544
LncRNA SNHG17 Contributes to Proliferation, Migration, and Poor Prognosis of Hepatocellular Carcinoma. PMID:34557456
Expression and prognosis of CDC45 in cervical cancer based on the GEO database. PMID:34557356
Transcriptome and Oxylipin Profiling Joint Analysis Reveals Opposite Roles of 9-Oxylipins and Jasmonic Acid in Maize Resistance to Gibberella Stalk Rot. PMID:34557211
Glycolysis-related gene expression profiling serves as a novel prognosis risk predictor for human hepatocellular carcinoma. PMID:34556750
Network neighbors of viral targets and differentially expressed genes in COVID-19 are drug target candidates. PMID:34556735
Examination of Gene Loss in the DNA Mismatch Repair Pathway and Its Mutational Consequences in a Fungal Phylum. PMID:34554246
Characterization of Mesenchymal Stem Cells Derived from Bisphosphonate-Related Osteonecrosis of the Jaw Patients' Gingiva. PMID:34553308
The role of metadata in reproducible computational research. PMID:34553169
A novel lncRNA Discn fine-tunes replication protein A (RPA) availability to promote genomic stability. PMID:34552092
Subcellular proteomics. PMID:34549195
Comprehensive molecular characterization of pediatric radiation-induced high-grade glioma. PMID:34545084
Automated conceptual model clustering: a relator-centric approach. PMID:34539311
KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases. PMID:34537014
Genetic dissection of complex traits using hierarchical biological knowledge. PMID:34534210
GRASP55 restricts early-stage autophagy and regulates spatial organization of the early secretory network. PMID:34533192
Role of competitive endogenous RNA networks in the pathogenesis of coronary artery disease. PMID:34532371
Identifying the dynamic gene regulatory network during latent HIV-1 reactivation using high-dimensional ordinary differential equations. PMID:34531927
Identification of Novel Gene Signatures using Next-Generation Sequencing Data from COVID-19 Infection Models: Focus on Neuro-COVID and Potential Therapeutics. PMID:34531741
Cell-specific gene association network construction from single-cell RNA sequence. PMID:34530677
Intercrypt sentinel macrophages tune antibacterial NF-κB responses in gut epithelial cells via TNF. PMID:34529751
Prognostic impact of a lymphocyte activation-associated gene signature in GBM based on transcriptome analysis. PMID:34527446
Integrative Analysis of the Roles of lncRNAs and mRNAs in Itaconate-Mediated Protection Against Liver Ischemia-Reperfusion Injury in Mice. PMID:34526799
Understanding Competitive Endogenous RNA Network Mechanism in Type 1 Diabetes Mellitus Using Computational and Bioinformatics Approaches. PMID:34526791
Multipotent progenitors and hematopoietic stem cells arise independently from hemogenic endothelium in the mouse embryo. PMID:34525376
MULocDeep: A deep-learning framework for protein subcellular and suborganellar localization prediction with residue-level interpretation. PMID:34522290
Bioinformatics analysis identified shared differentially expressed genes as potential biomarkers for Hashimoto's thyroiditis-related papillary thyroid cancer. PMID:34522174
Integrated analysis of the molecular mechanisms in idiopathic pulmonary fibrosis. PMID:34522168
Characterization of m6A-Related Genes Landscape in Skin Cutaneous Melanoma to Aid Immunotherapy and Assess Prognosis. PMID:34522131
Rapid Macrosatellite Evolution Promotes X-Linked Hybrid Male Sterility in a Feline Interspecies Cross. PMID:34519828
Podocyte-specific KLF4 is required to maintain parietal epithelial cell quiescence in the kidney. PMID:34516901
Rare variants in the endocytic pathway are associated with Alzheimer's disease, its related phenotypes, and functional consequences. PMID:34516545
SynWiki: Functional annotation of the first artificial organism Mycoplasma mycoides JCVI-syn3A. PMID:34515387
Bioinformatic analysis for potential biological processes and key targets of heart failure-related stroke. PMID:34514752
SCISSOR™: a single-cell inferred site-specific omics resource for tumor microenvironment association study. PMID:34514416
Effect of Tension on Human Periodontal Ligament Cells: Systematic Review and Network Analysis. PMID:34513810
Circulating microRNAs in Early Breast Cancer Patients and Its Association With Lymph Node Metastases. PMID:34513655
Protein function prediction with gene ontology: from traditional to deep learning models. PMID:34513334
Integrative analysis reveals clinically relevant molecular fingerprints in pancreatic cancer. PMID:34513290
Analysis of the Genome Sequence of Strain GiC-126 of Gloeostereum incarnatum with Genetic Linkage Map. PMID:34512084
Integrated analysis of lncRNA and mRNA in liver of Megalobrama amblycephala post Aeromonas hydrophila infection. PMID:34511071
Chromosomal neighbourhoods allow identification of organ specific changes in gene expression. PMID:34506480
Inferring Functional Epigenetic Modules by Integrative Analysis of Multiple Heterogeneous Networks. PMID:34504516
The Cancer Epitope Database and Analysis Resource: A Blueprint for the Establishment of a New Bioinformatics Resource for Use by the Cancer Immunology Community. PMID:34504503
Chondrocytes from Osteoarthritis Patients Adopt Distinct Phenotypes in Response to Central TH1/TH2/TH17 Cytokines. PMID:34502384
Investigating the Molecular Processes behind the Cell-Specific Toxicity Response to Titanium Dioxide Nanobelts. PMID:34502343
Classification and Treatment of Diseases in the Age of Genome Medicine Based on Pathway Pathology. PMID:34502326
Catalyzing Knowledge-Driven Discovery in Environmental Health Sciences through a Community-Driven Harmonized Language. PMID:34501574
Construction and analysis of a novel ferroptosis-related gene signature predicting prognosis in lung adenocarcinoma. PMID:34499810
A high-quality chromosome-level genome of wild Rosa rugosa. PMID:34499118
Specifying who delivers behaviour change interventions: development of an Intervention Source Ontology. PMID:34497878
Basement membrane proteins in various arterial beds from individuals with and without type 2 diabetes mellitus: a proteome study. PMID:34496837
An iteration model for identifying essential proteins by combining comprehensive PPI network with biological information. PMID:34496745
Single-cell heterogeneity analysis and CRISPR screens in MIN6 cell line reveal transcriptional regulators of insulin. PMID:34494921
Weakly activated core inflammation pathways were identified as a central signaling mechanism contributing to the chronic neurodegeneration in Alzheimer's disease. PMID:34494019
Integrative Analyses of Genes Associated with Hashimoto's Thyroiditis. PMID:34493981
Marine natural products targeting the eukaryotic cell membrane. PMID:34493848
Induction of dopaminergic neurons for neuronal subtype-specific modeling of psychiatric disease risk. PMID:34493831
Comparative analysis of the complete mitochondrial genome sequences and anther development cytology between maintainer and Ogura-type cytoplasm male-sterile cabbage (B. oleracea Var. capitata). PMID:34493212
Identification of direct transcriptional targets of NFATC2 that promote β cell proliferation. PMID:34491912
Integrative Analysis of Minichromosome Maintenance Proteins and Their Prognostic Significance in Melanoma. PMID:34490114
Interpretable, Scalable, and Transferrable Functional Projection of Large-Scale Transcriptome Data Using Constrained Matrix Decomposition. PMID:34490045
Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis. PMID:34489600
Learning interpretable cellular and gene signature embeddings from single-cell transcriptomic data. PMID:34489404
The genome sequence provides insights into salt tolerance of Achnatherum splendens (Gramineae), a constructive species of alkaline grassland. PMID:34487631
Modelling the impact of decidual senescence on embryo implantation in human endometrial assembloids. PMID:34487490
Proteomic Analysis of Copper Toxicity in Human Fungal Pathogen Cryptococcus neoformans. PMID:34485169
Inflammatory gene expression profiling in peripheral blood from patients with Alzheimer's disease reveals key pathways and hub genes with potential diagnostic utility: a preliminary study. PMID:34484988
Proteomic Analysis of Hypoxia-Induced Senescence of Human Bone Marrow Mesenchymal Stem Cells. PMID:34484348
Identification of EP300 as a Key Gene Involved in Antipsychotic-Induced Metabolic Dysregulation Based on Integrative Bioinformatics Analysis of Multi-Tissue Gene Expression Data. PMID:34483940
Centromere protein E as a novel biomarker and potential therapeutic target for retinoblastoma. PMID:34482803
Identification of anti-horn fly vaccine antigen candidates using a reverse vaccinology approach. PMID:34479607
FORUM: Building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases. PMID:34478489
Release of Notch activity coordinated by IL-1β signalling confers differentiation plasticity of airway progenitors via Fosl2 during alveolar regeneration. PMID:34475534
Human melanocyte development and melanoma dedifferentiation at single-cell resolution. PMID:34475532
A prelude to the proximity interaction mapping of CXXC5. PMID:34475492
Evolutionary history of two rare endemic conifer species from the eastern Qinghai-Tibet Plateau. PMID:34472580
Assembling stable syntrophic Escherichia coli communities by comprehensively identifying beneficiaries of secreted goods. PMID:34469744
Differential transcript usage analysis of bulk and single-cell RNA-seq data with DTUrtle. PMID:34469510
Nesterenkonia ebinurensis sp. nov., a Novel Actinobacterium Isolated From Populus euphratica. PMID:34468853
Human genetic analyses of organelles highlight the nucleus in age-related trait heritability. PMID:34467851
Chromosome-scale assembly of the Dendrobium chrysotoxum genome enhances the understanding of orchid evolution. PMID:34465765
Predictability of polygenic risk score for progression to dementia and its interaction with APOE ε4 in mild cognitive impairment. PMID:34465370
Upper airway gene expression reveals a more robust innate and adaptive immune response to SARS-CoV-2 in children compared with older adults. PMID:34462739
Deep learning from HE slides predicts the clinical benefit from adjuvant chemotherapy in hormone receptor-positive breast cancer patients. PMID:34462515
Host metabolic shift during systemic Salmonella infection revealed by comparative proteomics. PMID:34461813
Heparanase is a novel biomarker for immune infiltration and prognosis in breast cancer. PMID:34461608
A multi-objective genetic algorithm to find active modules in multiplex biological networks. PMID:34460810
A Birds-Eye (Re)View of Acid-Suppression Drugs, COVID-19, and the Highly Variable Literature. PMID:34456726
Will Plant Genome Editing Play a Decisive Role in "Quantum-Leap" Improvements in Crop Yield to Feed an Increasing Global Human Population? PMID:34451712
Microvesicles transfer mitochondria and increase mitochondrial function in brain endothelial cells. PMID:34450196
The blood transcriptome prior to ovarian cancer diagnosis: A case-control study in the NOWAC postgenome cohort. PMID:34449791
A Comprehensive Guide to Potato Transcriptome Assembly. PMID:34448160
An Overview of Cell-Based Assay Platforms for the Solute Carrier Family of Transporters. PMID:34447313
Icariin, an Up-and-Coming Bioactive Compound Against Neurological Diseases: Network Pharmacology-Based Study and Literature Review. PMID:34447243
Identification of key proteins in the signaling crossroads between wound healing and cancer hallmark phenotypes. PMID:34446793
Pan-cancer analysis of longitudinal metastatic tumors reveals genomic alterations and immune landscape dynamics associated with pembrolizumab sensitivity. PMID:34446728
Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes. PMID:34446072
Differential Retinal Protein Expression in Primary and Secondary Retinal Ganglion Cell Degeneration Identified by Integrated SWATH and Target-Based Proteomics. PMID:34445296
Hepatic Proteomic Analysis of Selenoprotein T Knockout Mice by TMT: Implications for the Role of Selenoprotein T in Glucose and Lipid Metabolism. PMID:34445217
Metatranscriptomic Analysis of Bacterial Communities on Laundered Textiles: A Pilot Case Study. PMID:34442670
Evaluating, Filtering and Clustering Genetic Disease Cohorts Based on Human Phenotype Ontology Data with Cohort Analyzer. PMID:34442375
JDSNMF: Joint Deep Semi-Non-Negative Matrix Factorization for Learning Integrative Representation of Molecular Signals in Alzheimer's Disease. PMID:34442330
Transcriptional Profiles of Diploid Mutant Apis mellifera Embryos after Knockout of csd by CRISPR/Cas9. PMID:34442270
A Genome-Wide Association Study on Liver Stiffness Changes during Hepatitis C Virus Infection Cure. PMID:34441435
DNA Methylation Alterations in Blood Cells of Toddlers with Down Syndrome. PMID:34440289
Comparative Transcriptomic Analysis Reveals the Effects of Drought on the Biosynthesis of Methyleugenol in Asarum sieboldii Miq. PMID:34439899
Application of Weighted Gene Coexpression Network Analysis to Identify Key Modules and Hub Genes in Systemic Juvenile Idiopathic Arthritis. PMID:34435051
Establishment of a ferroptosis-related gene signature for prognosis in lung adenocarcinoma patients. PMID:34434660
Ferroptosis-Related Genes in Lung Adenocarcinoma: Prognostic Signature and Immune, Drug Resistance, Mutation Analysis. PMID:34434214
A high-resolution temporal atlas of the SARS-CoV-2 translatome and transcriptome. PMID:34433827
Integrative analysis of metabolome and transcriptome profiles provides insight into the fruit pericarp pigmentation disorder caused by 'Candidatus Liberibacter asiaticus' infection. PMID:34433413
CANVS: an easy-to-use application for the analysis and visualization of mass spectrometry-based protein-protein interaction/association data. PMID:34432510
Depletion of TAX1BP1 Amplifies Innate Immune Responses during Respiratory Syncytial Virus Infection. PMID:34431698
Bacterial surface properties influence the activity of the TAT-RasGAP317-326 antimicrobial peptide. PMID:34430812
Transcriptional Analysis of Liver Tissue Identifies Distinct Phenotypes of Indeterminate Pediatric Acute Liver Failure. PMID:34430782
Plasma proteomic profiling reveals biomarkers associated with aortic dilation in patients with bicuspid aortic valve. PMID:34430623
Identification of new target proteins of a Urotensin-II receptor antagonist using transcriptome-based drug repositioning approach. PMID:34429474
Discovery of Cellular RhoA Functions by the Integrated Application of Gene Set Enrichment Analysis. PMID:34429388
Perturbed transcriptional profiles after chronic low dose rate radiation in mice. PMID:34428250
Identification of fibronectin 1 (FN1) and complement component 3 (C3) as immune infiltration-related biomarkers for diabetic nephropathy using integrated bioinformatic analysis. PMID:34424825
C-X-C motif chemokine ligand 12: a potential therapeutic target in Duchenne muscular dystrophy. PMID:34424816
Hypoxia-Inducible Factor 2-Alpha Mediated Gene Sets Differentiate Pulmonary Arterial Hypertension. PMID:34422822
TCF3 Regulates the Proliferation and Apoptosis of Human Spermatogonial Stem Cells by Targeting PODXL. PMID:34422820
CD86 Molecule Might Be a Novel Immune-Related Prognostic Biomarker for Patients With Bladder Cancer by Bioinformatics and Experimental Assays. PMID:34422632
Systematic Analysis Identifies a Specific RNA-Binding Protein-Related Gene Model for Prognostication and Risk-Adjustment in HBV-Related Hepatocellular Carcinoma. PMID:34422009
Long Non-coding RNA RP11-395G23.3 Acts as a Competing Endogenous RNA of miR-124-3p to Regulate ROR1 in Anaplastic Thyroid Carcinoma. PMID:34421987
Activation of FcRn Mediates a Primary Resistance Response to Sorafenib in Hepatocellular Carcinoma by Single-Cell RNA Sequencing. PMID:34421602
Identifying causal models between genetically regulated methylation patterns and gene expression in healthy colon tissue. PMID:34419169
Identification of significant alteration genes, pathways and TFs induced by LPS in ARDS via bioinformatical analysis. PMID:34418997
Comparative transcriptomic analyses of glucosinolate metabolic genes during the formation of Chinese kale seeds. PMID:34418959
Use of Network Pharmacology to Investigate the Mechanism of the Compound Xuanju Capsule in the Treatment of Rheumatoid Arthritis. PMID:34414237
Dynamic Patterns of N6-Methyladenosine Profiles of Messenger RNA Correlated with the Cardiomyocyte Regenerability during the Early Heart Development in Mice. PMID:34413927
Utilization of Transcriptome, Small RNA, and Degradome Sequencing to Provide Insights Into Drought Stress and Rewatering Treatment in Medicago ruthenica. PMID:34413864
Pathogenic variations in Germ Cell Nuclear Acidic Peptidase (GCNA) are associated with human male infertility. PMID:34413498
RNA-Seq, physiological, and biochemical analysis of burley tobacco response to nitrogen deficiency. PMID:34413327
Searchlight: automated bulk RNA-seq exploration and visualisation using dynamically generated R scripts. PMID:34412594
Dietary omega-3 fatty acid intake impacts peripheral blood DNA methylation -anti-inflammatory effects and individual variability in a pilot study. PMID:34411715
Cadherin and Wnt signaling pathways as key regulators in diabetic nephropathy. PMID:34411124
Modeling the effects of EMT-immune dynamics on carcinoma disease progression. PMID:34408236
Gene expression profile analysis of gallic acid-induced cell death process. PMID:34408198
PhenoDB, GeneMatcher and VariantMatcher, tools for analysis and sharing of sequence data. PMID:34407837
Human iPS-derived pre-epicardial cells direct cardiomyocyte aggregation expansion and organization in vitro. PMID:34404774
Evaluation of the molecular response of corpora lutea to manganese-amino acid complex supplementation in gilts. PMID:34402900
Gentamicin-induced hearing loss: A retrospective study using the Food and Drug Administration Adverse Event Reporting System and a toxicological study using drug-gene network analysis. PMID:34401547
MiR-508-3p promotes proliferation and inhibits apoptosis of middle ear cholesteatoma cells by targeting PTEN/PI3K/AKT pathway. PMID:34400892
A systematic comparison of data- and knowledge-driven approaches to disease subtype discovery. PMID:34396389
Deciphering the Therapeutic Mechanisms of Wuzi Ershen Decoction in Treating Oligoasthenozoospermia through the Network Pharmacology Approach. PMID:34394386
Genes and Pathways Affecting Sheep Productivity Traits: Genetic Parameters, Genome-Wide Association Mapping, and Pathway Enrichment Analysis. PMID:34394196
Insights from the cDNA and EST analysis of Antrodia cinnamomea. PMID:34393425
Employing bioinformatics analysis to identify hub genes and microRNAs involved in colorectal cancer. PMID:34390411
Comparison of gene expression in the red imported fire ant (Solenopsis invicta) under different temperature conditions. PMID:34389756
A single amino acid residue substitution in BraA04g017190.3C, a histone methyltransferase, results in premature bolting in Chinese cabbage (Brassica rapa L. ssp. Pekinensis). PMID:34388969
Mapping gene and gene pathways associated with coronary artery disease: a CARDIoGRAM exome and multi-ancestry UK biobank analysis. PMID:34385509
Comprior: facilitating the implementation and automated benchmarking of prior knowledge-based feature selection approaches on gene expression data sets. PMID:34384353
Transgenic modeling of Ndr2 gene amplification reveals disturbance of hippocampus circuitry and function. PMID:34381982
Data on the first functionally-annotated de novo transcriptome assembly for North American flying squirrels (genus Glaucomys). PMID:34381854
Exploring tissue architecture using spatial transcriptomics. PMID:34381231
Molecular and functional characterization of detrusor PDGFRα positive cells in spinal cord injury-induced detrusor overactivity. PMID:34381120
Downregulation of exhausted cytotoxic T cells in gene expression networks of multisystem inflammatory syndrome in children. PMID:34381049
GraphDTI: A robust deep learning predictor of drug-target interactions from multiple heterogeneous data. PMID:34380569
De novo genome assembly of the potent medicinal plant Rehmannia glutinosa using nanopore technology. PMID:34377362
A Novel miRNA-mRNA Axis Involves in Regulating Transcriptional Disorders in Pancreatic Adenocarcinoma. PMID:34377019
SERPINH1, Targeted by miR-29b, Modulated Proliferation and Migration of Human Retinal Endothelial Cells Under High Glucose Conditions. PMID:34377003
The molecular basis, genetic control and pleiotropic effects of local gene co-expression. PMID:34376650
From a genome assembly to full regulatory network prediction: the case study of Rhodotorula toruloides putative Haa1-regulon. PMID:34376148
Corticosterone pattern-dependent glucocorticoid receptor binding and transcriptional regulation within the liver. PMID:34375333
Identification of m6A-Related Biomarkers Associated with Prognosis of Colorectal Cancer. PMID:34373442
Identifying potential association on gene-disease network via dual hypergraph regularized least squares. PMID:34372777
CAD Genes: Genome-Wide Identification, Evolution, and Their Contribution to Lignin Biosynthesis in Pear (Pyrus bretschneideri). PMID:34371647
Exploring Chemical Information in PubChem. PMID:34370395
Transcriptional Profiling of Exosomes Derived from Staphylococcus aureus-Infected Bovine Mammary Epithelial Cell Line MAC-T by RNA-Seq Analysis. PMID:34367468
Limitations of Explainability for Established Prognostic Biomarkers of Prostate Cancer. PMID:34367234
Transcriptome and Small RNA Combined Sequencing Analysis of Cold Tolerance in Non-heading Chinese Cabbage. PMID:34367230
IRF7-Associated Immunophenotypes Have Dichotomous Responses to Virus/Allergen Coexposure and OM-85-Induced Reprogramming. PMID:34367159
Quantitative Peptidomics of Mouse Brain After Infection With Cyst-Forming Toxoplasma gondii. PMID:34367142
Hanseniaspora smithiae sp. nov., a Novel Apiculate Yeast Species From Patagonian Forests That Lacks the Typical Genomic Domestication Signatures for Fermentative Environments. PMID:34367085
An Ontology-Based Framework for Psychological Monitoring in Education During the COVID-19 Pandemic. PMID:34366992
Transcriptome analysis of differentially expressed genes in chrysanthemum MET1 RNA interference lines. PMID:34366589
TACR2 is associated with the immune microenvironment and inhibits migration and proliferation via the Wnt/β-catenin signaling pathway in prostate cancer. PMID:34364377
Sustained expression of inflammatory monocytes and activated T cells in COVID-19 patients and recovered convalescent plasma donors. PMID:34363351
Collagen fiber orientation disorder from H&E images is prognostic for early stage breast cancer: clinical trial validation. PMID:34362928
MAIT cells regulate NK cell-mediated tumor immunity. PMID:34362900
Association of CASC18/miR-20a-3p/TGFB2 ceRNA axis with occult lymph node metastasis in tongue squamous cell carcinoma. PMID:34362313
Regulatory Network Analysis in Estradiol-Treated Human Endothelial Cells. PMID:34360960
Identification of Rhythmically Expressed LncRNAs in the Zebrafish Pineal Gland and Testis. PMID:34360576
Two-Pore Channels Regulate Expression of Various Receptors and Their Pathway-Related Proteins in Multiple Ways. PMID:34359976
Integrated Analysis of Long Non-Coding RNA and mRNA Expression Profiles in Testes of Calves and Sexually Mature Wandong Bulls (Bos taurus). PMID:34359134
Investigation of RNA metabolism through large-scale genetic interaction profiling in yeast. PMID:34358317
Chronic Kidney Disease Cohort Studies: A Guide to Metabolome Analyses. PMID:34357354
The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research. PMID:34357286
Computational Probing the Methylation Sites Related to EGFR Inhibitor-Responsive Genes. PMID:34356665
Male Differentiation in the Marine Copepod Oithona nana Reveals the Development of a New Nervous Ganglion and Lin12-Notch-Repeat Protein-Associated Proteolysis. PMID:34356512
A Reassessment of Copy Number Variations in Congenital Heart Defects: Picturing the Whole Genome. PMID:34356064
Identification of Hub Genes Associated with Diabetes Mellitus and Tuberculosis Using Bioinformatic Analysis. PMID:34354368
Microfluidic device with brain extracellular matrix promotes structural and functional maturation of human brain organoids. PMID:34354063
Personalized single-cell networks: a framework to predict the response of any gene to any drug for any patient. PMID:34353329
Evaluating whole-genome expression differences in idiopathic and diabetic adhesive capsulitis. PMID:34352401
A general role for TANGO1, encoded by MIA3, in secretory pathway organization and function. PMID:34350936
Network Pharmacology Combined with Bioinformatics to Investigate the Mechanisms and Molecular Targets of Astragalus Radix-Panax notoginseng Herb Pair on Treating Diabetic Nephropathy. PMID:34349833
Genomic Analysis of the Mycoparasite Pestalotiopsis sp. PG52. PMID:34349810
Revealing protein-protein interactions at the transcriptome scale by sequencing. PMID:34348091
Ubiquitination-Related miRNA-mRNA Interaction Is a Potential Mechanism in the Progression of Retinoblastoma. PMID:34347012
Myeloid-resident neuropilin-1 influences brown adipose tissue in obesity. PMID:34344941
Effects of low lead exposure on sperm quality and sperm DNA methylation in adult men. PMID:34344450
Efficient Dicer processing of virus-derived double-stranded RNAs and its modulation by RIG-I-like receptor LGP2. PMID:34343211
Comprehensive Strain-Level Analysis of the Gut Microbe Faecalibacterium prausnitzii in Patients with Liver Cirrhosis. PMID:34342541
DeepMAge: A Methylation Aging Clock Developed with Deep Learning. PMID:34341706
Identifying molecular insight of synergistic complexities for SARS-CoV-2 infection with pre-existing type 2 diabetes. PMID:34340124
A systems-level study reveals host-targeted repurposable drugs against SARS-CoV-2 infection. PMID:34339582
Developmental lineage of human pluripotent stem cell-derived cardiac fibroblasts affects their functional phenotype. PMID:34339055
Identification and Confirmation of the miR-30 Family as a Potential Central Player in Tobacco-Related Head and Neck Squamous Cell Carcinoma. PMID:34336638
Comparative Transcriptome and Weighted Gene Co-expression Network Analysis Identify Key Transcription Factors of Rosa chinensis 'Old Blush' After Exposure to a Gradual Drought Stress Followed by Recovery. PMID:34335694
Comparing Host Module Activation Patterns and Temporal Dynamics in Infection by Influenza H1N1 Viruses. PMID:34335598
Genome-wide profiles of UV lesion susceptibility, repair, and mutagenic potential in melanoma. PMID:34333390
Aurora kinase A (AURKA) promotes the progression and imatinib resistance of advanced gastrointestinal stromal tumors. PMID:34332577
Computational identification of repurposed drugs against viruses causing epidemics and pandemics via drug-target network analysis. PMID:34332351
Global patterns of enhancer activity during sea urchin embryogenesis assessed by eRNA profiling. PMID:34330790
Epigenetic Analysis of the Chromatin Landscape Identifies a Repertoire of Murine Eosinophil-Specific PU.1-Bound Enhancers. PMID:34330753
Histone H2A.X phosphorylation and Caspase-Initiated Chromatin Condensation in late-stage erythropoiesis. PMID:34330317
Spectrum of Protein Location in Proteomes Captures Evolutionary Relationship Between Species. PMID:34328525
Clinical Genetic Risk Variants Inform a Functional Protein Interaction Network for Tetralogy of Fallot. PMID:34328347
Exosomal miR-218-5p/miR-363-3p from Endothelial Progenitor Cells Ameliorate Myocardial Infarction by Targeting the p53/JMY Signaling Pathway. PMID:34326916
Comparative transcriptome analysis reveals regulatory network and regulators associated with proanthocyanidin accumulation in persimmon. PMID:34325657
Genetic mapping of renal glutathione suggests a novel regulatory locus on the murine X chromosome and overlap with hepatic glutathione regulation. PMID:34324982
Transcriptional Profiling During Neural Conversion. PMID:34324187
Eukaryotic initiation factor EIF-3.G augments mRNA translation efficiency to regulate neuronal activity. PMID:34323215
Proteomic analysis reveals dexamethasone rescues matrix breakdown but not anabolic dysregulation in a cartilage injury model. PMID:34322675
Predicting Panel of Metabolism and Immune-Related Genes for the Prognosis of Human Ovarian Cancer. PMID:34322485
Genome Size Estimation and Full-Length Transcriptome of Sphingonotus tsinlingensis: Genetic Background of a Drought-Adapted Grasshopper. PMID:34322153
Gene expression profile of the murine ischemic retina and its response to Aflibercept (VEGF-Trap). PMID:34321516
Two Reference-Quality Sea Snake Genomes Reveal Their Divergent Evolution of Adaptive Traits and Venom Systems. PMID:34320652
RCA2: a scalable supervised clustering algorithm that reduces batch effects in scRNA-seq data. PMID:34320202
DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug-target interactions. PMID:34320178
Functionathon: a manual data mining workflow to generate functional hypotheses for uncharacterized human proteins and its application by undergraduate students. PMID:34318869
Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms. PMID:34318308
EVI1 activates tumor-promoting transcriptional enhancers in pancreatic cancer. PMID:34316710
LncRNA AC007255.1, an immune-related prognostic enhancer RNA in esophageal cancer. PMID:34316393
Analysis of long intergenic non-coding RNAs transcriptomic profiling in skeletal muscle growth during porcine embryonic development. PMID:34315913
Single-cell transcriptome of bronchoalveolar lavage fluid reveals sequential change of macrophages during SARS-CoV-2 infection in ferrets. PMID:34315893
Enhancing the interoperability of glycan data flow between ChEBI, PubChem and GlyGen. PMID:34314492
Study on potential differentially expressed genes in stroke by bioinformatics analysis. PMID:34313877
VarSAn: associating pathways with a set of genomic variants using network analysis. PMID:34313777
Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota. PMID:34312531
Transcriptome Characterization and Identification of Molecular Markers (SNP, SSR, and Indels) in the Medicinal Plant Sarcandra glabra spp. PMID:34307686
High Expression Levels of CDK1 and CDC20 in Patients With Lung Squamous Cell Carcinoma are Associated With Worse Prognosis. PMID:34307447
Autophagy-Related Genes in Atherosclerosis. PMID:34306596
The Role of INAPERTURATE POLLEN1 as a Pollen Aperture Factor Is Conserved in the Basal Eudicot Eschscholzia californica (Papaveraceae). PMID:34305989
The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns. PMID:34305969
The Compressed Vocabulary of Microbial Life. PMID:34305827
Identification of pathological transcription in autosomal dominant polycystic kidney disease epithelia. PMID:34301992
CFTR Lifecycle Map-A Systems Medicine Model of CFTR Maturation to Predict Possible Active Compound Combinations. PMID:34299207
Drugs and Epigenetic Molecular Functions. A Pharmacological Data Scientometric Analysis. PMID:34298869
SPTAN1 Expression Predicts Treatment and Survival Outcomes in Colorectal Cancer. PMID:34298848
ULK overexpression mitigates motor deficits and neuropathology in mouse models of Machado-Joseph disease. PMID:34298131
Systematic review of human post-mortem immunohistochemical studies and bioinformatics analyses unveil the complexity of astrocyte reaction in Alzheimer's disease. PMID:34297416
Bioinformatics analysis of PAE family in Populus trichocarpa and responsiveness to carbon and nitrogen treatment. PMID:34295610
Context-dependent effects of whole-genome duplication during mammary tumor recurrence. PMID:34294755
Transcriptome sequencing and multi-plex imaging of prostate cancer microenvironment reveals a dominant role for monocytic cells in progression. PMID:34294073
Genetic mapping of novel modifiers for ApcMin induced intestinal polyps' development using the genetic architecture power of the collaborative cross mice. PMID:34294033
Highly accurate protein structure prediction for the human proteome. PMID:34293799
Proteome plasticity in response to persistent environmental change. PMID:34293321
Key Candidate Genes - VSIG2 of Colon Cancer Identified by Weighted Gene Co-Expression Network Analysis. PMID:34290531
Identification of Key Genes and Underlying Mechanisms in Acute Kawasaki Disease Based on Bioinformatics Analysis. PMID:34290221
Sequence-based features that are determinant for tail-anchored membrane protein sorting in eukaryotes. PMID:34288289
Transcriptomic Analysis Exploring the Molecular Mechanisms of Hanchuan Zupa Granules in Alleviating Asthma in Rat. PMID:34285702
Full-length transcriptome assembly of andrias davidianus (amphibia: caudata) skin via hybrid sequencing. PMID:34282833
Analyzing the gonadal transcriptome of the frog Hoplobatrachus rugulosus to identify genes involved in sex development. PMID:34281525
Transcriptomic analyses of cacao flavonoids produced in photobioreactors. PMID:34281511
Identification of genes predicting unfavorable prognosis in hepatitis B virus-associated hepatocellular carcinoma. PMID:34277775
Biomarker Categorization in Transcriptomic Meta-Analysis by Concordant Patterns With Application to Pan-Cancer Studies. PMID:34276766
Comparative Label-Free Quantitative Proteomics Analysis Reveals the Essential Roles of N-Glycans in Salt Tolerance by Modulating Protein Abundance in Arabidopsis. PMID:34276718
Analysis of the Taxonomy and Pathogenic Factors of Pectobacterium aroidearum L6 Using Whole-Genome Sequencing and Comparative Genomics. PMID:34276610
Genomic Analysis of Sarcomyxa edulis Reveals the Basis of Its Medicinal Properties and Evolutionary Relationships. PMID:34276589
Differential Packaging Into Outer Membrane Vesicles Upon Oxidative Stress Reveals a General Mechanism for Cargo Selectivity. PMID:34276573
Dissecting the shared genetic basis of migraine and mental disorders using novel statistical tools. PMID:34273149
Correlation between targeted RNAseq signature of breast cancer CTCs and onset of bone-only metastases. PMID:34272498
FOXC2 controls adult lymphatic endothelial specialization, function, and gut lymphatic barrier preventing multiorgan failure. PMID:34272244
An ancestral recombination graph of human, Neanderthal, and Denisovan genomes. PMID:34272242
Transcriptome analysis of resistant and susceptible mulberry responses to Meloidogyne enterolobii infection. PMID:34271854
MSCFS: inferring circRNA functional similarity based on multiple data sources. PMID:34271851
Correlation guided Network Integration (CoNI) reveals novel genes affecting hepatic metabolism. PMID:34271221
Oxidation of Hemoglobin Drives a Proatherogenic Polarization of Macrophages in Human Atherosclerosis. PMID:34269613
Gene and protein expression profiles of olfactory ensheathing cells from olfactory bulb versus olfactory mucosa. PMID:34269221
Hippocampus chronic deep brain stimulation induces reversible transcript changes in a macaque model of mesial temporal lobe epilepsy. PMID:34267068
Global analysis of protein lysine 2-hydroxyisobutyrylation (Khib) profiles in Chinese herb rhubarb (Dahuang). PMID:34266380
Polychlorinated biphenyls induce oxidative stress and metabolic responses in astrocytes. PMID:34265337
Multimarker profiling identifies protective and harmful immune processes in heart failure: findings from BIOSTAT-CHF. PMID:34264317
A network-biology approach for identification of key genes and pathways involved in malignant peritoneal mesothelioma. PMID:34261301
A protein interactions map of multiple organ systems associated with COVID-19 disease. PMID:34261299
Identifying a Serum Exosomal-Associated lncRNA/circRNA-miRNA-mRNA Network in Coronary Heart Disease. PMID:34258055
Genome sequence of Apostasia ramifera provides insights into the adaptive evolution in orchids. PMID:34256691
Accurate transcriptome assembly by Nanopore RNA sequencing reveals novel functional transcripts in hepatocellular carcinoma. PMID:34255396
Computationally scalable regression modeling for ultrahigh-dimensional omics data with ParProx. PMID:34254998
Application across species of a one health approach to liquid sample handling for respiratory based -omics analysis. PMID:34253818
stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics. PMID:34252941
'Single-subject studies'-derived analyses unveil altered biomechanisms between very small cohorts: implications for rare diseases. PMID:34252934
DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction. PMID:34252926
Bioinformatics Analysis Reveals Crosstalk Among Platelets, Immune Cells, and the Glomerulus That May Play an Important Role in the Development of Diabetic Nephropathy. PMID:34249963
Transcriptomic Signature of Human Embryonic Thyroid Reveals Transition From Differentiation to Functional Maturation. PMID:34249923
In silico-driven analysis of the Glossina morsitans morsitans antennae transcriptome in response to repellent or attractant compounds. PMID:34249514
Comparative analysis of fatty acid metabolism based on transcriptome sequencing of wild and cultivated Ophiocordyceps sinensis. PMID:34249512
Overlapping Structures Detection in Protein-Protein Interaction Networks Using Community Detection Algorithm Based on Neighbor Clustering Coefficient. PMID:34249104
Genetic Divergence and Population Structure in Weedy and Cultivated Broomcorn Millets (Panicum miliaceum L.) Revealed by Specific-Locus Amplified Fragment Sequencing (SLAF-Seq). PMID:34249058
Trajectories of Homoeolog-Specific Expression in Allotetraploid Tragopogon castellanus Populations of Independent Origins. PMID:34249049
DNA methylation analysis reveals epimutation hotspots in patients with dilated cardiomyopathy-associated laminopathies. PMID:34246298
Transcriptomic and metabolomic profiles of Zea mays fed with urea and ammonium. PMID:34245168
TIDB: a comprehensive database of trained immunity. PMID:34244719
MicroRNA-378a-3p is overexpressed in psoriasis and modulates cell cycle arrest in keratinocytes via targeting BMP2 gene. PMID:34244572
Approximate search for known gene clusters in new genomes using PQ-trees. PMID:34243815
Full-Length Transcriptome Analysis Reveals Candidate Genes Involved in Terpenoid Biosynthesis in Artemisia argyi. PMID:34239538
Exosomes Derived From Heat Stroke Cases Carry miRNAs Associated With Inflammation and Coagulation Cascade. PMID:34239515
Dissecting immune cell stat regulation network reveals biomarkers to predict ICB therapy responders in melanoma. PMID:34238310
Bi-allelic mutations of DNAH10 cause primary male infertility with asthenoteratozoospermia in humans and mice. PMID:34237282
Identification of viral-mediated pathogenic mechanisms in neurodegenerative diseases using network-based approaches. PMID:34237135
Tumor Purity Coexpressed Genes Related to Immune Microenvironment and Clinical Outcomes of Lung Adenocarcinoma. PMID:34234827
Patient-derived iPSC-cerebral organoid modeling of the 17q11.2 microdeletion syndrome establishes CRLF3 as a critical regulator of neurogenesis. PMID:34233200
In-Cell Labeling and Mass Spectrometry for Systems-Level Structural Biology. PMID:34232610
Identification of endometriosis-associated genes and pathways based on bioinformatic analysis. PMID:34232189
Identification of potential core genes in esophageal carcinoma using bioinformatics analysis. PMID:34232175
Transcriptomic analysis of the black tiger shrimp (Penaeus monodon) reveals insights into immune development in their early life stages. PMID:34230553
A circular RNAs dataset landscape reveals potential signatures for the detection and prognosis of early-stage lung adenocarcinoma. PMID:34229638
Consensus clustering applied to multi-omics disease subtyping. PMID:34229612
Transcriptome analysis of chloride intracellular channel knockdown in Drosophila identifies oxidation-reduction function as possible mechanism of altered sensitivity to ethanol sedation. PMID:34228751
Shared genetic architecture between neuroticism, coronary artery disease and cardiovascular risk factors. PMID:34226488
Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation. PMID:34225769
Visual comprehension and orientation into the COVID-19 CIDO ontology. PMID:34224898
Identification of differential key biomarkers in the synovial tissue between rheumatoid arthritis and osteoarthritis using bioinformatics analysis. PMID:34224029
ReporterSeq reveals genome-wide dynamic modulators of the heat shock response across diverse stressors. PMID:34223816
A comprehensive review of integrative pharmacology-based investigation: A paradigm shift in traditional Chinese medicine. PMID:34221858
Comprehensive Analysis of Regulatory Network for LINC00472 in Clear Cell Renal Cell Carcinoma. PMID:34221297
Individuality in the Immune Repertoire and Induced Response of the Sponge Halichondria panicea. PMID:34220847
9-Gene Signature Correlated With CD8+ T Cell Infiltration Activated by IFN-γ: A Biomarker of Immune Checkpoint Therapy Response in Melanoma. PMID:34220795
A novel computational drug repurposing approach for Systemic Lupus Erythematosus (SLE) treatment using Semantic Web technologies. PMID:34220244
Axl-inhibitor bemcentinib alleviates mitochondrial dysfunction in the unilateral ureter obstruction murine model. PMID:34219376
Open chromatin in grapevine marks candidate CREs and with other chromatin features correlates with gene expression. PMID:34219317
Resident Kupffer cells and neutrophils drive liver toxicity in cancer immunotherapy. PMID:34215680
Fundamental limits on the rate of bacterial growth and their influence on proteomic composition. PMID:34214468
ACE2-lentiviral transduction enables mouse SARS-CoV-2 infection and mapping of receptor interactions. PMID:34214142
Linear functional organization of the omic embedding space. PMID:34213534
Control of tissue development and cell diversity by cell cycle-dependent transcriptional filtering. PMID:34212855
IGFBP2 Is a Potential Master Regulator Driving the Dysregulated Gene Network Responsible for Short Survival in Glioblastoma Multiforme. PMID:34211498
Comparative Transcriptome Analysis Reveals Regulatory Networks during the Maize Ear Shank Elongation Process. PMID:34209973
Annotating the Insect Regulatory Genome. PMID:34209769
Conservation of Zebrafish MicroRNA-145 and Its Role during Neural Crest Cell Development. PMID:34209401
Transcriptome Reveals Roles of Lignin-Modifying Enzymes and Abscisic Acid in the Symbiosis of Mycena and Gastrodia elata. PMID:34207287
Genome-Wide Transcriptomic Analysis of Non-Tumorigenic Tissues Reveals Aging-Related Prognostic Markers and Drug Targets in Renal Cell Carcinoma. PMID:34207247
Expression Status and Prognostic Value of m6A RNA Methylation Regulators in Lung Adenocarcinoma. PMID:34206803
Transcriptomic Profiling of Femoral Veins in Deep Vein Thrombosis in a Porcine Model. PMID:34206566
Secretory microRNA Profiles of Third- and Fourth-Stage Dirofilaria immitis Larvae with Different Macrocyclic Lactone Susceptibility: In Search of Biomarkers for Early Detection of Infection. PMID:34206439
Transcriptomic and Metabolic Profiling of High-Temperature Treated Storage Roots Reveals the Mechanism of Saccharification in Sweetpotato (Ipomoea batatas (L.) Lam.). PMID:34206151
A Comprehensive Bioinformatics Analysis of Notch Pathways in Bladder Cancer. PMID:34205690
Evaluation of Indigenous Olive Biocontrol Rhizobacteria as Protectants against Drought and Salt Stress. PMID:34204989
Short Time-Series Expression Transcriptome Data Reveal the Gene Expression Patterns of Dairy Cow Mammary Gland as Milk Yield Decreased Process. PMID:34203058
Relationship of the Pine Growth Promoting Pantoea eucalypti FBS135 with Type Strains P. eucalypti LMG 24197T and P. vagans 24199T. PMID:34202644
Global Proteomic Profiling of Pediatric AML: A Pilot Study. PMID:34202615
Analysing Complex Oral Protein Samples: Complete Workflow and Case Analysis of Salivary Pellicles. PMID:34202147
Predicting Lifestyle from Positive Selection Data and Genome Properties in Oomycetes. PMID:34202069
Differential Expression and Functional Analysis of CircRNA in the Ovaries of Low and High Fecundity Hanper Sheep. PMID:34201517
Differential Glycosite Profiling-A Versatile Method to Compare Membrane Glycoproteomes. PMID:34200965
S-Palmitoylation of Synaptic Proteins as a Novel Mechanism Underlying Sex-Dependent Differences in Neuronal Plasticity. PMID:34200797
Differential Transcript Profiles in Cumulus-Oocyte Complexes Originating from Pre-Ovulatory Follicles of Varied Physiological Maturity in Beef Cows. PMID:34200628
Neuronal Cytoskeleton in Intellectual Disability: From Systems Biology and Modeling to Therapeutic Opportunities. PMID:34200511
Genotoxicity and Gene Expression in the Rat Lung Tissue following Instillation and Inhalation of Different Variants of Amorphous Silica Nanomaterials (aSiO2 NM). PMID:34200147
Single-Cell Transcriptional Heterogeneity of Lymphatic Endothelial Cells in Normal and Inflamed Murine Lymph Nodes. PMID:34199492
Nanopore-based full-length transcriptome sequencing of Muscovy duck (Cairina moschata) ovary. PMID:34198095
Intra-heterogeneity in transcription and chemoresistant property of leukemia-initiating cells in murine Setd2-/- acute myeloid leukemia. PMID:34196511
Animals Models of Inherited Retinal Disease. PMID:34196320
A prognostic nomogram based on competing endogenous RNA network for clear-cell renal cell carcinoma. PMID:34196116
Crowdsourcing assessment of maternal blood multi-omics for predicting gestational age and preterm birth. PMID:34195686
Extracellular matrix remodeling associated with bleomycin-induced lung injury supports pericyte-to-myofibroblast transition. PMID:34195593
Enhancing the production of amphotericin B by Strepyomyces nodosus in a 50-ton bioreactor based on comparative genomic analysis. PMID:34194892
Characterization of Human Genes Modulated by Porphyromonas gingivalis Highlights the Ribosome, Hypothalamus, and Cholinergic Neurons. PMID:34194426
Multiple responses contribute to the enhanced drought tolerance of the autotetraploid Ziziphus jujuba Mill. var. spinosa. PMID:34193297
Altered hypothalamic DNA methylation and stress-induced hyperactivity following early life stress. PMID:34193254
Upregulated CD58 is associated with clinicopathological characteristics and poor prognosis of patients with pancreatic ductal adenocarcinoma. PMID:34193136
The subtype-specific molecular function of SPDEF in breast cancer and insights into prognostic significance. PMID:34191390
In-Frame and Frameshift Mutations in Zebrafish Presenilin 2 Affect Different Cellular Functions in Young Adult Brains. PMID:34189411
Identification of genes modulated by interferon gamma in breast cancer cells. PMID:34189281
Epigenetic effects of parasites and pesticides on captive and wild nestling birds. PMID:34188846
The amniotic fluid cell-free transcriptome in spontaneous preterm labor. PMID:34188072
Reconstruction of the full-length transcriptome of cigar tobacco without a reference genome and characterization of anion channel/transporter transcripts. PMID:34187357
Expression levels of specific microRNAs are increased after exercise and are associated with cognitive improvement in Parkinson's disease. PMID:34184078
Transcription in fungal conidia before dormancy produces phenotypically variable conidia that maximize survival in different environments. PMID:34183813
Protein Prenylation and Hsp40 in Thermotolerance of Plasmodium falciparum Malaria Parasites. PMID:34182772
Potential therapeutic target genes for systemic lupus erythematosus: a bioinformatics analysis. PMID:34180358
ACSNI: An unsupervised machine-learning tool for prediction of tissue-specific pathway components using gene expression profiles. PMID:34179848
Identification ACTA2 and KDR as key proteins for prognosis of PD-1/PD-L1 blockade therapy in melanoma. PMID:34179721
Identification of Dysregulated Complement Activation Pathways Driven by N-Glycosylation Alterations in T2D Patients. PMID:34178943
Low Expression of ADCY4 Predicts Worse Survival of Lung Squamous Cell Carcinoma Based on Integrated Analysis and Immunohistochemical Verification. PMID:34178627
Rapid Body-Wide Transcriptomic Turnover During Rhesus Macaque Perinatal Development. PMID:34177627
Acute Effects on the Human Peripheral Blood Transcriptome of Decompression Sickness Secondary to Scuba Diving. PMID:34177613
Proteomic and Transcriptomic Analyses Provide Novel Insights into the Crucial Roles of Host-Induced Carbohydrate Metabolism Enzymes in Xanthomonas oryzae pv. oryzae Virulence and Rice-Xoo Interaction. PMID:34176023
Single-cell analysis of mouse and human prostate reveals novel fibroblasts with specialized distribution and microenvironment interactions. PMID:34173975
The highly conserved FOXJ1 target CFAP161 is dispensable for motile ciliary function in mouse and Xenopus. PMID:34172766
Evolution of fibroblasts in the lung metastatic microenvironment is driven by stage-specific transcriptional plasticity. PMID:34169837
FINER: enhancing the prediction of tissue-specific functions of isoforms by refining isoform interaction networks. PMID:34169280
Single-Cell RNA-seq Identification of the Cellular Molecular Characteristics of Sporadic Bilateral Clear Cell Renal Cell Carcinoma. PMID:34168986
Bioinformatic Analysis of Hepatocellular Carcinoma Cell Lines to the Efficacy of Nimotuzumab. PMID:34168487
Genome instability-related long non-coding RNA in clear renal cell carcinoma determined using computational biology. PMID:34167490
Survival prediction based on the gene expression associated with cancer morphology and microenvironment in primary central nervous system lymphoma. PMID:34166375
Study of the Active Components and Molecular Mechanism of Tripterygium wilfordii in the Treatment of Diabetic Nephropathy. PMID:34164430
Identification and Validation of a Novel Prognosis Prediction Model in Adrenocortical Carcinoma by Integrative Bioinformatics Analysis, Statistics, and Machine Learning. PMID:34164395
Revealing the Characteristics of the Antarctic Snow Alga Chlorominima collina gen. et sp. nov. Through Taxonomy, Physiology, and Transcriptomics. PMID:34163502
Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant, "subfossil" koala lemur Megaladapis edwardsi. PMID:34162703
The brain transcriptome of the wolf spider, Schizocosa ocreata. PMID:34162407
Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research. PMID:34159360
Dissecting regulatory pathways for transcription recovery following DNA damage reveals a non-canonical function of the histone chaperone HIRA. PMID:34158510
Identification of Somatic Gene Signatures in Circulating Cell-Free DNA Associated with Disease Progression in Metastatic Prostate Cancer by a Novel Machine Learning Platform. PMID:34157173
MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses. PMID:34156446
Surface-Shaving Proteomics of Mycobacterium marinum Identifies Biofilm Subtype-Specific Changes Affecting Virulence, Tolerance, and Persistence. PMID:34156290
Identification of sex-specific biomarkers predicting new-onset heart failure. PMID:34156155
Disentangling transcriptional responses in plant defense against arthropod herbivores. PMID:34155286
A small RNA regulates pprM, a modulator of pleiotropic proteins promoting DNA repair, in Deinococcus radiodurans under ionizing radiation. PMID:34155239
Cell landscape atlas for patients with chronic thromboembolic pulmonary hypertension after pulmonary endarterectomy constructed using single-cell RNA sequencing. PMID:34153003
Analysis of differentially expressed genes responsible for the suppressive effect of anisomycin on cell proliferation of DLD-1 cells. PMID:34151031
Biological Mechanisms Induced by Soybean Agglutinin Using an Intestinal Cell Model of Monogastric Animals. PMID:34150879
Effect of the Expression of ELOVL5 and IGFBP6 Genes on the Metastatic Potential of Breast Cancer Cells. PMID:34149804
Agrobacterium VirE2 Protein Modulates Plant Gene Expression and Mediates Transformation From Its Location Outside the Nucleus. PMID:34149784
Transcriptome Analysis Reveals Putative Target Genes of APETALA3-3 During Early Floral Development in Nigella damascena L. PMID:34149759
Damage-Net: A program for DNA repair meta-analysis identifies a network of novel repair genes that facilitate cancer evolution. PMID:34147942
Combining QTL-seq and linkage mapping to fine map a candidate gene in qCTS6 for cold tolerance at the seedling stage in rice. PMID:34147069
A chromosome-level genome assembly of rugged rose (Rosa rugosa) provides insights into its evolution, ecology, and floral characteristics. PMID:34145222
RNA sequencing of long-term label-retaining colon cancer stem cells identifies novel regulators of quiescence. PMID:34142064
Somatic mutation subtypes of lung adenocarcinoma in East Asian reveal divergent biological characteristics and therapeutic vulnerabilities. PMID:34142036
Evolving Up-regulation of Biliary Fibrosis-Related Extracellular Matrix Molecules After Successful Portoenterostomy. PMID:34141988
Single-cell RNA-seq reveals fibroblast heterogeneity and increased mesenchymal fibroblasts in human fibrotic skin diseases. PMID:34140509
Mapping the multiscale structure of biological systems. PMID:34139169
Transcriptomic analyses of gastrulation-stage mouse embryos with differential susceptibility to alcohol. PMID:34137816
Association of medically assisted reproduction with offspring cord blood DNA methylation across cohorts. PMID:34136910
Pan-Genome Analysis of Vibrio cholerae and Vibrio metschnikovii Strains Isolated From Migratory Birds at Dali Nouer Lake in Chifeng, China. PMID:34136552
Transcriptome Profiling Analysis of the Testis After Eyestalk Ablation for Selection of the Candidate Genes Involved in the Male Sexual Development in Macrobrachium nipponense. PMID:34135943
Transcriptomic Signature Differences Between SARS-CoV-2 and Influenza Virus Infected Patients. PMID:34135895
Schistosomiasis Drug Discovery in the Era of Automation and Artificial Intelligence. PMID:34135888
An Axin2 mutation and perinatal risk factors contribute to sagittal craniosynostosis: evidence from a Chinese female monochorionic diamniotic twin family. PMID:34134783
Transcriptomics of type 2 diabetic and healthy human neutrophils. PMID:34134627
Transcriptomic coordination at hepatic steatosis indicates robust immune cell engagement prior to inflammation. PMID:34134614
RXRA DT448/9PP generates a dominant active variant capable of inducing maturation in acute myeloid leukemia cells. PMID:34134472
Protopanaxadiol improves endometriosis associated infertility and miscarriage in sex hormones receptors-dependent and independent manners. PMID:34131393
Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas. PMID:34131149
Microglia RAGE exacerbates the progression of neurodegeneration within the SOD1G93A murine model of amyotrophic lateral sclerosis in a sex-dependent manner. PMID:34130712
Identifying Genomic Regions Targeted During Eggplant Domestication Using Transcriptome Data. PMID:34130314
Tankyrase regulates epithelial lumen formation via suppression of Rab11 GEFs. PMID:34128958
A methyl esterase 1 (PvMES1) promotes the salicylic acid pathway and enhances Fusarium wilt resistance in common beans. PMID:34128089
Type I Interferon Transcriptional Network Regulates Expression of Coinhibitory Receptors in Human T cells. PMID:34127967
Interaction Between the Intestinal Microbial Community and Transcriptome Profile in Common Carp (Cyprinus carpio L.). PMID:34127924
Inter-individual body mass variations relate to fractionated functional brain hierarchies. PMID:34127795
A genetic interaction of NRXN2 with GABRE, SYT1 and CASK in migraine patients: a case-control study. PMID:34126933
Multiple Lesions Contribute to Infertility in Males Lacking Autoimmune Regulator. PMID:34126085
DGLinker: flexible knowledge-graph prediction of disease-gene associations. PMID:34125897
Droplet microarrays for cell culture: effect of surface properties and nanoliter culture volume on global transcriptomic landscape. PMID:34124640
Identification of CD8+ T Cell-Related Genes: Correlations with Immune Phenotypes and Outcomes of Liver Cancer. PMID:34124275
Highly connected, non-redundant microRNA functional control in breast cancer molecular subtypes. PMID:34123357
FGGA-lnc: automatic gene ontology annotation of lncRNA sequences based on secondary structures. PMID:34123354
Gene Instability-Related lncRNA Prognostic Model of Melanoma Patients via Machine Learning Strategy. PMID:34122546
Identification of Key Biomarkers and Immune Infiltration in Sciatic Nerve of Diabetic Neuropathy BKS-db/db Mice by Bioinformatics Analysis. PMID:34122109
Network Pharmacology-Based Validation of the Efficacy of Huiyangjiuji Decoction in the Treatment of Experimental Colitis. PMID:34122086
Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain. PMID:34121661
DNA methylation profile of liver of mice conceived by in vitro fertilization. PMID:34121654
The aging mouse lens transcriptome. PMID:34119483
miR-1224 contributes to ischemic stroke-mediated natural killer cell dysfunction by targeting Sp1 signaling. PMID:34118948
De novo genome assembly of a foxtail millet cultivar Huagu11 uncovered the genetic difference to the cultivar Yugu1, and the genetic mechanism of imazethapyr tolerance. PMID:34118890
Revealing the Modular Similarities and Differences Among Alzheimer's Disease, Vascular Dementia, and Parkinson's Disease in Genomic Networks. PMID:34117614
Mortalin/glucose-regulated protein 75 promotes the cisplatin-resistance of gastric cancer via regulating anti-oxidation/apoptosis and metabolic reprogramming. PMID:34117210
CCDC114, DNAI2 and TOP2A involves in the effects of tibolone treatment on postmenopausal endometrium. PMID:34116668
Integrating protein networks and machine learning for disease stratification in the Hereditary Spastic Paraplegias. PMID:34113825
Measuring pathway database coverage of the phosphoproteome. PMID:34113485
Characterization of the small RNA transcriptomes of cell protrusions and cell bodies of highly metastatic hepatocellular carcinoma cells via RNA sequencing. PMID:34113396
A report of two cases of bulbospinal form Alexander disease and preliminary exploration of the disease. PMID:34109421
Heat-killed endophytic bacterium induces robust plant defense responses against important pathogens. PMID:34108579
Gene expression changes and DNA damage after ex vivo exposure of peripheral blood cells to various CT photon spectra. PMID:34103547
Integrating longitudinal clinical laboratory tests with targeted proteomic and transcriptomic analyses reveal the landscape of host responses in COVID-19. PMID:34103487
Characterization of nucleic acids from extracellular vesicle-enriched human sweat. PMID:34103018
Protein functional module identification method combining topological features and gene expression data. PMID:34103008
Analysis of single-cell RNA sequencing data based on autoencoders. PMID:34103004
TNF blockade uncouples toxicity from antitumor efficacy induced with CD40 chemoimmunotherapy. PMID:34101617
Molecular omics resources should require sex annotation: a call for action. PMID:34099934
Systems genetics in diversity outbred mice inform BMD GWAS and identify determinants of bone strength. PMID:34099702
Comprehensive Phosphoproteomic Analysis of Nostoc flagelliforme in Response to Dehydration Provides Insights into Plant ROS Signaling Transduction. PMID:34095650
Transcriptome Analysis Reveals Differentially Expressed Genes and Long Non-coding RNAs Associated With Fecundity in Sheep Hypothalamus With Different FecB Genotypes. PMID:34095109
Gene Cascade Shift and Pathway Enrichment in Rat Kidney Induced by Acarbose Through Comparative Analysis. PMID:34095098
Sharp Downregulation of Hub Genes Associated With the Pathogenesis of Breast Cancer From Ductal Carcinoma In Situ to Invasive Ductal Carcinoma. PMID:34094915
Laryngeal squamous cell carcinoma cell lines show high tolerance for siRNA-mediated CDK1 knockdown. PMID:34094670
Cancer cell-selective modulation of mitochondrial respiration and metabolism by potent organogold(iii) dithiocarbamates. PMID:34094305
Comparing Statistical Tests for Differential Network Analysis of Gene Modules. PMID:34093641
Integrative Analysis of lncRNA and mRNA and Profiles in Postoperative Delirium Patients. PMID:34093168
Differential expression of striatal proteins in a mouse model of DOPA-responsive dystonia reveals shared mechanisms among dystonic disorders. PMID:34092491
The REASON score: an epigenetic and clinicopathologic score to predict risk of poor survival in patients with early stage oral squamous cell carcinoma. PMID:34090518
The effect of methanol fixation on single-cell RNA sequencing data. PMID:34090348
Beach sand oil spills select for generalist microbial populations. PMID:34088976
Chamber-enriched gene expression profiles in failing human hearts with reduced ejection fraction. PMID:34088950
PIGNON: a protein-protein interaction-guided functional enrichment analysis for quantitative proteomics. PMID:34088263
Mapping Proximity Associations of Core Spindle Assembly Checkpoint Proteins. PMID:34087075
Transmembrane adaptor protein PAG is a mediator of PD-1 inhibitory signaling in human T cells. PMID:34083754
A combination of Class-I fumarases and metabolites (α-ketoglutarate and fumarate) signal the DNA damage response in Escherichia coli. PMID:34083440
Patterns of recent natural selection on genetic loci associated with sexually differentiated human body size and shape phenotypes. PMID:34081690
Critical COVID-19 is associated with distinct leukocyte phenotypes and transcriptome patterns. PMID:34080738
Construction of a mammalian embryo model from stem cells organized by a morphogen signalling centre. PMID:34078907
Identification of biomarkers, pathways and potential therapeutic target for docetaxel resistant prostate cancer. PMID:34077304
Chromosome-level genome assembly of the Chinese longsnout catfish Leiocassis longirostris. PMID:34075735
Learning from Embryogenesis-A Comparative Expression Analysis in Melanoblast Differentiation and Tumorigenesis Reveals miRNAs Driving Melanoma Development. PMID:34073664
Proteomic Analyses of Vitreous in Proliferative Diabetic Retinopathy: Prior Studies and Future Outlook. PMID:34070658
Regulation of Oxalate Metabolism in Spinach Revealed by RNA-Seq-Based Transcriptomic Analysis. PMID:34069886
Identification of Critical Genes and Signaling Pathways in Human Monocytes Following High-Intensity Exercise. PMID:34067297
Integrating Transcriptome and Coexpression Network Analyses to Characterize Salicylic Acid- and Jasmonic Acid-Related Genes in Tolerant Poplars Infected with Rust. PMID:34066822
Microarray and qPCR Analysis of Mitochondrial Metabolism Activation during Prenatal and Early Postnatal Development in Rats and Humans with Emphasis on CoQ10 Biosynthesis. PMID:34066731
Effects of Three-Month Administration of High-Saturated Fat Diet and High-Polyunsaturated Fat Diets with Different Linoleic Acid (LA, C18:2n-6) to α-Linolenic Acid (ALA, C18:3n-3) Ratio on the Mouse Liver Proteome. PMID:34063343
Skeletal Muscle Gene Expression Profile in Response to Caloric Restriction and Aging: A Role for SirT1. PMID:34063079
Host Response of Atlantic Salmon (Salmo salar) Re-Inoculated with Paramoeba perurans. PMID:34062978
Identification of Potential Bisphenol A (BPA) Exposure Biomarkers in Ovarian Cancer. PMID:34062972
An in vitro model of tumor heterogeneity resolves genetic, epigenetic, and stochastic sources of cell state variability. PMID:34061819
The liver-clock coordinates rhythmicity of peripheral tissues in response to feeding. PMID:34059820
Role of cytoplasmic localization of maspin in promoting cell invasion in breast cancer with aggressive phenotype. PMID:34059749
The chromosome-level Stevia genome provides insights into steviol glycoside biosynthesis. PMID:34059662
Vesicle transporter GOLT1B mediates the cell membrane localization of DVL2 and PD-L2 and promotes colorectal cancer metastasis. PMID:34059062
The transcriptional repressor Rev-erbα regulates circadian expression of the astrocyte Fabp7 mRNA. PMID:34056625
Synthesis, Characterization, and Specific Localization of Mitochondrial-Targeted Antioxidant Peptide SS31 Probe. PMID:34056004
Comprehensive analysis of the long non-coding RNA expression profile and functional roles in a contrast-induced acute kidney injury rat model. PMID:34055056
Multi-Omics Approach in the Identification of Potential Therapeutic Biomolecule for COVID-19. PMID:34054532
Multi-Dimensional Transcriptome Analysis Reveals Modulation of Cholesterol Metabolism as Highly Integrated Response to Brain Injury. PMID:34054419
Synaptic proteins associated with cognitive performance and neuropathology in older humans revealed by multiplexed fractionated proteomics. PMID:34052751
Rapid evolution of mammalian APLP1 as a synaptic adhesion molecule. PMID:34050225
snpXplorer: a web application to explore human SNP-associations and annotate SNP-sets. PMID:34048563
Integrated Gene Co-expression Analysis and Metabolites Profiling Highlight the Important Role of ZmHIR3 in Maize Resistance to Gibberella Stalk Rot. PMID:34046051
Pneumolysin Is Responsible for Differential Gene Expression and Modifications in the Epigenetic Landscape of Primary Monocyte Derived Macrophages. PMID:34046027
Glycoproteomic analysis of the changes in protein N-glycosylation during neuronal differentiation in human-induced pluripotent stem cells and derived neuronal cells. PMID:34045517
Transcriptomic analysis of atopic dermatitis in African Americans is characterized by Th2/Th17-centered cutaneous immune activation. PMID:34045476
Inferring Genome-Wide Correlations of Mutation Fitness Effects between Populations. PMID:34043790
Transcriptional signatures of human peripheral blood mononuclear cells can identify the risk of tuberculosis progression from latent infection among individuals with silicosis. PMID:34042560
Linking Lysosomal Enzyme Targeting Genes and Energy Metabolism with Altered Gray Matter Volume in Children with Persistent Stuttering. PMID:34041495
In Arabidopsis thaliana Cd differentially impacts on hormone genetic pathways in the methylation defective ddc mutant compared to wild type. PMID:34040101
Structure-based protein function prediction using graph convolutional networks. PMID:34039967
Context-Dependent miR-21 Regulation of TLR7-Mediated Autoimmune and Foreign Antigen-Driven Antibody-Forming Cell and Germinal Center Responses. PMID:34039637
Adaptation to mitochondrial stress requires CHOP-directed tuning of ISR. PMID:34039602
Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers. PMID:34039407
Identification of significant genes as prognostic markers and potential tumor suppressors in lung adenocarcinoma via bioinformatical analysis. PMID:34039311
NetGO 2.0: improving large-scale protein function prediction with massive sequence, text, domain, family and network information. PMID:34038555
G2PDeep: a web-based deep-learning framework for quantitative phenotype prediction and discovery of genomic markers. PMID:34037802
CPA: a web-based platform for consensus pathway analysis and interactive visualization. PMID:34037798
ARHGDIA Confers Selective Advantage to Dissociated Human Pluripotent Stem Cells. PMID:34036793
AMOTL2‑knockdown promotes the proliferation, migration and invasion of glioma by regulating β‑catenin nuclear localization. PMID:34036399
Differential gene expression profile by RNA sequencing study of elderly osteoporotic hip fracture patients with sarcopenia. PMID:34036042
PhenCards: a data resource linking human phenotype information to biomedical knowledge. PMID:34034817
Gene Ontology Meta Annotator for Plants (GOMAP). PMID:34034755
De novo transcriptome sequencing and anthocyanin metabolite analysis reveals leaf color of Acer pseudosieboldianum in autumn. PMID:34034673
GWENA: gene co-expression networks analysis and extended modules characterization in a single Bioconductor package. PMID:34034647
Coordination of microbe-host homeostasis by crosstalk with plant innate immunity. PMID:34031541
Estimates of gene ensemble noise highlight critical pathways and predict disease severity in H1N1, COVID-19 and mortality in sepsis patients. PMID:34031464
Transcriptomic response of brain tissue to focused ultrasound-mediated blood-brain barrier disruption depends strongly on anesthesia. PMID:34027087
Genome sequence and transcriptome profiles of pathogenic fungus Paecilomyces penicillatus reveal its interactions with edible fungus Morchella importuna. PMID:34025947
TIGIT and PD-1 Immune Checkpoint Pathways Are Associated With Patient Outcome and Anti-Tumor Immunity in Glioblastoma. PMID:34025646
DNF: A differential network flow method to identify rewiring drivers for gene regulatory networks. PMID:34025035
Valproic Acid Protects Against Acute Kidney Injury in Hemorrhage and Trauma. PMID:34023578
Gene expression of intracortical bone demonstrates loading-induced increases in Wnt1 and Ngf and inhibition of bone remodeling processes. PMID:34023542
Up-regulated RFC2 predicts unfavorable progression in hepatocellular carcinoma. PMID:34022962
Transcriptome analysis reveals potential function of long non-coding RNAs in 20-hydroxyecdysone regulated autophagy in Bombyx mori. PMID:34022797
Chromosome-scale assembly of the Sparassis latifolia genome obtained using long-read and Hi-C sequencing. PMID:34021320
Chromatin-associated MRN complex protects highly transcribing genes from genomic instability. PMID:34020942
Genome-wide analysis identifies a novel LINC-PINT splice variant associated with vascular amyloid pathology in Alzheimer's disease. PMID:34020725
DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web. PMID:34019664
Rcl1 depletion impairs 18S pre-rRNA processing at the A1-site and up-regulates a cohort of ribosome biogenesis genes in zebrafish. PMID:34019640
Defining the role of the polyasparagine repeat domain of the S. cerevisiae transcription factor Azf1p. PMID:34019539
Hub biomarkers for the diagnosis and treatment of glioblastoma based on microarray technology. PMID:34018447
A method for benchmarking genetic screens reveals a predominant mitochondrial bias. PMID:34018332
Deciphering the architecture and interactome of hnRNP proteins and enigmRBPs. PMID:34017973
Temporal Transcriptome Analysis Reveals Dynamic Gene Expression Patterns Driving β-Cell Maturation. PMID:34017831
Platelets orchestrate the resolution of pulmonary inflammation in mice by T reg cell repositioning and macrophage education. PMID:34014253
Genome variation in colorectal cancer patient with liver metastasis measured by whole-exome sequencing. PMID:34012644
Cholesterol-Induced M4-Like Macrophages Recruit Neutrophils and Induce NETosis. PMID:34012454
Identification of the EMT-Related Genes Signature for Predicting Occurrence and Progression in Thyroid Cancer. PMID:34012269
Chromosomal instability by mutations in the novel minor spliceosome component CENATAC. PMID:34009673
Activated mast cells in skeletal muscle can be a potential mediator for cancer-associated cachexia. PMID:34008339
A novel diagnostic signature based on three circulating exosomal mircoRNAs for chronic obstructive pulmonary disease. PMID:34007326
Analyzing host-viral interactome of SARS-CoV-2 for identifying vulnerable host proteins during COVID-19 pathogenesis. PMID:34004362
Functionally distinct POMC-expressing neuron subpopulations in hypothalamus revealed by intersectional targeting. PMID:34002087
Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis. PMID:34002013
A miR-375/YAP axis regulates neuroendocrine differentiation and tumorigenesis in lung carcinoid cells. PMID:34001972
The nuclear receptor HNF4 drives a brush border gene program conserved across murine intestine, kidney, and embryonic yolk sac. PMID:34001900
Primordial super-enhancers: heat shock-induced chromatin organization in yeast. PMID:34001402
Learning adaptive representations for entity recognition in the biomedical domain. PMID:34001263
SynLeGG: analysis and visualization of multiomics data for discovery of cancer 'Achilles Heels' and gene function relationships. PMID:33997893
Evaluating the Consistency of Gene Methylation in Liver Cancer Using Bisulfite Sequencing Data. PMID:33996828
Simultaneous profiling of Arabidopsis thaliana and Vibrio vulnificus MO6-24/O transcriptomes by dual RNA-seq analysis. PMID:33995904
Cycad-Weevil Pollination Symbiosis Is Characterized by Rapidly Evolving and Highly Specific Plant-Insect Chemical Communication. PMID:33995438
Mutant PRPF8 Causes Widespread Splicing Changes in Spliceosome Components in Retinitis Pigmentosa Patient iPSC-Derived RPE Cells. PMID:33994920
Multimodality assessment of heart failure with preserved ejection fraction skeletal muscle reveals differences in the machinery of energy fuel metabolism. PMID:33991175
Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions. PMID:33988505
Mechanistic insight into the progressive retinal atrophy disease in dogs via pathway-based genome-wide association analysis. PMID:33987558
Properties and gene expression profiling of acquired radioresistance in mouse breast cancer cells. PMID:33987326
Centromere protein N may be a novel malignant prognostic biomarker for hepatocellular carcinoma. PMID:33987018
Identification of a five-gene signature in association with overall survival for hepatocellular carcinoma. PMID:33986994
ARTEMIS: A Novel Mass-Spec Platform for HLA-Restricted Self and Disease-Associated Peptide Discovery. PMID:33986749
Hypericum perforatum L. Regulates Glutathione Redox Stress and Normalizes Ggt1/Anpep Signaling to Alleviate OVX-Induced Kidney Dysfunction. PMID:33981220
Network-based identification of key master regulators associated with an immune-silent cancer phenotype. PMID:33979427
A termination-independent role of Rat1 in cotranscriptional splicing. PMID:33978753
Identification of a novel autophagy signature for predicting survival in patients with lung adenocarcinoma. PMID:33976960
Integrated analysis of three newly sequenced fern chloroplast genomes: Genome structure and comparative analysis. PMID:33976830
Haplotype-resolved genome assembly enables gene discovery in the red palm weevil Rhynchophorus ferrugineus. PMID:33976235
Integration of machine learning and genome-scale metabolic modeling identifies multi-omics biomarkers for radiation resistance. PMID:33976213
Overcoming false-positive gene-category enrichment in the analysis of spatially resolved transcriptomic brain atlas data. PMID:33976144
hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies. PMID:33973408
Comparative transcriptomics between Drosophila mojavensis and D. arizonae reveals transgressive gene expression and underexpression of spermatogenesis-related genes in hybrid testes. PMID:33972659
Genoppi is an open-source software for robust and standardized integration of proteomic and genetic data. PMID:33972534
Simultaneous learning of individual microRNA-gene interactions and regulatory comodules. PMID:33971820
Comparative Analysis of piRNA Profiles Helps to Elucidate Cryoinjury Between Giant Panda and Boar Sperm During Cryopreservation. PMID:33969033
Network Pharmacology-Based Prediction of Mechanism of Shenzhuo Formula for Application to DKD. PMID:33968154
Single-Cell Transcriptomics: Current Methods and Challenges in Data Acquisition and Analysis. PMID:33967674
Reactome and the Gene Ontology: Digital convergence of data resources. PMID:33964129
Collagen fiber regulation in human pediatric aortic valve development and disease. PMID:33963260
Intestinal mucosa-derived DNA methylation signatures in the penetrating intestinal mucosal lesions of Crohn's disease. PMID:33963246
Subtelomeric assembly of a multi-gene pathway for antimicrobial defense compounds in cereals. PMID:33963185
Generation of hypothalamic arcuate organoids from human induced pluripotent stem cells. PMID:33961804
Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. PMID:33961781
Retinoic acid induces NELFA-mediated 2C-like state of mouse embryonic stem cells associates with epigenetic modifications and metabolic processes in chemically defined media. PMID:33960560
Updates to HCOP: the HGNC comparison of orthology predictions tool. PMID:33959747
Common genetic associations between age-related diseases. PMID:33959723
The Links of Ghrelin to Incretins, Insulin, Glucagon, and Leptin After Bariatric Surgery. PMID:33959145
Comparison and Functional Analysis of Chemosensory Protein Genes From Eucryptorrhynchus scrobiculatus Motschulsky and Eucryptorrhynchus brandti Harold. PMID:33959040
Cell-Type-Specific Gene Modules Related to the Regional Homogeneity of Spontaneous Brain Activity and Their Associations With Common Brain Disorders. PMID:33958982
The genome of a wild Medicago species provides insights into the tolerant mechanisms of legume forage to environmental stress. PMID:33957908
Screening and identification of LMNB1 and DLGAP5, two key biomarkers in gliomas. PMID:33956061
Evidence for phloem loading via the abaxial bundle sheath cells in maize leaves. PMID:33955497
Transcriptional signatures of synaptic vesicle genes define myotonic dystrophy type I neurodegeneration. PMID:33955002
Knowledge-Based Biomedical Data Science. PMID:33954284
Bioinformatics analysis of laryngeal squamous cell carcinoma: seeking key candidate genes and pathways. PMID:33954053
Molecular evidence of the avocado defense response to Fusarium kuroshium infection: a deep transcriptome analysis using RNA-Seq. PMID:33954045
Use of Network Pharmacology to Explore the Mechanism of Gegen (Puerariae lobatae Radix) in the Treatment of Type 2 Diabetes Mellitus Associated with Hyperlipidemia. PMID:33953784
Identification and Analysis of Aux/IAA Family in Acer rubrum. PMID:33953533
Epigenetic silencing by SETDB1 suppresses tumour intrinsic immunogenicity. PMID:33953401
Osteocyte transcriptome mapping identifies a molecular landscape controlling skeletal homeostasis and susceptibility to skeletal disease. PMID:33953184
Transcriptomic meta-analysis of disuse muscle atrophy vs. resistance exercise-induced hypertrophy in young and older humans. PMID:33951310
Complete chloroplast genome sequencing of Job's tears (Coix L.): genome structure, comparative analysis, and phylogenetic relationships. PMID:33948493
The genomic basis of evolutionary differentiation among honey bees. PMID:33947700
Genome-wide histone acetylation analysis reveals altered transcriptional regulation in the Parkinson's disease brain. PMID:33947435
Characterization of Extracellular Vesicles Secreted in Lentiviral Producing HEK293SF Cell Cultures. PMID:33946875
Integrative Systems Biology Approaches to Identify Potential Biomarkers and Pathways of Cervical Cancer. PMID:33946372
An evolutionary genomic approach reveals both conserved and species-specific genetic elements related to human disease in closely related Aspergillus fungi. PMID:33944921
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. PMID:33944776
Protein structure-based gene expression signatures. PMID:33941686
Functional and genetic determinants of mutation rate variability in regulatory elements of cancer genomes. PMID:33941236
Strategies for detecting and identifying biological signals amidst the variation commonly found in RNA sequencing data. PMID:33941086
RIP1 Perturbation Induces Chondrocyte Necroptosis and Promotes Osteoarthritis Pathogenesis via Targeting BMP7. PMID:33937236
Predicting Tumor Cell Response to Synergistic Drug Combinations Using a Novel Simplified Deep Learning Model. PMID:33936513
Genome-Wide Gene Expression Analysis of Mtb-Infected DC Highlights the Rapamycin-Driven Modulation of Regulatory Cytokines via the mTOR/GSK-3β Axis. PMID:33936070
De-novo Assembly of Limnospira fusiformis Using Ultra-Long Reads. PMID:33936015
Transcriptomic and microRNA Expression Profiles Identify Biomarkers for Predicting Neo-Chemoradiotherapy Response in Esophageal Squamous Cell Carcinomas (ESCC). PMID:33935718
Comprehensive RNA-Seq Analysis of Potential Therapeutic Targets of Gan-Dou-Fu-Mu Decoction for Treatment of Wilson Disease Using a Toxic Milk Mouse Model. PMID:33935715
Basic leucine zipper (bZIP) transcription factor genes and their responses to drought stress in ginseng, Panax ginseng C.A. Meyer. PMID:33932982
Whole-genome resequencing of Osmanthus fragrans provides insights into flower color evolution. PMID:33931610
GAPGOM-an R package for gene annotation prediction using GO Metrics. PMID:33931103
Comparative transcriptomic analysis reveals the regulatory mechanism of the gibberellic acid pathway of Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) dwarf mutants. PMID:33931042
Transcriptome-Wide Gene Expression in a Murine Model of Ventilator-Induced Lung Injury. PMID:33927789
Genome-wide gene expression changes of Pseudomonas veronii 1YdBTEX2 during bioaugmentation in polluted soils. PMID:33926576
Best practices on the differential expression analysis of multi-species RNA-seq. PMID:33926528
Categorization of Orthologous Gene Clusters in 92 Ascomycota Genomes Reveals Functions Important for Phytopathogenicity. PMID:33925458
Assessing Various Control Samples for Microarray Gene Expression Profiling of Laryngeal Squamous Cell Carcinoma. PMID:33923685
Transcriptomic Analysis of Pseudomonas aeruginosa Response to Pine Honey via RNA Sequencing Indicates Multiple Mechanisms of Antibacterial Activity. PMID:33923242
Characterization of the Survival Influential Genes in Carcinogenesis. PMID:33922264
Connectivity Map Analysis of a Single-Cell RNA-Sequencing -Derived Transcriptional Signature of mTOR Signaling. PMID:33922083
Performance Comparison of Deep Learning Autoencoders for Cancer Subtype Detection Using Multi-Omics Data. PMID:33921978
A First Insight into the Gonad Transcriptome of Hong Kong Catfish (Clarias fuscus). PMID:33920938
Mapping of Genetic Locus for Leaf Trichome Formation in Chinese Cabbage Based on Bulked Segregant Analysis. PMID:33919922
Isolation and Characterization of Strain Exiguobacterium sp. KRL4, a Producer of Bioactive Secondary Metabolites from a Tibetan Glacier. PMID:33919419
Discovery of Post-Translational Modifications in Emiliania huxleyi. PMID:33918234
Investigation of the Initial Host Response of Naïve Atlantic Salmon (Salmo salar) Inoculated with Paramoeba perurans. PMID:33918228
Altered microRNA Transcriptome in Cultured Human Liver Cells upon Infection with Ebola Virus. PMID:33917562
Genome-Wide Mapping of Histone H3 Lysine 4 Trimethylation (H3K4me3) and Its Involvement in Fatty Acid Biosynthesis in Sunflower Developing Seeds. PMID:33917507
Genome and Pangenome Analysis of Lactobacillus hilgardii FLUB-A New Strain Isolated from Mead. PMID:33917427
Systematic Analysis of the Transcriptome Profiles and Co-Expression Networks of Tumour Endothelial Cells Identifies Several Tumour-Associated Modules and Potential Therapeutic Targets in Hepatocellular Carcinoma. PMID:33917186
Sphingosine Promotes Embryo Biomass in Upland Cotton: A Biochemical and Transcriptomic Analysis. PMID:33915924
Multi-Omics Approaches to Define Calcific Aortic Valve Disease Pathogenesis. PMID:33914608
Purification and quantitative proteomic analysis of cell bodies and protrusions. PMID:33912849
Single-Cell Atlas Reveals Fatty Acid Metabolites Regulate the Functional Heterogeneity of Mesenchymal Stem Cells. PMID:33912565
Identification of Expression Patterns and Potential Prognostic Significance of m5C-Related Regulators in Head and Neck Squamous Cell Carcinoma. PMID:33912441
Reproductive Proteins Evolve Faster Than Non-reproductive Proteins Among Solanum Species. PMID:33912206
In silico annotation of unreviewed acetylcholinesterase (AChE) in some lepidopteran insect pest species reveals the causes of insecticide resistance. PMID:33911936
The prognostic value of an autophagy-related lncRNA signature in hepatocellular carcinoma. PMID:33910497
5-hydroxymethylcytosine is dynamically regulated during forebrain organoid development and aberrantly altered in Alzheimer's disease. PMID:33910000
Boosting Detection of Low-Abundance Proteins in Thermal Proteome Profiling Experiments by Addition of an Isobaric Trigger Channel to TMT Multiplexes. PMID:33908254
Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator. PMID:33904398
Extracellular Vesicles from Human Adipose-Derived Mesenchymal Stem Cells: A Review of Common Cargos. PMID:33904115
Semantic standards of external exposome data. PMID:33901445
Identification of Metastasis-Associated MicroRNAs in Metastatic Melanoma by miRNA Expression Profile and Experimental Validation. PMID:33897771
Comprehensive RNA-Seq Profiling Reveals Temporal and Tissue-Specific Changes in Gene Expression in Sprague-Dawley Rats as Response to Heat Stress Challenges. PMID:33897767
The VRNetzer platform enables interactive network analysis in Virtual Reality. PMID:33893283
Transcriptomic analysis of α-linolenic acid content and biosynthesis in Paeonia ostii fruits and seeds. PMID:33892636
Transcriptome analysis reveals gene responses to herbicide, tribenuron methyl, in Brassica napus L. during seed germination. PMID:33892633
Chromosome-level genome assembly of the hard-shelled mussel Mytilus coruscus, a widely distributed species from the temperate areas of East Asia. PMID:33891010
Differential Expression of Insulin-Like Growth Factor 1 and Wnt Family Member 4 Correlates With Functional Heterogeneity of Human Dermal Fibroblasts. PMID:33889572
Controlling for cellular heterogeneity using single-cell deconvolution of gene expression reveals novel markers of colorectal tumors exhibiting microsatellite instability. PMID:33889300
System-Level Analysis of Alzheimer's Disease Prioritizes Candidate Genes for Neurodegeneration. PMID:33889174
The Chinese mitten crab genome provides insights into adaptive plasticity and developmental regulation. PMID:33888695
An atlas of the tissue and blood metagenome in cancer reveals novel links between bacteria, viruses and cancer. PMID:33888160
Isolation and genomic characterization of five novel strains of Erysipelotrichaceae from commercial pigs. PMID:33888068
Expression Profiles Reveal Involvement of VEGF, IGF1, BIRC5, and MMP1 in Vulvar Carcinogenesis. PMID:33888009
Resilience, plasticity and robustness in gene expression during aging in the brain of outbred deer mice. PMID:33882817
27-Hydroxycholesterol is a specific factor in the neoplastic microenvironment of HCC that causes MDR via GRP75 regulation of the redox balance and metabolic reprogramming. PMID:33880675
Transcriptomic alterations in malignant pleural mesothelioma cells in response to long‑term treatment with bullfrog sialic acid‑binding lectin. PMID:33880588
Brain proteomic changes by histone deacetylase inhibition after traumatic brain injury. PMID:33880414
Identification of key genes and pathways in discoid lupus skin via bioinformatics analysis. PMID:33879674
An ensemble of the iCluster method to analyze longitudinal lncRNA expression data for psoriasis patients. PMID:33879268
An EPIC predictor of gestational age and its application to newborns conceived by assisted reproductive technologies. PMID:33875015
Identification of the specific long-noncoding RNAs involved in night-break mediated flowering retardation in Chenopodium quinoa. PMID:33874907
Expression and prognosis analyses of BUB1, BUB1B and BUB3 in human sarcoma. PMID:33872216
Gut Microbiome Changes with Acute Diarrheal Disease in Urban Versus Rural Settings in Northern Ecuador. PMID:33872206
Predictive Models of Genetic Redundancy in Arabidopsis thaliana. PMID:33871641
Ontology-Based Graphs of Research Communities: A Tool for Understanding Threat Reduction Networks. PMID:33870041
An Extracellular Matrix-Based Signature Associated With Immune Microenvironment Predicts the Prognosis and Therapeutic Responses of Patients With Oesophageal Squamous Cell Carcinoma. PMID:33869274
CCR7 Has Potential to Be a Prognosis Marker for Cervical Squamous Cell Carcinoma and an Index for Tumor Microenvironment Change. PMID:33869272
Subtypes identification on heart failure with preserved ejection fraction via network enhancement fusion using multi-omics data. PMID:33868594
Is acupuncture effective in the treatment of COVID-19 related symptoms? Based on bioinformatics/network topology strategy. PMID:33866350
DUSP7 regulates the activity of ERK2 to promote proper chromosome alignment during cell division. PMID:33865857
Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease. PMID:33864768
The mechanism of TiaoGanYiPi formula for treating chronic hepatitis B by network pharmacology and molecular docking verification. PMID:33863948
Conserved long-range base pairings are associated with pre-mRNA processing of human genes. PMID:33863890
Bioinformatic analysis identifies potential biomarkers and therapeutic targets of septic-shock-associated acute kidney injury. PMID:33863396
IrGO: Iranian traditional medicine General Ontology and knowledge base. PMID:33863373
Silencing SHMT2 inhibits the progression of tongue squamous cell carcinoma through cell cycle regulation. PMID:33863325
Identification and Validation of a Tumor Microenvironment-Related Gene Signature for Prognostic Prediction in Advanced-Stage Non-Small-Cell Lung Cancer. PMID:33860055
Utilizing network pharmacology and molecular docking to explore the underlying mechanism of Guizhi Fuling Wan in treating endometriosis. PMID:33859874
Disparate Interferon Signaling and Shared Aberrant Basaloid Cells in Single-Cell Profiling of Idiopathic Pulmonary Fibrosis and Systemic Sclerosis-Associated Interstitial Lung Disease. PMID:33859634
PCprophet: a framework for protein complex prediction and differential analysis using proteomic data. PMID:33859439
A genome-wide atlas of co-essential modules assigns function to uncharacterized genes. PMID:33859415
Multi-omic profiling of pituitary thyrotropic cells and progenitors. PMID:33858413
Interacting impact of maternal inflammatory response and stress on the amygdala transcriptome of pigs. PMID:33856433
Unraveling Heterogeneity of Tumor Cells and Microenvironment and Its Clinical Implications for Triple Negative Breast Cancer. PMID:33854958
Integrated Genomic and Transcriptomic Analysis reveals key genes for predicting dual-phenotype Hepatocellular Carcinoma Prognosis. PMID:33854600
CD8+ T Lymphocyte Coexpression Genes Correlate with Immune Microenvironment and Overall Survival in Breast Cancer. PMID:33854546
Proteomic characterization of the human lens and Cataractogenesis. PMID:33849365
Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences. PMID:33849068
Lipoprotein DolP supports proper folding of BamA in the bacterial outer membrane promoting fitness upon envelope stress. PMID:33847565
Nanopore long-read RNA-seq and absolute quantification delineate transcription dynamics in early embryo development of an insect pest. PMID:33846393
Microbial community characterization of shrimp survivors to AHPND challenge test treated with an effective shrimp probiotic (Vibrio diabolicus). PMID:33845910
Improved characterisation of clinical text through ontology-based vocabulary expansion. PMID:33845909
Bioinformatics analysis of the expression and role of microRNA-221-3p in head and neck squamous cell carcinoma. PMID:33845800
The transcriptomic responses of Atlantic salmon (Salmo salar) to high temperature stress alone, and in combination with moderate hypoxia. PMID:33845767
Functional annotation of lung cancer‒associated genetic variants by cell type‒specific epigenome and long-range chromatin interactome. PMID:33840167
Editor's introduction to this issue (G&I 19:1, 2021). PMID:33840165
Machine learning revealed stemness features and a novel stemness-based classification with appealing implications in discriminating the prognosis, immunotherapy and temozolomide responses of 906 glioblastoma patients. PMID:33839757
Identification of transcriptomic signatures and crucial pathways involved in non-alcoholic steatohepatitis. PMID:33837926
Dual-process brain mitochondria isolation preserves function and clarifies protein composition. PMID:33836587
Large-Scale Phenomic and Genomic Analysis of Brain Asymmetrical Skew. PMID:33836062
Tumor Microenvironment Proteomics: Lessons From Multiple Myeloma. PMID:33833982
Molecular mechanisms detected in yak lung tissue via transcriptome-wide analysis provide insights into adaptation to high altitudes. PMID:33833362
Prediction of Streptococcus uberis clinical mastitis treatment success in dairy herds by means of mass spectrometry and machine-learning. PMID:33833319
lncRNA C2dat2 facilitates autophagy and apoptosis via the miR-30d-5p/DDIT4/mTOR axis in cerebral ischemia-reperfusion injury. PMID:33833132
Common low complexity regions for SARS-CoV-2 and human proteomes as potential multidirectional risk factor in vaccine development. PMID:33832440
MicroCellClust: mining rare and highly specific subpopulations from single-cell expression data. PMID:33830183
High BLM Expression Predicts Poor Clinical Outcome and Contributes to Malignant Progression in Human Cholangiocarcinoma. PMID:33828983
M2 Macrophage Co-Expression Factors Correlate With Immune Phenotype and Predict Prognosis of Bladder Cancer. PMID:33828973
Prognostic Implication of the Expression Level of PECAM-1 in Non-small Cell Lung Cancer. PMID:33828969
Transcriptomic Analysis of Mouse Brain After Traumatic Brain Injury Reveals That the Angiotensin Receptor Blocker Candesartan Acts Through Novel Pathways. PMID:33828448
The chromosome-level Hemerocallis citrina Borani genome provides new insights into the rutin biosynthesis and the lack of colchicine. PMID:33828071
Integrated genomic analysis reveals key features of long undecoded transcript isoform-based gene repression. PMID:33826921
Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations. PMID:33823788
JMJD6 Is a Druggable Oxygenase That Regulates AR-V7 Expression in Prostate Cancer. PMID:33822745
miRSM: an R package to infer and analyse miRNA sponge modules in heterogeneous data. PMID:33822666
Gene expression evaluation of antioxidant enzymes in patients with hepatocellular carcinoma: RT-qPCR and bioinformatic analyses. PMID:33821873
Age-dependent pathogenic characteristics of SARS-CoV-2 infection in ferrets. PMID:33821260
The construction and analysis of a ferroptosis-related gene prognostic signature for pancreatic cancer. PMID:33819918
Application and evaluation of knowledge graph embeddings in biomedical data. PMID:33816992
CogNet: classification of gene expression data based on ranked active-subnetwork-oriented KEGG pathway enrichment analysis. PMID:33816987
Immunogenomic Profiling Demonstrate AC003092.1 as an Immune-Related eRNA in Glioblastoma Multiforme. PMID:33815468
Identification of Novel Sensitive and Reliable Serovar-Specific Targets for PCR Detection of Salmonella Serovars Hadar and Albany by Pan-Genome Analysis. PMID:33815306
Weighted Gene Coexpression Network Analysis Reveals Essential Genes and Pathways in Bipolar Disorder. PMID:33815158
Comparative Analysis of Adelphocoris suturalis Jakovlev (Hemiptera: Miridae) Immune Responses to Fungal and Bacterial Pathogens. PMID:33815150
Proteomic reveals the influences of smoke-water and karrikinolide on the biosynthesis of salvianolic acids and lignins in Salvia miltiorrhiza hairy roots. PMID:33811528
Strategies to Modulate Specialized Metabolism in Mediterranean Crops: From Molecular Aspects to Field. PMID:33809189
Single-Molecule Long-Read Sequencing of Purslane (Portulaca oleracea) and Differential Gene Expression Related with Biosynthesis of Unsaturated Fatty Acids. PMID:33808162
Metabolome and Transcriptome Analyses Reveal the Regulatory Mechanisms of Photosynthesis in Developing Ginkgo biloba Leaves. PMID:33807564
Distinct miRNA Signatures and Networks Discern Fetal from Adult Erythroid Differentiation and Primary from Immortalized Erythroid Cells. PMID:33807258
CircRNA-Protein Interactions in Muscle Development and Diseases. PMID:33806945
Identification of Genomic Regions Associated with Concentrations of Milk Fat, Protein, Urea and Efficiency of Crude Protein Utilization in Grazing Dairy Cows. PMID:33806889
Transcriptomic Diversity in the Livers of South African Sardines Participating in the Annual Sardine Run. PMID:33806647
Mutations of Intrinsically Disordered Protein Regions Can Drive Cancer but Lack Therapeutic Strategies. PMID:33806614
Functional Annotation of a Full-Length Transcriptome and Identification of Genes Associated with Flower Development in Rhododendronsimsii (Ericaceae). PMID:33805478
Withholding of M-CSF Supplement Reprograms Macrophages to M2-Like via Endogenous CSF-1 Activation. PMID:33805444
Selective Activation of CNS and Reference PPARGC1A Promoters Is Associated with Distinct Gene Programs Relevant for Neurodegenerative Diseases. PMID:33804860
Innate Resistance and Phosphite Treatment Affect Both the Pathogen's and Host's Transcriptomes in the Tanoak-Phytophthora ramorum Pathosystem. PMID:33803362
A Comparison of the Transcriptomes of Cowpeas in Response to Two Different Ionizing Radiations. PMID:33802840
Rice Transcriptome Analysis Reveals Nitrogen Starvation Modulates Differential Alternative Splicing and Transcript Usage in Various Metabolism-Related Genes. PMID:33801769
Candidate Genes for the High-Altitude Adaptations of Two Mountain Pine Taxa. PMID:33801727
Transcriptome Analysis Reveals Genes Involved in Thermogenesis in Two Cold-Exposed Sheep Breeds. PMID:33800742
Regulation of Juvenile Hormone on Summer Diapause of Geleruca daurica and Its Pathway Analysis. PMID:33799822
Volume-constrained microcontainers enable myoepithelial functional differentiation in highly parallel mammary organoid culture. PMID:33796842
HARVESTMAN: a framework for hierarchical feature learning and selection from whole genome sequencing data. PMID:33794760
Anno genominis XX: 20 years of Arabidopsis genomics. PMID:33793861
Building blocks and blueprints for bacterial autolysins. PMID:33793553
Validation of intraosseous delivery of valproic acid in a swine model of polytrauma. PMID:33791436
Weighted Gene Coexpression Network Analysis Uncovers Critical Genes and Pathways for Multiple Brain Regions in Parkinson's Disease. PMID:33791366
Construction of a Prognostic Gene Signature Associated with Immune Infiltration in Glioma: A Comprehensive Analysis Based on the CGGA. PMID:33790966
Identification of Candidate Genes Conferring Cold Tolerance to Rice (Oryza sativa L.) at the Bud-Bursting Stage Using Bulk Segregant Analysis Sequencing and Linkage Mapping. PMID:33790929
Trans-acting genetic variation affects the expression of adjacent genes. PMID:33789351
Wormicloud: a new text summarization tool based on word clouds to explore the C. elegans literature. PMID:33787871
An expanding manifold in transmodal regions characterizes adolescent reconfiguration of structural connectome organization. PMID:33787489
FoxO1-GAB1 axis regulates homing capacity and tonic AKT activity in chronic lymphocytic leukemia. PMID:33786575
A Wnt-mediated phenotype switch along the epithelial-mesenchymal axis defines resistance and invasion downstream of ionising radiation in oral squamous cell carcinoma. PMID:33785878
Integration of multi-omics approaches for functional characterization of muscle related selective sweep genes in Nanchukmacdon. PMID:33785872
Deciphering the transcriptomic regulation of heat stress responses in Nothofagus pumilio. PMID:33784314
Clotting in COVID-19: Is It All in the Genes? PMID:33784208
Dysregulation of circRNA expression in the peripheral blood of individuals with schizophrenia and bipolar disorder. PMID:33782720
Modular genome-wide gene expression architecture shared by early traits of osteoporosis and atherosclerosis in the Young Finns Study. PMID:33782480
Screening of osteoarthritis diagnostic markers based on immune-related genes and immune infiltration. PMID:33782454
Perspective: targeting VEGF-A and YKL-40 in glioblastoma - matter matters. PMID:33779510
IL-8, MSPa, MIF, FGF-9, ANG-2 and AgRP collection were identified for the diagnosis of colorectal cancer based on the support vector machine model. PMID:33779485
Characterization of a Deep Sea Bacillus toyonensis Isolate: Genomic and Pathogenic Features. PMID:33777842
Transcriptome Analysis of Ovarian Follicles Reveals Potential Pivotal Genes Associated With Increased and Decreased Rates of Chicken Egg Production. PMID:33777097
Regulatory Function of Sympathetic Innervation on the Endo/Lysosomal Trafficking of Acetylcholine Receptor. PMID:33776791
CTD Anatomy: analyzing chemical-induced phenotypes and exposures from an anatomical perspective, with implications for environmental health studies. PMID:33768211
The deubiquitinase Usp9x regulates PRC2-mediated chromatin reprogramming during mouse development. PMID:33767158
Hepatic steatosis and steatohepatitis: a functional meta-analysis of sex-based differences in transcriptomic studies. PMID:33766130
The first complete mitochondrial genome of eggplant (Solanum melongena). PMID:33763537
A Comparative Transcriptome Analysis of Human and Porcine Choroid Plexus Cells in Response to Streptococcus suis Serotype 2 Infection Points to a Role of Hypoxia. PMID:33763387
Identification of a Metabolism-Related Signature for the Prediction of Survival in Endometrial Cancer Patients. PMID:33763366
Genomic Loci Affecting Milk Production in German Black Pied Cattle (DSN). PMID:33763120
Comparative transcriptome and metabolome analysis of Ostrinia furnacalis female adults under UV-A exposure. PMID:33762675
Genome-wide association analysis reveals regulation of at-risk loci by DNA methylation in prostate cancer. PMID:33762478
The identification of neutrophils-mediated mechanisms and potential therapeutic targets for the management of sepsis-induced acute immunosuppression using bioinformatics. PMID:33761636
Piggybacking on Niche Adaptation Improves the Maintenance of Multidrug-Resistance Plasmids. PMID:33760032
SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks. PMID:33758926
G-quadruplexes originating from evolutionary conserved L1 elements interfere with neuronal gene expression in Alzheimer's disease. PMID:33758195
Overexpression of CCNE1 confers a poorer prognosis in triple-negative breast cancer identified by bioinformatic analysis. PMID:33757543
Novel ultra-rare exonic variants identified in a founder population implicate cadherins in schizophrenia. PMID:33756103
PTENε suppresses tumor metastasis through regulation of filopodia formation. PMID:33755220
TALE: Transformer-based protein function Annotation with joint sequence-Label Embedding. PMID:33755048
Identification of pivotal genes associated with the prognosis of gastric carcinoma through integrated analysis. PMID:33754626
Genome-wide identification of MIKC-type genes related to stamen and gynoecium development in Liriodendron. PMID:33753780
The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai-Tibet Plateau. PMID:33753478
Critical role of the BAF chromatin remodeling complex during murine neural crest development. PMID:33750945
The identification of circular RNAs from peripheral blood mononuclear cells in systemic lupus erythematosus. PMID:33750387
Integrated microRNA and transcriptome profiling reveal key miRNA-mRNA interaction pairs associated with seed development in Tartary buckwheat (Fagopyrum tataricum). PMID:33750309
Noise regularization removes correlation artifacts in single-cell RNA-seq data preprocessing. PMID:33748795
Coexpressed Genes That Promote the Infiltration of M2 Macrophages in Melanoma Can Evaluate the Prognosis and Immunotherapy Outcome. PMID:33748290
Pleiotropic Roles for the Plasmodium berghei RNA Binding Protein UIS12 in Transmission and Oocyst Maturation. PMID:33747980
Comprehensive In Silico Analysis of a Novel Serum Exosome-Derived Competitive Endogenous RNA Network for Constructing a Prognostic Model for Glioblastoma. PMID:33747903
Pairwise Versus Multiple Global Network Alignment. PMID:33747670
Identification of Pivotal MicroRNAs and Target Genes Associated with Persistent Atrial Fibrillation Based on Bioinformatics Analysis. PMID:33747117
Transcriptome and Comparative Chloroplast Genome Analysis of Vincetoxicum versicolor: Insights Into Molecular Evolution and Phylogenetic Implication. PMID:33747039
The Molecular Basis of Kale Domestication: Transcriptional Profiling of Developing Leaves Provides New Insights Into the Evolution of a Brassica oleracea Vegetative Morphotype. PMID:33747016
Identification of molecular biomarkers and pathways of NSCLC: insights from a systems biomedicine perspective. PMID:33742334
Identification of disease treatment mechanisms through the multiscale interactome. PMID:33741907
Genetic-variant hotspots and hotspot clusters in the human genome facilitating adaptation while increasing instability. PMID:33741065
Differential microRNAs expression profiles in liver from three different lifestyle modification mice models. PMID:33740891
High expression of COL5A2, a member of COL5 family, indicates the poor survival and facilitates cell migration in gastric cancer. PMID:33739392
Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment. PMID:33737920
Prediction of LncRNA-encoded small peptides in glioma and oligomer channel functional analysis using in silico approaches. PMID:33735310
Natural variation in the regulation of neurodevelopmental genes modifies flight performance in Drosophila. PMID:33735180
Aberrant proteins expressed in skin fibroblasts of Parkinson's disease patients carrying heterozygous variants of glucocerebrosidase and parkin genes. PMID:33732455
Screening and verification of hub genes involved in osteoarthritis using bioinformatics. PMID:33732303
Ultrafast functional profiling of RNA-seq data for nonmodel organisms. PMID:33731361
Chronic villitis of unknown etiology: Investigations into viral pathogenesis. PMID:33730616
A KDM5-Prospero transcriptional axis functions during early neurodevelopment to regulate mushroom body formation. PMID:33729157
Integration of summary data from GWAS and eQTL studies identified novel risk genes for coronary artery disease. PMID:33725943
A perfusable, multifunctional epicardial device improves cardiac function and tissue repair. PMID:33723455
How to Get Started with Single Cell RNA Sequencing Data Analysis. PMID:33722930
Transcriptome Expression of Biomineralization Genes in Littoraria flava Gastropod in Brazilian Rocky Shore Reveals Evidence of Local Adaptation. PMID:33720344
Identification of genes that correlate clear cell renal cell carcinoma and obesity and exhibit potential prognostic value. PMID:33718070
Identification of the hub genes in gastric cancer through weighted gene co-expression network analysis. PMID:33717664
Comprehensive Quantitative Proteome Analysis of Aedes aegypti Identifies Proteins and Pathways Involved in Wolbachia pipientis and Zika Virus Interference Phenomenon. PMID:33716790
Soluble ACE2-mediated cell entry of SARS-CoV-2 via interaction with proteins related to the renin-angiotensin system. PMID:33713620
The Counteracting Effects of Demography on Functional Genomic Variation: The Roma Paradigm. PMID:33713133
Genome-wide transcriptome profiling uncovers differential miRNAs and lncRNAs in ovaries of Hu sheep at different developmental stages. PMID:33712687
Functional repertoire of EV-associated miRNA profiles after lipoprotein depletion via ultracentrifugation and size exclusion chromatography from autologous blood products. PMID:33712660
Identification of four key prognostic genes and three potential drugs in human papillomavirus negative head and neck squamous cell carcinoma. PMID:33712015
Identification of potential and novel target genes in pituitary prolactinoma by bioinformatics analysis. PMID:33709028
Coronary artery disease: differential expression of ceRNAs and interaction analyses. PMID:33708856
Transcriptome Analysis of the Inhibitory Effect of Sennoside A on the Metastasis of Hepatocellular Carcinoma Cells. PMID:33708105
Joint analysis of expression levels and histological images identifies genes associated with tissue morphology. PMID:33707455
Maternal Iron Deficiency Modulates Placental Transcriptome and Proteome in Mid-Gestation of Mouse Pregnancy. PMID:33693820
UbiNet 2.0: a verified, classified, annotated and updated database of E3 ubiquitin ligase-substrate interactions. PMID:33693667
Multi-influential genetic interactions alter behaviour and cognition through six main biological cascades in Down syndrome mouse models. PMID:33693642
Copper Availability Influences the Transcriptomic Response of Candida albicans to Fluconazole Stress. PMID:33693623
Data Analytics Applications for Streaming Data From Social Media: What to Predict? PMID:33693318
Four potential microRNAs affect the progression of pancreatic ductal adenocarcinoma by targeting MET via the PI3K/AKT signaling pathway. PMID:33692858
Macrophage M2 Co-expression Factors Correlate With the Immune Microenvironment and Predict Outcome of Renal Clear Cell Carcinoma. PMID:33692827
Stromal NRG1 in luminal breast cancer defines pro-fibrotic and migratory cancer-associated fibroblasts. PMID:33692466
Genome-wide association study in almost 195,000 individuals identifies 50 previously unidentified genetic loci for eye color. PMID:33692100
Changes in protein expression due to metformin treatment and hyperinsulinemia in a human endometrial cancer cell line. PMID:33690729
Biodegradation of lignin monomers and bioconversion of ferulic acid to vanillic acid by Paraburkholderia aromaticivorans AR20-38 isolated from Alpine forest soil. PMID:33687503
Long non-coding RNAs ENST00000429730.1 and MSTRG.93125.4 are associated with metabolic activity in tuberculosis lesions of sputum-negative tuberculosis patients. PMID:33686954
Identification and validation of three core genes in p53 signaling pathway in hepatitis B virus-related hepatocellular carcinoma. PMID:33685467
Identification of permissive amber suppression sites for efficient non-canonical amino acid incorporation in mammalian cells. PMID:33684219
The very early evolution of protein translocation across membranes. PMID:33684113
DeepViral: prediction of novel virus-host interactions from protein sequences and infectious disease phenotypes. PMID:33682875
Identification of Tumor Tissue of Origin with RNA-Seq Data and Using Gradient Boosting Strategy. PMID:33681364
Analysis of MicroRNAs Associated With Carotid Atherosclerotic Plaque Rupture With Thrombosis. PMID:33679879
Comprehensive circRNA Expression Profile and Construction of circRNAs-Related ceRNA Network in a Mouse Model of Autism. PMID:33679870
Analysing the yeast complexome-the Complex Portal rising to the challenge. PMID:33677561
MACMIC Reveals A Dual Role of CTCF in Epigenetic Regulation of Cell Identity Genes. PMID:33677108
Giant ankyrin-G regulates cardiac function. PMID:33675749
Comparative analysis of chloroplast genomes of kenaf cytoplasmic male sterile line and its maintainer line. PMID:33674697
Comparison of plasma and cerebrospinal fluid proteomes identifies gene products guiding adult neurogenesis and neural differentiation in birds. PMID:33674647
Mitochondrial arginase-2 is essential for IL-10 metabolic reprogramming of inflammatory macrophages. PMID:33674584
Unique Human and Mouse β-Cell Senescence-Associated Secretory Phenotype (SASP) Reveal Conserved Signaling Pathways and Heterogeneous Factors. PMID:33674410
AP-1 subunits converge promiscuously at enhancers to potentiate transcription. PMID:33674350
ETS-Domain Transcription Factor Elk-1 Regulates Stemness Genes in Brain Tumors and CD133+ BrainTumor-Initiating Cells. PMID:33672811
Integrative Analysis Identified Key Schizophrenia Risk Factors from an Abnormal Behavior Mouse Gene Set. PMID:33672431
Germline and Somatic Whole-Exome Sequencing Identifies New Candidate Genes Involved in Familial Predisposition to Serrated Polyposis Syndrome. PMID:33672345
Comprehensive Proteomics Analysis of In Vitro Canine Oviductal Cell-Derived Extracellular Vesicles. PMID:33672125
Accumulation of the Auxin Precursor Indole-3-Acetamide Curtails Growth through the Repression of Ribosome-Biogenesis and Development-Related Transcriptional Networks. PMID:33670805
Genomic Comparison of Lactobacillus casei AP and Lactobacillus plantarum DR131 with Emphasis on the Butyric Acid Biosynthetic Pathways. PMID:33669502
Patients with Proliferative Lupus Nephritis Have Autoantibodies That React to Moesin and Demonstrate Increased Glomerular Moesin Expression. PMID:33669337
Identify potential miRNA-mRNA regulatory networks contributing to high-risk neuroblastoma. PMID:33666785
Targeted molecular profiling of rare olfactory sensory neurons identifies fate, wiring, and functional determinants. PMID:33666172
Multiple Regionalized Genes and Their Putative Networks in the Interpeduncular Nucleus Suggest Complex Mechanisms of Neuron Development and Axon Guidance. PMID:33664652
The relationship among Girdin DNA methylation, its high expression, and immune infiltration in hepatocellular carcinoma: Clues from in silico analysis. PMID:33660763
Inheritance of Solanum chloroplast genomic DNA in interspecific hybrids. PMID:33659675
HoSeIn: A Workflow for Integrating Various Homology Search Results from Metagenomic and Metatranscriptomic Sequence Datasets. PMID:33659350
The Changes of Leukocytes in Brain and Blood After Intracerebral Hemorrhage. PMID:33659003
Transcriptome-Wide High-Throughput m6A Sequencing of Differential m6A Methylation Patterns in the Human Rheumatoid Arthritis Fibroblast-Like Synoviocytes Cell Line MH7A. PMID:33658830
Complex-dependent histone acetyltransferase activity of KAT8 determines its role in transcription and cellular homeostasis. PMID:33657400
Cooperation of LIM domain-binding 2 (LDB2) with EGR in the pathogenesis of schizophrenia. PMID:33656268
MMP7 as a potential biomarker of colon cancer and its prognostic value by bioinformatics analysis. PMID:33655961
OXPHOS deficiency activates global adaptation pathways to maintain mitochondrial membrane potential. PMID:33655635
Downregulation of miR‑146a inhibits osteoporosis in the jaws of ovariectomized rats by regulating the Wnt/β‑catenin signaling pathway. PMID:33655338
Exploring existing drugs: proposing potential compounds in the treatment of COVID-19. PMID:33655082
A Protocol to Map the Spatial Proteome Using HyperLOPIT in Saccharomyces cerevisiae. PMID:33654815
A developmental lineage-based gene co-expression network for mouse pancreatic β-cells reveals a role for Zfp800 in pancreas development. PMID:33653874
Cross-species data integration to prioritize causal genes in lipid metabolism. PMID:33651746
Human Chorionic Gonadotropin Modulates the Transcriptome of the Myometrium and Cervix in Late Gestation. PMID:33650091
Complete Genome Sequence Analysis of Brevibacillus laterosporus Bl-zj Reflects its Potential Algicidal Response. PMID:33649996
Peptidomics analysis revealed that a novel peptide VMP‑19 protects against Ang II‑induced injury in human umbilical vein endothelial cells. PMID:33649860
Complete genome sequencing of Bacillus sp. TK-2, analysis of its cold evolution adaptability. PMID:33649356
Differential regulation of β-catenin-mediated transcription via N- and C-terminal co-factors governs identity of murine intestinal epithelial stem cells. PMID:33649334
Genomically Complex Human Angiosarcoma and Canine Hemangiosarcoma Establish Convergent Angiogenic Transcriptional Programs Driven by Novel Gene Fusions. PMID:33649193
Construction of the optimization prognostic model based on differentially expressed immune genes of lung adenocarcinoma. PMID:33648465
Transcriptome and metabolome profiling provide insights into molecular mechanism of pseudostem elongation in banana. PMID:33648452
Pre-conditioning modifies the TME to enhance solid tumor CAR T cell efficacy and endogenous protective immunity. PMID:33647456
Comprehensive analysis of cancer breakpoints reveals signatures of genetic and epigenetic contribution to cancer genome rearrangements. PMID:33647036
RAMP2-AS1 Regulates Endothelial Homeostasis and Aging. PMID:33644072
Identification of mortality-risk-related missense variant for renal clear cell carcinoma using deep learning. PMID:33643601
Whole-Genome Diversification Analysis of the Hornbeam Species Reveals Speciation and Adaptation Among Closely Related Species. PMID:33643339
Potential Molecular Mechanism of TNF Superfamily-Related Genes in Glioblastoma Multiforme Based on Transcriptome and Epigenome. PMID:33643183
PIWI-interacting RNA sequencing profiles in maternal plasma-derived exosomes reveal novel non-invasive prenatal biomarkers for the early diagnosis of nonsyndromic cleft lip and palate. PMID:33639402
Identification of an N-acetylneuraminic acid-presenting bacteria isolated from a human microbiome. PMID:33637779
Retroviral integrations contribute to elevated host cancer rates during germline invasion. PMID:33637755
Tumor-specific cytolytic CD4 T cells mediate immunity against human cancer. PMID:33637530
Transcriptome analysis of the role of autophagy in plant response to heat stress. PMID:33635879
A novel DNA methylation-based model that effectively predicts prognosis in hepatocellular carcinoma. PMID:33634306
Knockdown of RIPK2 Inhibits Proliferation and Migration, and Induces Apoptosis via the NF-κB Signaling Pathway in Gastric Cancer. PMID:33633788
Genomic insight into diet adaptation in the biological control agent Cryptolaemus montrouzieri. PMID:33632122
PFP-WGAN: Protein function prediction by discovering Gene Ontology term correlations with generative adversarial networks. PMID:33630862
Genomic Expression Profiling and Bioinformatics Analysis of Chronic Recurrent Multifocal Osteomyelitis. PMID:33628812
Spatiotemporal dissection of the cell cycle with single-cell proteogenomics. PMID:33627808
Mass-spectrometry-based proteomic correlates of grade and stage reveal pathways and kinases associated with aggressive human cancers. PMID:33627787
Discovering microbe-disease associations from the literature using a hierarchical long short-term memory network and an ensemble parser model. PMID:33627732
Conserved Epigenetic Programming and Enhanced Heme Metabolism Drive Memory B Cell Reactivation. PMID:33627377
Genome-wide ancestry and introgression in a Zambian baboon hybrid zone. PMID:33624366
Comprehensive Analysis of Gene Expression Changes and Validation in Hepatocellular Carcinoma. PMID:33623390
Ontology-guided segmentation and object identification for developmental mouse lung immunofluorescent images. PMID:33622235
Seascape genomics reveals candidate molecular targets of heat stress adaptation in three coral species. PMID:33619812
Discovery of molecular features underlying the morphological landscape by integrating spatial transcriptomic data with deep features of tissue images. PMID:33619564
Mouse models for hereditary spastic paraplegia uncover a role of PI4K2A in autophagic lysosome reformation. PMID:33618608
RNA-binding protein syncrip regulates starvation-induced hyperactivity in adult Drosophila. PMID:33617535
Identification of miRNAs as diagnostic and prognostic markers in hepatocellular carcinoma. PMID:33617479
A New Family of Bacteriolytic Proteins in Dictyostelium discoideum. PMID:33614529
Identification of Primary and Metastatic Lung Cancer-Related lncRNAs and Potential Targeted Drugs Based on ceRNA Network. PMID:33614509
How value-sensitive design can empower sustainable consumption. PMID:33614080
20S proteasomes secreted by the malaria parasite promote its growth. PMID:33608523
Novel signaling pathways regulate SARS-CoV and SARS-CoV-2 infectious disease. PMID:33607766
redPATH: Reconstructing the Pseudo Development Time of Cell Lineages in Single-cell RNA-seq Data and Applications in Cancer. PMID:33607293
Local adaptation contributes to gene expression divergence in maize. PMID:33604670
Public data sources to support systems toxicology applications. PMID:33604492
Transcriptomic Signatures and Functional Network Analysis of Chronic Rhinosinusitis With Nasal Polyps. PMID:33603773
Enrichment analyses of diseases and pathways associated with precocious puberty using PrecocityDB. PMID:33602974
The immune-related biomarker TEK inhibits the development of clear cell renal cell carcinoma (ccRCC) by regulating AKT phosphorylation. PMID:33602230
Quantitative proteomic analysis of pear (Pyrus pyrifolia cv. "Hosui") flesh provides novel insights about development and quality characteristics of fruit. PMID:33599839
Curation of over 10 000 transcriptomic studies to enable data reuse. PMID:33599246
Systems biology analysis identifies TNFRSF9 as a functional marker of tumor-infiltrating regulatory T-cell enabling clinical outcome prediction in lung cancer. PMID:33598101
Limited effects of long-term daily cranberry consumption on the gut microbiome in a placebo-controlled study of women with recurrent urinary tract infections. PMID:33596852
The histone demethylase KDM5 is required for synaptic structure and function at the Drosophila neuromuscular junction. PMID:33596422
Ferroptosis-related gene signature as a prognostic marker for lower-grade gliomas. PMID:33594759
Genetic characteristics of Bursaphelenchus xylophilus third-stage dispersal juveniles. PMID:33594100
The KbvR Regulator Contributes to Capsule Production, Outer Membrane Protein Biosynthesis, Antiphagocytosis, and Virulence in Klebsiella pneumoniae. PMID:33593891
Role of opiorphin genes in prostate cancer growth and progression. PMID:33593085
Recent Evolutionary History of Tigers Highlights Contrasting Roles of Genetic Drift and Selection. PMID:33592092
Insulin-like 3 affects zebrafish spermatogenic cells directly and via Sertoli cells. PMID:33589679
Genome-wide analysis suggests the importance of vascular processes and neuroinflammation in late-life antidepressant response. PMID:33589590
Transcriptome analysis reveals major transcriptional changes during regrowth after mowing of red clover (Trifolium pratense). PMID:33588756
SARS-CoV-2 Proteins Exploit Host's Genetic and Epigenetic Mediators for the Annexation of Key Host Signaling Pathways. PMID:33585554
Identification of Protein Subcellular Localization With Network and Functional Embeddings. PMID:33584818
Identification of Key Modules and Hub Genes of Annulus Fibrosus in Intervertebral Disc Degeneration. PMID:33584795
The CLAIRE COVID-19 initiative: approach, experiences and recommendations. PMID:33584129
Guidelines for biomarker discovery in endometrium: correcting for menstrual cycle bias reveals new genes associated with uterine disorders. PMID:33576824
NetQuilt: Deep Multispecies Network-based Protein Function Prediction using Homology-informed Network Similarity. PMID:33576802
Integration of single-cell datasets reveals novel transcriptomic signatures of β-cells in human type 2 diabetes. PMID:33575641
An empirical bayesian approach for testing gene expression fold change and its application in detecting global dosage effects. PMID:33575620
Functional networks of co-expressed genes to explore iron homeostasis processes in the pathogenic yeast Candida glabrata. PMID:33575583
GSAn: an alternative to enrichment analysis for annotating gene sets. PMID:33575577
Family-specific analysis of variant pathogenicity prediction tools. PMID:33575576
Global variability analysis of mRNA and protein concentrations across and within human tissues. PMID:33575562
Potential Drug Prediction of Glioblastoma Based on Drug Perturbation-Induced Gene Expression Signatures. PMID:33575336
Screening and identification of hub genes in bladder cancer by bioinformatics analysis and KIF11 is a potential prognostic biomarker. PMID:33574944
Gene expression and epigenetics reveal species-specific mechanisms acting upon common molecular pathways in the evolution of task division in bees. PMID:33574391
Sinbase 2.0: An Updated Database to Study Multi-Omics in Sesamum indicum. PMID:33573226
MicroRNA Profiling of HL-1 Cardiac Cells-Derived Extracellular Vesicles. PMID:33573156
Correlation between cortical gene expression and resting-state functional network centrality in healthy young adults. PMID:33570215
Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program. PMID:33568819
Systematic auditing is essential to debiasing machine learning in biology. PMID:33568741
Comparative transcriptomic analysis revealed novel potential therapeutic targets of traditional Chinese medicine (Pinggan-Qianyang decoction) on vascular remodeling in spontaneously hypertensive rats. PMID:33568194
Ranking cancer drivers via betweenness-based outlier detection and random walks. PMID:33568049
Whole-genome comparative analysis of Malaysian Burkholderia pseudomallei clinical isolates. PMID:33565959
A Molecular network approach reveals shared cellular and molecular signatures between chronic fatigue syndrome and other fatiguing illnesses. PMID:33564792
Microarray Data Mining and Preliminary Bioinformatics Analysis of Hepatitis D Virus-Associated Hepatocellular Carcinoma. PMID:33564675
Integrated bioinformatic analysis identifies COL4A3, COL4A4, and KCNJ1 as key biomarkers in Wilms tumor. PMID:33564352
Classification of node-positive melanomas into prognostic subgroups using keratin, immune, and melanogenesis expression patterns. PMID:33564068
Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification. PMID:33563788
Modular Reorganization of Signaling Networks during the Development of Colon Adenoma and Carcinoma. PMID:33562960
Phosphoproteomic Landscape of AML Cells Treated with the ATP-Competitive CK2 Inhibitor CX-4945. PMID:33562780
The microRNA let-7b-5p Is Negatively Associated with Inflammation and Disease Severity in Multiple Sclerosis. PMID:33562569
Genome analysis of Plectus murrayi, a nematode from continental Antarctica. PMID:33561244
Activity of bacteria isolated from bats against Pseudogymnoascus destructans in China. PMID:33559264
Identification of differentially expressed genes involved in amino acid and lipid accumulation of winter turnip rape (Brassica rapa L.) in response to cold stress. PMID:33556109
Single-cell transcriptomes of developing and adult olfactory receptor neurons in Drosophila. PMID:33555999
Integrative Identification of Hub Genes Associated With Immune Cells in Atrial Fibrillation Using Weighted Gene Correlation Network Analysis. PMID:33553270
Transcriptome Based System Biology Exploration Reveals Homogeneous Tumorigenicity of Alimentary Tract Malignancy. PMID:33552958
The functional analysis of ABCG transporters in the adaptation of pigeon pea (Cajanus cajan) to abiotic stresses. PMID:33552725
Circulating plasma exosomal miRNA profiles serve as potential metastasis-related biomarkers for hepatocellular carcinoma. PMID:33552286
MUC4 is a novel mediator in H. pylori infection-related pancreatic cancer. PMID:33552244
Prior Biological Knowledge Improves Genomic Prediction of Growth-Related Traits in Arabidopsis thaliana. PMID:33552126
Host Transcriptomic Response Following Administration of Rotavirus Vaccine in Infants' Mimics Wild Type Infection. PMID:33552046
Integrative Analyses of Genes Associated With Osteoporosis in CD16+ Monocyte. PMID:33551990
Integrating Network Pharmacology and Experimental Validation to Investigate the Effects and Mechanism of Astragalus Flavonoids Against Hepatic Fibrosis. PMID:33551818
A Novel 10-Gene Signature Predicts Poor Prognosis in Low Grade Glioma. PMID:33550903
Inhibitory effect of sodium butyrate on colorectal cancer cells and construction of the related molecular network. PMID:33549042
Investigating the relevance of major signaling pathways in cancer survival using a biologically meaningful deep learning model. PMID:33546587
GMO Genetic Elements Thesaurus (GMO-GET): a controlled vocabulary for the consensus designation of introduced or modified genetic elements in genetically modified organisms. PMID:33546585
Prediction and analysis of hub genes between glioblastoma and low-grade glioma using bioinformatics analysis. PMID:33545929
Protuberances are organized distinct regions of long-term callus: histological and transcriptomic analyses in kiwifruit. PMID:33544186
In-silico definition of the Drosophila melanogaster matrisome. PMID:33543012
Genome Assembly and Analyses of the Macrofungus Macrocybe gigantea. PMID:33542921
Development of a prognostic signature for esophageal cancer based on nine immune related genes. PMID:33541291
The Genetics of Sudden Infant Death Syndrome-Towards a Gene Reference Resource. PMID:33540853
BSGatlas: a unified Bacillus subtilis genome and transcriptome annotation atlas with enhanced information access. PMID:33539279
Long non‑coding RNA LINC00491 promotes proliferation and inhibits apoptosis in esophageal squamous cell carcinoma. PMID:33537830
Genome annotation of disease-causing microorganisms. PMID:33537706
Regulatory genomic circuitry of human disease loci by integrative epigenomics. PMID:33536621
IgA transcytosis and antigen recognition govern ovarian cancer immunity. PMID:33536615
Analyses of transcriptomes and the first complete genome of Leucocalocybe mongolica provide new insights into phylogenetic relationships and conservation. PMID:33536487
Novel prognostic genes and subclasses of acute myeloid leukemia revealed by survival analysis of gene expression data. PMID:33536020
GEOlimma: differential expression analysis and feature selection using pre-existing microarray data. PMID:33535967
Identification of microRNA-16-5p and microRNA-21-5p in feces as potential noninvasive biomarkers for inflammatory bowel disease. PMID:33535181
A comprehensive evaluation of skin aging-related circular RNA expression profiles. PMID:33534927
ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways. PMID:33534793
A High-Throughput Method for Identifying Novel Genes That Influence Metabolic Pathways Reveals New Iron and Heme Regulation in Pseudomonas aeruginosa. PMID:33531406
An edge-based statistical analysis of long non-coding RNA expression profiles reveals a negative association between Parkinson's disease and colon cancer. PMID:33531021
Integrative analysis of chloroplast DNA methylation in a marine alga-Saccharina japonica. PMID:33528753
Identifying daily changes in circRNAs and circRNA-associated-ceRNA networks in the rat pineal gland. PMID:33526984
Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 infection induces dysregulation of immunity: in silico gene expression analysis. PMID:33526974
Functional Signatures in Non-Small-Cell Lung Cancer: A Systematic Review and Meta-Analysis of Sex-Based Differences in Transcriptomic Studies. PMID:33526761
Human keratinocyte-derived extracellular vesicles activate the MAPKinase pathway and promote cell migration and proliferation in vitro. PMID:33526070
Systematic Analysis of Functionally Related Gene Clusters in the Opportunistic Pathogen, Candida albicans. PMID:33525750
A Transcriptomic Approach Provides Insights on the Mycorrhizal Symbiosis of the Mediterranean Orchid Limodorum abortivum in Nature. PMID:33525474
Long-Term Waterlogging as Factor Contributing to Hypoxia Stress Tolerance Enhancement in Cucumber: Comparative Transcriptome Analysis of Waterlogging Sensitive and Tolerant Accessions. PMID:33525400
Decreased p53 is associated with a decline in asymmetric stem cell self-renewal in aged human epidermis. PMID:33524216
DeCompress: tissue compartment deconvolution of targeted mRNA expression panels using compressed sensing. PMID:33524140
Introduction to radiomics and radiogenomics in neuro-oncology: implications and challenges. PMID:33521636
Gene Expression Profiling Reveals the Shared and Distinct Transcriptional Signatures in Human Lung Epithelial Cells Infected With SARS-CoV-2, MERS-CoV, or SARS-CoV: Potential Implications in Cardiovascular Complications of COVID-19. PMID:33521069
American lobster postlarvae alter gene regulation in response to ocean warming and acidification. PMID:33520168
The Characteristics of Chemosensory and Opsin Genes in Newly Emerged and Sexually Mature Agrilus planipennis, an Important Quarantine Forest Beetle. PMID:33519910
Identifying RBM47, HCK, CD53, TYROBP, and HAVCR2 as Hub Genes in Advanced Atherosclerotic Plaques by Network-Based Analysis and Validation. PMID:33519905
Genome-Wide Association Study of Maize Aboveground Dry Matter Accumulation at Seedling Stage. PMID:33519889
Insights into triterpene synthesis and unsaturated fatty-acid accumulation provided by chromosomal-level genome analysis of Akebia trifoliata subsp. australis. PMID:33518712
Study on mechanism of matrine in treatment of COVID-19 combined with liver injury by network pharmacology and molecular docking technology. PMID:33517789
Computational resources for identifying and describing proteins driving liquid-liquid phase separation. PMID:33517364
Lipids, lysosomes and mitochondria: insights into Lewy body formation from rare monogenic disorders. PMID:33515275
Amynthas corticis genome reveals molecular mechanisms behind global distribution. PMID:33514865
The role of gene to gene interaction in the breast's genomic signature of pregnancy. PMID:33514799
Data-driven biological network alignment that uses topological, sequence, and functional information. PMID:33514304
Causal network inference from gene transcriptional time-series response to glucocorticoids. PMID:33513136
Transcriptome annotation in the cloud: complexity, best practices, and cost. PMID:33511996
High-throughput screening in postimplantation haploid epiblast stem cells reveals Hs3st3b1 as a modulator for reprogramming. PMID:33511777
Comprehensive Analysis of ceRNA Regulation Network Involved in the Development of Coronary Artery Disease. PMID:33511207
Elucidation of the Genomic-Epigenomic Interaction Landscape of Aggressive Prostate Cancer. PMID:33511206
Reporting on the Role of miRNAs and Affected Pathways on the Molecular Backbone of Ovarian Insufficiency: A Systematic Review and Critical Analysis Mapping of Future Research. PMID:33511114
Biocontrol Using Bacillus amyloliquefaciens PP19 Against Litchi Downy Blight Caused by Peronophythora litchii. PMID:33510732
Gene signature of children with severe respiratory syncytial virus infection. PMID:33510411
Meta-analysis of host transcriptional responses to SARS-CoV-2 infection reveals their manifestation in human tumors. PMID:33510359
The Epstein-Barr virus deubiquitinase BPLF1 targets SQSTM1/p62 to inhibit selective autophagy. PMID:33509017
SinEx DB 2.0 update 2020: database for eukaryotic single-exon coding sequences. PMID:33507271
biotoolsSchema: a formalized schema for bioinformatics software description. PMID:33506265
Transcriptome data for tissue-specific genes in four reproductive organs at three developmental stages of micro-tom tomato. PMID:33506081
Identified GNGT1 and NMU as Combined Diagnosis Biomarker of Non-Small-Cell Lung Cancer Utilizing Bioinformatics and Logistic Regression. PMID:33505535
Genome-Wide Identification and Analysis of Chitinase GH18 Gene Family in Mycogone perniciosa. PMID:33505368
Inflammation and regulatory T cell genes are differentially expressed in peripheral blood mononuclear cells of Parkinson's disease patients. PMID:33504893
Integrative analysis of transcriptomic data for identification of T-cell activation-related mRNA signatures indicative of preterm birth. PMID:33504832
DM3Loc: multi-label mRNA subcellular localization prediction and analysis based on multi-head self-attention mechanism. PMID:33503258
Screening and identification of potential biomarkers and therapeutic drugs in melanoma via integrated bioinformatics analysis. PMID:33501609
In Silico Inference of Synthetic Cytotoxic Interactions from Paclitaxel Responses. PMID:33499282
Genome Sequence and Adaptation Analysis of the Human and Rice Pathogenic Strain Burkholderia glumae AU6208. PMID:33498266
Comparative transcriptomics and host-specific parasite gene expression profiles inform on drivers of proliferative kidney disease. PMID:33495500
Cross-platform genomic identification and clinical validation of breast cancer diagnostic biomarkers. PMID:33493140
Short hairpin RNA attenuates liver fibrosis by regulating the PPAR‑γ and NF‑κB pathways in HBV‑induced liver fibrosis in mice. PMID:33491741
Pearl Sac Gene Expression Profiles Associated With Pearl Attributes in the Silver-Lip Pearl Oyster, Pinctada maxima. PMID:33488672
HELQ and EGR3 expression correlate with IGHV mutation status and prognosis in chronic lymphocytic leukemia. PMID:33485349
A mixed community of skin microbiome representatives influences cutaneous processes more than individual members. PMID:33482907
Gene co-expression network analysis of Trypanosoma brucei in tsetse fly vector. PMID:33482903
BSR-Seq analysis provides insights into the cold stress response of Actinidia arguta F1 populations. PMID:33482717
The BMP signaling gradient is interpreted through concentration thresholds in dorsal-ventral axial patterning. PMID:33481775
The Hunt for Ancient Prions: Archaeal Prion-Like Domains Form Amyloid-Based Epigenetic Elements. PMID:33480998
Likelihood ratio statistics for gene set enrichment in Alzheimer's disease pathways. PMID:33480182
Transcriptome profiling of cells exposed to particular and intense electromagnetic radiation emitted by the "SG-III" prototype laser facility. PMID:33479397
Integrative multiomics analysis of Premolis semirufa caterpillar venom in the search for molecules leading to a joint disease. PMID:33479267
Multi-omic analysis unveils biological pathways in peripheral immune system associated to minimal hepatic encephalopathy appearance in cirrhotic patients. PMID:33479266
Gene co-expression in the interactome: moving from correlation toward causation via an integrated approach to disease module discovery. PMID:33479222
An empirical meta-analysis of the life sciences linked open data on the web. PMID:33479214
Potential interactions between the TBX4-FGF10 and SHH-FOXF1 signaling during human lung development revealed using ChIP-seq. PMID:33478486
Effect of Aging on Homeostasis in the Soft Tissue of the Periodontium: A Narrative Review. PMID:33477537
The complete mitochondrial genome of sponge Tethya sp. (Demospongiae, Tethyida, Tethyidae). PMID:33473525
Deleterious variants in X-linked CFAP47 induce asthenoteratozoospermia and primary male infertility. PMID:33472045
Computational Functional Genomics-Based AmpliSeq™ Panel for Next-Generation Sequencing of Key Genes of Pain. PMID:33467215
RNA-Seq transcriptome analysis of ileum in Taiping chicken supplemented with the dietary probiotic. PMID:33462736
Identifying protein subcellular localisation in scientific literature using bidirectional deep recurrent neural network. PMID:33462256
Auxin is involved in arbuscular mycorrhizal fungi-promoted tomato growth and NADP-malic enzymes expression in continuous cropping substrates. PMID:33461504
HIV Protein Tat Induces Macrophage Dysfunction and Atherosclerosis Development in Low-Density Lipoprotein Receptor-Deficient Mice. PMID:33459922
Establishment and application of information resource of mutant mice in RIKEN BioResource Research Center. PMID:33455583
Infection trains the host for microbiota-enhanced resistance to pathogens. PMID:33453153
A systems-level gene regulatory network model for Plasmodium falciparum. PMID:33450011
A genome-wide strategy to identify causes and consequences of retrotransposon expression finds activation by BRCA1 in ovarian cancer. PMID:33447827
Ontologies relevant to behaviour change interventions: a method for their development. PMID:33447665
Changes on proteomic and metabolomic profile in serum of mice induced by chronic exposure to tramadol. PMID:33446901
HIF-1α promotes cellular growth in lymphatic endothelial cells exposed to chronically elevated pulmonary lymph flow. PMID:33446832
Late p65 nuclear translocation in glioblastoma cells indicates non-canonical TLR4 signaling and activation of DNA repair genes. PMID:33446690
A cortical immune network map identifies distinct microglial transcriptional programs associated with β-amyloid and Tau pathologies. PMID:33446646
An Integrative Transcriptomic Analysis of Systemic Juvenile Idiopathic Arthritis for Identifying Potential Genetic Markers and Drug Candidates. PMID:33445803
Knowledge Network Embedding of Transcriptomic Data from Spaceflown Mice Uncovers Signs and Symptoms Associated with Terrestrial Diseases. PMID:33445483
Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB. PMID:33445429
Transcript levels of keratin 1/5/6/14/15/16/17 as potential prognostic indicators in melanoma patients. PMID:33441834
Multiplex gene and phenotype network to characterize shared genetic pathways of epilepsy and autism. PMID:33441621
Ontological modeling and analysis of experimentally or clinically verified drugs against coronavirus infection. PMID:33441564
Blood-derived mitochondrial DNA copy number is associated with gene expression across multiple tissues and is predictive for incident neurodegenerative disease. PMID:33441415
Longitudinal saliva omics responses to immune perturbation: a case study. PMID:33436912
Post-transcriptional circadian regulation in macrophages organizes temporally distinct immunometabolic states. PMID:33436377
A modular master regulator landscape controls cancer transcriptional identity. PMID:33434495
Identification of loci associated with susceptibility to bovine paratuberculosis and with the dysregulation of the MECOM, eEF1A2, and U1 spliceosomal RNA expression. PMID:33432064
Novel circRNA discovery in sheep shows evidence of high backsplice junction conservation. PMID:33432020
Ascending dorsal column sensory neurons respond to spinal cord injury and downregulate genes related to lipid metabolism. PMID:33431991
A systems pharmacology approach to identify the autophagy-inducing effects of Traditional Persian medicinal plants. PMID:33431946
Induced organoids derived from patients with ulcerative colitis recapitulate colitic reactivity. PMID:33431859
Comprehensive assessments of germline deletion structural variants reveal the association between prognostic MUC4 and CEP72 deletions and immune response gene expression in colorectal cancer patients. PMID:33431054
A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions. PMID:33431024
Mapping the SARS-CoV-2-Host Protein-Protein Interactome by Affinity Purification Mass Spectrometry and Proximity-Dependent Biotin Labeling: A Rational and Straightforward Route to Discover Host-Directed Anti-SARS-CoV-2 Therapeutics. PMID:33430309
A novel Foxp3-related immune prognostic signature for glioblastoma multiforme based on immunogenomic profiling. PMID:33429364
Proteomic identification and validation of novel interactions of the putative tumor suppressor PRELP with membrane proteins including IGFI-R and p75NTR. PMID:33428936
Construction of an mRNA-miRNA-lncRNA network prognostic for triple-negative breast cancer. PMID:33428596
Absence of NLRP3 Inflammasome in Hematopoietic Cells Reduces Adverse Remodeling After Experimental Myocardial Infarction. PMID:33426377
Methods for isolation and transcriptional profiling of individual cells from the human heart. PMID:33426328
miR-140-5p in Small Extracellular Vesicles From Human Papilla Cells Stimulates Hair Growth by Promoting Proliferation of Outer Root Sheath and Hair Matrix Cells. PMID:33425897
ENPP4 overexpression is associated with no recovery from Barrett's esophagus. PMID:33425094
Selective Sweeps Lead to Evolutionary Success in an Amazonian Hyperdominant Palm. PMID:33424928
Integration of full-length transcriptomics and targeted metabolomics to identify benzylisoquinoline alkaloid biosynthetic genes in Corydalis yanhusuo. PMID:33423040
Re-purposing software for functional characterization of the microbiome. PMID:33422152
Biotin Proximity Labeling for Protein-Protein Interaction Discovery: The BioID Method. PMID:33421001
Prognostic gene expression signatures of breast cancer are lacking a sensible biological meaning. PMID:33420139
Identifying the miRNA Signature Association with Aging-Related Senescence in Glioblastoma. PMID:33419230
An Embryonic Diapause-like Adaptation with Suppressed Myc Activity Enables Tumor Treatment Persistence. PMID:33417832
The iPPI-DB initiative: A Community-centered database of Protein-Protein Interaction modulators. PMID:33416858
PC2P: Parameter-free network-based prediction of protein complexes. PMID:33416831
Candidate regulators and target genes of drought stress in needles and roots of Norway spruce. PMID:33416078
Integrative analysis of differential circular RNA and long non-coding RNA profiles and associated competing endogenous RNA networks in esophageal squamous cell carcinoma. PMID:33415515
Alcohol use disorder causes global changes in splicing in the human brain. PMID:33414398
HiDeF: identifying persistent structures in multiscale 'omics data. PMID:33413539
Transcriptome of nasopharyngeal samples from COVID-19 patients and a comparative analysis with other SARS-CoV-2 infection models reveal disparate host responses against SARS-CoV-2. PMID:33413422
Transcriptomic analysis identifies organ-specific metastasis genes and pathways across different primary sites. PMID:33413400
Computational analysis to repurpose drugs for COVID-19 based on transcriptional response of host cells to SARS-CoV-2. PMID:33413329
Evaluation of the potential of Pap test fluid and cervical swabs to serve as clinical diagnostic biospecimens for the detection of ovarian cancer by mass spectrometry-based proteomics. PMID:33413078
Integration of gene expression data identifies key genes and pathways in colorectal cancer. PMID:33411100
PM4NGS, a project management framework for next-generation sequencing data analysis. PMID:33410471
Machine Learning Models to Predict Primary Sites of Metastatic Cervical Carcinoma From Unknown Primary. PMID:33408743
Identification of Core Genes Involved in the Metastasis of Clear Cell Renal Cell Carcinoma. PMID:33408516
Bioinformatics analysis of common key genes and pathways of intracranial, abdominal, and thoracic aneurysms. PMID:33407182
Transcriptional response of Asarum heterotropoides Fr. Schmidt var. mandshuricum (Maxim.) Kitag. leaves grown under full and partial daylight conditions. PMID:33407099
Label-free proteomic analysis of serum exosomes from paroxysmal atrial fibrillation patients. PMID:33407078
An Integrated Platform for Skin Cancer Heterogenous and Multilayered Data Management. PMID:33404959
Identification of Seven Cell Cycle-Related Genes with Unfavorable Prognosis and Construction of their TF-miRNA-mRNA regulatory network in Breast Cancer. PMID:33403032
Relationships Between Vitamin D Status and Cytokine: Results from Interferon-Based Therapy in Non-Cirrhotic, Treatment-Naïve Patients with Chronic Hepatitis C Infection. PMID:33402842
Identification and validation of an immune-related gene signature predictive of overall survival in colon cancer. PMID:33401247
Restoration of type I interferon signaling in intrahepatically primed CD8+ T cells promotes functional differentiation. PMID:33400688
Genome sequencing and functional annotation of Bacillus sp. strain BS-Z15 isolated from cotton rhizosphere soil having antagonistic activity against Verticillium dahliae. PMID:33399892
The Biological Meaning of Radiomic Features. PMID:33399513
TriRNSC: triclustering of gene expression microarray data using restricted neighbourhood search. PMID:33399096
Mitochondrial bioenergetic deficits in C9orf72 amyotrophic lateral sclerosis motor neurons cause dysfunctional axonal homeostasis. PMID:33398403
Computationally predicted SARS-COV-2 encoded microRNAs target NFKB, JAK/STAT and TGFB signaling pathways. PMID:33398248
The Rcs stress response inversely controls surface and CRISPR-Cas adaptive immunity to discriminate plasmids and phages. PMID:33398095
Analysing the mechanism of mitochondrial oxidation-induced cell death using a multifunctional iridium(III) photosensitiser. PMID:33397915
Whole-Transcriptome RNA Sequencing Reveals the Global Molecular Responses and CeRNA Regulatory Network of mRNAs, lncRNAs, miRNAs and circRNAs in Response to Salt Stress in Sugar Beet (Beta vulgaris). PMID:33396637
Personalized beyond Precision: Designing Unbiased Gold Standards to Improve Single-Subject Studies of Personal Genome Dynamics from Gene Products. PMID:33396440
Transcriptomic Analysis of a Diabetic Skin-Humanized Mouse Model Dissects Molecular Pathways Underlying the Delayed Wound Healing Response. PMID:33396192
Metagenomics survey unravels diversity of biogas microbiomes with potential to enhance productivity in Kenya. PMID:33395690
DYRK1A regulates B cell acute lymphoblastic leukemia through phosphorylation of FOXO1 and STAT3. PMID:33393494
Immunological Role and Prognostic Value of APBB1IP in Pan-Cancer Analysis. PMID:33391455
Specific MiRNAs in naïve T cells associated with Hepatitis C Virus-induced Hepatocellular Carcinoma. PMID:33391397
RNA-Seq used to identify ipsdienone reductase (IDONER): A novel monoterpene carbon-carbon double bond reductase central to Ips confusus pheromone production. PMID:33388375
IFI27 may predict and evaluate the severity of respiratory syncytial virus infection in preterm infants. PMID:33388093
The Interactome of Cancer-Related Lysyl Oxidase and Lysyl Oxidase-Like Proteins. PMID:33383846
The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling. PMID:33378765
Effect of let-7c on the PI3K/Akt/FoxO signaling pathway in hepatocellular carcinoma. PMID:33376529
Identifying an Eight-Gene Signature to Optimize Overall Survival Prediction of Esophageal Adenocarcinoma Using Bioinformatics Analysis of ceRNA Network. PMID:33376353
Application of Biological Domain Knowledge Based Feature Selection on Gene Expression Data. PMID:33374969
Novel therapeutic compounds for prostate adenocarcinoma treatment: An analysis using bioinformatic approaches and the CMap database. PMID:33371142
Metric Labeling and Semimetric Embedding for Protein Annotation Prediction. PMID:33370163
Large-fragment insertion activates gene GaFZ (Ga08G0121) and is associated with the fuzz and trichome reduction in cotton (Gossypium arboreum). PMID:33369825
FIGNL1 promotes non‑small cell lung cancer cell proliferation. PMID:33367932
Proteome of the Triatomine Digestive Tract: From Catalytic to Immune Pathways; Focusing on Annexin Expression. PMID:33363206
iTRAQ-Based Phosphoproteomic Analysis of Toxoplasma gondii Tachyzoites Provides Insight Into the Role of Phosphorylation for its Invasion and Egress. PMID:33363051
Transcriptome Analysis of Juvenile Tilapia (Oreochromis niloticus) Blood, Fed With Different Concentrations of Resveratrol. PMID:33362577
Comprehensive Profiling of Gene Expression in the Cerebral Cortex and Striatum of BTBRTF/ArtRbrc Mice Compared to C57BL/6J Mice. PMID:33362469
Predictive network modeling in human induced pluripotent stem cells identifies key driver genes for insulin responsiveness. PMID:33362275
Salmonella enterica Serovars Dublin and Enteritidis Comparative Proteomics Reveals Differential Expression of Proteins Involved in Stress Resistance, Virulence, and Anaerobic Metabolism. PMID:33361201
A primer for generating and using transcriptome data and gene sets. PMID:33361089
Global insights to drought stress perturbed genes in oat (Avena sativa L.) seedlings using RNA sequencing. PMID:33356830
Knowledge Organization Systems for Systematic Chemical Assessments. PMID:33356525
Generation of an Interactome for the Tetratricopeptide Repeat Domain of O-GlcNAc Transferase Indicates a Role for the Enzyme in Intellectual Disability. PMID:33356293
Comparative genomics reveals dynamic genome evolution in host specialist ectomycorrhizal fungi. PMID:33355923
IiWRKY34 positively regulates yield, lignan biosynthesis and stress tolerance in Isatis indigotica. PMID:33354511
Fully Automated Sample Processing and Analysis Workflow for Low-Input Proteome Profiling. PMID:33352054
Multi-resolution visualization and analysis of biomolecular networks through hierarchical community detection and web-based graphical tools. PMID:33351828
ARPIR: automatic RNA-Seq pipelines with interactive report. PMID:33349239
Tumors Widely Express Hundreds of Embryonic Germline Genes. PMID:33348709
A review on viral data sources and search systems for perspective mitigation of COVID-19. PMID:33348368
Systematic review and meta-analysis of human transcriptomics reveals neuroinflammation, deficient energy metabolism, and proteostasis failure across neurodegeneration. PMID:33347974
A stress-induced tyrosine-tRNA depletion response mediates codon-based translational repression and growth suppression. PMID:33346941
Identification of Key Modules and Hub Genes Involved in Esophageal Squamous Cell Carcinoma Tumorigenesis Using WCGNA. PMID:33345608
Bioinformatics analysis identifies COL1A1, THBS2 and SPP1 as potential predictors of patient prognosis and immunotherapy response in gastric cancer. PMID:33345281
Ubiquitin-Like Modifier Activating Enzyme 1 as a Novel Diagnostic and Prognostic Indicator That Correlates With Ferroptosis and the Malignant Phenotypes of Liver Cancer Cells. PMID:33344241
Comprehensive analysis of circRNA expression profiles and circRNA-associated competing endogenous RNA networks in IgA nephropathy. PMID:33344076
Identification of significant genes signatures and prognostic biomarkers in cervical squamous carcinoma via bioinformatic data. PMID:33344075
A Novel Family of Acinetobacter Mega-Plasmids Are Disseminating Multi-Drug Resistance Across the Globe While Acquiring Location-Specific Accessory Genes. PMID:33343549
Episodic Decrease in Temperature Increases mcy Gene Transcription and Cellular Microcystin in Continuous Cultures of Microcystis aeruginosa PCC 7806. PMID:33343544
Transcriptional profiles of human islet and exocrine endothelial cells in subjects with or without impaired glucose metabolism. PMID:33339897
Competition between PRC2.1 and 2.2 subcomplexes regulates PRC2 chromatin occupancy in human stem cells. PMID:33338397
Screening and Identification of Prognostic Tumor-Infiltrating Immune Cells and Genes of Endometrioid Endometrial Adenocarcinoma: Based on The Cancer Genome Atlas Database and Bioinformatics. PMID:33335850
Upregulation of 5'-terminal oligopyrimidine mRNA translation upon loss of the ARF tumor suppressor. PMID:33335292
Cerina: systematic circRNA functional annotation based on integrative analysis of ceRNA interactions. PMID:33335165
Biological and physical approaches on the role of piplartine (piperlongumine) in cancer. PMID:33335138
The identification of co-expressed gene modules in Streptococcus pneumonia from colonization to infection to predict novel potential virulence genes. PMID:33334315
GAS2L1 Is a Potential Biomarker of Circulating Tumor Cells in Pancreatic Cancer. PMID:33333841
A Machine Learning Approach for Tracing Tumor Original Sites With Gene Expression Profiles. PMID:33330438
CD8+ T Cell Co-Expressed Genes Correlate With Clinical Phenotype and Microenvironments of Urothelial Cancer. PMID:33330025
Identification of Tumor Microenvironment-Related Prognostic Biomarkers in Luminal Breast Cancer. PMID:33329695
Creation of bladder assembloids mimicking tissue regeneration and cancer. PMID:33328632
A chromosome-scale reference genome of Lobularia maritima, an ornamental plant with high stress tolerance. PMID:33328471
Expression and Possible Molecular Mechanisms of microRNA-205-5p in Patients With Head and Neck Squamous Cell Carcinoma. PMID:33327871
Identification of Hub Genes of Mesio Temporal Lobe Epilepsy and Prognostic Biomarkers of Brain Low-grade Gliomas Based on Bioinformatics Analysis. PMID:33327771
Baseline SUVmax is related to tumor cell proliferation and patient outcome in follicular lymphoma. PMID:33327711
Comprehensive Transcriptomic Analysis Reveals Dysregulated Competing Endogenous RNA Network in Endocrine Resistant Breast Cancer Cells. PMID:33324567
Genetic Determinants of Gating Functions: Do We Get Closer to Understanding Schizophrenia Etiopathogenesis? PMID:33324248
Ancient microRNA profiles of a 14,300-year-old canid samples confirm taxonomic origin and give glimpses into tissue-specific gene regulation from the Pleistocene. PMID:33323528
Characterisation of gene and pathway expression in stabilised blood from children with coeliac disease. PMID:33323471
PEREGRINE: A genome-wide prediction of enhancer to gene relationships supported by experimental evidence. PMID:33320871
Distinct genomic profiles of gestational choriocarcinoma, a unique cancer of pregnant tissues. PMID:33319857
Outlier concepts auditing methodology for a large family of biomedical ontologies. PMID:33319713
Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies. PMID:33319712
Analysis of readability and structural accuracy in SNOMED CT. PMID:33319711
Missing lateral relationships in top-level concepts of an ontology. PMID:33319709
Extending import detection algorithms for concept import from two to three biomedical terminologies. PMID:33319702
Genome-wide correlation analysis to identify amplitude regulators of circadian transcriptome output. PMID:33318596
Olfactomedin 4 mediation of prostate stem/progenitor-like cell proliferation and differentiation via MYC. PMID:33318499
Identification of long non-coding RNA signatures for squamous cell carcinomas and adenocarcinomas. PMID:33318305
Hearing impairment due to Mir183/96/182 mutations suggests both loss and gain of function effects. PMID:33318051
Micronutrient supplementation affects transcriptional and epigenetic regulation of lipid metabolism in a dose-dependent manner. PMID:33315488
Hierarchical Canonical Correlation Analysis Reveals Phenotype, Genotype, and Geoclimate Associations in Plants. PMID:33313545
Computing on Phenotypic Descriptions for Candidate Gene Discovery and Crop Improvement. PMID:33313544
A bioinformatics analysis on the potential role of ACE2 in cardiac impairment of patients with coronavirus disease 2019. PMID:33313148
GWAS and Beyond: Using Omics Approaches to Interpret SNP Associations. PMID:33312764
Transcriptomic Profiling of Human Pluripotent Stem Cell-derived Retinal Pigment Epithelium over Time. PMID:33307245
The leukocyte non-coding RNA landscape in critically ill patients with sepsis. PMID:33305733
Immunogenetic and tolerance strategies against a novel parasitoid of wild field crickets. PMID:33304539
Draft Genome Sequence of Lactobacillus salivarius KZ-NCB, Isolated from Chicken Cecum. PMID:33303665
GCNG: graph convolutional networks for inferring gene interaction from spatial transcriptomics data. PMID:33303016
Composition and origin of lung fluid proteome in premature infants and relationship to respiratory outcome. PMID:33301538
Genome-wide investigation of the dynamic changes of epigenome modifications after global DNA methylation editing. PMID:33300025
ideal: an R/Bioconductor package for interactive differential expression analysis. PMID:33297942
Identification of an RNA binding protein-related gene signature in hepatocellular carcinoma patients. PMID:33297932
Integrated Physiological and Transcriptomic Analyses Reveal a Regulatory Network of Anthocyanin Metabolism Contributing to the Ornamental Value in a Novel Hybrid Cultivar of Camellia Japonica. PMID:33297392
COPD patients with chronic bronchitis and higher sputum eosinophil counts show increased type-2 and PDE4 gene expression in sputum. PMID:33295083
An Integrated Bioinformatic Analysis of the S100 Gene Family for the Prognosis of Colorectal Cancer. PMID:33294444
Network Pharmacology-Based Study on the Mechanism of Gegen Qinlian Decoction against Colorectal Cancer. PMID:33294000
Nuclear numbers in syncytial muscle fibers promote size but limit the development of larger myonuclear domains. PMID:33293533
Donkey genomes provide new insights into domestication and selection for coat color. PMID:33293529
PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API. PMID:33290554
Expression patterns and prognostic values of the cyclin-dependent kinase 1 and cyclin A2 gene cluster in pancreatic adenocarcinoma. PMID:33290118
Bioinformatic analysis of key pathways and genes involved in pediatric atopic dermatitis. PMID:33289509
Hidden in plain sight: The effects of BCG vaccination in the COVID-19 pandemic. PMID:33289122
Comparative transcriptome analysis of three gonadal development stages reveals potential genes involved in gametogenesis of the fluted giant clam (Tridacna squamosa). PMID:33287701
Transcriptome Remodeling in Gradual Development of Inverse Resistance between Paclitaxel and Cisplatin in Ovarian Cancer Cells. PMID:33287223
TMEA: A Thermodynamically Motivated Framework for Functional Characterization of Biological Responses to System Acclimation. PMID:33286800
Fifteen Years of Gene Set Analysis for High-Throughput Genomic Data: A Review of Statistical Approaches and Future Challenges. PMID:33286201
Chronic circadian shift leads to adipose tissue inflammation and fibrosis. PMID:33285245
Assembly of the non-heading pak choi genome and comparison with the genomes of heading Chinese cabbage and the oilseed yellow sarson. PMID:33283404
TTK, CDC25A, and ESPL1 as Prognostic Biomarkers for Endometrial Cancer. PMID:33282948
Identification of Dysregulated Genes for Late-Onset Alzheimer's Disease Using Gene Expression Data in Brain. PMID:33282526
Network Pharmacology Identifies the Mechanisms of Action of Tongxie Anchang Decoction in the Treatment of Irritable Bowel Syndrome with Diarrhea Predominant. PMID:33281910
Comparative Genomics Analysis Provides New Strategies for Bacteriostatic Ability of Bacillus velezensis HAB-2. PMID:33281792
Role of COL3A1 and POSTN on Pathologic Stages of Esophageal Cancer. PMID:33280513
Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus. PMID:33280122
Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity. PMID:33278344
Intercellular Mitochondria Transfer to Macrophages Regulates White Adipose Tissue Homeostasis and Is Impaired in Obesity. PMID:33278339
A Novel Proximity Biotinylation Assay Based on the Self-Associating Split GFP1-10/11. PMID:33276494
Targeted inhibition of ERα signaling and PIP5K1α/Akt pathways in castration-resistant prostate cancer. PMID:33275817
High levels of glucose alter Physcomitrella patens metabolism and trigger a differential proteomic response. PMID:33275616
Urinary vitronectin identifies patients with high levels of fibrosis in kidney grafts. PMID:33275196
Informatics Inference of Exercise-Induced Modulation of Brain Pathways Based on Cerebrospinal Fluid Micro-RNAs in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome. PMID:33274349
CovMulNet19, Integrating Proteins, Diseases, Drugs, and Symptoms: A Network Medicine Approach to COVID-19. PMID:33274348
Screening of T Cell-Related Long Noncoding RNA-MicroRNA-mRNA Regulatory Networks in Non-Small-Cell Lung Cancer. PMID:33274216
Identification of Monotonically Differentially Expressed Genes across Pathologic Stages for Cancers. PMID:33273919
NLRP3 inflammasome deficiency attenuates metabolic disturbances involving alterations in the gut microbial profile in mice exposed to high fat diet. PMID:33273482
The transcriptional repressors VAL1 and VAL2 recruit PRC2 for genome-wide Polycomb silencing in Arabidopsis. PMID:33270882
COVID-19 Knowledge Extractor (COKE): A Tool and a Web Portal to Extract Drug - Target Protein Associations from the CORD-19 Corpus of Scientific Publications on COVID-19. PMID:33269341
Reprogramming to recover youthful epigenetic information and restore vision. PMID:33268865
Humoral immune responses mediate the development of a restrictive phenotype of chronic lung allograft dysfunction. PMID:33268593
Supervised and Unsupervised End-to-End Deep Learning for Gene Ontology Classification of Neural In Situ Hybridization Images. PMID:33266936
Comparative Analysis of the Global Transcriptomic Response to Oxidative Stress of Bacillus anthracis htrA-Disrupted and Parental Wild Type Strains. PMID:33265965
YAP/TAZ deficiency reprograms macrophage phenotype and improves infarct healing and cardiac function after myocardial infarction. PMID:33264286
Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure. PMID:33262328
Transcriptome Sequencing and Comparative Analysis of Amphoteric ESCs and PGCs in Chicken (Gallus gallus). PMID:33261034
A hybrid approach toward biomedical relation extraction training corpora: combining distant supervision with crowdsourcing. PMID:33258966
Regulators of TNFα mediated insulin resistance elucidated by quantitative proteomics. PMID:33257747
Wide-ranging transcriptomic analysis of Poncirus trifoliata, Citrus sunki, Citrus sinensis and contrasting hybrids reveals HLB tolerance mechanisms. PMID:33257732
What Can Machine Learning Approaches in Genomics Tell Us about the Molecular Basis of Amyotrophic Lateral Sclerosis? PMID:33256133
MiR-215-5p Reduces Liver Metastasis in an Experimental Model of Colorectal Cancer through Regulation of ECM-Receptor Interactions and Focal Adhesion. PMID:33255928
Essential gene prediction using limited gene essentiality information-An integrative semi-supervised machine learning strategy. PMID:33253254
Mining GWAS and eQTL data for CF lung disease modifiers by gene expression imputation. PMID:33253230
Evolved bacterial resistance against fluoropyrimidines can lower chemotherapy impact in the Caenorhabditis elegans host. PMID:33252330
Dataset of full-length transcriptome assembly and annotation of apocynum venetum using pacbio sequel II. PMID:33251304
Identification of hsa-miR-1275 as a Novel Biomarker Targeting MECP2 for Human Epilepsy of Unknown Etiology. PMID:33251277
Transferrin Receptor Functionally Marks Thermogenic Adipocytes. PMID:33251209
Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome. PMID:33247132
RNA-mediated control of cell shape modulates antibiotic resistance in Vibrio cholerae. PMID:33247102
Transcriptome and proteome profiling reveal complementary scavenger and immune features of rat liver sinusoidal endothelial cells and liver macrophages. PMID:33246411
MicroRNA-based regulation of Aurora A kinase in breast cancer. PMID:33245732
Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer. PMID:33242424
Comprehensive Multi-omics Analysis Reveals Mitochondrial Stress as a Central Biological Hub for Spaceflight Impact. PMID:33242417
MutRank: an R shiny web-application for exploratory targeted mutual rank-based coexpression analyses integrated with user-provided supporting information. PMID:33240618
Polyphyllin VII suppresses cell proliferation, the cell cycle and cell migration in colorectal cancer. PMID:33240431
Functional characterisation of the transcriptome from leaf tissue of the fluoroacetate-producing plant, Dichapetalum cymosum, in response to mechanical wounding. PMID:33239700
Improving existing analysis pipeline to identify and analyze cancer driver genes using multi-omics data. PMID:33239644
Integrative genomic meta-analysis reveals novel molecular insights into cystic fibrosis and ΔF508-CFTR rescue. PMID:33239626
Identifying transcriptomic correlates of histology using deep learning. PMID:33237966
A thorough analysis of the contribution of experimental, derived and sequence-based predicted protein-protein interactions for functional annotation of proteins. PMID:33237964
Integration of the Drug-Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts. PMID:33237278
Insights into amphicarpy from the compact genome of the legume Amphicarpaea edgeworthii. PMID:33236503
Anti-inflammatory activity of Radix Angelicae biseratae in the treatment of osteoarthritis determined by systematic pharmacology and in vitro experiments. PMID:33235614
Reduced lipolysis in lipoma phenocopies lipid accumulation in obesity. PMID:33235355
Recent evolution of a TET-controlled and DPPA3/STELLA-driven pathway of passive DNA demethylation in mammals. PMID:33235224
CD74, a novel predictor for bronchopulmonary dysplasia in preterm infants. PMID:33235138
Donor-Specific Transcriptomic Analysis of Alzheimer's Disease-Associated Hypometabolism Highlights a Unique Donor, Ribosomal Proteins and Microglia. PMID:33234543
The Mediation of miR-34a/miR-449c for Immune Cytokines in Acute Cold/Heat-Stressed Broiler Chicken. PMID:33233727
Physiological Changes in Barley mlo-11 Powdery Mildew Resistance Conditioned by Tandem Repeat Copy Number. PMID:33233522
Epigenome-wide association scan identifies methylation sites associated with HIV infection. PMID:33232214
NECAB1 and NECAB2 are Prevalent Calcium-Binding Proteins of CB1/CCK-Positive GABAergic Interneurons. PMID:33230531
Conjoint Feature Representation of GO and Protein Sequence for PPI Prediction Based on an Inception RNN Attention Network. PMID:33230427
Haematopoietic stem cell-dependent Notch transcription is mediated by p53 through the Histone chaperone Supt16h. PMID:33230303
Spatial profiling of gastric cancer patient-matched primary and locoregional metastases reveals principles of tumour dissemination. PMID:33229445
Chicken cecal DNA methylome alteration in the response to Salmonella enterica serovar Enteritidis inoculation. PMID:33225883
Exploring biomarkers and therapeutic targets for pressure overload induced heart failure based on microarray data. PMID:33224746
Comprehensive proteomic atlas of skin biomatrix scaffolds reveals a supportive microenvironment for epidermal development. PMID:33224464
Investigation of the Potential Mechanism Governing the Effect of the Shen Zhu San on COVID-19 by Network Pharmacology. PMID:33224256
In-depth transcriptomic analyses of LncRNA and mRNA expression in the hippocampus of APP/PS1 mice by Danggui-Shaoyao-San. PMID:33221745
MolluscDB: an integrated functional and evolutionary genomics database for the hyper-diverse animal phylum Mollusca. PMID:33219670
A network-based comparative framework to study conservation and divergence of proteomes in plant phylogenies. PMID:33219668
Identification of Natural CRISPR Systems and Targets in the Human Microbiome. PMID:33217332
Vascular neutrophilic inflammation and immunothrombosis distinguish severe COVID-19 from influenza pneumonia. PMID:33217134
Predicted rat interactome database and gene set linkage analysis. PMID:33216897
Genome Sequence of Klebsiella pneumoniae YBQ, a Clinical Strain Isolated from the Sputum of a Patient with Severe Pneumonia. PMID:33214313
Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy. PMID:33212010
Prognostic Implication of a Metabolism-Associated Gene Signature in Lung Adenocarcinoma. PMID:33209981
Leaf shape in Populus tremula is a complex, omnigenic trait. PMID:33209260
Machine learning approaches reveal genomic regions associated with sugarcane brown rust resistance. PMID:33208862
ClusterM: a scalable algorithm for computational prediction of conserved protein complexes across multiple protein interaction networks. PMID:33208103
Functional Specialization of Human Salivary Glands and Origins of Proteins Intrinsic to Human Saliva. PMID:33207190
A Selective Autophagy Pathway for Phase-Separated Endocytic Protein Deposits. PMID:33207182
Genome-wide profiling of alternative splicing genes in hybrid poplar (P.alba×P.glandulosa cv.84K) leaves. PMID:33206683
DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier. PMID:33206638
LINC01235-TWIST2 feedback loop facilitates epithelial-mesenchymal transition in gastric cancer by inhibiting THBS2. PMID:33206629
Urinary glycoproteins associated with aggressive prostate cancer. PMID:33204318
Ensemble dimensionality reduction and feature gene extraction for single-cell RNA-seq data. PMID:33203837
Widespread regulation of gene expression by glucocorticoids in chondrocytes from patients with osteoarthritis as determined by RNA-Seq. PMID:33203447
Microarray expression profile analysis of circular RNAs and their potential regulatory role in bladder carcinoma. PMID:33200221
Genome-Wide Functional Screen for Calcium Transients in Escherichia coli Identifies Increased Membrane Potential Adaptation to Persistent DNA Damage. PMID:33199283
RBP2GO: a comprehensive pan-species database on RNA-binding proteins, their interactions and functions. PMID:33196814
NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants. PMID:33196801
A comparison of mRNA and circRNA expression between squamous cell carcinoma and adenocarcinoma of the lungs. PMID:33196759
Transcriptomic Data Analyses Reveal a Reprogramed Lipid Metabolism in HCV-Derived Hepatocellular Cancer. PMID:33195224
Epidermal Growth Factor Is Essential for the Maintenance of Novel Prostate Epithelial Cells Isolated From Patient-Derived Organoids. PMID:33195205
Proteomic Analysis of Exosome-Like Vesicles Isolated From Saliva of the Tick Haemaphysalis longicornis. PMID:33194791
Integrated transcriptome meta-analysis of pancreatic ductal adenocarcinoma and matched adjacent pancreatic tissues. PMID:33194391
Involvement of the Wnt/β-Catenin signaling pathway in the heterogenous nuclear ribonucleoprotein K-driven inhibition of proliferation and migration in head and neck squamous cell carcinoma. PMID:33193854
Transcriptome Analyses of β-Thalassemia -28(A>G) Mutation Using Isogenic Cell Models Generated by CRISPR/Cas9 and Asymmetric Single-Stranded Oligodeoxynucleotides (assODNs). PMID:33193694
Recurrent Drought Conditions Enhance the Induction of Drought Stress Memory Genes in Glycine max L. PMID:33193691
The Cyclically Seasonal Drosophila subobscura Inversion O7 Originated From Fragile Genomic Sites and Relocated Immunity and Metabolic Genes. PMID:33193649
Identification of RNA Transcript Makers Associated With Prognosis of Kidney Renal Clear Cell Carcinoma by a Competing Endogenous RNA Network Analysis. PMID:33193613
Identification of Potential Core Genes Associated With the Progression of Stomach Adenocarcinoma Using Bioinformatic Analysis. PMID:33193601
Hub Genes Identification in a Murine Model of Allergic Rhinitis Based on Bioinformatics Analysis. PMID:33193578
Transcriptomic Profiling of Mouse Brain During Acute and Chronic Infections by Toxoplasma gondii Oocysts. PMID:33193165
Inflammatory Response of Ischemic Tolerance in Circulating Plasma: Preconditioning-Induced by Transient Ischemic Attack (TIA) Phenomena in Acute Ischemia Patients (AIS). PMID:33192985
Embedding-based Silhouette community detection. PMID:33191975
Molecular estimation of neurodegeneration pseudotime in older brains. PMID:33188183
Dedifferentiation and neuronal repression define familial Alzheimer's disease. PMID:33188013
Virtual screening and network pharmacology-based synergistic mechanism identification of multiple components contained in Guanxin V against coronary artery disease. PMID:33187508
Quantitative Interactomics of Lck-TurboID in Living Human T Cells Unveils T Cell Receptor Stimulation-Induced Proximal Lck Interactors. PMID:33185455
The ZSWIM8 ubiquitin ligase mediates target-directed microRNA degradation. PMID:33184237
Gene Expression Signatures in AML-12 Hepatocyte Cells upon Dengue virus Infection and Acetaminophen Treatment. PMID:33182673
A Collection of Benchmark Data Sets for Knowledge Graph-based Similarity in the Biomedical Domain. PMID:33181823
Establishment of immune prognostic signature and analysis of prospective molecular mechanisms in childhood osteosarcoma patients. PMID:33181717
FunRes: resolving tissue-specific functional cell states based on a cell-cell communication network model. PMID:33179736
ID1 As a Prognostic Biomarker and Promising Drug Target Plays a Pivotal Role in Deterioration of Clear Cell Renal Cell Carcinoma. PMID:33178820
Bioinformatic Analysis Identifies Potential Key Genes in the Pathogenesis of Melanoma. PMID:33178610
Prolonged Targeted Cardiovascular Epidural Stimulation Improves Immunological Molecular Profile: A Case Report in Chronic Severe Spinal Cord Injury. PMID:33177997
Avian Immunome DB: an example of a user-friendly interface for extracting genetic information. PMID:33176685
Decoding myofibroblast origins in human kidney fibrosis. PMID:33176333
Insulin-promoted mobilization of GLUT4 from a perinuclear storage site requires RAB10. PMID:33175605
COVID-KOP: integrating emerging COVID-19 data with the ROBOKOP database. PMID:33175089
Anti‑inflammatory mechanism of berberine on lipopolysaccharide‑induced IEC‑18 models based on comparative transcriptomics. PMID:33174609
Co‑expression network analysis identified specific miRNAs and genes in association with slow‑transit constipation. PMID:33174045
Upregulated lnc‑HRK‑2:1 prompts nucleus pulposus cell senescence in intervertebral disc degeneration. PMID:33174041
Identification of inflammation‑associated circulating long non‑coding RNAs and genes in intracranial aneurysm rupture‑induced subarachnoid hemorrhage. PMID:33174039
Using mRNA deep sequencing to analyze differentially expressed genes during Panax notoginseng saponin treatment of ischemic stroke. PMID:33173991
Integrated microarray analysis of key genes and a miRNA‑mRNA regulatory network of early‑onset preeclampsia. PMID:33173953
Lung transcriptome of a COVID-19 patient and systems biology predictions suggest impaired surfactant production which may be druggable by surfactant therapy. PMID:33173052
Transcriptional Effects of Psychoactive Drugs on Genes Involved in Neurogenesis. PMID:33172123
Deciphering cell-cell interactions and communication from gene expression. PMID:33168968
Reprogramming of bone marrow myeloid progenitor cells in patients with severe coronary artery disease. PMID:33168134
A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection. PMID:33166281
Systematic Analysis of Protein-Protein and Gene-Environment Interactions to Decipher the Cognitive Mechanisms of Autism Spectrum Disorder. PMID:33165687
CYP27B1 Downregulation: A New Molecular Mechanism Regulating EZH2 in Ovarian Cancer Tumorigenicity. PMID:33163485
Expression Changes in Epigenetic Gene Pathways Associated With One-Carbon Nutritional Metabolites in Maternal Blood From Pregnancies Resulting in Autism and Non-Typical Neurodevelopment. PMID:33159718
CSF1R inhibition depletes tumor-associated macrophages and attenuates tumor progression in a mouse sonic Hedgehog-Medulloblastoma model. PMID:33159168
Bioinformatics-based identification of miRNA-, lncRNA-, and mRNA-associated ceRNA networks and potential biomarkers for preeclampsia. PMID:33157942
CLAVATA Signaling Ensures Reproductive Development in Plants across Thermal Environments. PMID:33157018
Lipopolysaccharide triggers different transcriptional signatures in taurine and indicine cattle macrophages: Reactive oxygen species and potential outcomes to the development of immune response to infections. PMID:33156842
TCRD and Pharos 2021: mining the human proteome for disease biology. PMID:33156327
Argonaut: A Web Platform for Collaborative Multi-omic Data Visualization and Exploration. PMID:33154995
Deep learning approach for predicting functional Z-DNA regions using omics data. PMID:33154517
Full function of exon junction complex factor, Rbm8a, is critical for interneuron development. PMID:33154347
The Transcriptome of Cunninghamia lanceolata male/female cone reveal the association between MIKC MADS-box genes and reproductive organs development. PMID:33153428
RNA Sequencing Reveals Diverse Functions of Amniotic Fluid Neutrophils and Monocytes/Macrophages in Intra-Amniotic Infection. PMID:33152737
DrugCentral 2021 supports drug discovery and repositioning. PMID:33151287
Constitution of a comprehensive phytochemical profile and network pharmacology based investigation to decipher molecular mechanisms of Teucrium polium L. in the treatment of type 2 diabetes mellitus. PMID:33150068
In-depth transcriptome reveals the potential biotechnological application of Bothrops jararaca venom gland. PMID:33149734
Desmoglein 3 and Keratin 14 for Distinguishing Between Lung Adenocarcinoma and Lung Squamous Cell Carcinoma. PMID:33149622
Circulating miR-1246 in the Progression of Chronic Obstructive Pulmonary Disease (COPD) in Patients from the BODE Cohort. PMID:33149570
Singular manifolds of proteomic drivers to model the evolution of inflammatory bowel disease status. PMID:33149233
Loss of PHF6 leads to aberrant development of human neuron-like cells. PMID:33149206
Systematic elucidation of neuron-astrocyte interaction in models of amyotrophic lateral sclerosis using multi-modal integrated bioinformatics workflow. PMID:33149111
Integrated Bioinformatics Analysis of Hub Genes and Pathways Associated with a Compression Model of Spinal Cord Injury in Rats. PMID:33149108
Blocking IL1 Beta Promotes Tumor Regression and Remodeling of the Myeloid Compartment in a Renal Cell Carcinoma Model: Multidimensional Analyses. PMID:33148676
Ubiquitinome Profiling Reveals the Landscape of Ubiquitination Regulation in Rice Young Panicles. PMID:33147495
Bone marrow microenvironments that contribute to patient outcomes in newly diagnosed multiple myeloma: A cohort study of patients in the Total Therapy clinical trials. PMID:33147277
Exploration in the Mechanism of Kaempferol for the Treatment of Gastric Cancer Based on Network Pharmacology. PMID:33145355
Investigation of hub genes involved in diabetic nephropathy using biological informatics methods. PMID:33145306
The draft genome of the blood pheasant (Ithaginis cruentus): Phylogeny and high-altitude adaptation. PMID:33144976
Transcriptomic profiling of feline teeth highlights the role of matrix metalloproteinase 9 (MMP9) in tooth resorption. PMID:33144645
Container-aided integrative QTL and RNA-seq analysis of Collaborative Cross mice supports distinct sex-oriented molecular modes of response in obesity. PMID:33143653
The Role of Salmonella Genomic Island 4 in Metal Tolerance of Salmonella enterica Serovar I 4,[5],12:i:- Pork Outbreak Isolate USDA15WA-1. PMID:33142960
Transcriptomic responses from improved murine sepsis models can better mimic human surgical sepsis. PMID:33140449
Type I Interferon Transcriptional Network Regulates Expression of Coinhibitory Receptors in Human T cells. PMID:33140047
Towards a foundational representation of potential drug-drug interaction knowledge. PMID:33139970
Proximity labeling in mammalian cells with TurboID and split-TurboID. PMID:33139955
Bacterial-fungal interactions revealed by genome-wide analysis of bacterial mutant fitness. PMID:33139882
β-Catenin signaling dynamics regulate cell fate in differentiating neural stem cells. PMID:33139571
A fully automated high-throughput workflow for 3D-based chemical screening in human midbrain organoids. PMID:33138918
Dual genome-wide CRISPR knockout and CRISPR activation screens identify mechanisms that regulate the resistance to multiple ATR inhibitors. PMID:33137164
Differential transcript usage in the Parkinson's disease brain. PMID:33137089
Quorum Sensing System in Bacteroides thetaiotaomicron Strain Identified by Genome Sequence Analysis. PMID:33134713
High Expression of UBB, RAC1, and ITGB1 Predicts Worse Prognosis among Nonsmoking Patients with Lung Adenocarcinoma through Bioinformatics Analysis. PMID:33134373
The Model of PPARγ-Downregulated Signaling in Psoriasis. PMID:33133175
A Systems Biology Approach to Identifying a Master Regulator That Can Transform the Fast Growing Cellular State to a Slowly Growing One in Early Colorectal Cancer Development Model. PMID:33133158
Identification of the Significant Genes Regulated by Estrogen Receptor in Estrogen Receptor-Positive Breast Cancer and Their Expression Pattern Changes When Tamoxifen or Fulvestrant Resistance Occurs. PMID:33133141
Plasma Proteome Responses in Salmonid Fish Following Immunization. PMID:33133099
Warming Climate Is Reducing the Diversity of Dominant Microbes in the Largest High Arctic Lake. PMID:33133035
Epitope prediction and identification- adaptive T cell responses in humans. PMID:33131981
System-level analyses of keystone genes required for mammalian tooth development. PMID:33128445
Higher miR-543 levels correlate with lower STK31 expression and longer pancreatic cancer survival. PMID:33128354
PAR-TERRA is the main contributor to telomeric repeat-containing RNA transcripts in normal and cancer mouse cells. PMID:33127860
Bufalin exerts antitumor effects in neuroblastoma via the induction of reactive oxygen species‑mediated apoptosis by targeting the electron transport chain. PMID:33125107
Characteristic and Phylogenetic Analysis of the Complete Chloroplast Genomes of Three Medicinal Plants of Schisandraceae. PMID:33123569
Transcriptome Profiling-Based Analysis of Carbohydrate-Active Enzymes in Aspergillus terreus Involved in Plant Biomass Degradation. PMID:33123513
Functional in vivo and in vitro effects of 20q11.21 genetic aberrations on hPSC differentiation. PMID:33122739
Paternal reprogramming-escape histone H3K4me3 marks located within promoters of RNA splicing genes. PMID:33119058
Transcriptome and proteome mapping in the sheep atria reveal molecular featurets of atrial fibrillation progression. PMID:33119050
Identification of key genes and pathways for melanoma in the TRIM family. PMID:33118318
A Phylogenetic Rate Parameter Indicates Different Sequence Divergence Patterns in Orthologs and Paralogs. PMID:33118098
Common Adaptive Strategies Underlie Within-Host Evolution of Bacterial Pathogens. PMID:33118035
OsteoBLAST: Computational Routine of Global Molecular Analysis Applied to Biomaterials Development. PMID:33117780
On the Logical Design of a Prototypical Data Lake System for Biological Resources. PMID:33117777
Increased M1 Macrophages Infiltration Correlated With Poor Survival Outcomes and Radiation Response in Gliomas. PMID:33117094
RUNX3 methylation drives hypoxia-induced cell proliferation and antiapoptosis in early tumorigenesis. PMID:33116296
Murine interfollicular epidermal differentiation is gradualistic with GRHL3 controlling progression from stem to transition cell states. PMID:33116143
Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells. PMID:33116115
Systematic Investigation of Resistance Evolution to Common Antibiotics Reveals Conserved Collateral Responses across Common Human Pathogens. PMID:33106260
Computational Identification of Human Biological Processes and Protein Sequence Motifs Putatively Targeted by SARS-CoV-2 Proteins Using Protein-Protein Interaction Networks. PMID:33103435
A curated list of genes that affect the plant ionome. PMID:33103043
Genomic and transcriptomic landscapes and evolutionary dynamics of molluscan glycoside hydrolase families with implications for algae-feeding biology. PMID:33101612
Plasmatic Membrane Expression of Adhesion Molecules in Human Cardiac Progenitor/Stem Cells Might Explain Their Superior Cell Engraftment after Cell Transplantation. PMID:33101423
Systematic Identification of Hub Genes in Placenta Accreta Spectrum Based on Integrated Transcriptomic and Proteomic Analysis. PMID:33101378
Haplotype Block Analysis Reveals Candidate Genes and QTLs for Meat Quality and Disease Resistance in Chinese Jiangquhai Pig Breed. PMID:33101353
Transcriptomic profile of Pea3 family members reveal regulatory codes for axon outgrowth and neuronal connection specificity. PMID:33097800
Predicting Drug Response and Synergy Using a Deep Learning Model of Human Cancer Cells. PMID:33096023
Meta-analysis of Transcriptomic Data Reveals Pathophysiological Modules Involved with Atrial Fibrillation. PMID:33095430
The efficacy of chemotherapeutic drug combinations may be predicted by concordance of gene response to the single agents. PMID:33093925
Maximized quantitative phosphoproteomics allows high confidence dissection of the DNA damage signaling network. PMID:33093574
A genome-wide association study of severe asthma exacerbations in Latino children and adolescents. PMID:33093117
Transcriptome analysis of Actinoplanes utahensis reveals molecular signature of saccharide impact on acarbose biosynthesis. PMID:33088668
Comparative morphological and transcriptomic analyses reveal chemosensory genes in the poultry red mite, Dermanyssus gallinae. PMID:33087814
De novo transcriptome assembly from the gonads of a scleractinian coral, Euphyllia ancora: molecular mechanisms underlying scleractinian gametogenesis. PMID:33087060
Differential gene regulatory pattern in the human brain from schizophrenia using transcriptomic-causal network. PMID:33087039
Dendritic Cells and Microglia Have Non-redundant Functions in the Inflamed Brain with Protective Effects of Type 1 cDCs. PMID:33086061
OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines. PMID:33084874
Integrative Analyses of Genes Associated with Fulminant Type 1 Diabetes. PMID:33083497
Exploration of ovine milk whey proteome during postnatal development using an iTRAQ approach. PMID:33083141
Genomic signatures of globally enhanced gene duplicate accumulation in the megadiverse higher Diptera fueling intralocus sexual conflict resolution. PMID:33083121
Examining the effector mechanisms of Xuebijing injection on COVID-19 based on network pharmacology. PMID:33082858
Mitochondrial-Y chromosome epistasis in Drosophila melanogaster. PMID:33081607
Common gene signatures and key pathways in hypopharyngeal and esophageal squamous cell carcinoma: Evidence from bioinformatic analysis. PMID:33080677
MARS: discovering novel cell types across heterogeneous single-cell experiments. PMID:33077966
Quantifying the distribution of protein oligomerization degree reflects cellular information capacity. PMID:33077848
Predicted functional interactome of Caenorhabditis elegans and a web tool for the functional interpretation of differentially expressed genes. PMID:33076954
SWI/SNF inactivation in the endometrial epithelium leads to loss of epithelial integrity. PMID:33075803
Differential Transcription and Alternative Splicing in Cotton Underly Specialized Defense Responses Against Pests. PMID:33072149
No Assembly Required: Using BTyper3 to Assess the Congruency of a Proposed Taxonomic Framework for the Bacillus cereus Group With Historical Typing Methods. PMID:33072050
Comparative Toxicogenomics Database (CTD): update 2021. PMID:33068428
Sexually dimorphic radiogenomic models identify distinct imaging and biological pathways that are prognostic of overall survival in glioblastoma. PMID:33068415
mRNA and miRNA expression profile reveals the role of miR-31 overexpression in neural stem cell. PMID:33067542
Increased RNA editing in maternal immune activation model of neurodevelopmental disease. PMID:33067431
Integrated Analysis of the Transcriptome and Metabolome of Cecropia obtusifolia: A Plant with High Chlorogenic Acid Content Traditionally Used to Treat Diabetes Mellitus. PMID:33066422
Genome Sequencing of Paecilomyces Penicillatus Provides Insights into Its Phylogenetic Placement and Mycoparasitism Mechanisms on Morel Mushrooms. PMID:33065983
Divergent Resistance Mechanisms to Immunotherapy Explain Responses in Different Skin Cancers. PMID:33065980
Circ-Tulp4 promotes β-cell adaptation to lipotoxicity by regulating soat1 expression. PMID:33064661
Identification of fertility-related genes for maize CMS-S via Bulked Segregant RNA-Seq. PMID:33062436
Bioinformatics-Based Identification of a circRNA-miRNA-mRNA Axis in Esophageal Squamous Cell Carcinomas. PMID:33061972
Identification of G2 and S Phase-Expressed-1 as a Potential Biomarker in Patients with Prostate Cancer. PMID:33061616
Exploration of the Potential Biomarkers of Papillary Thyroid Cancer (PTC) Based on RT2 Profiler PCR Arrays and Bioinformatics Analysis. PMID:33061614
Mapping scientific landscapes in UMLS research: a scientometric review. PMID:33059367
During bacteremia, Pseudomonas aeruginosa PAO1 adapts by altering the expression of numerous virulence genes including those involved in quorum sensing. PMID:33057423
Transcriptome sequencing and screening of genes related to sex determination of Trichosanthes kirilowii Maxim. PMID:33057394
Study of the differentially abundant proteins among Leishmania amazonensis, L. braziliensis, and L. infantum. PMID:33057350
The structural variation landscape in 492 Atlantic salmon genomes. PMID:33056985
smORFunction: a tool for predicting functions of small open reading frames and microproteins. PMID:33054771
Monosomy X in Female Mice Influences the Regional Formation and Augments the Severity of Angiotensin II-Induced Aortopathies. PMID:33054396
The Lethal(2)-Essential-for-Life [L(2)EFL] Gene Family Modulates Dengue Virus Infection in Aedes aegypti. PMID:33053895
Cytosolic TaGAPC2 Enhances Tolerance to Drought Stress in Transgenic Arabidopsis Plants. PMID:33053684
IurV, Encoded by ORF VCA0231, Is Involved in the Regulation of Iron Uptake Genes in Vibrio cholerae. PMID:33053678
A high-throughput CRISPR interference screen for dissecting functional regulators of GPCR/cAMP signaling. PMID:33052901
Free Wanderer Powder regulates AMPA receptor homeostasis in chronic restraint stress-induced rat model of depression with liver-depression and spleen-deficiency syndrome. PMID:33052137
Identification of potential key genes and miRNAs involved in Hepatoblastoma pathogenesis and prognosis. PMID:33051830
Predicting candidate genes from phenotypes, functions and anatomical site of expression. PMID:33051643
Integrated phosphoproteomic and metabolomic profiling reveals perturbed pathways in the hippocampus of gut microbiota dysbiosis mice. PMID:33051451
Semantic similarity and machine learning with ontologies. PMID:33049044
Maximizing cohesion and separation for detecting protein functional modules in protein-protein interaction networks. PMID:33048996
Prediction of a competing endogenous RNA co-expression network as a prognostic marker in glioblastoma. PMID:33047898
Early-pregnancy transcriptome signatures of preeclampsia: from peripheral blood to placenta. PMID:33046794
Electricity from lignocellulosic substrates by thermophilic Geobacillus species. PMID:33046790
Agasicles hygrophila attack increases nerolidol synthase gene expression in Alternanthera philoxeroides, facilitating host finding. PMID:33046727
Characterization of the TyrR Regulon in the Rhizobacterium Enterobacter ludwigii UW5 Reveals Overlap with the CpxR Envelope Stress Response. PMID:33046562
Transcriptome analysis revealed misregulated gene expression in blastoderms of interspecific chicken and Japanese quail F1 hybrids. PMID:33044996
RNA sequence analysis of dermal papilla cells' regeneration in 3D culture. PMID:33038058
The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals. PMID:33037820
In vivo mRNA display enables large-scale proteomics by next generation sequencing. PMID:33037152
Bioinformatic Identification of Potential Hub Genes in Muscle-Invasive Bladder Urothelial Carcinoma. PMID:33035117
Decoding the wheat awn transcriptome and overexpressing TaRca1β in rice for heat stress tolerance. PMID:33034884
Multi-ethnic GWAS and meta-analysis of sleep quality identify MPP6 as a novel gene that functions in sleep center neurons. PMID:33034629
Global gene expression analyses of the alkamide-producing plant Heliopsis longipes supports a polyketide synthase-mediated biosynthesis pathway. PMID:33033663
A review of protein-protein interaction network alignment: From pathway comparison to global alignment. PMID:33033584
Rewiring of gene expression in circulating white blood cells is associated with pregnancy outcome in heifers (Bos taurus). PMID:33033295
A realism-based approach to an ontological representation of symbiotic interactions. PMID:33032576
Graph-based exploitation of gene ontology using GOxploreR for scrutinizing biological significance. PMID:33028846
Identification of a new pseudogenes/lncRNAs-hsa-miR-26b-5p-COL12A1 competing endogenous RNA network associated with prognosis of pancreatic cancer using bioinformatics analysis. PMID:33027767
Root-Secreted Coumarins and the Microbiota Interact to Improve Iron Nutrition in Arabidopsis. PMID:33027611
Compartment-specific transcriptomics of ozone-exposed murine lungs reveals sex- and cell type-associated perturbations relevant to mucoinflammatory lung diseases. PMID:33026818
Development of a Cardiac Sarcomere Functional Genomics Platform to Enable Scalable Interrogation of Human TNNT2 Variants. PMID:33025817
A Novel Proteomic Method Reveals NLS Tagging of T-DM1 Contravenes Classical Nuclear Transport in a Model of HER2-Positive Breast Cancer. PMID:33024794
A high-quality chromosome-level genome assembly reveals genetics for important traits in eggplant. PMID:33024567
Transcript Isoforms of SLC7A11-AS1 Are Associated With Varicocele-Related Male Infertility. PMID:33024440
Perspective: Linkage Maps, Communities of Geneticists, and Genome Databases. PMID:33023927
Identification of Parkinson's disease-related pathways and potential risk factors. PMID:33021140
lncRNAKB, a knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA. PMID:33020484
Genetic circuit characterization by inferring RNA polymerase movement and ribosome usage. PMID:33020480
The Differential Composition of Whey Proteomes in Hu Sheep Colostrum and Milk during Different Lactation Periods. PMID:33019658
Development and Validation of a Novel DNA Methylation-Driven Gene Based Molecular Classification and Predictive Model for Overall Survival and Immunotherapy Response in Patients With Glioblastoma: A Multiomic Analysis. PMID:33015072
Pseudo2GO: A Graph-Based Deep Learning Method for Pseudogene Function Prediction by Borrowing Information From Coding Genes. PMID:33014009
Complete Genome Sequencing and Transcriptome Analysis of Nitrogen Metabolism of Succinivibrio dextrinosolvens Strain Z6 Isolated From Dairy Cow Rumen. PMID:33013723
Screening and Identification of Key Biomarkers in Acquired Lapatinib-Resistant Breast Cancer. PMID:33013420
Creating Neuroscientific Knowledge Organization System Based on Word Representation and Agglomerative Clustering Algorithm. PMID:33013345
Mouse Genetic Reference Populations: Cellular Platforms for Integrative Systems Genetics. PMID:33010949
Human Pluripotent Stem Cell-Derived Neural Cells and Brain Organoids Reveal SARS-CoV-2 Neurotropism Predominates in Choroid Plexus Epithelium. PMID:33010822
Sex-specific epigenetic profile of inner cell mass of mice conceived in vivo or by IVF. PMID:33010164
Genome-Wide Association Analysis of Neonatal White Matter Microstructure. PMID:33009551
Differential network analysis of bovine muscle reveals changes in gene coexpression patterns in response to changes in maternal nutrition. PMID:33008289
Functional Transcription Factor Target Networks Illuminate Control of Epithelial Remodelling. PMID:33007944
Discovering lethal alleles across the turkey genome using a transmission ratio distortion approach. PMID:33006154
iMDA-BN: Identification of miRNA-disease associations based on the biological network and graph embedding algorithm. PMID:33005302
Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis. PMID:33004908
Transcriptomic signatures of cold adaptation and heat stress in the winter ant (Prenolepis imparis). PMID:33002025
Phenotype-genotype comorbidity analysis of patients with rare disorders provides insight into their pathological and molecular bases. PMID:33001999
Altered expression of genes regulating inflammation and synaptogenesis during regrowth of afferent neurons to cochlear hair cells. PMID:33001981
Low-pass whole genome bisulfite sequencing of neonatal dried blood spots identifies a role for RUNX1 in Down syndrome DNA methylation profiles. PMID:33001180
Association of tricellulin expression with poor colorectal cancer prognosis and metastasis. PMID:33000262
Uncovering potential differentially expressed miRNAs and targeted mRNAs in myocardial infarction based on integrating analysis. PMID:33000230
Implication of ZNF217 in Accelerating Tumor Development and Therapeutically Targeting ZNF217-Induced PI3K-AKT Signaling for the Treatment of Metastatic Osteosarcoma. PMID:32999043
SlFERL Interacts with S-Adenosylmethionine Synthetase to Regulate Fruit Ripening. PMID:32999005
Efficient Propagation of Circulating Tumor Cells: A First Step for Probing Tumor Metastasis. PMID:32998338
Identification of the significant pathways of Banxia Houpu decoction in the treatment of depression based on network pharmacology. PMID:32997725
IL6-mediated HCoV-host interactome regulatory network and GO/Pathway enrichment analysis. PMID:32997660
Transcriptomic Analysis Reveals Common Adaptation Mechanisms Under Different Stresses for Moderately Piezophilic Bacteria. PMID:32995929
Immune response and endocytosis pathways are associated with the resilience against Alzheimer's disease. PMID:32994401
Aberration of the modulatory functions of intronic microRNA hsa-miR-933 on its host gene ATF2 results in type II diabetes mellitus and neurodegenerative disease development. PMID:32993798
Transcriptome analysis reveals underlying immune response mechanism of fungal (Penicillium oxalicum) disease in Gastrodia elata Bl. f. glauca S. chow (Orchidaceae). PMID:32993485
Inducible Deletion of YAP and TAZ in Adult Mouse Smooth Muscle Causes Rapid and Lethal Colonic Pseudo-Obstruction. PMID:32992050
Functional signatures of evolutionarily young CTCF binding sites. PMID:32988407
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. PMID:32986834
Expanded Chinese hamster organ and cell line proteomics profiling reveals tissue-specific functionalities. PMID:32985598
Cancer-associated fibroblasts of the prostate promote a compliant and more invasive phenotype in benign prostate epithelial cells. PMID:32984808
Single-Cell RNA-Sequencing From Mouse Incisor Reveals Dental Epithelial Cell-Type Specific Genes. PMID:32984333
Complement C7 (C7), a Potential Tumor Suppressor, Is an Immune-Related Prognostic Biomarker in Prostate Cancer (PC). PMID:32984006
Therapeutic mechanism of Toujie Quwen granules in COVID-19 based on network pharmacology. PMID:32983259
Identification of Hub Genes and Key Pathways Associated with Peripheral T-cell Lymphoma. PMID:32980897
pS421 huntingtin modulates mitochondrial phenotypes and confers neuroprotection in an HD hiPSC model. PMID:32978366
Genetic background dependent modifiers of craniosynostosis severity. PMID:32976998
TREND-DB-a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation. PMID:32976578
Molecular Characterization of the Coproduced Extracellular Vesicles in HEK293 during Virus-Like Particle Production. PMID:32975947
Analysis of Metabolites and Gene Expression Changes Relative to Apricot (Prunus armeniaca L.) Fruit Quality During Development and Ripening. PMID:32973833
The similarity of inherited diseases (II): clinical and biological similarity between the phenotypic series. PMID:32972400
Burden of rare deleterious variants in WNT signaling genes among 511 myelomeningocele patients. PMID:32970752
Aldh inhibitor restores auditory function in a mouse model of human deafness. PMID:32970669
Tobacco smoking induces metabolic reprogramming of renal cell carcinoma. PMID:32970633
An immune-related gene signature for determining Ewing sarcoma prognosis based on machine learning. PMID:32968877
Gaussian Embedding for Large-scale Gene Set Analysis. PMID:32968711
Genome-wide identification and expression analysis of bZIP gene family in Carthamus tinctorius L. PMID:32968100
Unveiling Sex-Based Differences in the Effects of Alcohol Abuse: A Comprehensive Functional Meta-Analysis of Transcriptomic Studies. PMID:32967293
Applications of Genome-Wide Screening and Systems Biology Approaches in Drug Repositioning. PMID:32967266
Identifying Risk Genes and Interpreting Pathogenesis for Parkinson's Disease by a Multiomics Analysis. PMID:32967142
Development of an Intervention Setting Ontology for behaviour change: Specifying where interventions take place. PMID:32964137
Systematic Elucidation of the Mechanism of Quercetin against Gastric Cancer via Network Pharmacology Approach. PMID:32964029
Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing. PMID:32962098
Identification of hub genes in colon cancer via bioinformatics analysis. PMID:32961078
Identification of Significant Genes and Pathways in Acute Pancreatitis via Bioinformatical Analysis. PMID:32960383
Localized inhibition in the Drosophila mushroom body. PMID:32955437
Identification of hub genes in diabetic kidney disease via multiple-microarray analysis. PMID:32953797
Network based analysis of microarray gene expression profiles in response to electroacupuncture. PMID:32953563
Designing custom CRISPR libraries for hypothesis-driven drug target discovery. PMID:32952937
Network pharmacology analysis of the therapeutic mechanisms of the traditional Chinese herbal formula Lian Hua Qing Wen in Corona virus disease 2019 (COVID-19), gives fundamental support to the clinical use of LHQW. PMID:32949888
An unanticipated tumor-suppressive role of the SUMO pathway in the intestine unveiled by Ubc9 haploinsufficiency. PMID:32948837
SPT6-driven error-free DNA repair safeguards genomic stability of glioblastoma cancer stem-like cells. PMID:32948765
Transcription factor expression defines subclasses of developing projection neurons highly similar to single-cell RNA-seq subtypes. PMID:32948690
Bioinformatics Data Mining Repurposes the JAK2 (Janus Kinase 2) Inhibitor Fedratinib for Treating Pancreatic Ductal Adenocarcinoma by Reversing the KRAS (Kirsten Rat Sarcoma 2 Viral Oncogene Homolog)-Driven Gene Signature. PMID:32947833
Multi-layered Spatial Transcriptomics Identify Secretory Factors Promoting Human Hematopoietic Stem Cell Development. PMID:32946788
Transcriptomics predicts compound synergy in drug and natural product treated glioblastoma cells. PMID:32946518
miR‑592 acts as an oncogene and promotes medullary thyroid cancer tumorigenesis by targeting cyclin‑dependent kinase 8. PMID:32945439
Resveratrol modulates the apoptosis and autophagic death of human lung adenocarcinoma A549 cells via a p53‑dependent pathway: Integrated bioinformatics analysis and experimental validation. PMID:32945383
The transcriptomic response of cells to a drug combination is more than the sum of the responses to the monotherapies. PMID:32945258
PAWER: protein array web exploreR. PMID:32942983
Enzyme-Constrained Models and Omics Analysis of Streptomyces coelicolor Reveal Metabolic Changes that Enhance Heterologous Production. PMID:32942174
Rps27a might act as a controller of microglia activation in triggering neurodegenerative diseases. PMID:32941527
The CRISPR-Cas9 crATIC HeLa transcriptome: Characterization of a novel cellular model of ATIC deficiency and ZMP accumulation. PMID:32939338
Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project. PMID:32939051
Revealing the full-length transcriptome of caucasian clover rhizome development. PMID:32938399
Long-read sequencing and de novo genome assembly of marine medaka (Oryzias melastigma). PMID:32938378
Whole-Genome Sequencing Analysis of Quorum Quenching Bacterial Strain Acinetobacter lactucae QL-1 Identifies the FadY Enzyme for Degradation of the Diffusible Signal Factor. PMID:32937869
Chitinase 3-Like 1 Contributes to Food Allergy via M2 Macrophage Polarization. PMID:32935492
Identification, Validation, and Functional Annotations of Genome-Wide Profile Variation between Melanocytic Nevus and Malignant Melanoma. PMID:32934956
Cellular expression profiles of Epstein-Barr virus-transformed B-lymphoblastoid cell lines. PMID:32934816
TMEM206 is a potential prognostic marker of hepatocellular carcinoma. PMID:32934741
Immunotyping of tumor-infiltrating lymphocytes in triple-negative breast cancer and genetic characterization. PMID:32934708
The extent of cyclin C promoter occupancy directs changes in stress-dependent transcription. PMID:32934007
Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses. PMID:32929263
Drosophila Voltage-Gated Sodium Channels Are Only Expressed in Active Neurons and Are Localized to Distal Axonal Initial Segment-like Domains. PMID:32928889
A Pilot Study on MicroRNA Profile in Tear Fluid to Predict Response to Anti-VEGF Treatments for Diabetic Macular Edema. PMID:32927780
A Systematic Pharmacology and In Vitro Study to Identify the Role of the Active Compounds of Achyranthes bidentata in the Treatment of Osteoarthritis. PMID:32925869
Using bioinformatics and metabolomics to identify altered granulosa cells in patients with diminished ovarian reserve. PMID:32923184
Identification of tumor-infiltrating immune cells and prognostic validation of tumor-infiltrating mast cells in adrenocortical carcinoma: results from bioinformatics and real-world data. PMID:32923148
The Phoebe genome sheds light on the evolution of magnoliids. PMID:32922818
Expression Profiles of Long Non-coding RNA and Messenger RNA in Human Traumatic Brain Injury. PMID:32919233
Functional Identification of the Dextransucrase Gene of Leuconostoc mesenteroides DRP105. PMID:32916950
Incorporating prior knowledge into regularized regression. PMID:32915960
Single-molecule real-time sequencing of the full-length transcriptome of loquat under low-temperature stress. PMID:32915882
Identification and validation of novel metastasis-related signatures of clear cell renal cell carcinoma using gene expression databases. PMID:32913492
Transcriptional analysis of cleft palate in TGFβ3 mutant mice. PMID:32913205
Cytotoxic lymphocytes are dysregulated in multisystem inflammatory syndrome in children. PMID:32909006
Identification of Biomarkers to Construct a Competing Endogenous RNA Network and Establishment of a Genomic-Clinicopathologic Nomogram to Predict Survival for Children with Rhabdoid Tumors of the Kidney. PMID:32908900
Bioinformatics Analysis of Key Genes and circRNA-miRNA-mRNA Regulatory Network in Gastric Cancer. PMID:32908877
Analysis of Differentially Expressed Genes in Necrotic Enteritis-infected Fayoumi Chickens using RNA Sequencing. PMID:32908417
A bilateral tumor model identifies transcriptional programs associated with patient response to immune checkpoint blockade. PMID:32907939
Finding semantic patterns in omics data using concept rule learning with an ontology-based refinement operator. PMID:32905086
Transcriptional signatures in histologic structures within glioblastoma tumors may predict personalized drug sensitivity and survival. PMID:32904984
Identification of Immune-Related Prognostic Biomarkers Based on the Tumor Microenvironment in 20 Malignant Tumor Types With Poor Prognosis. PMID:32903590
RNF40 exerts stage-dependent functions in differentiating osteoblasts and is essential for bone cell crosstalk. PMID:32901120
Conserved Patterns in Developmental Processes and Phases, Rather than Genes, Unite the Highly Divergent Bilateria. PMID:32899936
In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age. PMID:32898168
Understanding microcephaly through the study of centrosome regulation in Drosophila neural stem cells. PMID:32897294
Transcriptomic analysis links diverse hypothalamic cell types to fibroblast growth factor 1-induced sustained diabetes remission. PMID:32895383
Identification of a metabolism-related gene expression prognostic model in endometrial carcinoma patients. PMID:32894095
Functional, Morphological, and Evolutionary Characterization of Hearing in Subterranean, Eusocial African Mole-Rats. PMID:32888484
Osteopontin Expression Identifies a Subset of Recruited Macrophages Distinct from Kupffer Cells in the Fatty Liver. PMID:32888418
Environmental stability impacts the differential sensitivity of marine microbiomes to increases in temperature and acidity. PMID:32887943
Telomere-to-telomere assembled and centromere annotated genomes of the two main subspecies of the button mushroom Agaricus bisporus reveal especially polymorphic chromosome ends. PMID:32887908
Active Packaging of Immobilized Zinc Oxide Nanoparticles Controls Campylobacter jejuni in Raw Chicken Meat. PMID:32887715
De novo transcriptome sequencing of Rhododendron molle and identification of genes involved in the biosynthesis of secondary metabolites. PMID:32887550
Single-Cell NGS-Based Analysis of Copy Number Alterations Reveals New Insights in Circulating Tumor Cells Persistence in Early-Stage Breast Cancer. PMID:32887501
Cancer cell line-specific protein profiles in extracellular vesicles identified by proteomics. PMID:32886718
Identification of circular RNA hsa_circ_0044556 and its effect on the progression of colorectal cancer. PMID:32884449
Complete Genome Sequence of Pseudomonas aeruginosa XN-1, Isolated from the Sputum of a Severe Pneumonia Patient. PMID:32883796
De novo transcriptome assembly and population genetic analyses of an important coastal shrub, Apocynum venetum L. PMID:32883231
Pathogenic impact of transcript isoform switching in 1,209 cancer samples covering 27 cancer types using an isoform-specific interaction network. PMID:32879328
Secretome Proteomic Approaches for Biomarker Discovery: An Update on Colorectal Cancer. PMID:32878319
Changes in MicroRNA Expression during Rabbit Hemorrhagic Disease Virus (RHDV) Infection. PMID:32878241
Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns. PMID:32875947
Differential contribution of bone marrow-derived infiltrating monocytes and resident macrophages to persistent lung inflammation in chronic air pollution exposure. PMID:32873817
Analysis of key genes and pathways associated with the pathogenesis of intervertebral disc degeneration. PMID:32873329
Dissecting Transcription Factor-Target Interaction in Bovine Coronavirus Infection. PMID:32872640
Genome Wide Analysis Reveals the Role of VadA in Stress Response, Germination, and Sterigmatocystin Production in Aspergillus nidulans Conidia. PMID:32872591
Inference and multiscale model of epithelial-to-mesenchymal transition via single-cell transcriptomic data. PMID:32870263
Multivariate gene expression-based survival predictor model in esophageal adenocarcinoma. PMID:32869505
G protein-coupled receptor Gpr115 (Adgrf4) is required for enamel mineralization mediated by ameloblasts. PMID:32868297
Genomic landscape of the immune microenvironments of brain metastases in breast cancer. PMID:32867782
Comprehensive analysis of key genes associated with ceRNA networks in nasopharyngeal carcinoma based on bioinformatics analysis. PMID:32863767
Transcriptomic and anatomic profiling reveal the germination process of different wheat varieties in response to waterlogging stress. PMID:32859149
binomialRF: interpretable combinatoric efficiency of random forests to identify biomarker interactions. PMID:32859146
Proteomic and Transcriptomic Analyses Indicate Metabolic Changes and Reduced Defense Responses in Mycorrhizal Roots of Oeceoclades maculata (Orchidaceae) Collected in Nature. PMID:32858792
Systemic Mesenchymal Stem Cell Treatment Mitigates Structural and Functional Retinal Ganglion Cell Degeneration in a Mouse Model of Multiple Sclerosis. PMID:32855863
Identification of key differentially expressed mRNAs and microRNAs in non-small cell lung cancer using bioinformatics analysis. PMID:32855723
A cross-kingdom conserved ER-phagy receptor maintains endoplasmic reticulum homeostasis during stress. PMID:32851973
Single-cell RNA expression profiling of SARS-CoV-2-related ACE2 and TMPRSS2 in human trophectoderm and placenta. PMID:32851697
A Neural Network Framework for Predicting the Tissue-of-Origin of 15 Common Cancer Types Based on RNA-Seq Data. PMID:32850691
A Bioinformatics Research on Novel Mechanism of Compound Kushen Injection for Treating Breast Cancer by Network Pharmacology and Molecular Docking Verification. PMID:32849897
Genomics and Virulence of Fonsecaea pugnacius, Agent of Disseminated Chromoblastomycosis. PMID:32849816
Differently Expression Analysis and Function Prediction of Long Non-coding RNAs in Duck Embryo Fibroblast Cells Infected by Duck Tembusu Virus. PMID:32849615
Gonad-Specific Transcriptomes Reveal Differential Expression of Gene and miRNA Between Male and Female of the Discus Fish (Symphysodon aequifasciatus). PMID:32848810
Newly identified Gon4l/Udu-interacting proteins implicate novel functions. PMID:32848183
Experimental Evolution of Bacillus subtilis Reveals the Evolutionary Dynamics of Horizontal Gene Transfer and Suggests Adaptive and Neutral Effects. PMID:32847815
DEAD-Box Helicase 4 (Ddx4)+ Stem Cells Sustain Tumor Progression in Non-Serous Ovarian Cancers. PMID:32847044
SBML Level 3: an extensible format for the exchange and reuse of biological models. PMID:32845085
Mito-oncology agent: fermented extract suppresses the Warburg effect, restores oxidative mitochondrial activity, and inhibits in vivo tumor growth. PMID:32843660
An epigenome-wide association study of early-onset major depression in monozygotic twins. PMID:32843619
Screening and identification of miRNAs related to sexual differentiation of strobili in Ginkgo biloba by integration analysis of small RNA, RNA, and degradome sequencing. PMID:32842951
Identification of differentially expressed genes between mucinous adenocarcinoma and other adenocarcinoma of colorectal cancer using bioinformatics analysis. PMID:32840168
The NK cell granule protein NKG7 regulates cytotoxic granule exocytosis and inflammation. PMID:32839608
Transcriptomic Analysis of Short-Term Salt Stress Response in Watermelon Seedlings. PMID:32839408
Differential processing and localization of human Nocturnin controls metabolism of mRNA and nicotinamide adenine dinucleotide cofactors. PMID:32839274
Single-Cell RNA Sequencing for Precision Oncology: Current State-of-Art. PMID:32837038
ChIP-seq Profiling Identifies Histone Deacetylase 2 Targeting Genes Involved in Immune and Inflammatory Regulation Induced by Calcitonin Gene-Related Peptide in Microglial Cells. PMID:32832570
Study of Osteoarthritis-Related Hub Genes Based on Bioinformatics Analysis. PMID:32832544
Innate immune response in neuronopathic forms of Gaucher disease confers resistance against viral-induced encephalitis. PMID:32831144
Third-generation sequencing found LncRNA associated with heat shock protein response to heat stress in Populus qiongdaoensis seedlings. PMID:32831021
Comparative Analysis of the Extracellular Matrix Proteome across the Myotendinous Junction. PMID:32830507
Ambient Temperature is A Strong Selective Factor Influencing Human Development and Immunity. PMID:32822870
m6A-Atlas: a comprehensive knowledgebase for unraveling the N6-methyladenosine (m6A) epitranscriptome. PMID:32821938
Analyzing the lncRNA, miRNA, and mRNA-associated ceRNA networks to reveal potential prognostic biomarkers for glioblastoma multiforme. PMID:32821246
Risuteganib Protects against Hydroquinone-induced Injury in Human RPE Cells. PMID:32818234
Metalloproteins and apolipoprotein C: candidate plasma biomarkers of T2DM screened by comparative proteomics and lipidomics in ZDF rats. PMID:32817751
Analytical Guidelines for co-fractionation Mass Spectrometry Obtained through Global Profiling of Gold Standard Saccharomyces cerevisiae Protein Complexes. PMID:32817346
Experimental and Biological Insights from Proteomic Analyses of Extracellular Vesicle Cargos in Normalcy and Disease. PMID:32815324
A cosmopolitan fungal pathogen of dicots adopts an endophytic lifestyle on cereal crops and protects them from major fungal diseases. PMID:32814863
Paneth Cell-Derived Lysozyme Defines the Composition of Mucolytic Microbiota and the Inflammatory Tone of the Intestine. PMID:32814028
Paired Box 9 (PAX9), the RNA polymerase II transcription factor, regulates human ribosome biogenesis and craniofacial development. PMID:32813698
Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli. PMID:32813020
The Integrated Analyses of Driver Genes Identify Key Biomarkers in Thyroid Cancer. PMID:32812852
Screening and Identification of Potential Peripheral Blood Biomarkers for Alzheimer's Disease Based on Bioinformatics Analysis. PMID:32812532
The current landscape of coronavirus-host protein-protein interactions. PMID:32811513
Extreme Phenotype Approach Suggests Taste Transduction Pathway for Carotid Plaque in a Multi-Ethnic Cohort. PMID:32811377
Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment. PMID:32810438
Intrinsic Endocardial Defects Contribute to Hypoplastic Left Heart Syndrome. PMID:32810435
CRISPR interference of nucleotide biosynthesis improves production of a single-domain antibody in Escherichia coli. PMID:32808670
The chromosome-level draft genome of Dalbergia odorifera. PMID:32808664
Pregnancy-associated changes in cervical noncoding RNA. PMID:32808540
Large-scale tethered function assays identify factors that regulate mRNA stability and translation. PMID:32807991
Systems biology reveals reprogramming of the S-nitroso-proteome in the cortical and striatal regions of mice during aging process. PMID:32807865
HIF-1α and HIF-2α differently regulate tumour development and inflammation of clear cell renal cell carcinoma in mice. PMID:32807776
Computational Identification and Characterization of New microRNAs in Human Platelets Stored in a Blood Bank. PMID:32806499
Predicting Gram-Positive Bacterial Protein Subcellular Location by Using Combined Features. PMID:32802888
Construction and Investigation of MicroRNA-mRNA Regulatory Network of Gastric Cancer with Helicobacter pylori Infection. PMID:32802507
Network Pharmacology-Based Strategy for Predicting Active Ingredients and Potential Targets of Gegen Qinlian Decoction for Rotavirus Enteritis. PMID:32802121
Weighted single-step genomic best linear unbiased prediction integrating variants selected from sequencing data by association and bioinformatics analyses. PMID:32799816
Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function. PMID:32797179
Integrated Framework of the Immune-Defense Transcriptional Signatures in the Arabidopsis Shoot Apical Meristem. PMID:32796535
Development of a Nomogram With Alternative Splicing Signatures for Predicting the Prognosis of Glioblastoma: A Study Based on Large-Scale Sequencing Data. PMID:32793502
Deregulated High Affinity Copper Transport Alters Iron Homeostasis in Arabidopsis. PMID:32793263
Identification of a Recurrence Signature and Validation of Cell Infiltration Level of Thyroid Cancer Microenvironment. PMID:32793117
Genome-wide identification and characterization of bHLH family genes from Ginkgo biloba. PMID:32792673
Discovery of small molecules that normalize the transcriptome and enhance cysteine cathepsin activity in progranulin-deficient microglia. PMID:32792571
Mycoplasma hyopneumoniae J elicits an antioxidant response and decreases the expression of ciliary genes in infected swine epithelial cells. PMID:32792522
An autophagy-related model of 4 key genes for predicting prognosis of patients with laryngeal cancer. PMID:32791689
Isolating structural errors in reaction networks in systems biology. PMID:32790862
Combining Gene-Disease Associations with Single-Cell Gene Expression Data Provides Anatomy-Specific Subnetworks in Age-Related Macular Degeneration. PMID:32789304
Bacterial polyphosphates interfere with the innate host defense to infection. PMID:32788578
NPF:network propagation for protein function prediction. PMID:32787776
Genetic Mutations That Drive Evolutionary Rescue to Lethal Temperature in Escherichia coli. PMID:32785667
Computational Methods for Predicting Functions at the mRNA Isoform Level. PMID:32784445
Identification of transcriptomic markers for developing idiopathic pulmonary fibrosis: an integrative analysis of gene expression profiles. PMID:32782692
Mechanistic studies of cytotoxic activity of the mesoionic compound MIH 2.4Bl in MCF-7 breast cancer cells. PMID:32782546
Identification of Hidradenitis Suppurativa-Related mRNA Expression Patterns Through Analysis of Gene Expression Omnibus. PMID:32782449
A framework for pathway knowledge driven prioritization in genome-wide association studies. PMID:32779262
The chromosome-level wintersweet (Chimonanthus praecox) genome provides insights into floral scent biosynthesis and flowering in winter. PMID:32778152
Identification of key differentially expressed genes between ER-positive/HER2-negative breast cancer and ER-negative/HER2-negative breast cancer using integrated bioinformatics analysis. PMID:32775256
DHX36, BAX, and ARPC1B May Be Critical for the Diagnosis and Treatment of Tuberculosis. PMID:32774561
Role of CYP4F2 as a novel biomarker regulating malignant phenotypes of liver cancer cells via the Nrf2 signaling axis. PMID:32774486
Analysis and identification of novel biomarkers involved in neuroblastoma via integrated bioinformatics. PMID:32772341
Bioinformatics analysis of differentially expressed genes in subchondral bone in early experimental osteoarthritis using microarray data. PMID:32771051
SOX10-regulated promoter use defines isoform-specific gene expression in Schwann cells. PMID:32770939
Graph2GO: a multi-modal attributed network embedding method for inferring protein functions. PMID:32770210
Mutant p53 induces Golgi tubulo-vesiculation driving a prometastatic secretome. PMID:32770028
MicroRNA Profiling in Paired Left and Right Eyes, Lungs, and Testes of Normal Mice. PMID:32769059
Pseudohyphal differentiation in Komagataella phaffii: investigating the FLO gene family. PMID:32766781
A review of auditing techniques for the Unified Medical Language System. PMID:32766692
The regulatory genome constrains protein sequence evolution: implications for the search for disease-associated genes. PMID:32765967
Bioinformatics analysis shows that TOP2A functions as a key candidate gene in the progression of cervical cancer. PMID:32765860
Circular RNA profiling in plasma exosomes from patients with gastric cancer. PMID:32765789
Atherosclerosis prediction by microarray-based DNA methylation analysis. PMID:32765783
Epigenetic Regulator miRNA Pattern Differences Among SARS-CoV, SARS-CoV-2, and SARS-CoV-2 World-Wide Isolates Delineated the Mystery Behind the Epic Pathogenicity and Distinct Clinical Characteristics of Pandemic COVID-19. PMID:32765592
Analysis of the Antifungal Properties of Bacillus velezensis B-4 Through a Bioassay and Complete-Genome Sequencing. PMID:32765583
Transcriptome Analysis and Expression of Selected Cationic Amino Acid Transporters in the Liver of Broiler Chicken Fed Diets with Varying Concentrations of Lysine. PMID:32764289
Transcriptomic analysis reveals differential gene expression, alternative splicing, and novel exons during mouse trophoblast stem cell differentiation. PMID:32762732
Targeted cyclooxygenase-2 inhibiting nanomedicine results in pain-relief and differential expression of the RNA transcriptome in the dorsal root ganglia of injured male rats. PMID:32762277
FLUTE: Fast and reliable knowledge retrieval from biomedical literature. PMID:32761077
Identification and comparison of proteomic and peptide profiles of mung bean seeds and sprouts. PMID:32760914
Application of Transcriptional Gene Modules to Analysis of Caenorhabditis elegans' Gene Expression Data. PMID:32759329
Inducers of the endothelial cell barrier identified through chemogenomic screening in genome-edited hPSC-endothelial cells. PMID:32759214
The effect of Jiedu Huoxue decoction on rat model of experimental nonbacterial prostatitis via regulation of miRNAs. PMID:32758035
Circuits Regulating Superoxide and Nitric Oxide Production and Neutralization in Different Cell Types: Expression of Participating Genes and Changes Induced by Ionizing Radiation. PMID:32756515
Bioinformatics analysis of microRNA profiles and identification of microRNA-mRNA network and biological markers in intracranial aneurysm. PMID:32756097
Tousled-Like Kinases Suppress Innate Immune Signaling Triggered by Alternative Lengthening of Telomeres. PMID:32755577
Altered hemodynamics during arteriovenous fistula remodeling leads to reduced fistula patency in female mice. PMID:32754721
Differential proteomics study of postharvest Volvariella volvacea during storage at 4 °C. PMID:32753745
Hepatopancreas immune response during molt cycle in the mud crab, Scylla paramamosain. PMID:32753724
Complex landscape of alternative splicing in myeloid neoplasms. PMID:32753690
An interspecies translation model implicates integrin signaling in infliximab-resistant inflammatory bowel disease. PMID:32753478
iPS-Derived Early Oligodendrocyte Progenitor Cells from SPMS Patients Reveal Deficient In Vitro Cell Migration Stimulation. PMID:32751289
Metastasis of Uveal Melanoma with Monosomy-3 Is Associated with a Less Glycogenetic Gene Expression Profile and the Dysregulation of Glycogen Storage. PMID:32751097
RNAAgeCalc: A multi-tissue transcriptional age calculator. PMID:32750074
Characterization of a Protease Hyper-Productive Mutant of Bacillus pumilus by Comparative Genomic and Transcriptomic Analysis. PMID:32749522
Mitochondrial DNA drives abscopal responses to radiation that are inhibited by autophagy. PMID:32747819
Mapping the nucleolar proteome reveals a spatiotemporal organization related to intrinsic protein disorder. PMID:32744794
A human ESC-based screen identifies a role for the translated lncRNA LINC00261 in pancreatic endocrine differentiation. PMID:32744504
Large-scale Multi-omic Analysis of COVID-19 Severity. PMID:32743614
Identification of key genes of human bone marrow stromal cells adipogenesis at an early stage. PMID:32742785
Prognostic implication and functional annotations of APOBEC3G expression in patients with Melanoma. PMID:32742470
Genome-Wide Screen for Context-Dependent Tumor Suppressors Identified Using in Vivo Models for Neoplasia in Drosophila. PMID:32737065
Identification of Key Genes for the Ultrahigh Yield of Rice Using Dynamic Cross-tissue Network Analysis. PMID:32736037
IL-15 Preconditioning Augments CAR T Cell Responses to Checkpoint Blockade for Improved Treatment of Solid Tumors. PMID:32735774
The Anatomy of the SARS-CoV-2 Biomedical Literature: Introducing the CovidX Network Algorithm for Drug Repurposing Recommendation. PMID:32735546
Identification of the Key Regulatory Genes Involved in Elaborate Petal Development and Specialized Character Formation in Nigella damascena (Ranunculaceae). PMID:32732312
Research Note: Circular RNA expressing in different developmental stages of the chicken bursa of Fabricius. PMID:32731971
An Activity-Guided Map of Electrophile-Cysteine Interactions in Primary Human T Cells. PMID:32730809
Variants in SCAF4 Cause a Neurodevelopmental Disorder and Are Associated with Impaired mRNA Processing. PMID:32730804
An atlas of dynamic chromatin landscapes in mouse fetal development. PMID:32728240
Integrated bioinformatics analysis to decipher molecular mechanism of compound Kushen injection for esophageal cancer by combining WGCNA with network pharmacology. PMID:32728182
De novo assembly and Transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics. PMID:32727354
Protamine-2 Deficiency Initiates a Reactive Oxygen Species (ROS)-Mediated Destruction Cascade during Epididymal Sperm Maturation in Mice. PMID:32727081
Genome-wide effect of tetracycline, doxycycline and 4-epidoxycycline on gene expression in Saccharomyces cerevisiae. PMID:32726865
Breed Differences in Dog Cognition Associated with Brain-Expressed Genes and Neurological Functions. PMID:32726413
Optimization of skeletal protein preparation for LC-MS/MS sequencing yields additional coral skeletal proteins in Stylophora pistillata. PMID:32724895
Circulating miRNA-3552 as a Potential Biomarker for Ischemic Stroke in Rats. PMID:32724801
Delineation of the Germline and Somatic Mutation Interaction Landscape in Triple-Negative and Non-Triple-Negative Breast Cancer. PMID:32724790
Identifying key genes and drug screening for preeclampsia based on gene expression profiles. PMID:32724400
GGCT promotes colorectal cancer migration and invasion via epithelial-mesenchymal transition. PMID:32724344
Polyphosphate Functions In Vivo as an Iron Chelator and Fenton Reaction Inhibitor. PMID:32723918
Parental Selenium Nutrition Affects the One-Carbon Metabolism and the Hepatic DNA Methylation Pattern of Rainbow Trout (Oncorhynchus mykiss) in the Progeny. PMID:32722369
Tumorigenic effects of TLX overexpression in HEK 293T cells. PMID:32721119
Irradiation-Induced Upregulation of miR-711 Inhibits DNA Repair and Promotes Neurodegeneration Pathways. PMID:32718090
Genome-wide association study of corneal biomechanical properties identifies over 200 loci providing insight into the genetic etiology of ocular diseases. PMID:32716492
A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer's Disease Through Expert Curation of Key Protein Targets. PMID:32716361
Construction of a novel prognostic-predicting model correlated to ovarian cancer. PMID:32716025
Cancer-Testis Gene Expression in Hepatocellular Carcinoma: Identification of Prognostic Markers and Potential Targets for Immunotherapy. PMID:32715976
Complete Genome Sequence and Biodegradation Characteristics of Benzoic Acid-Degrading Bacterium Pseudomonas sp. SCB32. PMID:32714981
OASL as a Diagnostic Marker for Influenza Infection Revealed by Integrative Bioinformatics Analysis With XGBoost. PMID:32714913
A Network Pharmacology Approach to Investigate the Active Compounds and Mechanisms of Musk for Ischemic Stroke. PMID:32714405
Study on Mechanism of Iridoid Glycosides Derivatives from Fructus Gardeniae in Jiangxi Province by Network Pharmacology. PMID:32714404
The Construction and Comprehensive Prognostic Analysis of the LncRNA-Associated Competitive Endogenous RNAs Network in Colorectal Cancer. PMID:32714366
Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity. PMID:32711472
Transcriptome Analysis Provides Insights into Grain Filling in Foxtail Millet (Setaria italica L.). PMID:32708737
Shedding the Light on Litopenaeus vannamei Differential Muscle and Hepatopancreas Immune Responses in White Spot Syndrome Virus (WSSV) Exposure. PMID:32708590
Ribosomal Protein uL11 as a Regulator of Metabolic Circuits Related to Aging and Cell Cycle. PMID:32708309
Integrated transcriptomic and metabolomic analyses of yellow horn (Xanthoceras sorbifolia) in response to cold stress. PMID:32706804
Whole-genome analyses reveal gene content differences between nontypeable Haemophilus influenzae isolates from chronic obstructive pulmonary disease compared to other clinical phenotypes. PMID:32706329
Risk gene identification and support vector machine learning to construct an early diagnosis model of myocardial infarction. PMID:32705275
Genome‑wide analysis of DNA methylation and gene expression changes in an ovalbumin‑induced asthma mouse model. PMID:32705270
Effects of Egr1 on pancreatic acinar intracellular trypsinogen activation and the associated ceRNA network. PMID:32705196
Expression profiling of circular RNAs and their potential role in early‑stage diabetic cardiomyopathy. PMID:32705182
Stress response in periodontal ligament stem cells may contribute to bisphosphonate‑associated osteonecrosis of the jaw: A gene expression array analysis. PMID:32705175
Expanded Phenotypic Definition Identifies Hundreds of Potential Causative Genes for Leukodystrophies and Leukoencephalopathies. PMID:32704519
Transcriptomic differences between male and female Trachycarpus fortunei. PMID:32704095
Identification of key genes in calcific aortic valve disease by integrated bioinformatics analysis. PMID:32702920
Calmodulin-binding transcription activator (CAMTA) genes family: Genome-wide survey and phylogenetic analysis in flax (Linum usitatissimum). PMID:32702710
Identifying the novel key genes in renal cell carcinoma by bioinformatics analysis and cell experiments. PMID:32699530
Araport Lives: An Updated Framework for Arabidopsis Bioinformatics. PMID:32699173
The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest. PMID:32698880
iTRAQ protein profile analysis of sugar beet under salt stress: different coping mechanisms in leaves and roots. PMID:32698773
ClusterMine: A knowledge-integrated clustering approach based on expression profiles of gene sets. PMID:32698720
Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes. PMID:32697802
How to Annotate and Submit a Short Linear Motif to the Eukaryotic Linear Motif Resource. PMID:32696353
Functional identity of hypothalamic melanocortin neurons depends on Tbx3. PMID:32694784
Systematic mapping of genetic interactions for de novo fatty acid synthesis identifies C12orf49 as a regulator of lipid metabolism. PMID:32694731
Developing an automated mechanism to identify medical articles from wikipedia for knowledge extraction. PMID:32693245
Gut transcriptomic changes during hibernation in the greater horseshoe bat (Rhinolophus ferrumequinum). PMID:32690984
Zonal regulation of collagen-type proteins and posttranslational modifications in prostatic benign and cancer tissues by imaging mass spectrometry. PMID:32687633
DAZL mediates a broad translational program regulating expansion and differentiation of spermatogonial progenitors. PMID:32686646
Inhibition of the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs) stimulates osteoblastogenesis by potentiating bone morphogenetic protein 2 (BMP2) responses. PMID:32686190
Aberrant DNA methylation results in altered gene expression in non-alcoholic steatohepatitis-related hepatocellular carcinomas. PMID:32685988
Footprint-based functional analysis of multiomic data. PMID:32685770
Potential Prognostic Value and Mechanism of Stromal-Immune Signature in Tumor Microenvironment for Stomach Adenocarcinoma. PMID:32685487
The power and limitations of gene expression pathway analyses toward predicting population response to environmental stressors. PMID:32684953
Identification of potential crucial genes in atrial fibrillation: a bioinformatic analysis. PMID:32682418
Analysis of Transcriptome and miRNAome in the Muscle of Bamei Pigs at Different Developmental Stages. PMID:32679676
Identification of potential blood biomarkers for early diagnosis of Alzheimer's disease through RNA sequencing analysis. PMID:32677993
High-throughput discovery of phage receptors using transposon insertion sequencing of bacteria. PMID:32675236
RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus. PMID:32673562
Glyceroglycolipid Metabolism Regulations under Phosphate Starvation Revealed by Transcriptome Analysis in Synechococcus elongatus PCC 7942. PMID:32668657
Modeling Secondary Iron Overload Cardiomyopathy with Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes. PMID:32668256
Pathogenic Tau Causes a Toxic Depletion of Nuclear Calcium. PMID:32668249
Unified inference of missense variant effects and gene constraints in the human genome. PMID:32667917
Nonsense-Mediated RNA Decay Factor UPF1 Is Critical for Posttranscriptional and Translational Gene Regulation in Arabidopsis. PMID:32665305
A Long-Day Photoperiod and 6-Benzyladenine Promote Runner Formation through Upregulation of Soluble Sugar Content in Strawberry. PMID:32664642
Hsa_circ_0002320: a novel clinical biomarker for colorectal cancer prognosis. PMID:32664176
Leveraging the Comparative Toxicogenomics Database to Fill in Knowledge Gaps for Environmental Health: A Test Case for Air Pollution-induced Cardiovascular Disease. PMID:32663284
Investigating higher-order interactions in single-cell data with scHOT. PMID:32661426
Mapping signalling perturbations in myocardial fibrosis via the integrative phosphoproteomic profiling of tissue from diverse sources. PMID:32661320
Gold/alpha-lactalbumin nanoprobes for the imaging and treatment of breast cancer. PMID:32661307
The circular RNA landscape in specific peripheral blood mononuclear cells of critically ill patients with sepsis. PMID:32660590
Deciphering cellular transcriptional alterations in Alzheimer's disease brains. PMID:32660529
A trafficome-wide RNAi screen reveals deployment of early and late secretory host proteins and the entire late endo-/lysosomal vesicle fusion machinery by intracellular Salmonella. PMID:32658937
Chromatin network markers of leukemia. PMID:32657405
Factorized embeddings learns rich and biologically meaningful embedding spaces using factorized tensor decomposition. PMID:32657403
The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction. PMID:32657391
Benchmarking gene ontology function predictions using negative annotations. PMID:32657372
Network-principled deep generative models for designing drug combinations as graph sets. PMID:32657357
Immune cell infiltration features and related marker genes in lung cancer based on single-cell RNA-seq. PMID:32656582
Transcriptomic Analysis of Extracellular RNA Governed by the Endocytic Adaptor Protein Cin1 of Cryptococcus deneoformans. PMID:32656093
Comparison of Transcriptome Profiles of the Fungus Botrytis cinerea and Insect Pest Bradysia odoriphaga in Response to Benzothiazole. PMID:32655508
A bioinformatics investigation into molecular mechanism of Yinzhihuang granules for treating hepatitis B by network pharmacology and molecular docking verification. PMID:32651427
A Genomic Perspective on the Potential of Wild-Type Rumen Bacterium Enterobacter sp. LU1 as an Industrial Platform for Bio-Based Succinate Production. PMID:32650546
Comprehensive analysis of full genome sequence and Bd-milRNA/target mRNAs to discover the mechanism of hypovirulence in Botryosphaeria dothidea strains on pear infection with BdCV1 and BdPV1. PMID:32647612
Transcriptomic and Ultrastructural Signatures of K+-Induced Aggregation in Phytophthora parasitica Zoospores. PMID:32645882
Exploring the Molecular Mechanisms of Pterygium by Constructing lncRNA-miRNA-mRNA Regulatory Network. PMID:32645133
The Lyme disease bacterium, Borrelia burgdorferi, stimulates an inflammatory response in human choroid plexus epithelial cells. PMID:32645014
Comparative analysis of single-cell transcriptomics in human and Zebrafish oocytes. PMID:32640983
An expanded cell wall damage signaling network is comprised of the transcription factors Rlm1 and Sko1 in Candida albicans. PMID:32639995
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). PMID:32637990
Molecular atlas of the adult mouse brain. PMID:32637622
A Cancer Gene Module Mining Method Based on Bio-Network of Multi-Omics Gene Groups. PMID:32637361
Single-cell ATAC sequencing analysis: From data preprocessing to hypothesis generation. PMID:32637041
Genome-Scale Metabolic Model Driven Design of a Defined Medium for Campylobacter jejuni M1cam. PMID:32636809
Shared up-regulation and contrasting down-regulation of gene expression distinguish desiccation-tolerant from intolerant green algae. PMID:32636259
Low Oxygen Stress During Early Development Influences Regulation of Hypoxia-Response Genes in Farmed Atlantic Salmon (Salmo salar). PMID:32636218
WTO, an ontology for wheat traits and phenotypes in scientific publications. PMID:32634868
Bioinformatics analysis of high-throughput data to validate potential novel biomarkers and small molecule drugs for glioblastoma multiforme. PMID:32634050
RNA is essential for PRC2 chromatin occupancy and function in human pluripotent stem cells. PMID:32632336
Transcriptome Analyses of Candida albicans Biofilms, Exposed to Arachidonic Acid and Fluconazole, Indicates Potential Drug Targets. PMID:32631950
A systems biology-driven approach to construct a comprehensive protein interaction network of influenza A virus with its host. PMID:32631335
MMiRNA-Viewer2, a bioinformatics tool for visualizing functional annotation for MiRNA and MRNA pairs in a network. PMID:32631332
Proteomic Profiling of Emiliania huxleyi Using a Three-Dimensional Separation Method Combined with Tandem Mass Spectrometry. PMID:32630776
Screening and identification of key gene in sepsis development: Evidence from bioinformatics analysis. PMID:32629654
Placental exosomes isolated from urine of patients with gestational diabetes exhibit a differential profile expression of microRNAs across gestation. PMID:32626972
Key miRNAs associated with memory and learning disorder upon exposure to sevoflurane determined by RNA sequencing. PMID:32626949
Identification and Verification of Biomarker in Clear Cell Renal Cell Carcinoma via Bioinformatics and Neural Network Model. PMID:32626756
Glucose-mediated regulation of glycerol uptake in Rhodosporidium toruloides: Insights through transcriptomic analysis on dual substrate fermentation. PMID:32624774
Transcriptome analysis of testis reveals the effects of developmental exposure to bisphenol a or 17α-ethinylestradiol in medaka (Oryzias latipes). PMID:32622090
Breathing fresh air into respiratory research with single-cell RNA sequencing. PMID:32620586
Quantitative Translation of Dog-to-Human Aging by Conserved Remodeling of the DNA Methylome. PMID:32619550
Draft Genome Sequence of the Bacterium Paraburkholderia aromaticivorans AR20-38, a Gram-Negative, Cold-Adapted Degrader of Aromatic Compounds. PMID:32616634
Dietary genistein supplementation protects against lipopolysaccharide-induced intestinal injury through altering transcriptomic profile. PMID:32616235
Discovery, identification, and functional characterization of long noncoding RNAs in Arachis hypogaea L. PMID:32615935
Gene signatures of SARS-CoV/SARS-CoV-2-infected ferret lungs in short- and long-term models. PMID:32615317
Data-driven network alignment. PMID:32614833
RNA-sequencing and bioinformatics analysis of long noncoding RNAs and mRNAs in the asthenozoospermia. PMID:32614449
Protein profile of well-differentiated versus un-differentiated human bronchial/tracheal epithelial cells. PMID:32613119
Association study based on topological constraints of protein-protein interaction networks. PMID:32612246
Physiological blood-brain transport is impaired with age by a shift in transcytosis. PMID:32612231
Cardiac Transcriptome Analysis Reveals Nr4a1 Mediated Glucose Metabolism Dysregulation in Response to High-Fat Diet. PMID:32610475
The PD-1 Pathway Regulates Development and Function of Memory CD8+ T Cells following Respiratory Viral Infection. PMID:32610128
Identification of vital candidate microRNA/mRNA pairs regulating ovule development using high-throughput sequencing in hazel. PMID:32605594
Identification of Novel microRNA Profiles Dysregulated in Plasma and Tissue of Abdominal Aortic Aneurysm Patients. PMID:32605321
COVID-KOP: Integrating Emerging COVID-19 Data with the ROBOKOP Database. PMID:32601612
Genetic colocalization atlas points to common regulatory sites and genes for hematopoietic traits and hematopoietic contributions to disease phenotypes. PMID:32600345
Comparative analysis of full-length transcriptomes based on hybrid population reveals regulatory mechanisms of anthocyanin biosynthesis in sweet potato (Ipomoea batatas (L.) Lam). PMID:32600332
Comparative Pathway Integrator: A Framework of Meta-Analytic Integration of Multiple Transcriptomic Studies for Consensual and Differential Pathway Analysis. PMID:32599927
Experimentally Determined Long Intrinsically Disordered Protein Regions Are Now Abundant in the Protein Data Bank. PMID:32599863
Identification of Prognostic Organic Cation and Anion Transporters in Different Cancer Entities by In Silico Analysis. PMID:32599841
Fulvic acid increases forage legume growth inducing preferential up-regulation of nodulation and signalling-related genes. PMID:32599619
Use of Chou's 5-steps rule to predict the subcellular localization of gram-negative and gram-positive bacterial proteins by multi-label learning based on gene ontology annotation and profile alignment. PMID:32598314
Evolutionary History of the Globin Gene Family in Annelids. PMID:32597988
RNA Sequencing for Gene Expression Profiles in Peripheral Blood Mononuclear Cells with Ankylosing Spondylitis RNA. PMID:32596323
Network Pharmacology-Based Identification of the Mechanisms of Shen-Qi Compound Formula in Treating Diabetes Mellitus. PMID:32595730
Identification of miRNA-mRNA-TFs Regulatory Network and Crucial Pathways Involved in Tetralogy of Fallot. PMID:32595699
Novel Insights Into Triple-Negative Breast Cancer Prognosis by Comprehensive Characterization of Aberrant Alternative Splicing. PMID:32595697
Characterization of Hemerocallis citrina Transcriptome and Development of EST-SSR Markers for Evaluation of Genetic Diversity and Population Structure of Hemerocallis Collection. PMID:32595657
NF-κB/TWIST1 Mediates Migration and Phagocytosis of Macrophages in the Mice Model of Implant-Associated Staphylococcus aureus Osteomyelitis. PMID:32595631
PRC2-mediated H3K27me3 modulates shoot iron homeostasis in Arabidopsis thaliana. PMID:32594838
Time-resolved mRNA and miRNA expression profiling reveals crucial coregulation of molecular pathways involved in epithelial-pneumococcal interactions. PMID:32592597
Quantitative analysis of proteins which are members of the same protein complex but cause locus heterogeneity in disease. PMID:32591566
Expansions of chemosensory gene orthologs among selected tsetse fly species and their expressions in Glossina morsitans morsitans tsetse fly. PMID:32589659
Identifying persistent structures in multiscale 'omics data. PMID:32587977
Transcriptogram analysis reveals relationship between viral titer and gene sets responses during Corona-virus infection. PMID:32587961
Multiple Forms of Multifunctional Proteins in Health and Disease. PMID:32587857
Redox States of Protein Cysteines in Pathways of Protein Turnover and Cytoskeleton Dynamics Are Changed with Aging and Reversed by Slc7a11 Restoration in Mouse Lung Fibroblasts. PMID:32587657
Generation of High Yielding and Fragrant Rice (Oryza sativa L.) Lines by CRISPR/Cas9 Targeted Mutagenesis of Three Homoeologs of Cytochrome P450 Gene Family and OsBADH2 and Transcriptome and Proteome Profiling of Revealed Changes Triggered by Mutations. PMID:32586052
Transcriptomic microRNA Profiling of Dendritic Cells in Response to Gut Microbiota-Secreted Vesicles. PMID:32585977
Identification of Cell-Surface Proteins Endocytosed by Human Brain Microvascular Endothelial Cells In Vitro. PMID:32585920
Epigenome-450K-wide methylation signatures of active cigarette smoking: The Young Finns Study. PMID:32583859
Transcriptome Profiling of Pacu (Piaractus mesopotamicus) Challenged With Pathogenic Aeromonas hydrophila: Inference on Immune Gene Response. PMID:32582300
Phenotypic Responses to and Genetic Architecture of Sterility Following Exposure to Sub-Lethal Temperature During Development. PMID:32582294
Bioinformatics Analysis of Prognostic miRNA Signature and Potential Critical Genes in Colon Cancer. PMID:32582275
Identification of Target Genes and Transcription Factors in Mice with LMNA-Related Dilated Cardiomyopathy by Integrated Bioinformatic Analyses. PMID:32581210
Transcriptome Analysis of Wounding in the Model Grass Lolium temulentum. PMID:32580425
Deletion of the Dishevelled family of genes disrupts anterior-posterior axis specification and selectively prevents mesoderm differentiation. PMID:32579954
Identification of Conserved Proteomic Networks in Neurodegenerative Dementia. PMID:32579933
Drosophila models of pathogenic copy-number variant genes show global and non-neuronal defects during development. PMID:32579612
Detecting and correcting misclassified sequences in the large-scale public databases. PMID:32579213
Comparative and Phylogenetic Analyses of the Complete Chloroplast Genomes of Six Almond Species (Prunus spp. L.). PMID:32576920
Platelet-Released Growth Factors and Platelet-Rich Fibrin Induce Expression of Factors Involved in Extracellular Matrix Organization in Human Keratinocytes. PMID:32575800
A Knowledge-Based Machine Learning Approach to Gene Prioritisation in Amyotrophic Lateral Sclerosis. PMID:32575372
Skd3 (human ClpB) is a potent mitochondrial protein disaggregase that is inactivated by 3-methylglutaconic aciduria-linked mutations. PMID:32573439
Proteome-Wide Analyses Reveal the Diverse Functions of Lysine 2-Hydroxyisobutyrylation in Oryza sativa. PMID:32572646
Manumycin polyketides act as molecular glues between UBR7 and P53. PMID:32572277
The role of rare compound heterozygous events in autism spectrum disorder. PMID:32572023
Immune-related genes in tumor-specific CD4+ and CD8+ T cells in colon cancer. PMID:32571262
Dissecting the phenotypic components and genetic architecture of maize stem vascular bundles using high-throughput phenotypic analysis. PMID:32569428
Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples. PMID:32568231
Bioinformatics analysis of different candidate genes involved in hepatocellular carcinoma induced by HepG2 cells or tumor cells of patients. PMID:32567431
Identification of a Robust Five-Gene Risk Model in Prostate Cancer: A Robust Likelihood-Based Survival Analysis. PMID:32566639
Comprehensive characterization of driver genes in diffuse large B cell lymphoma. PMID:32565964
The Long Noncoding RNA NEAT1 Promotes Sarcoma Metastasis by Regulating RNA Splicing Pathways. PMID:32561656
Identification of lncRNAs Involved in PCV2 Infection of PK-15 Cells. PMID:32560439
Upregulation of cGMP-dependent Protein Kinase (PRKG1) in the Development of Adolescent Idiopathic Scoliosis. PMID:32558266
Transcriptome-Wide Regulation of Key Developmental Pathways in the Mouse Neural Tube by Prenatal Alcohol Exposure. PMID:32557641
Sequencing of RNA in single cells reveals a distinct transcriptome signature of hematopoiesis in GATA2 deficiency. PMID:32556286
FOBI: an ontology to represent food intake data and associate it with metabolomic data. PMID:32556148
Multi-omics network analysis reveals distinct stages in the human aging progression in epidermal tissue. PMID:32554863
System-wide analyses of the fission yeast poly(A)+ RNA interactome reveal insights into organization and function of RNA-protein complexes. PMID:32554781
The evolution of sex-biased gene expression in the Drosophila brain. PMID:32554780
An integrated chemical environment with tools for chemical safety testing. PMID:32553663
Cold priming uncouples light- and cold-regulation of gene expression in Arabidopsis thaliana. PMID:32552683
SMRT sequencing of the full-length transcriptome of the white-backed planthopper Sogatella furcifera. PMID:32551204
Draft genome of the famous ornamental plant Paeonia suffruticosa. PMID:32551041
An age-independent gene signature for monitoring acute rejection in kidney transplantation. PMID:32550916
Enhanced immortalization, HUWE1 mutations and other biological drivers of breast invasive carcinoma in Black/African American patients. PMID:32550556
Two new functions in the WormBase Enrichment Suite. PMID:32550381
Identification of Hub Genes in Type 2 Diabetes Mellitus Using Bioinformatics Analysis. PMID:32547141
Identification of Pannexin 2 as a Novel Marker Correlating with Ferroptosis and Malignant Phenotypes of Prostate Cancer Cells. PMID:32547072
Transcriptome, Spliceosome and Editome Expression Patterns of the Porcine Endometrium in Response to a Single Subclinical Dose of Salmonella Enteritidis Lipopolysaccharide. PMID:32545766
Transcription Analysis of the Chemerin Impact on Gene Expression Profile in the Luteal Cells of Gilts. PMID:32545672
Unraveling the Genomic-Epigenomic Interaction Landscape in Triple Negative and Non-Triple Negative Breast Cancer. PMID:32545594
RNA Binding Proteins as Drivers and Therapeutic Target Candidates in Pancreatic Ductal Adenocarcinoma. PMID:32545414
Relative Abundance of SARS-CoV-2 Entry Genes in the Enterocytes of the Lower Gastrointestinal Tract. PMID:32545271
Impact of Regulatory T Cells on Type 2 Alveolar Epithelial Cell Transcriptomes during Resolution of Acute Lung Injury and Contributions of IFN-γ. PMID:32543909
Genome-wide CRISPR synthetic lethality screen identifies a role for the ADP-ribosyltransferase PARP14 in DNA replication dynamics controlled by ATR. PMID:32542389
DNA methylation-based diagnostic and prognostic biomarkers of nasopharyngeal carcinoma patients. PMID:32541515
Long-term Changes in the Central Amygdala Proteome in Rats with a History of Chronic Cocaine Self-administration. PMID:32540363
Dynamic rewiring of the human interactome by interferon signaling. PMID:32539747
Identification of a competing endogenous RNA network associated with prognosis of pancreatic adenocarcinoma. PMID:32536819
Fatty acid bioconversion in harpacticoid copepods in a changing environment: a transcriptomic approach. PMID:32536309
CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis. PMID:32533075
Gene Expression Profiling in Fibromyalgia Indicates an Autoimmune Origin of the Disease and Opens New Avenues for Targeted Therapy. PMID:32532082
Expression of SARS-CoV-2 receptor ACE2 and coincident host response signature varies by asthma inflammatory phenotype. PMID:32531372
Insights into the mechanism of cyanobacteria removal by the algicidal fungi Bjerkandera adusta and Trametes versicolor. PMID:32529805
Data of de novo assembly and annotation of transcriptome from Aspidistra fenghuangensis (Asparagaceae: Nolinoideae). PMID:32529008
Whole-genome sequencing provides insights into the genetic diversity and domestication of bitter gourd (Momordica spp.). PMID:32528697
Differentially Regulated Transcription Factors and ABC Transporters in a Mitochondrial Dynamics Mutant Can Alter Azole Susceptibility of Aspergillus fumigatus. PMID:32528443
Pituispheres Contain Genetic Variants Characteristic to Pituitary Adenoma Tumor Tissue. PMID:32528411
Transcriptional regulation of strigolactone signalling in Arabidopsis. PMID:32528176
Screening and functional identification of lncRNAs in antler mesenchymal and cartilage tissues using high-throughput sequencing. PMID:32528134
PINOT: an intuitive resource for integrating protein-protein interactions. PMID:32527260
Identification, characterization and functional differentiation of the NAC gene family and its roles in response to cold stress in ginseng, Panax ginseng C.A. Meyer. PMID:32525906
GOcats: A tool for categorizing Gene Ontology into subgraphs of user-defined concepts. PMID:32525872
Deep belief network-Based Matrix Factorization Model for MicroRNA-Disease Associations Prediction. PMID:32523330
mTADA is a framework for identifying risk genes from de novo mutations in multiple traits. PMID:32522981
A selective inference approach for false discovery rate control using multiomics covariates yields insights into disease risk. PMID:32522875
Cell Type- and Stimulation-Dependent Transcriptional Programs Regulated by Atg16L1 and Its Crohn's Disease Risk Variant T300A. PMID:32522834
A Photo-clickable ATP-Mimetic Reveals Nucleotide Interactors in the Membrane Proteome. PMID:32521230
PSIONplusm Server for Accurate Multi-Label Prediction of Ion Channels and Their Types. PMID:32517331
Novel Insights Into the Effects of Interleukin 6 Antagonism in Non-ST-Segment-Elevation Myocardial Infarction Employing the SOMAscan Proteomics Platform. PMID:32515246
Multilayered VBC score predicts sgRNAs that efficiently generate loss-of-function alleles. PMID:32514112
An improved clear cell renal cell carcinoma stage prediction model based on gene sets. PMID:32513106
Transcriptome Profiling of Toxoplasma gondii-Infected Human Cerebromicrovascular Endothelial Cell Response to Treatment with Monensin. PMID:32512820
Database Mining of Genes of Prognostic Value for the Prostate Adenocarcinoma Microenvironment Using the Cancer Gene Atlas. PMID:32509861
Integration of Transcriptome and Metabolome Provides Unique Insights to Pathways Associated With Obese Breast Cancer Patients. PMID:32509585
SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae). PMID:32509454
High expression of stromal signatures correlated with macrophage infiltration, angiogenesis and poor prognosis in glioma microenvironment. PMID:32509446
Comprehensive identification of a two-genesignature as a novel potential prognostic model for patients with medulloblastoma. PMID:32509164
Construction of an Immunogenomic Risk Score for Prognostication in Colon Cancer. PMID:32508884
Common neural and transcriptional correlates of inhibitory control underlie emotion regulation and memory control. PMID:32507888
The core SWI/SNF catalytic subunit Brg1 regulates nephron progenitor cell proliferation and differentiation. PMID:32504627
Interpreting molecular similarity between patients as a determinant of disease comorbidity relationships. PMID:32504002
Comparative Target Analysis of Chlorinated Biphenyl Antimicrobials Highlights MenG as a Molecular Target of Triclocarban. PMID:32503913
Phen2Gene: rapid phenotype-driven gene prioritization for rare diseases. PMID:32500119
GC-AG Introns Features in Long Non-coding and Protein-Coding Genes Suggest Their Role in Gene Expression Regulation. PMID:32499820
Defining Critical Genes During Spherule Remodeling and Endospore Development in the Fungal Pathogen, Coccidioides posadasii. PMID:32499817
Developmental alterations in the transcriptome of three distinct rodent models of schizophrenia. PMID:32497066
MIPPIE: the mouse integrated protein-protein interaction reference. PMID:32496562
Expression profiling of small intestinal neuroendocrine tumors identified pathways and gene networks linked to tumorigenesis and metastasis. PMID:32496505
Identification of prognostic gene biomarkers for metastatic skin cancer using data mining. PMID:32494360
Draft genome sequence of Actinomadura sp. K4S16 and elucidation of the nonthmicin biosynthetic pathway. PMID:32494308
Excessive Homeostatic Gain in Spinal Motoneurons in a Mouse Model of Amyotrophic Lateral Sclerosis. PMID:32493926
A tissue level atlas of the healthy human virome. PMID:32493363
Assembly and Function of a Bioengineered Human Liver for Transplantation Generated Solely from Induced Pluripotent Stem Cells. PMID:32492423
Genome sequence and comparative analysis of reindeer (Rangifer tarandus) in northern Eurasia. PMID:32488117
Multiplexed relative and absolute quantitative immunopeptidomics reveals MHC I repertoire alterations induced by CDK4/6 inhibition. PMID:32488085
Proteomic signatures of metronidazole-resistant Trichomonas vaginalis reveal novel proteins associated with drug resistance. PMID:32487244
Urban air particulate matter induces mitochondrial dysfunction in human olfactory mucosal cells. PMID:32487172
Identification and characterization of male reproduction-related genes in pig (Sus scrofa) using transcriptome analysis. PMID:32487021
Using Reactome to build an autophagy mechanism knowledgebase. PMID:32486891
Transcriptome Analysis of Maternal Gene Transcripts in Unfertilized Eggs of Misgurnus anguillicaudatus and Identification of Immune-Related Maternal Genes. PMID:32485896
Cadmium, Smoking, and Human Blood DNA Methylation Profiles in Adults from the Strong Heart Study. PMID:32484362
Unraveling tumor-immune heterogeneity in advanced ovarian cancer uncovers immunogenic effect of chemotherapy. PMID:32483290
A-kinase-anchoring protein 1 (dAKAP1)-based signaling complexes coordinate local protein synthesis at the mitochondrial surface. PMID:32482893
A bibliometric analysis and visualization of medical data mining research. PMID:32481411
Differential gene expression in response to water deficit in leaf and root tissues of soybean genotypes with contrasting tolerance profiles. PMID:32478791
Possible key microRNAs and corresponding molecular mechanisms for atrial fibrillation. PMID:32478689
Draft genome sequence data of Microbacterium sp. strain Be9 isolated from uranium-mill tailings porewaters. PMID:32478160
A potential prognostic model based on miRNA expression profile in The Cancer Genome Atlas for bladder cancer patients. PMID:32477968
Expression Quantitative Trait Loci (eQTL) Mapping in Korean Patients With Crohn's Disease and Identification of Potential Causal Genes Through Integration With Disease Associations. PMID:32477412
Computational Prediction of Ubiquitination Proteins Using Evolutionary Profiles and Functional Domain Annotation. PMID:32476995
Serum proteomics analysis of feline mammary carcinoma based on label-free and PRM techniques. PMID:32476319
Comparative transcriptome analysis digs out genes related to antifreeze between fresh and frozen-thawed rooster sperm. PMID:32475417
Molecular signature of eutopic endometrium in endometriosis based on the multi-omics integrative synthesis. PMID:32474803
STAT5 is required for lipid breakdown and beta-adrenergic responsiveness of brown adipose tissue. PMID:32473405
Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum. PMID:32471448
X-ray Structure-Based Chemoinformatic Analysis Identifies Promiscuous Ligands Binding to Proteins from Different Classes with Varying Shapes. PMID:32471121
Silencing trust: confidence and familiarity in re-engineering knowledge infrastructures. PMID:32468194
Expression profile of circular RNAs in the peripheral blood of neonates with hypoxic‑ischemic encephalopathy. PMID:32468058
Principal component analysis on LC‑MS/MS and 2DE‑MALDI‑TOF in glioblastoma cell lines reveals that mitochondria act as organelle sensors of the metabolic state in glioblastoma. PMID:32468038
Drug screening and identification of key candidate genes and pathways of rheumatoid arthritis. PMID:32468016
Comparative Analyses of Five Complete Chloroplast Genomes from the Genus Pterocarpus (Fabacaeae). PMID:32466556
A memory of eS25 loss drives resistance phenotypes. PMID:32463448
Transcript expression-aware annotation improves rare variant interpretation. PMID:32461655
Itch attenuates CD4 T-cell proliferation in mice by limiting WBP2 protein stability. PMID:32459862
Third-Generation Sequencing Reveals LncRNA-Regulated HSP Genes in the Populus x canadensis Moench Heat Stress Response. PMID:32457788
Identification of Prognostic miRNA Signature and Lymph Node Metastasis-Related Key Genes in Cervical Cancer. PMID:32457603
Inferring Virus-Host relationship between HPV and its host Homo sapiens using protein interaction network. PMID:32457456
ARTDeco: automatic readthrough transcription detection. PMID:32456667
Proteomics of intracellular freezing survival. PMID:32453791
De novo identification of toxicants that cause irreparable damage to parasitic nematode intestinal cells. PMID:32453724
A transcriptomic map of murine and human alopecia areata. PMID:32453712
Integrated analysis of lncRNA-associated ceRNA network identified potential regulatory interactions in osteosarcoma. PMID:32453338
A disintegrin and metalloproteinase domain 17-epidermal growth factor receptor signaling contributes to oral cancer pain. PMID:32453136
Epigenetic deregulation of lamina-associated domains in Hutchinson-Gilford progeria syndrome. PMID:32450911
Multipathway synergy promotes testicular transition from growth to spermatogenesis in early-puberty goats. PMID:32450814
Functional Annotations of Single-Nucleotide Polymorphism (SNP)-Based and Gene-Based Genome-Wide Association Studies Show Genes Affecting Keratitis Susceptibility. PMID:32450567
ASAP 2020 update: an open, scalable and interactive web-based portal for (single-cell) omics analyses. PMID:32449934
Regulation of gene expression by MF63, a selective inhibitor of microsomal PGE synthase 1 (mPGES1) in human osteoarthritic chondrocytes. PMID:32449517
A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function. PMID:32449511
Network Pharmacology to Uncover the Molecular Mechanisms of Action of LeiGongTeng for the Treatment of Nasopharyngeal Carcinoma. PMID:32448862
Replicated umbilical cord blood DNA methylation loci associated with gestational age at birth. PMID:32448018
Research Techniques Made Simple: Whole-Transcriptome Sequencing by RNA-Seq for Diagnosis of Monogenic Disorders. PMID:32446329
Disease swamps molecular signatures of genetic-environmental associations to abiotic factors in Tasmanian devil (Sarcophilus harrisii) populations. PMID:32445281
Discrete populations of isotype-switched memory B lymphocytes are maintained in murine spleen and bone marrow. PMID:32444631
Screening and identification of key biomarkers for retinoblastoma: Evidence from bioinformatics analysis. PMID:32443297
ThETA: transcriptome-driven efficacy estimates for gene-based TArget discovery. PMID:32437556
Effect of aging on the transcriptomic changes associated with the expression of the HERV-K (HML-2) provirus at 1q22. PMID:32435269
Bioinformatics Analysis Identifies the Estrogen Receptor 1 (ESR1) Gene and hsa-miR-26a-5p as Potential Prognostic Biomarkers in Patients with Intrahepatic Cholangiocarcinoma. PMID:32435051
Transcriptome profiling of digital flexor tendons after injury in a chicken model. PMID:32432656
Gene regulation could be attributed to TCF3 and other key transcription factors in the muscle of pubertal heifers. PMID:32432381
Arsenic Disulfide Promoted Hypomethylation by Increasing DNA Methyltransferases Expression in Myelodysplastic Syndrome. PMID:32431489
TRPM7 Mediates Neuronal Cell Death Upstream of Calcium/Calmodulin-Dependent Protein Kinase II and Calcineurin Mechanism in Neonatal Hypoxic-Ischemic Brain Injury. PMID:32430797
Characterization of Stem-like Circulating Tumor Cells in Pancreatic Cancer. PMID:32429174
A Single-Cell Transcriptional Roadmap of the Mouse and Human Lymph Node Lymphatic Vasculature. PMID:32426372
Quantifying genetic effects on disease mediated by assayed gene expression levels. PMID:32424349
The genome of Mekong tiger perch (Datnioides undecimradiatus) provides insights into the phylogenetic position of Lobotiformes and biological conservation. PMID:32424221
Transcriptome-wide organization of subcellular microenvironments revealed by ATLAS-Seq. PMID:32421779
Molecular Signatures of Placentation and Secretion Uncovered in Poeciliopsis Maternal Follicles. PMID:32421768
Identification of potential novel differentially-expressed genes and their role in invasion and migration in renal cell carcinoma. PMID:32420905
Screening and Identification of Differentially Expressed Genes Expressed among Left and Right Colon Adenocarcinoma. PMID:32420374
Key genes of renal tubular necrosis: a bioinformatics analysis. PMID:32420172
Identification of significant genes with prognostic influence in clear cell renal cell carcinoma via bioinformatics analysis. PMID:32420151
A Network Pharmacology-Based Study on the Anti-Lung Cancer Effect of Dipsaci Radix. PMID:32419823
Gene Ontology Curation of Neuroinflammation Biology Improves the Interpretation of Alzheimer's Disease Gene Expression Data. PMID:32417785
Large-scale network analysis captures biological features of bacterial plasmids. PMID:32415210
Myocardial micro-biopsy procedure for molecular characterization with increased precision and reduced trauma. PMID:32415191
Identification of differentially expressed genes in actinic keratosis samples treated with ingenol mebutate gel. PMID:32413042
Plasma MicroRNA Expression Profiles in Psoriasis. PMID:32411787
SDN2GO: An Integrated Deep Learning Model for Protein Function Prediction. PMID:32411695
Global Transcriptional Profiling Reveals Novel Autocrine Functions of Interleukin 6 in Human Vascular Endothelial Cells. PMID:32410854
Tropomyosin 1 genetically constrains in vitro hematopoiesis. PMID:32408895
Identification of transforming growth factor beta induced (TGFBI) as an immune-related prognostic factor in clear cell renal cell carcinoma (ccRCC). PMID:32406866
Genome Sequencing and Analysis of the Fungal Symbiont of Sirex noctilio, Amylostereum areolatum: Revealing the Biology of Fungus-Insect Mutualism. PMID:32404513
Integrated small RNA and mRNA expression profiles reveal miRNAs and their target genes in response to Aspergillus flavus growth in peanut seeds. PMID:32404101
Therapeutic potential of lipids obtained from γ-irradiated PBMCs in dendritic cell-mediated skin inflammation. PMID:32403085
Alternative splicing of LSD1+8a in neuroendocrine prostate cancer is mediated by SRRM4. PMID:32403054
Ewastools: Infinium Human Methylation BeadChip pipeline for population epigenetics integrated into Galaxy. PMID:32401319
Revenant: a database of resurrected proteins. PMID:32400867
Transcriptional Sequencing and Gene Expression Analysis of Various Genes in Fruit Development of Three Different Black Pepper (Piper nigrum L.) Varieties. PMID:32399475
Transcriptomics in Toxicogenomics, Part II: Preprocessing and Differential Expression Analysis for High Quality Data. PMID:32397130
Zonation of Ribosomal DNA Transcription Defines a Stem Cell Hierarchy in Colorectal Cancer. PMID:32396863
Integrated urine proteomics and renal single-cell genomics identify an IFN-γ response gradient in lupus nephritis. PMID:32396533
Lower oxygen consumption and Complex I activity in mitochondria isolated from skeletal muscle of fetal sheep with intrauterine growth restriction. PMID:32396498
Suppression of Endothelial AGO1 Promotes Adipose Tissue Browning and Improves Metabolic Dysfunction. PMID:32393053
CoCoCoNet: conserved and comparative co-expression across a diverse set of species. PMID:32392296
CK14 Expression Identifies a Basal/Squamous-Like Type of Papillary Non-Muscle-Invasive Upper Tract Urothelial Carcinoma. PMID:32391279
Post-transcriptional regulation of several biological processes involved in latex production in Hevea brasiliensis. PMID:32391199
A Literature Review of Gene Function Prediction by Modeling Gene Ontology. PMID:32391061
Shared Regulatory Pathways Reveal Novel Genetic Correlations Between Grip Strength and Neuromuscular Disorders. PMID:32391060
Identifying Candida albicans Gene Networks Involved in Pathogenicity. PMID:32391057
Transcriptome Analysis Reveals the Flexibility of Cordycepin Network in Cordyceps militaris Activated by L-Alanine Addition. PMID:32390960
Functional genomics analysis of human colon organoids identifies key transcription factors. PMID:32390556
Compensatory combination of romidepsin with gemcitabine and cisplatin to effectively and safely control urothelial carcinoma. PMID:32390005
Bioinformatics Analysis and High-Throughput Sequencing to Identify Differentially Expressed Genes in Nebulin Gene (NEB) Mutations Mice. PMID:32390000
Applying knowledge-driven mechanistic inference to toxicogenomics. PMID:32387679
An improved high-quality genome assembly and annotation of Tibetan hulless barley. PMID:32385314
Tomato Atypical Receptor Kinase1 Is Involved in the Regulation of Preinvasion Defense. PMID:32385090
Comparative Transcriptome Analysis Combining SMRT- and Illumina-Based RNA-Seq Identifies Potential Candidate Genes Involved in Betalain Biosynthesis in Pitaya Fruit. PMID:32384685
Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era. PMID:32384671
Comprehensive analysis of mutations of renal cell carcinoma in an autosomal dominant polycystic kidney disease patient. PMID:32384474
A putative competing endogenous RNA network in cisplatin-resistant lung adenocarcinoma cells identifying potentially rewarding research targets. PMID:32382346
Proteomic Profiling of Small Extracellular Vesicles Secreted by Human Pancreatic Cancer Cells Implicated in Cellular Transformation. PMID:32382024
De novo transcriptome sequence of Senna tora provides insights into anthraquinone biosynthesis. PMID:32380515
Polygenic risk scores indicates genetic overlap between peripheral pain syndromes and chronic postsurgical pain. PMID:32377986
Chromosome-scale assembly of the Kandelia obovata genome. PMID:32377365
A high-quality reference genome of wild Cannabis sativa. PMID:32377363
Phenotypic Associations Among Cell Cycle Genes in Saccharomyces cerevisiae. PMID:32376676
A MicroRNA Signature Identifies Pancreatic Ductal Adenocarcinoma Patients at Risk for Lymph Node Metastases. PMID:32376411
Comparative analysis of tissue-specific transcriptomic responses to nitrogen stress in spinach (Spinacia oleracea). PMID:32374731
A Novel Computational Approach for Identifying Essential Proteins From Multiplex Biological Networks. PMID:32373163
Genome and Transcriptome Analyses Provide Insight Into the Omega-3 Long-Chain Polyunsaturated Fatty Acids Biosynthesis of Schizochytrium limacinum SR21. PMID:32373097
Genome Sequencing and Analysis of the Hypocrellin-Producing Fungus Shiraia bambusicola S4201. PMID:32373091
Cellular Analysis and Comparative Transcriptomics Reveal the Tolerance Mechanisms of Candida tropicalis Toward Phenol. PMID:32373081
Dark-rearing uncovers novel gene expression patterns in an obligate cave-dwelling fish. PMID:32372488
Transcriptome profiling reveals insertional mutagenesis suppressed the expression of candidate pathogenicity genes in honeybee fungal pathogen, Ascosphaera apis. PMID:32372055
A single-cell transcriptomic landscape of primate arterial aging. PMID:32371953
A Guide to Understanding "State-of-the-Art" Basic Research Techniques in Anesthesiology. PMID:32371742
Identification of key genes, pathways and potential therapeutic agents for IgA nephropathy using an integrated bioinformatics analysis. PMID:32370650
Analysis of differentially expressed genes and pathways associated with male sterility lines in watermelon via bulked segregant RNA-seq. PMID:32368431
Evaluation of the proteomic profiles of ejaculated spermatozoa from Saanen bucks ( Capra hircus ). PMID:32368270
In Vitro Evaluation of the Effects of Commercial Prebiotic GOS and FOS Products on Human Colonic Caco-2 Cells. PMID:32366023
The Influence of Methylating Mutations on Acute Myeloid Leukemia: Preliminary Analysis on 56 Patients. PMID:32365516
Population-Specific Genetic and Expression Differentiation in Europeans. PMID:32365201
Genome-wide association study of MRI markers of cerebral small vessel disease in 42,310 participants. PMID:32358547
CARD9-Associated Dectin-1 and Dectin-2 Are Required for Protective Immunity of a Multivalent Vaccine against Coccidioides posadasii Infection. PMID:32358020
Human adipose-derived mesenchymal stem cell-conditioned medium ameliorates polyneuropathy and foot ulceration in diabetic BKS db/db mice. PMID:32357914
Negative binomial additive model for RNA-Seq data analysis. PMID:32357831
Analysis of potential hub genes involved in the pathogenesis of Chinese type 1 diabetic patients. PMID:32355739
Identification and integrated analysis of hepatocellular carcinoma-related circular RNA signature. PMID:32355738
Identification of biomarkers for the transition from low-grade glioma to secondary glioblastoma by an integrated bioinformatic analysis. PMID:32355537
Comprehensive analysis of the SLC16A gene family in pancreatic cancer via integrated bioinformatics. PMID:32355273
The negative regulator SMAX1 controls mycorrhizal symbiosis and strigolactone biosynthesis in rice. PMID:32355217
Genetic Underpinnings of Host Manipulation by Ophiocordyceps as Revealed by Comparative Transcriptomics. PMID:32354705
Integrated Analysis of mRNA and microRNA Elucidates the Regulation of Glycyrrhizic Acid Biosynthesis in Glycyrrhiza uralensis Fisch. PMID:32353999
Community curation in PomBase: enabling fission yeast experts to provide detailed, standardized, sharable annotation from research publications. PMID:32353878
Comparative mitochondrial proteomics of Leishmania tropica clinical isolates resistant and sensitive to meglumine antimoniate. PMID:32350589
Polymorphisms in miRNA binding sites involved in metabolic diseases in mice and humans. PMID:32350386
Comprehensive Immunoprofiling of Pediatric Zika Reveals Key Role for Monocytes in the Acute Phase and No Effect of Prior Dengue Virus Infection. PMID:32348760
Contribution of common and rare damaging variants in familial forms of bipolar disorder and phenotypic outcome. PMID:32345981
Gene expression profiles for low-dose exposure to diethyl phthalate in rodents and humans: a translational study with implications for breast carcinogenesis. PMID:32341500
The phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia. PMID:32341346
Shared genetic architecture and casual relationship between leptin levels and type 2 diabetes: large-scale cross-trait meta-analysis and Mendelian randomization analysis. PMID:32341051
ABC Efflux Transporters and the Circuitry of miRNAs: Kinetics of Expression in Cancer Drug Resistance. PMID:32340269
Time Course of Changes in Sorafenib-Treated Hepatocellular Carcinoma Cells Suggests Involvement of Phospho-Regulated Signaling in Ferroptosis Induction. PMID:32336023
GATA2 and Progesterone Receptor Interaction in Endometrial Stromal Cells Undergoing Decidualization. PMID:32335672
Identification of Novel Targets of RBM5 in the Healthy and Injured Brain. PMID:32335213
Growth and elongation of axons through mechanical tension mediated by fluorescent-magnetic bifunctional Fe3O4·Rhodamine 6G@PDA superparticles. PMID:32334582
Transcriptomic profiling and discovery of key genes involved in adventitious root formation from green cuttings of highbush blueberry (Vaccinium corymbosum L.). PMID:32334538
A multiple genomic data fused SF2 prediction model, signature identification, and gene regulatory network inference for personalized radiotherapy. PMID:32329416
HIV-1 and Amyloid Beta Remodel Proteome of Brain Endothelial Extracellular Vesicles. PMID:32326569
Identification of AflR Binding Sites in the Genome of Aspergillus flavus by ChIP-Seq. PMID:32326370
Association of Proteins Modulating Immune Response and Insulin Clearance During Gestation with Antenatal Complications in Patients with Gestational or Type 2 Diabetes Mellitus. PMID:32326243
Red Chinese Cabbage Transcriptome Analysis Reveals Structural Genes and Multiple Transcription Factors Regulating Reddish Purple Color. PMID:32326209
Protein Synthesis by Day 16 Bovine Conceptuses during the Time of Maternal Recognition of Pregnancy. PMID:32325999
BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. PMID:32325033
STAT3-dependent analysis reveals PDK4 as independent predictor of recurrence in prostate cancer. PMID:32323921
Patient‑derived orthotopic xenograft glioma models fail to replicate the magnetic resonance imaging features of the original patient tumor. PMID:32323818
Application of weighted gene co‑expression network analysis to explore the potential diagnostic biomarkers for colorectal cancer. PMID:32323816
A novel plasma lncRNA ENST00000416361 is upregulated in coronary artery disease and is related to inflammation and lipid metabolism. PMID:32323776
Abnormal DNA methylation patterns in patients with infection‑caused leukocytopenia based on methylation microarrays. PMID:32323775
Pilot study and bioinformatics analysis of differentially expressed genes in adipose tissues of rats with excess dietary intake. PMID:32323762
A comparative chemogenic analysis for predicting Drug-Target Pair via Machine Learning Approaches. PMID:32322011
CRISPR-mediated gene targeting of CK1δ/ε leads to enhanced understanding of their role in endocytosis via phosphoregulation of GAPVD1. PMID:32321936
Identification of key miRNAs and genes for mouse retinal development using a linear model. PMID:32319662
Divergence of Peroxisome Membrane Gene Sequence and Expression Between Yeast Species. PMID:32317271
Common gene expression signatures in Parkinson's disease are driven by changes in cell composition. PMID:32317022
De Novo Transcriptome Assembly and Annotation of Liver and Brain Tissues of Common Brushtail Possums (Trichosurus vulpecula) in New Zealand: Transcriptome Diversity after Decades of Population Control. PMID:32316496
Fold-Change-Specific Enrichment Analysis (FSEA): Quantification of Transcriptional Response Magnitude for Functional Gene Groups. PMID:32316383
Prostate cancer cell-intrinsic interferon signaling regulates dormancy and metastatic outgrowth in bone. PMID:32314873
SPEED2: inferring upstream pathway activity from differential gene expression. PMID:32313938
RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis. PMID:32311035
Bioinformatics analysis and verification of gene targets for benign tracheal stenosis. PMID:32309912
Impaired Metabolic Pathways Related to Colorectal Cancer Progression and Therapeutic Implications. PMID:32309224
BioHackathon 2015: Semantics of data for life sciences and reproducible research. PMID:32308977
Full-length transcriptome sequencing and comparative transcriptomic analysis to uncover genes involved in early gametogenesis in the gonads of Amur sturgeon (Acipenser schrenckii). PMID:32308726
Genome of extreme halophyte Puccinellia tenuiflora. PMID:32306894
Enterovirus A71 Oncolysis of Malignant Gliomas. PMID:32304669
POLE2 Serves as a Prognostic Biomarker and Is Associated with Immune Infiltration in Squamous Cell Lung Cancer. PMID:32304567
Pleiotropy-Based Decomposition of Genetic Risk Scores: Association and Interaction Analysis for Type 2 Diabetes and CAD. PMID:32302534
A Five-Genes-Based Prognostic Signature for Cervical Cancer Overall Survival Prediction. PMID:32300605
Non-contiguous finished genome sequence and description of Bartonella saheliensis sp. nov. from the blood of Gerbilliscus gambianus from Senegal. PMID:32300480
Draft Genome Assembly for the Tibetan Black Bear (Ursus thibetanus thibetanus). PMID:32300354
Integrated Analysis to Evaluate the Prognostic Value of Signature mRNAs in Glioblastoma Multiforme. PMID:32296458
Learning-induced mRNA alterations in olfactory bulb mitral cells in neonatal rats. PMID:32295841
Insulin-Like Growth Factors Are Key Regulators of T Helper 17 Regulatory T Cell Balance in Autoimmunity. PMID:32294406
Transcriptomic diversity in seedling roots of European flint maize in response to cold. PMID:32293268
Stress-mediated convergence of splicing landscapes in male and female rock doves. PMID:32293250
Draft genome of Rosenbergiella nectarea strain 8N4T provides insights into the potential role of this species in its plant host. PMID:32292647
Transcriptomic Prediction of Pig Liver-Enriched Gene 1 Functions in a Liver Cell Line. PMID:32290278
Astrocyte-Derived Small Extracellular Vesicles Regulate Dendritic Complexity through miR-26a-5p Activity. PMID:32290095
Novel insight into theacrine metabolism revealed by transcriptome analysis in bitter tea (Kucha, Camellia sinensis). PMID:32286351
The morphology, molecular development and ecological function of pseudonectaries on Nigella damascena (Ranunculaceae) petals. PMID:32286317
Identification of Key Genes and Pathways for Enchondromas by Bioinformatics Analysis. PMID:32284694
Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution. PMID:32284579
Mutational landscape and genetic signatures of cell-free DNA in tumour-induced osteomalacia. PMID:32277576
Development of IFN-Stimulated Gene Expression from Embryogenesis through Adulthood, with and without Constitutive MDA5 Pathway Activation. PMID:32277054
Hydra: A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures. PMID:32275708
eXplainable Artificial Intelligence (XAI) for the identification of biologically relevant gene expression patterns in longitudinal human studies, insights from obesity research. PMID:32275707
Genome-wide DNA polymorphisms in four Actinidia arguta genotypes based on whole-genome re-sequencing. PMID:32275655
Modulator-Dependent RBPs Changes Alternative Splicing Outcomes in Kidney Cancer. PMID:32273884
GOMCL: a toolkit to cluster, evaluate, and extract non-redundant associations of Gene Ontology-based functions. PMID:32272889
Transcriptional and Spatial Resolution of Cell Types in the Mammalian Habenula. PMID:32272058
Diversity of peripheral blood human NK cells identified by single-cell RNA sequencing. PMID:32271902
Draft genome of multiple resistance donor plant Sinapis alba: An insight into SSRs, annotations and phylogenetics. PMID:32271806
Loci associated with conception rate in crossbred beef heifers. PMID:32271764
Integrative genomics analysis of eQTL and GWAS summary data identifies PPP1CB as a novel bone mineral density risk genes. PMID:32266926
Identification of core genes associated with prostate cancer progression and outcome via bioinformatics analysis in multiple databases. PMID:32266115
Integrated Analysis of Long Non-coding RNAs (lncRNAs) and mRNAs Reveals the Regulatory Role of lncRNAs Associated With Salt Resistance in Camellia sinensis. PMID:32265948
Test of Arabidopsis Space Transcriptome: A Discovery Environment to Explore Multiple Plant Biology Spaceflight Experiments. PMID:32265943
Exercise Training in Obese Rats Does Not Induce Browning at Thermoneutrality and Induces a Muscle-Like Signature in Brown Adipose Tissue. PMID:32265830
Identification of Co-expressed Genes Between Atrial Fibrillation and Stroke. PMID:32265825
Systems Pharmacology-Based Strategy to Investigate Pharmacological Mechanisms of Radix Puerariae for Treatment of Hypertension. PMID:32265716
Stable intronic sequence RNAs (sisRNAs) are selected regions in introns with distinct properties. PMID:32264855
A high-quality genome provides insights into the new taxonomic status and genomic characteristics of Cladopus chinensis (Podostemaceae). PMID:32257232
Chromosome doubling mediates superior drought tolerance in Lycium ruthenicum via abscisic acid signaling. PMID:32257226
Network Pharmacology-Based Strategy for Predicting Therapy Targets of Traditional Chinese Medicine Xihuang Pill on Liver Cancer. PMID:32256653
Cell type-specific transcriptomics of esophageal adenocarcinoma as a scalable alternative for single cell transcriptomics. PMID:32255255
A novel method to predict essential proteins based on tensor and HITS algorithm. PMID:32252824
Unveiling new disease, pathway, and gene associations via multi-scale neural network. PMID:32251458
Cell Type-Specific Intralocus Interactions Reveal Oligodendrocyte Mechanisms in MS. PMID:32246942
Activation of a Subset of Evolutionarily Young Transposable Elements and Innate Immunity Are Linked to Clinical Responses to 5-Azacytidine. PMID:32245794
Genomic Features of Cladobotryum dendroides, Which Causes Cobweb Disease in Edible Mushrooms, and Identification of Genes Related to Pathogenicity and Mycoparasitism. PMID:32245129
Cytoplasm Types Affect DNA Methylation among Different Cytoplasmic Male Sterility Lines and Their Maintainer Line in Soybean (Glycine max L.). PMID:32245080
Cardiac miRNA Expression and their mRNA Targets in a Rat Model of Prediabetes. PMID:32244869
Adaptive Shifts in Gene Regulation Underlie a Developmental Delay in Thermogenesis in High-Altitude Deer Mice. PMID:32243546
Single-cell analysis of a mutant library generated using CRISPR-guided deaminase in human melanoma cells. PMID:32242071
EpiMOLAS: an intuitive web-based framework for genome-wide DNA methylation analysis. PMID:32241255
Functional genomics by integrated analysis of transcriptome of sweet potato (Ipomoea batatas (L.) Lam.) during root formation. PMID:32240514
Altered expression of glycoprotein non‑metastatic melanoma protein B in the distal sciatic nerve following injury. PMID:32236569
Uncovering Prognosis-Related Genes and Pathways by Multi-Omics Analysis in Lung Cancer. PMID:32235589
To construct a ceRNA regulatory network as prognostic biomarkers for bladder cancer. PMID:32233022
Transcriptome sequencing and analysis reveals the molecular response to selenium stimuli in Pueraria lobata (willd.) Ohwi. PMID:32231880
Transcriptome Ortholog Alignment Sequence Tools (TOAST) for phylogenomic dataset assembly. PMID:32228442
Decreased Expression of NUSAP1 Predicts Poor Overall Survival in Cervical Cancer. PMID:32226503
CircRNA Expression Profiles and the Potential Role of CircZFP644 in Mice With Severe Acute Pancreatitis via Sponging miR-21-3p. PMID:32226441
WeiBI (web-based platform): Enriching integrated interaction network with increased coverage and functional proteins from genome-wide experimental OMICS data. PMID:32221380
Integrative differential expression and gene set enrichment analysis using summary statistics for scRNA-seq studies. PMID:32221292
Genetic Architecture of Gene Expression in European and African Americans: An eQTL Mapping Study in GENOA. PMID:32220292
Identification of hub genes associated with outcome of clear cell renal cell carcinoma. PMID:32218839
Comparative Transcriptome Analyses of Schistosoma japonicum Derived From SCID Mice and BALB/c Mice: Clues to the Abnormality in Parasite Growth and Development. PMID:32218772
Effect of Ionizing Radiation on Transcriptome during Neural Differentiation of Human Embryonic Stem Cells. PMID:32216708
Traditional Chinese Medicine Containing Arsenic Treated MDS Patients Effectively through Regulating Aberrant Hypomethylation. PMID:32215045
The transcriptome of the newt Cynops orientalis provides new insights into evolution and function of sexual gene networks in sarcopterygians. PMID:32214214
Endogenous siRNAs promote proteostasis and longevity in germline-less Caenorhabditis elegans. PMID:32213289
Dataset for de novo transcriptome assembly of the African bullfrog Pyxicephalus adspersus. PMID:32211462
CLING: Candidate Cancer-Related lncRNA Prioritization via Integrating Multiple Biological Networks. PMID:32211391
A Computational Approach for Mapping Heme Biology in the Context of Hemolytic Disorders. PMID:32211383
Divergent northern and southern populations and demographic history of the pearl oyster in the western Pacific revealed with genomic SNPs. PMID:32211071
Metadata Analysis of mcr-1-Bearing Plasmids Inspired by the Sequencing Evidence for Horizontal Transfer of Antibiotic Resistance Genes Between Polluted River and Wild Birds. PMID:32210943
Bioinformatic Analysis Identifies Potential Key Genes in the Pathogenesis of Turner Syndrome. PMID:32210915
Rewilding Nod2 and Atg16l1 Mutant Mice Uncovers Genetic and Environmental Contributions to Microbial Responses and Immune Cell Composition. PMID:32209431
Sergentomyia schwetzi: Salivary gland transcriptome, proteome and enzymatic activities in two lineages adapted to different blood sources. PMID:32208452
Secreted Phosphoprotein 1 (SPP1) and Fibronectin 1 (FN1) Are Associated with Progression and Prognosis of Esophageal Cancer as Identified by Integrated Expression Profiles Analysis. PMID:32208405
Drp1 modulates mitochondrial stress responses to mitotic arrest. PMID:32203171
Standard machine learning approaches outperform deep representation learning on phenotype prediction from transcriptomics data. PMID:32197580
Protein modification with ISG15 blocks coxsackievirus pathology by antiviral and metabolic reprogramming. PMID:32195343
Identification and validation of HELLS (Helicase, Lymphoid-Specific) and ICAM1 (Intercellular adhesion molecule 1) as potential diagnostic biomarkers of lung cancer. PMID:32195055
Tip of the iceberg: roles of circRNAs in hematological malignancies. PMID:32195014
A roadmap for research in octoploid strawberry. PMID:32194969
Integrated bioinformatics analysis of the association between apolipoprotein E expression and patient prognosis in papillary thyroid carcinoma. PMID:32194729
Genome-Wide Analysis and Function Prediction of Long Noncoding RNAs in Sheep Pituitary Gland Associated with Sexual Maturation. PMID:32192168
Identification of potential key genes in gastric cancer using bioinformatics analysis. PMID:32190306
Immune-related prognosis biomarkers associated with osteosarcoma microenvironment. PMID:32190007
Sexual-biased gene expression of olfactory-related genes in the antennae of Conogethes pinicolalis (Lepidoptera: Crambidae). PMID:32188403
A Gene-Set Enrichment and Protein-Protein Interaction Network-Based GWAS with Regulatory SNPs Identifies Candidate Genes and Pathways Associated with Carcass Traits in Hanwoo Cattle. PMID:32188084
PDGFD induces ibrutinib resistance of diffuse large B‑cell lymphoma through activation of EGFR. PMID:32186759
Absolute yeast mitochondrial proteome quantification reveals trade-off between biosynthesis and energy generation during diauxic shift. PMID:32184324
CuAS: a database of annotated transcripts generated by alternative splicing in cucumbers. PMID:32183712
Comprehensive Phosphoproteomic Analysis of Pepper Fruit Development Provides Insight into Plant Signaling Transduction. PMID:32183026
Comprehensive analysis of circular RNA profiles in skeletal muscles of aging mice and after aerobic exercise intervention. PMID:32182212
Identification of key genes and pathways of diagnosis and prognosis in cervical cancer by bioinformatics analysis. PMID:32181600
Integrated miRNA/mRNA Counter-Expression Analysis Highlights Oxidative Stress-Related Genes CCR7 and FOXO1 as Blood Markers of Coronary Arterial Disease. PMID:32178422
Comprehensive Analysis of Differentially Expressed Profiles of mRNA, lncRNA, and circRNA in the Uterus of Seasonal Reproduction Sheep. PMID:32178360
Systematical Analysis of the Cancer Genome Atlas Database Reveals EMCN/MUC15 Combination as a Prognostic Signature for Gastric Cancer. PMID:32175327
C-terminal binding proteins 1 and 2 in traumatic brain injury-induced inflammation and their inhibition as an approach for anti-inflammatory treatment. PMID:32174788
Whole transcriptome expression profiles in placenta samples from women with gestational diabetes mellitus. PMID:32174045
Sjögren syndrome/scleroderma autoantigen 1 is a direct Tankyrase binding partner in cancer cells. PMID:32170109
Myeloid-specific deficiency of pregnane X receptor decreases atherosclerosis in LDL receptor-deficient mice. PMID:32170024
Comparative Transcriptome-Based Mining and Expression Profiling of Transcription Factors Related to Cold Tolerance in Peanut. PMID:32168930
Gene transcription profiling of astheno- and normo-zoospermic sperm subpopulations. PMID:32167074
Acid ceramidase of macrophages traps herpes simplex virus in multivesicular bodies and protects from severe disease. PMID:32165633
Investigating global gene expression changes in a murine model of cherubism. PMID:32165349
Identification of molecules associated with response to abatacept in patients with rheumatoid arthritis. PMID:32164778
Genes associated with inflammation may serve as biomarkers for the diagnosis of coronary artery disease and ischaemic stroke. PMID:32164735
Hepatic transcriptome of the freeze-tolerant Cope's gray treefrog, Dryophytes chrysoscelis: responses to cold acclimation and freezing. PMID:32164545
Gill transcriptomes reveal expression changes of genes related with immune and ion transport under salinity stress in silvery pomfret (Pampus argenteus). PMID:32162151
DNA methylation QTL analysis identifies new regulators of human longevity. PMID:32160291
Genome Sequence, Assembly, and Characterization of the Antagonistic Yeast Candida oleophila Used as a Biocontrol Agent Against Post-harvest Diseases. PMID:32158440
Transcriptome Analyses of Diaphorina citri Midgut Responses to Candidatus Liberibacter Asiaticus Infection. PMID:32156093
Expression profiles of miRNAs in giant cell tumor of bone showed miR-187-5p and miR-1323 can regulate biological functions through inhibiting FRS2. PMID:32154662
Transcriptomic and metabolomic analyses of Lycium ruthenicum and Lycium barbarum fruits during ripening. PMID:32152358
Transcriptome analysis of Panax ginseng response to high light stress. PMID:32148414
Comprehensive RNA Sequencing in Adenoma-Cancer Transition Identified Predictive Biomarkers and Therapeutic Targets of Human CRC. PMID:32145677
Effect of VCP modulators on gene expression profiles of retinal ganglion cells in an acute injury mouse model. PMID:32144342
Genome sequencing of Aspergillus glaucus 'CCHA' provides insights into salt-stress adaptation. PMID:32140304
Temporal changes in the gene expression heterogeneity during brain development and aging. PMID:32139741
Functionally Enigmatic Genes in Cancer: Using TCGA Data to Map the Limitations of Annotations. PMID:32139709
Context-dependent genetic architecture of Drosophila life span. PMID:32134916
Whole Transcriptome Analysis of Mesenchyme Tissue in Sika Deer Antler Revealed the CeRNAs Regulatory Network Associated With Antler Development. PMID:32133026
A pathway coordinated by DELE1 relays mitochondrial stress to the cytosol. PMID:32132706
Identification of the Molecular Mechanisms of Peimine in the Treatment of Cough Using Computational Target Fishing. PMID:32131410
Supervised learning is an accurate method for network-based gene classification. PMID:32129827
Systematic metadata analysis of brown rot fungi gene expression data reveals the genes involved in Fenton's reaction and wood decay process. PMID:32128279
Gene regulatory network analysis with drug sensitivity reveals synergistic effects of combinatory chemotherapy in gastric cancer. PMID:32127608
Micromonospora zhangzhouensis sp. nov., a Novel Actinobacterium Isolated from Mangrove Soil, Exerts a Cytotoxic Activity in vitro. PMID:32127574
Comparative proteomics analysis of Tibetan hull-less barley under osmotic stress via data-independent acquisition mass spectrometry. PMID:32126136
ESHRD: deconvolution of brain homogenate RNA expression data to identify cell-type-specific alterations in Alzheimer's disease. PMID:32125278
MicroRNA‑449a regulates the progression of brain aging by targeting SCN2B in SAMP8 mice. PMID:32124967
Skeletal Toxicity of Coplanar Polychlorinated Biphenyl Congener 126 in the Rat Is Aryl Hydrocarbon Receptor Dependent. PMID:32119087
Pathogenic Gene Prediction Algorithm Based on Heterogeneous Information Fusion. PMID:32117433
Evaluation of Pathway Activation for a Single Sample Toward Inflammatory Bowel Disease Classification. PMID:32117426
Transcriptome Changes of Mycobacterium marinum in the Process of Resuscitation From Hypoxia-Induced Dormancy. PMID:32117415
An Anti-inflammatory microRNA Signature Distinguishes Group 3 Innate Lymphoid Cells From Natural Killer Cells in Human Decidua. PMID:32117280
Comparative Insights Into the Complete Genome Sequence of Highly Metal Resistant Cupriavidus metallidurans Strain BS1 Isolated From a Gold-Copper Mine. PMID:32117100
Identification of frailty-associated genes by coordination analysis of gene expression. PMID:32112643
The genetics of situs inversus without primary ciliary dyskinesia. PMID:32111882
Transcriptome differences in adipose stromal cells derived from pre- and postmenopausal women. PMID:32111240
In-depth Understanding of Camellia oleifera Self-incompatibility by Comparative Transcriptome, Proteome and Metabolome. PMID:32111089
Co-expression network analysis reveals the pivotal role of mitochondrial dysfunction and interferon signature in juvenile dermatomyositis. PMID:32110496
Genome-wide Association Analysis in Humans Links Nucleotide Metabolism to Leukocyte Telomere Length. PMID:32109421
MicroRNA-based recombinant AAV vector assembly improves efficiency of suicide gene transfer in a murine model of lymphoma. PMID:32108448
A comparative genomics study of 23 Aspergillus species from section Flavi. PMID:32107379
Genomic insight into the origins and evolution of symbiosis genes in Phaseolus vulgaris microsymbionts. PMID:32106817
Genetic Modifiers and Rare Mendelian Disease. PMID:32106447
Complete genome sequences of two Enterococcus faecium strains and comparative genomic analysis. PMID:32104261
Integrative module analysis of HCC gene expression landscapes. PMID:32104233
Electroacupuncture Alleviates Experimental Chronic Inflammatory Pain by Inhibiting Calcium Voltage-Gated Channel-Mediated Inflammation. PMID:32104194
Integrated Gene Expression Profiling Analysis Reveals Probable Molecular Mechanism and Candidate Biomarker in Anti-TNFα Non-Response IBD Patients. PMID:32104045
Predicted Drosophila Interactome Resource and web tool for functional interpretation of differentially expressed genes. PMID:32103267
Readthrough Errors Purge Deleterious Cryptic Sequences, Facilitating the Birth of Coding Sequences. PMID:32101291
Data libraries - the missing element for modeling biological systems. PMID:32100391
Informatics Approaches for Harmonized Intelligent Integration of Stem Cell Research. PMID:32099411
Integrated transcriptomic correlation network analysis identifies COPD molecular determinants. PMID:32099002
Integrative analysis suggests cell type-specific decoding of NF-κB dynamics. PMID:32098801
Draft Genome Assembly of Floccularia luteovirens, an Edible and Symbiotic Mushroom on Qinghai-Tibet Plateau. PMID:32098800
Exploring Integrative Analysis Using the BioMedical Evidence Graph. PMID:32097025
A Survey of Systematic Evidence Mapping Practice and the Case for Knowledge Graphs in Environmental Health and Toxicology. PMID:32096866
Detection and characterization of microRNA expression profiling and its target genes in response to canine parvovirus in Crandell Reese Feline Kidney cells. PMID:32095352
Genome-wide analysis of lncRNAs, miRNAs, and mRNAs forming a prognostic scoring system in esophageal squamous cell carcinoma. PMID:32095316
Identification, quantification and bioinformatic analysis of RNA-dependent proteins by RNase treatment and density gradient ultracentrifugation using R-DeeP. PMID:32094787
Toxicological response of the model fungus Saccharomyces cerevisiae to different concentrations of commercial graphene nanoplatelets. PMID:32094381
Pan-cancer mapping of differential protein-protein interactions. PMID:32094374
Equivalent change enrichment analysis: assessing equivalent and inverse change in biological pathways between diverse experiments. PMID:32093613
Transcriptome Analysis and Identification of Genes Associated with Starch Metabolism in Castanea henryi Seed (Fagaceae). PMID:32093295
Adaptation to Photooxidative Stress: Common and Special Strategies of the Alphaproteobacteria Rhodobacter sphaeroides and Rhodobacter capsulatus. PMID:32093084
Comparative Proteomic Analysis of Wild-Type Physcomitrella Patens and an OPDA-Deficient Physcomitrella Patens Mutant with Disrupted PpAOS1 and PpAOS2 Genes after Wounding. PMID:32093080
RNA-Seq Analysis of Genetic and Transcriptome Network Effects of Dual-Trait Selection for Ethanol Preference and Withdrawal Using SOT and NOT Genetic Models. PMID:32090358
Hierarchy and levels: analysing networks to study mechanisms in molecular biology. PMID:32089112
Transcriptomics at Maize Embryo/Endosperm Interfaces Identifies a Transcriptionally Distinct Endosperm Subdomain Adjacent to the Embryo Scutellum. PMID:32086366
Identification of Candidate Chemosensory Receptors in the Antennae of the Variegated Cutworm, Peridroma saucia Hübner, Based on a Transcriptome Analysis. PMID:32082194
Regulation of intrinsic polarity establishment by a differentiation-type MAPK pathway in S. cerevisiae. PMID:32079658
Radiogenomic-Based Survival Risk Stratification of Tumor Habitat on Gd-T1w MRI Is Associated with Biological Processes in Glioblastoma. PMID:32079590
In Vitro Zika Virus Infection of Human Neural Progenitor Cells: Meta-Analysis of RNA-Seq Assays. PMID:32079323
CRb and PbBa8.1 Synergically Increases Resistant Genes Expression upon Infection of Plasmodiophora brassicae in Brassica napus. PMID:32079196
Controllability analysis of molecular pathways points to proteins that control the entire interaction network. PMID:32076007
Predicting clinical benefit of immunotherapy by antigenic or functional mutations affecting tumour immunogenicity. PMID:32075964
Comparative genomics and association analysis identifies virulence genes of Cercospora sojina in soybean. PMID:32075575
Endogenous Retrovirus Activation as a Key Mechanism of Anti-Tumor Immune Response in Radiotherapy. PMID:32074012
Neutrophil-like HL-60 cells expressing only GFP-tagged β-actin exhibit nearly normal motility. PMID:32072765
Association of functional variants and protein-to-protein physical interactions of human MutY homolog linked with familial adenomatous polyposis and colorectal cancer syndrome. PMID:32072083
The MYCL and MXD1 transcription factors regulate the fitness of murine dendritic cells. PMID:32071205
Identification of core biomarkers associated with pathogenesis and prognostic outcomes of laryngeal squamous-cell cancer using bioinformatics analysis. PMID:32067095
A census of pathway maps in cancer systems biology. PMID:32066900
Machine Learning and Bioinformatics Models to Identify Pathways that Mediate Influences of Welding Fumes on Cancer Progression. PMID:32066756
Whole-exome sequencing of 81 individuals from 27 multiply affected bipolar disorder families. PMID:32066727
SSIF: Subsumption-based Sub-term Inference Framework to audit Gene Ontology. PMID:32065617
Network Pharmacology-Based Strategy to Investigate the Pharmacologic Mechanisms of Atractylodes macrocephala Koidz. for the Treatment of Chronic Gastritis. PMID:32063848
DDAPRED: a computational method for predicting drug repositioning using regularized logistic matrix factorization. PMID:32062701
Epigenomic analysis of 5-hydroxymethylcytosine (5hmC) reveals novel DNA methylation markers for lung cancers. PMID:32062069
A systems approach to infectious disease. PMID:32060427
The modular nature of protein evolution: domain rearrangement rates across eukaryotic life. PMID:32059645
Brassinosteroid signaling may regulate the germination of axillary buds in ratoon rice. PMID:32059642
Transcriptome profiles of Quercus rubra responding to increased O3 stress. PMID:32059640
Identification and validation of key genes with prognostic value in non-small-cell lung cancer via integrated bioinformatics analysis. PMID:32059076
Identification of Hub Genes and Pathways in Gastric Adenocarcinoma Based on Bioinformatics Analysis. PMID:32058995
SurfaceGenie: a web-based application for prioritizing cell-type-specific marker candidates. PMID:32053146
Poly-Enrich: count-based methods for gene set enrichment testing with genomic regions. PMID:32051932
Early-life trauma endophenotypes and brain circuit-gene expression relationships in functional neurological (conversion) disorder. PMID:32051548
Restricted immunological and cellular pathways are shared by murine models of chronic alcohol consumption. PMID:32051453
Cell Cycle Profiling Reveals Protein Oscillation, Phosphorylation, and Localization Dynamics. PMID:32051232
Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data. PMID:32051003
Characterization and whole genome sequencing of a novel strain of Bergeyella cardium related to infective endocarditis. PMID:32050896
Metabolome and Transcriptome Analysis of Hexaploid Solidago canadensis Roots Reveals its Invasive Capacity Related to Polyploidy. PMID:32050732
Selection in Australian Thoroughbred horses acts on a locus associated with early two-year old speed. PMID:32049967
Time-resolved proteomic profile of Amblyomma americanum tick saliva during feeding. PMID:32049966
Predict New Therapeutic Drugs for Hepatocellular Carcinoma Based on Gene Mutation and Expression. PMID:32047745
Identification of key genes and pathways associated with esophageal squamous cell carcinoma development based on weighted gene correlation network analysis. PMID:32047546
The Adipocyte Acquires a Fibroblast-Like Transcriptional Signature in Response to a High Fat Diet. PMID:32047213
Biomarkers for Traumatic Brain Injury: Data Standards and Statistical Considerations. PMID:32046588
Transcriptomic and Metabolomic Changes Triggered by Fusarium solani in Common Bean (Phaseolus vulgaris L.). PMID:32046085
Transcriptomic changes in the nasal epithelium associated with diesel engine exhaust exposure. PMID:32044442
The hornwort genome and early land plant evolution. PMID:32042158
The Personalisation of Glioblastoma Treatment Using Whole Exome Sequencing: A Pilot Study. PMID:32041307
Classification of Trispanins: A Diverse Group of Proteins That Function in Membrane Synthesis and Transport Mechanisms. PMID:32039202
Biocontrol Potential of a Novel Endophytic Bacterium From Mulberry (Morus) Tree. PMID:32039187
Quantifying Gene Essentiality Based on the Context of Cellular Components. PMID:32038710
Transcriptional and Functional Programming of Decidual Innate Lymphoid Cells. PMID:32038619
IGFBP6 Is Downregulated in Unstable Carotid Atherosclerotic Plaques According to an Integrated Bioinformatics Analysis and Experimental Verification. PMID:32037372
IGF1-mediated human embryonic stem cell self-renewal recapitulates the embryonic niche. PMID:32034154
Altered Hippocampal Epigenetic Regulation Underlying Reduced Cognitive Development in Response to Early Life Environmental Insults. PMID:32033187
Transcriptome-Wide Identification, Evolutionary Analysis, and GA Stress Response of the GRAS Gene Family in Panax ginseng C. A. Meyer. PMID:32033157
Genome-wide CRISPR screening identifies new regulators of glycoprotein secretion. PMID:32030357
Comparative RNA-Seq Analysis of Differentially Expressed Genes in the Epididymides of Yak and Cattleyak. PMID:32030088
iMTBGO: An Algorithm for Integrating Metabolic Networks with Transcriptomes Based on Gene Ontology Analysis. PMID:32030085
A rare subpopulation of melanoma cells with low expression of metastasis suppressor NME1 is highly metastatic in vivo. PMID:32029850
Electrophysiology-based stratification of pancreatic tumorigenicity by label-free single-cell impedance cytometry. PMID:32029124
PANEV: an R package for a pathway-based network visualization. PMID:32028885
PlaPPISite: a comprehensive resource for plant protein-protein interaction sites. PMID:32028878
Screening of Prognostic Factors in Early-Onset Breast Cancer. PMID:32028860
EHMT2 Inhibition Induces Cell Death in Human Non-Small Cell Lung Cancer by Altering the Cholesterol Biosynthesis Pathway. PMID:32028644
Genomic basis for RNA alterations in cancer. PMID:32025019
Pathway and network analysis of more than 2500 whole cancer genomes. PMID:32024854
Integrative pathway enrichment analysis of multivariate omics data. PMID:32024846
APOE genotype regulates pathology and disease progression in synucleinopathy. PMID:32024799
Establishment and Characterisation by Expression Microarray of Patient-Derived Xenograft Panel of Human Pancreatic Adenocarcinoma Patients. PMID:32024004
β-Catenin Preserves the Stem State of Murine Bone Marrow Stromal Cells Through Activation of EZH2. PMID:32022326
Transcriptome Analysis Reveals the Resistance Mechanism of Pseudomonas aeruginosa to Tachyplesin I. PMID:32021330
Mechanism of tanshinones and phenolic acids from Danshen in the treatment of coronary heart disease based on co-expression network. PMID:32020855
CDK1 serves as a potential prognostic biomarker and target for lung cancer. PMID:32020821
The IUPHAR Guide to Immunopharmacology: connecting immunology and pharmacology. PMID:32020584
Astrocyte-Derived Exosomal microRNA miR-200a-3p Prevents MPP+-Induced Apoptotic Cell Death Through Down-Regulation of MKK4. PMID:32016794
Quantitative analysis of protein crotonylation identifies its association with immunoglobulin A nephropathy. PMID:32016442
Clozapine-induced transcriptional changes in the zebrafish brain. PMID:32015324
Comparative Genomic Analysis of Closely Related Acetobacter pasteurianus Strains Provides Evidence of Horizontal Gene Transfer and Reveals Factors Necessary for Thermotolerance. PMID:32015144
Aging-associated decrease in the histone acetyltransferase KAT6B is linked to altered hematopoietic stem cell differentiation. PMID:32014431
Identification of transcriptome and fluralaner responsive genes in the common cutworm Spodoptera litura Fabricius, based on RNA-seq. PMID:32013879
Comparative Transcriptome Analysis of Different Dendrobium Species Reveals Active Ingredients-Related Genes and Pathways. PMID:32013237
Proteomic Analysis of Brain Region and Sex-Specific Synaptic Protein Expression in the Adult Mouse Brain. PMID:32012899
Complete Genome Sequence Reveals Evolutionary and Comparative Genomic Features of Xanthomonas albilineans Causing Sugarcane Leaf Scald. PMID:32012870
Identification of 34 genes conferring genetic and pharmacological risk for the comorbidity of schizophrenia and smoking behaviors. PMID:32012119
Single-cell morphology encodes metastatic potential. PMID:32010778
Inactivation of Zeb1 in GRHL2-deficient mouse embryos rescues mid-gestation viability and secondary palate closure. PMID:32005677
Analysis of circular RNA-associated competing endogenous RNA network in breast cancer. PMID:32002039
Automated Methods Enable Direct Computation on Phenotypic Descriptions for Novel Candidate Gene Prediction. PMID:31998331
Arginine π-stacking drives binding to fibrils of the Alzheimer protein Tau. PMID:31996674
Remethylation of Dnmt3a -/- hematopoietic cells is associated with partial correction of gene dysregulation and reduced myeloid skewing. PMID:31996479
Genomic analyses reveal selection footprints in rice landraces grown under on-farm conservation conditions during a short-term period of domestication. PMID:31993077
Zika virus targets the human thymic epithelium. PMID:31992777
A comparison of curated gene sets versus transcriptomics-derived gene signatures for detecting pathway activation in immune cells. PMID:31992182
Identification of Key Biomarkers in Bladder Cancer: Evidence from a Bioinformatics Analysis. PMID:31991631
Proteomic profiling of proteins in the dorsal horn of the spinal cord in dairy cows with chronic lameness. PMID:31990932
Topologically Guided Prioritization of Candidate Gene Transcripts Coexpressed with the 5-HT1A Receptor by Combining In Vivo PET and Allen Human Brain Atlas Data. PMID:31989157
Unravelling the role of long non-coding RNA - LINC01087 in breast cancer. PMID:31989062
Comparative transcriptome analysis revealed genes involved in the fruiting body development of Ophiocordyceps sinensis. PMID:31988806
Dissecting the genetic architecture of seed-cotton and lint yields in Upland cotton using genome-wide association mapping. PMID:31988625
Pro-efferocytic nanoparticles are specifically taken up by lesional macrophages and prevent atherosclerosis. PMID:31988506
Clostridioides difficile-Associated Antibiotics Alter Human Mucosal Barrier Functions by Microbiome-Independent Mechanisms. PMID:31988098
Enhanced cardiomyocyte reactive oxygen species signaling promotes ibrutinib-induced atrial fibrillation. PMID:31986467
Highly multiplexed proteomic assessment of human bone marrow in acute myeloid leukemia. PMID:31985806
Tentacle Transcriptomes of the Speckled Anemone (Actiniaria: Actiniidae: Oulactis sp.): Venom-Related Components and Their Domain Structure. PMID:31981004
The complete chloroplast genome of Microcycas calocoma (Miq.) A. DC. (Zamiaceae, Cycadales) and evolution in Cycadales. PMID:31976174
Comparative proteomic and genomic analyses of Brucella abortus biofilm and planktonic cells. PMID:31974592
ISOGO: Functional annotation of protein-coding splice variants. PMID:31974522
Q-Cell Glioblastoma Resource: Proteomics Analysis Reveals Unique Cell-States are Maintained in 3D Culture. PMID:31973233
Dipeptidyl peptidase-4 is increased in the abdominal aortic aneurysm vessel wall and is associated with aneurysm disease processes. PMID:31971988
Knowledge-guided analysis of "omics" data using the KnowEnG cloud platform. PMID:31971940
Imputation of Gene Expression Data in Blood Cancer and Its Significance in Inferring Biological Pathways. PMID:31970084
Biofilm formation displays intrinsic offensive and defensive features of Bacillus cereus. PMID:31969984
Physiological and Proteomic Changes in the Apoplast Accompany Leaf Senescence in Arabidopsis. PMID:31969890
Environmental arginine controls multinuclear giant cell metabolism and formation. PMID:31969567
Survival-Associated Metabolic Genes in Human Papillomavirus-Positive Head and Neck Cancers. PMID:31968678
MicroRNA and mRNA interactions coordinate the immune response in non-lethal heat stressed Litopenaeus vannamei against AHPND-causing Vibrio parahaemolyticus. PMID:31964916
A chromosome-level reference genome of the hornbeam, Carpinus fangiana. PMID:31964866
A Similar Genetic Architecture Underlies the Convergent Evolution of the Selfing Syndrome in Capsella. PMID:31964802
An operon consisting of a P-type ATPase gene and a transcriptional regulator gene responsible for cadmium resistances in Bacillus vietamensis 151-6 and Bacillus marisflavi 151-25. PMID:31964334
Novel Approaches for Identifying the Molecular Background of Schizophrenia. PMID:31963710
Transcriptional analysis of THP-1 cells infected with Leishmania infantum indicates no activation of the inflammasome platform. PMID:31961876
Tripal EUtils: a Tripal module to increase exchange and reuse of genome assembly metadata. PMID:31960040
Building a pipeline to solicit expert knowledge from the community to aid gene summary curation. PMID:31960022
Genetic studies of urinary metabolites illuminate mechanisms of detoxification and excretion in humans. PMID:31959995
A human ciliopathy reveals essential functions for NEK10 in airway mucociliary clearance. PMID:31959991
Immune gene signatures for predicting durable clinical benefit of anti-PD-1 immunotherapy in patients with non-small cell lung cancer. PMID:31959763
Profiling of the muscle-specific dystroglycan interactome reveals the role of Hippo signaling in muscular dystrophy and age-dependent muscle atrophy. PMID:31959160
Accumulation of genetic variants associated with immunity in the selective breeding of broilers. PMID:31952471
Dynamic post-translational modification profiling of Mycobacterium tuberculosis-infected primary macrophages. PMID:31951200
Cell Adhesion-Related Molecules Play a Key Role in Renal Cancer Progression by Multinetwork Analysis. PMID:31950034
Analysis of histological and microRNA profiles changes in rabbit skin development. PMID:31949201
Lag penalized weighted correlation for time series clustering. PMID:31948388
Role of Secreted Frizzled-Related Protein 1 in Early Mammary Gland Tumorigenesis and Its Regulation in Breast Microenvironment. PMID:31947616
A high-quality chromosomal genome assembly of Diospyros oleiferaCheng. PMID:31944244
Transcriptome meta-analysis reveals differences of immune profile between eutopic endometrium from stage I-II and III-IV endometriosis independently of hormonal milieu. PMID:31941945
De novo variants in exomes of congenital heart disease patients identify risk genes and pathways. PMID:31941532
Growth Mode and Physiological State of Cells Prior to Biofilm Formation Affect Immune Evasion and Persistence of Staphylococcus aureus. PMID:31940921
Whole Genome Analysis of the Red-Crowned Crane Provides Insight into Avian Longevity. PMID:31940721
Probiotic Bacillus subtilis Protects against α-Synuclein Aggregation in C. elegans. PMID:31940482
DNA methylation profiling in recurrent miscarriage. PMID:31938574
Effects of prenatal hypoxia on fetal sheep heart development and proteomics analysis. PMID:31938297
Bioinformatic analysis of differential expression and core GENEs in breast cancer. PMID:31938209
Distinct but Intertwined Evolutionary Histories of Multiple Salmonella enterica Subspecies. PMID:31937675
Enhanced genome assembly and a new official gene set for Tribolium castaneum. PMID:31937263
Water Deficit Transcriptomic Responses Differ in the Invasive Tamarix chinensis and T. ramosissima Established in the Southern and Northern United States. PMID:31936615
Comparative analysis of primary metabolites and transcriptome changes between ungrafted and pumpkin-grafted watermelon during fruit development. PMID:31934503
Parallel evolutionary paths to produce more than one Pseudomonas aeruginosa biofilm phenotype. PMID:31934344
The genome sequence of celery (Apium graveolens L.), an important leaf vegetable crop rich in apigenin in the Apiaceae family. PMID:31934340
Duodenum Intestine-Chip for preclinical drug assessment in a human relevant model. PMID:31933478
Maternal factor NELFA drives a 2C-like state in mouse embryonic stem cells. PMID:31932739
Combining lexical and context features for automatic ontology extension. PMID:31931870
Differential expression of microRNAs in tomato leaves treated with different light qualities. PMID:31931707
LINC01413/hnRNP-K/ZEB1 Axis Accelerates Cell Proliferation and EMT in Colorectal Cancer via Inducing YAP1/TAZ1 Translocation. PMID:31927328
Clonal kinetics and single-cell transcriptional profiling of CAR-T cells in patients undergoing CD19 CAR-T immunotherapy. PMID:31924795
Construction of asthma related competing endogenous RNA network revealed novel long non-coding RNAs and potential new drugs. PMID:31924195
Brief communication: Long-term absence of Langerhans cells alters the gene expression profile of keratinocytes and dendritic epidermal T cells. PMID:31923202
Gambogenic acid exerts anticancer effects in cisplatin‑resistant non‑small cell lung cancer cells. PMID:31922223
Novel Breast-Specific Long Non-coding RNA LINC00993 Acts as a Tumor Suppressor in Triple-Negative Breast Cancer. PMID:31921620
Mesostigma viride Genome and Transcriptome Provide Insights into the Origin and Evolution of Streptophyta. PMID:31921561
Computational identification of vesicular transport proteins from sequences using deep gated recurrent units architecture. PMID:31921391
The Cellular Transcriptome in the Maternal Circulation During Normal Pregnancy: A Longitudinal Study. PMID:31921132
Di (2-ethylhexyl) Phthalate Exposure Impairs the microRNAs Expression Profile During Primordial Follicle Assembly. PMID:31920986
Genome-wide association and Mendelian randomisation analysis provide insights into the pathogenesis of heart failure. PMID:31919418
Whole Genome Sequencing and Comparative Genomics of Two Nematicidal Bacillus Strains Reveals a Wide Range of Possible Virulence Factors. PMID:31919110
The transcriptional correlates of divergent electric organ discharges in Paramormyrops electric fish. PMID:31918666
Identification of Monotonically Differentially Expressed Genes for IFN-β-Treated Multiple Sclerosis Patients. PMID:31915697
Transcriptome analyses identify hub genes and potential mechanisms in adenoid cystic carcinoma. PMID:31914060
Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions. PMID:31913281
Comprehensive transcriptome analysis of cochlear spiral ganglion neurons at multiple ages. PMID:31913118
Fine-mapping of 150 breast cancer risk regions identifies 191 likely target genes. PMID:31911677
Generation and characterization of a mitotane-resistant adrenocortical cell line. PMID:31910152
Differential Expression in Testis and Liver Transcriptomes from Four Species of Peromyscus (Rodentia: Cricetidae). PMID:31909812
NHC-gold compounds mediate immune suppression through induction of AHR-TGFβ1 signalling in vitro and in scurfy mice. PMID:31909202
Presence and structure-activity relationship of intrinsically disordered regions across mucins. PMID:31908009
THAP11F80L cobalamin disorder-associated mutation reveals normal and pathogenic THAP11 functions in gene expression and cell proliferation. PMID:31905202
ASPM promotes glioblastoma growth by regulating G1 restriction point progression and Wnt-β-catenin signaling. PMID:31905171
Transcriptomic analyses of Pinus koraiensis under different cold stresses. PMID:31900194
Evolving knowledge graph similarity for supervised learning in complex biomedical domains. PMID:31900127
Tissue-specific gene expression and protein abundance patterns are associated with fractionation bias in maize. PMID:31900107
Sex-specific and opposite modulatory aspects revealed by PPI network and pathway analysis of ischemic stroke in humans. PMID:31899762
How to Illuminate the Druggable Genome Using Pharos. PMID:31898878
Leveraging complementary computational models for prioritizing chemicals of developmental and reproductive toxicity concern: an example of food contact materials. PMID:31897520
Translation of gastric disease progression at gene level expression. PMID:31897247
Identification of key candidate tumor biomarkers in non-small-cell lung cancer by in silico analysis. PMID:31897214
Expression profile of miRNA in NSCLC tissues in middle-altitude area. PMID:31897195
Identification of key genes for predicting colorectal cancer prognosis by integrated bioinformatics analysis. PMID:31897151
Genome and population sequencing of a chromosome-level genome assembly of the Chinese tapertail anchovy (Coilia nasus) provides novel insights into migratory adaptation. PMID:31895412
Weighted gene co‑expression network analysis to identify key modules and hub genes associated with atrial fibrillation. PMID:31894294
Recommendations for application of the functional evidence PS3/BS3 criterion using the ACMG/AMP sequence variant interpretation framework. PMID:31892348
The Acute Phase Response Is a Prominent Renal Proteome Change in Sepsis in Mice. PMID:31892161
The essentiality landscape of cell cycle related genes in human pluripotent and cancer cells. PMID:31889988
OHMI: the ontology of host-microbiome interactions. PMID:31888755
High-level integration of murine intestinal transcriptomics data highlights the importance of the complement system in mucosal homeostasis. PMID:31888466
Transcriptome-Wide Analysis Reveals Key DEGs in Flower Color Regulation of Hosta plantaginea (Lam.) Aschers. PMID:31888085
Integration of ATAC-Seq and RNA-Seq Identifies Key Genes in Light-Induced Primordia Formation of Sparassis latifolia. PMID:31888059
Enhancer jungles establish robust tissue-specific regulatory control in the human genome. PMID:31887344
Integrative Analysis of ceRNA Network Reveals Functional lncRNAs in Intrahepatic Cholangiocarcinoma. PMID:31886187
Study on the Multitarget Mechanism and Key Active Ingredients of Herba Siegesbeckiae and Volatile Oil against Rheumatoid Arthritis Based on Network Pharmacology. PMID:31885670
The impact of the genetic background on gene deletion phenotypes in Saccharomyces cerevisiae. PMID:31885205
A gene regulatory network controls the balance between mesendoderm and ectoderm at pluripotency exit. PMID:31885203
ShinyGO: a graphical gene-set enrichment tool for animals and plants. PMID:31882993
The Use of Whole Exome Sequencing in a Cohort of Transgender Individuals to Identify Rare Genetic Variants. PMID:31882810
Pan-genome diversification and recombination in Cronobacter sakazakii, an opportunistic pathogen in neonates, and insights to its xerotolerant lifestyle. PMID:31881843
Identifying miRNA synergism using multiple-intervention causal inference. PMID:31881825
RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism. PMID:31881735
CLIC4 and CLIC1 bridge plasma membrane and cortical actin network for a successful cytokinesis. PMID:31879279
Integrated analyses of miRNAome and transcriptome reveal zinc deficiency responses in rice seedlings. PMID:31878878
PROMO: an interactive tool for analyzing clinically-labeled multi-omic cancer datasets. PMID:31878868
Single Nucleotide Polymorphism rs6942067 Is a Risk Factor in Young and in Non-Smoking Patients with HPV Negative Head and Neck Squamous Cell Carcinoma. PMID:31878157
Chromosome-Level Comprehensive Genome of Mangrove Sediment-Derived Fungus Penicillium variabile HXQ-H-1. PMID:31878043
Immunity-related genes and signaling pathways under hypoxic stresses in Haliotis diversicolor: a transcriptome analysis. PMID:31874975
Refining modules to determine functionally significant clusters in molecular networks. PMID:31874644
Classification of adaptor proteins using recurrent neural networks and PSSM profiles. PMID:31874633
Joint learning improves protein abundance prediction in cancers. PMID:31870366
Identifying Acetylation Protein by Fusing Its PseAAC and Functional Domain Annotation. PMID:31867311
PHI-Nets: A Network Resource for Ascomycete Fungal Pathogens to Annotate and Identify Putative Virulence Interacting Proteins and siRNA Targets. PMID:31866958
A 2018 workshop: vaccine and drug ontology studies (VDOS 2018). PMID:31865905
Patterns of diverse gene functions in genomic neighborhoods predict gene function and phenotype. PMID:31863070
Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets. PMID:31862961
Profiling of the plasma proteome across different stages of human heart failure. PMID:31862877
Complete Genome Sequence of Acidithiobacillus Ferrooxidans YNTRS-40, a Strain of the Ferrous Iron- and Sulfur-Oxidizing Acidophile. PMID:31861345
Lipid and DHA-production in Aurantiochytrium sp. - Responses to nitrogen starvation and oxygen limitation revealed by analyses of production kinetics and global transcriptomes. PMID:31857635
MultiSourcDSim: an integrated approach for exploring disease similarity. PMID:31856813
Expression alteration of microRNAs in Nucleus Accumbens is associated with chronic stress and antidepressant treatment in rats. PMID:31856805
Direct comparison of Arabidopsis gene expression reveals different responses to melatonin versus auxin. PMID:31856719
Comparative transcriptome reveals the potential modulation mechanisms of estradiol affecting ovarian development of female Portunus trituberculatus. PMID:31856263
Identification of differentially expressed genes and signaling pathways involved in endometriosis by integrated bioinformatics analysis. PMID:31853298
Pulsed glucocorticoids enhance dystrophic muscle performance through epigenetic-metabolic reprogramming. PMID:31852847
Nuclear factor erythroid 2 - related factor 2 and its relationship with cellular response in nickel exposure: a systems biology analysis. PMID:31852525
Novel findings to the biosynthetic pathway of magnoflorine and taspine through transcriptomic and metabolomic analysis of Croton draco (Euphorbiaceae). PMID:31852435
The MathIOmica Toolbox: General Analysis Utilities for Dynamic Omics Datasets. PMID:31851777
The dynamics of DNA methylation during epigenetic reprogramming of primordial germ cells in medaka (Oryzias latipes). PMID:31851575
Screening, identification and validation of CCND1 and PECAM1/CD31 for predicting prognosis in renal cell carcinoma patients. PMID:31850854
Expression Quantitative Trait Loci in Equine Skeletal Muscle Reveals Heritable Variation in Metabolism and the Training Responsive Transcriptome. PMID:31850069
Master Regulators of Signaling Pathways: An Application to the Analysis of Gene Regulation in Breast Cancer. PMID:31850059
A Phylogenomic Analysis of the Floral Transcriptomes of Sexually Deceptive and Rewarding European Orchids, Ophrys and Gymnadenia. PMID:31850034
Transcriptome Analysis Identifies Immune Markers Related to Visceral Leishmaniasis Establishment in the Experimental Model of BALB/c Mice. PMID:31849951
Population History and Gene Divergence in Native Mexicans Inferred from 76 Human Exomes. PMID:31848607
Transcriptome analysis reveals plasticity in gene regulation due to environmental cues in Primula sikkimensis, a high altitude plant species. PMID:31847812
Genome-Wide Analysis of Whole Human Glycoside Hydrolases by Data-Driven Analysis in Silico. PMID:31847093
Evaluating the consistency of large-scale pharmacogenomic studies. PMID:31846027
GenFam: A web application and database for gene family-based classification and functional enrichment analysis. PMID:31844835
Multi-omics analysis of multiple missions to space reveal a theme of lipid dysregulation in mouse liver. PMID:31844325
Genome-wide analysis identifies molecular systems and 149 genetic loci associated with income. PMID:31844048
Development and validation of a nomogram with an autophagy-related gene signature for predicting survival in patients with glioblastoma. PMID:31844032
Wnt Signaling Drives Ectopic Gene Expression and Larval Arrest in the Absence of the Caenorhabditis elegans DREAM Repressor Complex. PMID:31843805
ReVac: a reverse vaccinology computational pipeline for prioritization of prokaryotic protein vaccine candidates. PMID:31842745
Combined De Novo Transcriptome and Metabolome Analysis of Common Bean Response to Fusarium oxysporum f. sp. phaseoli Infection. PMID:31842411
Battling Glioblastoma: A Novel Tyrosine Kinase Inhibitor with Multi-Dimensional Anti-Tumor Effect (Running Title: Cancer Cells Death Signalling Activation). PMID:31842391
Transcriptome-Guided Drug Repositioning. PMID:31842375
Drosophila RpS12 controls translation, growth, and cell competition through Xrp1. PMID:31841522
Whole genome sequencing and novel candidate genes for CAKUT and altered nephrogenesis in the HSRA rat. PMID:31841396
Neuroprotectants attenuate hypobaric hypoxia-induced brain injuries in cynomolgus monkeys. PMID:31840949
Predicting associations among drugs, targets and diseases by tensor decomposition for drug repositioning. PMID:31839008
High-resolution chromosomal microarray analysis for copy-number variations in high-functioning autism reveals large aberration typical for intellectual disability. PMID:31838600
Loss of the Epigenetic Mark 5-hmC in Psoriasis: Implications for Epidermal Stem Cell Dysregulation. PMID:31837302
An Integrated Pan-Cancer Analysis and Structure-Based Virtual Screening of GPR15. PMID:31835584
Draft Genome Sequence of Thermophilic Bacillus sp. TYF-LIM-B05 Directly Producing Ethanol from Various Carbon Sources Including Lignocellulose. PMID:31832840
Bioinformatic identification of key genes and molecular pathways in the spermatogenic process of cryptorchidism. PMID:31832523
Multiple freshwater invasions of the tapertail anchovy (Clupeiformes: Engraulidae) of the Yangtze River. PMID:31832154
Next-generation hypomethylating agent SGI-110 primes acute myeloid leukemia cells to IAP antagonist by activating extrinsic and intrinsic apoptosis pathways. PMID:31831875
TRANSNAP: a web database providing comprehensive information on Japanese pear transcriptome. PMID:31831861
Using mechanistic models for the clinical interpretation of complex genomic variation. PMID:31831811
Phosphoproteomic profiling reveals a defined genetic program for osteoblastic lineage commitment of human bone marrow-derived stromal stem cells. PMID:31831592
CD155 contributes to the mesenchymal phenotype of triple-negative breast cancer. PMID:31830330
Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools. PMID:31830054
Evolutionarily novel genes are expressed in transgenic fish tumors and their orthologs are involved in development of progressive traits in humans. PMID:31827597
Affected Sib-Pair Analyses Identify Signaling Networks Associated With Social Behavioral Deficits in Autism. PMID:31827489
Transcriptomic Characterization of the Human Insular Cortex and Claustrum. PMID:31827426
Schistosomal extracellular vesicle-enclosed miRNAs modulate host T helper cell differentiation. PMID:31825165
Integrated miRNA-seq analysis reveals the molecular mechanism underlying the effect of acupuncture on endometrial receptivity in patients undergoing fertilization: embryo transplantation. PMID:31824817
CircSLNN: Identifying RBP-Binding Sites on circRNAs via Sequence Labeling Neural Networks. PMID:31824574
Phenotype Prediction and Genome-Wide Association Study Using Deep Convolutional Neural Network of Soybean. PMID:31824557
Spermidine Increases the Sucrose Content in Inferior Grain of Wheat and Thereby Promotes Its Grain Filling. PMID:31824519
Comparative Network Pharmacology Analysis of Classical TCM Prescriptions for Chronic Liver Disease. PMID:31824313
Differential Proteome Analysis of Hybrid Bamboo (Bambusa pervariabilis × Dendrocalamopsis grandis) Under Fungal Stress (Arthrinium phaeospermum). PMID:31822726
On the possible origin of protein homochirality, structure, and biochemical function. PMID:31822617
Formal axioms in biomedical ontologies improve analysis and interpretation of associated data. PMID:31821406
Comparative genomics analysis of Nitriliruptoria reveals the genomic differences and salt adaptation strategies. PMID:31820112
Integrated Analysis To Identify Molecular Biomarkers Of High-Grade Serous Ovarian Cancer. PMID:31819501
Molecular Analysis of UV-C Induced Resveratrol Accumulation in Polygonum cuspidatum Leaves. PMID:31817915
Transcriptome of Chicken Liver Tissues Reveals the Candidate Genes and Pathways Responsible for Adaptation into Two Different Climatic Conditions. PMID:31816986
Extending the information content of the MALDI analysis of biological fluids via multi-million shot analysis. PMID:31815946
Identification of potential core genes in metastatic renal cell carcinoma using bioinformatics analysis. PMID:31814889
Mapping the Germline and Somatic Mutation Interaction Landscape in Indolent and Aggressive Prostate Cancers. PMID:31814827
Extracellular Vesicles in the Forebrain Display Reduced miR-346 and miR-331-3p in a Rat Model of Chronic Temporal Lobe Epilepsy. PMID:31813125
WormCat: An Online Tool for Annotation and Visualization of Caenorhabditis elegans Genome-Scale Data. PMID:31810987
Chromosome-level genome assembly for giant panda provides novel insights into Carnivora chromosome evolution. PMID:31810476
Association between breast cancer cell migration and radiosensitivity in vitro. PMID:31807191
Identification of key candidate genes and pathways in endometrial cancer: Evidence from bioinformatics analysis. PMID:31807178
Undulating changes in human plasma proteome profiles across the lifespan. PMID:31806903
Nongenic cancer-risk SNPs affect oncogenes, tumour-suppressor genes, and immune function. PMID:31806877
Identification of Key Genes Involved in Embryo Development and Differential Oil Accumulation in Two Contrasting Maize Genotypes. PMID:31805727
The genetic diversity and population structure of Sophora alopecuroides (Faboideae) as determined by microsatellite markers developed from transcriptome. PMID:31805153
A Combined Mass Spectrometry and Data Integration Approach to Predict the Mitochondrial Poly(A) RNA Interacting Proteome. PMID:31803741
Conjoint Analysis of SMRT- and Illumina-Based RNA-Sequencing Data of Fenneropenaeus chinensis Provides Insight Into Sex-Biased Expression Genes Involved in Sexual Dimorphism. PMID:31803244
Systematic evaluation of differential splicing tools for RNA-seq studies. PMID:31802105
The host jasmonic acid pathway regulates the transcriptomic changes of dodder and host plant under the scenario of caterpillar feeding on dodder. PMID:31801469
Integrative Omics Approach to Identifying Genes Associated With Atrial Fibrillation. PMID:31801406
DeepMiR2GO: Inferring Functions of Human MicroRNAs Using a Deep Multi-Label Classification Model. PMID:31801264
Evolution of C4 photosynthesis predicted by constraint-based modelling. PMID:31799932
Comparative analysis of the complete chloroplast genome sequences of six species of Pulsatilla Miller, Ranunculaceae. PMID:31798674
aTEMPO: Pathway-Specific Temporal Anomalies for Precision Therapeutics. PMID:31797638
Exploring Relationships between the Density of Charged Tracts within Disordered Regions and Phase Separation. PMID:31797598
From genome to phenome: Predicting multiple cancer phenotypes based on somatic genomic alterations via the genomic impact transformer. PMID:31797588
Full-Length Transcriptome Survey and Expression Analysis of Parasitoid Wasp Chouioia cunea upon Exposure to 1-Dodecene. PMID:31796851
Hypusine biosynthesis in β cells links polyamine metabolism to facultative cellular proliferation to maintain glucose homeostasis. PMID:31796630
The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases. PMID:31796553
Developmental hypomyelination in Wolfram syndrome: new insights from neuroimaging and gene expression analyses. PMID:31796109
QTL identification for seed weight and size based on a high-density SLAF-seq genetic map in peanut (Arachis hypogaea L.). PMID:31795931
Identifying gene-specific subgroups: an alternative to biclustering. PMID:31795929
Integrative In Silico and In Vitro Transcriptomics Analysis Revealed Gene Expression Changes and Oncogenic Features of Normal Cholangiocytes after Chronic Alcohol Exposure. PMID:31795085
Identification for Exploring Underlying Pathogenesis and Therapy Strategy of Oral Squamous Cell Carcinoma by Bioinformatics Analysis. PMID:31794546
Differences in the prognosis of gastric cancer patients of different sexes and races and the molecular mechanisms involved. PMID:31793655
Orchestrating single-cell analysis with Bioconductor. PMID:31792435
Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea. PMID:31792218
Electronic Cigarette (E-Cigarette) Vapor Exposure Alters the Streptococcus pneumoniae Transcriptome in a Nicotine-Dependent Manner without Affecting Pneumococcal Virulence. PMID:31791951
Transcriptomic and microstructural analyses in Liriodendron tulipifera Linn. reveal candidate genes involved in nectary development and nectar secretion. PMID:31791230
Navigating oxygen deprivation: liver transcriptomic responses of the red eared slider turtle to environmental anoxia. PMID:31788367
Identification of key candidate genes for colorectal cancer by bioinformatics analysis. PMID:31788116
Identification of hub genes and key pathways associated with the progression of gynecological cancer. PMID:31788113
PLCB4 upregulation is associated with unfavorable prognosis in pediatric acute myeloid leukemia. PMID:31788080
Identification of core differentially methylated genes in glioma. PMID:31788078
Bioinformatics analysis of Ewing's sarcoma: Seeking key candidate genes and pathways. PMID:31788075
Five extracellular matrix-associated genes upregulated in oral tongue squamous cell carcinoma: An integrated bioinformatics analysis. PMID:31788070
Predicting novel genomic regions linked to genetic disorders using GWAS and chromosome conformation data - a case study of schizophrenia. PMID:31784692
GPR108 Is a Highly Conserved AAV Entry Factor. PMID:31784416
Comparative analysis of functional assay evidence use by ClinGen Variant Curation Expert Panels. PMID:31783775
ATBS1-INTERACTING FACTOR 2 negatively regulates dark- and brassinosteroid-induced leaf senescence through interactions with INDUCER OF CBF EXPRESSION 1. PMID:31783407
Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop. PMID:31782791
A comparative analysis of gene expression induced by the embryo in the caprine endometrium. PMID:31782264
Identified the Synergistic Mechanism of Drynariae Rhizoma for Treating Fracture Based on Network Pharmacology. PMID:31781279
Brief Normothermic Machine Perfusion Rejuvenates Discarded Human Kidneys. PMID:31773055
Comprehensive analysis of differentially expressed microRNAs and mRNAs in MDBK cells expressing bovine papillomavirus E5 oncogene. PMID:31772843
Transcriptome profiling analysis reveals key genes of different coat color in sheep skin. PMID:31772839
Expression and potential prognostic value of histone family gene signature in breast cancer. PMID:31772649
Maternal Type-I interferon signaling adversely affects the microglia and the behavior of the offspring accompanied by increased sensitivity to stress. PMID:31772304
The in vivo ISGylome links ISG15 to metabolic pathways and autophagy upon Listeria monocytogenes infection. PMID:31772204
Repeated sex chromosome evolution in vertebrates supported by expanded avian sex chromosomes. PMID:31771477
Identification of a Major QTL (qRRs-10.1) That Confers Resistance to Ralstonia solanacearum in Pepper (Capsicum annuum) Using SLAF-BSA and QTL Mapping. PMID:31771239
Screening and identification of key biomarkers in nasopharyngeal carcinoma: Evidence from bioinformatic analysis. PMID:31770211
Molecular bases of responses to abiotic stress in trees. PMID:31768543
BNC1 regulates cell heterogeneity in human pluripotent stem cell-derived epicardium. PMID:31767620
Genomic Analysis of Spontaneous Abortion in Holstein Heifers and Primiparous Cows. PMID:31766405
The impact of genetic adaptation on chimpanzee subspecies differentiation. PMID:31765391
GPCRs show widespread differential mRNA expression and frequent mutation and copy number variation in solid tumors. PMID:31765370
Omega-3 Fatty Acids Activate Ciliary FFAR4 to Control Adipogenesis. PMID:31761534
TS-GOEA: a web tool for tissue-specific gene set enrichment analysis based on gene ontology. PMID:31760951
Candidate lncRNA-miRNA-mRNA network in predicting hepatocarcinogenesis with cirrhosis: an integrated bioinformatics analysis. PMID:31758243
Ontology-based prediction of cancer driver genes. PMID:31757986
ENCORE: A Visualization Tool for Insight into Circadian Omics. PMID:31754663
Monocytes affect bone mineral density in pre- and postmenopausal women through ribonucleoprotein complex biogenesis by integrative bioinformatics analysis. PMID:31754224
Full-length transcriptome sequencing from multiple tissues of duck, Anas platyrhynchos. PMID:31754106
Neogenin-1 distinguishes between myeloid-biased and balanced Hoxb5 + mouse long-term hematopoietic stem cells. PMID:31754028
Identifying gene function and module connections by the integration of multispecies expression compendia. PMID:31754022
A novel framework for horizontal and vertical data integration in cancer studies with application to survival time prediction models. PMID:31752974
The genomes of two parasitic wasps that parasitize the diamondback moth. PMID:31752718
Transcriptome analysis of the almond moth, Cadra cautella, female abdominal tissues and identification of reproduction control genes. PMID:31752675
Comparative Analysis of Transcriptome Responses to Cold Stress in Galeruca daurica (Coleoptera: Chrysomelidae). PMID:31752020
Single-cell transcriptomics of the naked mole-rat reveals unexpected features of mammalian immunity. PMID:31751331
Identification and Classification of Differentially Expressed Genes and Network Meta-Analysis Reveals Potential Molecular Signatures Associated With Tuberculosis. PMID:31749827
Early Root Transcriptomic Changes in Wheat Seedlings Colonized by Trichoderma harzianum Under Different Inorganic Nitrogen Supplies. PMID:31749777
An exome-wide rare variant analysis of Korean men identifies three novel genes predisposing to prostate cancer. PMID:31748686
Integrative analysis of mRNA and miRNA expression profiles reveals seven potential diagnostic biomarkers for non‑small cell lung cancer. PMID:31746439
LncRNA ROR1‑AS1 high expression and its prognostic significance in liver cancer. PMID:31746401
Screening and identification of key biomarkers in prostate cancer using bioinformatics. PMID:31746380
Prediction of crucial epigenetically‑associated, differentially expressed genes by integrated bioinformatics analysis and the identification of S100A9 as a novel biomarker in psoriasis. PMID:31746348
The transcriptional regulator CBX2 and ovarian function: A whole genome and whole transcriptome approach. PMID:31745224
The Cyclic AMP Receptor Protein Regulates Quorum Sensing and Global Gene Expression in Yersinia pestis during Planktonic Growth and Growth in Biofilms. PMID:31744922
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. PMID:31744546
Genome-Scale Metabolic Networks Shed Light on the Carotenoid Biosynthesis Pathway in the Brown Algae Saccharina japonica and Cladosiphon okamuranus. PMID:31744163
iTRAQ-based proteomics analysis of aqueous humor in patients with dry age-related macular degeneration. PMID:31741866
Fast, sensitive and accurate integration of single-cell data with Harmony. PMID:31740819
BubR1 allelic effects drive phenotypic heterogeneity in mosaic-variegated aneuploidy progeria syndrome. PMID:31738183
A Comparative Peptidomic Characterization of Cultured Skeletal Muscle Tissues Derived From db/db Mice. PMID:31736878
Methylation of drug resistance-related genes in chemotherapy-sensitive Epstein-Barr virus-associated gastric cancer. PMID:31736281
Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery. PMID:31735951
Bi-allelic Mutations in TTC29 Cause Male Subfertility with Asthenoteratospermia in Humans and Mice. PMID:31735294
Differential DNA methylation in experienced meditators after an intensive day of mindfulness-based practice: Implications for immune-related pathways. PMID:31733290
Arabidopsis ZINC FINGER PROTEIN1 Acts Downstream of GL2 to Repress Root Hair Initiation and Elongation by Directly Suppressing bHLH Genes. PMID:31732703
Transcriptional Regulation of Autophagy Genes via Stage-Specific Activation of CEBPB and PPARG during Adipogenesis: A Systematic Study Using Public Gene Expression and Transcription Factor Binding Datasets. PMID:31731552
Integrated transcriptome and miRNA analysis uncovers molecular regulators of aerial stem-to-rhizome transition in the medical herb Gynostemma pentaphyllum. PMID:31730459
Identification of key biomarkers associated with development and prognosis in patients with ovarian carcinoma: evidence from bioinformatic analysis. PMID:31729978
The assessment of efficient representation of drug features using deep learning for drug repositioning. PMID:31726977
Gold-standard ontology-based anatomical annotation in the CRAFT Corpus. PMID:31725864
Leveraging word embeddings and medical entity extraction for biomedical dataset retrieval using unstructured texts. PMID:31725862
The neXtProt knowledgebase in 2020: data, tools and usability improvements. PMID:31724716
A network-based predictive gene expression signature for recurrence risks in stage II colorectal cancer. PMID:31724326
Learning complex subcellular distribution patterns of proteins via analysis of immunohistochemistry images. PMID:31722369
Identification of the molecular mechanisms associated with acute type A aortic dissection through bioinformatics methods. PMID:31721906
Draft genome sequence data of Cercospora kikuchii, a causal agent of Cercospora leaf blight and purple seed stain of soybeans. PMID:31720340
Bartonella massiliensis sp. nov., a new bacterial species isolated from an Ornithodoros sonrai tick from Senegal. PMID:31719993
Dynamics of Non-Canonical Amino Acid-Labeled Intra- and Extracellular Proteins in the Developing Mouse. PMID:31719929
Exploring the Molecular Mechanism underlying the Stable Purple-Red Leaf Phenotype in Lagerstroemia indica cv. Ebony Embers. PMID:31718025
Comparative Proteomic Analysis Reveals Key Proteins Linked to the Accumulation of Soluble Sugars and Organic Acids in the Mature Fruits of the Wild Malus Species. PMID:31717908
The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform. PMID:31713623
New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. PMID:31713622
Oncogenes, tumor suppressor and differentiation genes represent the oldest human gene classes and evolve concurrently. PMID:31712655
NLRP2 Regulates Proinflammatory and Antiapoptotic Responses in Proximal Tubular Epithelial Cells. PMID:31709256
A Bioinformatics Guide to Plant Microbiome Analysis. PMID:31708944
Excluding Oct4 from Yamanaka Cocktail Unleashes the Developmental Potential of iPSCs. PMID:31708402
Integrated transcriptomic analysis reveals hub genes involved in diagnosis and prognosis of pancreatic cancer. PMID:31706267
Mutation of the PTCH1 gene predicts recurrence of breast cancer. PMID:31704974
Trophectoderm regeneration to support full-term development in the inner cell mass isolated from bovine blastocyst. PMID:31704705
The Rhododendron Genome and Chromosomal Organization Provide Insight into Shared Whole-Genome Duplications across the Heath Family (Ericaceae). PMID:31702783
Comparative analysis of cellular expression pattern of schizophrenia risk genes in human versus mouse cortex. PMID:31700606
MiR-146a is over-expressed and controls IL-6 production in cystic fibrosis macrophages. PMID:31700158
Genomic interrogation of familial short stature contributes to the discovery of the pathophysiological mechanisms and pharmaceutical drug repositioning. PMID:31699087
MGnify: the microbiome analysis resource in 2020. PMID:31696235
Transcriptomic Analysis of mRNA-lncRNA-miRNA Interactions in Hepatocellular Carcinoma. PMID:31695090
Hemagglutinin Stability Regulates H1N1 Influenza Virus Replication and Pathogenicity in Mice by Modulating Type I Interferon Responses in Dendritic Cells. PMID:31694942
Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale. PMID:31694533
Transcriptome sequencing of Salvia miltiorrhiza after infection by its endophytic fungi and identification of genes related to tanshinone biosynthesis. PMID:31694427
Distinct gene expression characteristics in epithelial cell-Porphyromonas gingivalis interactions by integrating transcriptome analyses. PMID:31692996
Systematic identification of lncRNA-based prognostic biomarkers for glioblastoma. PMID:31692451
The IUPHAR/BPS Guide to PHARMACOLOGY in 2020: extending immunopharmacology content and introducing the IUPHAR/MMV Guide to MALARIA PHARMACOLOGY. PMID:31691834
Complete Genome Sequence of Strain YCSC6, a Marine Bacterium Isolated from Saturated Saltpan with Activity Against Uronema marinum. PMID:31691022
Genomic Resources for Darters (Percidae: Etheostominae) Provide Insight into Postzygotic Barriers Implicated in Speciation. PMID:31688927
Chlorella vulgaris supplementation effects on performances, oxidative stress and antioxidant genes expression in liver and ovaries of New Zealand White rabbits. PMID:31687566
Identification of key genes and pathways associated with cholangiocarcinoma development based on weighted gene correlation network analysis. PMID:31687280
Lignin degradation potential and draft genome sequence of Trametes trogii S0301. PMID:31687044
A specific fungal transcription factor controls effector gene expression and orchestrates the establishment of the necrotrophic pathogen lifestyle on wheat. PMID:31685928
The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation. PMID:31685817
Cisplatin-resistant triple-negative breast cancer subtypes: multiple mechanisms of resistance. PMID:31684899
Deconvolution of the Genomic and Epigenomic Interaction Landscape of Triple-Negative Breast Cancer. PMID:31683572
Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences. PMID:31682632
Differential regulatory network-based quantification and prioritization of key genes underlying cancer drug resistance based on time-course RNA-seq data. PMID:31682596
Mabellini: a genome-wide database for understanding the structural proteome and evaluating prospective antimicrobial targets of the emerging pathogen Mycobacterium abscessus. PMID:31681953
Profiling Transcriptional Regulation and Functional Roles of Schistosoma mansoni c-Jun N-Terminal Kinase. PMID:31681440
Rice Genome-Scale Network Integration Reveals Transcriptional Regulators of Grass Cell Wall Synthesis. PMID:31681374
IFN-Lambda 3 Mediates Antiviral Protection Against Porcine Epidemic Diarrhea Virus by Inducing a Distinct Antiviral Transcript Profile in Porcine Intestinal Epithelia. PMID:31681286
Expression of Protein-Coding Gene Orthologs in Zebrafish and Mouse Inner Ear Non-sensory Supporting Cells. PMID:31680844
SCNBase: a genomics portal for the soybean cyst nematode (Heterodera glycines). PMID:31680133
Computational Methods for Identifying Similar Diseases. PMID:31678735
Comparative gene expression analysis in melanocytes driven by tumor cell-derived exosomes. PMID:31678172
Tissue-specific expression profiles and positive selection analysis in the tree swallow (Tachycineta bicolor) using a de novo transcriptome assembly. PMID:31676844
Identification of DNAH6 mutations in infertile men with multiple morphological abnormalities of the sperm flagella. PMID:31676830
Immune Suppressive Extracellular Vesicle Proteins of Leptopilina heterotoma Are Encoded in the Wasp Genome. PMID:31676506
Transcriptomic and metabolomic profiling provide novel insights into fruit development and flesh coloration in Prunus mira Koehne, a special wild peach species. PMID:31675926
Investigation of the genes associated with a male sterility mutant (msm) in Chinese cabbage (Brassica campestris ssp. pekinensis) using RNA-Seq. PMID:31673754
Analysis of Arabidopsis thaliana Redox Gene Network Indicates Evolutionary Expansion of Class III Peroxidase in Plants. PMID:31673065
Genetic Regulators and Physiological Significance of Glycogen Storage in Candida albicans. PMID:31671578
Neurofilament-lysosomal genetic intersections in the cortical network of stuttering. PMID:31669185
Physiological and transcriptome analyses of photosynthesis and chlorophyll metabolism in variegated Citrus (Shiranuhi and Huangguogan) seedlings. PMID:31666652
Microevolution within ST11 group Clostridioides difficile isolates through mobile genetic elements based on complete genome sequencing. PMID:31666016
Weighted single-step GWAS identified candidate genes associated with semen traits in a Duroc boar population. PMID:31666004
Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes. PMID:31665645
SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update. PMID:31665520
Multi-breed genome-wide association studies across countries for electronically recorded behavior traits in local dual-purpose cows. PMID:31665138
RACS: rapid analysis of ChIP-Seq data for contig based genomes. PMID:31664892
Downregulation of GRK5 hampers the migration of breast cancer cells. PMID:31664083
miR-29a Is Repressed by MYC in Pancreatic Cancer and Its Restoration Drives Tumor-Suppressive Effects via Downregulation of LOXL2. PMID:31662451
Rewiring of Cancer Cell Metabolism by Mitochondrial VDAC1 Depletion Results in Time-Dependent Tumor Reprogramming: Glioblastoma as a Proof of Concept. PMID:31661894
Proteasome inhibition preserves longitudinal growth of denervated muscle and prevents neonatal neuromuscular contractures. PMID:31661460
Network inference with ensembles of bi-clustering trees. PMID:31660848
Synthetic Activators of Cell Migration Designed by Constructive Machine Learning. PMID:31660283
Phenome-wide association study of TTR and RBP4 genes in 361,194 individuals reveals novel insights in the genetics of hereditary and wildtype transthyretin amyloidoses. PMID:31659433
Ionizing radiation induces endothelial transdifferentiation of glioblastoma stem-like cells through the Tie2 signaling pathway. PMID:31659157
NaCl treatment markedly enhanced pollen viability and pollen preservation time of euhalophyte Suaeda salsa via up regulation of pollen development-related genes. PMID:31654246
Autologous micrograft accelerates endogenous wound healing response through ERK-induced cell migration. PMID:31654035
The whole-genome sequence analysis of Morchella sextelata. PMID:31653932
Biological process activity transformation of single cell gene expression for cross-species alignment. PMID:31653878
Dietary tryptophan links encephalogenicity of autoreactive T cells with gut microbial ecology. PMID:31653831
Promising Prognosis Marker Candidates on the Status of Epithelial-Mesenchymal Transition and Glioma Stem Cells in Glioblastoma. PMID:31653034
Comprehensive anatomic ontologies for lung development: A comparison of alveolar formation and maturation within mouse and human lung. PMID:31651362
Hepatic gene expression variations in response to high-fat diet-induced impaired glucose tolerance using RNAseq analysis in collaborative cross mouse population. PMID:31650267
Analysis of tumour ecological balance reveals resource-dependent adaptive strategies of ovarian cancer. PMID:31648981
Knockdown of formin mDia2 alters lamin B1 levels and increases osteogenesis in stem cells. PMID:31648392
gep2pep: a Bioconductor package for the creation and analysis of pathway-based expression profiles. PMID:31647521
Bovine Genome Database: new annotation tools for a new reference genome. PMID:31647100
MiRNA expression patterns are associated with tumor mutational burden in lung adenocarcinoma. PMID:31646073
A high-quality Actinidia chinensis (kiwifruit) genome. PMID:31645971
Draft genome sequence of cauliflower (Brassica oleracea L. var. botrytis) provides new insights into the C genome in Brassica species. PMID:31645943
Multi-tissue network analysis for drug prioritization in knee osteoarthritis. PMID:31645614
The Genome Sequence of the Eastern Woodchuck (Marmota monax) - A Preclinical Animal Model for Chronic Hepatitis B. PMID:31645421
Network-Based Functional Prediction Augments Genetic Association To Predict Candidate Genes for Histamine Hypersensitivity in Mice. PMID:31645420
Adult sox10+ Cardiomyocytes Contribute to Myocardial Regeneration in the Zebrafish. PMID:31644901
Elevated serum alpha-1 antitrypsin is a major component of GlycA-associated risk for future morbidity and mortality. PMID:31644575
WormBase: a modern Model Organism Information Resource. PMID:31642470
Integrated bioinformatics analysis reveals role of the LINC01093/miR-96-5p/ZFAND5/NF-κB signaling axis in hepatocellular carcinoma. PMID:31641376
Induction of metabolic quiescence defines the transitional to follicular B cell switch. PMID:31641080
An in silico Approach for Integrating Phenotypic and Target-based Approaches in Drug Discovery. PMID:31638744
Whole Genome Mapping Reveals Novel Genes and Pathways Involved in Milk Production Under Heat Stress in US Holstein Cows. PMID:31636656
Fermentation innovation through complex hybridization of wild and domesticated yeasts. PMID:31636426
Transcriptional Regulator TonEBP Mediates Oxidative Damages in Ischemic Kidney Injury. PMID:31635160
Complex patterns of dopamine-related gene expression in the ventral tegmental area of male zebra finches relate to dyadic interactions with long-term female partners. PMID:31634415
Genomic Analyses Provide Insights Into the Evolutionary History and Genetic Diversity of Auricularia Species. PMID:31632371
Massive computational identification of somatic variants in exonic splicing enhancers using The Cancer Genome Atlas. PMID:31631560
The Dynamic Chromatin Architecture of the Regenerating Liver. PMID:31629814
Differential expression and co-expression gene network analyses reveal molecular mechanisms and candidate biomarkers involved in breast muscle myopathies in chicken. PMID:31624339
An integrated epigenome and transcriptome analysis identifies PAX2 as a master regulator of drug resistance in high grade pancreatic ductal adenocarcinoma. PMID:31622355
Identification of prognostic biomarkers for malignant melanoma using microarray datasets. PMID:31620197
Characterization of an Environmental Multidrug-Resistant Acinetobacter seifertii and Comparative Genomic Analysis Reveals Co-occurrence of Antimicrobial Resistance and Metal Tolerance Determinants. PMID:31620107
Search for Nutritional Fitness Traits in a Biological Pest Control Agent Harmonia axyridis Using Comparative Transcriptomics. PMID:31620008
GENAVi: a shiny web application for gene expression normalization, analysis and visualization. PMID:31619158
Polymorphic Immune Mechanisms Regulate Commensal Repertoire. PMID:31618625
Concordance between gene expression in peripheral whole blood and colonic tissue in children with inflammatory bowel disease. PMID:31618209
Identification of potential key genes in esophageal adenocarcinoma using bioinformatics. PMID:31616504
Differential Expression of Circular RNAs in Polytocous and Monotocous Uterus during the Reproductive Cycle of Sheep. PMID:31615050
Transcriptomics of Tasmanian Devil (Sarcophilus Harrisii) Ear Tissue Reveals Homogeneous Gene Expression Patterns across a Heterogeneous Landscape. PMID:31614864
Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives. PMID:31614509
Inferring targeting modes of Argonaute-loaded tRNA fragments. PMID:31613177
DNAproDB: an expanded database and web-based tool for structural analysis of DNA-protein complexes. PMID:31612957
Screening and identification of key biomarkers in lung squamous cell carcinoma by bioinformatics analysis. PMID:31612029
Exosome complex genes mediate RNA degradation and predict survival in mantle cell lymphoma. PMID:31612023
Four targeted genes for predicting the prognosis of colorectal cancer: A bioinformatics analysis case. PMID:31612015
Screening and identification of key biomarkers in adrenocortical carcinoma based on bioinformatics analysis. PMID:31611976
Screening and authentication of molecular markers in malignant glioblastoma based on gene expression profiles. PMID:31611967
Myo-REG: A Portal for Signaling Interactions in Muscle Regeneration. PMID:31611808
In silico approach to calculate the transcript capacity. PMID:31610627
pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks. PMID:31608109
A Computational Pipeline for the Extraction of Actionable Biological Information From NGS-Phage Display Experiments. PMID:31607941
The Long Noncoding RNA Paupar Modulates PAX6 Regulatory Activities to Promote Alpha Cell Development and Function. PMID:31607563
Loss of methionine sulfoxide reductases increases resistance to oxidative stress. PMID:31606431
The MTH1 inhibitor TH588 is a microtubule-modulating agent that eliminates cancer cells by activating the mitotic surveillance pathway. PMID:31604991
ZC3H18 specifically binds and activates the BRCA1 promoter to facilitate homologous recombination in ovarian cancer. PMID:31604914
Transcriptomic analysis of early fruit development in Chinese white pear (Pyrus bretschneideri Rehd.) and functional identification of PbCCR1 in lignin biosynthesis. PMID:31604417
A Graphic Encoding Method for Quantitative Classification of Protein Structure and Representation of Conformational Changes. PMID:31603792
Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. PMID:31602618
ModelBricks-modules for reproducible modeling improving model annotation and provenance. PMID:31602314
Genetic interaction networks mediate individual statin drug response in Saccharomyces cerevisiae. PMID:31602312
Investigating the Multi-Target Pharmacological Mechanism of Hedyotis diffusa Willd Acting on Prostate Cancer: A Network Pharmacology Approach. PMID:31600936
Zinc binding proteome of a phytopathogen Xanthomonas translucens pv. undulosa. PMID:31598288
sRNA OsiA Stabilizes Catalase mRNA during Oxidative Stress Response of Deincoccus radiodurans R1. PMID:31597319
The U1 spliceosomal RNA is recurrently mutated in multiple cancers. PMID:31597163
DNA hypermethylation of Fgf16 and Tbx22 associated with cleft palate during palatal fusion. PMID:31596367
Stereotyped transcriptomic transformation of somatosensory neurons in response to injury. PMID:31592768
Rhizophagus intraradices promotes alfalfa (Medicago sativa) defense against pea aphids (Acyrthosiphon pisum) revealed by RNA-Seq analysis. PMID:31588522
Identification and characterization of jasmonic acid- and linolenic acid-mediated transcriptional regulation of secondary laticifer differentiation in Hevea brasiliensis. PMID:31586098
Changes of Gene Expression in Euglena gracilis Obtained During the 29th DLR Parabolic Flight Campaign. PMID:31582787
Cognitive impairment and transcriptomic profile in hippocampus of young mice after multiple neonatal exposures to sevoflurane. PMID:31582589
Blinded Testing of Function Annotation for uPE1 Proteins by I-TASSER/COFACTOR Pipeline Using the 2018-2019 Additions to neXtProt and the CAFA3 Challenge. PMID:31581775
Binding to medium and long chain fatty acyls is a common property of HEAT and ARM repeat modules. PMID:31578417
Comparative Genomics Reveals a Well-Conserved Intrinsic Resistome in the Emerging Multidrug-Resistant Pathogen Cupriavidus gilardii. PMID:31578249
Comparative transcript profiling and cytological observation of the newly bred recessive genic male sterility non-heading Chinese cabbage (Brassica rapa ssp. chinensis) line WS24-3A. PMID:31576519
Identification of lncRNAs associated with lung squamous cell carcinoma prognosis in the competitive endogenous RNA network. PMID:31576252
Genomics Analysis of L-DOPA Exposure in Drosophila sechellia. PMID:31575638
Protective Role of Leaf Variegation in Pittosporum tobira under Low Temperature: Insights into the Physio-Biochemical and Molecular Mechanisms. PMID:31574927
Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome. PMID:31574156
S‑allyl‑cysteine sulfoxide (alliin) alleviates myocardial infarction by modulating cardiomyocyte necroptosis and autophagy. PMID:31573046
Screening and Identification of Potential Prognostic Biomarkers in Adrenocortical Carcinoma. PMID:31572440
Characterization of the Long Terminal Repeat of the Endogenous Retrovirus-derived microRNAs in the Olive Flounder. PMID:31570746
Expression of microRNA in human retinal pigment epithelial cells following infection with Zaire ebolavirus. PMID:31570108
CircRNA Expression Pattern and ceRNA and miRNA-mRNA Networks Involved in Anther Development in the CMS Line of Brassica campestris. PMID:31569708
Molecular Characterization of the Transcription Factors in Susceptible Poplar Infected with Virulent Melampsora larici-populina. PMID:31569685
Diesel exhaust particles dysregulate multiple immunological pathways in murine macrophages: Lessons from microarray and scRNA-seq technologies. PMID:31568751
The in vivo transcriptome of Schistosoma mansoni in the prominent vector species Biomphalaria pfeifferi with supporting observations from Biomphalaria glabrata. PMID:31568484
Identification of key genes and pathways associated with different immune statuses of hepatitis B virus infection. PMID:31565863
Metric learning on expression data for gene function prediction. PMID:31562759
Dynamic changes in epithelial cell morphology control thymic organ size during atrophy and regeneration. PMID:31562306
Pathway Analysis Integrating Genome-Wide and Functional Data Identifies PLCG2 as a Candidate Gene for Age-Related Macular Degeneration. PMID:31560769
Genome Sequence of Lactobacillus futsaii Y97, a Potential Probiotic Strain Isolated from Futsai of Taiwan. PMID:31558628
Drosophila Heterochromatin Stabilization Requires the Zinc-Finger Protein Small Ovary. PMID:31558581
Induction of human hemogenesis in adult fibroblasts by defined factors and hematopoietic coculture. PMID:31557312
Genome-wide analysis of methylation in giant pandas with cataract by methylation-dependent restriction-site associated DNA sequencing (MethylRAD). PMID:31553743
Global agricultural concept space: lightweight semantics for pragmatic interoperability. PMID:31552293
Integrated Analysis of Multiple Microarray Studies to Identify Novel Gene Signatures in Non-alcoholic Fatty Liver Disease. PMID:31551930
Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems. PMID:31548717
Comprehensive characterization of the rRNA metabolism-related genes in human cancer. PMID:31548613
The IBD-associated long noncoding RNA IFNG-AS1 regulates the balance between inflammatory and anti-inflammatory cytokine production after T-cell stimulation. PMID:31545920
Reconstruction and analysis of competitive endogenous RNA network reveals regulatory role of long non‑coding RNAs in hepatic fibrosis. PMID:31545470
Comprehensive expression profiles and bioinformatics analysis reveal special circular RNA expression and potential predictability in the peripheral blood of humans with idiopathic membranous nephropathy. PMID:31545426
Screening and identification of biomarkers for systemic sclerosis via microarray technology. PMID:31545397
Draft Genome and Complete Hox-Cluster Characterization of the Sterlet (Acipenser ruthenus). PMID:31543900
Multi-Omics Analysis of Fatty Alcohol Production in Engineered Yeasts Saccharomyces cerevisiae and Yarrowia lipolytica. PMID:31543895
Association study reveals Th17, Treg, and Th2 loci related to resistance to Haemonchus contortus in Florida Native sheep1. PMID:31541548
Lossless Compression of Binary Trees with Correlated Vertex Names. PMID:31537945
Genome-wide identification of DNA methylation QTLs in whole blood highlights pathways for cardiovascular disease. PMID:31537805
Complete Genome Sequence of Bacteriocin-Producing Enterococcus faecium HY07. PMID:31537656
Additive and heterozygous (dis)advantage GWAS models reveal candidate genes involved in the genotypic variation of maize hybrids to Azospirillum brasilense. PMID:31536609
Bioinformatic identification of key candidate genes and pathways in axon regeneration after spinal cord injury in zebrafish. PMID:31535658
Network-based approach to identify biomarkers predicting response and prognosis for HER2-negative breast cancer treatment with taxane-anthracycline neoadjuvant chemotherapy. PMID:31534839
High-coverage genomes to elucidate the evolution of penguins. PMID:31531675
Identifying Protein Complexes from Dynamic Temporal Interval Protein-Protein Interaction Networks. PMID:31531351
Photoreceptor Activity Contributes to Contrasting Responses to Shade in Cardamine and Arabidopsis Seedlings. PMID:31530733
cellHarmony: cell-level matching and holistic comparison of single-cell transcriptomes. PMID:31529053
Synergistic Cytotoxicity of Renieramycin M and Doxorubicin in MCF-7 Breast Cancer Cells. PMID:31527453
Molecular Profiling of the Drosophila Antenna Reveals Conserved Genes Underlying Olfaction in Insects. PMID:31527046
An in silico survey of Clostridioides difficile extrachromosomal elements . PMID:31526450
Predicting Sequence Features, Function, and Structure of Proteins Using MESSA. PMID:31524991
Chronic Inflammation Directs an Olfactory Stem Cell Functional Switch from Neuroregeneration to Immune Defense. PMID:31523027
Microbial Metabolism Modulates Antibiotic Susceptibility within the Murine Gut Microbiome. PMID:31523007
Proteomics-Based Monitoring of Pathway Activity Reveals that Blocking Diacylglycerol Biosynthesis Rescues from Alpha-Synuclein Toxicity. PMID:31521608
Proteogenomic Network Analysis of Context-Specific KRAS Signaling in Mouse-to-Human Cross-Species Translation. PMID:31521603
Identifying protein complexes based on an edge weight algorithm and core-attachment structure. PMID:31521132
Favorable Alleles of GRAIN-FILLING RATE1 Increase the Grain-Filling Rate and Yield of Rice. PMID:31519786
The CRISPR-Cas9 crADSL HeLa transcriptome: A first step in establishing a model for ADSL deficiency and SAICAR accumulation. PMID:31516833
Identification of differentially expressed genes between primary lung cancer and lymph node metastasis via bioinformatic analysis. PMID:31516588
Effect of hyperoside on cervical cancer cells and transcriptome analysis of differentially expressed genes. PMID:31516392
TEADs, Yap, Taz, Vgll4s transcription factors control the establishment of Left-Right asymmetry in zebrafish. PMID:31513014
An integrative pan-cancer analysis of biological and clinical impacts underlying ubiquitin-specific-processing proteases. PMID:31511647
Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. PMID:31510914
scOrange-a tool for hands-on training of concepts from single-cell data analytics. PMID:31510695
MEK1/2 Inhibitors Unlock the Constrained Interferon Response in Macrophages Through IRF1 Signaling. PMID:31507609
Broad regulation of gene isoform expression by Wnt signaling in cancer. PMID:31506381
Regulatory annotation of genomic intervals based on tissue-specific expression QTLs. PMID:31504167
Protein functional annotation of simultaneously improved stability, accuracy and false discovery rate achieved by a sequence-based deep learning. PMID:31504150
Persistence of skewed X-chromosome inactivation in pre-B acute lymphoblastic leukemia of a female ATRX mutation carrier. PMID:31501157
BINDER: computationally inferring a gene regulatory network for Mycobacterium abscessus. PMID:31500560
Differential Regulation of Anthocyanins in Green and Purple Turnips Revealed by Combined De Novo Transcriptome and Metabolome Analysis. PMID:31500111
Migratory Neural Crest Cells Phagocytose Dead Cells in the Developing Nervous System. PMID:31495570
A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases. PMID:31494632
Prognostic value and immune infiltration of novel signatures in clear cell renal cell carcinoma microenvironment. PMID:31493764
Metaproteomics reveal that rapid perturbations in organic matter prioritize functional restructuring over taxonomy in western Arctic Ocean microbiomes. PMID:31492961
Auxin-sensitive Aux/IAA proteins mediate drought tolerance in Arabidopsis by regulating glucosinolate levels. PMID:31492889
Genetic variants in Forkhead box O1 associated with predisposition to sepsis in a Chinese Han population. PMID:31492105
H3K4me3, H3K9ac, H3K27ac, H3K27me3 and H3K9me3 Histone Tags Suggest Distinct Regulatory Evolution of Open and Condensed Chromatin Landmarks. PMID:31491936
Voluntary exercise normalizes the proteomic landscape in muscle and brain and improves the phenotype of progeroid mice. PMID:31489782
SamPler - a novel method for selecting parameters for gene functional annotation routines. PMID:31488049
TPM2 as a potential predictive biomarker for atherosclerosis. PMID:31487691
Signaling pathways and gene co-expression modules associated with cytoskeleton and axon morphology in breast cancer survivors with chronic paclitaxel-induced peripheral neuropathy. PMID:31486345
Integrative genomics analysis of hub genes and their relationship with prognosis and signaling pathways in esophageal squamous cell carcinoma. PMID:31485619
The Functional 3D Organization of Unicellular Genomes. PMID:31484964
Transcriptome Analysis Reveals Key Seed-Development Genes in Common Buckwheat (Fagopyrum esculentum). PMID:31484314
Pituitary cell translation and secretory capacities are enhanced cell autonomously by the transcription factor Creb3l2. PMID:31481663
The Role of Extracellular Matrix Expression, ERK1/2 Signaling and Cell Cohesiveness for Cartilage Yield from iPSCs. PMID:31480758
Comparative Analysis of MicroRNA and mRNA Profiles of Sperm with Different Freeze Tolerance Capacities in Boar (Sus scrofa) and Giant Panda (Ailuropoda melanoleuca). PMID:31480517
Detection of copy number variation and selection signatures on the X chromosome in Chinese indigenous sheep with different types of tail. PMID:31480185
A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition. PMID:31477929
Gene set enrichment analysis to create polygenic scores: a developmental examination of aggression. PMID:31477688
A Structure-Informed Atlas of Human-Virus Interactions. PMID:31474372
De novo transcriptome assembly for four species of crustose coralline algae and analysis of unique orthologous genes. PMID:31471551
Integration analysis for novel lncRNA markers predicting tumor recurrence in human colon adenocarcinoma. PMID:31470869
The Reason for Growth Inhibition of Ulmus pumila 'Jinye': Lower Resistance and Abnormal Development of Chloroplasts Slow Down the Accumulation of Energy. PMID:31470529
Identification of modules and functional analysis in CRC subtypes by integrated bioinformatics analysis. PMID:31469863
P4HB, a Novel Hypoxia Target Gene Related to Gastric Cancer Invasion and Metastasis. PMID:31467922
Protein identification from the parotoid macrogland secretion of Duttaphrynus melanostictus. PMID:31467513
Novel computational model of gastrula morphogenesis to identify spatial discriminator genes by self-organizing map (SOM) clustering. PMID:31467377
Comparative analysis demonstrates cell type-specific conservation of SOX9 targets between mouse and chicken. PMID:31467356
Draft Genome Sequence of a Chryseobacterium indologenes Strain Isolated from a Blood Culture of a Hospitalized Child in Antananarivo, Madagascar. PMID:31467100
Raptor genomes reveal evolutionary signatures of predatory and nocturnal lifestyles. PMID:31464627
A human endogenous retrovirus encoded protease potentially cleaves numerous cellular proteins. PMID:31462935
Function Prediction for G Protein-Coupled Receptors through Text Mining and Induction Matrix Completion. PMID:31459527
Multi-study reanalysis of 2,213 acute myeloid leukemia patients reveals age- and sex-dependent gene expression signatures. PMID:31455838
Comparative transcription analysis of photosensitive and non-photosensitive eggplants to identify genes involved in dark regulated anthocyanin synthesis. PMID:31455222
Integration of curated and high-throughput screening data to elucidate environmental influences on disease pathways. PMID:31453412
Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes. PMID:31452935
Identification of key genes and pathways between type I and type II endometrial cancer using bioinformatics analysis. PMID:31452737
On Finding and Enumerating Maximal and Maximum k-Partite Cliques in k-Partite Graphs. PMID:31448059
ComplexBrowser: A Tool for Identification and Quantification of Protein Complexes in Large-scale Proteomics Datasets. PMID:31447428
Customizing Functionalized Cofactor Mimics to Study the Human Pyridoxal 5'-Phosphate-Binding Proteome. PMID:31447350
Regulation of Co-transcriptional Pre-mRNA Splicing by m6A through the Low-Complexity Protein hnRNPG. PMID:31445886
Gene co-expression network analysis reveals pathways associated with graft healing by asymmetric profiling in tomato. PMID:31445524
Proteomics Links Ubiquitin Chain Topology Change to Transcription Factor Activation. PMID:31444107
Genome-Wide SNPs and InDels Characteristics of Three Chinese Cattle Breeds. PMID:31443466
Clinical and Genetic Analysis of Children with Kartagener Syndrome. PMID:31443223
Randomized trial of weight loss in primary breast cancer: Impact on body composition, circulating biomarkers and tumor characteristics. PMID:31442303
Revisiting the Phylogenetic History of Helminths Through Genomics, the Case of the New Echinococcus oligarthrus Genome. PMID:31440275
Statistical genomics in rare cancer. PMID:31437624
A high-quality genome assembly for the endangered golden snub-nosed monkey (Rhinopithecus roxellana). PMID:31437279
Cross comparison and prognostic assessment of breast cancer multigene signatures in a large population-based contemporary clinical series. PMID:31434940
Replication timing networks reveal a link between transcription regulatory circuits and replication timing control. PMID:31434679
Exploration of fine-scale recombination rate variation in the domestic horse. PMID:31434677
Chronic cadmium exposure decreases the dependency of MCF7 breast cancer cells on ERα. PMID:31431634
Distinct signatures of lung cancer types: aberrant mucin O-glycosylation and compromised immune response. PMID:31429720
Using Large Datasets to Understand Nanotechnology. PMID:31429126
Compression-induced expression of glycolysis genes in CAFs correlates with EMT and angiogenesis gene expression in breast cancer. PMID:31428701
I-TASSER gateway: A protein structure and function prediction server powered by XSEDE. PMID:31427836
Homogeneity tests of covariance matrices with high-dimensional longitudinal data. PMID:31427823
Syndromic immune disorder caused by a viable hypomorphic allele of spliceosome component Snrnp40. PMID:31427773
Synergistic Genetic Interactions between Pkhd1 and Pkd1 Result in an ARPKD-Like Phenotype in Murine Models. PMID:31427367
A mechanistic evaluation of the angiogenic properties of a dehydrated amnion chorion membrane in vitro and in vivo. PMID:31425636
Intrinsically disordered proteins and structured proteins with intrinsically disordered regions have different functional roles in the cell. PMID:31425549
KEGG Mapper for inferring cellular functions from protein sequences. PMID:31423653
LAMTOR/Ragulator regulates lipid metabolism in macrophages and foam cell differentiation. PMID:31423582
Dysregulation of DNA methylation patterns may identify patients with breast cancer resistant to endocrine therapy: A predictive classifier based on differentially methylated regions. PMID:31423189
Integrated bioinformatics analysis to identify 15 hub genes in breast cancer. PMID:31423162
Nucleo-cytoplasmic Partitioning of ARF Proteins Controls Auxin Responses in Arabidopsis thaliana. PMID:31421981
Possible epigenetic regulatory effect of dysregulated circular RNAs in Alzheimer's disease model. PMID:31420566
Mapping anatomical related entities to human body parts based on wikipedia in discharge summaries. PMID:31419946
ITRAQ-based proteomic analysis reveals possible target-related proteins in human adrenocortical adenomas. PMID:31419939
Investigation into the underlying regulatory mechanisms shaping inflorescence architecture in Chenopodium quinoa. PMID:31419932
Chromosomal level assembly and population sequencing of the Chinese tree shrew genome. PMID:31418539
Complete Genome Sequence of Azoarcus sp. Strain DD4, a Gram-Negative Propanotroph That Degrades 1,4-Dioxane and 1,1-Dichloroethylene. PMID:31416874
In silico evidence of de novo interactions between ribosomal and Epstein - Barr virus proteins. PMID:31416416
Advances in gene ontology utilization improve statistical power of annotation enrichment. PMID:31415589
IRNdb: the database of immunologically relevant non-coding RNAs. PMID:31414702
Decreased metabolism and increased tolerance to extreme environments in Staphylococcus warneri during long-term spaceflight. PMID:31414557
Genome-wide analysis sheds light on the high-altitude adaptation of the buff-throated partridge (Tetraophasis szechenyii). PMID:31414227
Application of the High-throughput TAB-Array for the Discovery of Novel 5-Hydroxymethylcytosine Biomarkers in Pancreatic Ductal Adenocarcinoma. PMID:31413874
mRNAs expression profiles of high glucose-induced memory in human umbilical vein endothelial cells. PMID:31413614
Gene expression profiling reveals candidate biomarkers and probable molecular mechanism in diabetic peripheral neuropathy. PMID:31413612
Transcriptomic analysis of immune response to bacterial lipopolysaccharide in zebra finch (Taeniopygia guttata). PMID:31412766
Identification of crucial genes based on expression profiles of hepatocellular carcinomas by bioinformatics analysis. PMID:31410310
Establishment and characterisation of a new patient-derived model of myxoid liposarcoma with acquired resistance to trabectedin. PMID:31409911
Network Pharmacology Identifies the Mechanisms of Action of Shaoyao Gancao Decoction in the Treatment of Osteoarthritis. PMID:31409761
ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity. PMID:31406507
Link clustering explains non-central and contextually essential genes in protein interaction networks. PMID:31406201
Differential Proteomics Based on TMT and PRM Reveal the Resistance Response of Bambusa pervariabilis × Dendrocalamopisis grandis Induced by AP-Toxin. PMID:31405188
Transcriptomic Analysis of Marine Gastropod Hemifusus tuba Provides Novel Insights into Conotoxin Genes. PMID:31405144
miRDRN-miRNA disease regulatory network: a tool for exploring disease and tissue-specific microRNA regulatory networks. PMID:31404401
Structural Basis of the Subcellular Topology Landscape of Escherichia coli. PMID:31404336
Discovery of core genes in colorectal cancer by weighted gene co-expression network analysis. PMID:31402962
Clinical value of microRNA-198-5p downregulation in lung adenocarcinoma and its potential pathways. PMID:31402959
Construction of subtype-specific prognostic gene signatures for early-stage non-small cell lung cancer using meta feature selection methods. PMID:31402939
Omics Driven Understanding of the Intestines of Parasitic Nematodes. PMID:31402928
Multilayered Tuning of Dosage Compensation and Z-Chromosome Masculinization in the Wood White (Leptidea sinapis) Butterfly. PMID:31400207
Gene Fusions Derived by Transcriptional Readthrough are Driven by Segmental Duplication in Human. PMID:31400206
Obese Individuals with and without Type 2 Diabetes Show Different Gut Microbial Functional Capacity and Composition. PMID:31399369
Differential gene and protein expression between rat tibial nerve and common peroneal nerve during Wallerian degeneration. PMID:31397358
Serial gene co-expression network approach to mine biological meanings from integrated transcriptomes of the porcine endometrium during estrous cycle. PMID:31396752
A Systematic View Exploring the Role of Chloroplasts in Plant Abiotic Stress Responses. PMID:31396532
Integrated mRNA and miRNA profiling in NIH/3T3 cells in response to bovine papillomavirus E6 gene expression. PMID:31396463
Single-Cell RNA Sequencing of Visceral Adipose Tissue Leukocytes Reveals that Caloric Restriction Following Obesity Promotes the Accumulation of a Distinct Macrophage Population with Features of Phagocytic Cells. PMID:31396408
Head Start Immunity: Characterizing the Early Protection of C Strain Vaccine Against Subsequent Classical Swine Fever Virus Infection. PMID:31396205
Identification of Wolbachia-Responsive miRNAs in the Small Brown Planthopper, Laodelphax striatellus. PMID:31396100
Protein Complex Identification and quantitative complexome by CN-PAGE. PMID:31395906
Cell-specific ablation of Hsp47 defines the collagen-producing cells in the injured heart. PMID:31393098
Discovery of stroke-related blood biomarkers from gene expression network models. PMID:31391037
A seed-extended algorithm for detecting protein complexes based on density and modularity with topological structure and GO annotations. PMID:31390979
Long Non-Coding RNA Expression Levels Modulate Cell-Type-Specific Splicing Patterns by Altering Their Interaction Landscape with RNA-Binding Proteins. PMID:31390792
An improved genome assembly of the fluke Schistosoma japonicum. PMID:31390359
Identifying subpathway signatures for individualized anticancer drug response by integrating multi-omics data. PMID:31387579
Novel deep learning model for more accurate prediction of drug-drug interaction effects. PMID:31387547
Characterization of the prognostic values of the NDRG family in gastric cancer. PMID:31384305
Effect of short-term oral prednisone therapy on blood gene expression: a randomised controlled clinical trial. PMID:31382977
Hybrid sequencing of the Gynostemma pentaphyllum transcriptome provides new insights into gypenoside biosynthesis. PMID:31382891
Long Non-Coding RNAs Target Pathogenetically Relevant Genes and Pathways in Rheumatoid Arthritis. PMID:31382516
The Natural Compound Neobractatin Induces Cell Cycle Arrest by Regulating E2F1 and Gadd45α. PMID:31380287
Pan-Cancer and Single-Cell Modeling of Genomic Alterations Through Gene Expression. PMID:31379928
Uncovering the Transcriptional Correlates of Hub Connectivity in Neural Networks. PMID:31379515
Cholestatic liver disease results increased production of reactive aldehydes and an atypical periportal hepatic antioxidant response. PMID:31377417
Analysis of methylation datasets identified significantly changed genes and functional pathways in osteoarthritis. PMID:31376087
Development of a Chimeric Model to Study and Manipulate Human Microglia In Vivo. PMID:31375314
Identification of key candidate targets and pathways for the targeted treatment of leukemia stem cells of chronic myelogenous leukemia using bioinformatics analysis. PMID:31373443
From the Amazon: A comprehensive liver transcriptome dataset of the teleost fish tambaqui, Colossoma macropomum. PMID:31372415
Spatial Regulation of Mitochondrial Heterogeneity by Stromal Confinement in Micropatterned Tumor Models. PMID:31371796
Whole Genome Sequence of the Commercially Relevant Mushroom Strain Agaricus bisporus var. bisporus ARP23. PMID:31371382
Comparative Proteomics and Physiological Analyses Reveal Important Maize Filling-Kernel Drought-Responsive Genes and Metabolic Pathways. PMID:31370198
Multigene Biomarkers of Pyrethroid Exposure: Exploratory Experiments. PMID:31365144
Comparative transcriptome analysis reveals the genetic basis underlying the biosynthesis of polysaccharides in Hericium erinaceus. PMID:31363932
Genetically diverse Pseudomonas aeruginosa populations display similar transcriptomic profiles in a cystic fibrosis explanted lung. PMID:31363089
Detailed modeling of positive selection improves detection of cancer driver genes. PMID:31363082
Bioactive Proteins in Channa striata Promote Wound Healing through Angiogenesis and Cell Proliferation. PMID:31362651
Extensive post-transcriptional buffering of gene expression in the response to severe oxidative stress in baker's yeast. PMID:31358845
Lack of long-term acclimation in Antarctic encrusting species suggests vulnerability to warming. PMID:31358752
Challenges in funding and developing genomic software: roots and remedies. PMID:31358028
Whole genome sequence and de novo assembly revealed genomic architecture of Indian Mithun (Bos frontalis). PMID:31357931
MicroRNA Sequencing Reveals the Effect of Different Levels of Non-Fibrous Carbohydrate/Neutral Detergent Fiber on Rumen Development in Calves. PMID:31357699
RITAN: rapid integration of term annotation and network resources. PMID:31355053
Bioinformatics analysis of dysregulated microRNAs in exosomes from docetaxel-resistant and parental human breast cancer cells. PMID:31354350
RNA sequencing profiling of the retina in C57BL/6J and DBA/2J mice: Enhancing the retinal microarray data sets from GeneNetwork. PMID:31354228
Mammalian Annotation Database for improved annotation and functional classification of Omics datasets from less well-annotated organisms. PMID:31353404
Predicting Phenotypic Diversity from Molecular and Genetic Data. PMID:31352366
The Gene Master Regulators (GMR) Approach Provides Legitimate Targets for Personalized, Time-Sensitive Cancer Gene Therapy. PMID:31349573
Integrated identification of key genes and pathways in Alzheimer's disease via comprehensive bioinformatical analyses. PMID:31346329
Complete Genome Sequence of Brevibacillus laterosporus Bl-zj, an Algicidal Bacterium Isolated from Soil. PMID:31346010
Analysis of gene expression in rheumatoid arthritis and related conditions offers insights into sex-bias, gene biotypes and co-expression patterns. PMID:31344123
Identification and Interaction Analysis of Significant Genes and MicroRNAs in Pterygium. PMID:31341891
Chromosome assembly of Collichthys lucidus, a fish of Sciaenidae with a multiple sex chromosome system. PMID:31341172
Identification of differentially expressed genes in small and non-small cell lung cancer based on meta-analysis of mRNA. PMID:31338439
Exploiting Differential Gene Expression to Discover Ionic and Osmotic-Associated Transcripts in the Halophyte Grass Aeluropus littoralis. PMID:31337987
Label-Free Proteomic Analysis of Molecular Effects of 2-Methoxy-1,4-naphthoquinone on Penicillium italicum. PMID:31337149
Using deep maxout neural networks to improve the accuracy of function prediction from protein interaction networks. PMID:31335894
Genetic mapping in Diversity Outbred mice identifies a Trpa1 variant influencing late-phase formalin response. PMID:31335644
AraPPINet: An Updated Interactome for the Analysis of Hormone Signaling Crosstalk in Arabidopsis thaliana. PMID:31333706
Proteomic Data Integration Highlights Central Actors Involved in Einkorn (Triticum monococcum ssp. monococcum) Grain Filling in Relation to Grain Storage Protein Composition. PMID:31333693
Identification of gene co-expression modules and hub genes associated with lymph node metastasis of papillary thyroid cancer. PMID:31332712
Transcriptome profiling of Gerbera hybrida reveals that stem bending is caused by water stress and regulation of abscisic acid. PMID:31331262
Why do eukaryotic proteins contain more intrinsically disordered regions? PMID:31329574
Differential regulation of mycelial growth and aflatoxin biosynthesis by Aspergillus flavus under different temperatures as revealed by strand-specific RNA-Seq. PMID:31328901
Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases. PMID:31328773
A step-by-step guide to analyzing CAGE data using R/Bioconductor. PMID:31327999
Estimating dispensable content in the human interactome. PMID:31324802
Identification and characterization of sexual dimorphism‑linked gene expression profile in hepatocellular carcinoma. PMID:31322260
Diagnostic and prognostic values of integrin α subfamily mRNA expression in colon adenocarcinoma. PMID:31322253
Identification of important invasion and proliferation related genes in adrenocortical carcinoma. PMID:31321566
Shiny-Seq: advanced guided transcriptome analysis. PMID:31319888
FunFam protein families improve residue level molecular function prediction. PMID:31319797
Functionally significant metabolic differences between B and T lymphocyte lineages. PMID:31318442
Computational Drug Screening Identifies Compounds Targeting Renal Age-associated Molecular Profiles. PMID:31316728
Plasma proteomic changes during therapeutic hypothermia in resuscitated patients after cardiac arrest. PMID:31316602
The ER Lumenal Hsp70 Protein FpLhs1 Is Important for Conidiation and Plant Infection in Fusarium pseudograminearum. PMID:31316483
RAC1 inhibition reverses cisplatin resistance in esophageal squamous cell carcinoma and induces downregulation of glycolytic enzymes. PMID:31314174
The draft genome of a wild barley genotype reveals its enrichment in genes related to biotic and abiotic stresses compared to cultivated barley. PMID:31314154
iOmicsPASS: network-based integration of multiomics data for predictive subnetwork discovery. PMID:31312515
Replication and transcriptionomic analysis of human noroviruses in human intestinal enteroids. PMID:31312350
Gene Amplification-Driven Long Noncoding RNA SNHG17 Regulates Cell Proliferation and Migration in Human Non-Small-Cell Lung Cancer. PMID:31310946
Long Noncoding RNA Expression Profile in BV2 Microglial Cells Exposed to Lipopolysaccharide. PMID:31309106
NGSEA: Network-Based Gene Set Enrichment Analysis for Interpreting Gene Expression Phenotypes with Functional Gene Sets. PMID:31307154
Ligand Binding Site Structure Shapes Folding, Assembly and Degradation of Homomeric Protein Complexes. PMID:31306664
Co-expression analysis reveals dysregulated miRNAs and miRNA-mRNA interactions in the development of contrast-induced acute kidney injury. PMID:31306435
ParaDB: A manually curated database containing genomic annotation for the human pathogenic fungi Paracoccidioides spp. PMID:31306428
Comprehensive analysis of an lncRNA-miRNA-mRNA competing endogenous RNA network in pulpitis. PMID:31304055
PRPF40A as a potential diagnostic and prognostic marker is upregulated in pancreatic cancer tissues and cell lines: an integrated bioinformatics data analysis. PMID:31303762
Identification of Fusarium graminearum-responsive miRNAs and their targets in wheat by sRNA sequencing and degradome analysis. PMID:31302787
Inferring Regulatory Programs Governing Region Specificity of Neuroepithelial Stem Cells during Early Hindbrain and Spinal Cord Development. PMID:31302154
A gene expression network analysis of the pancreatic islets from lean and obese mice identifies complement 1q like-3 secreted protein as a regulator of β-cell function. PMID:31300714
Royal jelly-derived proteins enhance proliferation and migration of human epidermal keratinocytes in an in vitro scratch wound model. PMID:31299973
A role for the Saccharomyces cerevisiae ABCF protein New1 in translation termination/recycling. PMID:31299085
Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps. PMID:31296857
Regulation of tumor angiogenesis and mesenchymal-endothelial transition by p38α through TGF-β and JNK signaling. PMID:31296856
Comprehensive in vivo identification of the c-Myc mRNA protein interactome using HyPR-MS. PMID:31296583
A transcriptional and functional analysis of heat hardening in two invasive fruit fly species, Bactrocera dorsalis and Bactrocera correcta. PMID:31293628
The Transcriptome Landscape of Walnut Interspecies Hybrid (Juglans hindsii × Juglans regia) and Regulation of Cambial Activity in Relation to Grafting. PMID:31293615
Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment. PMID:31293610
Finding Functional Differences Between Species in a Microbial Community: Case Studies in Wine Fermentation and Kefir Culture. PMID:31293529
Quorum Quenching Enzyme APTM01, an Acylhomoserine-Lactone Acylase from Marine Bacterium of Pseudoalteromonas tetraodonis Strain MQS005. PMID:31292680
Hybrid gene misregulation in multiple developing tissues within a recent adaptive radiation of Cyprinodon pupfishes. PMID:31291291
Epimutations in Developmental Genes Underlie the Onset of Domestication in Farmed European Sea Bass. PMID:31289822
Investigation of differentially expressed genes in nasopharyngeal carcinoma by integrated bioinformatics analysis. PMID:31289570
Identification of potential diagnostic and therapeutic target genes for lung squamous cell carcinoma. PMID:31289486
Unveiling the presence of biosynthetic pathways for bioactive compounds in the Thalassiosira rotula transcriptome. PMID:31289324
Genetic interactions of G-quadruplexes in humans. PMID:31287417
The Farmed Atlantic Salmon (Salmo salar) Skin-Mucus Proteome and Its Nutrient Potential for the Resident Bacterial Community. PMID:31284681
Moonlighting Proteins and Cardiopathy in the Spatial Response of MCF-7 Breast Cancer Cells to Tamoxifen. PMID:31282103
Genome-wide functional association networks: background, data & state-of-the-art resources. PMID:31281921
Three Biomarkers Predict Gastric Cancer Patients' Susceptibility To Fluorouracil-based Chemotherapy. PMID:31281472
A Novel Genes Signature Associated with the Progression of Polycystic Ovary Syndrome. PMID:31278444
Restoration of histone acetylation ameliorates disease and metabolic abnormalities in a FUS mouse model. PMID:31277703
Novel significant stage-specific differentially expressed genes in hepatocellular carcinoma. PMID:31277598
ET-GRU: using multi-layer gated recurrent units to identify electron transport proteins. PMID:31277574
Bioinformatics analysis of key biomarkers and pathways in KSHV infected endothelial cells. PMID:31277155
Disease gene prediction for molecularly uncharacterized diseases. PMID:31276496
RNA Sequencing of Osteosarcoma Gene Expression Profile Revealed that miR-214-3p Facilitates Osteosarcoma Cell Proliferation via Targeting Ubiquinol-Cytochrome c Reductase Core Protein 1 (UQCRC1). PMID:31276465
Whole Transcriptome Sequencing Reveals How Acupuncture and Moxibustion Increase Pregnancy Rate in Patients Undergoing In Vitro Fertilization-Embryo Transplantation. PMID:31275970
Combinatorial perturbation analysis reveals divergent regulations of mesenchymal genes during epithelial-to-mesenchymal transition. PMID:31275609
Analysis of the Escherichia coli extracellular vesicle proteome identifies markers of purity and culture conditions. PMID:31275533
Chemoproteomic Method for Profiling Inhibitor-Bound Kinase Complexes. PMID:31274292
Reporting and connecting cell type names and gating definitions through ontologies. PMID:31272390
An ontology for representing hematologic malignancies: the cancer cell ontology. PMID:31272372
Physical confinement induces malignant transformation in mammary epithelial cells. PMID:31271857
ProtDCal-Suite: A web server for the numerical codification and functional analysis of proteins. PMID:31271472
Exploring the dark genome: implications for precision medicine. PMID:31270560
FGF family members differentially regulate maturation and proliferation of stem cell-derived astrocytes. PMID:31270389
Deep evolutionary origin of limb and fin regeneration. PMID:31270239
Qianggan extract improved nonalcoholic steatohepatitis by modulating lncRNA/circRNA immune ceRNA networks. PMID:31269941
Cross-species functional modules link proteostasis to human normal aging. PMID:31269015
Evolutionary Proteomics Reveals Distinct Patterns of Complexity and Divergence between Lepidopteran Sperm Morphs. PMID:31268533
Glial α-synuclein promotes neurodegeneration characterized by a distinct transcriptional program in vivo. PMID:31267577
Common and specific responses to iron and phosphorus deficiencies in roots of apple tree (Malus × domestica). PMID:31267256
A systems biology pipeline identifies regulatory networks for stem cell engineering. PMID:31267104
Long noncoding RNA NEAT1 mediates neuronal histone methylation and age-related memory impairment. PMID:31266852
The Genome Sequence of the Anthelmintic-Susceptible New Zealand Haemonchus contortus. PMID:31263885
Cloudy with a Chance of Insights: Context Dependent Gene Regulation and Implications for Evolutionary Studies. PMID:31261769
GAIL: An interactive webserver for inference and dynamic visualization of gene-gene associations based on gene ontology guided mining of biomedical literature. PMID:31260503
Isatin inhibits the invasion of human neuroblastoma SH‑SY5Y cells, based on microarray analysis. PMID:31257543
Analysis of potential functional significance of microRNA‑3613‑3p in human umbilical vein endothelial cells affected by heat stress. PMID:31257536
Identification of key pathways and genes in different types of chronic kidney disease based on WGCNA. PMID:31257514
Detecting the long non‑coding RNA signature related to spinal cord ependymal tumor subtype using a genome‑wide methylome analysis approach. PMID:31257484
Significantly dysregulated genes in osteoarthritic labrum cells identified through gene expression profiling. PMID:31257478
HPO2Vec+: Leveraging heterogeneous knowledge resources to enrich node embeddings for the Human Phenotype Ontology. PMID:31255713
Multimapping confounds ribosome profiling analysis: A case-study of the Hsp90 molecular chaperone. PMID:31254414
Osteoclasts Modulate Bone Erosion in Cholesteatoma via RANKL Signaling. PMID:31254133
A genetics-led approach defines the drug target landscape of 30 immune-related traits. PMID:31253980
A periodic table of cell types. PMID:31249003
FunSet: an open-source software and web server for performing and displaying Gene Ontology enrichment analysis. PMID:31248361
Transcriptomic Insights into the Response of the Olfactory Bulb to Selenium Treatment in a Mouse Model of Alzheimer's Disease. PMID:31248178
Pigeon foot feathering reveals conserved limb identity networks. PMID:31247188
The Knowledge Object Reference Ontology (KORO): A formalism to support management and sharing of computable biomedical knowledge for learning health systems. PMID:31245583
Co-expression Network Analysis Elucidated a Core Module in Association With Prognosis of Non-functioning Non-invasive Human Pituitary Adenoma. PMID:31244774
Survey of the Bradysia odoriphaga Transcriptome Using PacBio Single-Molecule Long-Read Sequencing. PMID:31242713
Complete Genome Sequences of Colwellia sp. Arc7-635, a Denitrifying Bacterium Isolated from Arctic Seawater. PMID:31240393
CTCF variants in 39 individuals with a variable neurodevelopmental disorder broaden the mutational and clinical spectrum. PMID:31239556
Visualization and prediction of CRISPR incidence in microbial trait-space to identify drivers of antiviral immune strategy. PMID:31239539
DNA methylome and transcriptome alterations and cancer prevention by triterpenoid ursolic acid in UVB-induced skin tumor in mice. PMID:31237383
Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm. PMID:31236786
RNA polymerase II (RNAP II)-associated factors are recruited to tRNA loci, revealing that RNAP II- and RNAP III-mediated transcriptions overlap in yeast. PMID:31235518
Partial defoliation of Brachypodium distachyon plants grown in petri dishes under low light increases P and other nutrient levels concomitantly with transcriptional changes in the roots. PMID:31223535
Identification and prioritization of macrolideresistance genes with hypothetical annotation inStreptococcus pneumoniae. PMID:31223208
Systems-level Analysis Reveals Multiple Modulators of Epithelial-mesenchymal Transition and Identifies DNAJB4 and CD81 as Novel Metastasis Inducers in Breast Cancer. PMID:31221721
Proteomics Analysis of Extracellular Matrix Remodeling During Zebrafish Heart Regeneration. PMID:31221719
Methylation analysis for postpartum depression: a case control study. PMID:31221108
Age-dependent alterations of Kir4.1 expression in neural crest-derived cells of the mouse and human cochlea. PMID:31220650
Genomic knockout of alms1 in zebrafish recapitulates Alström syndrome and provides insight into metabolic phenotypes. PMID:31220269
Comparison of liver transcriptome from high- and low-intramuscular fat Chaohu ducks provided additional candidate genes for lipid selection. PMID:31218175
Buyang Huanwu Tang alleviates inflammation and improves motor endplate functions in DSMA rat models by activating several biological molecules and associated signaling pathways. PMID:31217875
Gene Information eXtension (GIX): effortless retrieval of gene product information on any website. PMID:31217594
Current best practices in single-cell RNA-seq analysis: a tutorial. PMID:31217225
Comprehensive epigenetic analyses reveal master regulators driving lung metastasis of breast cancer. PMID:31215771
A First Study of the Virulence Potential of a Bacillus subtilis Isolate From Deep-Sea Hydrothermal Vent. PMID:31214515
Health information technology: promise and progress. PMID:31214346
The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species. PMID:31214208
miR-142-3p suppresses uveal melanoma by targeting CDC25C, TGFβR1, GNAQ, WASL, and RAC1. PMID:31213897
Transcriptomic correlates of electrophysiological and morphological diversity within and across excitatory and inhibitory neuron classes. PMID:31211786
Shigella promotes major alteration of gut epithelial physiology and tissue invasion by shutting off host intracellular transport. PMID:31209035
Novel interconnections of HOG signaling revealed by combined use of two proteomic software packages. PMID:31208443
Combining learning and constraints for genome-wide protein annotation. PMID:31208327
Machine learning with the TCGA-HNSC dataset: improving usability by addressing inconsistency, sparsity, and high-dimensionality. PMID:31208324
Genetic Diversity of Indigenous Pigs from South China Area Revealed by SNP Array. PMID:31208134
Rational discovery of dual-indication multi-target PDE/Kinase inhibitor for precision anti-cancer therapy using structural systems pharmacology. PMID:31206508
Rational creation and systematic analysis of cervical cancer kinase-inhibitor binding profile. PMID:31203490
An expanded proteome of cardiac t-tubules. PMID:31202980
Protein interactions and consensus clustering analysis uncover insights into herpesvirus virion structure and function relationships. PMID:31199794
Screening of differentially expressed genes and identification of NUF2 as a prognostic marker in breast cancer. PMID:31198978
Comprehensive bioinformatics analysis of trabecular meshwork gene expression data to unravel the molecular pathogenesis of primary open-angle glaucoma. PMID:31197946
Contribution of Gene Regulatory Networks to Heritability of Coronary Artery Disease. PMID:31196451
Predicting instances of pathway ontology classes for pathway integration. PMID:31196182
Clinical expression and antigenic profiles of a Plasmodium vivax vaccine candidate: merozoite surface protein 7 (PvMSP-7). PMID:31196098
pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components. PMID:31195976
Limits to a classic paradigm: most transcription factors in E. coli regulate genes involved in multiple biological processes. PMID:31194874
Genome-wide association study of multisite chronic pain in UK Biobank. PMID:31194737
Transcriptomic Analysis of Trichoderma atroviride Overgrowing Plant-Wilting Verticillium dahliae Reveals the Role of a New M14 Metallocarboxypeptidase CPA1 in Biocontrol. PMID:31191472
Identification of key genes and pathways in seminoma by bioinformatics analysis. PMID:31190870
Identification of novel biomarkers and candidate small molecule drugs in non-small-cell lung cancer by integrated microarray analysis. PMID:31190860
A perfusion bioreactor-based 3D model of the subarachnoid space based on a meningeal tissue construct. PMID:31189484
Specialized eRpL22 paralogue-specific ribosomes regulate specific mRNA translation in spermatogenesis in Drosophila melanogaster. PMID:31188709
Development of a Zebrafish S1500+ Sentinel Gene Set for High-Throughput Transcriptomics. PMID:31188086
Deciphering the non-coding RNA-level response to arsenic stress in rice (Oryza sativa). PMID:31187662
Prediction of key regulators and downstream targets of E. coli induced mastitis. PMID:31187384
Analysis of the role of DAMTC in lung adenocarcinoma cells based on the DNA microarrays. PMID:31186684
The initiation of puberty in Atlantic salmon brings about large changes in testicular gene expression that are modulated by the energy status. PMID:31185904
Identification of miRNAs and their target genes in Larix olgensis and verified of differential expression miRNAs. PMID:31185902
Phenotypical profile and global transcriptomic profile of Hypervirulent Klebsiella pneumoniae due to carbapenemase-encoding plasmid acquisition. PMID:31185888
Protein-protein interaction prediction using a hybrid feature representation and a stacked generalization scheme. PMID:31182027
Bioinformatics analysis of the regulatory lncRNA‑miRNA‑mRNA network and drug prediction in patients with hypertrophic cardiomyopathy. PMID:31180540
Identify CRNDE and LINC00152 as the key lncRNAs in age-related degeneration of articular cartilage through comprehensive and integrative analysis. PMID:31179196
Detection of condition-specific marker genes from RNA-seq data with MGFR. PMID:31179178
ANASTASIA: An Automated Metagenomic Analysis Pipeline for Novel Enzyme Discovery Exploiting Next Generation Sequencing Data. PMID:31178894
Identification of Temporal Characteristic Networks of Peripheral Blood Changes in Alzheimer's Disease Based on Weighted Gene Co-expression Network Analysis. PMID:31178714
Identification of Key Genes and Pathway for Ovarian Neoplasms Using the OVDM1 Cell Line Based on Bioinformatics Analysis. PMID:31177266
Comparative transcriptomic and proteomic analysis of yellow shell and black shell pearl oysters, Pinctada fucata martensii. PMID:31176356
AtTRAPPC11/ROG2: A Role for TRAPPs in Maintenance of the Plant Trans-Golgi Network/Early Endosome Organization and Function. PMID:31175171
Regional Heterogeneity in Gene Expression, Regulation, and Coherence in the Frontal Cortex and Hippocampus across Development and Schizophrenia. PMID:31174959
Culturing C2C12 myotubes on micromolded gelatin hydrogels accelerates myotube maturation. PMID:31174599
Identification of microRNAs associated with the aggressiveness of prolactin pituitary tumors using bioinformatic analysis. PMID:31173251
Screening key genes and signaling pathways in colorectal cancer by integrated bioinformatics analysis. PMID:31173250
Identification of diagnostic long non‑coding RNA biomarkers in patients with hepatocellular carcinoma. PMID:31173205
Identification of key candidate genes involved in melanoma metastasis. PMID:31173190
Comparison of long non‑coding RNA expression profiles in human dental follicle cells and human periodontal ligament cells. PMID:31173189
The complexity of alternative splicing and landscape of tissue-specific expression in lotus (Nelumbo nucifera) unveiled by Illumina- and single-molecule real-time-based RNA-sequencing. PMID:31173073
Aberrant NFATc1 signaling counteracts TGFβ-mediated growth arrest and apoptosis induction in pancreatic cancer progression. PMID:31171768
Identification of core genes and clinical roles in pregnancy-associated breast cancer based on integrated analysis of different microarray profile datasets. PMID:31171715
SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse. PMID:31171447
High expression of Annexin A2 is associated with DNA repair, metabolic alteration, and worse survival in pancreatic ductal adenocarcinoma. PMID:31171367
A survey of transcriptome complexity using PacBio single-molecule real-time analysis combined with Illumina RNA sequencing for a better understanding of ricinoleic acid biosynthesis in Ricinus communis. PMID:31170917
PTEN interacts with the transcription machinery on chromatin and regulates RNA polymerase II-mediated transcription. PMID:31169889
Endometriosis Knowledgebase: a gene-based resource on endometriosis. PMID:31169291
Ontology-Based Interactive Visualization of Patient-Generated Research Questions. PMID:31167249
Endodermal Maternal Transcription Factors Establish Super-Enhancers during Zygotic Genome Activation. PMID:31167141
Transcriptome and excretory-secretory proteome of infective-stage larvae of the nematode Gnathostoma spinigerum reveal potential immunodiagnostic targets for development. PMID:31166909
Monozygotic twins and triplets discordant for amyotrophic lateral sclerosis display differential methylation and gene expression. PMID:31164693
Prediction of competing endogenous RNA coexpression network as prognostic markers in AML. PMID:31164492
IL-27 promotes the expansion of self-renewing CD8+ T cells in persistent viral infection. PMID:31164392
Maternal Experience Leads to Lasting Gene Expression Changes in Some Regions of the Mouse Brain. PMID:31164388
Comprehensive transcriptome analysis reveals genes potentially involved in isoflavone biosynthesis in Pueraria thomsonii Benth. PMID:31163077
The prediction of early preeclampsia: Results from a longitudinal proteomics study. PMID:31163045
Genome-wide survey and expression analyses of the GRAS gene family in Brassica napus reveals their roles in root development and stress response. PMID:31161396
VCF/Plotein: visualization and prioritization of genomic variants from human exome sequencing projects. PMID:31161195
Global serum proteomic changes in water buffaloes infected with Fasciola gigantica. PMID:31159882
Trait ontology analysis based on association mapping studies bridges the gap between crop genomics and Phenomics. PMID:31159731
NetR and AttR, Two New Bioinformatic Tools to Integrate Diverse Datasets into Cytoscape Network and Attribute Files. PMID:31159440
PRC2-Mediated H3K27me3 Contributes to Transcriptional Regulation of FIT-Dependent Iron Deficiency Response. PMID:31156682
Identification of Proteins Differentially Expressed by Adipose-derived Mesenchymal Stem Cells Isolated from Immunodeficient Mice. PMID:31151297
The genomes of polyextremophilic cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions. PMID:31149898
LnCompare: gene set feature analysis for human long non-coding RNAs. PMID:31147707
Genome Analysis of Hypomyces perniciosus, the Causal Agent of Wet Bubble Disease of Button Mushroom (Agaricus bisporus). PMID:31146507
Distinct fibroblast subsets drive inflammation and damage in arthritis. PMID:31142839
Transcriptomics Analysis Reveals New Insights into the Roles of Notch1 Signaling on Macrophage Polarization. PMID:31142802
Graph Algorithms for Condensing and Consolidating Gene Set Analysis Results. PMID:31142576
LION/web: a web-based ontology enrichment tool for lipidomic data analysis. PMID:31141612
Map and model-moving from observation to prediction in toxicogenomics. PMID:31140561
Genomic characterization of Escherichia coli LCT-EC001, an extremely multidrug-resistant strain with an amazing number of resistance genes. PMID:31139265
Identify differential gene expressions in fatty infiltration process in rotator cuff. PMID:31138249
Altered microRNA profiles of testicular biopsies from patients with nonobstructive azoospermia. PMID:31134916
Human pancreatic cancer cell exosomes, but not human normal cell exosomes, act as an initiator in cell transformation. PMID:31134894
eIF2B Mutations Cause Mitochondrial Malfunction in Oligodendrocytes. PMID:31134486
Identification of Genes Differentially Expressed in Simvastatin-Induced Alveolar Bone Formation. PMID:31131344
Genomic insights into a robust gamma-aminobutyric acid-producer Lactobacillus brevis CD0817. PMID:31127390
Exploratory Gene Ontology Analysis with Interactive Visualization. PMID:31127124
Genetic analyses of human fetal retinal pigment epithelium gene expression suggest ocular disease mechanisms. PMID:31123710
A Brief History of Protein Sorting Prediction. PMID:31119599
The genome resources for conservation of Indo-Pacific humpback dolphin, Sousa chinensis. PMID:31118413
Overlapping and unique roles played by ROCK1 and 2 in the modulation of coding and long noncoding RNA expression. PMID:31117934
Transcriptomics analysis of sirolimus treatment in lupus nephritis. PMID:31115581
Informatics and Computational Methods in Natural Product Drug Discovery: A Review and Perspectives. PMID:31114606
Differential gene expression analysis in blood of first episode psychosis patients. PMID:31113746
Preclinical rationale for entinostat in embryonal rhabdomyosarcoma. PMID:31113472
Iso-Seq analysis of the Taxus cuspidata transcriptome reveals the complexity of Taxol biosynthesis. PMID:31113367
Morpholinos Do Not Elicit an Innate Immune Response during Early Xenopus Embryogenesis. PMID:31112700
The human amniotic fluid mesenchymal stem cells therapy on, SKOV3, ovarian cancer cell line. PMID:31111674
Tracking transcriptomic responses to endogenous and exogenous variation in cetaceans in the Southern California Bight. PMID:31110768
Transcriptomic profiles of 33 opium poppy samples in different tissues, growth phases, and cultivars. PMID:31110243
Involvement of Salicylic Acid in Anthracnose Infection in Tea Plants Revealed by Transcriptome Profiling. PMID:31108845
Testosterone Influence on Gene Expression in Lacrimal Glands of Mouse Models of Sjögren Syndrome. PMID:31108549
Pergola-web: a web server for the visualization and analysis of longitudinal behavioral data using repurposed genomics tools and standards. PMID:31106365
NetGO: improving large-scale protein function prediction with massive network information. PMID:31106361
Impact of ROS-Induced Damage of TCA Cycle Enzymes on Metabolism and Virulence of Salmonella enterica serovar Typhimurium. PMID:31105651
Use of Genome-Scale Integrated Analysis to Identify Key Genes and Potential Molecular Mechanisms in Recurrence of Lower-Grade Brain Glioma. PMID:31104065
A comparative analysis of egg provisioning using mass spectrometry during rapid life history evolution in sea urchins. PMID:31102332
A deficiency in SUMOylation activity disrupts multiple pathways leading to neural tube and heart defects in Xenopus embryos. PMID:31101013
Transcriptome analysis of activated sludge microbiomes reveals an unexpected role of minority nitrifiers in carbon metabolism. PMID:31098412
Draft genome of the big-headed turtle Platysternon megacephalum. PMID:31097710
Identification of a regeneration-organizing cell in the Xenopus tail. PMID:31097661
CiliaCarta: An integrated and validated compendium of ciliary genes. PMID:31095607
Hayai-Annotation Plants: an ultra-fast and comprehensive functional gene annotation system in plants. PMID:31093654
Reconstructed Skin Models Revealed Unexpected Differences in Epidermal African and Caucasian Skin. PMID:31092846
The Paf1 Complex Broadly Impacts the Transcriptome of Saccharomyces cerevisiae. PMID:31092540
Unbiased Boolean analysis of public gene expression data for cell cycle gene identification. PMID:31091168
Identification of novel biomarkers and small molecule drugs in human colorectal cancer by microarray and bioinformatics analysis. PMID:31087508
Protein-Protein Interaction Analysis of Common Top Genes in Obsessive-Compulsive Disorder (OCD) and Schizophrenia: Towards New Drug Approach Obsessive-Compulsive disorder (OCD) and Schizophrenia Comorbidity Gene Analysis. PMID:31086558
Interscapular and Perivascular Brown Adipose Tissue Respond Differently to a Short-Term High-Fat Diet. PMID:31086124
Transcriptional changes associated with advancing stages of heart failure underlie atrial and ventricular arrhythmogenesis. PMID:31083689
TRPV2 Calcium Channel Gene Expression and Outcomes in Gastric Cancer Patients: A Clinically Relevant Association. PMID:31083561
RNA-seq Transcriptome Analysis in Ovarian Tissue of Pelibuey Breed to Explore the Regulation of Prolificacy. PMID:31083386
Exact hypothesis testing for shrinkage-based Gaussian graphical models. PMID:31077287
Germline Structural Variations Are Preferential Sites of DNA Replication Timing Plasticity during Development. PMID:31076752
R-DeeP: Proteome-wide and Quantitative Identification of RNA-Dependent Proteins by Density Gradient Ultracentrifugation. PMID:31076284
ODAE: Ontology-based systematic representation and analysis of drug adverse events and its usage in study of adverse events given different patient age and disease conditions. PMID:31074377
Incorporating Pathway Information into Feature Selection towards Better Performed Gene Signatures. PMID:31073522
What lies beneath? Molecular evolution during the radiation of caecilian amphibians. PMID:31072350
Comparative transcriptome analysis of trout skin pigment cells. PMID:31072301
modEnrichr: a suite of gene set enrichment analysis tools for model organisms. PMID:31069376
Detection and analysis of RNA methylation. PMID:31069058
Immunophenotypic, cytotoxic, proteomic and genomic characterization of human cord blood vs. peripheral blood CD56Dim NK cells. PMID:31068047
Genome-Wide Signatures of Selection Detection in Three South China Indigenous Pigs. PMID:31067806
g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update). PMID:31066453
Genome-wide association studies for 30 haematological and blood clinical-biochemical traits in Large White pigs reveal genomic regions affecting intermediate phenotypes. PMID:31065004
PhyloToL: A Taxon/Gene-Rich Phylogenomic Pipeline to Explore Genome Evolution of Diverse Eukaryotes. PMID:31062861
Novel transcriptional responses to heat revealed by turning up the heat at night. PMID:31062216
Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry. PMID:31061532
A novel mRNA-miRNA-lncRNA competing endogenous RNA triple sub-network associated with prognosis of pancreatic cancer. PMID:31061236
Disrupted folate metabolism with anesthesia leads to myelination deficits mediated by epigenetic regulation of ERMN. PMID:31060905
Small Molecule Inhibitors of KDM5 Histone Demethylases Increase the Radiosensitivity of Breast Cancer Cells Overexpressing JARID1B. PMID:31060229
Assessing the Functional Relevance of Variants in the IKAROS Family Zinc Finger Protein 1 (IKZF1) in a Cohort of Patients With Primary Immunodeficiency. PMID:31057532
Quantitative proteomic study of arsenic treated mouse liver sinusoidal endothelial cells using a reverse super-SILAC method. PMID:31056257
Benchmarker: An Unbiased, Association-Data-Driven Strategy to Evaluate Gene Prioritization Algorithms. PMID:31056107
Superantigen SpeA attenuates the biofilm forming capacity of Streptococcus pyogenes. PMID:31054134
Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks. PMID:31053864
PiPred - a deep-learning method for prediction of π-helices in protein sequences. PMID:31053765
Differential methylation of enhancer at IGF2 is associated with abnormal dopamine synthesis in major psychosis. PMID:31053723
Filamentation Regulatory Pathways Control Adhesion-Dependent Surface Responses in Yeast. PMID:31053593
Muscle Gene Sets: a versatile methodological aid to functional genomics in the neuromuscular field. PMID:31053169
Genes with High Network Connectivity Are Enriched for Disease Heritability. PMID:31051114
The genomes of pecan and Chinese hickory provide insights into Carya evolution and nut nutrition. PMID:31049561
Analyses of circRNA profiling during the development from pre-receptive to receptive phases in the goat endometrium. PMID:31049198
Ten quick tips for biocuration. PMID:31048830
A Multigene Assay Determines Risk of Recurrence in Patients with Triple-Negative Breast Cancer. PMID:31048497
Alternative classification of identical concepts in different terminologies: Different ways to view the world. PMID:31048072
Comparative analysis of microRNA expression profiles of adult Schistosoma japonicum isolated from water buffalo and yellow cattle. PMID:31046821
m6Acomet: large-scale functional prediction of individual m6A RNA methylation sites from an RNA co-methylation network. PMID:31046660
Comprehensive transcriptome analysis based on RNA sequencing identifies critical genes for lipopolysaccharide-induced epididymitis in a rat model. PMID:31044753
Promiscuous Targeting of Cellular Proteins by Vpr Drives Systems-Level Proteomic Remodeling in HIV-1 Infection. PMID:31042482
Distinct Requirements of CHD4 during B Cell Development and Antibody Response. PMID:31042474
Dual inhibition of glutaminase and carnitine palmitoyltransferase decreases growth and migration of glutaminase inhibition-resistant triple-negative breast cancer cells. PMID:31040181
Protein Interaction Mapping related to Becker Muscular Dystrophy. PMID:31037085
Cyclin C Regulated Oxidative Stress Responsive Transcriptome in Mus musculus Embryonic Fibroblasts. PMID:31036676
High-density genetic map construction and QTL mapping of first flower node in pepper (Capsicum annuum L.). PMID:31035914
Conserved Secondary Structures in Viral mRNAs. PMID:31035717
Identification and characterization of a novel stay-green QTL that increases yield in maize. PMID:31033139
The Transcriptomic Toolbox: Resources for Interpreting Large Gene Expression Data within a Precision Medicine Context for Metabolic Disease Atherosclerosis. PMID:31032818
In Silico Integration Approach Reveals Key MicroRNAs and Their Target Genes in Follicular Thyroid Carcinoma. PMID:31032340
The Promoter Regions of Intellectual Disability-Associated Genes Are Uniquely Enriched in LTR Sequences of the MER41 Primate-Specific Endogenous Retrovirus: An Evolutionary Connection Between Immunity and Cognition. PMID:31031802
Parallel repulsive logic regression with biological adjacency. PMID:31030217
Loss of Msh2 and a single-radiation hit induce common, genome-wide, and persistent epigenetic changes in the intestine. PMID:31029155
An annual cycle of gene regulation in the red-legged salamander mental gland: from hypertrophy to expression of rapidly evolving pheromones. PMID:31029098
Multi-species transcriptome analyses for the regulation of crocins biosynthesis in Crocus. PMID:31029081
PseudoFuN: Deriving functional potentials of pseudogenes from integrative relationships with genes and microRNAs across 32 cancers. PMID:31029062
Deciphering the three-domain architecture in schlafens and the structures and roles of human schlafen12 and serpinB12 in transcriptional regulation. PMID:31026779
Extended Multitarget Pharmacology of Anticancer Drugs. PMID:31025863
Screening common signaling pathways associated with drug resistance in non-small cell lung cancer via gene expression profile analysis. PMID:31025554
Plasma Protein and MicroRNA Biomarkers of Insulin Resistance: A Network-Based Integrative -Omics Analysis. PMID:31024340
Chemical suppression of specific C-C chemokine signaling pathways enhances cardiac reprogramming. PMID:31023824
An Open Science Approach to Artificial Intelligence in Healthcare. PMID:31022753
DNAmod: the DNA modification database. PMID:31016417
Feature Selection for Longitudinal Data by Using Sign Averages to Summarize Gene Expression Values over Time. PMID:31016185
A small molecule promotes cartilage extracellular matrix generation and inhibits osteoarthritis development. PMID:31015473
In silico learning of tumor evolution through mutational time series. PMID:31015295
Detailed prediction of protein sub-nuclear localization. PMID:31014229
Anticandidal Potential of Stem Bark Extract from Schima superba and the Identification of Its Major Anticandidal Compound. PMID:31013655
Sex-specific Tau methylation patterns and synaptic transcriptional alterations are associated with neural vulnerability during chronic neuroinflammation. PMID:31010726
Identification of significant genes with poor prognosis in ovarian cancer via bioinformatical analysis. PMID:31010415
Placental DNA methylation levels at CYP2E1 and IRS2 are associated with child outcome in a prospective autism study. PMID:31009952
Integration of Multiple Data Sources for Gene Network Inference Using Genetic Perturbation Data. PMID:31009236
Interactions between Germline and Somatic Mutated Genes in Aggressive Prostate Cancer. PMID:31007957
AXL knockdown gene signature reveals a drug repurposing opportunity for a class of antipsychotics to reduce growth and metastasis of triple-negative breast cancer. PMID:31007848
TAF5L and TAF6L Maintain Self-Renewal of Embryonic Stem Cells via the MYC Regulatory Network. PMID:31005419
FuncTree2: an interactive radial tree for functional hierarchies and omics data visualization. PMID:31004476
In silico markers: an evolutionary and statistical approach to select informative genes of human breast cancer subtypes. PMID:31004329
CACNA2D3 Enhances the Chemosensitivity of Esophageal Squamous Cell Carcinoma to Cisplatin via Inducing Ca2+-Mediated Apoptosis and Suppressing PI3K/Akt Pathways. PMID:31001468
Identifying Disease-Gene Associations With Graph-Regularized Manifold Learning. PMID:31001321
De novo Mutations From Whole Exome Sequencing in Neurodevelopmental and Psychiatric Disorders: From Discovery to Application. PMID:31001316
Alkylaminophenol Induces G1/S Phase Cell Cycle Arrest in Glioblastoma Cells Through p53 and Cyclin-Dependent Kinase Signaling Pathway. PMID:31001122
BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing. PMID:30999927
A robust data-driven genomic signature for idiopathic pulmonary fibrosis with applications for translational model selection. PMID:30998768
The acute transcriptional response to resistance exercise: impact of age and contraction mode. PMID:30996129
Evolutionary conservation of MLO gene promoter signatures. PMID:30995906
Predicting synthetic lethal interactions using conserved patterns in protein interaction networks. PMID:30995217
Studying alcohol use disorder using Drosophila melanogaster in the era of 'Big Data'. PMID:30992041
Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes. PMID:30991941
A photocleavable surfactant for top-down proteomics. PMID:30988469
Highly efficient hypothesis testing methods for regression-type tests with correlated observations and heterogeneous variance structure. PMID:30987598
Aligning the Aligners: Comparison of RNA Sequencing Data Alignment and Gene Expression Quantification Tools for Clinical Breast Cancer Research. PMID:30987214
MicroRNA-related transcription factor regulatory networks in human colorectal cancer. PMID:30985693
Simultaneous Interrogation of Cancer Omics to Identify Subtypes With Significant Clinical Differences. PMID:30984238
Salt-Enhanced Reproductive Development of Suaeda salsa L. Coincided With Ion Transporter Gene Upregulation in Flowers and Increased Pollen K+ Content. PMID:30984214
Transcriptional Reprogramming of Arabidopsis thaliana Defence Pathways by the Entomopathogen Beauveria bassiana Correlates With Resistance Against a Fungal Pathogen but Not Against Insects. PMID:30984142
Yeast Ataxin-2 Forms an Intracellular Condensate Required for the Inhibition of TORC1 Signaling during Respiratory Growth. PMID:30982600
Fine-tuned adaptation of embryo-endometrium pairs at implantation revealed by transcriptome analyses in Bos taurus. PMID:30978203
Genomic characterization of Kerstersia gyiorum SWMUKG01, an isolate from a patient with respiratory infection in China. PMID:30978196
Mapping the transcriptional diversity of genetically and anatomically defined cell populations in the mouse brain. PMID:30977723
Transcriptomic analysis of the interaction of choriocarcinoma spheroids with receptive vs. non-receptive endometrial epithelium cell lines: an in vitro model for human implantation. PMID:30972518
Genome-wide analysis of differentially expressed lncRNA in sporadic parathyroid tumors. PMID:30972448
The behavioral origins of novelty: did increased aggression lead to scale-eating in pupfishes? PMID:30971862
Differential expression analysis of Trichoderma virens RNA reveals a dynamic transcriptome during colonization of Zea mays roots. PMID:30971198
Mining Featured Biomarkers Linked with Epithelial Ovarian CancerBased on Bioinformatics. PMID:30970615
Network and Pathway-Based Analysis of Single-Nucleotide Polymorphism of miRNA in Temporal Lobe Epilepsy. PMID:30968344
Apple whole genome sequences: recent advances and new prospects. PMID:30962944
Prunus genetics and applications after de novo genome sequencing: achievements and prospects. PMID:30962943
Draft genome of the river water buffalo. PMID:30962899
Association Analysis of Deep Genomic Features Extracted by Denoising Autoencoders in Breast Cancer. PMID:30959966
Androgen deprivation therapy promotes an obesity-like microenvironment in periprostatic fat. PMID:30959474
Identification of pharmacodynamic biomarker hypotheses through literature analysis with IBM Watson. PMID:30958864
Gene Expression Pattern and Regulatory Network of α-Toxin Treatment in Bombyx mori. PMID:30956974
Latent Model-Based Clustering for Biological Discovery. PMID:30954780
Clinical and Genome-wide Analysis of Cisplatin-induced Tinnitus Implicates Novel Ototoxic Mechanisms. PMID:30952644
exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids. PMID:30951672
Genome sequencing for rightward hemispheric language dominance. PMID:30950222
Transcriptional profiling of Auricularia cornea in selenium accumulation. PMID:30948778
Identification of Key Genes and Circular RNAs in Human Gastric Cancer. PMID:30948703
Elucidating the transcriptional program of feline injection-site sarcoma using a cross-species mRNA-sequencing approach. PMID:30947707
Identification of candidate cancer predisposing variants by performing whole-exome sequencing on index patients from BRCA1 and BRCA2-negative breast cancer families. PMID:30947698
Comparative transcriptome analyses revealed different heat stress responses in high- and low-GS Brassica alboglabra sprouts. PMID:30947685
Differential changes in bone strength of two inbred mouse strains following administration of a sclerostin-neutralizing antibody during growth. PMID:30947279
Independent Microevolution Mediated by Mobile Genetic Elements of Individual Clostridium difficile Isolates from Clade 4 Revealed by Whole-Genome Sequencing. PMID:30944881
Transcriptome sequencing of Himalayan Raspberry (Rubus ellipticus) and development of simple sequence repeat markers. PMID:30944808
Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. PMID:30944313
Mutational spectrum and associations with clinical features in patients with acute myeloid leukaemia based on next‑generation sequencing. PMID:30942411
Systematic Review of the Prognostic Role of the Immune System After Surgery of Colorectal Liver Metastases. PMID:30941301
Meta-path Based Prioritization of Functional Drug Actions with Multi-Level Biological Networks. PMID:30940832
Prioritizing candidate genes for fertility in dairy cows using gene-based analysis, functional annotation and differential gene expression. PMID:30935378
Uterine fluid proteome changes during diapause and resumption of embryo development in roe deer (Capreolus capreolus). PMID:30933930
Discovery of Covalent CDK14 Inhibitors with Pan-TAIRE Family Specificity. PMID:30930164
The identification of differentially expressed genes between extremes of placental efficiency in maternal line gilts on day 95 of gestation. PMID:30925895
Genetic control of cellular morphogenesis in Müller glia. PMID:30924555
Genome-Wide Identification, Characterization, and Expression Analysis of the Grapevine Superoxide Dismutase (SOD) Family. PMID:30923713
A Pathway-Based Strategy to Identify Biomarkers for Lung Cancer Diagnosis and Prognosis. PMID:30923439
α1ACT Is Essential for Survival and Early Cerebellar Programming in a Critical Neonatal Window. PMID:30922876
Genomic signature of parity in the breast of premenopausal women. PMID:30922380
Too Many False Targets for MicroRNAs: Challenges and Pitfalls in Prediction of miRNA Targets and Their Gene Ontology in Model and Non-model Organisms. PMID:30919506
A siphonous macroalgal genome suggests convergent functions of homeobox genes in algae and land plants. PMID:30918953
Maternal diet deficient in riboflavin induces embryonic death associated with alterations in the hepatic proteome of duck embryos. PMID:30918526
Adapting Community Detection Algorithms for Disease Module Identification in Heterogeneous Biological Networks. PMID:30918511
Developing a vocabulary and ontology for modeling insect natural history data: example data, use cases, and competency questions. PMID:30918448
GO functional similarity clustering depends on similarity measure, clustering method, and annotation completeness. PMID:30917779
Integrative transcriptomic analysis suggests new autoregulatory splicing events coupled with nonsense-mediated mRNA decay. PMID:30916337
Integrative Bioinformatics Analysis Reveals Potential Gene Biomarkers and Analysis of Function in Human Degenerative Disc Annulus Fibrosus Cells. PMID:30915367
Selection of a Real-Time PCR Housekeeping Gene Panel in Human Endothelial Colony Forming Cells for Cellular Senescence Studies. PMID:30915334
Encircling the regions of the pharmacogenomic landscape that determine drug response. PMID:30914058
Dynamic host immune response in virus-associated cancers. PMID:30911684
Plastid genome and composition analysis of two medical ferns: Dryopteris crassirhizoma Nakai and Osmunda japonica Thunb. PMID:30911328
Gene expression imputation across multiple brain regions provides insights into schizophrenia risk. PMID:30911161
Text mining tools for extracting information about microbial biodiversity in food. PMID:30910089
Combining microfluidics and RNA-sequencing to assess the inducible defensome of a mushroom against nematodes. PMID:30909884
Integrating Germline and Somatic Mutation Information for the Discovery of Biomarkers in Triple-Negative Breast Cancer. PMID:30909550
Prediction of key gene function in spinal muscular atrophy using guilt by association method based on network and gene ontology. PMID:30906446
High levels of PIWI-interacting RNAs are present in the small RNA landscape of prostate epithelium from vitamin D clinical trial specimens. PMID:30905091
High-Resolution Mapping of the Escherichia coli Chromosome Reveals Positions of High and Low Transcription. PMID:30904377
Transcriptomic analysis of contrasting inbred lines and F2 segregant of Chinese cabbage provides valuable information on leaf morphology. PMID:30900192
Proteomic profiling and integrated analysis with transcriptomic data bring new insights in the stress responses of Kluyveromyces marxianus after an arrest during high-temperature ethanol fermentation. PMID:30899329
Drosophila mRNA Localization During Later Development: Past, Present, and Future. PMID:30899273
Comparative Genome and Transcriptome Study of the Gene Expression Difference Between Pathogenic and Environmental Strains of Prototheca zopfii. PMID:30899253
Transcriptional effects of 177Lu-octreotate therapy using a priming treatment schedule on GOT1 tumor in nude mice. PMID:30895393
Combined Genomic, Transcriptomic, Proteomic, and Physiological Characterization of the Growth of Pecoramyces sp. F1 in Monoculture and Co-culture With a Syntrophic Methanogen. PMID:30894845
micro-RNAs dependent regulation of DNMT and HIF1α gene expression in thrombotic disorders. PMID:30894555
Identifying and exploiting gene-pathway interactions from RNA-seq data for binary phenotype. PMID:30890140
Curating gene sets: challenges and opportunities for integrative analysis. PMID:30888410
Primate piRNA Cluster Evolution Suggests Limited Relevance of Pseudogenes in piRNA-Mediated Gene Regulation. PMID:30888404
Comparative transcriptome analysis of salt-sensitive and salt-tolerant maize reveals potential mechanisms to enhance salt resistance. PMID:30887305
Human iPSC-derived MSCs (iMSCs) from aged individuals acquire a rejuvenation signature. PMID:30885246
Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects. PMID:30885123
MGSEA - a multivariate Gene set enrichment analysis. PMID:30885118
Neuronal Apolipoprotein E4 Expression Results in Proteome-Wide Alterations and Compromises Bioenergetic Capacity by Disrupting Mitochondrial Function. PMID:30883359
Genome-wide genotyping uncovers genetic diversity, phylogeny, signatures of selection, and population structure of Chinese Jiangquhai pigs in a global perspective1. PMID:30882885
KIF15 promotes bladder cancer proliferation via the MEK-ERK signaling pathway. PMID:30881113
The Balancing Act of Intrinsically Disordered Proteins: Enabling Functional Diversity while Minimizing Promiscuity. PMID:30878482
Dependence on Myb expression is attenuated in myeloid leukaemia with N-terminal CEBPA mutations. PMID:30877232
Powerful gene set analysis in GWAS with the Generalized Berk-Jones statistic. PMID:30875371
Comprehensive analysis of the GATA transcription factor gene family in breast carcinoma using gene microarrays, online databases and integrated bioinformatics. PMID:30872657
Integrating germline and somatic variation information using genomic data for the discovery of biomarkers in prostate cancer. PMID:30871495
Differentially expressed genes ASPN, COL1A1, FN1, VCAN and MUC5AC are potential prognostic biomarkers for gastric cancer. PMID:30867749
Combined analysis and validation for DNA methylation and gene expression profiles associated with prostate cancer. PMID:30867653
Genetic contributions to two special factors of neuroticism are associated with affluence, higher intelligence, better health, and longer life. PMID:30867560
Metatranscriptomic exploration of microbial functioning in clouds. PMID:30867542
Field transcriptome revealed a novel relationship between nitrate transport and flowering in Japanese beech. PMID:30867453
In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived species' adaptability to environmental cues. PMID:30866823
Expression and regulatory asymmetry of retained Arabidopsis thaliana transcription factor genes derived from whole genome duplication. PMID:30866803
Both Peripheral Blood and Urinary miR-195-5p, miR-192-3p, miR-328-5p and Their Target Genes PPM1A, RAB1A and BRSK1 May Be Potential Biomarkers for Membranous Nephropathy. PMID:30865617
The Genome of Drosophila innubila Reveals Lineage-Specific Patterns of Selection in Immune Genes. PMID:30865231
Identification of hub genes in chronically hypoxic myocardium using bioinformatics analysis. PMID:30864710
Precision drug repurposing via convergent eQTL-based molecules and pathway targeting independent disease-associated polymorphisms. PMID:30864332
SNPs2ChIP: Latent Factors of ChIP-seq to infer functions of non-coding SNPs. PMID:30864321
The Protein-Protein Interaction Network of Litopenaeus vannamei Haemocytes. PMID:30863321
Xenbase: Facilitating the Use of Xenopus to Model Human Disease. PMID:30863320
Transcriptome analysis of the curry tree (Bergera koenigii L., Rutaceae) during leaf development. PMID:30862864
GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes. PMID:30862647
Characterization of the Rosa roxburghii Tratt transcriptome and analysis of MYB genes. PMID:30860996
Single cell RNA-seq identifies the origins of heterogeneity in efficient cell transdifferentiation and reprogramming. PMID:30860479
MorCVD: A Unified Database for Host-Pathogen Protein-Protein Interactions of Cardiovascular Diseases Related to Microbes. PMID:30858555
Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies. PMID:30858527
Mechanism-based disease similarity. PMID:30854526
Genome-wide analysis of yeast expression data based on a priori generated co-regulation cliques. PMID:30854393
A Systems Pharmacology Approach for Identifying the Multiple Mechanisms of Action of the Wei Pi Xiao Decoction for the Treatment of Gastric Precancerous Lesions. PMID:30854000
The Ethylene Signaling Pathway Negatively Impacts CBF/DREB-Regulated Cold Response in Soybean (Glycine max). PMID:30853961
Comprehensive Analysis of Driver Genes in Personal Genomes of Clear Cell Renal Cell Carcinoma. PMID:30852945
Collective influencers in protein interaction networks. PMID:30850642
Integrated analyses of lncRNAs microarray profiles and mRNA-lncRNA coexpression in smooth muscle cells under hypoxic and normoxic conditions. PMID:30850398
Functional protein representations from biological networks enable diverse cross-species inference. PMID:30847485
Automated exploration of gene ontology term and pathway networks with ClueGO-REST. PMID:30847467
Connective Tissue Growth Factor Inhibition Enhances Cardiac Repair and Limits Fibrosis After Myocardial Infarction. PMID:30847422
A microRNA profile of pediatric glioblastoma: The role of NUCKS1 upregulation. PMID:30847170
Investigating the role of Osiris genes in Drosophila sechellia larval resistance to a host plant toxin. PMID:30847082
TACCO, a Database Connecting Transcriptome Alterations, Pathway Alterations and Clinical Outcomes in Cancers. PMID:30846808
Gene expression profiling meta-analysis reveals novel gene signatures and pathways shared between tuberculosis and rheumatoid arthritis. PMID:30845171
Epigenetic loss of the endoplasmic reticulum-associated degradation inhibitor SVIP induces cancer cell metabolic reprogramming. PMID:30843871
Ontological representation-oriented term normalization and standardization of the Research Domain Criteria. PMID:30843449
LncRNAs GIHCG and SPINT1-AS1 Are Crucial Factors for Pan-Cancer Cells Sensitivity to Lapatinib. PMID:30842786
Hepatocytes direct the formation of a pro-metastatic niche in the liver. PMID:30842658
PAI-1 augments mucosal damage in colitis. PMID:30842312
Growth Factor Screening in Dystrophic Muscles Reveals PDGFB/PDGFRB-Mediated Migration of Interstitial Stem Cells. PMID:30841538
Integrative Analysis Reveals Key Circular RNA in Atrial Fibrillation. PMID:30838031
Succinyl-proteome profiling of Pyricularia oryzae, a devastating phytopathogenic fungus that causes rice blast disease. PMID:30837482
Gonadal microRNA Expression Profiles and Their Potential Role in Sex Differentiation and Gonadal Maturation of Mud Crab Scylla paramamosain. PMID:30835008
Genome-wide analysis reveals the genomic features of the turkey vulture (Cathartes aura) as a scavenger. PMID:30834967
Integrated Analysis of Whole Exome Sequencing and Copy Number Evaluation in Parkinson's Disease. PMID:30833663
A transcriptome-wide analysis deciphers distinct roles of G1 cyclins in temporal organization of the yeast cell cycle. PMID:30833602
Genome Sequencing Illustrates the Genetic Basis of the Pharmacological Properties of Gloeostereum incarnatum. PMID:30832255
Proteomic Identification of Protein Glutathionylation in Cardiomyocytes. PMID:30831029
Transcriptomics Identifies Modules of Differentially Expressed Genes and Novel Cyclotides in Viola pubescens. PMID:30828342
Expression Divergence as an Evolutionary Alternative Mechanism Adopted by Two Rice Subspecies Against Rice Blast Infection. PMID:30825020
Identification of Potential Genes Responsible for Thermotolerance in Wheat under High Temperature Stress. PMID:30823586
Functional geometry of protein interactomes. PMID:30821317
High-throughput sequencing of small RNAs and analysis of differentially expressed microRNAs associated with high-fat diet-induced hepatic insulin resistance in mice. PMID:30820263
Complete Genome Sequence of Arthrobacter sp. Strain MN05-02, a UV-Resistant Bacterium from a Manganese Deposit in the Sonoran Desert. PMID:30820258
Genetic meta-analysis of diagnosed Alzheimer's disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing. PMID:30820047
A modular analysis of microglia gene expression, insights into the aged phenotype. PMID:30819113
Integrated Analysis of miRNA and mRNA Expression Profiles in Spleen of Specific Pathogen-Free Chicken Infected with Avian Reticuloendotheliosis Virus Strain SNV. PMID:30818863
Identifying Genome-Wide Sequence Variations and Candidate Genes Implicated in Self-Incompatibility by Resequencing Fragaria viridis. PMID:30818833
Genome‑wide DNA methylation profile of thymomas and potential epigenetic regulation of thymoma subtypes. PMID:30816514
Identification of survival‑associated key genes and long non‑coding RNAs in glioblastoma multiforme by weighted gene co‑expression network analysis. PMID:30816427
Overlapping Complex Concepts Have More Commission Errors, Especially in Intensive Terminology Auditing. PMID:30815158
How Sustainable are Biomedical Ontologies? PMID:30815087
FAIRness and Usability for Open-access Omics Data Systems. PMID:30815061
The analysis of a time-course transcriptome profile by systems biology approaches reveals key molecular processes in acute kidney injury. PMID:30815016
Analysis of Predicted Host-Parasite Interactomes Reveals Commonalities and Specificities Related to Parasitic Lifestyle and Tissues Tropism. PMID:30815000
Integrative analysis of Paneth cell proteomic and transcriptomic data from intestinal organoids reveals functional processes dependent on autophagy. PMID:30814064
Handling Big Data Scalability in Biological Domain Using Parallel and Distributed Processing: A Case of Three Biological Semantic Similarity Measures. PMID:30809545
Shared Gene Expression Between Multiple Sclerosis and Ischemic Stroke. PMID:30809253
Characterization of Endothelial and Smooth Muscle Cells From Different Canine Vessels. PMID:30809157
Metabolic gene NR4A1 as a potential therapeutic target for non-smoking female non-small cell lung cancer patients. PMID:30806032
Identification of Candidate Genes for the Plateau Adaptation of a Tibetan Amphipod, Gammarus lacustris, Through Integration of Genome and Transcriptome Sequencing. PMID:30804987
Identification of common genetic risk variants for autism spectrum disorder. PMID:30804558
Circadian regulation in human white adipose tissue revealed by transcriptome and metabolic network analysis. PMID:30804433
Genetic variants differentially associated with rheumatoid arthritis and systemic lupus erythematosus reveal the disease-specific biology. PMID:30804378
Death of female flower microsporocytes progresses independently of meiosis-like process and can be accelerated by specific transcripts in Asparagus officinalis. PMID:30804374
Decreased mRNA and protein stability of W1282X limits response to modulator therapy. PMID:30803905
Comparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing. PMID:30802266
Optimal Penalized Function-on-Function Regression under a Reproducing Kernel Hilbert Space Framework. PMID:30799886
A Model Information Management Plan for Molecular Pathology Sequence Data Using Standards: From Sequencer to Electronic Health Record. PMID:30797065
Predicted secreted protein analysis reveals synaptogenic function of Clstn3 during WAT browning and BAT activation in mice. PMID:30796355
Repository of Enriched Structures of Proteins Involved in the Red Blood Cell Environment (RESPIRE). PMID:30794542
The promising novel biomarkers and candidate small molecule drugs in kidney renal clear cell carcinoma: Evidence from bioinformatics analysis of high-throughput data. PMID:30793530
Stress-induced mRNP granules: Form and function of processing bodies and stress granules. PMID:30793528
CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination. PMID:30793173
Identification of Potential Key Genes and Pathways in Early-Onset Colorectal Cancer Through Bioinformatics Analysis. PMID:30786729
Integrative Gene Selection on Gene Expression Data: Providing Biological Context to Traditional Approaches. PMID:30785707
Comparative genomics sheds light on the predatory lifestyle of accipitrids and owls. PMID:30783131
A MST1-FOXO1 cascade establishes endothelial tip cell polarity and facilitates sprouting angiogenesis. PMID:30783090
Genomic evidence for shared common ancestry of East African hunting-gathering populations and insights into local adaptation. PMID:30782801
Human IFIT proteins inhibit lytic replication of KSHV: A new feed-forward loop in the innate immune system. PMID:30779786
Towards a data-integrated cell. PMID:30778056
Quantification and discovery of sequence determinants of protein-per-mRNA amount in 29 human tissues. PMID:30777893
Targeting JUN, CEBPB, and HDAC3: A Novel Strategy to Overcome Drug Resistance in Hypoxic Glioblastoma. PMID:30775317
Barrett's esophagus network analysis revealed that arginine, alanine, aspartate, glutamate, valine, leucine and isoleucine can be biomarkers. PMID:30774814
H3.3 K27M depletion increases differentiation and extends latency of diffuse intrinsic pontine glioma growth in vivo. PMID:30770999
Identification of novel candidate indicators for assessing zinc status during pregnancy in mice from microarray data. PMID:30770772
Phosphoregulated FMRP phase separation models activity-dependent translation through bidirectional control of mRNA granule formation. PMID:30765518
Gene expression atlas of embryo development in Arabidopsis. PMID:30762127
Transcriptome dataset of trunk neural crest cells migrating along the ventral pathway of chick embryos. PMID:30761336
Predicting Gene Ontology Function of Human MicroRNAs by Integrating Multiple Networks. PMID:30761178
RNA Sequencing Characterizes Transcriptomes Differences in Cold Response Between Northern and Southern Alternanthera philoxeroides and Highlight Adaptations Associated With Northward Expansion. PMID:30761169
Repurposing of Drugs as Novel Influenza Inhibitors From Clinical Gene Expression Infection Signatures. PMID:30761132
Unveiling the Link Between Inflammation and Adaptive Immunity in Breast Cancer. PMID:30761130
Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks. PMID:30760546
Secretome profiling of heterotypic spheroids suggests a role of fibroblasts in HIF-1 pathway modulation and colorectal cancer photodynamic resistance. PMID:30756254
The identification of gene signature and critical pathway associated with childhood-onset type 2 diabetes. PMID:30755828
A genome-wide scan shows evidence for local adaptation in a widespread keystone Neotropical forest tree. PMID:30755734
Development of Orthogonal Linear Separation Analysis (OLSA) to Decompose Drug Effects into Basic Components. PMID:30755704
Transcriptional analysis of Foxp3+ Tregs and functions of two identified molecules during resolution of ALI. PMID:30753170
Identification of critical genes associated with spinal cord injury based on the gene expression profile of spinal cord tissues from trkB.T1 knockout mice. PMID:30747207
A new genomic blueprint of the human gut microbiota. PMID:30745586
mTORC2-mediated PDHE1α nuclear translocation links EBV-LMP1 reprogrammed glucose metabolism to cancer metastasis in nasopharyngeal carcinoma. PMID:30745576
Hypersensitive IFN Responses in Lupus Keratinocytes Reveal Key Mechanistic Determinants in Cutaneous Lupus. PMID:30745462
Identification of potential blood biomarkers for Parkinson's disease by gene expression and DNA methylation data integration analysis. PMID:30744671
Comparative transcriptome analysis reveals K+ transporter gene contributing to salt tolerance in eggplant. PMID:30744551
Genome Sequencing of Cladobotryum protrusum Provides Insights into the Evolution and Pathogenic Mechanisms of the Cobweb Disease Pathogen on Cultivated Mushroom. PMID:30744046
Retinal transcriptome and eQTL analyses identify genes associated with age-related macular degeneration. PMID:30742112
Molecular signature of human bone marrow-derived mesenchymal stromal cell subsets. PMID:30742027
Obesity-associated inflammation triggers an autophagy-lysosomal response in adipocytes and causes degradation of perilipin 1. PMID:30741926
Generation and classification of transcriptomes in two Croomia species and molecular evolution of CYC/TB1 genes in Stemonaceae. PMID:30740572
Generation and characterization of expressed sequence tags (ESTs) from coralloid root cDNA library of Cycas debaoensis. PMID:30740571
A network biology approach to unraveling inherited axonopathies. PMID:30737464
Lymphocyte innateness defined by transcriptional states reflects a balance between proliferation and effector functions. PMID:30737409
Targeted mutation detection in breast cancer using MammaSeq™. PMID:30736836
Retroelement-Linked Transcription Factor Binding Patterns Point to Quickly Developing Molecular Pathways in Human Evolution. PMID:30736359
Genomic Characterization of the Zinc Transcriptional Regulatory Element Reveals Potential Functional Roles of ZNF658. PMID:30734197
Smp38 MAP Kinase Regulation in Schistosoma mansoni: Roles in Survival, Oviposition, and Protection Against Oxidative Stress. PMID:30733716
O-GlcNAcylation alters the selection of mRNAs for translation and promotes 4E-BP1-dependent mitochondrial dysfunction in the retina. PMID:30733333
Genome-wide associations and detection of potential candidate genes for direct genetic and maternal genetic effects influencing dairy cattle body weight at different ages. PMID:30727969
CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features. PMID:30727967
First RNA-seq approach to study fruit set and parthenocarpy in zucchini (Cucurbita pepo L.). PMID:30727959
Comparative Analysis of Normalization Methods for Network Propagation. PMID:30723490
Integrative analysis of cancer driver genes in prostate adenocarcinoma. PMID:30720096
Construction of a cDNA library and preliminary analysis of the expressed sequence tags of the earthworm Eisenia fetida (Savigny, 1826). PMID:30720084
Ulcerative colitis: functional analysis of the in-depth proteome. PMID:30718987
Label-free Quantitative Analysis of Protein Expression Alterations in miR-26a-Knockout HeLa Cells using SWATH-MS Technology. PMID:30718521
Functional homogeneity and specificity of topological modules in human proteome. PMID:30717667
Quantitative insights into the cyanobacterial cell economy. PMID:30714903
Conserved Disease Modules Extracted From Multilayer Heterogeneous Disease and Gene Networks for Understanding Disease Mechanisms and Predicting Disease Treatments. PMID:30713550
Sex-Dependent Sensory Phenotypes and Related Transcriptomic Expression Profiles Are Differentially Affected by Angelman Syndrome. PMID:30706369
Interaction of roses with a biotrophic and a hemibiotrophic leaf pathogen leads to differences in defense transcriptome activation. PMID:30706286
Complete Genome Sequence of Streptomyces olivoreticuli ATCC 31159 Which can Produce Anticancer Bestatin and Show Diverse Secondary Metabolic Potentials. PMID:30706083
WNT signaling modulates PD-L1 expression in the stem cell compartment of triple-negative breast cancer. PMID:30705400
Transcriptome Analysis of Mesenchymal Stem Cells from Multiple Myeloma Patients Reveals Downregulation of Genes Involved in Cell Cycle Progression, Immune Response, and Bone Metabolism. PMID:30705326
De Novo Transcriptome Assembly of Agave H11648 by Illumina Sequencing and Identification of Cellulose Synthase Genes in Agave Species. PMID:30704153
Network Analysis Reveals TNF as a Major Hub of Reactive Inflammation Following Spinal Cord Injury. PMID:30700814
Candidate Gene Selection for Cytoplasmic Male Sterility in Pepper (Capsicum annuum L.) through Whole Mitochondrial Genome Sequencing. PMID:30699994
Transcriptional Analysis of Immunohistochemically Defined Subgroups of Non-Muscle-Invasive Papillary High-Grade Upper Tract Urothelial Carcinoma. PMID:30699951
Abrogation of Stem Loop Binding Protein (Slbp) function leads to a failure of cells to transition from proliferation to differentiation, retinal coloboma and midline axon guidance deficits. PMID:30695021
White Matter is the Predilection Site of Late-Delayed Radiation-Induced Brain Injury in Non-Human Primates. PMID:30694733
Fibroblast activation and abnormal extracellular matrix remodelling as common hallmarks in three cancer-prone genodermatoses. PMID:30693469
High Throughput mRNA Sequencing Reveals Potential Therapeutic Targets of Tao-Hong-Si-Wu Decoction in Experimental Middle Cerebral Artery Occlusion. PMID:30692926
Circular RNA Expression Alteration and Bioinformatics Analysis in Rats After Traumatic Spinal Cord Injury. PMID:30692912
Draft Genome Analysis Offers Insights Into the Mechanism by Which Streptomyces chartreusis WZS021 Increases Drought Tolerance in Sugarcane. PMID:30687260
Choice of Alternative Polyadenylation Sites, Mediated by the RNA-Binding Protein Elavl3, Plays a Role in Differentiation of Inhibitory Neuronal Progenitors. PMID:30687010
The Short Chain Fatty Acid Butyrate Imprints an Antimicrobial Program in Macrophages. PMID:30683619
Exosomes Cause Preterm Birth in Mice: Evidence for Paracrine Signaling in Pregnancy. PMID:30679631
Transcriptome analysis identifies strong candidate genes for ginsenoside biosynthesis and reveals its underlying molecular mechanism in Panax ginseng C.A. Meyer. PMID:30679448
Widespread inter-individual gene expression variability in Arabidopsis thaliana. PMID:30679203
s ·nr: a visual analytics framework for contextual analyses of private and public RNA-seq data. PMID:30678634
Identification of Key Candidate Genes and Pathways for Relationship between Ovarian Cancer and Diabetes Mellitus Using Bioinformatical Analysis. PMID:30678426
Integrative analysis of gene expression profiles reveals distinct molecular characteristics in oral tongue squamous cell carcinoma. PMID:30675303
Robust predictions of specialized metabolism genes through machine learning. PMID:30674669
Impact of Homologous Recombination on the Evolution of Prokaryotic Core Genomes. PMID:30670614
Transcriptional Basis of Copper-Induced Olfactory Impairment in the Sea Lamprey, a Primitive Invasive Fish. PMID:30670609
Thiol isomerase ERp57 targets and modulates the lectin pathway of complement activation. PMID:30670593
OGER++: hybrid multi-type entity recognition. PMID:30666476
Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap. PMID:30664679
Identification of key genes and pathways involved in microsatellite instability in colorectal cancer. PMID:30664178
EFNB2 acts as the target of miR-557 to facilitate cell proliferation, migration and invasion in pancreatic ductal adenocarcinoma by bioinformatics analysis and verification. PMID:30662604
Identification of hub genes and pathways in glioblastoma by bioinformatics analysis. PMID:30655863
Identification of core genes and prediction of miRNAs associated with osteoporosis using a bioinformatics approach. PMID:30655789
Assessment of somatic single-nucleotide variation in brain tissue of cases with schizophrenia. PMID:30655504
Coexpression modules constructed by weighted gene co-expression network analysis indicate ubiquitin-mediated proteolysis as a potential biomarker of uveal melanoma. PMID:30651788
p.E95K mutation in Indian hedgehog causing brachydactyly type A1 impairs IHH/Gli1 downstream transcriptional regulation. PMID:30651074
Genomic changes associated with adaptation to arid environments in cactophilic Drosophila species. PMID:30651071
Rbf Activates the Myogenic Transcriptional Program to Promote Skeletal Muscle Differentiation. PMID:30650361
The Evolutionary Traceability of a Protein. PMID:30649284
The Genetics of Mating Song Evolution Underlying Rapid Speciation: Linking Quantitative Variation to Candidate Genes for Behavioral Isolation. PMID:30647070
Complete Genome Sequence of Pseudomonas sp. Strain phDV1, an Isolate Capable of Efficient Degradation of Aromatic Hydrocarbons. PMID:30643876
Robust analysis of novel mRNA-lncRNA cross talk based on ceRNA hypothesis uncovers carcinogenic mechanism and promotes diagnostic accuracy in esophageal cancer. PMID:30643460
Identification of hub genes and outcome in colon cancer based on bioinformatics analysis. PMID:30643458
Mature IgDlow/- B cells maintain tolerance by promoting regulatory T cell homeostasis. PMID:30643147
Investigation of the Underlying Genes and Mechanism of Macrophage-Enriched Ruptured Atherosclerotic Plaques Using Bioinformatics Method. PMID:30643084
Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle. PMID:30642389
Multi-omics integration reveals molecular networks and regulators of psoriasis. PMID:30642337
RCBTB1 Deletion Is Associated with Metastatic Outcome and Contributes to Docetaxel Resistance in Nontranslocation-Related Pleomorphic Sarcomas. PMID:30641971
A novel alternative splicing-based prediction model for uteri corpus endometrial carcinoma. PMID:30640723
Mesenchymal-Epithelial Interactome Analysis Reveals Essential Factors Required for Fibroblast-Free Alveolosphere Formation. PMID:30639966
Identification of candidate diagnostic and prognostic biomarkers for pancreatic carcinoma. PMID:30639415
GOTrapper: a tool to navigate through branches of gene ontology hierarchy. PMID:30634902
CALD1, CNN1, and TAGLN identified as potential prognostic molecular markers of bladder cancer by bioinformatics analysis. PMID:30633156
Determination of host proteins composing the microenvironment of coronavirus replicase complexes by proximity-labeling. PMID:30632963
Cytokines in adipose-derived mesenchymal stem cells promote the healing of liver disease. PMID:30631390
Computational translation of genomic responses from experimental model systems to humans. PMID:30629591
Biological Pathways Leading From ANGPTL8 to Diabetes Mellitus-A Co-expression Network Based Analysis. PMID:30627105
Transcriptome network analysis identifies protective role of the LXR/SREBP-1c axis in murine pulmonary fibrosis. PMID:30626759
Meta-analysis of gene expression profiles in long-term non-progressors infected with HIV-1. PMID:30626383
Breaking the paradigm: Dr Insight empowers signature-free, enhanced drug repurposing. PMID:30624606
eIF2B activator prevents neurological defects caused by a chronic integrated stress response. PMID:30624206
Bacillus velezensis YC7010 Enhances Plant Defenses Against Brown Planthopper Through Transcriptomic and Metabolic Changes in Rice. PMID:30622550
Maternal choline supplementation ameliorates Alzheimer's disease pathology by reducing brain homocysteine levels across multiple generations. PMID:30622336
Chemically induced vesiculation as a platform for studying TMEM16F activity. PMID:30622179
Analysis of the distribution of assimilation products and the characteristics of transcriptomes in rice by submergence during the ripening stage. PMID:30621581
Gene expression changes elicited by a parasitic B chromosome in the grasshopper Eyprepocnemis plorans are consistent with its phenotypic effects. PMID:30617552
Pathological priming causes developmental gene network heterochronicity in autistic subject-derived neurons. PMID:30617258
Akt and SGK protein kinases are required for efficient feeding by macropinocytosis. PMID:30617109
BO-LSTM: classifying relations via long short-term memory networks along biomedical ontologies. PMID:30616557
The embryonic transcriptome of Arabidopsis thaliana. PMID:30610360
Genome-wide analysis reveals extensive genetic overlap between schizophrenia, bipolar disorder, and intelligence. PMID:30610197
Quantitative Proteomic Analysis of Small and Large Extracellular Vesicles (EVs) Reveals Enrichment of Adhesion Proteins in Small EVs. PMID:30608700
Recombination of ecologically and evolutionarily significant loci maintains genetic cohesion in the Pseudomonas syringae species complex. PMID:30606234
Noncoding rare variants of TBX6 in congenital anomalies of the kidney and urinary tract. PMID:30604070
Whole-exome sequencing reveals SALL4 variants in premature ovarian insufficiency: an update on genotype-phenotype correlations. PMID:30603774
The Major RNA-Binding Protein ProQ Impacts Virulence Gene Expression in Salmonella enterica Serovar Typhimurium. PMID:30602583
Loss of Estrogen-Related Receptor Alpha Facilitates Angiogenesis in Endothelial Cells. PMID:30602497
Analysis of transcripts and splice isoforms in Medicago sativa L. by single-molecule long-read sequencing. PMID:30600412
Analysis of dynamic molecular networks for pancreatic ductal adenocarcinoma progression. PMID:30598639
Optimizing gene set annotations combining GO structure and gene expression data. PMID:30598093
Analysis of Dendrobium huoshanense transcriptome unveils putative genes associated with active ingredients synthesis. PMID:30594136
Time-resolved mapping of genetic interactions to model rewiring of signaling pathways. PMID:30592458
EDEn-Electroceutical Design Environment: Ion Channel Tissue Expression Database with Small Molecule Modulators. PMID:30590250
Arabidopsis thaliana responds to colonisation of Piriformospora indica by secretion of symbiosis-specific proteins. PMID:30589877
Ischemia-reperfusion injury in a rat microvascular skin free flap model: A histological, genetic, and blood flow study. PMID:30589864
Transcriptomic and proteomic host response to Aspergillus fumigatus conidia in an air-liquid interface model of human bronchial epithelium. PMID:30589860
Clinical significance and effect of MTDH/AEG-1 in bladder urothelial cancer: a study based on immunohistochemistry, RNA-seq, and in vitro verification. PMID:30588098
From Matrices to Knowledge: Using Semantic Networks to Annotate the Connectome. PMID:30581382
Identifying Potential Ageing-Modulating Drugs In Silico. PMID:30581056
Identifying Principles for the Construction of an Ontology-Based Knowledge Base: A Case Study Approach. PMID:30578220
Gene expression analysis of heat-shock proteins and redox regulators reveals combinatorial prognostic markers in carcinomas of the gastrointestinal tract. PMID:30578123
Accelerating annotation of articles via automated approaches: evaluation of the neXtA5 curation-support tool by neXtProt. PMID:30576492
Conservation of location of several specific inhibitory codon pairs in the Saccharomyces sensu stricto yeasts reveals translational selection. PMID:30576464
Precious cargo: Modulation of the mesenteric lymph exosome payload after hemorrhagic shock. PMID:30576304
A role for MED14 and UVH6 in heterochromatin transcription upon destabilization of silencing. PMID:30574575
Integrated analysis of microRNA and mRNA expression profiles in splenomegaly induced by non-cirrhotic portal hypertension in rats. PMID:30573742
High-resolution mapping of cancer cell networks using co-functional interactions. PMID:30573688
HLA-DO Modulates the Diversity of the MHC-II Self-peptidome. PMID:30573663
Identification of co-located QTLs and genomic regions affecting grapevine cluster architecture. PMID:30569367
Expression and potential molecular mechanisms of miR‑204‑5p in breast cancer, based on bioinformatics and a meta‑analysis of 2,306 cases. PMID:30569120
A Novel Inorganic Sulfur Compound Metabolizing Ferroplasma-Like Population Is Suggested to Mediate Extracellular Electron Transfer. PMID:30568637
Measures of co-expression for improved function prediction of long non-coding RNAs. PMID:30567492
iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data. PMID:30567491
Transcriptomic Characterization of the South American Freshwater Stingray Potamotrygon motoro Venom Apparatus. PMID:30567320
Expression reflects population structure. PMID:30566439
Early-onset inflammatory bowel disease as a model disease to identify key regulators of immune homeostasis mechanisms. PMID:30565237
Identification of biomarkers of chromophobe renal cell carcinoma by weighted gene co-expression network analysis. PMID:30564062
GLUE: a flexible software system for virus sequence data. PMID:30563445
The Prognostic Value of Cell Cycle Gene Expression Signatures in Muscle Invasive, High-Grade Bladder Cancer. PMID:30561442
Up-Regulation of hsa-miR-210 Promotes Venous Metastasis and Predicts Poor Prognosis in Hepatocellular Carcinoma. PMID:30560088
Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life. PMID:30559407
Rapid Recapitulation of Nonalcoholic Steatohepatitis upon Loss of Host Cell Factor 1 Function in Mouse Hepatocytes. PMID:30559308
Induced Resistance Mechanism of Novel Curcumin Analogs Bearing a Quinazoline Moiety to Plant Virus. PMID:30558295
Higher gene expression stability during aging in long-lived giant mole-rats than in short-lived rats. PMID:30557854
Elucidating the Role of Chromatin State and Transcription Factors on the Regulation of the Yeast Metabolic Cycle: A Multi-Omic Integrative Approach. PMID:30555512
Comparative Transcriptome and iTRAQ Proteome Analyses Reveal the Mechanisms of Diapause in Aphidius gifuensis Ashmead (Hymenoptera: Aphidiidae). PMID:30555341
Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis. PMID:30554520
Circadian Proteomic Analysis Uncovers Mechanisms of Post-Transcriptional Regulation in Metabolic Pathways. PMID:30553726
Mechanotransduction of vocal fold fibroblasts and mesenchymal stromal cells in the context of the vocal fold mechanome. PMID:30553439
Daphnia galeata responds to the exposure to an ichthyosporean gut parasite by down-regulation of immunity and lipid metabolism. PMID:30547741
Neuroinflammatory signals drive spinal curve formation in zebrafish models of idiopathic scoliosis. PMID:30547092
Deuterium induces a distinctive Escherichia coli proteome that correlates with the reduction in growth rate. PMID:30545941
RNA sequencing and anthocyanin synthesis-related genes expression analyses in white-fruited Vaccinium uliginosum. PMID:30545307
Functional genomics of the digestive tract in broilers. PMID:30545300
Transcriptome Sequencing and Biochemical Analysis of Perianths and Coronas Reveal Flower Color Formation in Narcissus pseudonarcissus. PMID:30545084
A two‑circRNA signature predicts tumour recurrence in clinical non‑functioning pituitary adenoma. PMID:30542712
Identifying the key genes and microRNAs in colorectal cancer liver metastasis by bioinformatics analysis and in vitro experiments. PMID:30542696
Connecting nutrition composition measures to biomedical research. PMID:30541615
A multi-omics approach for identifying important pathways and genes in human cancer. PMID:30541428
Developmental toxicity and apoptosis in zebrafish embryos induced by low-dose γ-ray irradiation. PMID:30539402
Integrated analysis reveals key genes with prognostic value in lung adenocarcinoma. PMID:30538558
Role of miRNAs in skeletal muscle aging. PMID:30538437
Differential responses of Lasiopodomys mandarinus and Lasiopodomys brandtii to chronic hypoxia: a cross-species brain transcriptome analysis. PMID:30537924
Identification of key genes and pathways in diabetic nephropathy by bioinformatics analysis. PMID:30536626
Identification of tissue-specific tumor biomarker using different optimization algorithms. PMID:30535858
DeepIsoFun: a deep domain adaptation approach to predict isoform functions. PMID:30535380
Comparative Analysis of Oomycete Genome Evolution Using the Oomycete Gene Order Browser (OGOB). PMID:30535146
Complete genome of Rhizobium leguminosarum Norway, an ineffective Lotus micro-symbiont. PMID:30534351
Effects of Icariin on Atherosclerosis and Predicted Function Regulatory Network in ApoE Deficient Mice. PMID:30533443
RNA Sequencing for Gene Expression Profiles in a Rat Model of Middle Cerebral Artery Occlusion. PMID:30533429
Mitoproteomics: Tackling Mitochondrial Dysfunction in Human Disease. PMID:30533169
Building an octaploid genome and transcriptome of the medicinal plant Pogostemon cablin from Lamiales. PMID:30532075
Chromatin Immunoprecipitation of Murine Brown Adipose Tissue. PMID:30531713
Comprehensive Transcriptional Profiling of the Gastrointestinal Tract of Ruminants from Birth to Adulthood Reveals Strong Developmental Stage Specific Gene Expression. PMID:30530642
Practical considerations on performing and analyzing CLIP-seq experiments to identify transcriptomic-wide RNA-protein interactions. PMID:30527764
A longitudinal feature selection method identifies relevant genes to distinguish complicated injury and uncomplicated injury over time. PMID:30526581
GOnet: a tool for interactive Gene Ontology analysis. PMID:30526489
Genome-wide differences in DNA methylation changes in caprine ovaries between oestrous and dioestrous phases. PMID:30524725
Type 1 Diabetes Mellitus-Associated Genetic Variants Contribute to Overlapping Immune Regulatory Networks. PMID:30524468
Identification and Analysis of Rice Yield-Related Candidate Genes by Walking on the Functional Network. PMID:30524460
GPCR-specific autoantibody signatures are associated with physiological and pathological immune homeostasis. PMID:30523250
Accurate and efficient estimation of small P-values with the cross-entropy method: applications in genomic data analysis. PMID:30521030
The comparative analysis of phenotypic and whole transcriptome gene expression data of ascites susceptible versus ascites resistant chickens. PMID:30519813
Derivation and Validation of the Potential Core Genes in Pancreatic Cancer for Tumor-Stroma Crosstalk. PMID:30519576
Preliminary insights into the genetics of bank vole tolerance to Puumala hantavirus in Sweden. PMID:30519443
Draft genomes of Cronobacter sakazakii strains isolated from dried spices bring unique insights into the diversity of plant-associated strains. PMID:30519380
Identification of Grade-associated MicroRNAs in Brainstem Gliomas Based on Microarray Data. PMID:30519352
Comprehensive Analysis of BAP1 Somatic Mutation in Clear Cell Renal Cell Carcinoma to Explore Potential Mechanisms in Silico. PMID:30519310
Stable-protein Pair Analysis as A Novel Strategy to Identify Proteomic Signatures: Application To Seminal Plasma From Infertile Patients. PMID:30518674
The Transcriptomic Landscape of Yaks Reveals Molecular Pathways for High Altitude Adaptation. PMID:30517636
Analysis of the transcriptome data in Litopenaeus vannamei reveals the immune basis and predicts the hub regulation-genes in response to high-pH stress. PMID:30517152
Glucose intake hampers PKA-regulated HSP90 chaperone activity. PMID:30516470
An integrative machine learning approach for prediction of toxicity-related drug safety. PMID:30515477
Comparative transcriptomics between high and low rubber producing Taraxacum kok-saghyz R. plants. PMID:30514210
De novo male gonad transcriptome draft for the marine mussel Perumytilus purpuratus with a focus on its reproductive-related proteins. PMID:30510598
G-quadruplexes formation in the 5'UTRs of mRNAs associated with colorectal cancer pathways. PMID:30507959
The Hsp70/J-protein machinery of the African trypanosome, Trypanosoma brucei. PMID:30506377
High-quality-draft genome sequence of the heavy metal resistant and exopolysaccharides producing bacterium Mucilaginibacter pedocola TBZ30T. PMID:30505390
Complete genome sequence of Arcticibacterium luteifluviistationis SM1504T, a cytophagaceae bacterium isolated from Arctic surface seawater. PMID:30505389
Identification and validation of NOLC1 as a potential target for enhancing sensitivity in multidrug resistant non-small cell lung cancer cells. PMID:30505321
Genome-wide identification of lncRNAs and mRNAs differentially expressed in non-functioning pituitary adenoma and construction of an lncRNA-mRNA co-expression network. PMID:30504132
The subcellular organisation of Saccharomyces cerevisiae. PMID:30503867
Improving the Gene Ontology Resource to Facilitate More Informative Analysis and Interpretation of Alzheimer's Disease Data. PMID:30501127
Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy. PMID:30500839
Inflammatory Cytokine TNFα Promotes the Long-Term Expansion of Primary Hepatocytes in 3D Culture. PMID:30500539
Impact of human milk on the transcriptomic response of fetal intestinal epithelial cells reveals expression changes of immune-related genes. PMID:30499575
A systematic screen of conserved Ralstonia solanacearum effectors reveals the role of RipAB, a nuclear-localized effector that suppresses immune responses in potato. PMID:30499228
Characterization of drought stress-responsive root transcriptome of faba bean (Vicia faba L.) using RNA sequencing. PMID:30498675
The draft genome sequence of "Nitrospira lenta" strain BS10, a nitrite oxidizing bacterium isolated from activated sludge. PMID:30498561
Representativeness of variation benchmark datasets. PMID:30497376
SWIM tool application to expression data of glioblastoma stem-like cell lines, corresponding primary tumors and conventional glioma cell lines. PMID:30497369
Genome-wide search of nucleosome patterns using visual analytics. PMID:30496344
Comparative Transcriptomic and Metagenomic Analyses of Influenza Virus-Infected Nasal Epithelial Cells From Multiple Individuals Reveal Specific Nasal-Initiated Signatures. PMID:30487780
Prognostic value of sorting nexin 10 weak expression in stomach adenocarcinoma revealed by weighted gene co-expression network analysis. PMID:30487700
Selective expansion of myeloid and NK cells in humanized mice yields human-like vaccine responses. PMID:30487575
Automatic detection of genomic regions with informative epigenetic patterns. PMID:30486775
Semantic Multi-Classifier Systems Identify Predictive Processes in Heart Failure Models across Species. PMID:30486323
Unified Transcriptomic Signature of Arbuscular Mycorrhiza Colonization in Roots of Medicago truncatula by Integration of Machine Learning, Promoter Analysis, and Direct Merging Meta-Analysis. PMID:30483277
Linking single-cell measurements of mass, growth rate, and gene expression. PMID:30482222
Sex Effects on Gene Expression in Lacrimal Glands of Mouse Models of Sjögren Syndrome. PMID:30481277
SkeletalVis: an exploration and meta-analysis data portal of cross-species skeletal transcriptomics data. PMID:30481257
A new method for evaluating the impacts of semantic similarity measures on the annotation of gene sets. PMID:30481204
Adipocyte-secreted BMP8b mediates adrenergic-induced remodeling of the neuro-vascular network in adipose tissue. PMID:30478315
Metabolomics and proteomics identify the toxic form and the associated cellular binding targets of the anti-proliferative drug AICAR. PMID:30478173
NeVOmics: An Enrichment Tool for Gene Ontology and Functional Network Analysis and Visualization of Data from OMICs Technologies. PMID:30477135
The genome of an underwater architect, the caddisfly Stenopsyche tienmushanensis Hwang (Insecta: Trichoptera). PMID:30476205
RT States: systematic annotation of the human genome using cell type-specific replication timing programs. PMID:30475980
CMTCN: a web tool for investigating cancer-specific microRNA and transcription factor co-regulatory networks. PMID:30473937
Evidence for genetic contribution to the increased risk of type 2 diabetes in schizophrenia. PMID:30470734
Ontology-based semantic mapping of chemical toxicities. PMID:30468866
Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities. PMID:30467459
CCNA2 acts as a novel biomarker in regulating the growth and apoptosis of colorectal cancer. PMID:30464611
MicroRNA 399 as a potential integrator of photo-response, phosphate homeostasis, and sucrose signaling under long day condition. PMID:30463514
Harmonizing semantic annotations for computational models in biology. PMID:30462164
Benchtop-compatible sample processing workflow for proteome profiling of < 100 mammalian cells. PMID:30460388
Small RNA-Seq reveals novel miRNAs shaping the transcriptomic identity of rat brain structures. PMID:30456375
Genome-wide transcriptome profiling and spatial expression analyses identify signals and switches of development in tapeworms. PMID:30455861
Complete genome sequence of Planococcus sp. PAMC21323 isolated from Antarctica and its metabolic potential to detoxify pollutants. PMID:30455841
Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow. PMID:30455444
ALS mutations of FUS suppress protein translation and disrupt the regulation of nonsense-mediated decay. PMID:30455313
Evaluating the impact of topological protein features on the negative examples selection. PMID:30453879
Computational discovery of direct associations between GO terms and protein domains. PMID:30453875
Assembly of a parts list of the human mitotic cell cycle machinery. PMID:30452682
Elevation in Cell Cycle and Protein Metabolism Gene Transcription in Inactive Colonic Tissue From Icelandic Patients With Ulcerative Colitis. PMID:30452647
Spen limits intestinal stem cell self-renewal. PMID:30452449
Integrated PTR-ToF-MS, GWAS and biological pathway analyses reveal the contribution of cow's genome to cheese volatilome. PMID:30451907
Large-scale protein function prediction using heterogeneous ensembles. PMID:30450194
Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis. PMID:30445518
The codon sequences predict protein lifetimes and other parameters of the protein life cycle in the mouse brain. PMID:30443017
Screening and clinical significance of tumor markers in head and neck squamous cell carcinoma through bioinformatics analysis. PMID:30431092
Bioinformatics-based study to detect chemical compounds that show potential as treatments for pulmonary thromboembolism. PMID:30431066
De novo assembly and comparative transcriptome analysis: novel insights into terpenoid biosynthesis in Chamaemelum nobile L. PMID:30430213
Prioritization of Candidate Genes for Congenital Diaphragmatic Hernia in a Critical Region on Chromosome 4p16 using a Machine-Learning Algorithm. PMID:30430034
Transcriptomic Characterization of the Human Habenula Highlights Drug Metabolism and the Neuroimmune System. PMID:30429765
Identification of hub genes with diagnostic values in pancreatic cancer by bioinformatics analyses and supervised learning methods. PMID:30428899
Transcriptome and Resistance-Related Genes Analysis of Botrytis cinerea B05.10 Strain to Different Selective Pressures of Cyprodinil and Fenhexamid. PMID:30425701
Transcriptomics Study on Staphylococcus aureus Biofilm Under Low Concentration of Ampicillin. PMID:30425687
CMV2b-Dependent Regulation of Host Defense Pathways in the Context of Viral Infection. PMID:30423959
miRBase: from microRNA sequences to function. PMID:30423142
Hierarchical HotNet: identifying hierarchies of altered subnetworks. PMID:30423088
Ontology-based validation and identification of regulatory phenotypes. PMID:30423068
Prioritising candidate genes causing QTL using hierarchical orthologous groups. PMID:30423067
Born to Cry: A Genetic Dissection of Infant Vocalization. PMID:30420800
Whole exome sequencing identifies recessive germline mutations in FAM160A1 in familial NK/T cell lymphoma. PMID:30420729
SynerClust: a highly scalable, synteny-aware orthologue clustering tool. PMID:30418868
Gold-containing compound BDG-I inhibits the growth of A549 lung cancer cells through the deregulation of miRNA expression. PMID:30416360
ComClus: A Self-Grouping Framework for Multi-Network Clustering. PMID:30416320
Whole exome sequencing identifies novel predisposing genes in neural tube defects. PMID:30415495
Screening of key candidate genes and pathways for osteocytes involved in the differential response to different types of mechanical stimulation using a bioinformatics analysis. PMID:30413886
Arabidopsis molybdenum cofactor sulfurase ABA3 contributes to anthocyanin accumulation and oxidative stress tolerance in ABA-dependent and independent ways. PMID:30413758
Two histologically colorectal carcinomas subsets from the serrated pathway show different methylome signatures and diagnostic biomarkers. PMID:30413173
The Overexpression of CD80 and ISG15 Are Associated with the Progression and Metastasis of Breast Cancer by a Meta-Analysis Integrating Three Microarray Datasets. PMID:30411299
Extracellular Vesicles Secreted by Hypoxic AC10 Cardiomyocytes Modulate Fibroblast Cell Motility. PMID:30410918
Draft genome sequence of Bacillus amyloliquefaciens subsp. plantarum strain Fito_F321, an endophyte microorganism from Vitis vinifera with biocontrol potential. PMID:30410642
Integrated whole genome microarray analysis and immunohistochemical assay identifies COL11A1, GJB2 and CTRL as predictive biomarkers for pancreatic cancer. PMID:30410422
Identification of critically carcinogenesis-related genes in basal cell carcinoma. PMID:30410353
A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference. PMID:30408409
Resequencing of cv CRI-12 family reveals haplotype block inheritance and recombination of agronomically important genes in artificial selection. PMID:30407717
PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools. PMID:30407594
IID 2018 update: context-specific physical protein-protein interactions in human, model organisms and domesticated species. PMID:30407591
ECO, the Evidence & Conclusion Ontology: community standard for evidence information. PMID:30407590
Building a livestock genetic and genomic information knowledgebase through integrative developments of Animal QTLdb and CorrDB. PMID:30407520
The EcoCyc Database. PMID:30406744
Identification of Core Biomarkers Associated with Outcome in Glioma: Evidence from Bioinformatics Analysis. PMID:30405856
Global Transcriptome Analysis During Adipogenic Differentiation and Involvement of Transthyretin Gene in Adipogenesis in Cattle. PMID:30405687
Uncovering the Changing Gene Expression Profile of Honeybee (Apis mellifera) Worker Larvae Transplanted to Queen Cells. PMID:30405683
Maternal depression during pregnancy and cord blood DNA methylation: findings from the Avon Longitudinal Study of Parents and Children. PMID:30405117
Quantitative proteomic analysis of aqueous humor from patients with drusen and reticular pseudodrusen in age-related macular degeneration. PMID:30404605
A Comparison of Proteins Expressed between Human and Mouse Adipose-Derived Mesenchymal Stem Cells by a Proteome Analysis through Liquid Chromatography with Tandem Mass Spectrometry. PMID:30404232
Transcriptome profile analysis of leg muscle tissues between slow- and fast-growing chickens. PMID:30403718
SyNDI: synchronous network data integration framework. PMID:30400817
MitoMiner v4.0: an updated database of mitochondrial localization evidence, phenotypes and diseases. PMID:30398659
InterPro in 2019: improving coverage, classification and access to protein sequence annotations. PMID:30398656
Lineage-Specific Expression Divergence in Grasses Is Associated with Male Reproduction, Host-Pathogen Defense, and Domestication. PMID:30398650
The protein interaction networks of mucolipins and two-pore channels. PMID:30395881
Comparative transcriptomics identifies genes differentially expressed in the intestine of a new fast-growing strain of common carp with higher unsaturated fatty acid content in muscle. PMID:30395585
FAM92A Underlies Nonsyndromic Postaxial Polydactyly in Humans and an Abnormal Limb and Digit Skeletal Phenotype in Mice. PMID:30395363
RNAcentral: a hub of information for non-coding RNA sequences. PMID:30395267
High-complexity regions in mammalian genomes are enriched for developmental genes. PMID:30395202
Comparative transcriptome analysis to elucidate the enhanced thermotolerance of tea plants (Camellia sinensis) treated with exogenous calcium. PMID:30392143
Transcriptome analysis of Xenopus orofacial tissues deficient in retinoic acid receptor function. PMID:30390632
Proteomics based analysis of the nicotine catabolism in Paenarthrobacter nicotinovorans pAO1. PMID:30390017
Comparative Transcriptional Profiling and Physiological Responses of Two Contrasting Oat Genotypes under Salt Stress. PMID:30389990
An RNAi screen in human cell lines reveals conserved DNA damage repair pathways that mitigate formaldehyde sensitivity. PMID:30389308
Strategies for Pathway Analysis Using GWAS and WGS Data. PMID:30387919
High-quality-draft genome sequence of the multiple heavy metal resistant bacterium Pseudaminobacter manganicus JH-7T. PMID:30386456
Interplay Between MicroRNAs and Targeted Genes in Cellular Homeostasis of Adult Zebrafish (Danio rerio). PMID:30386173
Identification of highly connected and differentially expressed gene subnetworks in metastasizing endometrial cancer. PMID:30383835
Variation in Mitochondria-Derived Transcript Levels Associated With DDT Resistance in the 91-R Strain of Drosophila melanogaster (Diptera: Drosophilidae). PMID:30383265
Identification of glioblastoma gene prognosis modules based on weighted gene co-expression network analysis. PMID:30382873
Blastic plasmacytoid dendritic cell neoplasm: genomics mark epigenetic dysregulation as a primary therapeutic target. PMID:30381297
Translocatome: a novel resource for the analysis of protein translocation between cellular organelles. PMID:30380112
Genomic distribution of a novel Pyrenophora tritici-repentis ToxA insertion element. PMID:30379913
Proteomic analysis of human prostate cancer PC-3M-1E8 cells and PC-3M-2B4 cells of same origin but with different metastatic potential. PMID:30379883
Gene ontology concept recognition using named concept: understanding the various presentations of the gene functions in biomedical literature. PMID:30376045
Genome sequence of the cauliflower mushroom Sparassis crispa (Hanabiratake) and its association with beneficial usage. PMID:30375506
Neurogenetic contributions to amyloid beta and tau spreading in the human cortex. PMID:30374196
Deep sequencing and miRNA profiles in alcohol-induced neuroinflammation and the TLR4 response in mice cerebral cortex. PMID:30374194
Analysis of the Trichuris suis excretory/secretory proteins as a function of life cycle stage and their immunomodulatory properties. PMID:30374177
Feature related multi-view nonnegative matrix factorization for identifying conserved functional modules in multiple biological networks. PMID:30373534
De novo transcriptome based on next-generation sequencing reveals candidate genes with sex-specific expression in Arapaima gigas (Schinz, 1822), an ancient Amazonian freshwater fish. PMID:30372461
PubChem 2019 update: improved access to chemical data. PMID:30371825
MatrixDB: integration of new data with a focus on glycosaminoglycan interactions. PMID:30371822
Machine Learning in Human Olfactory Research. PMID:30371751
Molecular Atlas of Postnatal Mouse Heart Development. PMID:30371266
A Transcriptomic Method to Determine Airway Immune Dysfunction in T2-High and T2-Low Asthma. PMID:30371106
A GPU-based algorithm for fast node label learning in large and unbalanced biomolecular networks. PMID:30367594
Multiple model species selection for transcriptomics analysis of non-model organisms. PMID:30367568
Identification of Potential miRNAs Biomarkers for High-Grade Prostate Cancer by Integrated Bioinformatics Analysis. PMID:30367364
Determinants of promoter and enhancer transcription directionality in metazoans. PMID:30367057
De Novo Hepatic Transcriptome Assembly and Systems Level Analysis of Three Species of Dietary Fish, Sardinops sagax, Scomber japonicus, and Pleuronichthys verticalis. PMID:30366465
Victors: a web-based knowledge base of virulence factors in human and animal pathogens. PMID:30365026
Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions. PMID:30364468
Identification of candidate genes or microRNAs associated with the lymph node metastasis of SCLC. PMID:30364292
The Hierarchical Modular Structure of HER2+ Breast Cancer Network. PMID:30364267
Innexins: Expression, Regulation, and Functions. PMID:30364195
Gene Mapping and Gene-Set Analysis for Milk Fever Incidence in Holstein Dairy Cattle. PMID:30364193
Whole Genome Transcriptome Analysis of the Association between Obesity and Triple-Negative Breast Cancer in Caucasian Women. PMID:30360534
Comparative De Novo transcriptome analysis of the Australian black-lip and Sydney rock oysters reveals expansion of repetitive elements in Saccostrea genomes. PMID:30359422
Clust: automatic extraction of optimal co-expressed gene clusters from gene expression data. PMID:30359297
Proteomic changes in traumatic brain injury: experimental approaches. PMID:30358641
15 years of GDR: New data and functionality in the Genome Database for Rosaceae. PMID:30357347
Candidate Biomarkers and Molecular Mechanism Investigation for Glioblastoma Multiforme Utilizing WGCNA. PMID:30356407
The human gut microbiome in early-onset type 1 diabetes from the TEDDY study. PMID:30356183
Complete genome sequence of the nitrogen-fixing bacterium Azospirillum humicireducens type strain SgZ-5T. PMID:30349619
Comparative Transcriptomic Analysis of Two Actinorhizal Plants and the Legume Medicago truncatula Supports the Homology of Root Nodule Symbioses and Is Congruent With a Two-Step Process of Evolution in the Nitrogen-Fixing Clade of Angiosperms. PMID:30349546
Parasitic Nematodes Exert Antimicrobial Activity and Benefit From Microbiota-Driven Support for Host Immune Regulation. PMID:30349532
From Affective Science to Psychiatric Disorder: Ontology as a Semantic Bridge. PMID:30349491
Species groups distributed across elevational gradients reveal convergent and continuous genetic adaptation to high elevations. PMID:30348757
Draft genome sequences of Cylindrospermopsis raciborskii strains CS-508 and MVCC14, isolated from freshwater bloom events in Australia and Uruguay. PMID:30344889
Insights into the draft genome sequence of bioactives-producing Bacillus thuringiensis DNG9 isolated from Algerian soil-oil slough. PMID:30344888
Complete Genome Sequence of Bacillus cereus CC-1, A Novel Marine Selenate/Selenite Reducing Bacterium Producing Metallic Selenides Nanomaterials. PMID:30343326
HSP90-incorporating chaperome networks as biosensor for disease-related pathways in patient-specific midbrain dopamine neurons. PMID:30341316
Indirubin attenuates mouse psoriasis-like skin lesion in a CD274-dependent manner: an achievement of RNA sequencing. PMID:30341238
Comparative Proteomic and Physiological Analyses of Two Divergent Maize Inbred Lines Provide More Insights into Drought-Stress Tolerance Mechanisms. PMID:30340410
Draft genome sequences of 'Candidatus Chloroploca asiatica' and 'Candidatus Viridilinea mediisalina', candidate representatives of the Chloroflexales order: phylogenetic and taxonomic implications. PMID:30338027
One complete and three draft genome sequences of four Brochothrix thermosphacta strains, CD 337, TAP 175, BSAS1 3 and EBP 3070. PMID:30338025
First genome sequencing and comparative analyses of Corynebacterium pseudotuberculosis strains from Mexico. PMID:30338024
Prediction of Target Genes and Pathways Associated With Cetuximab Insensitivity in Colorectal Cancer. PMID:30336768
Genomic heterogeneity differentiates clinical and environmental subgroups of Legionella pneumophila sequence type 1. PMID:30335848
A Comparative Assessment of Human and Chimpanzee iPSC-derived Cardiomyocytes with Primary Heart Tissues. PMID:30333510
Genetic and Epigenetic Determinants of Aggressiveness in Cribriform Carcinoma of the Prostate. PMID:30333152
Bioinformatics Analysis and Functional Prediction of Transmembrane Proteins in Entamoeba histolytica. PMID:30332795
Small RNA and degradome profiling involved in seed development and oil synthesis of Brassica napus. PMID:30332454
REDfly: the transcriptional regulatory element database for Drosophila. PMID:30329093
Tissue-Specific Profiling of Oxidative Stress-Associated Transcriptome in a Healthy Mouse Model. PMID:30326626
Distinct co-expression networks using multi-omic data reveal novel interventional targets in HPV-positive and negative head-and-neck squamous cell cancer. PMID:30323202
MicroRNA-664-5p promotes myoblast proliferation and inhibits myoblast differentiation by targeting serum response factor and Wnt1. PMID:30323063
PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information. PMID:30321395
CRISPR Activation Screens Systematically Identify Factors that Drive Neuronal Fate and Reprogramming. PMID:30318302
Systems vaccinology and big data in the vaccine development chain. PMID:30317555
Insight into the evolution and functional characteristics of the pan-genome assembly from sesame landraces and modern cultivars. PMID:30315621
CUP-SHAPED COTYLEDON1 (CUC1) and CUC2 regulate cytokinin homeostasis to determine ovule number in Arabidopsis. PMID:30312436
FAANG, establishing metadata standards, validation and best practices for the farmed and companion animal community. PMID:30311252
A miRNA Combination as Promising Biomarker for Hepatocellular Carcinoma Diagnosis: A Study Based on Bioinformatics Analysis. PMID:30310500
Genome-wide association studies and meta-analysis uncovers new candidate genes for growth and carcass traits in pigs. PMID:30308042
Sequence Alterations of Cortical Genes Linked to Individual Connectivity of the Human Brain. PMID:30307489
GOGO: An improved algorithm to measure the semantic similarity between gene ontology terms. PMID:30305653
Towards region-specific propagation of protein functions. PMID:30304483
Transcriptomics reveal potential vaccine antigens and a drastic increase of upregulated genes during Theileria parva development from arthropod to bovine infective stages. PMID:30303978
Transcriptomic analyses identify albino-associated genes of a novel albino tea germplasm 'Huabai 1'. PMID:30302258
Induction of antibacterial proteins and peptides in the coprophilous mushroom Coprinopsis cinerea in response to bacteria. PMID:30301946
Pathogenicity Induced by Invasive Infection of Streptococcus dysgalactiae subsp. equisimilis in a Mouse Model of Diabetes. PMID:30298057
Food perception without ingestion leads to metabolic changes and irreversible developmental arrest in C. elegans. PMID:30296941
MicroRNA-transcription factor network analysis reveals miRNAs cooperatively suppress RORA in oral squamous cell carcinoma. PMID:30293994
Differential Gene Expression Common to Acquired and Intrinsic Resistance to BRAF Inhibitor Revealed by RNA-Seq Analysis. PMID:30293252
The Bear Giant-Skipper genome suggests genetic adaptations to living inside yucca roots. PMID:30293092
Gene ontology enrichment analysis of congenital diaphragmatic hernia-associated genes. PMID:30287891
Mutation pattern analysis reveals polygenic mini-drivers associated with relapse after surgery in lung adenocarcinoma. PMID:30287876
Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties. PMID:30286077
MiRNA expression profiles in healthy OSAHS and OSAHS with arterial hypertension: potential diagnostic and early warning markers. PMID:30285853
Environmental pH modulates transcriptomic responses in the fungus Fusarium sp. associated with KSHB Euwallacea sp. near fornicatus. PMID:30285612
Parallel evolution of gene expression between trophic specialists despite divergent genotypes and morphologies. PMID:30283665
The genomic basis of cichlid fish adaptation within the deepwater "twilight zone" of Lake Malawi. PMID:30283648
Development of an AmpliSeqTM Panel for Next-Generation Sequencing of a Set of Genetic Predictors of Persisting Pain. PMID:30283335
Unraveling Rice Tolerance Mechanisms Against Schizotetranychus oryzae Mite Infestation. PMID:30279693
A systems-approach reveals human nestin is an endothelial-enriched, angiogenesis-independent intermediate filament protein. PMID:30279450
Integrated systems analysis reveals conserved gene networks underlying response to spinal cord injury. PMID:30277459
A survey of inter-individual variation in DNA methylation identifies environmentally responsive co-regulated networks of epigenetic variation in the human genome. PMID:30273333
Identification of COL1A1 as an invasion‑related gene in malignant astrocytoma. PMID:30272346
Gene expression differences between thyroid carcinoma, thyroid adenoma and normal thyroid tissue. PMID:30272326
Examining the key genes and pathways in hepatocellular carcinoma development from hepatitis B virus‑positive cirrhosis. PMID:30272310
Gene module analysis of juvenile myelomonocytic leukemia and screening of anticancer drugs. PMID:30272300
Cardiac recovery via extended cell-free delivery of extracellular vesicles secreted by cardiomyocytes derived from induced pluripotent stem cells. PMID:30271672
To select relevant features for longitudinal gene expression data by extending a pathway analysis method. PMID:30271585
The Diurnal Timing of Starvation Differently Impacts Murine Hepatic Gene Expression and Lipid Metabolism - A Systems Biology Analysis Using Self-Organizing Maps. PMID:30271348
A mitochondrial proteome profile indicative of type 2 diabetes mellitus in skeletal muscles. PMID:30266947
WEADE: A workflow for enrichment analysis and data exploration. PMID:30265728
Identification and comparison of microRNAs in pituitary gland during prenatal and postnatal stages of sheep by deep sequencing. PMID:30262709
Systematic analysis of lncRNA-miRNA-mRNA competing endogenous RNA network identifies four-lncRNA signature as a prognostic biomarker for breast cancer. PMID:30261893
Differentially Expressed Genes Associated with the Cabbage Yellow-Green-Leaf Mutant in the ygl-1 Mapping Interval with Recombination Suppression. PMID:30261688
Single-Run Mass Spectrometry Analysis Provides Deep Insight into E. coli Proteome. PMID:30259409
Investigation of post-translational modifications in type 2 diabetes. PMID:30258344
De Novo Sequence and Copy Number Variants Are Strongly Associated with Tourette Disorder and Implicate Cell Polarity in Pathogenesis. PMID:30257206
SemGen: a tool for semantics-based annotation and composition of biosimulation models. PMID:30256901
Methods and results from the genome-wide association group at GAW20. PMID:30255814
Microenvironmental niche divergence shapes BRCA1-dysregulated ovarian cancer morphological plasticity. PMID:30254278
The cargo receptor SURF4 promotes the efficient cellular secretion of PCSK9. PMID:30251625
Identification of a 3'-Untranslated Genetic Variant of RARB Associated With Carotid Intima-Media Thickness in Rheumatoid Arthritis: A Genome-Wide Association Study. PMID:30251476
MaxMIF: A New Method for Identifying Cancer Driver Genes through Effective Data Integration. PMID:30250803
A new tool for studying waterfowl immune and metabolic responses: Molecular level analysis using kinome profiling. PMID:30250721
Complete genome sequence of the Robinia pseudoacacia L. symbiont Mesorhizobium amorphae CCNWGS0123. PMID:30250634
Identification of six key miRNAs associated with breast cancer through screening large-scale microarray data. PMID:30250531
Comparative Transcriptome Profiling of mRNA and lncRNA Related to Tail Adipose Tissues of Sheep. PMID:30250481
Neurogenetic profiles delineate large-scale connectivity dynamics of the human brain. PMID:30250030
Evolutionary insights from comparative transcriptome and transcriptome-wide coalescence analyses in Tetrastigma hemsleyanum. PMID:30249188
Granulocyte-Colony-Stimulating Factor Alters the Proteomic Landscape of the Ventral Tegmental Area. PMID:30249060
Comprehensive Transcriptome Profiling and Identification of Potential Genes Responsible for Salt Tolerance in Tall Fescue Leaves under Salinity Stress. PMID:30248970
Genome-wide identification and characterization of CONSTANS-like gene family in radish (Raphanus sativus). PMID:30248137
The Comparative Toxicogenomics Database: update 2019. PMID:30247620
Exome sequencing study of 20 patients with high myopia. PMID:30245926
Context-dependent prediction of protein complexes by SiComPre. PMID:30245847
Shared Biological Pathways Between Alzheimer's Disease and Ischemic Stroke. PMID:30245614
ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature. PMID:30241466
Computerized Approach to Creating a Systematic Ontology of Hematology/Oncology Regimens. PMID:30238070
Identification of an eight-gene prognostic signature for lung adenocarcinoma. PMID:30237740
Habitual aerobic exercise and circulating proteomic patterns in healthy adults: relation to indicators of healthspan. PMID:30236049
Robust Innate Immunity of Young Rabbits Mediates Resistance to Rabbit Hemorrhagic Disease Caused by Lagovirus Europaeus GI.1 But Not GI.2. PMID:30235853
Genetic variants analysis of three dromedary camels using whole genome sequencing data. PMID:30235280
Bioinformatics Analysis Identifies p53 as a Candidate Prognostic Biomarker for Neuropathic Pain. PMID:30233637
Exome scale map of genetic alterations promoting metastasis in colorectal cancer. PMID:30231850
Analysis of Transcription Factor-Related Regulatory Networks Based on Bioinformatics Analysis and Validation in Hepatocellular Carcinoma. PMID:30228980
Identification of Missing Carbon Fixation Enzymes as Potential Drug Targets in Mycobacterium Tuberculosis. PMID:30218604
Robust interferon signature and suppressed tissue repair gene expression in synovial tissue from patients with postinfectious, Borrelia burgdorferi-induced Lyme arthritis. PMID:30218476
DNA methylation in adolescents with anxiety disorder: a longitudinal study. PMID:30218003
PAX5A and PAX5B isoforms are both efficient to drive B cell differentiation. PMID:30214688
Identifying miRNA-mRNA regulation network of major depressive disorder in ovarian cancer patients. PMID:30214617
A Robust Methodology for Assessing Differential Homeolog Contributions to the Transcriptomes of Allopolyploids. PMID:30213855
B cells with aberrant activation of Notch1 signaling promote Treg and Th2 cell-dominant T-cell responses via IL-33. PMID:30213787
Gene co-expression network analysis identifies the hub genes associated with immune functions for nocturnal hemodialysis in patients with end-stage renal disease. PMID:30212930
MetaHCR: a web-enabled metagenome data management system for hydrocarbon resources. PMID:30212909
Transcriptomic profile analysis of brain microvascular pericytes in spontaneously hypertensive rats by RNA-Seq. PMID:30210677
A comprehensive investigation using meta-analysis and bioinformatics on miR-34a-5p expression and its potential role in head and neck squamous cell carcinoma. PMID:30210668
Identification of Genes and Pathways Involved in Ovarian Epithelial Cancer by Bioinformatics Analysis. PMID:30210623
Cycles of gene expression and genome response during mammalian tissue regeneration. PMID:30208973
Proteomic analysis of human T cell-derived exosomes reveals differential RAS/MAPK signaling. PMID:30207595
Transcriptomic analyses of cacao cell suspensions in light and dark provide target genes for controlled flavonoid production. PMID:30206304
Proteomic Analysis of Rapeseed Root Response to Waterlogging Stress. PMID:30205432
The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer's disease. PMID:30204156
SMRT-Cappable-seq reveals complex operon variants in bacteria. PMID:30201986
Analysis of miRNA signature differentially expressed in exosomes from adriamycin-resistant and parental human breast cancer cells. PMID:30201690
Comparative gene expression profile and DNA methylation status in diabetic patients of Kazak and Han people. PMID:30200077
Cx26 partial loss causes accelerated presbycusis by redox imbalance and dysregulation of Nfr2 pathway. PMID:30199819
DNA damage-induced dynamic changes in abundance and cytosol-nuclear translocation of proteins involved in translational processes, metabolism, and autophagy. PMID:30196736
Implications of Newly Identified Brain eQTL Genes and Their Interactors in Schizophrenia. PMID:30195780
Nuclear Factor I Represses the Notch Effector HEY1 in Glioblastoma. PMID:30195713
Transcriptome analysis of differentially expressed unigenes involved in flavonoid biosynthesis during flower development of Chrysanthemum morifolium 'Chuju'. PMID:30194355
Copy Number Alterations in Tumor Genomes Deleting Antineoplastic Drug Targets Partially Compensated by Complementary Amplifications. PMID:30194077
Data on genome annotation and analysis of earthworm Eisenia fetida. PMID:30191166
Genomic analysis reveals genes affecting distinct phenotypes among different Chinese and western pig breeds. PMID:30190566
Plasma membrane profiling during enterohemorrhagic E. coli infection reveals that the metalloprotease StcE cleaves CD55 from host epithelial surfaces. PMID:30190327
Prioritizing candidate genes post-GWAS using multiple sources of data for mastitis resistance in dairy cattle. PMID:30189836
Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells. PMID:30188322
[Retinal transcriptome profile in mice following dexamethasone treatment for endotoxin-induced uveitis]. PMID:30187873
Comparison of gene expression profiles between human erythroid cells derived from fetal liver and adult peripheral blood. PMID:30186694
Microarray data analysis to identify differentially expressed genes and biological pathways associated with asthma. PMID:30186379
In silico Study of Iron, Zinc and Copper Binding Proteins of Pseudomonas syringae pv. lapsa: Emphasis on Secreted Metalloproteins. PMID:30186242
Metabolome and molecular basis for carbohydrate increase and nitrate reduction in burley tobacco seedlings by glycerol through upregulating carbon and nitrogen metabolism. PMID:30185870
Tomato DCL2b is required for the biosynthesis of 22-nt small RNAs, the resulting secondary siRNAs, and the host defense against ToMV. PMID:30181890
Identification of key pathways and genes in response to trastuzumab treatment in breast cancer using bioinformatics analysis. PMID:30181805
A network pharmacology approach to explore the mechanisms of Erxian decoction in polycystic ovary syndrome. PMID:30181771
Systematic pharmacological screens uncover novel pathways involved in cerebral cavernous malformations. PMID:30181117
Sequence and structural variation in the genome of the Biomphalaria glabrata embryonic (Bge) cell line. PMID:30180879
Single-Locus and Multi-Locus Genome-Wide Association Studies in the Genetic Dissection of Fiber Quality Traits in Upland Cotton (Gossypium hirsutum L.). PMID:30177935
Transcriptomic Insights Into the Growth Phase- and Sugar-Associated Changes in the Exopolysaccharide Production of a High EPS-Producing Streptococcus thermophilus ASCC 1275. PMID:30177921
Genome-wide analysis of the FleQ direct regulon in Pseudomonas fluorescens F113 and Pseudomonas putida KT2440. PMID:30177764
Molecular mechanism of activated T cells in breast cancer. PMID:30174439
Integrated analysis of a competing endogenous RNA network reveals key lncRNAs as potential prognostic biomarkers for human bladder cancer. PMID:30170380
Improving protein function prediction using protein sequence and GO-term similarities. PMID:30169569
FGFR1/FOXM1 pathway: a key regulator of glioblastoma stem cells radioresistance and a prognosis biomarker. PMID:30167084
CEA: Combination-based gene set functional enrichment analysis. PMID:30166636
PirVP genes causing AHPND identified in a new Vibrio species (Vibrio punensis) within the commensal Orientalis clade. PMID:30166588
Predictions of novel Schistosoma mansoni - human protein interactions consistent with experimental data. PMID:30166569
Silent Witness: Dual-Species Transcriptomics Reveals Epithelial Immunological Quiescence to Helminth Larval Encounter and Fostered Larval Development. PMID:30158930
Exploring the Mechanism of Flavonoids Through Systematic Bioinformatics Analysis. PMID:30158870
Mushroom Body Specific Transcriptome Analysis Reveals Dynamic Regulation of Learning and Memory Genes After Acquisition of Long-Term Courtship Memory in Drosophila. PMID:30158319
Differentially expressed proteins in positive versus negative HNSCC lymph nodes. PMID:30157864
A head transcriptome provides insights into odorant binding proteins of the bamboo grasshopper. PMID:30155713
Genome-Wide Characterization of Selection Signatures and Runs of Homozygosity in Ugandan Goat Breeds. PMID:30154830
Computational characterization and identification of human polycystic ovary syndrome genes. PMID:30154492
FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes. PMID:30152809
Normal and Abortive Buds Transcriptomic Profiling of Broccoli ogu Cytoplasmic Male Sterile Line and Its Maintainer. PMID:30149512
Identification of key genes and pathways using bioinformatics analysis in septic shock children. PMID:30147344
Effects of 5-Aminolevulinic Acid on Gene Expression, Immunity, and ATP Levels in Pacific White Shrimp, Litopenaeus vannamei. PMID:30145744
Pan-cancer analysis of neoepitopes. PMID:30143704
ESCC ATLAS: A population wide compendium of biomarkers for Esophageal Squamous Cell Carcinoma. PMID:30143675
A compendium of conserved cleavage and polyadenylation events in mammalian genes. PMID:30143597
Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation. PMID:30143032
Deacetylase activity-independent transcriptional activation by HDAC2 during TPA-induced HL-60 cell differentiation. PMID:30142192
A systemic approach to identify signaling pathways activated during short-term exposure to traffic-related urban air pollution from human blood. PMID:30141164
BdorOR88a Modulates the Responsiveness to Methyl Eugenol in Mature Males of Bactrocera dorsalis (Hendel). PMID:30140233
Instant Clue: A Software Suite for Interactive Data Visualization and Analysis. PMID:30140043
Transcriptomic Analysis of Aedes aegypti in Response to Mosquitocidal Bacillus thuringiensis LLP29 Toxin. PMID:30140020
Construction and analysis of mRNA, miRNA, lncRNA, and TF regulatory networks reveal the key genes associated with prostate cancer. PMID:30138363
Identification of biomarkers for Barcelona Clinic Liver Cancer staging and overall survival of patients with hepatocellular carcinoma. PMID:30138346
Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655. PMID:30137486
Divergent brain gene expression patterns associate with distinct cell-specific tau neuropathology traits in progressive supranuclear palsy. PMID:30136084
Physiological characterization of the emergence from diapause: A transcriptomics approach. PMID:30135598
Alterations of 63 hub genes during lingual carcinogenesis in C57BL/6J mice. PMID:30135512
Models of cell signaling uncover molecular mechanisms of high-risk neuroblastoma and predict disease outcome. PMID:30134948
Prediction of key genes and pathways involved in trastuzumab-resistant gastric cancer. PMID:30134903
Transcriptome analysis of Valsa mali reveals its response mechanism to the biocontrol actinomycete Saccharothrix yanglingensis Hhs.015. PMID:30134836
Specific expression pattern of IMP metabolism related-genes in chicken muscle between cage and free range conditions. PMID:30133460
Bioinformatics analyses of significant genes, related pathways and candidate prognostic biomarkers in glioblastoma. PMID:30132538
Deletion of the formin Diaph1 protects from structural and functional abnormalities in the murine diabetic kidney. PMID:30132346
From homogeneous to heterogeneous network alignment via colored graphlets. PMID:30131590
Dissecting the expression landscape of mitochondrial genes in lung squamous cell carcinoma and lung adenocarcinoma. PMID:30128019
Screening and identification of key biomarkers in bladder carcinoma: Evidence from bioinformatics analysis. PMID:30127900
TRIQ: a new method to evaluate triclusters. PMID:30127855
Selective gene dependencies in MYCN-amplified neuroblastoma include the core transcriptional regulatory circuitry. PMID:30127528
Epigenetic regulation of the circadian gene Per1 contributes to age-related changes in hippocampal memory. PMID:30127461
Robust prediction of response to immune checkpoint blockade therapy in metastatic melanoma. PMID:30127394
One Way to Achieve Germination: Common Molecular Mechanism Induced by Ethylene and After-Ripening in Sunflower Seeds. PMID:30127315
Efficient proximity labeling in living cells and organisms with TurboID. PMID:30125270
Bioinformatics analysis of microarray data to reveal the pathogenesis of diffuse intrinsic pontine glioma. PMID:30124166
Alternate splicing of transcripts upon Mycobacterium tuberculosis infection impacts the expression of functional protein domains. PMID:30120868
Identification of key genes and pathways involved in response to pain in goat and sheep by transcriptome sequencing. PMID:30119702
Comprehensive analysis of differentially expressed microRNAs and mRNAs in dorsal root ganglia from streptozotocin-induced diabetic rats. PMID:30118515
PRSS8 suppresses colorectal carcinogenesis and metastasis. PMID:30115975
Volatile Oil of Amomum villosum Inhibits Nonalcoholic Fatty Liver Disease via the Gut-Liver Axis. PMID:30112382
Identification of key genes and pathways for esophageal squamous cell carcinoma by bioinformatics analysis. PMID:30112053
Unraveling the Plasmodium vivax sporozoite transcriptional journey from mosquito vector to human host. PMID:30111801
Comprehensive gene expression profiling identifies distinct and overlapping transcriptional profiles in non-specific interstitial pneumonia and idiopathic pulmonary fibrosis. PMID:30111332
Genetic dissection of bull fertility in US Jersey dairy cattle. PMID:30109710
Identification of a panel of MYC and Tip60 co-regulated genes functioning primarily in cell cycle and DNA replication. PMID:30108681
Microgravity-Induced Alterations of Inflammation-Related Mechanotransduction in Endothelial Cells on Board SJ-10 Satellite. PMID:30108515
Unbiased shRNA screening, using a combination of FACS and high-throughput sequencing, enables identification of novel modifiers of Polycomb silencing. PMID:30108332
Gene Ontology Enrichment Improves Performances of Functional Similarity of Genes. PMID:30108262
A Methodological Assessment and Characterization of Genetically-Driven Variation in Three Human Phosphoproteomes. PMID:30108239
Monitoring changes in the Gene Ontology and their impact on genomic data analysis. PMID:30107399
Nuclear localized Raf1 isoform alters DNA-dependent protein kinase activity and the DNA damage response. PMID:30106602
C5aR1 regulates migration of suppressive myeloid cells required for costimulatory blockade-induced murine allograft survival. PMID:30106232
Transcriptome sequencing identifies key pathways and genes involved in gastric adenocarcinoma. PMID:30106143
Proteomics: Clinical and research applications in respiratory diseases. PMID:30105802
PMLPR: A novel method for predicting subcellular localization based on recommender systems. PMID:30104743
EMBLmyGFF3: a converter facilitating genome annotation submission to European Nucleotide Archive. PMID:30103816
Transcriptome profiling of anti-müllerian hormone treated preantral/small antral mouse ovary follicles. PMID:30100987
Dysfunction of Sister Chromatids Separation Promotes Progression of Hepatocellular Carcinoma According to Analysis of Gene Expression Profiling. PMID:30100882
Identification of prognostic risk factors for esophageal adenocarcinoma using bioinformatics analysis. PMID:30100738
Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain. PMID:30097089
Assisted gene expression-based clustering with AWNCut. PMID:30094873
A clinical-pathogenetic approach on associated anomalies and chromosomal defects supports novel candidate critical regions and genes for gastroschisis. PMID:30094464
Rat BodyMap transcriptomes reveal unique circular RNA features across tissue types and developmental stages. PMID:30093490
Analysis of differentially expressed genes among human hair follicle-derived iPSCs, induced hepatocyte-like cells, and primary hepatocytes. PMID:30092828
Genome-wide transcriptional analysis of silica nanoparticle-induced toxicity in zebrafish embryos. PMID:30090375
Identification of potential target genes of USP22 via ChIP-seq and RNA-seq analysis in HeLa cells. PMID:30088609
Reconstruction of the Protein-Protein Interaction Network for Protein Complexes Identification by Walking on the Protein Pair Fingerprints Similarity Network. PMID:30087694
Dehydration Stress Memory: Gene Networks Linked to Physiological Responses During Repeated Stresses of Zea mays. PMID:30087686
Proteomic distinction of renal oncocytomas and chromophobe renal cell carcinomas. PMID:30087584
Effusion: prediction of protein function from sequence similarity networks. PMID:30084920
Comprehensive profiling of transcriptional networks specific for lactogenic differentiation of HC11 mammary epithelial stem-like cells. PMID:30082875
Studies on Aminoglycoside Susceptibility Identify a Novel Function of KsgA To Secure Translational Fidelity during Antibiotic Stress. PMID:30082289
Pan-Cancer Analysis Reveals Differential Susceptibility of Bidirectional Gene Promoters to DNA Methylation, Somatic Mutations, and Copy Number Alterations. PMID:30081598
Factors Associated with Heritable Pulmonary Arterial Hypertension Exert Convergent Actions on the miR-130/301-Vascular Matrix Feedback Loop. PMID:30081553
Active N6-Methyladenine Demethylation by DMAD Regulates Gene Expression by Coordinating with Polycomb Protein in Neurons. PMID:30078725
Conducting metagenomic studies in microbiology and clinical research. PMID:30078138
Regional differences in thermal adaptation of a cold-water fish Rhynchocypris oxycephalus revealed by thermal tolerance and transcriptomic responses. PMID:30076386
GFAP Mutations in Astrocytes Impair Oligodendrocyte Progenitor Proliferation and Myelination in an hiPSC Model of Alexander Disease. PMID:30075130
Genome Variation in the Model Halophilic Bacterium Salinibacter ruber. PMID:30072959
Transcriptome analysis highlights key differentially expressed genes involved in cellulose and lignin biosynthesis of sugarcane genotypes varying in fiber content. PMID:30072760
Alternatively spliced variants in Atlantic cod (Gadus morhua) support response to variable salinity environment. PMID:30072755
Gene expression analysis indicates reduced memory and cognitive functions in the hippocampus and increase in synaptic reorganization in the frontal cortex 3 weeks after MDMA administration in Dark Agouti rats. PMID:30071829
An overview of Phoneutria nigriventer spider venom using combined transcriptomic and proteomic approaches. PMID:30067761
CLEC3B is downregulated and inhibits proliferation in clear cell renal cell carcinoma. PMID:30066941
A proteomic analysis of chemoresistance development via sequential treatment with doxorubicin reveals novel players in MCF‑7 breast cancer cells. PMID:30066829
A semantics-oriented computational approach to investigate microRNA regulation on glucocorticoid resistance in pediatric acute lymphoblastic leukemia. PMID:30066657
OC-2-KB: integrating crowdsourcing into an obesity and cancer knowledge base curation system. PMID:30066655
Gonadal transcriptome sequencing of the critically endangered Acipenser dabryanus to discover candidate sex-related genes. PMID:30065900
Use of Proteomic Imaging Coupled With Transcriptomic Analysis to Identify Biomolecules Responsive to Cochlear Injury. PMID:30065626
Monoassociation with Lactobacillus plantarum Disrupts Intestinal Homeostasis in Adult Drosophila melanogaster. PMID:30065090
Single-cell transcriptomic analyses reveal distinct dorsal/ventral pancreatic programs. PMID:30065074
Application of Transcriptomics to Compare the Carbohydrate Active Enzymes That Are Expressed by Diverse Genera of Anaerobic Fungi to Degrade Plant Cell Wall Carbohydrates. PMID:30061875
Discovery and control of culturable and viable but non-culturable cells of a distinctive Lactobacillus harbinensis strain from spoiled beer. PMID:30061572
d Rhamnose β-hederin reverses chemoresistance of breast cancer cells by regulating exosome-mediated resistance transmission. PMID:30061173
Efflux Pumps Represent Possible Evolutionary Convergence onto the β-Barrel Fold. PMID:30057025
Irf3 from mandarin fish thymus initiates interferon transcription. PMID:30056593
Transcriptomic Analysis of Hepatic Cells in Multicellular Organotypic Liver Models. PMID:30054499
The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders. PMID:30053424
ChemDIS 2: an update of chemical-disease inference system. PMID:30053236
Systems Pharmacological Approach to Investigate the Mechanism of Acori Tatarinowii Rhizoma for Alzheimer's Disease. PMID:30050590
A Meta-Analysis Characterizing Stem-Like Gene Expression in the Suprachiasmatic Nucleus and Its Circadian Clock. PMID:30046594
Mitofusin2 Induces Cell Autophagy of Pancreatic Cancer through Inhibiting the PI3K/Akt/mTOR Signaling Pathway. PMID:30046371
KampoDB, database of predicted targets and functional annotations of natural medicines. PMID:30046160
Genome sequence and genetic transformation of a widely distributed and cultivated poplar. PMID:30044051
Full-length transcriptome sequences and the identification of putative genes for flavonoid biosynthesis in safflower. PMID:30041604
Early Transcriptomic Response to Phosphate Deprivation in Soybean Leaves as Revealed by RNA-Sequencing. PMID:30041471
Leveraging Experimental Details for an Improved Understanding of Host-Pathogen Interactome. PMID:30040202
Differential aging of growth plate cartilage underlies differences in bone length and thus helps determine skeletal proportions. PMID:30036371
The Ontology of Biological and Clinical Statistics (OBCS)-based statistical method standardization and meta-analysis of host responses to yellow fever vaccines. PMID:30034908
TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations. PMID:30032202
RNA-seq assistant: machine learning based methods to identify more transcriptional regulated genes. PMID:30029596
Molecular mechanism of estrogen-mediated neuroprotection in the relief of brain ischemic injury. PMID:30029590
High-throughput profiling of the circulating proteome suggests sexually dimorphic corticosteroid signaling following ischemic stroke. PMID:30029587
Murine cytomegalovirus M72 promotes acute virus replication in vivo and is a substrate of the TRiC/CCT complex. PMID:30029015
Identification and characterization of known and novel microRNAs in strawberry fruits induced by Botrytis cinerea. PMID:30026481
Inhibiting the integrated stress response pathway prevents aberrant chondrocyte differentiation thereby alleviating chondrodysplasia. PMID:30024379
GOATOOLS: A Python library for Gene Ontology analyses. PMID:30022098
Overexpression of the Rybp Gene Inhibits Differentiation of Bovine Myoblasts into Myotubes. PMID:30021933
ProfPPIdb: Pairs of physical protein-protein interactions predicted for entire proteomes. PMID:30020956
Triflic Acid Treatment Enables LC-MS/MS Analysis of Insoluble Bacterial Biomass. PMID:30019906
InDePTH: detection of hub genes for developing gene expression networks under anticancer drug treatment. PMID:30018738
Methods for Physical Characterization of Phase-Separated Bodies and Membrane-less Organelles. PMID:30017918
Analysis of codon usage patterns in Hirudinaria manillensis reveals a preference for GC-ending codons caused by dominant selection constraints. PMID:30016953
An unsupervised machine learning method for discovering patient clusters based on genetic signatures. PMID:30016722
Bioinformatics approach reveals the key role of C‑X‑C motif chemokine receptor 2 in endometriosis development. PMID:30015967
Increased Alternative Splicing as a Host Response to Edwardsiella ictaluri Infection in Catfish. PMID:30014301
Identification of SNPs potentially related to immune responses and growth performance in Litopenaeus vannamei by RNA-seq analyses. PMID:30013834
Identification of potential target genes in pancreatic ductal adenocarcinoma by bioinformatics analysis. PMID:30013637
Genome-Wide Characterization and Expression Analyses of Pleurotus ostreatus MYB Transcription Factors during Developmental Stages and under Heat Stress Based on de novo Sequenced Genome. PMID:30011913
A Liquid Chromatography with Tandem Mass Spectrometry-Based Proteomic Analysis of Cells Cultured in DMEM 10% FBS and Chemically Defined Medium Using Human Adipose-Derived Mesenchymal Stem Cells. PMID:30011845
A plant diterpene counteracts juvenile hormone-mediated gene regulation during Drosophila melanogaster larval development. PMID:30011330
Sex-Dependent Variation of Pumpkin (Cucurbita maxima cv. Big Max) Nectar and Nectaries as Determined by Proteomics and Metabolomics. PMID:30008725
Exosomal zinc transporter ZIP4 promotes cancer growth and is a novel diagnostic biomarker for pancreatic cancer. PMID:30007115
Socio-demographic, Clinical, and Genetic Determinants of Quality of Life in Lung Cancer Patients. PMID:30006595
Decoding the chromatin proteome of a single genomic locus by DNA sequencing. PMID:30005073
A Systems Biology Approach to Understanding the Pathophysiology of High-Grade Serous Ovarian Cancer: Focus on Iron and Fatty Acid Metabolism. PMID:30004845
Genome-wide association meta-analysis of age at first cannabis use. PMID:30003630
Nonredundant, Highly Connected MicroRNAs Control Functionality in Breast Cancer Networks. PMID:30003085
Gene expression profiles in neurological tissues during West Nile virus infection: a critical meta-analysis. PMID:30001706
FindSim: A Framework for Integrating Neuronal Data and Signaling Models. PMID:29997492
Transcriptional Alterations in the Trigeminal Ganglia, Nucleus and Peripheral Blood Mononuclear Cells in a Rat Orofacial Pain Model. PMID:29997476
The effect of chronic and acute stressors, and their interaction, on testes function: an experimental test during testicular recrudescence. PMID:29997161
Identification of differential gene expression profile from peripheral blood cells of military pilots with hypertension by RNA sequencing analysis. PMID:29996846
Molecular genetic overlap between migraine and major depressive disorder. PMID:29995844
CeleryDB: a genomic database for celery. PMID:29992323
A comprehensive review of web-based resources of non-coding RNAs for plant science research. PMID:29989090
Identifying differentially expressed genes from cross-site integrated data based on relative expression orderings. PMID:29989020
PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia. PMID:29988723
An integrated analysis of genome-wide DNA methylation and gene expression data in hepatocellular carcinoma. PMID:29988590
Shank3 mutation in a mouse model of autism leads to changes in the S-nitroso-proteome and affects key proteins involved in vesicle release and synaptic function. PMID:29988084
A promoter interaction map for cardiovascular disease genetics. PMID:29988018
Semantics for an Integrative and Immersive Pipeline Combining Visualization and Analysis of Molecular Data. PMID:29982236
A comprehensive analysis of the Korean fir (Abies koreana) genes expressed under heat stress using transcriptome analysis. PMID:29980711
A transcriptome study on Macrobrachium nipponense hepatopancreas experimentally challenged with white spot syndrome virus (WSSV). PMID:29979781
Characteristics of microbial communities and intestinal pathogenic bacteria for migrated Larus ridibundus in southwest China. PMID:29978594
Transcriptome analysis reveals candidate genes involved in splay leg syndrome in piglets. PMID:29978277
LCK as a Potential Therapeutic Target for Acute Rejection after Kidney Transplantation: A Bioinformatics Clue. PMID:29977931
Taxon-Driven Functional Shifts Associated with Storm Flow in an Urban Stream Microbial Community. PMID:29976643
Effects of Sepantronium Bromide (YM-155) on the Whole Transcriptome of MDA-MB-231 Cells: Highlight on Impaired ATR/ATM Fanconi Anemia DNA Damage Response. PMID:29976630
Expression and network analysis of YBX1 interactors for identification of new drug targets in lung adenocarcinoma. PMID:29973960
Transcriptome analysis of alternative splicing in peanut (Arachis hypogaea L.). PMID:29973157
Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism. PMID:29973148
Genetic modifiers of radon-induced lung cancer risk: a genome-wide interaction study in former uranium miners. PMID:29971594
Combining Targeted Metabolites Analysis and Transcriptomics to Reveal Chemical Composition Difference and Underlying Transcriptional Regulation in Maca (Lepidium Meyenii Walp.) Ecotypes. PMID:29970867
Switching roles for DNA and histone methylation depend on evolutionary ages of human endogenous retroviruses. PMID:29970451
Genomic variations and association study of agronomic traits in flax. PMID:29969983
ChemDIS-Mixture: an online tool for analyzing potential interaction effects of chemical mixtures. PMID:29968796
Gene expression-based drug repurposing to target aging. PMID:29959820
Prioritizing network communities. PMID:29959323
Non-classical monocytes as mediators of tissue destruction in arthritis. PMID:29959183
Feature Selection via Swarm Intelligence for Determining Protein Essentiality. PMID:29958434
Histology and Transcriptome Profiles of the Mammary Gland across Critical Windows of Development in Sprague Dawley Rats. PMID:29956080
Correlated Selection on Amino Acid Deletion and Replacement in Mammalian Protein Sequences. PMID:29955898
SLIDE - a web-based tool for interactive visualization of large-scale - omics data. PMID:29955804
Transferring knowledge of bacterial protein interaction networks to predict pathogen targeted human genes and immune signaling pathways: a case study on M. tuberculosis. PMID:29954330
Transcriptional and Translational Landscape of Equine Torovirus. PMID:29950409
HFSP: high speed homology-driven function annotation of proteins. PMID:29950013
Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations. PMID:29949999
Enumerating consistent sub-graphs of directed acyclic graphs: an insight into biomedical ontologies. PMID:29949985
Transcriptome analysis demonstrates that long noncoding RNA is involved in the hypoxic response in Larimichthys crocea. PMID:29948448
PanACEA: a bioinformatics tool for the exploration and visualization of bacterial pan-chromosomes. PMID:29945570
A whole-genome transcriptome analysis of articular chondrocytes in secondary osteoarthritis of the hip. PMID:29944724
Genome-wide association meta-analysis in 269,867 individuals identifies new genetic and functional links to intelligence. PMID:29942086
Genomewide phenotypic analysis of growth, cell morphogenesis, and cell cycle events in Escherichia coli. PMID:29941428
High-quality assembly of the reference genome for scarlet sage, Salvia splendens, an economically important ornamental plant. PMID:29931210
RBPMetaDB: a comprehensive annotation of mouse RNA-Seq datasets with perturbations of RNA-binding proteins. PMID:29931156
Potential candidate treatment agents for targeting of cholangiocarcinoma identified by gene expression profile analysis. PMID:29930804
Idiopathic Scoliosis Families Highlight Actin-Based and Microtubule-Based Cellular Projections and Extracellular Matrix in Disease Etiology. PMID:29930198
Pan-cancer adaptive immune resistance as defined by the Tumor Inflammation Signature (TIS): results from The Cancer Genome Atlas (TCGA). PMID:29929551
Exploring the molecular pathogenesis associated with T-cell prolymphocytic leukemia based on a comprehensive bioinformatics analysis. PMID:29928415
Transcriptome profiling analysis reveals biomarkers in colon cancer samples of various differentiation. PMID:29928385
Identification of proteins associated with paclitaxel resistance of epithelial ovarian cancer using iTRAQ-based proteomics. PMID:29928353
MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis. PMID:29927748
Elevated T cell levels in peripheral blood predict poor clinical response following rituximab treatment in new-onset type 1 diabetes. PMID:29925930
Regulators of Long-Term Memory Revealed by Mushroom Body-Specific Gene Expression Profiling in Drosophila melanogaster. PMID:29925565
A machine-learned analysis of human gene polymorphisms modulating persisting pain points to major roles of neuroimmune processes. PMID:29923268
Key Genes and Pathways Associated With Inner Ear Malformation in SOX10 p.R109W Mutation Pigs. PMID:29922125
Co-Expression Network Analysis of AMPK and Autophagy Gene Products during Adipocyte Differentiation. PMID:29921805
dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments. PMID:29921301
Effects of Experimental Terrestrialization on the Skin Mucus Proteome of African Lungfish (Protopterus dolloi). PMID:29915597
Uncovering global metabolic response to cordycepin production in Cordyceps militaris through transcriptome and genome-scale network-driven analysis. PMID:29915355
Massive expression of germ cell-specific genes is a hallmark of cancer and a potential target for novel treatment development. PMID:29907769
LncRNA expression profiling of BMSCs in osteonecrosis of the femoral head associated with increased adipogenic and decreased osteogenic differentiation. PMID:29904151
Deep Transcriptomic Analysis of Black Rockfish (Sebastes schlegelii) Provides New Insights on Responses to Acute Temperature Stress. PMID:29904092
Signature of Pareto optimization in the Escherichia coli proteome. PMID:29904084
System analysis of teratozoospermia mRNA profile based on integrated bioinformatics tools. PMID:29901159
Weighted gene co‑expression network analysis in identification of key genes and networks for ischemic‑reperfusion remodeling myocardium. PMID:29901145
Identification and functional analysis of differentially expressed genes associated with cerebral ischemia/reperfusion injury through bioinformatics methods. PMID:29901134
Proteomic comparison of the EWS-FLI1 expressing cells EF with NIH-3T3 and actin remodeling effect of (R/W)9 cell-penetrating peptide. PMID:29900093
Mapping biological process relationships and disease perturbations within a pathway network. PMID:29900005
Gas41 links histone acetylation to H2A.Z deposition and maintenance of embryonic stem cell identity. PMID:29900004
Quantitative phosphoproteomic analysis of the molecular substrates of sleep need. PMID:29899451
A data mining paradigm for identifying key factors in biological processes using gene expression data. PMID:29899432
The Holo-Transcriptome of the Zoantharian Protopalythoa variabilis (Cnidaria: Anthozoa): A Plentiful Source of Enzymes for Potential Application in Green Chemistry, Industrial and Pharmaceutical Biotechnology. PMID:29899267
Enhancer of zeste homolog 2 (Ezh2) controls bone formation and cell cycle progression during osteogenesis in mice. PMID:29899112
Secretome Screening Reveals Fibroblast Growth Factors as Novel Inhibitors of Viral Replication. PMID:29899088
Systematic Identification, Characterization, and Conservation of Adjacent-Gene Coregulation in the Budding Yeast Saccharomyces cerevisiae. PMID:29898982
Stratification of candidate genes for Parkinson's disease using weighted protein-protein interaction network analysis. PMID:29898659
Traditional and systems biology based drug discovery for the rare tumor syndrome neurofibromatosis type 2. PMID:29897904
BioSankey: Visualization of Microbial Communities Over Time. PMID:29897884
iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites. PMID:29897410
A resource for sustainable management: De novo assembly and annotation of the liver transcriptome of the Atlantic chub mackerel, Scomber colias. PMID:29896516
Comparative transcriptome analysis of dikaryotic mycelia and mature fruiting bodies in the edible mushroom Lentinula edodes. PMID:29895888
Prion-like Domains in Eukaryotic Viruses. PMID:29895872
Transcriptomic response to GABA-producing Lactobacillus plantarum CGMCC 1.2437T induced by L-MSG. PMID:29894506
EviNet: a web platform for network enrichment analysis with flexible definition of gene sets. PMID:29893885
Evidence of the Red-Queen Hypothesis from Accelerated Rates of Evolution of Genes Involved in Biotic Interactions in Pneumocystis. PMID:29893833
Transcriptome analysis of the threatened snail Ellobium chinense reveals candidate genes for adaptation and identifies SSRs for conservation genetics. PMID:29892840
Association analyses of more than 140,000 men identify 63 new prostate cancer susceptibility loci. PMID:29892016
Genome-Wide Identification and Characterization of Warming-Related Genes in Brassica rapa ssp. pekinensis. PMID:29891774
Chemoproteomics reveals baicalin activates hepatic CPT1 to ameliorate diet-induced obesity and hepatic steatosis. PMID:29891721
Comparative Proteomic Analysis of Rana chensinensis Oviduct. PMID:29890619
Differentially Expressed Genes in Osteomyelitis Induced by Staphylococcus aureus Infection. PMID:29887852
Genome-wide association study identifies genes associated with neuropathy in patients with head and neck cancer. PMID:29884837
Gene set analysis methods: a systematic comparison. PMID:29881462
Family specific genetic predisposition to breast cancer: results from Tunisian whole exome sequenced breast cancer cases. PMID:29879995
Identification of specific metabolic pathways as druggable targets regulating the sensitivity to cyanide poisoning. PMID:29879736
LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis. PMID:29878235
Genomic atlas of the human plasma proteome. PMID:29875488
Hypoxia-derived exosomes induce putative altered pathways in biosynthesis and ion regulatory channels in glioblastoma cells. PMID:29872742
Construction of a specific SVM classifier and identification of molecular markers for lung adenocarcinoma based on lncRNA-miRNA-mRNA network. PMID:29872324
RNA Sequencing Reveals Novel Transcripts from Sympathetic Stellate Ganglia During Cardiac Sympathetic Hyperactivity. PMID:29872217
Expanding the horizons of microRNA bioinformatics. PMID:29871895
MGOGP: a gene module-based heuristic algorithm for cancer-related gene prioritization. PMID:29871590
A comparison of mechanistic signaling pathway activity analysis methods. PMID:29868818
Identification of Putative Precursor Genes for the Biosynthesis of Cannabinoid-Like Compound in Radula marginata. PMID:29868043
Metagenomic Approaches to Investigate the Contribution of the Vineyard Environment to the Quality of Wine Fermentation: Potentials and Difficulties. PMID:29867889
Evolutionary divergence of 3' UTRs in cichlid fishes. PMID:29866078
Analysis and expression of the carotenoid biosynthesis genes from Deinococcus wulumuqiensis R12 in engineered Escherichia coli. PMID:29860613
De novo sequencing, assembly and characterisation of Aloe vera transcriptome and analysis of expression profiles of genes related to saponin and anthraquinone metabolism. PMID:29859051
Strong correlation of downregulated genes related to synaptic transmission and mitochondria in post-mortem autism cerebral cortex. PMID:29859039
A Deep Learning Framework for Robust and Accurate Prediction of ncRNA-Protein Interactions Using Evolutionary Information. PMID:29858068
The proteome of perilymph in patients with vestibular schwannoma. A possibility to identify biomarkers for tumor associated hearing loss? PMID:29856847
Melittin Constrains the Expression of Identified Key Genes Associated with Bladder Cancer. PMID:29854840
Leveraging Collaborative Filtering to Accelerate Rare Disease Diagnosis. PMID:29854225
Deep Learning Meets Biomedical Ontologies: Knowledge Embeddings for Epilepsy. PMID:29854192
Network Pharmacology-Based Approach to Investigate the Mechanisms of Hedyotis diffusa Willd. in the Treatment of Gastric Cancer. PMID:29853970
Identification of key genes in rheumatoid arthritis and osteoarthritis based on bioinformatics analysis. PMID:29851858
Systems analysis of phosphate-limitation-induced lipid accumulation by the oleaginous yeast Rhodosporidium toruloides. PMID:29849765
Gene family innovation, conservation and loss on the animal stem lineage. PMID:29848444
Metabolic co-dependence drives the evolutionarily ancient Hydra-Chlorella symbiosis. PMID:29848439
Chemical-Induced Phenotypes at CTD Help Inform the Predisease State and Construct Adverse Outcome Pathways. PMID:29846728
RNA‑sequencing analysis of aberrantly expressed long non‑coding RNAs and mRNAs in a mouse model of ventilator‑induced lung injury. PMID:29845294
Genes associated with inflammation and the cell cycle may serve as biomarkers for the diagnosis and prognosis of acute myocardial infarction in a Chinese population. PMID:29845217
Divergent and convergent evolution of housekeeping genes in human-pig lineage. PMID:29844985
Study of 300,486 individuals identifies 148 independent genetic loci influencing general cognitive function. PMID:29844566
Molecular Composition of Vestibular Hair Bundles. PMID:29844221
Genome sequencing and protein domain annotations of Korean Hanwoo cattle identify Hanwoo-specific immunity-related and other novel genes. PMID:29843617
Landscape of copy number variations in Bos taurus: individual - and inter-breed variability. PMID:29843606
Transcriptome analysis of the typical freshwater rhodophytes Sheathia arcuata grown under different light intensities. PMID:29813098
Identification of key candidate genes and pathways in hepatocellular carcinoma by integrated bioinformatical analysis. PMID:29805517
An ERK-Dependent Feedback Mechanism Prevents Hematopoietic Stem Cell Exhaustion. PMID:29804890
Sorting Five Human Tumor Types Reveals Specific Biomarkers and Background Classification Genes. PMID:29802335
RNA-binding proteins with basic-acidic dipeptide (BAD) domains self-assemble and aggregate in Alzheimer's disease. PMID:29802200
QTLTableMiner++: semantic mining of QTL tables in scientific articles. PMID:29801439
GIANT 2.0: genome-scale integrated analysis of gene networks in tissues. PMID:29800226
Elevated Nrf-2 responses are insufficient to mitigate protein carbonylation in hepatospecific PTEN deletion mice. PMID:29799837
Transcriptomic response of breast cancer cells to anacardic acid. PMID:29795261
Towards a complete map of the human long non-coding RNA transcriptome. PMID:29795125
Identification of Biological Targets of Therapeutic Intervention for Hepatocellular Carcinoma by Integrated Bioinformatical Analysis. PMID:29795057
Identification of differentially expressed genes in childhood asthma. PMID:29794786
Genome-Wide Analysis of Multidrug and Toxic Compound Extrusion (MATE) Family in Gossypium raimondii and Gossypium arboreum and Its Expression Analysis Under Salt, Cadmium, and Drought Stress. PMID:29794162
De novo assembly and annotation of Hyalomma dromedarii tick (Acari: Ixodidae) sialotranscriptome with regard to gender differences in gene expression. PMID:29793520
Embryonic transcriptome and proteome analyses on hepatic lipid metabolism in chickens divergently selected for abdominal fat content. PMID:29792171
Long non-coding RNA Gm2199 rescues liver injury and promotes hepatocyte proliferation through the upregulation of ERK1/2. PMID:29789577
Transcriptome analysis of the adult human Klinefelter testis and cellularity-matched controls reveals disturbed differentiation of Sertoli- and Leydig cells. PMID:29789566
Correlated Gene Expression and Anatomical Communication Support Synchronized Brain Activity in the Mouse Functional Connectome. PMID:29789379
WEGO 2.0: a web tool for analyzing and plotting GO annotations, 2018 update. PMID:29788377
Gender-Specific Effects of Selection for Drinking in the Dark on the Network Roles of Coding and Noncoding RNAs. PMID:29786871
Molecular characterization of proton beam-induced mutations in soybean using genotyping-by-sequencing. PMID:29785615
A genome-wide cross-trait analysis from UK Biobank highlights the shared genetic architecture of asthma and allergic diseases. PMID:29785011
Integration of multi-omics data and deep phenotyping enables prediction of cytokine responses. PMID:29784908
Quantitative Proteome and Phosphoproteome Analyses of Streptomyces coelicolor Reveal Proteins and Phosphoproteins Modulating Differentiation and Secondary Metabolism. PMID:29784711
Differences between fast and slow muscles in scallops revealed through proteomics and transcriptomics. PMID:29783952
Transcriptomic Analysis of Pseudoscorpion Venom Reveals a Unique Cocktail Dominated by Enzymes and Protease Inhibitors. PMID:29783636
Ontology translation: A case study on translating the Gene Ontology from English to German. PMID:29780975
Comparative Metatranscriptomics of Wheat Rhizosphere Microbiomes in Disease Suppressive and Non-suppressive Soils for Rhizoctonia solani AG8. PMID:29780371
Systems Biology-Based Investigation of Host-Plasmodium Interactions. PMID:29779985
Altered mitochondrial acetylation profiles in a kainic acid model of temporal lobe epilepsy. PMID:29778462
Progression of whole-blood transcriptional signatures from interferon-induced to neutrophil-associated patterns in severe influenza. PMID:29777224
Developmental vascular regression is regulated by a Wnt/β-catenin, MYC and CDKN1A pathway that controls cell proliferation and cell death. PMID:29777010
Ecological Engineering Helps Maximize Function in Algal Oil Production. PMID:29776927
The developmental transcriptomes of two sea biscuit species with differing larval types. PMID:29776340
Complete genome sequence of "Thiodictyon syntrophicum" sp. nov. strain Cad16T, a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno. PMID:29774086
Computational identification of specific genes for glioblastoma stem-like cells identity. PMID:29773872
Transcriptome and miRNA analyses of the response to Corynespora cassiicola in cucumber. PMID:29773833
The aquatic animals' transcriptome resource for comparative functional analysis. PMID:29764375
Using ZFIN: Data Types, Organization, and Retrieval. PMID:29761463
A Primer for the Rat Genome Database (RGD). PMID:29761460
EuPathDB: The Eukaryotic Pathogen Genomics Database Resource. PMID:29761457
PomBase: The Scientific Resource for Fission Yeast. PMID:29761456
Using the Candida Genome Database. PMID:29761455
Genomewide DNA Methylation Responses in Patients with β-Thalassemia Treated with Yisui Shengxue Granules (). PMID:29761313
Anti-tumoral effects of exercise on hepatocellular carcinoma growth. PMID:29761175
Transcriptome analysis of alcohol-treated microglia reveals downregulation of beta amyloid phagocytosis. PMID:29759078
The Algicidal Fungus Trametes versicolor F21a Eliminating Blue Algae via Genes Encoding Degradation Enzymes and Metabolic Pathways Revealed by Transcriptomic Analysis. PMID:29755442
Decoding Common Features of Neurodegenerative Disorders: From Differentially Expressed Genes to Pathways. PMID:29755292
Effects of Zhizi Chuanxiong Capsule () on the Abnormal Methylation in Rabbits with Atherosclerosis. PMID:29752693
Microarray‑based bioinformatics analysis of the prospective target gene network of key miRNAs influenced by long non‑coding RNA PVT1 in HCC. PMID:29749550
Bioinformatics analysis of microarray data to reveal the pathogenesis of brain ischemia. PMID:29749511
Functional signaling and gene regulatory networks between the oocyte and the surrounding cumulus cells. PMID:29747587
Identification of novel drug targets for diamond-blackfan anemia based on RPS19 gene mutation using protein-protein interaction network. PMID:29745857
Multi-target drug repositioning by bipartite block-wise sparse multi-task learning. PMID:29745839
GraphTeams: a method for discovering spatial gene clusters in Hi-C sequencing data. PMID:29745835
Regulation of osteogenesis by long noncoding RNAs: An epigenetic mechanism contributing to bone formation. PMID:29745821
Transcriptome sequencing and analysis during seed growth and development in Euryale ferox Salisb. PMID:29743016
Widespread epigenomic, transcriptomic and proteomic differences between hip osteophytic and articular chondrocytes in osteoarthritis. PMID:29741735
PANNZER2: a rapid functional annotation web server. PMID:29741643
Candidate genes associated with red colour formation revealed by comparative genomic variant analysis of red- and green-skinned fruits of Japanese apricot (Prunus mume). PMID:29740511
Identification of target genes regulated by the Drosophila histone methyltransferase Eggless reveals a role of Decapentaplegic in apoptotic signaling. PMID:29740006
De novo and inherited private variants in MAP1B in periventricular nodular heterotopia. PMID:29738522
Identifying Cancer Specific Driver Modules Using a Network-Based Method. PMID:29738475
Activation of disease resistance against Botryosphaeria dothidea by downregulating the expression of MdSYP121 in apple. PMID:29736249
Data Mining Mycobacterium tuberculosis Pathogenic Gene Transcription Factors and Their Regulatory Network Nodes. PMID:29725597
High quality draft genome sequences of Mycoplasma agassizii strains PS6T and 723 isolated from Gopherus tortoises with upper respiratory tract disease. PMID:29725499
ResearchMaps.org for integrating and planning research. PMID:29723213
Strategies for high-altitude adaptation revealed from high-quality draft genome of non-violacein producing Janthinobacterium lividum ERGS5:01. PMID:29721151
Sex Determination in Ceratopteris richardii Is Accompanied by Transcriptome Changes That Drive Epigenetic Reprogramming of the Young Gametophyte. PMID:29720393
Identification of key gene modules for human osteosarcoma by co-expression analysis. PMID:29720180
Biomarker enhanced risk prediction for development of AKI after cardiac surgery. PMID:29720115
Adar3 Is Involved in Learning and Memory in Mice. PMID:29719497
A Strategy for Discovery of Endocrine Interactions with Application to Whole-Body Metabolism. PMID:29719227
PVCbase: an integrated web resource for the PVC bacterial proteomes. PMID:29718141
Exploring intrinsically disordered proteins in Chlamydomonas reinhardtii. PMID:29717210
Functional and structural characterization of osteocytic MLO-Y4 cell proteins encoded by genes differentially expressed in response to mechanical signals in vitro. PMID:29712973
Environmental fluctuations accelerate molecular evolution of thermal tolerance in a marine diatom. PMID:29712900
Remote Memory and Cortical Synaptic Plasticity Require Neuronal CCCTC-Binding Factor (CTCF). PMID:29712785
Development of a computational promoter with highly efficient expression in tumors. PMID:29703163
Transcriptome profiling provides insights into dormancy release during cold storage of Lilium pumilum. PMID:29703130
Regularized Multi-View Subspace Clustering for Common Modules Across Cancer Stages. PMID:29701681
A comprehensive comparison of four species of Onchidiidae provides insights on the morphological and molecular adaptations of invertebrates from shallow seas to wetlands. PMID:29698429
The multiple myeloma risk allele at 5q15 lowers ELL2 expression and increases ribosomal gene expression. PMID:29695719
Tumor-Independent Host Secretomes Induced By Angiogenesis and Immune-Checkpoint Inhibitors. PMID:29695634
Transcriptomic analysis between self- and cross-pollinated pistils of tea plants (Camellia sinensis). PMID:29695246
Identifying genes as potential prognostic indicators in patients with serous ovarian cancer resistant to carboplatin using integrated bioinformatics analysis. PMID:29693178
Inflammatory genes are novel prognostic biomarkers for colorectal cancer. PMID:29693170
Analysis of NFKB2‑mediated regulation of mechanisms underlying the development of Hodgkin's lymphoma. PMID:29693141
Litopenaeus vannamei Transcriptome Profile of Populations Evaluated for Growth Performance and Exposed to White Spot Syndrome Virus (WSSV). PMID:29692800
Updated regulation curation model at the Saccharomyces Genome Database. PMID:29688362
Identification of errors in the IEDB using ontologies. PMID:29688357
Chromosome-scale assembly of the Monopterus genome. PMID:29688346
EMUDRA: Ensemble of Multiple Drug Repositioning Approaches to improve prediction accuracy. PMID:29688306
Community-driven roadmap for integrated disease maps. PMID:29688273
Microarray Analysis of the Molecular Mechanism Involved in Parkinson's Disease. PMID:29686831
High-quality draft genome of the methanotroph Methylovulum psychrotolerans Str. HV10-M2 isolated from plant material at a high-altitude environment. PMID:29686747
A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development. PMID:29686312
Systemic surfaceome profiling identifies target antigens for immune-based therapy in subtypes of advanced prostate cancer. PMID:29686080
Navigating the disease landscape: knowledge representations for contextualizing molecular signatures. PMID:29684165
High quality draft genome sequence of Mycoplasma testudineum strain BH29T, isolated from the respiratory tract of a desert tortoise. PMID:29682170
Draft genome sequence of Fermentimonas caenicola strain SIT8, isolated from the human gut. PMID:29682169
Genome sequence of Planktotalea frisia type strain (SH6-1T), a representative of the Roseobacter group isolated from the North Sea during a phytoplankton bloom. PMID:29682168
De Novo Sequencing of a Sparassis latifolia Genome and Its Associated Comparative Analyses. PMID:29682127
Proteome-wide analysis of cysteine oxidation reveals metabolic sensitivity to redox stress. PMID:29679077
Divergent genome evolution caused by regional variation in DNA gain and loss between human and mouse. PMID:29677183
Genome sequence and description of Gracilibacillus timonensis sp. nov. strain Marseille-P2481T , a moderate halophilic bacterium isolated from the human gut microflora. PMID:29675845
FSPP: A Tool for Genome-Wide Prediction of smORF-Encoded Peptides and Their Functions. PMID:29675032
Implications of publicly available genomic data resources in searching for therapeutic targets of obesity and type 2 diabetes. PMID:29674722
Complete Genome Sequence of the Heavy-Metal-Tolerant Endophytic Type Strain of Salinicola tamaricis. PMID:29674561
Menin regulates the serine biosynthetic pathway in Ewing sarcoma. PMID:29672864
RNA-Seq transcriptome analysis of Amaranthus palmeri with differential tolerance to glufosinate herbicide. PMID:29672568
Comparisons of gene coexpression network modules in breast cancer and ovarian cancer. PMID:29671401
Identification of a cold-tolerant locus in rice (Oryza sativa L.) using bulked segregant analysis with a next-generation sequencing strategy. PMID:29671148
Genomic prediction applied to high-biomass sorghum for bioenergy production. PMID:29670457
Starvation during pregnancy impairs fetal oogenesis and folliculogenesis in offspring in the mouse. PMID:29670080
miRNAome expression profiles in the gonads of adult Melopsittacus undulatus. PMID:29666766
p52 expression enhances lung cancer progression. PMID:29666445
Whole Genome Sequence of an Edible and Potential Medicinal Fungus, Cordyceps guangdongensis. PMID:29666196
Effect of Larval Nutrition on Maternal mRNA Contribution to the Drosophila Egg. PMID:29666195
The LuxR Regulators PcoR and RfiA Co-regulate Antimicrobial Peptide and Alginate Production in Pseudomonas corrugata. PMID:29662475
miR-148b-3p functions as a tumor suppressor in GISTs by directly targeting KIT. PMID:29661252
Synergistic co-regulation and competition by a SOX9-GLI-FOXA phasic transcriptional network coordinate chondrocyte differentiation transitions. PMID:29659575
Biocuration: Distilling data into knowledge. PMID:29659566
Analysis of potential genes and pathways associated with the colorectal normal mucosa-adenoma-carcinoma sequence. PMID:29659199
Key signaling pathways, genes and transcription factors associated with hepatocellular carcinoma. PMID:29658607
Detecting Disease Specific Pathway Substructures through an Integrated Systems Biology Approach. PMID:29657291
Transcriptome Network Analysis Reveals Aging-Related Mitochondrial and Proteasomal Dysfunction and Immune Activation in Human Thyroid. PMID:29652618
Lymphatic exosomes promote dendritic cell migration along guidance cues. PMID:29650776
Gene-level differential analysis at transcript-level resolution. PMID:29650040
Systematic characterization of autophagy-related genes during the adipocyte differentiation using public-access data. PMID:29643990
Peripherally derived macrophages can engraft the brain independent of irradiation and maintain an identity distinct from microglia. PMID:29643186
Global Transcriptome Analysis of Brown Adipose Tissue of Diet-Induced Obese Mice. PMID:29642370
BiOnIC: A Catalog of User Interactions with Biomedical Ontologies. PMID:29637199
Reduction of Proliferating Olfactory Cells and Low Expression of Extracellular Matrix Genes Are Hallmarks of the Aged Olfactory Mucosa. PMID:29636678
Massive mining of publicly available RNA-seq data from human and mouse. PMID:29636450
Biological signaling pathways and potential mathematical network representations: biological discovery through optimization. PMID:29635835
The latent geometry of the human protein interaction network. PMID:29635317
Profiling expression of coding genes, long noncoding RNA, and circular RNA in lung adenocarcinoma by ribosomal RNA-depleted RNA sequencing. PMID:29632808
Open chromatin dynamics reveals stage-specific transcriptional networks in hiPSC-based neurodevelopmental model. PMID:29631039
Protein CoAlation and antioxidant function of coenzyme A in prokaryotic cells. PMID:29626155
A Beginner's Guide to Analysis of RNA Sequencing Data. PMID:29624415
New computational approaches to understanding molecular protein function. PMID:29621256
Role of COL6A3 in colorectal cancer. PMID:29620224
A study of the key genes and inflammatory signaling pathways involved in HLA-B27-associated acute anterior uveitis families. PMID:29620146
Proteomic analysis of protein interactions between Eimeria maxima sporozoites and chicken jejunal epithelial cells by shotgun LC-MS/MS. PMID:29618377
From SNPs to pathways: Biological interpretation of type 2 diabetes (T2DM) genome wide association study (GWAS) results. PMID:29617380
A comprehensive analysis of the predicted targets of miR-642b-3p associated with the long non-coding RNA HOXA11-AS in NSCLC cells. PMID:29616096
MorphDB: Prioritizing Genes for Specialized Metabolism Pathways and Gene Ontology Categories in Plants. PMID:29616063
De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution. PMID:29615780
MTGO: PPI Network Analysis Via Topological and Functional Module Identification. PMID:29615773
Human Sertoli cells support high levels of Zika virus replication and persistence. PMID:29615760
Modeling and rescue of defective blood-brain barrier function of induced brain microvascular endothelial cells from childhood cerebral adrenoleukodystrophy patients. PMID:29615068
Pairwise gene GO-based measures for biclustering of high-dimensional expression data. PMID:29610579
Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss. PMID:29608732
A computational biology approach of a genome-wide screen connected miRNAs to obesity and type 2 diabetes. PMID:29605715
The non-human primate kidney transcriptome in fetal development. PMID:29603257
MicroRNA Expression Levels Are Altered in the Cerebrospinal Fluid of Patients with Young-Onset Alzheimer's Disease. PMID:29603092
Functional Precision Medicine Identifies Novel Druggable Targets and Therapeutic Options in Head and Neck Cancer. PMID:29599409
Identification of key genes and miRNAs associated with carotid atherosclerosis based on mRNA-seq data. PMID:29595698
Molecular cloning, expression, and functional characterization of the β-agarase AgaB-4 from Paenibacillus agarexedens. PMID:29594843
Metazoan Parasite Vaccines: Present Status and Future Prospects. PMID:29594064
Circulating MicroRNA Expression Levels Associated With Internet Gaming Disorder. PMID:29593587
Automated brightfield morphometry of 3D organoid populations by OrganoSeg. PMID:29593296
Cross-species multiple environmental stress responses: An integrated approach to identify candidate genes for multiple stress tolerance in sorghum (Sorghum bicolor (L.) Moench) and related model species. PMID:29590108
Constraints on signaling network logic reveal functional subgraphs on Multiple Myeloma OMIC data. PMID:29589566
A hidden Markov tree model for testing multiple hypotheses corresponding to Gene Ontology gene sets. PMID:29587646
Transcriptional regulatory networks underlying gene expression changes in Huntington's disease. PMID:29581148
Identification of a newly described OsHV-1 µvar from the North Adriatic Sea (Italy). PMID:29580370
Where to search top-K biomedical ontologies? PMID:29579141
In silico identification of microRNAs predicted to regulate N-myristoyltransferase and Methionine Aminopeptidase 2 functions in cancer and infectious diseases. PMID:29579063
Gene microarray analysis of lncRNA and mRNA expression profiles in patients with high‑grade ovarian serous cancer. PMID:29577163
Role for Wnt Signaling in Retinal Neuropil Development: Analysis via RNA-Seq and In Vivo Somatic CRISPR Mutagenesis. PMID:29576390
Interpretation of biological experiments changes with evolution of the Gene Ontology and its annotations. PMID:29572502
Identification of potential key protein interaction networks of BK virus nephropathy in patients receiving kidney transplantation. PMID:29567951
Transcriptomic characterization of MRI contrast with focus on the T1-w/T2-w ratio in the cerebral cortex. PMID:29567503
Sigmoid colon mucosal gene expression supports alterations of neuronal signaling in irritable bowel syndrome with constipation. PMID:29565640
RNA cytosine methylation and methyltransferases mediate chromatin organization and 5-azacytidine response and resistance in leukaemia. PMID:29563491
Inter-replicon Gene Flow Contributes to Transcriptional Integration in the Sinorhizobium meliloti Multipartite Genome. PMID:29563186
Screening of Genes Related to Early and Late Flowering in Tree Peony Based on Bulked Segregant RNA Sequencing and Verification by Quantitative Real-Time PCR. PMID:29562683
Transcriptome Analysis of Epithelioma Papulosum Cyprini Cells Infected by Reovirus Isolated from Allogynogenetic Silver Crucian Carp. PMID:29562634
Comparative transcriptome profiling of the human and mouse dorsal root ganglia: an RNA-seq-based resource for pain and sensory neuroscience research. PMID:29561359
QSurface: fast identification of surface expression markers in cancers. PMID:29560830
The mRNA and miRNA transcriptomic landscape of Panax ginseng under the high ambient temperature. PMID:29560829
A homologous mapping method for three-dimensional reconstruction of protein networks reveals disease-associated mutations. PMID:29560828
System analysis of the regulation of the immune response by CD147 and FOXC1 in cancer cell lines. PMID:29560120
Genome-Wide Identification and Characterization of Long Non-Coding RNA in Wheat Roots in Response to Ca2+ Channel Blocker. PMID:29559983
Molecular Networks of Postia placenta Involved in Degradation of Lignocellulosic Biomass Revealed from Metadata Analysis of Open Access Gene Expression Data. PMID:29559843
New drug candidates for treatment of atypical meningiomas: An integrated approach using gene expression signatures for drug repurposing. PMID:29558515
Vascular restenosis in coronary artery bypass grafting might be associated with VEGF-C/VEGFR-3 signaling pathway. PMID:29557990
U-Index, a dataset and an impact metric for informatics tools and databases. PMID:29557976
Human blood gene signature as a marker for smoking exposure: computational approaches of the top ranked teams in the sbv IMPROVER Systems Toxicology challenge. PMID:29556588
Species translatable blood gene signature as a marker of exposure to smoking: computational approaches of the top ranked teams in the sbv IMPROVER Systems Toxicology challenge. PMID:29556587
Studying microbial functionality within the gut ecosystem by systems biology. PMID:29556373
Identification of functional modules induced by bare-metal stents and paclitaxel-eluting stents in coronary heart disease. PMID:29556263
Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing. PMID:29554982
Transcriptome profiling of genes related to light-induced anthocyanin biosynthesis in eggplant (Solanum melongena L.) before purple color becomes evident. PMID:29554865
Mesenchymal Stem Cells Isolated from the Anterior Cruciate Ligament: Characterization and Comparison of Cells from Young and Old Donors. PMID:29554721
The Pathway Coexpression Network: Revealing pathway relationships. PMID:29554099
Identification and analysis of hub genes and networks related to hypoxia preconditioning in mice (No 035215). PMID:29552280
Proceedings of the 2017 annual meeting of the Fetal Alcohol Spectrum Disorders study group. PMID:29550584
Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness. PMID:29549885
Comprehensive analysis of differential expression profiles reveals potential biomarkers associated with the cell cycle and regulated by p53 in human small cell lung cancer. PMID:29545845
Comprehensive subcellular topologies of polypeptides in Streptomyces. PMID:29544487
Discovery and validation of a glioblastoma co-expressed gene module. PMID:29541392
LINC00152 is a potential biomarker involved in the modulation of biological characteristics of residual colorectal cancer cells following chemoradiotherapy. PMID:29541183
LMTK3 confers chemo-resistance in breast cancer. PMID:29540829
A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex. PMID:29539641
Genomic insights into the broad antifungal activity, plant-probiotic properties, and their regulation, in Pseudomonas donghuensis strain SVBP6. PMID:29538430
Hepatitis C virus core impacts expression of miR122 and miR204 involved in carcinogenic progression via regulation of TGFBRAP1 and HOTTIP expression. PMID:29535540
MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein-Protein Network Mapping. PMID:29534977
Genome-Wide Analysis of the PYL Gene Family and Identification of PYL Genes That Respond to Abiotic Stress in Brassica napus. PMID:29534558
Identification of the key genes associated with neuropathic pain. PMID:29532897
Investigation of mechanisms of mesenchymal stem cells for treatment of diabetic nephropathy via construction of a miRNA-TF-mRNA network. PMID:29532746
Multiscale analysis of a regenerative therapy for treatment of volumetric muscle loss injury. PMID:29531830
Effect of single nucleotide polymorphisms on intramuscular fat content in Hungarian Simmental cattle. PMID:29531185
Argonaute2 and LaminB modulate gene expression by controlling chromatin topology. PMID:29529026
LAILAPS-QSM: A RESTful API and JAVA library for semantic query suggestions. PMID:29529024
Insulin resistance causes inflammation in adipose tissue. PMID:29528335
Indigenous Pseudomonas spp. Strains from the Olive (Olea europaea L.) Rhizosphere as Effective Biocontrol Agents against Verticillium dahliae: From the Host Roots to the Bacterial Genomes. PMID:29527195
A Novel Five-Node Feed-Forward Loop Unravels miRNA-Gene-TF Regulatory Relationships in Ischemic Stroke. PMID:29524052
The bromodomain-containing protein Ibd1 links multiple chromatin-related protein complexes to highly expressed genes in Tetrahymena thermophila. PMID:29523178
Co-expression of TIMP-1 and its cell surface binding partner CD63 in glioblastomas. PMID:29523123
Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides. PMID:29521624
Association study between copy number variation and beef fatty acid profile of Nellore cattle. PMID:29520708
Functional Validation of Candidate Genes Detected by Genomic Feature Models. PMID:29519937
CD40 ligand deficiency causes functional defects of peripheral neutrophils that are improved by exogenous IFN-γ. PMID:29518426
Why West? Comparisons of clinical, genetic and molecular features of infants with and without spasms. PMID:29518120
Primate fetal hepatic responses to maternal obesity: epigenetic signalling pathways and lipid accumulation. PMID:29516496
Gene expression differs in susceptible and resistant amphibians exposed to Batrachochytrium dendrobatidis. PMID:29515828
Genome-wide transcriptome analysis identifies alternative splicing regulatory network and key splicing factors in mouse and human psoriasis. PMID:29515135
A peripheral blood transcriptomic signature predicts autoantibody development in infants at risk of type 1 diabetes. PMID:29515040
Spatiotemporal compartmentalization of hepatic NADH and NADPH metabolism. PMID:29514978
Epistasis analysis of microRNAs on pathological stages in colon cancer based on an Empirical Bayesian Elastic Net method. PMID:29513198
Identification of potential genes and miRNAs associated with sepsis based on microarray analysis. PMID:29512785
Screening for key lncRNAs in the progression of gallbladder cancer using bioinformatics analyses. PMID:29512694
Evaluation of involved proteins in colon adenocarcinoma: an interactome analysis. PMID:29511483
The chemokine receptor CCR1 is identified in mast cell-derived exosomes. PMID:29511430
A multi-omic analysis reveals the regulatory role of CD180 during the response of macrophages to Borrelia burgdorferi. PMID:29511161
An integrative transcriptomic approach to identify depot differences in genes and microRNAs in adipose tissues from high fat fed mice. PMID:29507687
Analysis of a gene panel for targeted sequencing of colorectal cancer samples. PMID:29507673
Brain-specific functional relationship networks inform autism spectrum disorder gene prediction. PMID:29507298
Petri net-based prediction of therapeutic targets that recover abnormally phosphorylated proteins in muscle atrophy. PMID:29506508
The Immunome of Colon Cancer: Functional In Silico Analysis of Antigenic Proteins Deduced from IgG Microarray Profiling. PMID:29505855
TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities. PMID:29505613
Hereditary cancer genes are highly susceptible to splicing mutations. PMID:29505604
Novel candidate genes important for asthma and hypertension comorbidity revealed from associative gene networks. PMID:29504915
Gene expression in retinal ischemic post-conditioning. PMID:29504043
Transcriptome analysis of wheat seedling and spike tissues in the hybrid Jingmai 8 uncovered genes involved in heterosis. PMID:29504038
Effect of Qinghuang Powder () Combined with Bupi Yishen Decoction () in Treating Patients with Refractory Cytopenia with Multilineage Dysplasia through Regulating DNA Methylation. PMID:29500545
Identification of genomic differences among peripheral arterial beds in atherosclerotic and healthy arteries. PMID:29500419
The genome sequence of 'Kurodagosun', a major carrot variety in Japan and China, reveals insights into biological research and carrot breeding. PMID:29497811
Genetic variants in two pathways influence serum urate levels and gout risk: a systematic pathway analysis. PMID:29497127
Landscape of the spliced leader trans-splicing mechanism in Schistosoma mansoni. PMID:29497070
Quantitative proteomic and phosphoproteomic comparison of human colon cancer DLD-1 cells differing in ploidy and chromosome stability. PMID:29496963
Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism. PMID:29496885
Direct Reprogramming of Spiral Ganglion Non-neuronal Cells into Neurons: Toward Ameliorating Sensorineural Hearing Loss by Gene Therapy. PMID:29492404
Transcriptomic data reanalysis allows for a contribution of embryonic transcriptional change-induced gene expression reprogramming in transgenerational epigenetic inheritance. PMID:29492289
Surfaceome and Proteosurfaceome in Parietal Monoderm Bacteria: Focus on Protein Cell-Surface Display. PMID:29491848
Mutations in DNA repair genes are associated with increased neo-antigen load and activated T cell infiltration in lung adenocarcinoma. PMID:29487705
Different Modes of Gene Duplication Show Divergent Evolutionary Patterns and Contribute Differently to the Expansion of Gene Families Involved in Important Fruit Traits in Pear (Pyrus bretschneideri). PMID:29487610
Investigation of hypoxia networks in ovarian cancer via bioinformatics analysis. PMID:29482638
Unexplored therapeutic opportunities in the human genome. PMID:29472638
PANDA: Protein function prediction using domain architecture and affinity propagation. PMID:29472600
Evolution, functional differentiation, and co-expression of the RLK gene family revealed in Jilin ginseng, Panax ginseng C.A. Meyer. PMID:29468273
Potential prognostic biomarkers identified by DNA methylation profiling analysis for patients with lung adenocarcinoma. PMID:29467875
Toward an integrated map of genetic interactions in cancer cells. PMID:29467179
Network modules uncover mechanisms of skeletal muscle dysfunction in COPD patients. PMID:29463285
Mendelian Disease Associations Reveal Novel Insights into Inflammatory Bowel Disease. PMID:29462399
Exploring autophagy with Gene Ontology. PMID:29455577
AOP-DB: A database resource for the exploration of Adverse Outcome Pathways through integrated association networks. PMID:29454060
Transcriptomics reveals a cross-modulatory effect between riboflavin and iron and outlines responses to riboflavin biosynthesis and uptake in Vibrio cholerae. PMID:29453341
Species-specific regulation of angiogenesis by glucocorticoids reveals contrasting effects on inflammatory and angiogenic pathways. PMID:29447208
A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts. PMID:29447159
Time- and polarity-dependent proteomic changes associated with homeostatic scaling at central synapses. PMID:29447110
Urine proteomics of primary membranous nephropathy using nanoscale liquid chromatography tandem mass spectrometry analysis. PMID:29445323
Draft genomes of two blister beetles Hycleus cichorii and Hycleus phaleratus. PMID:29444297
Increased proteomic complexity in Drosophila hybrids during development. PMID:29441361
Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology. PMID:29440116
Exploring the Antimicrobial Action of Quaternary Amines against Acinetobacter baumannii. PMID:29437928
Mutational Pleiotropy and the Strength of Stabilizing Selection Within and Between Functional Modules of Gene Expression. PMID:29437825
hsa-mir183/EGR1-mediated regulation of E2F1 is required for CML stem/progenitor cell survival. PMID:29437554
Microarray analysis for the identification of specific proteins and functional modules involved in the process of hepatocellular carcinoma originating from cirrhotic liver. PMID:29436633
Gene expression profile analysis of the progression of carotid atherosclerotic plaques. PMID:29436628
microRNA expression profiles of scar and normal tissue from patients with posterior urethral stricture caused by pelvic fracture urethral distraction defects. PMID:29436608
Genome sequence and description of Haloferax massiliense sp. nov., a new halophilic archaeon isolated from the human gut. PMID:29435649
Bioinformatical analysis of gene expression signatures of different glioma subtypes. PMID:29435008
Bioinformatic analysis of gene expression profiles of pituitary gonadotroph adenomas. PMID:29434861
Comprehensive characterization of cancer genes in hepatocellular carcinoma genomes. PMID:29434842
Matrine Is Identified as a Novel Macropinocytosis Inducer by a Network Target Approach. PMID:29434546
Quantification of glioblastoma mass effect by lateral ventricle displacement. PMID:29434275
Transcriptome analysis in tissue sectors with contrasting crocins accumulation provides novel insights into apocarotenoid biosynthesis and regulation during chromoplast biogenesis. PMID:29434251
Hub connectivity, neuronal diversity, and gene expression in the Caenorhabditis elegans connectome. PMID:29432412
Molecular Correlates of In Vitro Responses to Dacomitinib and Afatinib in Bladder Cancer. PMID:29430509
Differential gene expression induced by anti-cancer agent plumbagin is mediated by androgen receptor in prostate cancer cells. PMID:29426892
Differences in MWCNT- and SWCNT-induced DNA methylation alterations in association with the nuclear deposition. PMID:29426343
Network Analysis of UBE3A/E6AP-Associated Proteins Provides Connections to Several Distinct Cellular Processes. PMID:29426014
Integrated Systems Approach Reveals Sphingolipid Metabolism Pathway Dysregulation in Association with Late-Onset Alzheimer's Disease. PMID:29425116
Dietary Safety Assessment of Flk1-Transgenic Fish. PMID:29422865
Supporting shared hypothesis testing in the biomedical domain. PMID:29422110
Dissection of the Mechanism for Compatible and Incompatible Graft Combinations of Citrus grandis (L.) Osbeck ('Hongmian Miyou'). PMID:29419732
A DP-like transcription factor protein interacts with E2fl1 to regulate meiosis in Tetrahymena thermophila. PMID:29417875
Identification of human age-associated gene co-expressions in functional modules using liquid association. PMID:29416677
Analysis of Homologs of Cry-toxin Receptor-Related Proteins in the Midgut of a Non-Bt Target, Nilaparvata lugens (Stål) (Hemiptera: Delphacidae). PMID:29415259
Proteome Data Improves Protein Function Prediction in the Interactome of Helicobacter pylori. PMID:29414760
Effects of predation stress and food ration on perch gut microbiota. PMID:29409543
Ribonuclease inhibitor 1 regulates erythropoiesis by controlling GATA1 translation. PMID:29408805
Chromatin Modification and Global Transcriptional Silencing in the Oocyte Mediated by the mRNA Decay Activator ZFP36L2. PMID:29408237
Region-Specific Methylation Profiling in Acute Myeloid Leukemia. PMID:29405013
Evaluating the adaptive evolutionary convergence of carnivorous plant taxa through functional genomics. PMID:29404217
In vitro RNA-seq-based toxicogenomics assessment shows reduced biological effect of tobacco heating products when compared to cigarette smoke. PMID:29402904
Bio-SimVerb and Bio-SimLex: wide-coverage evaluation sets of word similarity in biomedicine. PMID:29402212
Activation of JAK/STAT3 restores NK-cell function and improves immune defense after brain ischemia. PMID:29401578
Oxygen drives hepatocyte differentiation and phenotype stability in liver cell lines. PMID:29399736
Switch of Mitochondrial Superoxide Dismutase into a Prooxidant Peroxidase in Manganese-Deficient Cells and Mice. PMID:29398562
SMRT sequencing of full-length transcriptome of flea beetle Agasicles hygrophila (Selman and Vogt). PMID:29396453
Comparative transcriptome analysis reveals molecular response to salinity stress of salt-tolerant and sensitive genotypes of indica rice at seedling stage. PMID:29391416
Decellularization and Solubilization of Porcine Liver for Use as a Substrate for Porcine Hepatocyte Culture: Method Optimization and Comparison. PMID:29390876
Co-complex protein membership evaluation using Maximum Entropy on GO ontology and InterPro annotation. PMID:29390084
Differentially expressed miRNAs in hepatocellular carcinoma cells under hypoxic conditions are associated with transcription and phosphorylation. PMID:29387230
Gene expression profile analysis of the bone microenvironment in patients with spinal metastases. PMID:29387210
High-throughput sequencing analysis revealed the regulation patterns of small RNAs on the development of A. comosus var. bracteatus leaves. PMID:29386560
Arabidopsis mRNA decay landscape arises from specialized RNA decay substrates, decapping-mediated feedback, and redundancy. PMID:29386391
Comparative Transcriptome Analyses Uncover Key Candidate Genes Mediating Flight Capacity in Bactrocera dorsalis (Hendel) and Bactrocera correcta (Bezzi) (Diptera: Tephritidae). PMID:29385681
Transcriptomic alterations during ageing reflect the shift from cancer to degenerative diseases in the elderly. PMID:29382830
Ubiquitin C decrement plays a pivotal role in replicative senescence of bone marrow mesenchymal stromal cells. PMID:29382826
Identification of regulatory role of DNA methylation in colon cancer gene expression via systematic bioinformatics analysis. PMID:29381923
RNA-seq transcriptome analysis of the immature seeds of two Brassica napus lines with extremely different thousand-seed weight to identify the candidate genes related to seed weight. PMID:29381708
Highly Efficient Exosome Isolation and Protein Analysis by an Integrated Nanomaterial-Based Platform. PMID:29381333
Regulation of Adult CNS Axonal Regeneration by the Post-transcriptional Regulator Cpeb1. PMID:29379413
GO FEAT: a rapid web-based functional annotation tool for genomic and transcriptomic data. PMID:29379090
Commensal microbiota modulate gene expression in the skin. PMID:29378633
Integrated multi-omic analysis of host-microbiota interactions in acute oak decline. PMID:29378627
Interleukins and their signaling pathways in the Reactome biological pathway database. PMID:29378288
The extent of ribosome queuing in budding yeast. PMID:29377894
Identification of key genes associated with bladder cancer using gene expression profiles. PMID:29375713
Dynamic Changes in Chemosensory Gene Expression during the Dendrolimus punctatus Mating Process. PMID:29375398
MiRNA Signaling in Viral Myocarditis Novel and Unique Pathological Features. PMID:29375227
Sparse simultaneous signal detection for identifying genetically controlled disease genes. PMID:29375169
Implication of molecular vascular smooth muscle cell heterogeneity among arterial beds in arterial calcification. PMID:29373585
Draft genome sequence of Streptomyces hyaluromycini MB-PO13T, a hyaluromycin producer. PMID:29371910
The Biotrophic Development of Ustilago maydis Studied by RNA-Seq Analysis. PMID:29371439
PhenoDis: a comprehensive database for phenotypic characterization of rare cardiac diseases. PMID:29370821
Assessing the Role of Muscle Protein Breakdown in Response to Nutrition and Exercise in Humans. PMID:29368185
InfAcrOnt: calculating cross-ontology term similarities using information flow by a random walk. PMID:29363423
Biclustering of transcriptome sequencing data reveals human tissue-specific circular RNAs. PMID:29363420
Use of DAVID algorithms for clustering custom annotated gene lists in a non-model organism, rainbow trout. PMID:29361978
miR-9a mediates the role of Lethal giant larvae as an epithelial growth inhibitor in Drosophila. PMID:29361610
RGBM: regularized gradient boosting machines for identification of the transcriptional regulators of discrete glioma subtypes. PMID:29361062
Dynamic genome wide expression profiling of Drosophila head development reveals a novel role of Hunchback in retinal glia cell development and blood-brain barrier integrity. PMID:29360820
Gene annotation bias impedes biomedical research. PMID:29358745
Herpesvirus deconjugases inhibit the IFN response by promoting TRIM25 autoubiquitination and functional inactivation of the RIG-I signalosome. PMID:29357390
Complete Genome Sequence of Pseudomonas Parafulva PRS09-11288, a Biocontrol Strain Produces the Antibiotic Phenazine-1-carboxylic Acid. PMID:29356878
Sphingolipid Metabolism Is Dysregulated at Transcriptomic and Metabolic Levels in the Spinal Cord of an Animal Model of Amyotrophic Lateral Sclerosis. PMID:29354030
ERα-Mediated Nuclear Sequestration of RSK2 Is Required for ER+ Breast Cancer Tumorigenesis. PMID:29351904
Systematic Gene-to-Phenotype Arrays: A High-Throughput Technique for Molecular Phenotyping. PMID:29351850
Large-scale mapping of bioactive peptides in structural and sequence space. PMID:29351315
Identification of genetic elements in metabolism by high-throughput mouse phenotyping. PMID:29348434
Draft Genome Sequence of the Crude Oil-Degrading and Biosurfactant-Producing Strain Cobetia sp. QF-1. PMID:29348342
MIRO: guidelines for minimum information for the reporting of an ontology. PMID:29347969
Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D. PMID:29346625
Analyzing DNA Methylation Patterns During Tumor Evolution. PMID:29344884
Microarray analysis reveals Tmub1 as a cell cycle-associated protein in rat hepatocytes. PMID:29344642
Identification of differentially expressed molecular functions associated with breast cancer using Gibbs sampling. PMID:29344193
Downregulated miRNA-1269a variant (rs73239138) decreases the susceptibility to gastric cancer via targeting ZNF70. PMID:29344113
The protective role of DOT1L in UV-induced melanomagenesis. PMID:29343685
LocText: relation extraction of protein localizations to assist database curation. PMID:29343218
Prediction of novel target genes and pathways involved in bevacizumab-resistant colorectal cancer. PMID:29342159
RBiomirGS: an all-in-one miRNA gene set analysis solution featuring target mRNA mapping and expression profile integration. PMID:29340253
Differential gene expression profiles between two subtypes of ischemic stroke with blood stasis syndromes. PMID:29340078
Gene expression profiling and construction of a putative gene regulatory network of bladder cancer tumor-initiating cells. PMID:29340052
Genomic insights into Mycobacterium simiae human colonization. PMID:29340007
Using intracellular markers to identify a novel set of surface markers for live cell purification from a heterogeneous hIPSC culture. PMID:29339826
Loss of disease tolerance during Citrobacter rodentium infection is associated with impaired epithelial differentiation and hyperactivation of T cell responses. PMID:29339782
Clustering gene expression time series data using an infinite Gaussian process mixture model. PMID:29337990
Identification of Potential MR-Derived Biomarkers for Tumor Tissue Response to 177Lu-Octreotate Therapy in an Animal Model of Small Intestine Neuroendocrine Tumor. PMID:29331677
Large-scale aggregation analysis of eukaryotic proteins reveals an involvement of intrinsically disordered regions in protein folding. PMID:29330519
Integration of GWAS, pathway and network analyses reveals novel mechanistic insights into the synthesis of milk proteins in dairy cows. PMID:29330500
Discovery of microRNA-target modules of African rice (Oryza glaberrima) under salinity stress. PMID:29330361
The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability. PMID:29329592
Transcriptome profiling with focus on potential key genes for wing development and evolution in Megaloprepus caerulatus, the damselfly species with the world's largest wings. PMID:29329292
Bioinformatic analysis of gene expression profiling of intracranial aneurysm. PMID:29328431
Investigation into the underlying molecular mechanisms of hypertensive nephrosclerosis using bioinformatics analyses. PMID:29328390
Genetic analysis of very obese children with autism spectrum disorder. PMID:29327328
An Integrated Analysis of miRNAs and Methylated Genes Encoding mRNAs and lncRNAs in Sheep Breeds with Different Fecundity. PMID:29326596
A combined analysis of genetically correlated traits identifies 187 loci and a role for neurogenesis and myelination in intelligence. PMID:29326435
Whole-Genome Sequences of Brucella melitensis Strain QH61, Isolated from Yak in Qinghai, China. PMID:29326214
Systematic target function annotation of human transcription factors. PMID:29325558
Antibacterial Evaluation and Virtual Screening of New Thiazolyl-Triazole Schiff Bases as Potential DNA-Gyrase Inhibitors. PMID:29324679
An amebic protein disulfide isomerase (PDI) complements the yeast PDI1 mutation but is unable to support cell viability under ER or thermal stress. PMID:29321956
Enhanced MYC association with the NuA4 histone acetyltransferase complex mediated by the adenovirus E1A N-terminal domain activates a subset of MYC target genes highly expressed in cancer cells. PMID:29321817
Comparative analysis of low complexity regions in Plasmodia. PMID:29321589
CUILESS2016: a clinical corpus applying compositional normalization of text mentions. PMID:29316970
Improving the interoperability of biomedical ontologies with compound alignments. PMID:29316968
Biotea: semantics for Pubmed Central. PMID:29312824
Update on 13 Syndromes Affecting Craniofacial and Dental Structures. PMID:29311971
The muscle development transcriptome landscape of ovariectomized goat. PMID:29308264
An epigenome-wide methylation study of healthy individuals with or without depressive symptoms. PMID:29305581
Integration of multiple networks and pathways identifies cancer driver genes in pan-cancer analysis. PMID:29304754
Inferring ontology graph structures using OWL reasoning. PMID:29304741
Transcriptome analysis of response to Plasmodiophora brassicae infection in the Arabidopsis shoot and root. PMID:29304736
Comparative analysis of miRNA and mRNA abundance in determinate cucumber by high-throughput sequencing. PMID:29304061
Genome sequence of Acuticoccus yangtzensis JL1095T (DSM 28604T) isolated from the Yangtze Estuary. PMID:29299111
Genome of Russian wheat aphid an economically important cereal aphid. PMID:29299110
Complete genome sequence of esterase-producing bacterium Croceicoccus marinus E4A9T. PMID:29299108
The gonadal transcriptome of the unisexual Amazon molly Poecilia formosa in comparison to its sexual ancestors, Poecilia mexicana and Poecilia latipinna. PMID:29298680
DisSetSim: an online system for calculating similarity between disease sets. PMID:29297411
Investigations on factors influencing HPO-based semantic similarity calculation. PMID:29297376
Measuring disease similarity and predicting disease-related ncRNAs by a novel method. PMID:29297338
Integrative biological simulation praxis: Considerations from physics, philosophy, and data/model curation practices. PMID:29296511
Semantic Relations in Compound Nouns: Perspectives from Inter-Annotator Agreement. PMID:29295175
Phenotypic Analysis of Clinical Narratives Using Human Phenotype Ontology. PMID:29295162
Improving pairwise comparison of protein sequences with domain co-occurrence. PMID:29293498
Genetic variation associated with healthy traits and environmental conditions in Vaccinium vitis-idaea. PMID:29291734
Protein-Protein Interaction Network Analysis for a Biomarker Panel Related to Human Esophageal Adenocarcinoma. PMID:29286604
Identifying hub genes and potential mechanisms associated with senescence in human annulus cells by gene expression profiling and bioinformatics analysis. PMID:29286093
Genome expression profiling predicts the molecular mechanism of peripheral myelination. PMID:29286075
Changes in microRNA expression in the brachial plexus avulsion model of neuropathic pain. PMID:29286067
A molecular signature of lung cancer: potential biomarkers for adenocarcinoma and squamous cell carcinoma. PMID:29285267
Platform-independent gene expression signature differentiates sessile serrated adenomas/polyps and hyperplastic polyps of the colon. PMID:29284484
MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data. PMID:29280960
Genome sequence of the model plant pathogen Pectobacterium carotovorum SCC1. PMID:29276572
Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565T an anaerobic, slightly halophilic bacterium isolated from a Colombian saline spring. PMID:29276571
Complete genome of a novel virulent phage ST0 lysing Escherichia coli H8. PMID:29276570
Comparison of multiple transcriptomes exposes unified and divergent features of quiescent and activated skeletal muscle stem cells. PMID:29273087
Developing a 'personalome' for precision medicine: emerging methods that compute interpretable effect sizes from single-subject transcriptomes. PMID:29272327
The integration of weighted gene association networks based on information entropy. PMID:29272314
The pomegranate (Punica granatum L.) genome provides insights into fruit quality and ovule developmental biology. PMID:29271050
A network-based meta-analysis for characterizing the genetic landscape of human aging. PMID:29270911
Physiological and transcriptomic analyses of a yellow-green mutant with high photosynthetic efficiency in wheat (Triticum aestivum L.). PMID:29270875
Draft genome sequence of Acidithiobacillus thiooxidans CLST isolated from the acidic hypersaline Gorbea salt flat in northern Chile. PMID:29270251
Complete genome sequence analysis of Archaeoglobus fulgidus strain 7324 (DSM 8774), a hyperthermophilic archaeal sulfate reducer from a North Sea oil field. PMID:29270248
Transcriptomic characterization of Caecomyces churrovis: a novel, non-rhizoid-forming lignocellulolytic anaerobic fungus. PMID:29270219
Sequential feature selection and inference using multi-variate random forests. PMID:29267851
PECAplus: statistical analysis of time-dependent regulatory changes in dynamic single-omics and dual-omics experiments. PMID:29263799
A framework for exploring associations between biomedical terms in PubMed. PMID:29262548
A conserved maternal-specific repressive domain in Zelda revealed by Cas9-mediated mutagenesis in Drosophila melanogaster. PMID:29261646
Integrating phenotype ontologies with PhenomeNET. PMID:29258588
Identification of the Sex-Biased Gene Expression and Putative Sex-Associated Genes in Eucommia ulmoides Oliver Using Comparative Transcriptome Analyses. PMID:29258253
Bioinformatics analysis of differentially expressed gene profiles associated with systemic lupus erythematosus. PMID:29257335
Gene Network Analysis of Interstitial Macrophages After Treatment with Induced Pluripotent Stem Cells Secretome (iPSC-cm) in the Bleomycin Injured Rat Lung. PMID:29256173
Draft genome of Paraburkholderia caballeronis TNe-841T, a free-living, nitrogen-fixing, tomato plant-associated bacterium. PMID:29255574
Draft genome sequence of Pseudomonas extremaustralis strain USBA-GBX 515 isolated from Superparamo soil samples in Colombian Andes. PMID:29255573
Draft genome sequence of the type strain of the sulfur-oxidizing acidophile, Acidithiobacillus albertensis (DSM 14366). PMID:29255572
The complete genome sequence of Ensifer meliloti strain CCMM B554 (FSM-MA), a highly effective nitrogen-fixing microsymbiont of Medicago truncatula Gaertn. PMID:29255570
A flexible ontology for inference of emergent whole cell function from relationships between subcellular processes. PMID:29255142
Evolutionary transition from blood feeding to obligate nonbiting in a mosquito. PMID:29255013
cFLIP critically modulates apoptotic resistance in epithelial-to-mesenchymal transition. PMID:29254146
A polygenic score for schizophrenia predicts glycemic control. PMID:29249829
Proteomic Analysis Shows Constitutive Secretion of MIF and p53-associated Activity of COX-2-/- Lung Fibroblasts. PMID:29247872
Proteome profiling of clear cell renal cell carcinoma in von Hippel-Lindau patients highlights upregulation of Xaa-Pro aminopeptidase-1, an anti-proliferative and anti-migratory exoprotease. PMID:29245961
Proteomic analysis of six- and twelve-month hippocampus and cerebellum in a murine Down syndrome model. PMID:29245059
Minichromosome maintenance complex component 6 (MCM6) expression correlates with histological grade and survival in endometrioid endometrial adenocarcinoma. PMID:29243125
Insights into the Proteome of Gastrointestinal Stromal Tumors-Derived Exosomes Reveals New Potential Diagnostic Biomarkers. PMID:29242380
Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking. PMID:29239719
Gene and miRNA expression profiles in PBMCs from patients with severe and mild emphysema and PiZZ alpha1-antitrypsin deficiency. PMID:29238183
A Case Study Application of the Aggregate Exposure Pathway (AEP) and Adverse Outcome Pathway (AOP) Frameworks to Facilitate the Integration of Human Health and Ecological End Points for Cumulative Risk Assessment (CRA). PMID:29236470
Evidence for a hierarchical transcriptional circuit in Drosophila male germline involving testis-specific TAF and two gene-specific transcription factors, Mod and Acj6. PMID:29235675
Differential Expression of Serum MicroRNAs Supports CD4⁺ T Cell Differentiation into Th2/Th17 Cells in Severe Equine Asthma. PMID:29231896
A Comprehensive Overview of Online Resources to Identify and Predict Bacterial Essential Genes. PMID:29230204
SNP co-association and network analyses identify E2F3, KDM5A and BACH2 as key regulators of the bovine milk fatty acid profile. PMID:29230020
Ensemble Modeling Approach Targeting Heterogeneous RNA-Seq data: Application to Melanoma Pseudogenes. PMID:29229974
PTEN regulates spindle assembly checkpoint timing through MAD1 in interphase. PMID:29228672
Draft genome sequences of Bradyrhizobium shewense sp. nov. ERR11T and Bradyrhizobium yuanmingense CCBAU 10071T. PMID:29225730
Draft genome sequence of Bacillus velezensis 2A-2B strain: a rhizospheric inhabitant of Sporobolus airoides (Torr.) Torr., with antifungal activity against root rot causing phytopathogens. PMID:29225729
The complete genome sequence of the rumen bacterium Butyrivibrio hungatei MB2003. PMID:29225728
The genomic study of an environmental isolate of Scedosporium apiospermum shows its metabolic potential to degrade hydrocarbons. PMID:29225727
Prediction of cassava protein interactome based on interolog method. PMID:29222529
Differently expressed long noncoding RNAs and mRNAs in TK6 cells exposed to low dose hydroquinone. PMID:29221148
Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium. PMID:29220487
EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species. PMID:29220468
SFMetaDB: a comprehensive annotation of mouse RNA splicing factor RNA-Seq datasets. PMID:29220461
The Grass Carp Genome Database (GCGD): an online platform for genome features and annotations. PMID:29220445
Triage by ranking to support the curation of protein interactions. PMID:29220432
In silico characterization of tandem repeats in Trichophyton rubrum and related dermatophytes provides new insights into their role in pathogenesis. PMID:29220431
A multi-network clustering method for detecting protein complexes from multiple heterogeneous networks. PMID:29219066
Annotating gene sets by mining large literature collections with protein networks. PMID:29218918
Convergent downstream candidate mechanisms of independent intergenic polymorphisms between co-classified diseases implicate epistasis among noncoding elements. PMID:29218911
Emergence of pathway-level composite biomarkers from converging gene set signals of heterogeneous transcriptomic responses. PMID:29218907
Single subject transcriptome analysis to identify functionally signed gene set or pathway activity. PMID:29218900
PRECISION MEDICINE: FROM DIPLOTYPES TO DISPARITIES TOWARDS IMPROVED HEALTH AND THERAPIES. PMID:29218899
Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencoders. PMID:29218871
Aging and neurodegeneration are associated with increased mutations in single human neurons. PMID:29217584
A comparative transcriptomic analysis of replicating and dormant liver stages of the relapsing malaria parasite Plasmodium cynomolgi. PMID:29215331
Genome overview of eight Candida boidinii strains isolated from human activities and wild environments. PMID:29213357
High-quality draft genome sequence of Aquidulcibacter paucihalophilus TH1-2T isolated from cyanobacterial aggregates in a eutrophic lake. PMID:29213356
Draft genome sequence of Venturia carpophila, the causal agent of peach scab. PMID:29213355
Human hair follicle transcriptome profiling: a minimally invasive tool to assess molecular adaptations upon low-volume, high-intensity interval training. PMID:29212859
Ultra-low input transcriptomics reveal the spore functional content and phylogenetic affiliations of poorly studied arbuscular mycorrhizal fungi. PMID:29211832
The mouse Jhy gene regulates ependymal cell differentiation and ciliogenesis. PMID:29211732
Analysis of the Salivary Gland Transcriptome of Unfed and Partially Fed Amblyomma sculptum Ticks and Descriptive Proteome of the Saliva. PMID:29209593
pH Stress-Induced Cooperation between Rhodococcus ruber YYL and Bacillus cereus MLY1 in Biodegradation of Tetrahydrofuran. PMID:29209303
VEGF121, is predictor for survival in activated B-cell-like diffuse large B-cell lymphoma and is related to an immune response gene signature conserved in cancers. PMID:29207605
Biochemical, Physiological and Transcriptomic Comparison between Burley and Flue-Cured Tobacco Seedlings in Relation to Carbohydrates and Nitrate Content. PMID:29207483
Mountain hare transcriptome and diagnostic markers as resources to monitor hybridization with European hares. PMID:29206218
Annotation of nerve cord transcriptome in earthworm Eisenia fetida. PMID:29204349
Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists. PMID:29202807
Global gene expression reveals stress-responsive genes in Aspergillus fumigatus mycelia. PMID:29202712
Single-cell RNA-Seq analysis reveals dynamic trajectories during mouse liver development. PMID:29202695
Identification of key genes influenced by fixation stability in early fracture hematoma and elucidation of their roles in fracture healing. PMID:29201161
Complete genome sequence of the Vibrio vulnificus strain VV2014DJH, a human-pathogenic bacterium isolated from a death case in China. PMID:29201149
A time-course microarray data analysis reveals consistent dysregulated genes and upstream microRNAs in autoantibody-mediated arthritis. PMID:29197380
Differential prioritization of therapies to subtypes of triple negative breast cancer using a systems medicine method. PMID:29190967
MicroRNA-21 inhibits mitochondria-mediated apoptosis in keloid. PMID:29190966
Proteomic analysis of lung metastases in a murine breast cancer model reveals divergent influence of CTSB and CTSL overexpression. PMID:29187882
Subchronic olanzapine exposure leads to increased expression of myelination-related genes in rat fronto-medial cortex. PMID:29187753
Integrative Bioinformatic Analysis of Transcriptomic Data Identifies Conserved Molecular Pathways Underlying Ionizing Radiation-Induced Bystander Effects (RIBE). PMID:29186820
The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics. PMID:29186578
Long-read sequence assembly of the firefly Pyrocoelia pectoralis genome. PMID:29186486
Improving amphibian genomic resources: a multitissue reference transcriptome of an iconic invader. PMID:29186423
The OncoPPi Portal: an integrative resource to explore and prioritize protein-protein interactions for cancer target discovery. PMID:29186335
Bacterial endosymbionts influence host sexuality and reveal reproductive genes of early divergent fungi. PMID:29184190
First gene-ontology enrichment analysis based on bacterial coregenome variants: insights into adaptations of Salmonella serovars to mammalian- and avian-hosts. PMID:29183286
Whole transcriptome RNA-Seq analysis reveals extensive cell type-specific compartmentalization in Volvox carteri. PMID:29179763
Production of poly-γ-glutamic acid by a thermotolerant glutamate-independent strain and comparative analysis of the glutamate dependent difference. PMID:29177886
The Gene Ontology of eukaryotic cilia and flagella. PMID:29177046
Mechanisms of action of Coxiella burnetii effectors inferred from host-pathogen protein interactions. PMID:29176882
Phosphoproteomics of cAMP signaling of Bordetella adenylate cyclase toxin in mouse dendritic cells. PMID:29176673
Shared genetic etiology of hypertension and stroke: evidence from bioinformatics analysis of genome-wide association studies. PMID:29176593
Genome-wide identification and differential analysis of translational initiation. PMID:29170441
Genome-wide meta-analysis in Japanese populations identifies novel variants at the TMC6-TMC8 and SIX3-SIX2 loci associated with HbA1c. PMID:29170429
A post-gene silencing bioinformatics protocol for plant-defence gene validation and underlying process identification: case study of the Arabidopsis thaliana NPR1. PMID:29169324
Graph-theoretical comparison of normal and tumor networks in identifying BRCA genes. PMID:29166896
ADAGE signature analysis: differential expression analysis with data-defined gene sets. PMID:29166858
Novel phosphate deficiency-responsive long non-coding RNAs in the legume model plant Medicago truncatula. PMID:29165588
Identification of diverse target RNAs that are functionally regulated by human Pumilio proteins. PMID:29165587
Systemic Responses of Multidrug-Resistant Pseudomonas aeruginosa and Acinetobacter baumannii Following Exposure to the Antimicrobial Peptide Cathelicidin-BF Imply Multiple Intracellular Targets. PMID:29164074
Identification of molecular mechanisms of glutamine in pancreatic cancer. PMID:29163679
Identification of MsHsp20 Gene Family in Malus sieversii and Functional Characterization of MsHsp16.9 in Heat Tolerance. PMID:29163556
Whole Exome Sequencing reveals new candidate genes in host genomic susceptibility to Respiratory Syncytial Virus Disease. PMID:29162850
A 16-gene signature predicting prognosis of patients with oral tongue squamous cell carcinoma. PMID:29158988
Insights into gene expression profiles induced by Socs3 depletion in keratinocytes. PMID:29158586
Highly expressed genes evolve under strong epistasis from a proteome-wide scan in E. coli. PMID:29158562
ChIP-Seq analysis identifies p27(Kip1)-target genes involved in cell adhesion and cell signalling in mouse embryonic fibroblasts. PMID:29155860
Investigation of common, low-frequency and rare genome-wide variation in anorexia nervosa. PMID:29155802
Complete genome sequence of Pseudomonas corrugata strain RM1-1-4, a stress protecting agent from the rhizosphere of an oilseed rape bait plant. PMID:29152037
Molecular Characterization of an Endozoicomonas-Like Organism Causing Infection in the King Scallop (Pecten maximus L.). PMID:29150518
The IUPHAR/BPS Guide to PHARMACOLOGY in 2018: updates and expansion to encompass the new guide to IMMUNOPHARMACOLOGY. PMID:29149325
Draft genome analysis provides insights into the fiber yield, crude protein biosynthesis, and vegetative growth of domesticated ramie (Boehmeria nivea L. Gaud). PMID:29149285
Human Accelerated Regions and Other Human-Specific Sequence Variations in the Context of Evolution and Their Relevance for Brain Development. PMID:29149249
Using Next-Generation Sequencing to Detect Differential Expression Genes in Bradysia odoriphaga after Exposure to Insecticides. PMID:29149030
A transcriptomic insight into the impacts of mast cells in lung, breast, and colon cancers. PMID:29147625
Migrainomics - identifying brain and genetic markers of migraine. PMID:29146952
Proteome-wide identification of lysine 2-hydroxyisobutyrylation reveals conserved and novel histone modifications in Physcomitrella patens. PMID:29138512
Comprehensive microRNA-sequencing of exosomes derived from head and neck carcinoma cells in vitro reveals common secretion profiles and potential utility as salivary biomarkers. PMID:29137278
MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins. PMID:29136219
Modelling pyruvate dehydrogenase under hypoxia and its role in cancer metabolism. PMID:29134060
Weighted gene co-expression network analysis of expression data of monozygotic twins identifies specific modules and hub genes related to BMI. PMID:29132311
Differential transcriptome analysis reveals genes related to cold tolerance in seabuckthorn carpenter moth, Eogystia hippophaecolus. PMID:29131867
Automated visualization of rule-based models. PMID:29131816
Identification of a novel gene in ROD9 island of Salmonella Enteritidis involved in the alteration of virulence-associated genes expression. PMID:29130383
Statistical Contributions to Bioinformatics: Design, Modeling, Structure Learning, and Integration. PMID:29129969
Protein Moonlighting Revealed by Noncatalytic Phenotypes of Yeast Enzymes. PMID:29127264
ActiveDriverDB: human disease mutations and genome variation in post-translational modification sites of proteins. PMID:29126202
Comparative Genome Analysis Reveals Adaptation to the Ectophytic Lifestyle of Sooty Blotch and Flyspeck Fungi. PMID:29126189
Deep sequencing and comprehensive expression analysis identifies several molecules potentially related to human poorly differentiated hepatocellular carcinoma. PMID:29123978
Identification and Characterization of MicroRNAs in the Goat (Capra hircus) Rumen during Embryonic Development. PMID:29123545
Entity recognition in the biomedical domain using a hybrid approach. PMID:29122011
The combinatorial control of alternative splicing in C. elegans. PMID:29121637
Pectin methylesterase inhibitor (PMEI) family can be related to male sterility in Chinese cabbage (Brassica rapa ssp. pekinensis). PMID:29119365
Guanylate-binding protein-1 is a potential new therapeutic target for triple-negative breast cancer. PMID:29115931
Genome-wide DNA methylome alterations in acute coronary syndrome. PMID:29115576
Abnormal DNA methylation may contribute to the progression of osteosarcoma. PMID:29115427
Gene expression profiles and protein‑protein interaction networks during tongue carcinogenesis in the tumor microenvironment. PMID:29115421
Global gene expression analysis combined with a genomics approach for the identification of signal transduction networks involved in postnatal mouse myocardial proliferation and development. PMID:29115400
Common mechanism of pathogenesis in various types of metastatic osteosarcoma. PMID:29113282
CommWalker: correctly evaluating modules in molecular networks in light of annotation bias. PMID:29112702
Bacterial colonization stimulates a complex physiological response in the immature human intestinal epithelium. PMID:29110754
Chemical Similarity Enrichment Analysis (ChemRICH) as alternative to biochemical pathway mapping for metabolomic datasets. PMID:29109515
Transcriptomic Profiling of MDA-MB-231 Cells Exposed to Boswellia Serrata and 3-O-Acetyl-B-Boswellic Acid; ER/UPR Mediated Programmed Cell Death. PMID:29109091
Insight into glucocorticoid receptor signalling through interactome model analysis. PMID:29107989
Signatures of adaptation and symbiosis in genomes and transcriptomes of Symbiodinium. PMID:29101370
Comparative transcriptome analysis reveals potentially novel roles of Homeobox genes in adipose deposition in fat-tailed sheep. PMID:29101335
Contribution of epigenetic landscapes and transcription factors to X-chromosome reactivation in the inner cell mass. PMID:29101321
Endothelial dysfunction is a superinducer of syndecan-4: fibrogenic role of its ectodomain. PMID:29101181
Cellular, ultrastructural and molecular analyses of epidermal cell development in the planarian Schmidtea mediterranea. PMID:29100657
Differentially expressed genes in the caecal and colonic mucosa of Landrace finishing pigs with high and low food conversion ratios. PMID:29097775
GRAFENE: Graphlet-based alignment-free network approach integrates 3D structural and sequence (residue order) data to improve protein structural comparison. PMID:29097661
A Long Noncoding RNA Signature That Predicts Pathological Complete Remission Rate Sensitively in Neoadjuvant Treatment of Breast Cancer. PMID:29096247
Draft genome sequence of Marinobacterium rhizophilum CL-YJ9T (DSM 18822T), isolated from the rhizosphere of the coastal tidal-flat plant Suaeda japonica. PMID:29093768
Genome-wide discovery of long intergenic noncoding RNAs and their epigenetic signatures in the rat. PMID:29093522
SABIO-RK: an updated resource for manually curated biochemical reaction kinetics. PMID:29092055
Insight into cordycepin biosynthesis of Cordyceps militaris: Comparison between a liquid surface culture and a submerged culture through transcriptomic analysis. PMID:29091925
Physiological and transcriptome response to cadmium in cosmos (Cosmos bipinnatus Cav.) seedlings. PMID:29089633
MARK3-mediated phosphorylation of ARHGEF2 couples microtubules to the actin cytoskeleton to establish cell polarity. PMID:29089450
Post-weaning epiphysiolysis causes distal femur dysplasia and foreshortened hindlimbs in fetuin-A-deficient mice. PMID:29088242
Dorsal and Ventral Hippocampus Differentiate in Functional Pathways and Differentially Associate with Neurological Disease-Related Genes during Postnatal Development. PMID:29085281
Hypoxia tolerance, longevity and cancer-resistance in the mole rat Spalax - a liver transcriptomics approach. PMID:29084988
miRNA alteration is an important mechanism in sugarcane response to low-temperature environment. PMID:29084515
CGC: A Flexible and Robust Approach to Integrating Co-Regularized Multi-Domain Graph for Clustering. PMID:29081726
Genetic diversity and structure of wild and cultivated Amorphophallus paeoniifolius populations in southwestern China as revealed by RAD-seq. PMID:29079830
A proteome view of structural, functional, and taxonomic characteristics of major protein domain clusters. PMID:29079755
PLATO software provides analytic framework for investigating complexity beyond genome-wide association studies. PMID:29079728
Hsp90-downregulation influences the heat-shock response, innate immune response and onset of oocyte development in nematodes. PMID:29078207
Proteomics and phosphoproteomics in precision medicine: applications and challenges. PMID:29077858
Reactome enhanced pathway visualization. PMID:29077811
First draft genome sequence of a strain belonging to the Zoogloea genus and its gene expression in situ. PMID:29075368
iTRAQ Proteomic Analysis Reveals That Metabolic Pathways Involving Energy Metabolism Are Affected by Tea Tree Oil in Botrytis cinerea. PMID:29075250
Transcriptome analysis of mRNA and microRNAs in intramuscular fat tissues of castrated and intact male Chinese Qinchuan cattle. PMID:29073274
An effective approach to detecting both small and large complexes from protein-protein interaction networks. PMID:29072136
Genome-wide functional analysis on the molecular mechanism of specifically biosynthesized fluorescence Eu complex. PMID:29069770
Endoplasmic reticulum chaperone prolyl 4-hydroxylase, beta polypeptide (P4HB) promotes malignant phenotypes in glioma via MAPK signaling. PMID:29069756
Expanded and updated data and a query pipeline for iBeetle-Base. PMID:29069517
EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies. PMID:29069476
The DifferentialNet database of differential protein-protein interactions in human tissues. PMID:29069447
The maternal-zygotic transition and zygotic activation of the Mnemiopsis leidyi genome occurs within the first three cleavage cycles. PMID:29068507
RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education. PMID:29067736
DNA N6-methyladenine is dynamically regulated in the mouse brain following environmental stress. PMID:29066820
Role of the luxS gene in bacteriocin biosynthesis by Lactobacillus plantarum KLDS1.0391: A proteomic analysis. PMID:29066774
Ontology-based systematical representation and drug class effect analysis of package insert-reported adverse events associated with cardiovascular drugs used in China. PMID:29061976
Genome-wide profiling of transcribed enhancers during macrophage activation. PMID:29061167
A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE). PMID:29061110
Association analysis identifies 65 new breast cancer risk loci. PMID:29059683
Diverse type 2 diabetes genetic risk factors functionally converge in a phenotype-focused gene network. PMID:29059180
Hemodynamic Forces Sculpt Developing Heart Valves through a KLF2-WNT9B Paracrine Signaling Axis. PMID:29056552
iPhemap: an atlas of phenotype to genotype relationships of human iPSC models of neurological diseases. PMID:29051230
Identification of core genes and outcome in gastric cancer using bioinformatics analysis. PMID:29050278
Panax ginseng genome examination for ginsenoside biosynthesis. PMID:29048480
The Human Behaviour-Change Project: harnessing the power of artificial intelligence and machine learning for evidence synthesis and interpretation. PMID:29047393
Analysis of Genes with Alternatively Spliced Transcripts in the Leaf, Root, Panicle and Seed of Rice Using a Long Oligomer Microarray and RNA-Seq. PMID:29047256
Complete genome sequence of Paenibacillus yonginensis DCY84T, a novel plant Symbiont that promotes growth via induced systemic resistance. PMID:29046742
Complete genome sequence of Thermotoga sp. strain RQ7. PMID:29046741
Draft genome sequence and characterization of commensal Escherichia coli strain BG1 isolated from bovine gastro-intestinal tract. PMID:29046740
High-quality-draft genomic sequence of Paenibacillus ferrarius CY1T with the potential to bioremediate Cd, Cr and Se contamination. PMID:29046739
Global Analysis of Small RNA Dynamics during Seed Development of Picea glauca and Arabidopsis thaliana Populations Reveals Insights on their Evolutionary Trajectories. PMID:29046688
Novel Insights into miRNA Regulation of Storage Protein Biosynthesis during Wheat Caryopsis Development under Drought Stress. PMID:29046684
Integrated genomic characterization of cancer genes in glioma. PMID:29046615
Early Transcriptional Divergence Marks Virus-Specific Primary Human CD8+ T Cells in Chronic versus Acute Infection. PMID:29045899
Transcriptomic responses of Biomphalaria pfeifferi to Schistosoma mansoni: Investigation of a neglected African snail that supports more S. mansoni transmission than any other snail species. PMID:29045404
Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster. PMID:29045400
Evaluating phenotype-driven approaches for genetic diagnoses from exomes in a clinical setting. PMID:29044180
Biotoxicity of Cry1Ab protein on wolf spider Pardosa pseudoannulata. PMID:29043472
ProLanGO: Protein Function Prediction Using Neural Machine Translation Based on a Recurrent Neural Network. PMID:29039790
Prokineticin receptor-1-dependent paracrine and autocrine pathways control cardiac tcf21+ fibroblast progenitor cell transformation into adipocytes and vascular cells. PMID:29038558
Genome-wide trait-trait dynamics correlation study dissects the gene regulation pattern in maize kernels. PMID:29037150
Enhanced Desiccation Tolerance in Mature Cultures of the Streptophytic Green Alga Zygnema circumcarinatum Revealed by Transcriptomics. PMID:29036673
The Proteome of Biologically Active Membrane Vesicles from Piscirickettsia salmonis LF-89 Type Strain Identifies Plasmid-Encoded Putative Toxins. PMID:29034215
Microarray Analysis Identifies the Potential Role of Long Non-Coding RNA in Regulating Neuroinflammation during Japanese Encephalitis Virus Infection. PMID:29033949
Identification of genes and pathways potentially related to PHF20 by gene expression profile analysis of glioblastoma U87 cell line. PMID:29033691
Widespread Post-transcriptional Attenuation of Genomic Copy-Number Variation in Cancer. PMID:29032074
Unwavering Pathobiology of Volumetric Muscle Loss Injury. PMID:29030619
MicroRNA Signature of Cigarette Smoking and Evidence for a Putative Causal Role of MicroRNAs in Smoking-Related Inflammation and Target Organ Damage. PMID:29030400
LiverWiki: a wiki-based database for human liver. PMID:29029599
DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier. PMID:29028931
Review of computational methods for virus-host protein interaction prediction: a case study on novel Ebola-human interactions. PMID:29028879
Affected pathways and transcriptional regulators in gene expression response to an ultra-marathon trail: Global and independent activity approaches. PMID:29028836
Native KCC2 interactome reveals PACSIN1 as a critical regulator of synaptic inhibition. PMID:29028184
The Plasticizer Bisphenol A Perturbs the Hepatic Epigenome: A Systems Level Analysis of the miRNome. PMID:29027980
Trichostatin A and 5-Aza-2'-Deoxycytidine influence the expression of cold-induced genes in Arabidopsis. PMID:29027833
Genomic insights into the thiamin metabolism of Paenibacillus thiaminolyticus NRRL B-4156 and P. apiarius NRRL B-23460. PMID:29026451
Prediction of Human Phenotype Ontology terms by means of hierarchical ensemble methods. PMID:29025394
RNA-Seq Analysis of Differentiated Keratinocytes Reveals a Massive Response to Late Events during Human Papillomavirus 16 Infection, Including Loss of Epithelial Barrier Function. PMID:29021401
Co-expression networks reveal the tissue-specific regulation of transcription and splicing. PMID:29021288
Transcriptomic Analysis of Octanoic Acid Response in Drosophila sechellia Using RNA-Sequencing. PMID:29021218
Knowledge Management Framework for Emerging Infectious Diseases Preparedness and Response: Design and Development of Public Health Document Ontology. PMID:29021130
The draft genome assembly of Rhododendron delavayi Franch. var. delavayi. PMID:29020749
A novel network analysis approach reveals DNA damage, oxidative stress and calcium/cAMP homeostasis-associated biomarkers in frontotemporal dementia. PMID:29020091
Reconstructing cancer drug response networks using multitask learning. PMID:29017547
A genome-by-environment interaction classifier for precision medicine: personal transcriptome response to rhinovirus identifies children prone to asthma exacerbations. PMID:29016970
Meta-analysis of peripheral blood gene expression modules for COPD phenotypes. PMID:29016655
Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data. PMID:28994825
Isolation and complete genome sequence of Halorientalis hydrocarbonoclasticus sp. nov., a hydrocarbon-degrading haloarchaeon. PMID:28994006
Long non-coding RNA expression profiles in different severity EV71-infected hand foot and mouth disease patients. PMID:28993196
Identification of key genes for diabetic kidney disease using biological informatics methods. PMID:28990106
Genome‑wide analysis and prediction of functional long noncoding RNAs in osteoblast differentiation under simulated microgravity. PMID:28990099
A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines. PMID:28988802
Differential carbonylation of proteins in end-stage human fatty and nonfatty NASH. PMID:28988798
Identification of differential genomic DNA Methylation in the hypothalamus of pubertal rat using reduced representation Bisulfite sequencing. PMID:28985764
RNA sequencing identifies novel non-coding RNA and exon-specific effects associated with cigarette smoking. PMID:28985737
Congenic mice demonstrate the presence of QTLs conferring obesity and hypercholesterolemia on chromosome 1 in the TALLYHO mouse. PMID:28983685
Principles for the regulation of multiple developmental pathways by a versatile transcriptional factor, BLIMP1. PMID:28981894
Selective Constraints on Coding Sequences of Nervous System Genes Are a Major Determinant of Duplicate Gene Retention in Vertebrates. PMID:28981708
The Encyclopedia of Proteome Dynamics: a big data ecosystem for (prote)omics. PMID:28981707
A draft genome sequence of the rose black spot fungus Diplocarpon rosae reveals a high degree of genome duplication. PMID:28981525
Hybrid Sequencing of Full-Length cDNA Transcripts of Stems and Leaves in Dendrobium officinale. PMID:28981454
Quantitative proteomics analysis of mitochondrial proteins in lung adenocarcinomas and normal lung tissue using iTRAQ and tandem mass spectrometry. PMID:28979670
Comprehensive analysis of long non-coding RNA PVT1 gene interaction regulatory network in hepatocellular carcinoma using gene microarray and bioinformatics. PMID:28979669
Functional 5' UTR motif discovery with LESMoN: Local Enrichment of Sequence Motifs in biological Networks. PMID:28977652
Towards enhanced and interpretable clustering/classification in integrative genomics. PMID:28977511
The ESRP1-GPR137 axis contributes to intestinal pathogenesis. PMID:28975893
High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain. PMID:28975015
Caspase-1 cleaves PPARγ for potentiating the pro-tumor action of TAMs. PMID:28974683
Transcriptome Profiling in Systems Vascular Medicine. PMID:28970795
Ant-infecting Ophiocordyceps genomes reveal a high diversity of potential behavioral manipulation genes and a possible major role for enterotoxins. PMID:28970504
RNA-seq based gene expression analysis of ovarian granulosa cells exposed to zearalenone in vitro: significance to steroidogenesis. PMID:28969048
Large-scale Meta-analysis Suggests Low Regional Modularity in Lateral Frontal Cortex. PMID:28968758
Preliminary identification of key miRNAs, signaling pathways, and genes associated with Hirschsprung's disease by analysis of tissue microRNA expression profiles. PMID:28965333
Adenovirus E1A TRRAP-targeting domain-mediated enhancement of MYC association with the NuA4 complex activates a panel of MYC target genes enriched for gene expression and ribosome biogenesis. PMID:28965007
High rate of adaptation of mammalian proteins that interact with Plasmodium and related parasites. PMID:28957326
Comparative Genomics of Ralstonia solanacearum Identifies Candidate Genes Associated with Cool Virulence. PMID:28955357
Metatranscriptomics Reveals the Functions and Enzyme Profiles of the Microbial Community in Chinese Nong-Flavor Liquor Starter. PMID:28955318
Inflammasome-driven catecholamine catabolism in macrophages blunts lipolysis during ageing. PMID:28953873
γ-Carboxymuconolactone decarboxylase: a novel cell cycle-related basal body protein in the early branching eukaryote Trichomonas vaginalis. PMID:28950916
Mimvec: a deep learning approach for analyzing the human phenome. PMID:28950906
NetGen: a novel network-based probabilistic generative model for gene set functional enrichment analysis. PMID:28950861
BRWLDA: bi-random walks for predicting lncRNA-disease associations. PMID:28947982
Comparative proteomic analysis of pituitary glands from Huoyan geese between pre-laying and laying periods using an iTRAQ-based approach. PMID:28945779
Upregulation of long noncoding RNA AP003419.16 predicts high risk of aging‑associated idiopathic pulmonary fibrosis. PMID:28944926
Exploring the key genes and pathways of osteosarcoma with pulmonary metastasis using a gene expression microarray. PMID:28944885
Gene expression analysis: Regulation of key genes associated with mycophenolate mofetil treatment of symptomatic carotid artery stenosis. PMID:28944878
MuMADS1 and MaOFP1 regulate fruit quality in a tomato ovate mutant. PMID:28944538
A Statistical Framework for Pathway and Gene Identification from Integrative Analysis. PMID:28943673
Computational Approaches to Identify Genetic Interactions for Cancer Therapeutics. PMID:28941356
The draft genome sequence of a desert tree Populus pruinosa. PMID:28938721
Differential expression of circulating biomarkers of tumor phenotype and outcomes in previously treated non-small cell lung cancer patients receiving erlotinib vs. cytotoxic chemotherapy. PMID:28938541
Integrating omics data and protein interaction networks to prioritize driver genes in cancer. PMID:28938536
Systematic integration of biomedical knowledge prioritizes drugs for repurposing. PMID:28936969
Automatic identification of informative regions with epigenomic changes associated to hematopoiesis. PMID:28934481
Evaluation of shared genetic aetiology between osteoarthritis and bone mineral density identifies SMAD3 as a novel osteoarthritis risk locus. PMID:28934396
Transcriptome analysis of Callery pear (Pyrus calleryana) reveals a comprehensive signalling network in response to Alternaria alternata. PMID:28934298
Insights from the draft genome into the pathogenicity of a clinical isolate of Elizabethkingia meningoseptica Em3. PMID:28932346
Integrated analysis of microRNA and mRNA expression profiles during the sex-differentiation sensitive period in oriental river prawn, Macrobrachium nipponense. PMID:28931848
CellNetVis: a web tool for visualization of biological networks using force-directed layout constrained by cellular components. PMID:28929969
Fish Ontology framework for taxonomy-based fish recognition. PMID:28929028
Screening of candidate key genes associated with human osteosarcoma using bioinformatics analysis. PMID:28928828
Genome-wide imaging association study implicates functional activity and glial homeostasis of the caudate in smoking addiction. PMID:28927378
Transcription Factors Responding to Pb Stress in Maize. PMID:28927013
Apophysomyces variabilis: draft genome sequence and comparison of predictive virulence determinants with other medically important Mucorales. PMID:28923009
An individualized gene expression signature for prediction of lung adenocarcinoma metastases. PMID:28922552
Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. PMID:28922347
Nε- and O-Acetylation in Mycobacterium tuberculosis Lineage 7 and Lineage 4 Strains: Proteins Involved in Bioenergetics, Virulence, and Antimicrobial Resistance Are Acetylated. PMID:28920697
The DREAM complex through its subunit Lin37 cooperates with Rb to initiate quiescence. PMID:28920576
Genome sequence of the white-rot fungus Irpex lacteus F17, a type strain of lignin degrader fungus. PMID:28919942
Genome sequence of the ectophytic fungus Ramichloridium luteum reveals unique evolutionary adaptations to plant surface niche. PMID:28915794
Detecting the genetic link between Alzheimer's disease and obesity using bioinformatics analysis of GWAS data. PMID:28915562
A high resolution atlas of gene expression in the domestic sheep (Ovis aries). PMID:28915238
Triportheus albus Cope, 1872 in the Blackwater, Clearwater, and Whitewater of the Amazon: A Case of Phenotypic Plasticity? PMID:28912799
Extending XNAT Platform with an Incremental Semantic Framework. PMID:28912709
Deconvolution of DNA methylation identifies differentially methylated gene regions on 1p36 across breast cancer subtypes. PMID:28912426
Microarray Analysis and Detection of MicroRNAs Associated with Chronic Thromboembolic Pulmonary Hypertension. PMID:28904974
Complete genome sequence of the sulfur-oxidizing chemolithoautotrophic Sulfurovum lithotrophicum 42BKTT. PMID:28904743
Draft genome sequence of the cellulolytic endophyte Chitinophaga costaii A37T2T. PMID:28904742
Transcriptomic profiling of genes in matured dimorphic seeds of euhalophyte Suaeda salsa. PMID:28903734
Hsp70/J-protein machinery from Glossina morsitans morsitans, vector of African trypanosomiasis. PMID:28902917
Screening and identification of key biomarkers in hepatocellular carcinoma: Evidence from bioinformatic analysis. PMID:28901457
Transcriptome Analysis of Induced Pluripotent Stem Cell (iPSC)-derived Pancreatic β-like Cell Differentiation. PMID:28901190
Molecular Resources from Transcriptomes in the Brassicaceae Family. PMID:28900436
Gene expression profiling of calcifications in breast cancer. PMID:28900139
Evolution and genome specialization of Brucella suis biovar 2 Iberian lineages. PMID:28899413
De Novo Assembly and Analysis of Polygonatum sibiricum Transcriptome and Identification of Genes Involved in Polysaccharide Biosynthesis. PMID:28895881
Navigating the Functional Landscape of Transcription Factors via Non-Negative Tensor Factorization Analysis of MEDLINE Abstracts. PMID:28894735
A Preliminary List of Horizontally Transferred Genes in Prokaryotes Determined by Tree Reconstruction and Reconciliation. PMID:28894459
Monitoring storage induced changes in the platelet proteome employing label free quantitative mass spectrometry. PMID:28887518
MicroRNA expression changes following synthesis of three full-sib Populus triploid populations with different heterozygosities. PMID:28884266
Draft Genome Sequence of Lactobacillus brevis Strain 3M004, a Probiotic with Potential Quorum-Sensing Regulation. PMID:28883127
Multiple network-constrained regressions expand insights into influenza vaccination responses. PMID:28881994
Predicting multicellular function through multi-layer tissue networks. PMID:28881986
Integrating Imaging Genomic Data in the Quest for Biomarkers of Schizophrenia Disease. PMID:28880187
Intracellular spectral recompositioning of light enhances algal photosynthetic efficiency. PMID:28879232
Assessment of Whole-Exome Sequence Data in Attempted Suicide within a Bipolar Disorder Cohort. PMID:28879196
A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog. PMID:28879061
Onset of human preterm and term birth is related to unique inflammatory transcriptome profiles at the maternal fetal interface. PMID:28879060
Genome sequence of the sulfur-oxidizing Bathymodiolus thermophilus gill endosymbiont. PMID:28878861
Draft genome sequences of two opportunistic pathogenic strains of Staphylococcus cohnii isolated from human patients. PMID:28878860
FunctionAnnotator, a versatile and efficient web tool for non-model organism annotation. PMID:28874813
BUFET: boosting the unbiased miRNA functional enrichment analysis using bitsets. PMID:28874117
De novo transcriptome assembly and analysis of differential gene expression in response to drought in European beech. PMID:28873454
De novo assembly of a transcriptome from the eggs and early embryos of Astropecten aranciacus. PMID:28873438
Characterization of 2 Novel Ependymoma Cell Lines With Chromosome 1q Gain Derived From Posterior Fossa Tumors of Childhood. PMID:28863455
Identification of Genes under Positive Selection Reveals Differences in Evolutionary Adaptation between Brown-Algal Species. PMID:28861104
Protein-Protein Interactions in Virus-Host Systems. PMID:28861068
Genomic and transcriptomic analyses reveal differential regulation of diverse terpenoid and polyketides secondary metabolites in Hericium erinaceus. PMID:28860534
Small molecule-based lineage switch of human adipose-derived stem cells into neural stem cells and functional GABAergic neurons. PMID:28860504
Whole-Genome Sequences of Brucella melitensis Strain QY1, Isolated from Sheep in Gansu, China. PMID:28860252
Whole-Genome Sequence of the 1,4-Dioxane-Degrading Bacterium Mycobacterium dioxanotrophicus PH-06. PMID:28860235
Gene expression profile data for mouse facial development. PMID:28856179
Transposable Element Misregulation Is Linked to the Divergence between Parental piRNA Pathways in Drosophila Hybrids. PMID:28854624
New Genes and Functional Innovation in Mammals. PMID:28854603
Multiplexed quantification of proteins and transcripts in single cells. PMID:28854175
Gene expression profiling and functional analysis reveals that p53 pathway-related gene expression is highly activated in cancer cells treated by cold atmospheric plasma-activated medium. PMID:28852598
Effect of fluoride treatment on gene expression in tea plant (Camellia sinensis). PMID:28851890
Exploring regulation in tissues with eQTL networks. PMID:28851834
MicroRNA-induced silencing in epilepsy: Opportunities and challenges for clinical application. PMID:28850760
RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes. PMID:28850115
Identification of prognostic markers of high grade prostate cancer through an integrated bioinformatics approach. PMID:28849390
Alterations in the long non‑coding RNA transcriptome in mesangial cells treated with aldosterone in vitro. PMID:28849035
The effect of Bu Zhong Yi Qi decoction on simulated weightlessness‑induced muscle atrophy and its mechanisms. PMID:28849026
Phenotypic and Comparative Transcriptome Analysis of Different Ploidy Plants in Dendrocalamus latiflorus Munro. PMID:28848575
Mycobacterium bovis Bacillus Calmette-Guérin Alters Melanoma Microenvironment Favoring Antitumor T Cell Responses and Improving M2 Macrophage Function. PMID:28848560
Integrated Computational Analysis of Genes Associated with Human Hereditary Insensitivity to Pain. A Drug Repurposing Perspective. PMID:28848388
Proteome dynamics and physiological responses to short-term salt stress in Leymus chinensis leaves. PMID:28846722
Novel and ultra-rare damaging variants in neuropeptide signaling are associated with disordered eating behaviors. PMID:28846695
Whole-genome sequencing reveals mutational landscape underlying phenotypic differences between two widespread Chinese cattle breeds. PMID:28841720
cDNA microarray analysis of human keratinocytes cells of patients submitted to chemoradiotherapy and oral photobiomodulation therapy: pilot study. PMID:28840431
Effects of short indels on protein structure and function in human genomes. PMID:28839204
Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse. PMID:28838066
Logic programming reveals alteration of key transcription factors in multiple myeloma. PMID:28835615
Rapid functional and evolutionary changes follow gene duplication in yeast. PMID:28835561
Multi-tissue RNA-seq and transcriptome characterisation of the spiny dogfish shark (Squalus acanthias) provides a molecular tool for biological research and reveals new genes involved in osmoregulation. PMID:28832628
Single-Nucleotide Polymorphisms in Vitamin D-Related Genes May Modify Vitamin D-Breast Cancer Associations. PMID:28830874
Protein microarray analysis identifies key cytokines associated with malignant middle cerebral artery infarction. PMID:28828208
Evolutionary shifts in gene expression decoupled from gene duplication across functionally distinct spider silk glands. PMID:28827773
Viral Infection Identifies Micropeptides Differentially Regulated in smORF-Containing lncRNAs. PMID:28825667
Genome-Wide Mapping of Transcriptional Regulation and Metabolism Describes Information-Processing Units in Escherichia coli. PMID:28824593
Neural Precursor-Derived Pleiotrophin Mediates Subventricular Zone Invasion by Glioma. PMID:28823557
A Systematic Analysis of Term Reuse and Term Overlap across Biomedical Ontologies. PMID:28819351
Discovering Condition-Specific Gene Co-Expression Patterns Using Gaussian Mixture Models: A Cancer Case Study. PMID:28819158
The impact of RNA sequence library construction protocols on transcriptomic profiling of leukemia. PMID:28818039
Time-resolved transcriptome analysis and lipid pathway reconstruction of the oleaginous green microalga Monoraphidium neglectum reveal a model for triacylglycerol and lipid hyperaccumulation. PMID:28814974
Assisted clustering of gene expression data using ANCut. PMID:28814280
Genome-wide association analysis reveals genetic loci and candidate genes for feeding behavior and eating efficiency in Duroc boars. PMID:28813538
Characterization of the Rosellinia necatrix Transcriptome and Genes Related to Pathogenesis by Single-Molecule mRNA Sequencing. PMID:28811753
Joint inflammation related citrullination of functional arginines in extracellular proteins. PMID:28811641
Identification of key genes and pathways associated with obesity in children. PMID:28810559
Strategies and tools to improve crop productivity by targeting photosynthesis. PMID:28808096
From Saccharomyces cerevisiae to human: The important gene co-expression modules. PMID:28804628
Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis. PMID:28804499
Use of biological priors enhances understanding of genetic architecture and genomic prediction of complex traits within and between dairy cattle breeds. PMID:28797230
ODG: Omics database generator - a tool for generating, querying, and analyzing multi-omics comparative databases to facilitate biological understanding. PMID:28797229
Similarities between plant traits based on their connection to underlying gene functions. PMID:28797052
Equine skeletal muscle adaptations to exercise and training: evidence of differential regulation of autophagosomal and mitochondrial components. PMID:28793853
Implicating candidate genes at GWAS signals by leveraging topologically associating domains. PMID:28792001
Molecular mechanisms of breast cancer metastasis by gene expression profile analysis. PMID:28791367
Identification of the anticancer effects of a novel proteasome inhibitor, ixazomib, on colorectal cancer using a combined method of microarray and bioinformatics analysis. PMID:28790851
CODA: Integrating multi-level context-oriented directed associations for analysis of drug effects. PMID:28790372
The purplish bifurcate mussel Mytilisepta virgata gene expression atlas reveals a remarkable tissue functional specialization. PMID:28789640
Hedgehog inhibitor sonidegib potentiates 177Lu-octreotate therapy of GOT1 human small intestine neuroendocrine tumors in nude mice. PMID:28789624
Identification of potential key genes associated with glioblastoma based on the gene expression profile. PMID:28789435
Cutaneous transcriptome analysis in NIH hairless mice. PMID:28787439
Commensal microbiota maintains alveolar macrophages with a low level of CCL24 production to generate anti-metastatic tumor activity. PMID:28785009
TROM: A Testing-Based Method for Finding Transcriptomic Similarity of Biological Samples. PMID:28781712
Systematic Selection of Reference Genes for the Normalization of Circulating RNA Transcripts in Pregnant Women Based on RNA-Seq Data. PMID:28777335
Genome-wide signatures of complex introgression and adaptive evolution in the big cats. PMID:28776029
High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460. PMID:28775794
Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins. PMID:28775330
Complete genome sequence of human pathogen Kosakonia cowanii type strain 888-76T. PMID:28774637
Characterization of the genome of a phylogenetically distinct tospovirus and its interactions with the local lesion-induced host Chenopodium quinoa by whole-transcriptome analyses. PMID:28771638
Complete genome sequence of the sand-sediment actinobacterium Nocardioides dokdonensis FR1436T. PMID:28770029
First draft genome sequence of a strain from the genus Fusibacter isolated from Salar de Ascotán in Northern Chile. PMID:28770028
The genome of the cotton bacterial blight pathogen Xanthomonas citri pv. malvacearum strain MSCT1. PMID:28770027
Quantitative Temporal in Vivo Proteomics Deciphers the Transition of Virus-Driven Myeloid Cells into M2 Macrophages. PMID:28768414
In silico analyses of conservational, functional and phylogenetic distribution of the LuxI and LuxR homologs in Gram-positive bacteria. PMID:28765541
PhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection. PMID:28761071
Differential regulation of germ line apoptosis and germ cell differentiation by CPEB family members in C. elegans. PMID:28759574
Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species. PMID:28756777
Transcriptome profiling of monocytes from XLA patients revealed the innate immune function dysregulation due to the BTK gene expression deficiency. PMID:28754963
Krüppel-like factor 4 acts as a potential therapeutic target of Sijunzi decoction for treatment of colorectal cancer. PMID:28752861
Prediction of novel target genes and pathways involved in irinotecan-resistant colorectal cancer. PMID:28749961
Insights into Cedecea neteri strain M006 through complete genome sequence, a rare bacterium from aquatic environment. PMID:28748024
Active nuclear transcriptome analysis reveals inflammasome-dependent mechanism for early neutrophil response to Mycobacterium marinum. PMID:28747644
Rapid evolution of female-biased genes among four species of Anopheles malaria mosquitoes. PMID:28747381
Protein Function Prediction Using Deep Restricted Boltzmann Machines. PMID:28744460
Transcriptomes and expression profiling of deep-sea corals from the Red Sea provide insight into the biology of azooxanthellate corals. PMID:28743941
The evolution of duplicate gene expression in mammalian organs. PMID:28743766
Novel Blood Pressure Locus and Gene Discovery Using Genome-Wide Association Study and Expression Data Sets From Blood and the Kidney. PMID:28739976
The prediction of late-onset preeclampsia: Results from a longitudinal proteomics study. PMID:28738067
Community detection in sequence similarity networks based on attribute clustering. PMID:28738060
Identification and Expression Profiling of Chemosensory Genes in Dendrolimus punctatus Walker. PMID:28736530
NoGOA: predicting noisy GO annotations using evidences and sparse representation. PMID:28732468
Identification of pivotal genes and pathways for spinal cord injury via bioinformatics analysis. PMID:28731189
iTRAQ-based Proteomic Analysis of APPSw,Ind Mice Provides Insights into the Early Changes in Alzheimer's Disease. PMID:28730955
The Functional Genetics of Handedness and Language Lateralization: Insights from Gene Ontology, Pathway and Disease Association Analyses. PMID:28729848
Draft Genome Sequence of the Polysaccharide-Degrading Marine Bacterium Pseudoalteromonas sp. Strain A601. PMID:28729260
Using Closure Tables to Enable Cross-Querying of Ontologies in Database-Driven Applications. PMID:28725879
Not just a colourful metaphor: modelling the landscape of cellular development using Hopfield networks. PMID:28725466
Gene expression reversal toward pre-adult levels in the aging human brain and age-related loss of cellular identity. PMID:28724976
Thioredoxin-Mediated ROS Homeostasis Explains Natural Variation in Plant Regeneration. PMID:28724620
Assessment of genome annotation using gene function similarity within the gene neighborhood. PMID:28724412
Quality assurance of chemical ingredient classification for the National Drug File - Reference Terminology. PMID:28723580
iTRAQ-based quantitative proteomic analysis reveals alterations in the metabolism of Actinidia arguta. PMID:28720800
CLIC, a tool for expanding biological pathways based on co-expression across thousands of datasets. PMID:28719601
Mutation intolerant genes and targets of FMRP are enriched for nonsynonymous alleles in schizophrenia. PMID:28719003
Transcriptome analysis uncovers Arabidopsis F-BOX STRESS INDUCED 1 as a regulator of jasmonic acid and abscisic acid stress gene expression. PMID:28716048
Resequencing and variation identification of whole genome of the japonica rice variety "Longdao24" with high yield. PMID:28715430
Gene microarray analysis of expression profiles in liver ischemia and reperfusion. PMID:28713993
Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks. PMID:28711280
Assessing glycolytic flux alterations resulting from genetic perturbations in E. coli using a biosensor. PMID:28709932
Molecular Mechanisms behind the Physiological Resistance to Intense Transient Warming in an Iconic Marine Plant. PMID:28706528
Lower Expression of SLC27A1 Enhances Intramuscular Fat Deposition in Chicken via Down-Regulated Fatty Acid Oxidation Mediated by CPT1A. PMID:28706492
Transcriptional consequences of XPA disruption in human cell lines. PMID:28704716
Opposing roles of Toll-like receptor and cytosolic DNA-STING signaling pathways for Staphylococcus aureus cutaneous host defense. PMID:28704551
A density-based approach for detecting complexes in weighted PPI networks by semantic similarity. PMID:28704455
Long noncoding RNA expression profile changes associated with dietary energy in the sheep testis during sexual maturation. PMID:28701734
HDNetDB: A Molecular Interaction Database for Network-Oriented Investigations into Huntington's Disease. PMID:28701700
Activating transcription factor 3 promotes loss of the acinar cell phenotype in response to cerulein-induced pancreatitis in mice. PMID:28701342
Lightweight predicate extraction for patient-level cancer information and ontology development. PMID:28699547
Genome-wide differential mRNA expression profiles in follicles of two breeds and at two stages of estrus cycle of gilts. PMID:28698542
Genome Sequence of Pseudomonas stutzeri 273 and Identification of the Exopolysaccharide EPS273 Biosynthesis Locus. PMID:28698510
GeNNet: an integrated platform for unifying scientific workflows and graph databases for transcriptome data analysis. PMID:28695067
Complete genome sequence of Microbulbifer sp. CCB-MM1, a halophile isolated from Matang Mangrove Forest, Malaysia. PMID:28694917
Whole-transcriptome analysis delineates the human placenta gene network and its associations with fetal growth. PMID:28693416
Metabolic modeling to identify engineering targets for Komagataella phaffii: The effect of biomass composition on gene target identification. PMID:28691262
Reduced Circulating Levels of miR-433 and miR-133b Are Potential Biomarkers for Parkinson's Disease. PMID:28690499
Salivary gland transcripts of the kissing bug, Panstrongylus chinai, a vector of Chagas disease. PMID:28690145
Replicable and Coupled Changes in Innate and Adaptive Immune Gene Expression in Two Case-Control Studies of Blood Microarrays in Major Depressive Disorder. PMID:28688579
Transcriptome and metabolome analysis of Ferula gummosa Boiss. to reveal major biosynthetic pathways of galbanum compounds. PMID:28687892
Strength of functional signature correlates with effect size in autism. PMID:28687074
The viable but nonculturable state induction and genomic analyses of Lactobacillus casei BM-LC14617, a beer-spoilage bacterium. PMID:28685978
Interpreting whole genome and exome sequencing data of individual gastric cancer samples. PMID:28683819
Microarray expression profile of circular RNAs in chronic thromboembolic pulmonary hypertension. PMID:28682884
Enriching plausible new hypothesis generation in PubMed. PMID:28678852
Transcriptomic profiling of Melilotus albus near-isogenic lines contrasting for coumarin content. PMID:28676637
Shaping functional gut microbiota using dietary bioactives to reduce colon cancer risk. PMID:28676459
A statistical framework for biomedical literature mining. PMID:28675924
Differential regulation of miRNA and mRNA expression in the myocardium of Nrf2 knockout mice. PMID:28673258
De novo transcriptome analysis shows differential expression of genes in salivary glands of edible bird's nest producing swiftlets. PMID:28673247
In-Depth Proteomic Analysis of the Hippocampus in a Rat Model after Cerebral Ischaemic Injury and Repair by Danhong Injection (DHI). PMID:28672812
[Screening of biomarkers related with leukocyte responses early after burn injury in mice by differential gene expression profiling]. PMID:28669950
Dissecting the role of non-coding RNAs in the accumulation of amyloid and tau neuropathologies in Alzheimer's disease. PMID:28668092
A molecular hypothesis to explain direct and inverse co-morbidities between Alzheimer's Disease, Glioblastoma and Lung cancer. PMID:28667284
RBM10 promotes transformation-associated processes in small cell lung cancer and is directly regulated by RBM5. PMID:28662214
Systematic bacterialization of yeast genes identifies a near-universally swappable pathway. PMID:28661399
Ten-eleven translocation 2 interacts with forkhead box O3 and regulates adult neurogenesis. PMID:28660881
System Level Meta-analysis of Microarray Datasets for Elucidation of Diabetes Mellitus Pathobiology. PMID:28659725
Predicting human protein subcellular localization by heterogeneous and comprehensive approaches. PMID:28658305
WetA bridges cellular and chemical development in Aspergillus flavus. PMID:28658268
Melatonin Suppresses Neuropathic Pain via MT2-Dependent and -Independent Pathways in Dorsal Root Ganglia Neurons of Mice. PMID:28656058
Alterations of expression of inflammation/immune-related genes in the dorsal and ventral striatum of adult C57BL/6J mice following chronic oxycodone self-administration: a RNA sequencing study. PMID:28653080
Identification of Jak-STAT signaling involvement in sarcoidosis severity via a novel microRNA-regulated peripheral blood mononuclear cell gene signature. PMID:28652588
Downregulation of PKCζ/Pard3/Pard6b is responsible for lung adenocarcinoma cell EMT and invasion. PMID:28652146
Data- and expert-driven rule induction and filtering framework for functional interpretation and description of gene sets. PMID:28651634
Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expression. PMID:28651633
Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction. PMID:28651538
Data on the genome-wide identification of CNL R-genes in Setaria italica (L.) P. Beauv. PMID:28649585
Integrating personalized gene expression profiles into predictive disease-associated gene pools. PMID:28649437
Comparative transcriptomic analysis of Gardnerella vaginalis biofilms vs. planktonic cultures using RNA-seq. PMID:28649404
Locally adapted populations of a copepod can evolve different gene expression patterns under the same environmental pressures. PMID:28649343
Identification of regulators of germ stem cell enwrapment by its niche in C. elegans. PMID:28648843
Analysis of MAP kinase MPK4/MEKK1/MKK genes of Carica papaya L. comparative to other plant homologues. PMID:28642634
Characterisation of Plasmodium falciparum populations selected on the human endothelial receptors P-selectin, E-selectin, CD9 and CD151. PMID:28642573
A sorghum (Sorghum bicolor) mutant with altered carbon isotope ratio. PMID:28640841
A Transcriptomic Analysis of Physiological Significance of Hypoxia-inducible Factor-1α in Myogenesis and Carbohydrate Metabolism of Genioglossus in Mice. PMID:28639573
Integration of transcriptomic and metabolic data reveals hub transcription factors involved in drought stress response in sunflower (Helianthus annuus L.). PMID:28639116
Weighted Gene Co-expression Network Analysis of the Dioscin Rich Medicinal Plant Dioscorea nipponica. PMID:28638386
Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges. PMID:28634997
Proteomic analysis reveals large amounts of decomposition enzymes and major metabolic pathways involved in algicidal process of Trametes versicolor F21a. PMID:28634367
Autophagy gene FIP200 in neural progenitors non-cell autonomously controls differentiation by regulating microglia. PMID:28634261
Reconstructing cell cycle pseudo time-series via single-cell transcriptome data. PMID:28630425
Exposure of Induced Pluripotent Stem Cell-Derived Vascular Endothelial and Smooth Muscle Cells in Coculture to Hemodynamics Induces Primary Vascular Cell-Like Phenotypes. PMID:28628273
Bioinformatics analysis of transcription profiling of solid pseudopapillary neoplasm of the pancreas. PMID:28627654
DUSP1 and KCNJ2 mRNA upregulation can serve as a biomarker of mechanical asphyxia-induced death in cardiac tissue. PMID:28624985
Drug repurposing for aging research using model organisms. PMID:28620943
ELIXIR pilot action: Marine metagenomics - towards a domain specific set of sustainable services. PMID:28620454
HGPEC: a Cytoscape app for prediction of novel disease-gene and disease-disease associations and evidence collection based on a random walk on heterogeneous network. PMID:28619054
Proteome profiling in IL-1β and VEGF-activated human umbilical vein endothelial cells delineates the interlink between inflammation and angiogenesis. PMID:28617818
In silico re-identification of properties of drug target proteins. PMID:28617227
Plasticity in gene transcription explains the differential performance of two invasive fish species. PMID:28616064
Differential effects of a post-anthesis heat stress on wheat (Triticum aestivum L.) grain proteome determined by iTRAQ. PMID:28615669
Improving the detection of pathways in genome-wide association studies by combined effects of SNPs from Linkage Disequilibrium blocks. PMID:28615668
De novo transcriptomic analysis and development of EST-SSRs for Sorbus pohuashanensis (Hance) Hedl. PMID:28614366
Multilineage communication regulates human liver bud development from pluripotency. PMID:28614297
Exosomes and Homeostatic Synaptic Plasticity Are Linked to Each other and to Huntington's, Parkinson's, and Other Neurodegenerative Diseases by Database-Enabled Analyses of Comprehensively Curated Datasets. PMID:28611571
Integration of quantitated expression estimates from polyA-selected and rRNA-depleted RNA-seq libraries. PMID:28610557
CHOmine: an integrated data warehouse for CHO systems biology and modeling. PMID:28605771
Workflow and web application for annotating NCBI BioProject transcriptome data. PMID:28605765
RNA-Sequence Analysis Reveals Differentially Expressed Genes (DEGs) in Patients Exhibiting Different Risks of Tumor Metastasis. PMID:28601889
Omics Data Complementarity Underlines Functional Cross-Communication in Yeast. PMID:28600905
Transcriptome of Pterospermum kingtungense provides implications on the mechanism underlying its rapid vegetative growth and limestone adaption. PMID:28600559
Functional dissection of human targets for KSHV-encoded miRNAs using network analysis. PMID:28600495
Uniform neural tissue models produced on synthetic hydrogels using standard culture techniques. PMID:28599598
mTFkb: a knowledgebase for fundamental annotation of mouse transcription factors. PMID:28596516
Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes. PMID:28596423
Sequencing, de novo assembling, and annotating the genome of the endangered Chinese crocodile lizard Shinisaurus crocodilurus. PMID:28595343
De novo transcriptome assembly and quantification reveal differentially expressed genes between soft-seed and hard-seed pomegranate (Punica granatum L.). PMID:28594931
Genomics insights into production of 2-methylisoborneol and a putative cyanobactin by Planktothricoides sp. SR001. PMID:28593028
Plasmobase: a comparative database of predicted domain architectures for Plasmodium genomes. PMID:28592293
NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation. PMID:28592275
Statistical analysis of fractionation resistance by functional category and expression. PMID:28589858
N-of-1-pathways MixEnrich: advancing precision medicine via single-subject analysis in discovering dynamic changes of transcriptomes. PMID:28589853
Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access. PMID:28588568
RNA sequencing and transcriptome arrays analyses show opposing results for alternative splicing in patient derived samples. PMID:28587590
Microarray profiling of long non-coding RNAs associated with idiopathic pulmonary arterial hypertension. PMID:28587327
Fine Mapping and Transcriptome Analysis Reveal Candidate Genes Associated with Hybrid Lethality in Cabbage (Brassica Oleracea). PMID:28587228
The IDA-LIKE peptides IDL6 and IDL7 are negative modulators of stress responses in Arabidopsis thaliana. PMID:28586470
MYC and hsa‑miRNA‑423‑5p as biomarkers in nasopharyngeal carcinoma revealed by miRNA‑mRNA‑pathway network integrated analysis. PMID:28586063
Identification and functional analysis of the risk microRNAs associated with cerebral low-grade glioma prognosis. PMID:28586047
Comparative transcriptome analysis of isonuclear-alloplasmic lines unmask key transcription factor genes and metabolic pathways involved in sterility of maize CMS-C. PMID:28584730
Physiological characteristics of Magnetospirillum gryphiswaldense MSR-1 that control cell growth under high-iron and low-oxygen conditions. PMID:28584275
An empirical analysis of ontology reuse in BioPortal. PMID:28583809
Gene expression and adaptive noncoding changes during human evolution. PMID:28583075
JDINAC: joint density-based non-parametric differential interaction network analysis and classification using high-dimensional sparse omics data. PMID:28582486
Co-expression analysis among microRNAs, long non-coding RNAs, and messenger RNAs to understand the pathogenesis and progression of diabetic kidney disease at the genetic level. PMID:28577935
The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies. PMID:28576844
Catch and Release of Cytokines Mediated by Tumor Phosphatidylserine Converts Transient Exposure into Long-Lived Inflammation. PMID:28575659
Databases, Repositories, and Other Data Resources in Structural Biology. PMID:28573593
Genetic subclone architecture of tumor clone-initiating cells in colorectal cancer. PMID:28572216
De novo characterization of the pine aphid Cinara pinitabulaeformis Zhang et Zhang transcriptome and analysis of genes relevant to pesticides. PMID:28570707
Identification of key genes and pathways for peri-implantitis through the analysis of gene expression data. PMID:28565775
Identification of potential biomarkers of sepsis using bioinformatics analysis. PMID:28565754
Properties of genes essential for mouse development. PMID:28562614
MicroRNA profiling in the dentate gyrus in epileptic rats: The role of miR-187-3p. PMID:28562528
Systematic discovery of mutation-specific synthetic lethals by mining pan-cancer human primary tumor data. PMID:28561042
Bioinformatics analyses of the differences between lung adenocarcinoma and squamous cell carcinoma using The Cancer Genome Atlas expression data. PMID:28560415
DNA methylation in schizophrenia in different patient-derived cell types. PMID:28560252
Gene Set Enrichment Analyses: lessons learned from the heart failure phenotype. PMID:28559929
Auxin regulates functional gene groups in a fold-change-specific manner in Arabidopsis thaliana roots. PMID:28559568
In vitro expansion of mouse primordial germ cell-like cells recapitulates an epigenetic blank slate. PMID:28559416
In-depth genome characterization of a Brazilian common bean core collection using DArTseq high-density SNP genotyping. PMID:28558696
A dual-strategy expression screen for candidate connectivity labels in the developing thalamus. PMID:28558017
Bactericidal potential of silver nanoparticles synthesized using cell-free extract of Comamonas acidovorans: in vitro and in silico approaches. PMID:28555428
Methylated cis-regulatory elements mediate KLF4-dependent gene transactivation and cell migration. PMID:28553926
Co-Inflammatory Roles of TGFβ1 in the Presence of TNFα Drive a Pro-inflammatory Fate in Mesenchymal Stem Cells. PMID:28553282
Biallelic Mutations in CFAP43 and CFAP44 Cause Male Infertility with Multiple Morphological Abnormalities of the Sperm Flagella. PMID:28552195
Testing for differentially expressed genetic pathways with single-subject N-of-1 data in the presence of inter-gene correlation. PMID:28552011
Genomic Analysis of Genotype-by-Social Environment Interaction for Drosophila melanogaster Aggressive Behavior. PMID:28550016
Genomic adaptation to agricultural environments: cabbage white butterflies (Pieris rapae) as a case study. PMID:28549454
Multiple Trait Covariance Association Test Identifies Gene Ontology Categories Associated with Chill Coma Recovery Time in Drosophila melanogaster. PMID:28546557
Type 2 diabetes and obesity induce similar transcriptional reprogramming in human myocytes. PMID:28545587
Optimizing complex phenotypes through model-guided multiplex genome engineering. PMID:28545477
Bacterial Virus Ontology; Coordinating across Databases. PMID:28545254
A resource of potential drug targets and strategic decision-making for obstructive sleep apnoea pharmacotherapy. PMID:28544082
Genes and gene clusters related to genotype and drought-induced variation in saccharification potential, lignin content and wood anatomical traits in Populus nigra. PMID:28541580
GLANET: genomic loci annotation and enrichment tool. PMID:28541490
The genome sequence of sweet cherry (Prunus avium) for use in genomics-assisted breeding. PMID:28541388
Plasma and White Blood Cells Show Different miRNA Expression Profiles in Parkinson's Disease. PMID:28540642
Dynamic regulation of VEGF-inducible genes by an ERK/ERG/p300 transcriptional network. PMID:28536097
HGVA: the Human Genome Variation Archive. PMID:28535294
The draft genome of blunt snout bream (Megalobrama amblycephala) reveals the development of intermuscular bone and adaptation to herbivorous diet. PMID:28535200
Transcriptome analyses provide insights into the difference of alkaloids biosynthesis in the Chinese goldthread (Coptis chinensis Franch.) from different biotopes. PMID:28533961
Genome-wide association meta-analysis of 78,308 individuals identifies new loci and genes influencing human intelligence. PMID:28530673
Identification of Transcriptional Modules and Key Genes in Chickens Infected with Salmonella enterica Serovar Pullorum Using Integrated Coexpression Analyses. PMID:28529955
Gene expression of Vibrio parahaemolyticus growing in laboratory isolation conditions compared to those common in its natural ocean environment. PMID:28525966
Gene co-expression network analysis for identifying modules and functionally enriched pathways in SCA2. PMID:28525545
A computational framework for distinguishing direct versus indirect interactions in human functional protein-protein interaction networks. PMID:28524201
Label-Free Quantitative Proteomic Analysis of Chitosan Oligosaccharide-Treated Rice Infected with Southern Rice Black-Streaked Dwarf Virus. PMID:28524115
Drosophila melanogaster positive transcriptional elongation factors regulate metabolic and sex-biased expression in adults. PMID:28521739
GeMSTONE: orchestrated prioritization of human germline mutations in the cloud. PMID:28521008
De novo assembly and comparative transcriptome analysis of the foot from Chinese green mussel (Perna viridis) in response to cadmium stimulation. PMID:28520756
Computational Exploration of Putative LuxR Solos in Archaea and Their Functional Implications in Quorum Sensing. PMID:28515720
Architecture of the human interactome defines protein communities and disease networks. PMID:28514442
Insights into the Mechanism of Proliferation on the Special Microbes Mediated by Phenolic Acids in the Radix pseudostellariae Rhizosphere under Continuous Monoculture Regimes. PMID:28512464
Global gene expression analysis provides insight into local adaptation to geothermal streams in tadpoles of the Andean toad Rhinella spinulosa. PMID:28512324
Long noncoding RNA expression profile in HLE B-3 cells during TGF-β2-induced epithelial-mesenchymal transition. PMID:28511643
Application of a systems approach to study developmental gene regulation. PMID:28510076
Functional annotation of a novel toxin-antitoxin system Xn-RelT of Xenorhabdus nematophila; a combined in silico and in vitro approach. PMID:28508139
Deletion Extents Are Not the Cause of Clinical Variability in 22q11.2 Deletion Syndrome: Does the Interaction between DGCR8 and miRNA-CNVs Play a Major Role? PMID:28507561
Aberrant promoter methylation profiles and association with survival in patients with hepatocellular carcinoma. PMID:28507442
Expansion of the redox-sensitive proteome coincides with the plastid endosymbiosis. PMID:28504699
Transcriptomic and macroevolutionary evidence for phenotypic uncoupling between frog life history phases. PMID:28504275
The Distinct Transcriptional Response of the Midgut of Amblyomma sculptum and Amblyomma aureolatum Ticks to Rickettsia rickettsii Correlates to Their Differences in Susceptibility to Infection. PMID:28503490
Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks. PMID:28499419
Genome-wide characterization and expression analyses of superoxide dismutase (SOD) genes in Gossypium hirsutum. PMID:28499417
Specific MicroRNA Pattern in Colon Tissue of Young Children with Eosinophilic Colitis. PMID:28498330
Chromosomal features of Escherichia coli serotype O2:K2, an avian pathogenic E. coli. PMID:28496941
Leveraging multiple genomic data to prioritize disease-causing indels from exome sequencing data. PMID:28496131
A new two-stage method for revealing missing parts of edges in protein-protein interaction networks. PMID:28493910
High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482T, isolated from raw cow milk. PMID:28491240
Transcriptional response profiles of paired tumor-normal samples offer novel perspectives in pan-cancer analysis. PMID:28489584
Investigating the neuroimmunogenic architecture of schizophrenia. PMID:28485405
Exosomes in mammals with greater habitat variability contain more proteins and RNAs. PMID:28484642
Genome sequencing and description of Oerskovia enterophila VJag, an agar- and cellulose-degrading bacterium. PMID:28484582
Transcriptome Analysis of Arabidopsis thaliana in Response to Plasmodiophora brassicae during Early Infection. PMID:28484434
Altered interactions between unicellular and multicellular genes drive hallmarks of transformation in a diverse range of solid tumors. PMID:28484005
Substrates and oxygen dependent citric acid production by Yarrowia lipolytica: insights through transcriptome and fluxome analyses. PMID:28482902
Inferring miRNA sponge co-regulation of protein-protein interactions in human breast cancer. PMID:28482794
Hypoxia-driven splicing into noncoding isoforms regulates the DNA damage response. PMID:28480052
Effects of dietary physical or nutritional factors on morphology of rumen papillae and transcriptome changes in lactating dairy cows based on three different forage-based diets. PMID:28477620
Tradict enables accurate prediction of eukaryotic transcriptional states from 100 marker genes. PMID:28474674
Annotating function to differentially expressed LincRNAs in myelodysplastic syndrome using a network-based method. PMID:28472271
The highly buffered Arabidopsis immune signaling network conceals the functions of its components. PMID:28472137
Transcriptome analysis of muskrat scented glands degeneration mechanism. PMID:28472080
Using hyperLOPIT to perform high-resolution mapping of the spatial proteome. PMID:28471460
PAIRS: Prediction of Activation/Inhibition Regulation Signaling Pathway. PMID:28469669
Use of Biomedical Ontologies for Integration of Biological Knowledge for Learning and Prediction of Adverse Drug Reactions. PMID:28469412
An Integrative Genomics Approach for Associating Genome-Wide Association Studies Information With Localized and Metastatic Prostate Cancer Phenotypes. PMID:28469398
Transcriptional dissection of melanoma identifies a high-risk subtype underlying TP53 family genes and epigenome deregulation. PMID:28469092
Proteomic anaysis of aged microglia: shifts in transcription, bioenergetics, and nutrient response. PMID:28468668
A subset of microRNAs defining the side population of a human malignant mesothelioma cell line. PMID:28467812
The natural history of molecular functions inferred from an extensive phylogenomic analysis of gene ontology data. PMID:28467492
Gene co-expression network analysis identifies porcine genes associated with variation in metabolizing fenbendazole and flunixin meglumine in the liver. PMID:28465592
Oxidation of protein-bound methionine in Photofrin-photodynamic therapy-treated human tumor cells explored by methionine-containing peptide enrichment and quantitative proteomics approach. PMID:28465586
Expression profile of mitochondrial voltage-dependent anion channel-1 (VDAC1) influenced genes is associated with pulmonary hypertension. PMID:28461778
Accumulation, elimination, sequestration, and genetic variation of lead (Pb2+) loads within and between generations of Drosophila melanogaster. PMID:28458212
QueryOR: a comprehensive web platform for genetic variant analysis and prioritization. PMID:28454514
Identification of molecular characteristics induced by radiotherapy in rectal cancer based on microarray data. PMID:28454466
A comprehensive analysis of cancer-driving mutations and genes in kidney cancer. PMID:28454375
Exploring a causal role of DNA methylation in the relationship between maternal vitamin B12 during pregnancy and child's IQ at age 8, cognitive performance and educational attainment: a two-step Mendelian randomization study. PMID:28453778
1000 Genomes-based meta-analysis identifies 10 novel loci for kidney function. PMID:28452372
An integrated RNAseq-1H NMR metabolomics approach to understand soybean primary metabolism regulation in response to Rhizoctonia foliar blight disease. PMID:28449662
Neuro-symbolic representation learning on biological knowledge graphs. PMID:28449114
Evolutionary history of Tibetans inferred from whole-genome sequencing. PMID:28448578
Tracking disease progression by searching paths in a temporal network of biological processes. PMID:28448511
Little Cigars are More Toxic than Cigarettes and Uniquely Change the Airway Gene and Protein Expression. PMID:28447619
PARP3 is a promoter of chromosomal rearrangements and limits G4 DNA. PMID:28447610
Mining a differential sialotranscriptome of Rhipicephalus microplus guides antigen discovery to formulate a vaccine that reduces tick infestations. PMID:28446245
Draft genome of the lined seahorse, Hippocampus erectus. PMID:28444302
Prediction of optimal gene functions for osteosarcoma using network-based- guilt by association method based on gene oncology and microarray profile. PMID:28443230
Transcriptome Analysis of a Female-sterile Mutant (fsm) in Chinese Cabbage (Brassica campestris ssp. pekinensis). PMID:28443127
Genome Sequencing Reveals the Complex Polysaccharide-Degrading Ability of Novel Deep-Sea Bacterium Flammeovirga pacifica WPAGA1. PMID:28443080
Proteomic mapping of cytosol-facing outer mitochondrial and ER membranes in living human cells by proximity biotinylation. PMID:28441135
Next-generation DNA sequencing identifies novel gene variants and pathways involved in specific language impairment. PMID:28440294
Modulated evaluation metrics for drug-based ontologies. PMID:28438189
The predictive nature of transcript expression levels on protein expression in adult human brain. PMID:28438116
Peripheral leukocyte microRNAs as novel biomarkers for COPD. PMID:28435243
Hierarchical Feature Selection Incorporating Known and Novel Biological Information: Identifying Genomic Features Related to Prostate Cancer Recurrence. PMID:28435175
Transcriptional Dependencies in Diffuse Intrinsic Pontine Glioma. PMID:28434841
Systematic Synergy of Glucose and GLP-1 to Stimulate Insulin Secretion Revealed by Quantitative Phosphoproteomics. PMID:28432305
A microRNA-mRNA expression network during oral siphon regeneration in Ciona. PMID:28432214
Mapping genes for calcium signaling and their associated human genetic disorders. PMID:28430858
A large-scale benchmark of gene prioritization methods. PMID:28429739
A mouse tissue transcription factor atlas. PMID:28429721
Gene expression profiling during the embryo-to-larva transition in the giant red sea urchin Mesocentrotus franciscanus. PMID:28428870
Genome sequencing and analysis of Ralstonia solanacearum phylotype I strains FJAT-91, FJAT-452 and FJAT-462 isolated from tomato, eggplant, and chili pepper in China. PMID:28428834
Complete genome sequence of Kosakonia oryzae type strain Ola 51T. PMID:28428833
A meta-analysis testing eusocial co-option theories in termite gut physiology and symbiosis. PMID:28428832
Identification of Candidate Genes and Biosynthesis Pathways Related to Fertility Conversion by Wheat KTM3315A Transcriptome Profiling. PMID:28428792
Draft Genome Sequence of Methylocaldum sp. Strain 14B, an Obligate Hydrogen Sulfide-Tolerant Methanotrophic Strain That Can Convert Biogas to Methanol. PMID:28428289
Pan genome and CRISPR analyses of the bacterial fish pathogen Moritella viscosa. PMID:28427330
Detection of QTL for traits related to adaptation to sub-optimal climatic conditions in chickens. PMID:28427323
Multiple components of PKA and TGF-β pathways are mutated in pseudomyxoma peritonei. PMID:28426742
Unified Alignment of Protein-Protein Interaction Networks. PMID:28424527
Chromatin module inference on cellular trajectories identifies key transition points and poised epigenetic states in diverse developmental processes. PMID:28424352
Transcriptome and proteome responses in RNAlater preserved tissue of Arabidopsis thaliana. PMID:28423006
SEL120-34A is a novel CDK8 inhibitor active in AML cells with high levels of serine phosphorylation of STAT1 and STAT5 transactivation domains. PMID:28422713
Delineating the Common Biological Pathways Perturbed by ASD's Genetic Etiology: Lessons from Network-Based Studies. PMID:28420080
The E. coli molecular phenotype under different growth conditions. PMID:28417974
Comparative Transcriptome Sequence Analysis of Sporulation-Related Genes of Aspergillus cristatus in Response to Low and High Osmolarity. PMID:28417188
Identification of driver modules in pan-cancer via coordinating coverage and exclusivity. PMID:28415609
Constructing a biodiversity terminological inventory. PMID:28414821
Cyclosporine A alters expression of renal microRNAs: New insights into calcineurin inhibitor nephrotoxicity. PMID:28414804
Semantic prioritization of novel causative genomic variants. PMID:28414800
L1000CDS2: LINCS L1000 characteristic direction signatures search engine. PMID:28413689
Identification of genes associated with the effect of inflammation on the neurotransmission of vascular smooth muscle cell. PMID:28413470
goSTAG: gene ontology subtrees to tag and annotate genes within a set. PMID:28413437
Poplar stem transcriptome is massively remodelled in response to single or repeated mechanical stimuli. PMID:28412928
Comparison of different cell type correction methods for genome-scale epigenetics studies. PMID:28410574
Genetic variant of miR-4293 rs12220909 is associated with susceptibility to non-small cell lung cancer in a Chinese Han population. PMID:28410417
Exploring the key genes and pathways in enchondromas using a gene expression microarray. PMID:28410203
Outlier analyses to test for local adaptation to breeding grounds in a migratory arctic seabird. PMID:28405300
Comparative Analysis of Expression Profiles of Panicle Development among Tolerant and Sensitive Rice in Response to Drought Stress. PMID:28405199
Atrial electrophysiological and molecular remodelling induced by obstructive sleep apnoea. PMID:28402037
IGF2BP3 functions as a potential oncogene and is a crucial target of miR-34a in gastric carcinogenesis. PMID:28399871
Comparative transcriptome profiling and morphology provide insights into endocarp cleaving of apricot cultivar (Prunus armeniaca L.). PMID:28399812
Rare copy number variants in patients with congenital conotruncal heart defects. PMID:28398664
Systemic evaluation of cellular reprogramming processes exploiting a novel R-tool: eegc. PMID:28398503
Genetic architecture of gene expression underlying variation in host response to porcine reproductive and respiratory syndrome virus infection. PMID:28393889
Microarray‑based screening of differentially expressed genes in glucocorticoid‑induced avascular necrosis. PMID:28393228
eTumorType, An Algorithm of Discriminating Cancer Types for Circulating Tumor Cells or Cell-free DNAs in Blood. PMID:28389380
Sex-specific differences in transcriptome profiles of brain and muscle tissue of the tropical gar. PMID:28388875
Integrated network analysis reveals potentially novel molecular mechanisms and therapeutic targets of refractory epilepsies. PMID:28388656
Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells. PMID:28388430
An Approach to Spatiotemporally Resolve Protein Interaction Networks in Living Cells. PMID:28388416
The anatomy of phenotype ontologies: principles, properties and applications. PMID:28387809
Whole-transcriptome RNA-seq, gene set enrichment pathway analysis, and exon coverage analysis of two plastid RNA editing mutants. PMID:28387567
Identification of prognostic genes and gene sets for early-stage non-small cell lung cancer using bi-level selection methods. PMID:28387364
Transcriptome Analyses of Two Citrus Cultivars (Shiranuhi and Huangguogan) in Seedling Etiolation. PMID:28387303
Bioinformatics and co-expression network analysis of differentially expressed lncRNAs and mRNAs in hippocampus of APP/PS1 transgenic mice with Alzheimer disease. PMID:28386363
Case-control analysis of truncating mutations in DNA damage response genes connects TEX15 and FANCD2 with hereditary breast cancer susceptibility. PMID:28386063
Protease-Inhibitor Interaction Predictions: Lessons on the Complexity of Protein-Protein Interactions. PMID:28385878
Glucocorticoid receptor binding to chromatin is selectively controlled by the coregulator Hic-5 and chromatin remodeling enzymes. PMID:28381557
Fuento: functional enrichment for bioinformatics. PMID:28379299
Comparative Genomics Analysis of a New Exiguobacterium Strain from Salar de Huasco Reveals a Repertoire of Stress-Related Genes and Arsenic Resistance. PMID:28377753
The Transcriptome of Leishmania major Developmental Stages in Their Natural Sand Fly Vector. PMID:28377524
The Biological Function of the Prion Protein: A Cell Surface Scaffold of Signaling Modules. PMID:28373833
A New Natural Product Analog of Blasticidin S Reveals Cellular Uptake Facilitated by the NorA Multidrug Transporter. PMID:28373194
Tracking the evolution of 3D gene organization demonstrates its connection to phenotypic divergence. PMID:28369658
Stress-dependent opposing roles for mitophagy in aging of the ascomycete Podospora anserina. PMID:28368682
Genome-wide sequencing of longan (Dimocarpus longan Lour.) provides insights into molecular basis of its polyphenol-rich characteristics. PMID:28368449
Genetic variation in the exome: Associations with alcohol and tobacco co-use. PMID:28368157
Protein-coding genes in B chromosomes of the grasshopper Eyprepocnemis plorans. PMID:28367986
Proteomic signature of muscle fibre hyperplasia in response to faba bean intake in grass carp. PMID:28367976
Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD). PMID:28365740
Better living through ontologies at the Immune Epitope Database. PMID:28365732
PCPPI: a comprehensive database for the prediction of Penicillium-crop protein-protein interactions. PMID:28365721
BELMiner: adapting a rule-based relation extraction system to extract biological expression language statements from bio-medical literature evidence sentences. PMID:28365720
Comparative analysis of MBD-seq and MeDIP-seq and estimation of gene expression changes in a rodent model of schizophrenia. PMID:28365388
Neuroserpin polymers cause oxidative stress in a neuronal model of the dementia FENIB. PMID:28363799
Systems biology of facial development: contributions of ectoderm and mesenchyme. PMID:28363736
Interrogating the topological robustness of gene regulatory circuits by randomization. PMID:28362798
Finding low-conductance sets with dense interactions (FLCD) for better protein complex prediction. PMID:28361714
SEQUOIA: significance enhanced network querying through context-sensitive random walk and minimization of network conductance. PMID:28361708
In silico prediction of lncRNA function using tissue specific and evolutionary conserved expression. PMID:28361701
NEArender: an R package for functional interpretation of 'omics' data via network enrichment analysis. PMID:28361684
Comparative network stratification analysis for identifying functional interpretable network biomarkers. PMID:28361683
Identifying miRNA sponge modules using biclustering and regulatory scores. PMID:28361682
DIGNiFI: Discovering causative genes for orphan diseases using protein-protein interaction networks. PMID:28361678
Enhancement of Arabidopsis growth characteristics using genome interrogation with artificial transcription factors. PMID:28358915
Olfactory effects of a hypervariable multicomponent pheromone in the red-legged salamander, Plethodon shermani. PMID:28358844
Construction and evaluation of yeast expression networks by database-guided predictions. PMID:28357360
The druggable genome and support for target identification and validation in drug development. PMID:28356508
Distribution of Secretion Systems in the Genus Legionella and Its Correlation with Pathogenicity. PMID:28352254
Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines. PMID:28350380
Identification of Key Candidate Genes and Pathways in Colorectal Cancer by Integrated Bioinformatical Analysis. PMID:28350360
Time-matched analysis of DNA adduct formation and early gene expression as predictive tool for renal carcinogenesis in methylazoxymethanol acetate treated Eker rats. PMID:28349193
Integrated analysis of microRNA and mRNA expression profiles in HBx-expressing hepatic cells. PMID:28348484
Draft genome analysis of Dietzia sp. 111N12-1, isolated from the South China Sea with bioremediation activity. PMID:28347590
Gene Expression, Protein Function and Pathways of Arabidopsis thaliana Responding to Silver Nanoparticles in Comparison to Silver Ions, Cold, Salt, Drought, and Heat. PMID:28347022
Computational identifying and characterizing circular RNAs and their associated genes in hepatocellular carcinoma. PMID:28346469
A Genome-wide Analysis of Human Pluripotent Stem Cell-Derived Endothelial Cells in 2D or 3D Culture. PMID:28343999
PML protein organizes heterochromatin domains where it regulates histone H3.3 deposition by ATRX/DAXX. PMID:28341773
Genomic Comparison of Indigenous African and Northern European Chickens Reveals Putative Mechanisms of Stress Tolerance Related to Environmental Selection Pressure. PMID:28341699
Genome evolutionary dynamics followed by diversifying selection explains the complexity of the Sesamum indicum genome. PMID:28340563
RNA Editing During Sexual Development Occurs in Distantly Related Filamentous Ascomycetes. PMID:28338982
EXPath tool-a system for comprehensively analyzing regulatory pathways and coexpression networks from high-throughput transcriptome data. PMID:28338930
Exploring Approaches for Detecting Protein Functional Similarity within an Orthology-based Framework. PMID:28336965
APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins. PMID:28334975
High resolution time-course mapping of early transcriptomic, molecular and cellular phenotypes in Huntington's disease CAG knock-in mice across multiple genetic backgrounds. PMID:28334820
Introducing crucial protein panel of gastric adenocarcinoma disease. PMID:28331560
Transcriptome analysis of endometrial tissues following GnRH agonist treatment in a mouse adenomyosis model. PMID:28331289
De novo transcriptome sequencing in Monsonia burkeana revealed putative genes for key metabolic pathways involved in tea quality and medicinal value. PMID:28330322
Hugonella massiliensis gen. nov., sp. nov., genome sequence, and description of a new strictly anaerobic bacterium isolated from the human gut. PMID:28326685
Disease Risk Assessment Using a Voronoi-Based Network Analysis of Genes and Variants Scores. PMID:28326099
TheCellMap.org: A Web-Accessible Database for Visualizing and Mining the Global Yeast Genetic Interaction Network. PMID:28325812
In search of genome annotation consistency: solid gene clusters and how to use them. PMID:28324432
Exploring the FGFR3-related oncogenic mechanism in bladder cancer using bioinformatics strategy. PMID:28320388
NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology. PMID:28320317
Comparative transcriptome analyses of flower development in four species of Achimenes (Gesneriaceae). PMID:28320315
The histone demethylase KDM3A, and its downstream target MCAM, promote Ewing Sarcoma cell migration and metastasis. PMID:28319067
Isocitrate dehydrogenase mutations suppress STAT1 and CD8+ T cell accumulation in gliomas. PMID:28319047
SWIM: a computational tool to unveiling crucial nodes in complex biological networks. PMID:28317894
Complete genome sequencing and antibiotics biosynthesis pathways analysis of Streptomyces lydicus 103. PMID:28317865
Functional proteomic analysis of corticosteroid pharmacodynamics in rat liver: Relationship to hepatic stress, signaling, energy regulation, and drug metabolism. PMID:28315483
Comprehensive Analysis of MILE Gene Expression Data Set Advances Discovery of Leukaemia Type and Subtype Biomarkers. PMID:28303531
NEUROD2 Regulates Stim1 Expression and Store-Operated Calcium Entry in Cortical Neurons. PMID:28303257
Deciphering the Acute Cellular Phosphoproteome Response to Irradiation with X-rays, Protons and Carbon Ions. PMID:28302921
Complete genome sequence of Pseudomonas citronellolis P3B5, a candidate for microbial phyllo-remediation of hydrocarbon-contaminated sites. PMID:28300228
Systems-level understanding of ethanol-induced stresses and adaptation in E. coli. PMID:28300180
Transcriptomic Analysis Reveals Mechanisms of Sterile and Fertile Flower Differentiation and Development in Viburnum macrocephalum f. keteleeri. PMID:28298915
Systematic protein-protein interaction mapping for clinically relevant human GPCRs. PMID:28298427
Network reconstruction of the mouse secretory pathway applied on CHO cell transcriptome data. PMID:28298216
Autism gene Ube3a and seizures impair sociability by repressing VTA Cbln1. PMID:28297715
Approximating the correction of weighted and unweighted orthology and paralogy relations. PMID:28293276
Comprehensive discovery of subsample gene expression components by information explanation: therapeutic implications in cancer. PMID:28292312
Modeling anorexia nervosa: transcriptional insights from human iPSC-derived neurons. PMID:28291261
Meta-Analysis of Gene Expression Profiles in Acute Promyelocytic Leukemia Reveals Involved Pathways. PMID:28286608
Global Transcriptome Analysis and Identification of Differentially Expressed Genes in Strawberry after Preharvest Application of Benzothiadiazole and Chitosan. PMID:28286508
Proteome-Scale Human Interactomics. PMID:28284537
Mitochondrial chaperone HSP-60 regulates anti-bacterial immunity via p38 MAP kinase signaling. PMID:28283579
Gene Expression Profiling with Cre-Conditional Pseudorabies Virus Reveals a Subset of Midbrain Neurons That Participate in Reward Circuitry. PMID:28283558
The essential and downstream common proteins of amyotrophic lateral sclerosis: A protein-protein interaction network analysis. PMID:28282387
Gene expression metadata analysis reveals molecular mechanisms employed by Phanerochaete chrysosporium during lignin degradation and detoxification of plant extractives. PMID:28275822
Systemic QSAR and phenotypic virtual screening: chasing butterflies in drug discovery. PMID:28274840
MC4R-dependent suppression of appetite by bone-derived lipocalin 2. PMID:28273060
Transcriptomic insight into terpenoid and carbazole alkaloid biosynthesis, and functional characterization of two terpene synthases in curry tree (Murraya koenigii). PMID:28272514
Identification and characterization of differentially expressed miRNAs in subcutaneous adipose between Wagyu and Holstein cattle. PMID:28272430
High-quality permanent draft genome sequence of the Bradyrhizobium elkanii type strain USDA 76T, isolated from Glycine max (L.) Merr. PMID:28270909
Differential Transcriptional Regulation in Roots of Tomato Near-Isogenic Lines in Response to Rapid-Onset Water Stress. PMID:28270818
Tracking the Remodeling of SNOMED CT's Bacterial Infectious Diseases. PMID:28269894
Mapping the function of neuronal ion channels in model and experiment. PMID:28267430
The Role of Lipid Droplets in Mortierella alpina Aging Revealed by Integrative Subcellular and Whole-Cell Proteome Analysis. PMID:28266581
High quality draft genome sequence of an extremely halophilic archaeon Natrinema altunense strain AJ2T. PMID:28265340
Transcriptomes of three species of Tipuloidea (Diptera, Tipulomorpha) and implications for phylogeny of Tipulomorpha. PMID:28264066
The maternal plasma proteome changes as a function of gestational age in normal pregnancy: a longitudinal study. PMID:28263753
Social network architecture of human immune cells unveiled by quantitative proteomics. PMID:28263321
Whole-genome sequencing identifies common-to-rare variants associated with human blood metabolites. PMID:28263315
Screening of potential gene markers for predicting carotid atheroma plaque formation using bioinformatics approaches. PMID:28260035
Identification of key genes and pathways associated with spinal cord injury. PMID:28259986
Avoiding the pitfalls of gene set enrichment analysis with SetRank. PMID:28259142
Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem. PMID:28258138
Sharing Big Data. PMID:28250936
High-quality-draft genome sequence of the fermenting bacterium Anaerobium acetethylicum type strain GluBS11T (DSM 29698). PMID:28250895
Medical Subject Heading (MeSH) annotations illuminate maize genetics and evolution. PMID:28250803
The amyloid interactome: Exploring protein aggregation. PMID:28249044
Evolution of protein-protein interaction networks in yeast. PMID:28248977
Dynamic gene expression analysis in a H1N1 influenza virus mouse pneumonia model. PMID:28243843
Computer-Aided Experiment Planning toward Causal Discovery in Neuroscience. PMID:28243197
The Echinococcus canadensis (G7) genome: a key knowledge of parasitic platyhelminth human diseases. PMID:28241794
Cyclin Y-mediated transcript profiling reveals several important functional pathways regulated by Cyclin Y in hippocampal neurons. PMID:28241067
Asymmetric interactions between doublesex and tissue- and sex-specific target genes mediate sexual dimorphism in beetles. PMID:28239147
Genes encoding intrinsic disorder in Eukaryota have high GC content. PMID:28232902
Exploratory bioinformatics investigation reveals importance of "junk" DNA in early embryo development. PMID:28231763
Mining Cancer Transcriptomes: Bioinformatic Tools and the Remaining Challenges. PMID:28229366
Transcriptomic responses of the olive fruit fly Bactrocera oleae and its symbiont Candidatus Erwinia dacicola to olive feeding. PMID:28225009
Identification of novel cancer therapeutic targets using a designed and pooled shRNA library screen. PMID:28223711
Identification of miRNA-mRNA crosstalk in CD4+ T cells during HIV-1 infection by integrating transcriptome analyses. PMID:28222782
ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data. PMID:28222698
The fire ant social chromosome supergene variant Sb shows low diversity but high divergence from SB. PMID:28220980
Chronic nicotine differentially affects murine transcriptome profiling in isolated cortical interneurons and pyramidal neurons. PMID:28219337
The effects of shared information on semantic calculations in the gene ontology. PMID:28217262
Analyzing structural changes in SNOMED CT's Bacterial infectious diseases using a visual semantic delta. PMID:28215561
SCALEUS: Semantic Web Services Integration for Biomedical Applications. PMID:28214993
Genome-wide identification of direct HBx genomic targets. PMID:28212627
De novo assembly of the sea trout (Salmo trutta m. trutta) skin transcriptome to identify putative genes involved in the immune response and epidermal mucus secretion. PMID:28212382
The Effect of the Human Peptide GHK on Gene Expression Relevant to Nervous System Function and Cognitive Decline. PMID:28212278
gsSKAT: Rapid gene set analysis and multiple testing correction for rare-variant association studies using weighted linear kernels. PMID:28211093
Resequencing and annotation of the Nostoc punctiforme ATTC 29133 genome: facilitating biofuel and high-value chemical production. PMID:28211005
RNA-Seq of Guar (Cyamopsis tetragonoloba, L. Taub.) Leaves: De novo Transcriptome Assembly, Functional Annotation and Development of Genomic Resources. PMID:28210265
The ins and outs of eukaryotic viruses: Knowledge base and ontology of a viral infection. PMID:28207819
A familial study of azoospermic men identifies three novel causative mutations in three new human azoospermia genes. PMID:28206990
Association of 15-hydroxyprostaglandin dehydrogenate and poor prognosis of obese breast cancer patients. PMID:28206964
The OncoPPi network of cancer-focused protein-protein interactions to inform biological insights and therapeutic strategies. PMID:28205554
CisMapper: predicting regulatory interactions from transcription factor ChIP-seq data. PMID:28204599
Using predictive specificity to determine when gene set analysis is biologically meaningful. PMID:28204549
The complete genome sequence of the phytopathogenic fungus Sclerotinia sclerotiorum reveals insights into the genome architecture of broad host range pathogens. PMID:28204478
Predicting disease-related genes using integrated biomedical networks. PMID:28198675
Dynamic changes in the transcriptome of Populus hopeiensis in response to abscisic acid. PMID:28198429
Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. PMID:28196534
Genetic analysis of impaired trimethylamine metabolism using whole exome sequencing. PMID:28196478
Leveraging Online Resources to Prioritize Candidate Genes for Functional Analyses: Using the Fetal Testis as a Test Case. PMID:28196369
Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site. PMID:28194258
Exploring soybean metabolic pathways based on probabilistic graphical model and knowledge-based methods. PMID:28194174
The post-genomic era of biological network alignment. PMID:28194172
Evaluating the effect of annotation size on measures of semantic similarity. PMID:28193260
Anopheline salivary protein genes and gene families: an evolutionary overview after the whole genome sequence of sixteen Anopheles species. PMID:28193177
Opportunities and challenges of whole-genome and -exome sequencing. PMID:28193154
Transcriptome analysis of hexaploid hulless oat in response to salinity stress. PMID:28192458
Personalized Identification of Differentially Expressed Modules in Osteosarcoma. PMID:28190021
Proteomics Profiling of Chimeric-Truncated Tissue Plasminogen activator Producing- Chinese Hamster Ovary Cells Cultivated in a Chemically Defined Medium Supplemented with Protein Hydrolysates. PMID:28187683
Var2GO: a web-based tool for gene variants selection. PMID:28185576
From comorbidities of chronic obstructive pulmonary disease to identification of shared molecular mechanisms by data integration. PMID:28185567
Gene set analysis controlling for length bias in RNA-seq experiments. PMID:28184252
How can functional annotations be derived from profiles of phenotypic annotations? PMID:28183267
Expression of β-globin by cancer cells promotes cell survival during blood-borne dissemination. PMID:28181495
Synthetic vulnerabilities of mesenchymal subpopulations in pancreatic cancer. PMID:28178232
Canalization Leads to Similar Whole Bone Mechanical Function at Maturity in Two Inbred Strains of Mice. PMID:28177139
Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana. PMID:28175342
Complete genome sequence of Thermus brockianus GE-1 reveals key enzymes of xylan/xylose metabolism. PMID:28174620
Complete genome sequence of Jiangella gansuensis strain YIM 002T (DSM 44835T), the type species of the genus Jiangella and source of new antibiotic compounds. PMID:28174619
Transcriptome analysis reveals rod/cone photoreceptor specific signatures across mammalian retinas. PMID:28172828
Cis-acting single nucleotide polymorphisms alter MicroRNA-mediated regulation of human brain-expressed transcripts. PMID:28171541
Protein-Induced Pluripotent Stem Cells Ameliorate Cognitive Dysfunction and Reduce Aβ Deposition in a Mouse Model of Alzheimer's Disease. PMID:28170178
Genomic and transcriptomic resources for assassin flies including the complete genome sequence of Proctacanthus coquilletti (Insecta: Diptera: Asilidae) and 16 representative transcriptomes. PMID:28168115
Complete genome sequence of Pseudoalteromonas phage vB_PspS-H40/1 (formerly H40/1) that infects Pseudoalteromonas sp. strain H40 and is used as biological tracer in hydrological transport studies. PMID:28168014
A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma. PMID:28166733
Identification of shared risk loci and pathways for bipolar disorder and schizophrenia. PMID:28166306
Genetic loci associated with chronic obstructive pulmonary disease overlap with loci for lung function and pulmonary fibrosis. PMID:28166215
Potential probiotic-associated traits revealed from completed high quality genome sequence of Lactobacillus fermentum 3872. PMID:28163828
The complete genome sequence of the yogurt isolate Streptococcus thermophilus ACA-DC 2. PMID:28163827
Draft genome sequences of eight bacteria isolated from the indoor environment: Staphylococcus capitis strain H36, S. capitis strain H65, S. cohnii strain H62, S. hominis strain H69, Microbacterium sp. strain H83, Mycobacterium iranicum strain H39, Plantibacter sp. strain H53, and Pseudomonas oryzihabitans strain H72. PMID:28163826
Draft genome sequence of Lactobacillus plantarum strains E2C2 and E2C5 isolated from human stool culture. PMID:28163824
Draft genome sequence of type strain HBR26T and description of Rhizobium aethiopicum sp. nov. PMID:28163823
Characterization of Leaf Transcriptome in Banksia hookeriana. PMID:28161492
p27Kip1, PCAF and PAX5 cooperate in the transcriptional regulation of specific target genes. PMID:28158851
A whole-blood transcriptome meta-analysis identifies gene expression signatures of cigarette smoking. PMID:28158590
An improved method for functional similarity analysis of genes based on Gene Ontology. PMID:28155727
Interspecies gene function prediction using semantic similarity. PMID:28155711
PARRoT- a homology-based strategy to quantify and compare RNA-sequencing from non-model organisms. PMID:28155708
Between-species differences in gene copy number are enriched among functions critical for adaptive evolution in Arabidopsis halleri. PMID:28155655
A network-based pathway-expanding approach for pathway analysis. PMID:28155638
Robust Inference of Genetic Exchange Communities from Microbial Genomes Using TF-IDF. PMID:28154557
Clinical significance and effect of AEG-1 on the proliferation, invasion, and migration of NSCLC: a study based on immunohistochemistry, TCGA, bioinformatics, in vitro and in vivo verification. PMID:28152520
Expression Quantitative Trait loci (QTL) in tumor adjacent normal breast tissue and breast tumor tissue. PMID:28152060
Differential lactate and cholesterol synthetic activities in XY and XX Sertoli cells. PMID:28150810
Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks. PMID:28150250
Epigenome-wide association study of DNA methylation in panic disorder. PMID:28149334
Genes2GO: A web application for querying gene sets for specific GO terms. PMID:28149059
The Plasma Proteome Is Associated with Anthropometric Status of Undernourished Nepalese School-Aged Children. PMID:28148680
Analysis of gene expression profiles between apical papilla tissues, stem cells from apical papilla and cell sheet to identify the key modulators in MSCs niche. PMID:28145066
Aberrant coordination geometries discovered in the most abundant metalloproteins. PMID:28142195
De novo transcriptome assemblies of four accessions of the metal hyperaccumulator plant Noccaea caerulescens. PMID:28140388
Genome sequence of a high agarase-producing strain Flammeovirga sp. SJP92. PMID:28138357
Genome features of moderately halophilic polyhydroxyalkanoate-producing Yangia sp. CCB-MM3. PMID:28138356
Draft genome sequence of Arthrobacter sp. strain B6 isolated from the high-arsenic sediments in Datong Basin, China. PMID:28138355
Multiple network algorithm for epigenetic modules via the integration of genome-wide DNA methylation and gene expression data. PMID:28137264
An Asymmetrically Balanced Organization of Kinases versus Phosphatases across Eukaryotes Determines Their Distinct Impacts. PMID:28135269
SWATH label-free proteomics analyses revealed the roles of oxidative stress and antioxidant defensing system in sclerotia formation of Polyporus umbellatus. PMID:28134344
Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy. PMID:28132844
Genome-Scale Networks Link Neurodegenerative Disease Genes to α-Synuclein through Specific Molecular Pathways. PMID:28131822
Identification of protein complexes by integrating multiple alignment of protein interaction networks. PMID:28130237
Identification of Entry Factors Involved in Hepatitis C Virus Infection Based on Host-Mimicking Short Linear Motifs. PMID:28129350
Permanent draft genome of Thiobacillus thioparus DSM 505T, an obligately chemolithoautotrophic member of the Betaproteobacteria. PMID:28127420
Lipidome determinants of maximal lifespan in mammals. PMID:28127055
Selecting the most appropriate time points to profile in high-throughput studies. PMID:28124972
Systematic analysis of the achaete-scute complex-like gene signature in clinical cancer patients. PMID:28123722
Identification of the molecular mechanisms underlying dilated cardiomyopathy via bioinformatic analysis of gene expression profiles. PMID:28123501
CyNetSVM: A Cytoscape App for Cancer Biomarker Identification Using Network Constrained Support Vector Machines. PMID:28122019
Heat Stress Regulates the Expression of Genes at Transcriptional and Post-Transcriptional Levels, Revealed by RNA-seq in Brachypodium distachyon. PMID:28119730
Whole-exome sequencing of 228 patients with sporadic Parkinson's disease. PMID:28117402
High quality draft genome sequence of Janthinobacterium psychrotolerans sp. nov., isolated from a frozen freshwater pond. PMID:28116042
High-quality draft genome sequence of Rhizobium mesoamericanum strain STM6155, a Mimosa pudica microsymbiont from New Caledonia. PMID:28116041
A systematic comparative evaluation of biclustering techniques. PMID:28114903
Underexpression of Specific Interferon Genes Is Associated with Poor Prognosis of Melanoma. PMID:28114321
Transcriptomic and hormone analyses reveal mechanisms underlying petal elongation in Chrysanthemum morifolium 'Jinba'. PMID:28108965
Integrity of Induced Pluripotent Stem Cell (iPSC) Derived Megakaryocytes as Assessed by Genetic and Transcriptomic Analysis. PMID:28107356
Using Network Extracted Ontologies to Identify Novel Genes with Roles in Appressorium Development in the Rice Blast Fungus Magnaporthe oryzae. PMID:28106722
The antineoplastic drug, trastuzumab, dysregulates metabolism in iPSC-derived cardiomyocytes. PMID:28101782
The histone demethylase PHF8 is a molecular safeguard of the IFNγ response. PMID:28100697
Talin-1 interaction network promotes hepatocellular carcinoma progression. PMID:28099903
Priming increases the anti-tumor effect and therapeutic window of 177Lu-octreotate in nude mice bearing human small intestine neuroendocrine tumor GOT1. PMID:28097640
Transcriptome Sequencing of Gynostemma pentaphyllum to Identify Genes and Enzymes Involved in Triterpenoid Biosynthesis. PMID:28097124
Comparative interactomics for virus-human protein-protein interactions: DNA viruses versus RNA viruses. PMID:28097092
Genome-scale transcriptional study of hybrid effects and regulatory divergence in an F1 hybrid Ruellia (Wild Petunias: Acanthaceae) and its parents. PMID:28095782
Chronic drug-induced effects on contractile motion properties and cardiac biomarkers in human induced pluripotent stem cell-derived cardiomyocytes. PMID:28094846
Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts. PMID:28094347
Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. PMID:28092920
Long-lasting antinociceptive effects of green light in acute and chronic pain in rats. PMID:28092651
Genome Analysis of a Zygomycete Fungus Choanephora cucurbitarum Elucidates Necrotrophic Features Including Bacterial Genes Related to Plant Colonization. PMID:28091548
Landscape of Fluid Sets of Hairpin-Derived 21-/24-nt-Long Small RNAs at Seed Set Uncovers Special Epigenetic Features in Picea glauca. PMID:28082604
Genome Sequence of Christensenella minuta DSM 22607T. PMID:28082495
Whole-Genome Sequence of Streptococcus parauberis Strain SP-llh, Isolated from Cows with Mastitis in Western China. PMID:28082485
Modeling gene-wise dependencies improves the identification of drug response biomarkers in cancer studies. PMID:28082455
Human Lacrimal Gland Gene Expression. PMID:28081151
Comparative Genomics of H. pylori and Non-Pylori Helicobacter Species to Identify New Regions Associated with Its Pathogenicity and Adaptability. PMID:28078297
Complete genome sequence of Pseudomonas brassicacearum strain L13-6-12, a biological control agent from the rhizosphere of potato. PMID:28078051
Complete genome sequence of Lutibacter profundi LP1T isolated from an Arctic deep-sea hydrothermal vent system. PMID:28078050
Transcriptomic evidence for the control of soybean root isoflavonoid content by regulation of overlapping phenylpropanoid pathways. PMID:28077078
Structure alignment-based classification of RNA-binding pockets reveals regional RNA recognition motifs on protein surfaces. PMID:28077065
Transcriptome and Gene Expression Analysis of Cylas formicarius (Coleoptera: Brentidae) During Different Development Stages. PMID:28076281
High quality draft genome of Nakamurella lactea type strain, a rock actinobacterium, and emended description of Nakamurella lactea. PMID:28074122
Complete genome sequence and whole-genome phylogeny of Kosmotoga pacifica type strain SLHLJ1T from an East Pacific hydrothermal sediment. PMID:28074121
Complete genome sequence of the heavy metal resistant bacterium Agromyces aureus AR33T and comparison with related Actinobacteria. PMID:28074120
Complete genome sequence of the salmonella enterica serovar enteritidis bacteriophages fSE1C and fSE4C isolated from food matrices. PMID:28074119
De novo assembly, annotation, and characterization of the whole brain transcriptome of male and female Syrian hamsters. PMID:28071753
A next-generation microarray further reveals stage-enriched gene expression pattern in the blood fluke Schistosoma japonicum. PMID:28069074
FirebrowseR: an R client to the Broad Institute's Firehose Pipeline. PMID:28062517
DEIVA: a web application for interactive visual analysis of differential gene expression profiles. PMID:28061742
Temporal quantitative phosphoproteomics of ADP stimulation reveals novel central nodes in platelet activation and inhibition. PMID:28060719
Effects of selection for ethanol preference on gene expression in the nucleus accumbens of HS-CC mice. PMID:28058793
Genome-Wide DNA Methylation Patterns Analysis of Noncoding RNAs in Temporal Lobe Epilepsy Patients. PMID:28058582
PanViz: interactive visualization of the structure of functionally annotated pangenomes. PMID:28057677
De novo transcriptome and expression profile analyses of the Asian corn borer (Ostrinia furnacalis) reveals relevant flubendiamide response genes. PMID:28056803
Immune adaptation to chronic intense exercise training: new microarray evidence. PMID:28056786
Age influences the olfactory profiles of the migratory oriental armyworm mythimna separate at the molecular level. PMID:28056777
LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells. PMID:28056766
Integration of MicroRNA, mRNA, and Protein Expression Data for the Identification of Cancer-Related MicroRNAs. PMID:28056026
Autophagy orchestrates adaptive responses to targeted therapy in endometrial cancer. PMID:28055301
Functional constraints on adaptive evolution of protein ubiquitination sites. PMID:28054638
Functional Transcriptomics in Diverse Intestinal Epithelial Cell Types Reveals Robust MicroRNA Sensitivity in Intestinal Stem Cells to Microbial Status. PMID:28053090
Linking Hematopoietic Differentiation to Co-Expressed Sets of Pluripotency-Associated and Imprinted Genes and to Regulatory microRNA-Transcription Factor Motifs. PMID:28052084
Deep Transcriptomic Profiling of M1 Macrophages Lacking Trpc3. PMID:28051144
Comparative transcriptome analysis of two contrasting watermelon genotypes during fruit development and ripening. PMID:28049426
Network Centrality Analysis in Fungi Reveals Complex Regulation of Lost and Gained Genes. PMID:28046110
High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes. PMID:28042959
A Genome-wide Association Study Identifies Risk Alleles in Plasminogen and P4HA2 Associated with Giant Cell Arteritis. PMID:28041642
Sixty-five years of the long march in protein secondary structure prediction: the final stretch? PMID:28040746
Non-Coding RNAs in Lung Cancer: Contribution of Bioinformatics Analysis to the Development of Non-Invasive Diagnostic Tools. PMID:28035947
Gene-based analyses reveal novel genetic overlap and allelic heterogeneity across five major psychiatric disorders. PMID:28035465
Integrated Analysis of Long Noncoding RNA and mRNA Expression Profile in Advanced Laryngeal Squamous Cell Carcinoma. PMID:28033431
Complete genome sequence of the actinomycete Actinoalloteichus hymeniacidonis type strain HPA 177T isolated from a marine sponge. PMID:28031775
The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature. PMID:28031747
Drug-drug interaction discovery and demystification using Semantic Web technologies. PMID:28031284
Gene regulatory network inference using PLS-based methods. PMID:28031031
Evolution of Chemosensory Gene Families in Arthropods: Insight from the First Inclusive Comparative Transcriptome Analysis across Spider Appendages. PMID:28028122
m6A-Driver: Identifying Context-Specific mRNA m6A Methylation-Driven Gene Interaction Networks. PMID:28027310
Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes. PMID:28025345
Alternative splicing in tomato pollen in response to heat stress. PMID:28025318
Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution. PMID:28024147
Network Analysis-Based Approach for Exploring the Potential Diagnostic Biomarkers of Acute Myocardial Infarction. PMID:28018242
Kinase impact assessment in the landscape of fusion genes that retain kinase domains: a pan-cancer study. PMID:28013235
Driver gene classification reveals a substantial overrepresentation of tumor suppressors among very large chromatin-regulating proteins. PMID:28008934
Long-term propagation of tree shrew spermatogonial stem cells in culture and successful generation of transgenic offspring. PMID:28008926
Stable Binding of the Conserved Transcription Factor Grainy Head to its Target Genes Throughout Drosophila melanogaster Development. PMID:28007888
kMEn: Analyzing noisy and bidirectional transcriptional pathway responses in single subjects. PMID:28007582
Developing the Quantitative Histopathology Image Ontology (QHIO): A case study using the hot spot detection problem. PMID:28003147
Genome sequence and overview of Oligoflexus tunisiensis Shr3T in the eighth class Oligoflexia of the phylum Proteobacteria. PMID:27999625
Complete genome sequence of new bacteriophage phiE142, which causes simultaneously lysis of multidrug-resistant Escherichia coli O157:H7 and Salmonella enterica. PMID:27999624
Mapping the membrane proteome of anaerobic gut fungi identifies a wealth of carbohydrate binding proteins and transporters. PMID:27998268
Prediction of Possible Biomarkers and Novel Pathways Conferring Risk to Post-Traumatic Stress Disorder. PMID:27997584
Physiological Adjustments and Circulating MicroRNA Reprogramming Are Involved in Early Acclimatization to High Altitude in Chinese Han Males. PMID:27994555
The development of non-coding RNA ontology. PMID:27990175
Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency. PMID:27986076
Dual-seq transcriptomics reveals the battle for iron during Pseudomonas aeruginosa acute murine pneumonia. PMID:27982111
Co-expression analysis and identification of fecundity-related long non-coding RNAs in sheep ovaries. PMID:27982099
Overexpression of protein kinase STK25 in mice exacerbates ectopic lipid accumulation, mitochondrial dysfunction and insulin resistance in skeletal muscle. PMID:27981357
Discovery of biomarkers in rare diseases: innovative approaches by predictive and personalized medicine. PMID:27980697
Cardiovascular proteomics in the era of big data: experimental and computational advances. PMID:27980500
Comprehensive analysis of the long noncoding RNA HOXA11-AS gene interaction regulatory network in NSCLC cells. PMID:27980454
Integrating Information in Biological Ontologies and Molecular Networks to Infer Novel Terms. PMID:27976738
Arsenic resistance strategy in Pantoea sp. IMH: Organization, function and evolution of ars genes. PMID:27966630
Identification of Development-Related Genes in the Ovaries of Adult Harmonia axyridis (Pallas) Lady Beetles Using a Time- Series Analysis by RNA-seq. PMID:27966611
Integrative modelling of tumour DNA methylation quantifies the contribution of metabolism. PMID:27966532
Modeling Rice Metabolism: From Elucidating Environmental Effects on Cellular Phenotype to Guiding Crop Improvement. PMID:27965696
XGR software for enhanced interpretation of genomic summary data, illustrated by application to immunological traits. PMID:27964755
Functional Analyses of the Crohn's Disease Risk Gene LACC1. PMID:27959965
Distinct Molecular Signature of Murine Fetal Liver and Adult Hematopoietic Stem Cells Identify Novel Regulators of Hematopoietic Stem Cell Function. PMID:27958775
PROPER: global protein interaction network alignment through percolation matching. PMID:27955623
Development of an in vitro human liver system for interrogating nonalcoholic steatohepatitis. PMID:27942596
Complete genome anatomy of the emerging potato pathogen Dickeya solani type strain IPO 2222T. PMID:27942352
Bursaphelenchus xylophilus and B. mucronatus secretomes: a comparative proteomic analysis. PMID:27941947
Identification of Potential Biomarkers for Rhegmatogenous Retinal Detachment Associated with Choroidal Detachment by Vitreous iTRAQ-Based Proteomic Profiling. PMID:27941623
An Optimized Chromatographic Strategy for Multiplexing In Parallel Reaction Monitoring Mass Spectrometry: Insights from Quantitation of Activated Kinases. PMID:27940637
Impaired liver regeneration in aged mice can be rescued by silencing Hippo core kinases MST1 and MST2. PMID:27940445
A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells. PMID:27939218
Robust multi-group gene set analysis with few replicates. PMID:27938331
The evolution of function within the Nudix homology clan. PMID:27936487
Insecticidal Activity of Melaleuca alternifolia Essential Oil and RNA-Seq Analysis of Sitophilus zeamais Transcriptome in Response to Oil Fumigation. PMID:27936192
Searching the Mouse Genome Informatics (MGI) Resources for Information on Mouse Biology from Genotype to Phenotype. PMID:27930808
Transcriptomic Changes in Liver of Young Bulls Caused by Diets Low in Mineral and Protein Contents and Supplemented with n-3 Fatty Acids and Conjugated Linoleic Acid. PMID:27930681
De Novo Sequencing and Comparative Analysis of Schima superba Seedlings to Explore the Response to Drought Stress. PMID:27930677
Long noncoding RNA HIT000218960 promotes papillary thyroid cancer oncogenesis and tumor progression by upregulating the expression of high mobility group AT-hook 2 (HMGA2) gene. PMID:27929737
Tribbles ortholog NIPI-3 and bZIP transcription factor CEBP-1 regulate a Caenorhabditis elegans intestinal immune surveillance pathway. PMID:27927200
Altered microRNA profiles in plasma exosomes from mesial temporal lobe epilepsy with hippocampal sclerosis. PMID:27926529
Datasets for the validation of the "in vivo" siRNA-silencing of CD40 and for the detection of new markers of atherosclerosis progression in ApoE-deficient mice. PMID:27924297
Molecular mechanisms underlying the positive role of treadmill training in locomotor recovery after spinal cord injury. PMID:27922623
Identification of critical paralog groups with indispensable roles in the regulation of signaling flow. PMID:27922122
Human Intervention Study to Assess the Effects of Supplementation with Olive Leaf Extract on Peripheral Blood Mononuclear Cell Gene Expression. PMID:27918443
Distinct and Shared Determinants of Cardiomyocyte Contractility in Multi-Lineage Competent Ethnically Diverse Human iPSCs. PMID:27917881
Towards an open grapevine information system. PMID:27917288
Brain transcriptome atlases: a computational perspective. PMID:27909802
Global Deletion of TSPO Does Not Affect the Viability and Gene Expression Profile. PMID:27907096
Bone morphogenetic protein-2-mediated pain and inflammation in a rat model of posterolateral arthrodesis. PMID:27905881
Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes. PMID:27903897
Pharos: Collating protein information to shed light on the druggable genome. PMID:27903890
The Genomic Architecture of Interactions Between Natural Genetic Polymorphisms and Environments in Yeast Growth. PMID:27903611
Differential variation patterns between hubs and bottlenecks in human protein-protein interaction networks. PMID:27903259
Identification of laryngeal cancer prognostic biomarkers using an inflammatory gene-related, competitive endogenous RNA network. PMID:27902487
Microarray analysis of differentially-expressed genes and linker genes associated with the molecular mechanism of colorectal cancer. PMID:27899990
InterPro in 2017-beyond protein family and domain annotations. PMID:27899635
CATH: an expanded resource to predict protein function through structure and sequence. PMID:27899584
The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching. PMID:27899582
Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse. PMID:27899570
WormBase ParaSite - a comprehensive resource for helminth genomics. PMID:27899279
Identification and Characterization of MicroRNAs in the Liver of Blunt Snout Bream (Megalobrama amblycephala) Infected by Aeromonas hydrophila. PMID:27898025
Genome-wide analysis of miRNAs in the ovaries of Jining Grey and Laiwu Black goats to explore the regulation of fecundity. PMID:27897262
Changes in the Membrane-Associated Proteins of Exosomes Released from Human Macrophages after Mycobacterium tuberculosis Infection. PMID:27897233
PROSNET: INTEGRATING HOMOLOGY WITH MOLECULAR NETWORKS FOR PROTEIN FUNCTION PREDICTION. PMID:27896959
Transcriptome analysis reveals the genetic basis underlying the seasonal development of keratinized nuptial spines in Leptobrachium boringii. PMID:27894252
E2fl1 is a meiosis-specific transcription factor in the protist Tetrahymena thermophila. PMID:27892792
Comprehensive Gene expression meta-analysis and integrated bioinformatic approaches reveal shared signatures between thrombosis and myeloproliferative disorders. PMID:27892526
Compact Integration of Multi-Network Topology for Functional Analysis of Genes. PMID:27889536
Text mining resources for the life sciences. PMID:27888231
MathIOmica: An Integrative Platform for Dynamic Omics. PMID:27883025
Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences. PMID:27881428
Global gene expression analysis for evaluation and design of biomaterials. PMID:27877315
Genome Sequence of Pseudomonas koreensis CRS05-R5, an Antagonistic Bacterium Isolated from Rice Paddy Field. PMID:27877162
De-novo protein function prediction using DNA binding and RNA binding proteins as a test case. PMID:27869118
Integrative representations and analyses of vaccine-induced intended protective immunity and unintended adverse events using ontology-based and theory-guided approaches. PMID:27868103
ClassyFire: automated chemical classification with a comprehensive, computable taxonomy. PMID:27867422
Investigation of candidate genes for osteoarthritis based on gene expression profiles. PMID:27866912
Evaluation of the genetic basis of primary hypoadrenocorticism in Standard Poodles using SNP array genotyping and whole-genome sequencing. PMID:27864587
Computational approaches for the identification of cancer genes and pathways. PMID:27863091
Transcriptome Profiling of Watermelon Root in Response to Short-Term Osmotic Stress. PMID:27861528
Draft Genome Sequence of Lactobacillus plantarum XJ25 Isolated from Chinese Red Wine. PMID:27856576
Systems analysis identifies miR-29b regulation of invasiveness in melanoma. PMID:27852308
Identification of potential genes for human ischemic cardiomyopathy based on RNA-Seq data. PMID:27852050
Large-scale identification of human protein function using topological features of interaction network. PMID:27849060
Characterization of genes and pathways that respond to heat stress in Holstein calves through transcriptome analysis. PMID:27848120
GEN3VA: aggregation and analysis of gene expression signatures from related studies. PMID:27846806
Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences. PMID:27846802
Identification of Genes Discriminating Multiple Sclerosis Patients from Controls by Adapting a Pathway Analysis Method. PMID:27846233
Unravelling the genomic architecture of bull fertility in Holstein cattle. PMID:27842509
Early pregnancy vitamin D status and risk of preeclampsia. PMID:27841759
Leaf transcriptome of two highly divergent genotypes of Urochloa humidicola (Poaceae), a tropical polyploid forage grass adapted to acidic soils and temporary flooding areas. PMID:27835957
Cocaine promotes primary human astrocyte proliferation via JNK-dependent up-regulation of cyclin A2. PMID:27834787
Two draft genome sequences of Pseudomonas jessenii strains isolated from a copper contaminated site in Denmark. PMID:27833718
Knowledge Representation and Management: a Linked Data Perspective. PMID:27830248
AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations. PMID:27830058
Potential molecular characteristics in situ in response to repetitive UVB irradiation. PMID:27829444
Differential Gene Expression in Rhododendron fortunei Roots Colonized by an Ericoid Mycorrhizal Fungus and Increased Nitrogen Absorption and Plant Growth. PMID:27826312
Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir. PMID:27822552
ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions. PMID:27822512
De novo assembly and analysis of changes in the protein-coding transcriptome of the freshwater shrimp Paratya australiensis (Decapoda: Atyidae) in response to acid sulfate drainage water. PMID:27821072
Multi-label ℓ2-regularized logistic regression for predicting activation/inhibition relationships in human protein-protein interaction networks. PMID:27819359
Insights into a novel nuclear function for Fascin in the regulation of the amino-acid transporter SLC3A2. PMID:27819326
Transcriptomic analysis on the formation of the viable putative non-culturable state of beer-spoilage Lactobacillus acetotolerans. PMID:27819317
Analysis of the interplay between methylation and expression reveals its potential role in cancer aetiology. PMID:27819121
Discovery of the molecular mechanisms of the novel chalcone-based Magnaporthe oryzae inhibitor C1 using transcriptomic profiling and co-expression network analysis. PMID:27818889
Identification of the Key Genes and Pathways in Esophageal Carcinoma. PMID:27818681
The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations. PMID:27812948
Evaluating Functional Annotations of Enzymes Using the Gene Ontology. PMID:27812939
Primer on the Gene Ontology. PMID:27812933
The Gene Ontology and the Meaning of Biological Function. PMID:27812932
The Genome of the Toluene-Degrading Pseudomonas veronii Strain 1YdBTEX2 and Its Differential Gene Expression in Contaminated Sand. PMID:27812150
Changes in mammary histology and transcriptome profiles by low-dose exposure to environmental phenols at critical windows of development. PMID:27810681
Exploring Human Diseases and Biological Mechanisms by Protein Structure Prediction and Modeling. PMID:27807743
Functional insights into the testis transcriptome of the edible sea urchin Loxechinus albus. PMID:27805042
An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography. PMID:27803195
ATR maintains chromosomal integrity during postnatal cerebellar neurogenesis and is required for medulloblastoma formation. PMID:27803059
An Integrative Analysis of Preeclampsia Based on the Construction of an Extended Composite Network Featuring Protein-Protein Physical Interactions and Transcriptional Relationships. PMID:27802351
Draft genome sequence of Streptomyces sp. TP-A0867, an alchivemycin producer. PMID:27800124
Hypoxia increases genome-wide bivalent epigenetic marking by specific gain of H3K27me3. PMID:27800026
Expression of HIV-1 matrix protein p17 and association with B-cell lymphoma in HIV-1 transgenic mice. PMID:27799525
Genenames.org: the HGNC and VGNC resources in 2017. PMID:27799471
OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines. PMID:27799467
Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana). PMID:27799338
Deregulated expression of HDAC9 in B cells promotes development of lymphoproliferative disease and lymphoma in mice. PMID:27799148
Genome-wide analysis identifies 12 loci influencing human reproductive behavior. PMID:27798627
Expression Variations of miRNAs and mRNAs in Rice (Oryza sativa). PMID:27797952
Comparison of miRNA profiling during airway epithelial repair in undifferentiated and differentiated cells in vitro. PMID:27796942
Draft genome sequence of Micromonospora sp. DSW705 and distribution of biosynthetic gene clusters for depsipeptides bearing 4-amino-2,4-pentadienoate in actinomycetes. PMID:27795808
A network-biology perspective of microRNA function and dysfunction in cancer. PMID:27795564
Complete Genome Sequence of Bacillus pumilus PDSLzg-1, a Hydrocarbon-Degrading Bacterium Isolated from Oil-Contaminated Soil in China. PMID:27795249
Complete Genome Sequence of Pontibacter akesuensis Strain AKS 1T, Which Exhibits Robust Nutrient Metabolism in Harsh Environments. PMID:27795233
RNA-binding profiles of Drosophila CPEB proteins Orb and Orb2. PMID:27791065
Transcriptome Analysis and Ultrastructure Observation Reveal that Hawthorn Fruit Softening Is due to Cellulose/Hemicellulose Degradation. PMID:27790234
Draft Genome Sequence of Botryosphaeria dothidea, the Pathogen of Apple Ring Rot. PMID:27789635
Changes to the Aqueous Humor Proteome during Glaucoma. PMID:27788204
The Pre-Eclampsia Ontology: A Disease Ontology Representing the Domain Knowledge Specific to Pre-Eclampsia. PMID:27788142
Draft genome sequence of Streptomyces sp. MWW064 for elucidating the rakicidin biosynthetic pathway. PMID:27785333
Draft genome of the leopard gecko, Eublepharis macularius. PMID:27784328
Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat. PMID:27784266
Maternal Chromium Restriction Leads to Glucose Metabolism Imbalance in Mice Offspring through Insulin Signaling and Wnt Signaling Pathways. PMID:27782077
Non-targeted transcriptomic effects upon thyroid irradiation: similarity between in-field and out-of-field responses varies with tissue type. PMID:27779251
Draft genome of Prochlorothrix hollandica CCAP 1490/1T (CALU1027), the chlorophyll a/b-containing filamentous cyanobacterium. PMID:27777652
Draft genome sequence of the marine Rhodobacteraceae strain O3.65, cultivated from oil-polluted seawater of the Deepwater Horizon oil spill. PMID:27777651
Complete genome sequence of Methanoculleus bourgensis strain MAB1, the syntrophic partner of mesophilic acetate-oxidising bacteria (SAOB). PMID:27777650
Genome sequences and annotation of two urinary isolates of E. coli. PMID:27777649
A draft genome sequence of Pseudomonas veronii R4: a grapevine (Vitis vinifera L.) root-associated strain with high biocontrol potential. PMID:27777646
Mapping wild-type and R345W fibulin-3 intracellular interactomes. PMID:27777122
Loss of variation of state detected in soybean metabolic and human myelomonocytic leukaemia cell transcriptional networks under external stimuli. PMID:27775018
Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns. PMID:27774140
A computational interactome and functional annotation for the human proteome. PMID:27770567
Microenvironmental Gene Expression Plasticity Among Individual Drosophila melanogaster. PMID:27770026
Genetic Adaptation and Neandertal Admixture Shaped the Immune System of Human Populations. PMID:27768888
Dissecting the Origin of Breast Cancer Subtype Stem Cell and the Potential Mechanism of Malignant Transformation. PMID:27768723
The Terroir Concept Interpreted through Grape Berry Metabolomics and Transcriptomics. PMID:27768042
Prioritization, clustering and functional annotation of MicroRNAs using latent semantic indexing of MEDLINE abstracts. PMID:27766940
Effective comparative analysis of protein-protein interaction networks by measuring the steady-state network flow using a Markov model. PMID:27766938
Draft genome sequence of Staphylococcus hominis strain Hudgins isolated from human skin implicates metabolic versatility and several virulence determinants. PMID:27766204
Proteomic analysis reveals diverse proline hydroxylation-mediated oxygen-sensing cellular pathways in cancer cells. PMID:27764789
Microbial culturomics unravels the halophilic microbiota repertoire of table salt: description of Gracilibacillus massiliensis sp. nov. PMID:27760679
Signal-Oriented Pathway Analyses Reveal a Signaling Complex as a Synthetic Lethal Target for p53 Mutations. PMID:27758891
Gene expression, signal transduction pathways and functional networks associated with growth of sporadic vestibular schwannomas. PMID:27752882
Introducing the Big Knowledge to Use (BK2U) challenge. PMID:27750400
Tissue Specificity of Human Disease Module. PMID:27748412
miRPathDB: a new dictionary on microRNAs and target pathways. PMID:27742822
Notions of similarity for systems biology models. PMID:27742665
Characterization of factors underlying the metabolic shifts in developing kernels of colored maize. PMID:27739524
Graphlet-based Characterization of Directed Networks. PMID:27734973
Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration. PMID:27733503
Gene expression and metabolism preceding soft scald, a chilling injury of 'Honeycrisp' apple fruit. PMID:27733113
Activity-Dependent Changes in Gene Expression in Schizophrenia Human-Induced Pluripotent Stem Cell Neurons. PMID:27732689
KinView: a visual comparative sequence analysis tool for integrated kinome research. PMID:27731453
Ovarian transcriptomic study reveals the differential regulation of miRNAs and lncRNAs related to fecundity in different sheep. PMID:27731399
Mutational Analysis of Extranodal NK/T-Cell Lymphoma Using Targeted Sequencing with a Comprehensive Cancer Panel. PMID:27729836
Nuclear receptors control pro-viral and antiviral metabolic responses to hepatitis C virus infection. PMID:27723751
High-quality draft genome sequence of Sedimenticola selenatireducens strain AK4OH1T, a gammaproteobacterium isolated from estuarine sediment. PMID:27721915
Identification of large disjoint motifs in biological networks. PMID:27716036
Transcriptome Analysis of Sucrose Metabolism during Bulb Swelling and Development in Onion (Allium cepa L.). PMID:27713754
Transcriptome Profile of the Chicken Thrombocyte: New Implications as an Advanced Immune Effector Cell. PMID:27711235
Self-Contained Statistical Analysis of Gene Sets. PMID:27711232
Permanent draft genome of Thermithiobaclillus tepidarius DSM 3134T, a moderately thermophilic, obligately chemolithoautotrophic member of the Acidithiobacillia. PMID:27708749
Genome sequence of the basal haplorrhine primate Tarsius syrichta reveals unusual insertions. PMID:27708261
A global genetic interaction network maps a wiring diagram of cellular function. PMID:27708008
Transcriptomic characterization of differential gene expression in oral squamous cell carcinoma: a meta-analysis of publicly available microarray data sets. PMID:27704359
Network analysis of mitonuclear GWAS reveals functional networks and tissue expression profiles of disease-associated genes. PMID:27704213
Identification and Characterization of Small Noncoding RNAs in Genome Sequences of the Edible Fungus Pleurotus ostreatus. PMID:27703969
Importance of metabolic rate to the relationship between the number of genes in a functional category and body size in Peto's paradox for cancer. PMID:27703689
Screening and identification of microRNA involved in unstable angina using gene-chip analysis. PMID:27703515
Transcriptome and Metabolite analysis reveal candidate genes of the cardiac glycoside biosynthetic pathway from Calotropis procera. PMID:27703261
OAHG: an integrated resource for annotating human genes with multi-level ontologies. PMID:27703231
Draft genome sequence and detailed analysis of Pantoea eucrina strain Russ and implication for opportunistic pathogenesis. PMID:27699151
Draft genome sequence of Microbacterium oleivorans strain Wellendorf implicates heterotrophic versatility and bioremediation potential. PMID:27699150
An Integrated Analysis of the Genome-Wide Profiles of DNA Methylation and mRNA Expression Defining the Side Population of a Human Malignant Mesothelioma Cell Line. PMID:27698904
Bioinformatics analysis of the molecular mechanism of diffuse intrinsic pontine glioma. PMID:27698822
A machine-learned computational functional genomics-based approach to drug classification. PMID:27695919
Ongoing resolution of duplicate gene functions shapes the diversification of a metabolic network. PMID:27690225
Aberrant LncRNA Expression Profile in a Contusion Spinal Cord Injury Mouse Model. PMID:27689092
Whole genome shotgun sequence of Bacillus amyloliquefaciens TF28, a biocontrol entophytic bacterium. PMID:27688836
NUCLEAR FACTOR Y, Subunit C (NF-YC) Transcription Factors Are Positive Regulators of Photomorphogenesis in Arabidopsis thaliana. PMID:27685091
Immunoproteomic analysis of house dust mite antigens reveals distinct classes of dominant T cell antigens according to function and serological reactivity. PMID:27684489
Characterization and phosphoproteomic analysis of a human immortalized podocyte model of Fabry disease generated using CRISPR/Cas9 technology. PMID:27681560
An efficient method for protein function annotation based on multilayer protein networks. PMID:27678214
A drug target slim: using gene ontology and gene ontology annotations to navigate protein-ligand target space in ChEMBL. PMID:27678076
Unconventional secretory processing diversifies neuronal ion channel properties. PMID:27677849
Microgravity induces proteomics changes involved in endoplasmic reticulum stress and mitochondrial protection. PMID:27670941
Identification of Genes Potentially Associated with the Fertility Instability of S-Type Cytoplasmic Male Sterility in Maize via Bulked Segregant RNA-Seq. PMID:27669430
Gene expression elucidates functional impact of polygenic risk for schizophrenia. PMID:27668389
Finding lost genes in GWAS via integrative-omics analysis reveals novel sub-networks associated with preterm birth. PMID:27664809
Transcriptomic analysis of the highly efficient oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization. PMID:27664055
O-fucosylated glycoproteins form assemblies in close proximity to the nuclear pore complexes of Toxoplasma gondii. PMID:27663739
Pathway-Specific Polygenic Risk Scores as Predictors of Amyloid-β Deposition and Cognitive Function in a Sample at Increased Risk for Alzheimer's Disease. PMID:27662287
Genome sequence of Candidatus Arsenophonus lipopteni, the exclusive symbiont of a blood sucking fly Lipoptena cervi (Diptera: Hippoboscidae). PMID:27660670
Profiling of downregulated blood-circulating miR-150-5p as a novel tumor marker for cholangiocarcinoma. PMID:27658773
Trinitrobenzene sulfonic acid-induced intestinal injury in neonatal mice activates transcriptional networks similar to those seen in human necrotizing enterocolitis. PMID:27656771
Clinical Application of a Modular Genomics Technique in Systemic Lupus Erythematosus: Progress towards Precision Medicine. PMID:27656648
Identification potential biomarkers in pulmonary tuberculosis and latent infection based on bioinformatics analysis. PMID:27655333
Development and Validation of a Six-Gene Recurrence Risk Score Assay for Gastric Cancer. PMID:27654712
Systems Analysis of Early Host Gene Expression Provides Clues for Transient Mycobacterium avium ssp avium vs. Persistent Mycobacterium avium ssp paratuberculosis Intestinal Infections. PMID:27653506
miRNA targeted signaling pathway in the early stage of denervated fast and slow muscle atrophy. PMID:27651778
The Comparative Toxicogenomics Database: update 2017. PMID:27651457
DBSecSys 2.0: a database of Burkholderia mallei and Burkholderia pseudomallei secretion systems. PMID:27650316
Translational Advances in the Field of Pulmonary Hypertension. Translating MicroRNA Biology in Pulmonary Hypertension. It Will Take More Than "miR" Words. PMID:27648944
Perturbation Detection Through Modeling of Gene Expression on a Latent Biological Pathway Network: A Bayesian hierarchical approach. PMID:27647944
Comparative transcriptome profiling of longissimus muscle tissues from Qianhua Mutton Merino and Small Tail Han sheep. PMID:27645777
Identification of 2-oxohistidine Interacting Proteins Using E. coli Proteome Chips. PMID:27644758
Autophagy induction stabilizes microtubules and promotes axon regeneration after spinal cord injury. PMID:27638205
Large-scale analysis of intrinsic disorder flavors and associated functions in the protein sequence universe. PMID:27636733
Annotating the Function of the Human Genome with Gene Ontology and Disease Ontology. PMID:27635398
Transcriptome analysis of colored calla lily (Zantedeschia rehmannii Engl.) by Illumina sequencing: de novo assembly, annotation and EST-SSR marker development. PMID:27635342
v-Src Oncogene Induces Trop2 Proteolytic Activation via Cyclin D1. PMID:27634768
Investigation of rare and low-frequency variants using high-throughput sequencing with pooled DNA samples. PMID:27633116
The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis. PMID:27627881
Constructing Bayesian networks by integrating gene expression and copy number data identifies NLGN4Y as a novel regulator of prostate cancer progression. PMID:27626693
High-throughput discovery of novel developmental phenotypes. PMID:27626380
The PathoYeastract database: an information system for the analysis of gene and genomic transcription regulation in pathogenic yeasts. PMID:27625390
Protein complex detection based on partially shared multi-view clustering. PMID:27623844
An intestinal microRNA modulates the homeostatic adaptation to chronic oxidative stress in C. elegans. PMID:27623524
First Draft Assembly and Annotation of the Genome of a California Endemic Oak Quercus lobata Née (Fagaceae). PMID:27621377
CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data. PMID:27620863
Conservation and diversification of the transcriptomes of adult Paragonimus westermani and P. skrjabini. PMID:27619014
GeneSCF: a real-time based functional enrichment tool with support for multiple organisms. PMID:27618934
Tissue enrichment analysis for C. elegans genomics. PMID:27618863
Functional Annotations of Paralogs: A Blessing and a Curse. PMID:27618105
Higher expression of somatic repair genes in long-lived ant queens than workers. PMID:27617474
Complete genome sequence of the Antarctic Halorubrum lacusprofundi type strain ACAM 34. PMID:27617060
Draft genome sequence of Thermoactinomyces sp. strain AS95 isolated from a Sebkha in Thamelaht, Algeria. PMID:27617058
An improved high-quality draft genome sequence of Carnobacterium inhibens subsp. inhibens strain K1(T). PMID:27617056
PGD: a pangolin genome hub for the research community. PMID:27616775
Positive Selection Linked with Generation of Novel Mammalian Dentition Patterns. PMID:27613398
Comparative analysis of housekeeping and tissue-specific driver nodes in human protein interaction networks. PMID:27612563
Meta-Analysis of Parkinson's Disease Transcriptome Data Using TRAM Software: Whole Substantia Nigra Tissue and Single Dopamine Neuron Differential Gene Expression. PMID:27611585
Lipid Biosynthesis Coordinates a Mitochondrial-to-Cytosolic Stress Response. PMID:27610574
Draft genome sequence of Lampropedia cohaerens strain CT6(T) isolated from arsenic rich microbial mats of a Himalayan hot water spring. PMID:27610214
Draft genome sequence of Enterococcus faecium strain LMG 8148. PMID:27610213
24-hour-restraint stress induces long-term depressive-like phenotypes in mice. PMID:27609090
Information and organization in public health institutes: an ontology-based modeling of the entities in the reception-analysis-report phases. PMID:27608917
De Novo Transcriptome Assembly and Sex-Biased Gene Expression in the Cyclical Parthenogenetic Daphnia galeata. PMID:27604882
An expanded evaluation of protein function prediction methods shows an improvement in accuracy. PMID:27604469
Complete genome sequences of the Serratia plymuthica strains 3Rp8 and 3Re4-18, two rhizosphere bacteria with antagonistic activity towards fungal phytopathogens and plant growth promoting abilities. PMID:27602183
Near complete genome sequence of the animal feed probiotic, Bacillus amyloliquefaciens H57. PMID:27602182
The complete genome sequence of the methanogenic archaeon ISO4-H5 provides insights into the methylotrophic lifestyle of a ruminal representative of the Methanomassiliicoccales. PMID:27602181
Candida albicans triggers the expression of inflammatory genes in human umbilical vein endothelial cells. PMID:27602073
Comparative transcriptomics of anal fin pigmentation patterns in cichlid fishes. PMID:27600936
Data Integration for Microarrays: Enhanced Inference for Gene Regulatory Networks. PMID:27600224
Enhancing Interpretability of Gene Signatures with Prior Biological Knowledge. PMID:27600081
Emergence and evolution of inter-specific segregating retrocopies in cynomolgus monkey (Macaca fascicularis) and rhesus macaque (Macaca mulatta). PMID:27600022
Genotypes of cancer stem cells characterized by epithelial-to-mesenchymal transition and proliferation related functions. PMID:27597445
NEAT: an efficient network enrichment analysis test. PMID:27597310
Tissue-specific Co-expression of Long Non-coding and Coding RNAs Associated with Breast Cancer. PMID:27597120
Reconstruction of the Fatty Acid Biosynthetic Pathway of Exiguobacterium antarcticum B7 Based on Genomic and Bibliomic Data. PMID:27595107
Insights from the draft genome of the subsection V (Stigonematales) cyanobacterium Hapalosiphon sp. Strain MRB220 associated with 2-MIB production. PMID:27594977
Draft genome sequence of Acinetobacter baumannii strain NCTC 13423, a multidrug-resistant clinical isolate. PMID:27594976
Modeling biochemical pathways in the gene ontology. PMID:27589964
The green ash transcriptome and identification of genes responding to abiotic and biotic stresses. PMID:27589953
Genome-wide co-localization of active EGFR and downstream ERK pathway kinases mirrors mitogen-inducible RNA polymerase 2 genomic occupancy. PMID:27587583
Draft genome sequence of Pseudomonas moraviensis strain Devor implicates metabolic versatility and bioremediation potential. PMID:27583206
Draft genome sequence of Micrococcus luteus strain O'Kane implicates metabolic versatility and the potential to degrade polyhydroxybutyrates. PMID:27583205
A biologically informed method for detecting rare variant associations. PMID:27582876
Discover the network underlying the connections between aging and age-related diseases. PMID:27582315
ANGIOGENES: knowledge database for protein-coding and noncoding RNA genes in endothelial cells. PMID:27582018
Transcriptional Analysis of The Adaptive Digestive System of The Migratory Locust in Response to Plant Defensive Protease Inhibitors. PMID:27581362
Identification of key pathways and genes in colorectal cancer using bioinformatics analysis. PMID:27581154
Automated detection of discourse segment and experimental types from the text of cancer pathway results sections. PMID:27580922
Predicting Diagnostic Gene Biomarkers for Non-Small-Cell Lung Cancer. PMID:27579312
Fusing literature and full network data improves disease similarity computation. PMID:27578323
Differential expression of genes in the alate and apterous morphs of the brown citrus aphid, Toxoptera citricida. PMID:27577531
Transcriptome sequencing reveals genome-wide variation in molecular evolutionary rate among ferns. PMID:27577050
Effects of early feeding on the host rumen transcriptome and bacterial diversity in lambs. PMID:27576848
Transcriptome sequencing of Mycosphaerella fijiensis during association with Musa acuminata reveals candidate pathogenicity genes. PMID:27576702
Overexpression of Differentially Expressed Genes Identified in Non-pathogenic and Pathogenic Entamoeba histolytica Clones Allow Identification of New Pathogenicity Factors Involved in Amoebic Liver Abscess Formation. PMID:27575775
Impact of outdated gene annotations on pathway enrichment analysis. PMID:27575621
Gene transcription profiles associated with inter-modular hubs and connection distance in human functional magnetic resonance imaging networks. PMID:27574314
Overexpression of CD44 is associated with the occurrence and migration of non-small cell lung cancer. PMID:27573351
Insight: An ontology-based integrated database and analysis platform for epilepsy self-management research. PMID:27573308
Analysis of gene expression profile identifies potential biomarkers for atherosclerosis. PMID:27573188
Long noncoding RNA linc00598 regulates CCND2 transcription and modulates the G1 checkpoint. PMID:27572135
rG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome. PMID:27571552
Sexually Dimorphic Gene Expression Associated with Growth and Reproduction of Tongue Sole (Cynoglossus semilaevis) Revealed by Brain Transcriptome Analysis. PMID:27571066
Draft genome sequence of pathogenic bacteria Vibrio parahaemolyticus strain Ba94C2, associated with acute hepatopancreatic necrosis disease isolate from South America. PMID:27570736
Community-based Ontology Development, Annotation and Discussion with MediaWiki extension Ontokiwi and Ontokiwi-based Ontobedia. PMID:27570653
Ion Channel ElectroPhysiology Ontology (ICEPO) - a case study of text mining assisted ontology development. PMID:27570648
Transient resistance to DNA damaging agents is associated with expression of microRNAs-135b and -196b in human leukemia cell lines. PMID:27570640
First high quality draft genome sequence of a plant growth promoting and cold active enzyme producing psychrotrophic Arthrobacter agilis strain L77. PMID:27570579
Fast Inference for the Latent Space Network Model Using a Case-Control Approximate Likelihood. PMID:27570438
Statistical inference for time course RNA-Seq data using a negative binomial mixed-effect model. PMID:27565575
Transcriptome responses to temperature, water availability and photoperiod are conserved among mature trees of two divergent Douglas-fir provenances from a coastal and an interior habitat. PMID:27565139
A novel mass spectrometric strategy "BEMAP" reveals Extensive O-linked protein glycosylation in Enterotoxigenic Escherichia coli. PMID:27562176
FFPred 3: feature-based function prediction for all Gene Ontology domains. PMID:27561554
Permanent draft genome of strain ESFC-1: ecological genomics of a newly discovered lineage of filamentous diazotrophic cyanobacteria. PMID:27559430
A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: insights into plant-microbe interactions and legume evolution. PMID:27557478
Network analysis reveals potential markers for pediatric adrenocortical carcinoma. PMID:27555782
Dynamic DNA methylation regulates neuronal intrinsic membrane excitability. PMID:27555660
Neural stem cells secrete factors facilitating brain regeneration upon constitutive Raf-Erk activation. PMID:27554447
FastProject: a tool for low-dimensional analysis of single-cell RNA-Seq data. PMID:27553427
Several type 2 diabetes-associated variants in genes annotated to WNT signaling interact with dietary fiber in relation to incidence of type 2 diabetes. PMID:27551309
msBiodat analysis tool, big data analysis for high-throughput experiments. PMID:27547241
Draft genome sequence of subterranean clover, a reference for genus Trifolium. PMID:27545089
Resolvin E1 Reverses Experimental Periodontitis and Dysbiosis. PMID:27543615
STAMS: STRING-assisted module search for genome wide association studies and application to autism. PMID:27542772
The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation. PMID:27538448
Draft genome sequences of three Xanthomonas translucens pathovar reference strains (pv. arrhenatheri, pv. poae and pv. phlei) with different specificities for forage grasses. PMID:27536340
The complete genome sequence of the rumen methanogen Methanobrevibacter millerae SM9. PMID:27536339
Nitrogen Metabolism and Growth Enhancement in Tomato Plants Challenged with Trichoderma harzianum Expressing the Aspergillus nidulans Acetamidase amdS Gene. PMID:27536277
Differential Biphasic Transcriptional Host Response Associated with Coevolution of Hemagglutinin Quasispecies of Influenza A Virus. PMID:27536272
Human INO80/YY1 chromatin remodeling complex transcriptionally regulates the BRCA2- and CDKN1A-interacting protein (BCCIP) in cells. PMID:27535137
Gene signatures associated with adaptive humoral immunity following seasonal influenza A/H1N1 vaccination. PMID:27534615
Eliciting the Functional Taxonomy from protein annotations and taxa. PMID:27534507
The Effects of Ivermectin on Brugia malayi Females In Vitro: A Transcriptomic Approach. PMID:27529747
Gene Set-Based Integrative Analysis Revealing Two Distinct Functional Regulation Patterns in Four Common Subtypes of Epithelial Ovarian Cancer. PMID:27527159
PDZD7-MYO7A complex identified in enriched stereocilia membranes. PMID:27525485
Regulatory complexity revealed by integrated cytological and RNA-seq analyses of meiotic substages in mouse spermatocytes. PMID:27519264
NF-Y Binding Site Architecture Defines a C-Fos Targeted Promoter Class. PMID:27517874
New insights in Rett syndrome using pathway analysis for transcriptomics data. PMID:27517371
Highlighting the Need for Systems-Level Experimental Characterization of Plant Metabolic Enzymes. PMID:27516767
Navigating the Phenotype Frontier: The Monarch Initiative. PMID:27516611
RNA-seq-based evaluation of bicolor tepal pigmentation in Asiatic hybrid lilies (Lilium spp.). PMID:27516339
Transcriptomics of liver and muscle in Holstein cows genetically divergent for fertility highlight differences in nutrient partitioning and inflammation processes. PMID:27514375
Comparative Digital Gene Expression Analysis of the Arabidopsis Response to Volatiles Emitted by Bacillus amyloliquefaciens. PMID:27513952
VHLdb: A database of von Hippel-Lindau protein interactors and mutations. PMID:27511743
Evaluation of artificial selection in Standard Poodles using whole-genome sequencing. PMID:27510710
Transcriptome sequencing and de novo characterization of Korean endemic land snail, Koreanohadra kurodana for functional transcripts and SSR markers. PMID:27507702
Genes Interacting with Occupational Exposures to Low Molecular Weight Agents and Irritants on Adult-Onset Asthma in Three European Studies. PMID:27504716
The Role of Retrotransposons in Gene Family Expansions in the Human and Mouse Genomes. PMID:27503295
Imaging-genomics reveals driving pathways of MRI derived volumetric tumor phenotype features in Glioblastoma. PMID:27502180
Functional Implications of Biochemical and Molecular Characteristics of Donation After Circulatory Death Livers. PMID:27500220
Draft genomic sequence of a chromate- and sulfate-reducing Alishewanella strain with the ability to bioremediate Cr and Cd contamination. PMID:27499827
Schistosome sex matters: a deep view into gonad-specific and pairing-dependent transcriptomes reveals a complex gender interplay. PMID:27499125
A transcriptional blueprint for a spiral-cleaving embryo. PMID:27496340
Computational Identification of Novel Genes: Current and Future Perspectives. PMID:27493475
Draft Genome Sequence of Pseudoalteromonas tetraodonis Strain MQS005, a Bacterium with Potential Quorum-Sensing Regulation. PMID:27491986
Cell-free Determination of Binary Complexes That Comprise Extended Protein-Protein Interaction Networks of Yersinia pestis. PMID:27489291
Global Transcriptional Analysis of Virus-Host Interactions between Phage ϕ29 and Bacillus subtilis. PMID:27489274
Transcriptomic analysis of mouse liver reveals a potential hepato-enteric pathogenic mechanism in acute Toxoplasma gondii infection. PMID:27488578
Health Concept and Knowledge Management: Twenty-five Years of Evolution. PMID:27488404
Repair of UVB-induced DNA damage is reduced in melanoma due to low XPC and global genome repair. PMID:27487145
Identification and Comparative Analysis of Differential Gene Expression in Soybean Leaf Tissue under Drought and Flooding Stress Revealed by RNA-Seq. PMID:27486466
Genome-wide characterization of non-reference transposons in crops suggests non-random insertion. PMID:27485608
Genetic analysis of variation in lifespan using a multiparental advanced intercross Drosophila mapping population. PMID:27485207
Statistical Methods in Integrative Genomics. PMID:27482531
Integrative genomics analyses unveil downstream biological effectors of disease-specific polymorphisms buried in intergenic regions. PMID:27482468
On the study of microbial transcriptomes using second- and third-generation sequencing technologies. PMID:27480632
Gene-Disease Interaction Retrieval from Multiple Sources: A Network Based Method. PMID:27478829
High-concentrate feeding upregulates the expression of inflammation-related genes in the ruminal epithelium of dairy cattle. PMID:27478614
Identification of differentially expressed genes in salivary adenoid cystic carcinoma cells associated with metastasis. PMID:27478471
Comparative Proteome Analysis in Schizosaccharomyces pombe Identifies Metabolic Targets to Improve Protein Production and Secretion. PMID:27477394
The Genome of Undifilum oxytropis Provides Insights into Swainsonine Biosynthesis and Locoism. PMID:27477109
Cutaneous wound healing through paradoxical MAPK activation by BRAF inhibitors. PMID:27476449
Prediction of FAD binding sites in electron transport proteins according to efficient radial basis function networks and significant amino acid pairs. PMID:27475771
Immune competence assessment in marine medaka (Orzyias melastigma)-a holistic approach for immunotoxicology. PMID:27473621
TopoICSim: a new semantic similarity measure based on gene ontology. PMID:27473391
CicerTransDB 1.0: a resource for expression and functional study of chickpea transcription factors. PMID:27472917
The Anisakis Transcriptome Provides a Resource for Fundamental and Applied Studies on Allergy-Causing Parasites. PMID:27472517
Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil. PMID:27471578
Partial Activation of SA- and JA-Defensive Pathways in Strawberry upon Colletotrichum acutatum Interaction. PMID:27471515
eSNPO: An eQTL-based SNP Ontology and SNP functional enrichment analysis platform. PMID:27470167
Comparison of miRNAs and Their Targets in Seed Development between Two Maize Inbred Lines by High-Throughput Sequencing and Degradome Analysis. PMID:27463682
Partial loss of interleukin 2 receptor gamma function in pigs provides mechanistic insights for the study of human immunodeficiency syndrome. PMID:27463006
Representing and querying disease networks using graph databases. PMID:27462371
Hypomethylation coordinates antagonistically with hypermethylation in cancer development: a case study of leukemia. PMID:27461342
Sarcoidosis activates diverse transcriptional programs in bronchoalveolar lavage cells. PMID:27460362
Ontology-based Vaccine and Drug Adverse Event Representation and Theory-guided Systematic Causal Network Analysis toward Integrative Pharmacovigilance Research. PMID:27458549
Divergent Transcriptional Responses to Physiological and Xenobiotic Stress in Giardia duodenalis. PMID:27458219
DisSim: an online system for exploring significant similar diseases and exhibiting potential therapeutic drugs. PMID:27457921
Transcriptomic Analysis of Compromise Between Air-Breathing and Nutrient Uptake of Posterior Intestine in Loach (Misgurnus anguillicaudatus), an Air-Breathing Fish. PMID:27457889
Transcriptome analysis reveals global regulation in response to CO2 supplementation in oleaginous microalga Coccomyxa subellipsoidea C-169. PMID:27453726
A Network of Conserved Synthetic Lethal Interactions for Exploration of Precision Cancer Therapy. PMID:27453043
PreImplantation factor (PIF) therapy provides comprehensive protection against radiation induced pathologies. PMID:27449294
MicroRNA expression and gene regulation drive breast cancer progression and metastasis in PyMT mice. PMID:27449149
Classification of Non-Small Cell Lung Cancer Using Significance Analysis of Microarray-Gene Set Reduction Algorithm. PMID:27446945
Identification of key target genes and pathways in laryngeal carcinoma. PMID:27446427
Genome-Wide Sequence Variation Identification and Floral-Associated Trait Comparisons Based on the Re-sequencing of the 'Nagafu No. 2' and 'Qinguan' Varieties of Apple (Malus domestica Borkh.). PMID:27446138
Identification of miRNAs Involved in Stolon Formation in Tulipa edulis by High-Throughput Sequencing. PMID:27446103
A scientist's guide for submitting data to ZFIN. PMID:27443940
Comparative Transcriptome Analysis Reveals Heat-Responsive Genes in Chinese Cabbage (Brassica rapa ssp. chinensis). PMID:27443222
A highly multiplexed and sensitive RNA-seq protocol for simultaneous analysis of host and pathogen transcriptomes. PMID:27442864
The De Novo Transcriptome and Its Functional Annotation in the Seed Beetle Callosobruchus maculatus. PMID:27442123
Comparative Transcriptome Analysis of Resistant and Susceptible Common Bean Genotypes in Response to Soybean Cyst Nematode Infection. PMID:27441552
Transcriptomic Analysis of Multipurpose Timber Yielding Tree Neolamarckia cadamba during Xylogenesis Using RNA-Seq. PMID:27438485
SILAC-MS Based Characterization of LPS and Resveratrol Induced Changes in Adipocyte Proteomics - Resveratrol as Ameliorating Factor on LPS Induced Changes. PMID:27438462
Association of multiparametric MRI quantitative imaging features with prostate cancer gene expression in MRI-targeted prostate biopsies. PMID:27438142
Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition. PMID:27436874
The myocardial regenerative potential of three-dimensional engineered cardiac tissues composed of multiple human iPS cell-derived cardiovascular cell lineages. PMID:27435115
Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla. PMID:27434306
Revisiting the role of the Gcm transcription factor, from master regulator to Swiss army knife. PMID:27434165
Systematic investigation of transcription factors critical in the protection against cerebral ischemia by Danhong injection. PMID:27431009
Community-Reviewed Biological Network Models for Toxicology and Drug Discovery Applications. PMID:27429547
De Novo Assembly and Developmental Transcriptome Analysis of the Small White Butterfly Pieris rapae. PMID:27428371
Histone deacetylase inhibitor induces cell apoptosis and cycle arrest in lung cancer cells via mitochondrial injury and p53 up-acetylation. PMID:27423454
Protein function in precision medicine: deep understanding with machine learning. PMID:27423136
Grasses suppress shoot-borne roots to conserve water during drought. PMID:27422554
Identification of biomarkers for pseudo and true progression of GBM based on radiogenomics study. PMID:27421136
Cdk3, a conjugation-specific cyclin-dependent kinase, is essential for the initiation of meiosis in Tetrahymena thermophila. PMID:27420775
Complete genome sequencing and comparative genomic analysis of functionally diverse Lysinibacillus sphaericus III(3)7. PMID:27419068
Biosynthesis of Antibiotic Leucinostatins in Bio-control Fungus Purpureocillium lilacinum and Their Inhibition on Phytophthora Revealed by Genome Mining. PMID:27416025
Characterization and target genes of nine human PRD-like homeobox domain genes expressed exclusively in early embryos. PMID:27412763
Permanent draft genome sequence of sulfoquinovose-degrading Pseudomonas putida strain SQ1. PMID:27408681
High quality genome sequence and description of Enterobacter mori strain 5-4, isolated from a mixture of formation water and crude-oil. PMID:27408680
Obtaining Human Ischemic Stroke Gene Expression Biomarkers from Animal Models: A Cross-species Validation Study. PMID:27407070
Identification of candidate genes for myeloma-induced osteocyte death based on microarray data. PMID:27405725
Overcoming the matched-sample bottleneck: an orthogonal approach to integrate omic data. PMID:27403564
Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens. PMID:27403523
Relative contributions of the structural and catalytic roles of Rrp6 in exosomal degradation of individual mRNAs. PMID:27402898
COMODI: an ontology to characterise differences in versions of computational models in biology. PMID:27401413
Genome-Wide Identification of Regulatory Sequences Undergoing Accelerated Evolution in the Human Genome. PMID:27401230
Here We Are, But Where Do We Go? A Systematic Review of Crustacean Transcriptomic Studies from 2014-2015. PMID:27400974
Piriformospora indica Stimulates Root Metabolism of Arabidopsis thaliana. PMID:27399695
Whole Genome Pathway Analysis Identifies an Association of Cadmium Response Gene Loss with Copy Number Variation in Mutant p53 Bearing Uterine Endometrial Carcinomas. PMID:27391266
A novel single cell method to identify the genetic composition at a single nuclear body. PMID:27389808
Expression and methylation patterns partition luminal-A breast tumors into distinct prognostic subgroups. PMID:27386846
The complete genome sequence and analysis of vB_VorS-PVo5, a Vibrio phage infectious to the pathogenic bacterium Vibrio ordalii ATCC-33509. PMID:27382430
Suppressing Farnesyl Diphosphate Synthase Alters Chloroplast Development and Triggers Sterol-Dependent Induction of Jasmonate- and Fe-Related Responses. PMID:27382138
Nuclear import sequence identification in hOAS3 protein. PMID:27379722
Transcriptome- Assisted Label-Free Quantitative Proteomics Analysis Reveals Novel Insights into Piper nigrum-Phytophthora capsici Phytopathosystem. PMID:27379110
A Pathway Proteomic Profile of Ischemic Stroke Survivors Reveals Innate Immune Dysfunction in Association with Mild Symptoms of Depression - A Pilot Study. PMID:27379006
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. PMID:27377652
Transcriptome Analysis on Monocytes from Patients with Neovascular Age-Related Macular Degeneration. PMID:27374485
HPIDB 2.0: a curated database for host-pathogen interactions. PMID:27374121
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
neXtA5: accelerating annotation of articles via automated approaches in neXtProt. PMID:27374119
The Zfhx3-Mediated Axis Regulates Sleep and Interval Timing in Mice. PMID:27373158
Antennal transcriptome and differential expression of olfactory genes in the yellow peach moth, Conogethes punctiferalis (Lepidoptera: Crambidae). PMID:27364081
A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies. PMID:27363390
Comprehensive analysis of lncRNAs microarray profile and mRNA-lncRNA co-expression in oncogenic HPV-positive cervical cancer cell lines. PMID:27363024
DNA methylation signature of human fetal alcohol spectrum disorder. PMID:27358653
Evolution of the Calcium-Based Intracellular Signaling System. PMID:27358427
Screening of gene signatures for rheumatoid arthritis and osteoarthritis based on bioinformatics analysis. PMID:27356888
High-throughput sequencing reveals differential regulation of miRNAs in fenoxaprop-P-ethyl-resistant Beckmannia syzigachne. PMID:27353151
Novel proteases from the genome of the carnivorous plant Drosera capensis: Structural prediction and comparative analysis. PMID:27353064
SorghumFDB: sorghum functional genomics database with multidimensional network analysis. PMID:27352859
Transcriptome analysis of maize resistance to Fusarium graminearum. PMID:27352627
Innate immune defects in HIV permissive cell lines. PMID:27350062
A new strategy for exploring the hierarchical structure of cancers by adaptively partitioning functional modules from gene expression network. PMID:27349736
Probing chromatin landscape reveals roles of endocardial TBX20 in septation. PMID:27348591
Use of RNA-seq to identify cardiac genes and gene pathways differentially expressed between dogs with and without dilated cardiomyopathy. PMID:27347821
Identification of novel biomarkers for preeclampsia on the basis of differential expression network analysis. PMID:27347039
A unified software framework for deriving, visualizing, and exploring abstraction networks for ontologies. PMID:27345947
Genomic Characteristics of Genetic Creutzfeldt-Jakob Disease Patients with V180I Mutation and Associations with Other Neurodegenerative Disorders. PMID:27341347
Genome sequence of the organohalide-respiring Dehalogenimonas alkenigignens type strain (IP3-3(T)). PMID:27340512
High-quality permanent draft genome sequence of Ensifer sp. PC2, isolated from a nitrogen-fixing root nodule of the legume tree (Khejri) native to the Thar Desert of India. PMID:27340511
Draft Genome Sequence of Fungus Clonostachys rosea Strain YKD0085. PMID:27340057
Transcriptome, genetic editing, and microRNA divergence substantiate sympatric speciation of blind mole rat, Spalax. PMID:27339131
Functional coherence metrics in protein families. PMID:27338101
Salinity-induced changes in gene expression from anterior and posterior gills of Callinectes sapidus (Crustacea: Portunidae) with implications for crustacean ecological genomics. PMID:27337176
Epigenome-wide DNA methylation analysis implicates neuronal and inflammatory signaling pathways in adult murine hepatic tumorigenesis following perinatal exposure to bisphenol A. PMID:27334623
CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs. PMID:27334471
Generalized enrichment analysis improves the detection of adverse drug events from the biomedical literature. PMID:27333889
Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta-Lactamases. PMID:27332861
De novo Transcriptome Analysis of Chinese Citrus Fly, Bactrocera minax (Diptera: Tephritidae), by High-Throughput Illumina Sequencing. PMID:27331903
Transcriptome analysis of immature xylem in the Chinese fir at different developmental phases. PMID:27330860
Comprehensive analysis of high-throughput screens with HiTSeekR. PMID:27330136
Functional characterization of three trehalase genes regulating the chitin metabolism pathway in rice brown planthopper using RNA interference. PMID:27328657
MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data. PMID:27327495
A Mechanistic Beta-Binomial Probability Model for mRNA Sequencing Data. PMID:27326762
Transcriptional similarity in couples reveals the impact of shared environment and lifestyle on gene regulation through modified cytosines. PMID:27326381
Molecular serum signature of treatment resistant depression. PMID:27325393
Identification of the key regulating genes of diminished ovarian reserve (DOR) by network and gene ontology analysis. PMID:27324248
Integrated gene set analysis for microRNA studies. PMID:27324197
Functional characterization of somatic mutations in cancer using network-based inference of protein activity. PMID:27322546
Human Milk Cells Contain Numerous miRNAs that May Change with Milk Removal and Regulate Multiple Physiological Processes. PMID:27322254
Evolution of domain-peptide interactions to coadapt specificity and affinity to functional diversity. PMID:27317745
Toward reliable biomarker signatures in the age of liquid biopsies - how to standardize the small RNA-Seq workflow. PMID:27317696
Transcriptional signatures of influenza A/H1N1-specific IgG memory-like B cell response in older individuals. PMID:27317456
Acute Stress Responses Are Early Molecular Events of Retinal Degeneration in Abca4-/-Rdh8-/- Mice After Light Exposure. PMID:27315541
High-quality draft genome sequence of Flavobacterium suncheonense GH29-5(T) (DSM 17707(T)) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5(T). PMID:27313837
Defining the consequences of genetic variation on a proteome-wide scale. PMID:27309819
Approaches to uncovering cancer diagnostic and prognostic molecular signatures. PMID:27308330
Jumping across biomedical contexts using compressive data fusion. PMID:27307649
An integer programming framework for inferring disease complexes from network data. PMID:27307626
Identification of S-phase DNA damage-response targets in fission yeast reveals conservation of damage-response networks. PMID:27298342
Donor age and long-term culture do not negatively influence the stem potential of limbal fibroblast-like stem cells. PMID:27296060
An Adaptive Hybrid Algorithm for Global Network Alignment. PMID:27295633
Inferring active regulatory networks from gene expression data using a combination of prior knowledge and enrichment analysis. PMID:27295045
Mechanisms of transcription factor evolution in Metazoa. PMID:27288445
Evolution of Gene Duplication in Plants. PMID:27288366
Long noncoding RNA EGOT negatively affects the antiviral response and favors HCV replication. PMID:27283940
Distinct properties of proteases and nucleases in the gut, salivary gland and saliva of southern green stink bug, Nezara viridula. PMID:27282882
Virus-induced gene silencing of the RPC5-like subunit of RNA polymerase III caused pleiotropic effects in Nicotiana benthamiana. PMID:27282827
Genome-wide detection of CNVs in Chinese indigenous sheep with different types of tails using ovine high-density 600K SNP arrays. PMID:27282145
Antiinflammatory Effects of Budesonide in Human Fetal Lung. PMID:27281349
Insights into Sexual Precocity of Female Oriental River Prawn Macrobrachium nipponense through Transcriptome Analysis. PMID:27280288
Next-generation profiling to identify the molecular etiology of Parkinson dementia. PMID:27275011
Complete genome sequence of the haloalkaliphilic, obligately chemolithoautotrophic thiosulfate and sulfide-oxidizing γ-proteobacterium Thioalkalimicrobium cyclicum type strain ALM 1 (DSM 14477(T)). PMID:27274784
Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae UST040801-001(T) (DSM 23547(T)), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictoriae Lau et al. 2005. PMID:27274783
Draft genome sequence of Fusicladium effusum, cause of pecan scab. PMID:27274782
Complete genome sequence of Leuconostoc gelidum subsp. gasicomitatum KG16-1, isolated from vacuum-packaged vegetable sausages. PMID:27274361
Tools for Predicting the Functional Impact of Nonsynonymous Genetic Variation. PMID:27270698
Antimalarial Benzoxaboroles Target Plasmodium falciparum Leucyl-tRNA Synthetase. PMID:27270277
Horizontal gene transfer events reshape the global landscape of arm race between viruses and homo sapiens. PMID:27270140
Comparative genomic and transcriptomic analyses of the Fuzhuan brick tea-fermentation fungus Aspergillus cristatus. PMID:27267057
miR-30 Family Controls Proliferation and Differentiation of Intestinal Epithelial Cell Models by Directing a Broad Gene Expression Program That Includes SOX9 and the Ubiquitin Ligase Pathway. PMID:27261459
MeSH-Informed Enrichment Analysis and MeSH-Guided Semantic Similarity Among Functional Terms and Gene Products in Chicken. PMID:27261003
Transcriptome sequences spanning key developmental states as a resource for the study of the cestode Schistocephalus solidus, a threespine stickleback parasite. PMID:27259971
The Proteasix Ontology. PMID:27259807
De novo assembly and characterization of the Chinese three-keeled pond turtle (Mauremys reevesii) transcriptome: presence of longevity-related genes. PMID:27257545
High-quality genome sequence and description of Bacillus ndiopicus strain FF3(T) sp. nov. PMID:27257496
Noncontiguous finished genome sequence and description of Paenibacillus antibioticophila sp. nov. GD11(T), the type strain of Paenibacillus antibioticophila. PMID:27257493
Noncontiguous finished genome sequence and description of Nocardioides massiliensis sp. nov. GD13(T). PMID:27257488
Generation of open biomedical datasets through ontology-driven transformation and integration processes. PMID:27255189
A dataset for assessing temporal changes in gene expression during the aging process of adult Drosophila melanogaster. PMID:27252981
Reactive oxygen species-associated molecular signature predicts survival in patients with sepsis. PMID:27252846
Transcriptomic and proteomic analysis of mouse radiation-induced acute myeloid leukaemia (AML). PMID:27250028
Differentially Expressed miRNAs in Tumor, Adjacent, and Normal Tissues of Lung Adenocarcinoma. PMID:27247934
Combinatorial Gene Regulatory Functions Underlie Ultraconserved Elements in Drosophila. PMID:27247329
Label-Free Proteomics Assisted by Affinity Enrichment for Elucidating the Chemical Reactivity of the Liver Mitochondrial Proteome toward Adduction by the Lipid Electrophile 4-hydroxy-2-nonenal (HNE). PMID:27242993
CoopTFD: a repository for predicted yeast cooperative transcription factor pairs. PMID:27242036
Abasy Atlas: a comprehensive inventory of systems, global network properties and systems-level elements across bacteria. PMID:27242034
Variation in serum biomarkers with sex and female hormonal status: implications for clinical tests. PMID:27240929
High-resolution copy number variation analysis of schizophrenia in Japan. PMID:27240532
Pre-mRNA splicing is modulated by antifungal drugs in the filamentous fungus Neurospora crassa. PMID:27239448
Coronary artery disease susceptibility gene ADTRP regulates cell cycle progression, proliferation, and apoptosis by global gene expression regulation. PMID:27235449
Genomic Prediction for Quantitative Traits Is Improved by Mapping Variants to Gene Ontology Categories in Drosophila melanogaster. PMID:27235308
Plasma-derived Extracellular Vesicles Contain Predictive Biomarkers and Potential Therapeutic Targets for Myocardial Ischemic (MI) Injury. PMID:27234505
Identification and characterization of miRNAs and targets in flax (Linum usitatissimum) under saline, alkaline, and saline-alkaline stresses. PMID:27234464
Germline APOBEC3B deletion is associated with breast cancer risk in an Asian multi-ethnic cohort and with immune cell presentation. PMID:27233495
Data integration to prioritize drugs using genomics and curated data. PMID:27231484
Genome-wide identification of microRNAs in pomegranate (Punica granatum L.) by high-throughput sequencing. PMID:27230657
OCT4 Remodels the Phenotype and Promotes Angiogenesis of HUVECs by Changing the Gene Expression Profile. PMID:27226779
Glucocorticoid receptor isoforms direct distinct mitochondrial programs to regulate ATP production. PMID:27226058
Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling. PMID:27224977
Massive Shift in Gene Expression during Transitions between Developmental Stages of the Gall Midge, Mayetiola Destructor. PMID:27224654
Transcriptome analysis of cortical tissue reveals shared sets of downregulated genes in autism and schizophrenia. PMID:27219343
RNA-seq analysis of virR and revR mutants of Clostridium perfringens. PMID:27216822
Integrated Analysis of Expression Profile Based on Differentially Expressed Genes in Middle Cerebral Artery Occlusion Animal Models. PMID:27213359
Ontology-based collection, representation and analysis of drug-associated neuropathy adverse events. PMID:27213033
Altered gene expression in the lower respiratory tract of Car6 (-/-) mice. PMID:27209317
Genome-Wide Inference of Protein-Protein Interaction Networks Identifies Crosstalk in Abscisic Acid Signaling. PMID:27208273
Transcriptomic Responses of the Interactions between Clostridium cellulovorans 743B and Rhodopseudomonas palustris CGA009 in a Cellulose-Grown Coculture for Enhanced Hydrogen Production. PMID:27208134
Editor's Highlight: Analysis of the Effects of Cell Stress and Cytotoxicity on In Vitro Assay Activity Across a Diverse Chemical and Assay Space. PMID:27208079
DIANA-mirExTra v2.0: Uncovering microRNAs and transcription factors with crucial roles in NGS expression data. PMID:27207881
Reprogramming human A375 amelanotic melanoma cells by catalase overexpression: Upregulation of antioxidant genes correlates with regression of melanoma malignancy and with malignant progression when downregulated. PMID:27206673
Representation of anatomy in online atlases and databases: a survey and collection of patterns for interface design. PMID:27206491
Reactome from a WikiPathways Perspective. PMID:27203685
Leveraging Comparative Genomics to Identify and Functionally Characterize Genes Associated with Sperm Phenotypes in Python bivittatus (Burmese Python). PMID:27200191
The Classification of Sini Decoction Pattern in Traditional Chinese Medicine by Gene Expression Profiling. PMID:27200105
SUR1 Receptor Interaction with Hesperidin and Linarin Predicts Possible Mechanisms of Action of Valeriana officinalis in Parkinson. PMID:27199743
Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis. PMID:27199545
Survey of the genome of Pogostemon cablin provides insights into its evolutionary history and sesquiterpenoid biosynthesis. PMID:27198881
The cellular microscopy phenotype ontology. PMID:27195102
Heterozygote Advantage Is a Common Outcome of Adaptation in Saccharomyces cerevisiae. PMID:27194750
Identification and Characterization of miRNAs in Chondrus crispus by High-Throughput Sequencing and Bioinformatics Analysis. PMID:27193824
Peptide-based systems analysis of inflammation induced myeloid-derived suppressor cells reveals diverse signaling pathways. PMID:27193397
Cyc17, a meiosis-specific cyclin, is essential for anaphase initiation and chromosome segregation in Tetrahymena thermophila. PMID:27192402
Practical aspects of NGS-based pathways analysis for personalized cancer science and medicine. PMID:27191992
The Role of Transcription Factors at Antisense-Expressing Gene Pairs in Yeast. PMID:27190003
Whole-transcriptome analysis of UUO mouse model of renal fibrosis reveals new molecular players in kidney diseases. PMID:27189340
Selective forces and mutational biases drive stop codon usage in the human genome: a comparison with sense codon usage. PMID:27188984
SOX7 co-regulates Wnt/β-catenin signaling with Axin-2: both expressed at low levels in breast cancer. PMID:27188720
Viruses are a dominant driver of protein adaptation in mammals. PMID:27187613
Chronic Heat Stress Induces Immune Response, Oxidative Stress Response, and Apoptosis of Finishing Pig Liver: A Proteomic Approach. PMID:27187351
Successful establishment of patient-derived tumor xenografts from gastrointestinal stromal tumor-a single center experience. PMID:27186422
Comparative transcriptome analysis revealing dormant conidia and germination associated genes in Aspergillus species: an essential role for AtfA in conidial dormancy. PMID:27185182
The effect of growth rate on pyrazinamide activity in Mycobacterium tuberculosis - insights for early bactericidal activity? PMID:27184366
Complete genome sequence of 'Halanaeroarchaeum sulfurireducens' M27-SA2, a sulfur-reducing and acetate-oxidizing haloarchaeon from the deep-sea hypersaline anoxic lake Medee. PMID:27182430
Identification of the anti-tumor activity and mechanisms of nuciferine through a network pharmacology approach. PMID:27180984
Transcription Analysis of the Myometrium of Labouring and Non-Labouring Women. PMID:27176052
Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancer. PMID:27175787
Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics. PMID:27175778
Filtering large-scale event collections using a combination of supervised and unsupervised learning for event trigger classification. PMID:27175227
OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data. PMID:27175225
BELTracker: evidence sentence retrieval for BEL statements. PMID:27173525
Interconnections Between RNA-Processing Pathways Revealed by a Sequencing-Based Genetic Screen for Pre-mRNA Splicing Mutants in Fission Yeast. PMID:27172183
Generating Gene Ontology-Disease Inferences to Explore Mechanisms of Human Disease at the Comparative Toxicogenomics Database. PMID:27171405
Advancing Exposure Science through Chemical Data Curation and Integration in the Comparative Toxicogenomics Database. PMID:27170236
Six Tissue Transcriptomics Reveals Specific Immune Suppression in Spleen by Dietary Polyunsaturated Fatty Acids. PMID:27166587
Identification of a new gene regulatory circuit involving B cell receptor activated signaling using a combined analysis of experimental, clinical and global gene expression data. PMID:27166259
Exploiting single-cell expression to characterize co-expression replicability. PMID:27165153
Targeted Sequencing and Meta-Analysis of Preterm Birth. PMID:27163930
Model-based contextualization of in vitro toxicity data quantitatively predicts in vivo drug response in patients. PMID:27161439
Comparative Genomics of Pathogens Causing Brown Spot Disease of Tobacco: Alternaria longipes and Alternaria alternata. PMID:27159564
Developmental Acquisition of Regulomes Underlies Innate Lymphoid Cell Functionality. PMID:27156451
Dynamic metabolic and transcriptomic profiling of methyl jasmonate-treated hairy roots reveals synthetic characters and regulators of lignan biosynthesis in Isatis indigotica Fort. PMID:27155368
Characterizing gene sets using discriminative random walks with restart on heterogeneous biological networks. PMID:27153592
Independent Evolution of Winner Traits without Whole Genome Duplication in Dekkera Yeasts. PMID:27152421
The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology. PMID:27152146
Complete genome sequence of an agr-dysfunctional variant of the ST239 lineage of the methicillin-resistant Staphylococcus aureus strain GV69 from Brazil. PMID:27152133
DrugGenEx-Net: a novel computational platform for systems pharmacology and gene expression-based drug repurposing. PMID:27151405
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. PMID:27141961
The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing. PMID:27138043
Comprehensive Transcriptome Analysis of Sex-Biased Expressed Genes Reveals Discrete Biological and Physiological Features of Male and Female Schistosoma japonicum. PMID:27128440
The Ontology for Biomedical Investigations. PMID:27128319
The omic approach to parasitic trematode research-a review of techniques and developments within the past 5 years. PMID:27126082
Complete genome sequences of Geobacillus sp. WCH70, a thermophilic strain isolated from wood compost. PMID:27123157
Identification of potential therapeutic target genes and mechanisms in head and neck squamous cell carcinoma by bioinformatics analysis. PMID:27123054
PTIR: Predicted Tomato Interactome Resource. PMID:27121261
Metabolomics in epidemiology: from metabolite concentrations to integrative reaction networks. PMID:27118561
From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF. PMID:27114493
Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons. PMID:27113915
Human somatic cells subjected to genetic induction with six germ line-related factors display meiotic germ cell-like features. PMID:27112843
Network-driven plasma proteomics expose molecular changes in the Alzheimer's brain. PMID:27112350
An inter-species protein-protein interaction network across vast evolutionary distance. PMID:27107014
Companion: a web server for annotation and analysis of parasite genomes. PMID:27105845
Active and Repressive Chromatin-Associated Proteome after MPA Treatment and the Role of Midkine in Epithelial Monolayer Permeability. PMID:27104530
Gene Expression Profiling Identifies Cell Proliferation and Inflammation as the Predominant Pathways Regulated by Aryl Hydrocarbon Receptor in Primary Human Fetal Lung Cells Exposed to Hyperoxia. PMID:27103661
Standardized Profiling of The Membrane-Enriched Proteome of Mouse Dorsal Root Ganglia (DRG) Provides Novel Insights Into Chronic Pain. PMID:27103637
Single-Cell Co-expression Analysis Reveals Distinct Functional Modules, Co-regulation Mechanisms and Clinical Outcomes. PMID:27100869
g:Profiler-a web server for functional interpretation of gene lists (2016 update). PMID:27098042
Spaceflight Activates Lipotoxic Pathways in Mouse Liver. PMID:27097220
Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package. PMID:27096930
Sequencing and characterization of leaf transcriptomes of six diploid Nicotiana species. PMID:27096138
Computing the origin and evolution of the ribosome from its structure - Uncovering processes of macromolecular accretion benefiting synthetic biology. PMID:27096056
Bioinformatics analysis of the gene expression profile of hepatocellular carcinoma: preliminary results. PMID:27095935
Interferon-α signaling promotes embryonic HSC maturation. PMID:27095787
In Vitro Model for Hepatotoxicity Studies Based on Primary Human Hepatocyte Cultivation in a Perfused 3D Bioreactor System. PMID:27092500
Learning from Co-expression Networks: Possibilities and Challenges. PMID:27092161
Gene Prioritization for Imaging Genetics Studies Using Gene Ontology and a Stratified False Discovery Rate Approach. PMID:27092072
Controllability analysis of the directed human protein interaction network identifies disease genes and drug targets. PMID:27091990
ChemiRs: a web application for microRNAs and chemicals. PMID:27091357
Genome-wide association study of antidepressant response: involvement of the inorganic cation transmembrane transporter activity pathway. PMID:27091189
Gene set of chemosensory receptors in the polyembryonic endoparasitoid Macrocentrus cingulum. PMID:27090020
The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts. PMID:27089831
Identification and Evolutionary Analysis of Potential Candidate Genes in a Human Eating Disorder. PMID:27088090
Transcriptome changes in apple peel tissues during CO2 injury symptom development under controlled atmosphere storage regimens. PMID:27087982
Non contiguous-finished genome sequence and description of Microbacterium gorillae sp. nov. PMID:27087892
The link between orthology relations and gene trees: a correction perspective. PMID:27087831
Microarray-Based Phospho-Proteomic Profiling of Complex Biological Systems. PMID:27084428
AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression. PMID:27082953
High-quality genome sequencing and description of Dermabacter indicis sp. nov. PMID:27081494
High-quality draft genome sequence and description of Haemophilus massiliensis sp. nov. PMID:27081435
A Network of Splice Isoforms for the Mouse. PMID:27079421
Novel Biomarker Proteins in Chronic Lymphocytic Leukemia: Impact on Diagnosis, Prognosis and Treatment. PMID:27078856
Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system. PMID:27078110
Computational Reconstruction of NFκB Pathway Interaction Mechanisms during Prostate Cancer. PMID:27078000
Coordinated Evolution of Transcriptional and Post-Transcriptional Regulation for Mitochondrial Functions in Yeast Strains. PMID:27077367
Extending gene ontology in the context of extracellular RNA and vesicle communication. PMID:27076901
MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions. PMID:27076900
Human Milk Cells and Lipids Conserve Numerous Known and Novel miRNAs, Some of Which Are Differentially Expressed during Lactation. PMID:27074017
Process Pharmacology: A Pharmacological Data Science Approach to Drug Development and Therapy. PMID:27069773
Functional test of PCDHB11, the most human-specific neuronal surface protein. PMID:27068704
Unbiased identification of substrates of protein tyrosine phosphatase ptp-3 in C. elegans. PMID:27067626
Transcriptome Analysis of Differentially Expressed Genes Provides Insight into Stolon Formation in Tulipa edulis. PMID:27064558
Core Circadian Clock Genes Regulate Leukemia Stem Cells in AML. PMID:27058663
Comprehensive Transcriptome Meta-analysis to Characterize Host Immune Responses in Helminth Infections. PMID:27058578
RegenBase: a knowledge base of spinal cord injury biology for translational research. PMID:27055827
Proteome-wide dataset supporting functional study of tyrosine kinases in breast cancer. PMID:27054188
Integrated analysis of proteome and transcriptome changes in the mucopolysaccharidosis type VII mouse hippocampus. PMID:27053151
The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable. PMID:27051515
A physiome interoperability roadmap for personalized drug development. PMID:27051513
ATG9A loss confers resistance to trastuzumab via c-Cbl mediated Her2 degradation. PMID:27050377
A Querying Method over RDF-ized Health Level Seven v2.5 Messages Using Life Science Knowledge Resources. PMID:27050304
A Novel Prioritization Method in Identifying Recurrent Venous Thromboembolism-Related Genes. PMID:27050193
The Genome and Methylome of a Subsocial Small Carpenter Bee, Ceratina calcarata. PMID:27048475
Genome-Wide Expression Profiling Reveals S100B as Biomarker for Invasive Aspergillosis. PMID:27047454
Transcriptome Analysis of Differentially Expressed Genes Involved in Proanthocyanidin Accumulation in the Rhizomes of Fagopyrum dibotrys and an Irradiation-Induced Mutant. PMID:27047386
Transcriptome Remodeling in Trypanosoma cruzi and Human Cells during Intracellular Infection. PMID:27046031
MicroRNA profiling of cisplatin-resistant oral squamous cell carcinoma cell lines enriched with cancer-stem-cell-like and epithelial-mesenchymal transition-type features. PMID:27045798
SoftPanel: a website for grouping diseases and related disorders for generation of customized panels. PMID:27044653
Compensation of Dosage-Sensitive Genes on the Chicken Z Chromosome. PMID:27044516
Webulous and the Webulous Google Add-On--a web service and application for ontology building from templates. PMID:27042287
Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment. PMID:27042262
Comparative transcriptome analyses of seven anurans reveal functions and adaptations of amphibian skin. PMID:27040083
GAMDB: a web resource to connect microRNAs with autophagy in gerontology. PMID:27037912
Using biological networks to integrate, visualize and analyze genomics data. PMID:27036106
Characterization of long non-coding RNA expression profiles in lymph node metastasis of early-stage cervical cancer. PMID:27035672
Expression profile analysis of head and neck squamous cell carcinomas using data from The Cancer Genome Atlas. PMID:27035117
System-Wide Associations between DNA-Methylation, Gene Expression, and Humoral Immune Response to Influenza Vaccination. PMID:27031986
Topology based identification and comprehensive classification of four-transmembrane helix containing proteins (4TMs) in the human genome. PMID:27030248
A generic schema and data collection forms applicable to diverse entomological studies of mosquitoes. PMID:27022408
CoDNaS 2.0: a comprehensive database of protein conformational diversity in the native state. PMID:27022160
Independent and Parallel Evolution of New Genes by Gene Duplication in Two Origins of C4 Photosynthesis Provides New Insight into the Mechanism of Phloem Loading in C4 Species. PMID:27016024
In-depth analysis of secretome and N-glycosecretome of human hepatocellular carcinoma metastatic cell lines shed light on metastasis correlated proteins. PMID:27014972
Insights into the single cell draft genome of "Candidatus Achromatium palustre". PMID:27014417
Contextualizing the Genes Altered in Bladder Neoplasms in Pediatric andTeen Patients Allows Identifying Two Main Classes of Biological ProcessesInvolved and New Potential Therapeutic Targets. PMID:27013923
HNdb: an integrated database of gene and protein information on head and neck squamous cell carcinoma. PMID:27013077
Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation. PMID:27011785
IQSEC2 and X-linked syndromal intellectual disability. PMID:27010919
Using PSEA-Quant for Protein Set Enrichment Analysis of Quantitative Mass Spectrometry-Based Proteomics. PMID:27010334
The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database. PMID:27009807
Differences in environmental stress response among yeasts is consistent with species-specific lifestyles. PMID:27009200
Illuminating drug action by network integration of disease genes: a case study of myocardial infarction. PMID:27004607
Proteomic Profiling of Mouse Liver following Acute Toxoplasma gondii Infection. PMID:27003162
CCAR1 5' UTR as a natural miRancer of miR-1254 overrides tamoxifen resistance. PMID:27002217
The Hsp70 homolog Ssb and the 14-3-3 protein Bmh1 jointly regulate transcription of glucose repressed genes in Saccharomyces cerevisiae. PMID:27001512
Sparse regression models for unraveling group and individual associations in eQTL mapping. PMID:27000043
FlyOde - a platform for community curation and interactive visualization of dynamic gene regulatory networks in Drosophila eye development. PMID:26998229
BRG1/SMARCA4 is essential for neuroblastoma cell viability through modulation of cell death and survival pathways. PMID:26996667
Identification of genes for controlling swine adipose deposition by integrating transcriptome, whole-genome resequencing, and quantitative trait loci data. PMID:26996612
GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations. PMID:26994912
New features of desiccation tolerance in the lichen photobiont Trebouxia gelatinosa are revealed by a transcriptomic approach. PMID:26992400
dbWGFP: a database and web server of human whole-genome single nucleotide variants and their functional predictions. PMID:26989155
Wikidata as a semantic framework for the Gene Wiki initiative. PMID:26989148
An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework. PMID:26989145
Utilizing a structural meta-ontology for family-based quality assurance of the BioPortal ontologies. PMID:26988001
Comparison of module detection algorithms in protein networks and investigation of the biological meaning of predicted modules. PMID:26987731
Genes with high penetrance for syndromic and non-syndromic autism typically function within the nucleus and regulate gene expression. PMID:26985359
Transcriptomic Signature of the SHATTERPROOF2 Expression Domain Reveals the Meristematic Nature of Arabidopsis Gynoecial Medial Domain. PMID:26983993
ENTPRISE: An Algorithm for Predicting Human Disease-Associated Amino Acid Substitutions from Sequence Entropy and Predicted Protein Structures. PMID:26982818
Analysis of copy number variations in Mexican Holstein cattle using axiom genome-wide Bos 1 array. PMID:26981375
The complete genome sequence of Eubacterium limosum SA11, a metabolically versatile rumen acetogen. PMID:26981167
Genetic Evidence of Human Adaptation to a Cooked Diet. PMID:26979798
Integrated Drug Expression Analysis for leukemia: an integrated in silico and in vivo approach to drug discovery. PMID:26975228
Comprehensive transcriptome analysis identifies novel molecular subtypes and subtype-specific RNAs of triple-negative breast cancer. PMID:26975198
Sequencing and comparative analyses of the genomes of zoysiagrasses. PMID:26975196
Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage. PMID:26973616
Human fibroblasts display a differential focal adhesion phenotype relative to chimpanzee. PMID:26971204
Biofilms on Hospital Shower Hoses: Characterization and Implications for Nosocomial Infections. PMID:26969701
Comparative Single-Cell Genomics of Chloroflexi from the Okinawa Trough Deep-Subsurface Biosphere. PMID:26969693
Comprehensive profiling of EBV gene expression in nasopharyngeal carcinoma through paired-end transcriptome sequencing. PMID:26969667
Long genes and genes with multiple splice variants are enriched in pathways linked to cancer and other multigenic diseases. PMID:26968808
Challenges in horizontal model integration. PMID:26968798
GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data. PMID:26968614
Draft genome sequence and overview of the purple non sulfur bacterium Rhodopseudomonas palustris 42OL. PMID:26966509
Identifying genetic modulators of the connectivity between transcription factors and their transcriptional targets. PMID:26966232
Medullary carcinoma of the colon: a distinct morphology reveals a distinctive immunoregulatory microenvironment. PMID:26965581
Activation of Myenteric Glia during Acute Inflammation In Vitro and In Vivo. PMID:26964064
Expression Profiles of miRNA Subsets Distinguish Human Colorectal Carcinoma and Normal Colonic Mucosa. PMID:26963002
Genetic Divergence between Camellia sinensis and Its Wild Relatives Revealed via Genome-Wide SNPs from RAD Sequencing. PMID:26962860
Illumina microRNA profiles reveal the involvement of miR397a in Citrus adaptation to long-term boron toxicity via modulating secondary cell-wall biosynthesis. PMID:26962011
Data in support of the identification of neuronal and astrocyte proteins interacting with extracellularly applied oligomeric and fibrillar α-synuclein assemblies by mass spectrometry. PMID:26958642
High-quality genome sequence and description of Paenibacillus dakarensis sp. nov. PMID:26958345
Drug-drug Interaction Discovery Using Abstraction Networks for "National Drug File - Reference Terminology" Chemical Ingredients. PMID:26958234
De novo Transcriptome Assembly of Floral Buds of Pineapple and Identification of Differentially Expressed Genes in Response to Ethephon Induction. PMID:26955375
Transcriptome Profiling of Two Asparagus Bean (Vigna unguiculata subsp. sesquipedalis) Cultivars Differing in Chilling Tolerance under Cold Stress. PMID:26954786
Analysis of the Phialocephala subalpina Transcriptome during Colonization of Its Host Plant Picea abies. PMID:26954682
miR-130b-3p Modulates Epithelial-Mesenchymal Crosstalk in Lung Fibrosis by Targeting IGF-1. PMID:26953888
Stable engineered vascular networks from human induced pluripotent stem cell-derived endothelial cells cultured in synthetic hydrogels. PMID:26945632
Common DNA methylation alterations of Alzheimer's disease and aging in peripheral whole blood. PMID:26943045
shRNA target prediction informed by comprehensive enquiry (SPICE): a supporting system for high-throughput screening of shRNA library. PMID:26941783
Identification of biological targets of therapeutic intervention for clear cell renal cell carcinoma based on bioinformatics approach. PMID:26941587
Health and population effects of rare gene knockouts in adult humans with related parents. PMID:26940866
Genome sequence and description of Anaerosalibacter massiliensis sp. nov. PMID:26937282
Integrated microRNA‑gene analysis of coronary artery disease based on miRNA and gene expression profiles. PMID:26936111
Comparative transcriptomics and proteomics of three different aphid species identifies core and diverse effector sets. PMID:26935069
High-quality genome sequence and description of Chryseobacterium senegalense sp. nov. PMID:26933502
Genome sequences of Knoxdaviesia capensis and K. proteae (Fungi: Ascomycota) from Protea trees in South Africa. PMID:26933475
GEMC1 is a critical regulator of multiciliated cell differentiation. PMID:26933123
Draft genomic sequence of Nereida ignava CECT 5292(T), a marine bacterium of the family Rhodobacteraceae. PMID:26929790
Expression profile analysis of long noncoding RNA in HER-2-enriched subtype breast cancer by next-generation sequencing and bioinformatics. PMID:26929647
Hologenome analysis of two marine sponges with different microbiomes. PMID:26926518
KENeV: A web-application for the automated reconstruction and visualization of the enriched metabolic and signaling super-pathways deriving from genomic experiments. PMID:26925206
High-quality draft genome sequence of the Thermus amyloliquefaciens type strain YIM 77409(T) with an incomplete denitrification pathway. PMID:26925197
Draft genome sequence of chloride-tolerant Leptospirillum ferriphilum Sp-Cl from industrial bioleaching operations in northern Chile. PMID:26925196
Label-free proteomic methodology for the analysis of human kidney stone matrix composition. PMID:26924944
Mutations in Subunits of the Activating Signal Cointegrator 1 Complex Are Associated with Prenatal Spinal Muscular Atrophy and Congenital Bone Fractures. PMID:26924529
Comparative Transcriptomics Indicates a Role for SHORT VEGETATIVE PHASE (SVP) Genes in Mimulus guttatus Vernalization Response. PMID:26921300
Smokescreen: a targeted genotyping array for addiction research. PMID:26921259
Draft genome sequence of Sphingomonas paucimobilis strain LCT-SP1 isolated from the Shenzhou X spacecraft of China. PMID:26918090
Guidelines for the functional annotation of microRNAs using the Gene Ontology. PMID:26917558
Venom gland transcriptome analyses of two freshwater stingrays (Myliobatiformes: Potamotrygonidae) from Brazil. PMID:26916342
Strong Components of Epigenetic Memory in Cultured Human Fibroblasts Related to Site of Origin and Donor Age. PMID:26913521
Isolation and complete genome sequence of the thermophilic Geobacillus sp. 12AMOR1 from an Arctic deep-sea hydrothermal vent site. PMID:26913091
Examining non-syndromic autosomal recessive intellectual disability (NS-ARID) genes for an enriched association with intelligence differences. PMID:26912939
Novel loci and pathways significantly associated with longevity. PMID:26912274
Identity, proliferation capacity, genomic stability and novel senescence markers of mesenchymal stem cells isolated from low volume of human bone marrow. PMID:26910916
Prediction of Candidate Drugs for Treating Pancreatic Cancer by Using a Combined Approach. PMID:26910401
The Lungfish Transcriptome: A Glimpse into Molecular Evolution Events at the Transition from Water to Land. PMID:26908371
Transcriptome Sequencing and Development of Genic SSR Markers of an Endangered Chinese Endemic Genus Dipteronia Oliver (Aceraceae). PMID:26907245
Using Multi-objective Optimization to Identify Dynamical Network Biomarkers as Early-warning Signals of Complex Diseases. PMID:26906975
Comparative transcriptome analysis of fruiting body and sporulating mycelia of Villosiclava virens reveals genes with putative functions in sexual reproduction. PMID:26905382
Genetic features of Mycobacterium tuberculosis modern Beijing sublineage. PMID:26905026
Systems Perturbation Analysis of a Large-Scale Signal Transduction Model Reveals Potentially Influential Candidates for Cancer Therapeutics. PMID:26904540
The transcriptomic basis of tissue- and nutrition-dependent sexual dimorphism in the beetle Onthophagus taurus. PMID:26904187
Quantitative proteomic analyses of mammary organoids reveals distinct signatures after exposure to environmental chemicals. PMID:26903627
An interactive web-based application for Comprehensive Analysis of RNAi-screen Data. PMID:26902267
Tissue-specific Proteogenomic Analysis of Plutella xylostella Larval Midgut Using a Multialgorithm Pipeline. PMID:26902207
Natural variation in non-coding regions underlying phenotypic diversity in budding yeast. PMID:26898953
Differentially expressed lncRNAs and mRNAs identified by microarray analysis in GBS patients vs healthy controls. PMID:26898505
EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation. PMID:26896844
Identification of genes and pathways associated with pancreatic ductal adenocarcinoma by bioinformatics analyses. PMID:26893748
Identification of genes and signaling pathways associated with squamous cell carcinoma by bioinformatics analysis. PMID:26893747
Revealing the role of VEGFA in clear cell sarcoma of the kidney by protein-protein interaction network and significant pathway analysis. PMID:26893674
Cinacalcet inhibits neuroblastoma tumor growth and upregulates cancer-testis antigens. PMID:26893368
Epigenome-wide profiling of DNA methylation in paired samples of adipose tissue and blood. PMID:26891033
Population structure and minimum core genome typing of Legionella pneumophila. PMID:26888563
Application of biclustering of gene expression data and gene set enrichment analysis methods to identify potentially disease causing nanomaterials. PMID:26885455
LEAFDATA: a literature-curated database for Arabidopsis leaf development. PMID:26884807
Cross-platform comparison of independent datasets identifies an immune signature associated with improved survival in metastatic melanoma. PMID:26883106
Revisiting cobalt chloride preconditioning to prevent hypobaric hypoxia-induced damage: identification of global proteomic alteration and key networks. PMID:26882918
Functional screen identifies regulators of murine hematopoietic stem cell repopulation. PMID:26880577
Deep-sequencing identification of differentially expressed miRNAs in decidua and villus of recurrent miscarriage patients. PMID:26879955
BATMAN-TCM: a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine. PMID:26879404
Translational bioinformatics in the era of real-time biomedical, health care and wellness data streams. PMID:26876889
Expression Profiling of Macrophages Reveals Multiple Populations with Distinct Biological Roles in an Immunocompetent Orthotopic Model of Lung Cancer. PMID:26873985
Is the crowd better as an assistant or a replacement in ontology engineering? An exploration through the lens of the Gene Ontology. PMID:26873781
Structural and Functional Characterization of a Caenorhabditis elegans Genetic Interaction Network within Pathways. PMID:26871911
Laying a Community-Based Foundation for Data-Driven Semantic Standards in Environmental Health Sciences. PMID:26871594
Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals. PMID:26870952
Signal transduction by M3 muscarinic acetylcholine receptor in prostate cancer. PMID:26870222
Ten Simple Rules for Selecting a Bio-ontology. PMID:26867217
Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2. PMID:26866790
Genome sequence of Shinella sp. strain DD12, isolated from homogenized guts of starved Daphnia magna. PMID:26865909
Predicting physiologically relevant SH3 domain mediated protein-protein interactions in yeast. PMID:26861823
Quorum sensing activity of Citrobacter amalonaticus L8A, a bacterium isolated from dental plaque. PMID:26860259
Physiological Characterization and Comparative Transcriptome Analysis of a Slow-Growing Reduced-Thylakoid Mutant of Chinese Cabbage (Brassica campestris ssp. pekinensis). PMID:26858733
Sequencing, De novo Assembly, Functional Annotation and Analysis of Phyllanthus amarus Leaf Transcriptome Using the Illumina Platform. PMID:26858723
New insights into the Plasmodium vivax transcriptome using RNA-Seq. PMID:26858037
Lack of tRNA-i6A modification causes mitochondrial-like metabolic deficiency in S. pombe by limiting activity of cytosolic tRNATyr, not mito-tRNA. PMID:26857223
Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines. PMID:26856248
Selectivity profiling of BCRP versus P-gp inhibition: from automated collection of polypharmacology data to multi-label learning. PMID:26855674
Comparative analysis of Cu (I)-catalyzed alkyne-azide cycloaddition (CuAAC) and strain-promoted alkyne-azide cycloaddition (SPAAC) in O-GlcNAc proteomics. PMID:26853435
The exploration of network motifs as potential drug targets from post-translational regulatory networks. PMID:26853265
Bridging semantics and syntax with graph algorithms-state-of-the-art of extracting biomedical relations. PMID:26851224
Erosion of Conserved Binding Sites in Personal Genomes Points to Medical Histories. PMID:26845687
Prime, Shock, and Kill: Priming CD4 T Cells from HIV Patients with a BCL-2 Antagonist before HIV Reactivation Reduces HIV Reservoir Size. PMID:26842479
Time-Series Transcriptomics Reveals That AGAMOUS-LIKE22 Affects Primary Metabolism and Developmental Processes in Drought-Stressed Arabidopsis. PMID:26842464
Recruitment of the Mammalian Histone-modifying EMSY Complex to Target Genes Is Regulated by ZNF131. PMID:26841866
Transcriptome and Expression Patterns of Chemosensory Genes in Antennae of the Parasitoid Wasp Chouioia cunea. PMID:26841106
Characterising Complex Enzyme Reaction Data. PMID:26840640
A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics. PMID:26838676
PHENOstruct: Prediction of human phenotype ontology terms using heterogeneous data sources. PMID:26834980
Multi-Omics Approach Identifies Molecular Mechanisms of Plant-Fungus Mycorrhizal Interaction. PMID:26834754
Different evolutionary patterns of SNPs between domains and unassigned regions in human protein-coding sequences. PMID:26833483
Vibrio cholerae FeoA, FeoB, and FeoC Interact To Form a Complex. PMID:26833408
Probiotic (Enterococcus faecium) induced responses of the hepatic proteome improves metabolic efficiency of broiler chickens (Gallus gallus). PMID:26830196
An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma. PMID:26829750
Rapid Identification of Candidate Genes for Seed Weight Using the SLAF-Seq Method in Brassica napus. PMID:26824525
Complete genome sequence and characterization of avian pathogenic Escherichia coli field isolate ACN001. PMID:26823959
Draft genome sequence for virulent and avirulent strains of Xanthomonas arboricola isolated from Prunus spp. in Spain. PMID:26823958
Complete genome sequence and genomic characterization of Microcystis panniformis FACHB 1757 by third-generation sequencing. PMID:26823957
Differences in gene expression profiles and signaling pathways in rhabdomyolysis-induced acute kidney injury. PMID:26823722
Genomic Analyses Reveal Demographic History and Temperate Adaptation of the Newly Discovered Honey Bee Subspecies Apis mellifera sinisxinyuan n. ssp. PMID:26823447
Targeted Next-Generation Sequencing Identifies a Recurrent Mutation in MCPH1 Associating with Hereditary Breast Cancer Susceptibility. PMID:26820313
The Iflaviruses Sacbrood virus and Deformed wing virus evoke different transcriptional responses in the honeybee which may facilitate their horizontal or vertical transmission. PMID:26819848
Draft genome sequence of Paenibacillus sp. strain A2. PMID:26819653
Missing value imputation for microRNA expression data by using a GO-based similarity measure. PMID:26818962
Learning a hierarchical representation of the yeast transcriptomic machinery using an autoencoder model. PMID:26818848
A Bayesian approach for estimating allele-specific expression from RNA-Seq data with diploid genomes. PMID:26818838
Consolidating and Exploring Antibiotic Resistance Gene Data Resources. PMID:26818666
Gene expression profiling identifies candidate biomarkers for active and latent tuberculosis. PMID:26818387
Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome. PMID:26818233
Identification of Genes Relevant to Pesticides and Biology from Global Transcriptome Data of Monochamus alternatus Hope (Coleoptera: Cerambycidae) Larvae. PMID:26815657
A survey of best practices for RNA-seq data analysis. PMID:26813401
A Genome-Wide mRNA Expression Profile in Caenorhabditis elegans under Prolonged Exposure to 1750MHz Radiofrequency Fields. PMID:26811916
Transcriptional response to heat shock in liver of snow trout (Schizothorax richardsonii)--a vulnerable Himalayan Cyprinid fish. PMID:26810178
Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics. PMID:26808494
Transcriptomic Determinants of Scrapie Prion Propagation in Cultured Ovine Microglia. PMID:26807844
Dysregulated expression of microRNAs and mRNAs in myocardial infarction. PMID:26807177
Expression Profiles and Biological Roles of miR-196a in Swine. PMID:26805888
Semantic interrogation of a multi knowledge domain ontological model of tendinopathy identifies four strong candidate risk genes. PMID:26804977
Divergence and Functional Degradation of a Sex Chromosome-like Supergene. PMID:26804558
Developmental alcohol exposure leads to a persistent change on astrocyte secretome. PMID:26801685
Uncovering New Pathogen-Host Protein-Protein Interactions by Pairwise Structure Similarity. PMID:26799490
Advanced Running Performance by Genetic Predisposition in Male Dummerstorf Marathon Mice (DUhTP) Reveals Higher Sterol Regulatory Element-Binding Protein (SREBP) Related mRNA Expression in the Liver and Higher Serum Levels of Progesterone. PMID:26799318
Orphan Crops Browser: a bridge between model and orphan crops. PMID:26798323
An endometrial gene expression signature accurately predicts recurrent implantation failure after IVF. PMID:26797113
Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation. PMID:26795250
Integrative analyses of proteomics and RNA transcriptomics implicate mitochondrial processes, protein folding pathways and GWAS loci in Parkinson disease. PMID:26793951
A Proteomic Analysis of Sarcoptes scabiei (Acari: Sarcoptidae). PMID:26792847
Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis. PMID:26791995
Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins. PMID:26787667
Proteomic peptide phage display uncovers novel interactions of the PDZ1-2 supramodule of syntenin. PMID:26787460
A comparative gene analysis with rice identified orthologous group II HKT genes and their association with Na(+) concentration in bread wheat. PMID:26786911
Lamina Associated Polypeptide 1 (LAP1) Interactome and Its Functional Features. PMID:26784240
Interaction between dietary lipids and gut microbiota regulates hepatic cholesterol metabolism. PMID:26783361
Draft genome of the Arabidopsis thaliana phyllosphere bacterium, Williamsia sp. ARP1. PMID:26779305
Complete genome sequence of the potato pathogen Ralstonia solanacearum UY031. PMID:26779304
Permanent draft genome sequence of the probiotic strain Propionibacterium freudenreichii CIRM-BIA 129 (ITG P20). PMID:26779303
Commentary: Comparative Transcriptome Analysis of Raphanus sativus Tissues. PMID:26779225
Transcriptome Analysis of Brassica rapa Near-Isogenic Lines Carrying Clubroot-Resistant and -Susceptible Alleles in Response to Plasmodiophora brassicae during Early Infection. PMID:26779217
Proteome-Wide Effect of 17-β-Estradiol and Lipoxin A4 in an Endometriotic Epithelial Cell Line. PMID:26779118
An evaluation of the accuracy and speed of metagenome analysis tools. PMID:26778510
SEPARATING THE CAUSES AND CONSEQUENCES IN DISEASE TRANSCRIPTOME. PMID:26776202
Repeated exposure to neurotoxic levels of chlorpyrifos alters hippocampal expression of neurotrophins and neuropeptides. PMID:26775027
Genome Reduction Uncovers a Large Dispensable Genome and Adaptive Role for Copy Number Variation in Asexually Propagated Solanum tuberosum. PMID:26772996
Combinatorial Cis-regulation in Saccharomyces Species. PMID:26772747
A transcriptional signature of hub connectivity in the mouse connectome. PMID:26772314
MicroRNA Species in Follicular Fluid Associating With Polycystic Ovary Syndrome and Related Intermediary Phenotypes. PMID:26771704
A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human. PMID:26771498
Developing of the Computer Method for Annotation of Bacterial Genes. PMID:26770195
Comparative genome-wide analysis reveals that Burkholderia contaminans MS14 possesses multiple antimicrobial biosynthesis genes but not major genetic loci required for pathogenesis. PMID:26769582
High quality permanent draft genome sequence of Phaseolibacter flectens ATCC 12775(T), a plant pathogen of French bean pods. PMID:26767091
Permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, a thermoacidophilic sulfur-reducing crenarchaeon isolated from acidic hot springs of Hveravellir, Iceland. PMID:26767090
Transcription Factors Exhibit Differential Conservation in Bacteria with Reduced Genomes. PMID:26766575
De Novo Transcriptome Assembly of the Chinese Swamp Buffalo by RNA Sequencing and SSR Marker Discovery. PMID:26766209
Synthetic cycle of the initiation module of a formylating nonribosomal peptide synthetase. PMID:26762462
An ontology for major histocompatibility restriction. PMID:26759709
Slowed aging during reproductive dormancy is reflected in genome-wide transcriptome changes in Drosophila melanogaster. PMID:26758761
Comprehensive analysis of schizophrenia-associated loci highlights ion channel pathways and biologically plausible candidate causal genes. PMID:26755824
The Dynamics of Transcript Abundance during Cellularization of Developing Barley Endosperm. PMID:26754666
The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution. PMID:26754549
Comparative Transcriptome Profile of the Cytoplasmic Male Sterile and Fertile Floral Buds of Radish (Raphanus sativus L.). PMID:26751440
Ixodes scapularis Tick Saliva Proteins Sequentially Secreted Every 24 h during Blood Feeding. PMID:26751078
LEGO: a novel method for gene set over-representation analysis by incorporating network-based gene weights. PMID:26750448
Microvirga massiliensis sp. nov., the human commensal with the largest genome. PMID:26749561
Transcriptome profiling of immune tissues reveals habitat-specific gene expression between lake and river sticklebacks. PMID:26749022
Systematic Phenomics Analysis Deconvolutes Genes Mutated in Intellectual Disability into Biologically Coherent Modules. PMID:26748517
Introgression of Neandertal- and Denisovan-like Haplotypes Contributes to Adaptive Variation in Human Toll-like Receptors. PMID:26748514
Genomic Signatures of Selective Pressures and Introgression from Archaic Hominins at Human Innate Immunity Genes. PMID:26748513
SNaPP: Simplified Nanoproteomics Platform for Reproducible Global Proteomic Analysis of Nanogram Protein Quantities. PMID:26745641
Complete genome sequence of Methanospirillum hungatei type strain JF1. PMID:26744606
Label-Free, In-Solution Screening of Peptide Libraries for Binding to Protein Targets Using Hydrogen Exchange Mass Spectrometry. PMID:26741284
Exome arrays capture polygenic rare variant contributions to schizophrenia. PMID:26740555
A proteogenomic approach to understand splice isoform functions through sequence and expression-based computational modeling. PMID:26740460
Effect of chronic uremia on the transcriptional profile of the calcified aorta analyzed by RNA sequencing. PMID:26739890
The cytomegalovirus protein UL138 induces apoptosis of gastric cancer cells by binding to heat shock protein 70. PMID:26735338
The complete genome sequence and analysis of a plasmid-bearing myxobacterial strain Myxococcus fulvus 124B02 (M 206081). PMID:26734118
RNA Sequencing Analysis of the msl2msl3, crl, and ggps1 Mutants Indicates that Diverse Sources of Plastid Dysfunction Do Not Alter Leaf Morphology Through a Common Signaling Pathway. PMID:26734046
Pathway Analysis: State of the Art. PMID:26733877
Cross-Study Comparison Reveals Common Genomic, Network, and Functional Signatures of Desiccation Resistance in Drosophila melanogaster. PMID:26733490
Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome. PMID:26731733
Label-Free Quantitative Proteomic Analysis of Puccinia psidii Uredospores Reveals Differences of Fungal Populations Infecting Eucalyptus and Guava. PMID:26731728
dEMBF: A Comprehensive Database of Enzymes of Microalgal Biofuel Feedstock. PMID:26727469
The Effect of In Vitro Cultivation on the Transcriptome of Adult Brugia malayi. PMID:26727204
Genetic code expansion in stable cell lines enables encoded chromatin modification. PMID:26727110
Differentially expressed genes and microRNAs in bladder carcinoma cell line 5637 and T24 detected by RNA sequencing. PMID:26722457
Proteomics and bioinformatics analysis of mouse hypothalamic neurogenesis with or without EPHX2 gene deletion. PMID:26722453
iTRAQ proteomic analysis of salinity acclimation proteins in the gill of tropical marbled eel (Anguilla marmorata). PMID:26721661
Role of NSC319726 in ovarian cancer based on the bioinformatics analyses. PMID:26719703
An in vivo molecular response analysis of colorectal cancer treated with Astragalus membranaceus extract. PMID:26719057
Identification and characterization of microRNAs in Eucheuma denticulatum by high-throughput sequencing and bioinformatics analysis. PMID:26717154
miRLAB: An R Based Dry Lab for Exploring miRNA-mRNA Regulatory Relationships. PMID:26716983
Using host-pathogen protein interactions to identify and characterize Francisella tularensis virulence factors. PMID:26714771
p38 Mitogen-Activated Protein Kinase Pathway Regulates Genes during Proliferation and Differentiation in Oligodendrocytes. PMID:26714323
Schizophrenia-Associated MIR204 Regulates Noncoding RNAs and Affects Neurotransmitter and Ion Channel Gene Sets. PMID:26714269
Tissue Restricted Splice Junctions Originate Not Only from Tissue-Specific Gene Loci, but Gene Loci with a Broad Pattern of Expression. PMID:26713731
Brain Transcriptomic Response to Social Eavesdropping in Zebrafish (Danio rerio). PMID:26713440
Prediction of the anti-inflammatory mechanisms of curcumin by module-based protein interaction network analysis. PMID:26713275
Identifying communities from multiplex biological networks. PMID:26713261
Emerging semantics to link phenotype and environment. PMID:26713234
Proteomic profiling of maize opaque endosperm mutants reveals selective accumulation of lysine-enriched proteins. PMID:26712829
Comprehensive Proteomic and Metabolomic Signatures of Nontypeable Haemophilus influenzae-Induced Acute Otitis Media Reveal Bacterial Aerobic Respiration in an Immunosuppressed Environment. PMID:26711468
MycoBASE: expanding the functional annotation coverage of mycobacterial genomes. PMID:26704706
TauCstF-64 Mediates Correct mRNA Polyadenylation and Splicing of Activator and Repressor Isoforms of the Cyclic AMP-Responsive Element Modulator (CREM) in Mouse Testis. PMID:26700942
The evolution of standards and data management practices in systems biology. PMID:26700851
A high-resolution gene expression atlas of epistasis between gene-specific transcription factors exposes potential mechanisms for genetic interactions. PMID:26700642
Generating and evaluating a ranked candidate gene list for potential vertebrate heart field regulators. PMID:26697374
Androgen Modulates Functions of Endothelial Progenitor Cells through Activated Egr1 Signaling. PMID:26697079
Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods. PMID:26694353
Haem-activated promiscuous targeting of artemisinin in Plasmodium falciparum. PMID:26694030
Prediction of tissue-specific effects of gene knockout on apoptosis in different anatomical structures of human brain. PMID:26693857
Predictive Modeling of Drug Treatment in the Area of Personalized Medicine. PMID:26692759
A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants. PMID:26691988
Developmental genes significantly afflicted by aberrant promoter methylation and somatic mutation predict overall survival of late-stage colorectal cancer. PMID:26691761
Dintor: functional annotation of genomic and proteomic data. PMID:26691694
Cyclophilin C Participates in the US2-Mediated Degradation of Major Histocompatibility Complex Class I Molecules. PMID:26691022
Microarray analysis of Long non-coding RNA expression profiles in human gastric cells and tissues with Helicobacter pylori Infection. PMID:26690385
Genomic analysis of Luteimonas abyssi XH031(T): insights into its adaption to the subseafloor environment of South Pacific Gyre and ecological role in biogeochemical cycle. PMID:26690083
Genome-wide transcriptome profiling reveals functional networks involving the Plasmodium falciparum drug resistance transporters PfCRT and PfMDR1. PMID:26689807
De Novo Assembly of the Pea (Pisum sativum L.) Nodule Transcriptome. PMID:26688806
Postmortem human brain genomics in neuropsychiatric disorders--how far can we go? PMID:26685806
traseR: an R package for performing trait-associated SNP enrichment analysis in genomic intervals. PMID:26685307
Transcriptional regulatory networks in Arabidopsis thaliana during single and combined stresses. PMID:26681689
Multiple target drug cocktail design for attacking the core network markers of four cancers using ligand-based and structure-based virtual screening methods. PMID:26680552
LENS: web-based lens for enrichment and network studies of human proteins. PMID:26680011
Screening of potential biomarkers for cholangiocarcinoma by integrated analysis of microarray data sets. PMID:26679756
Signal reachability facilitates characterization of probabilistic signaling networks. PMID:26679404
Disentangling the multigenic and pleiotropic nature of molecular function. PMID:26678917
Functional redundancy of transcription factors explains why most binding targets of a transcription factor are not affected when the transcription factor is knocked out. PMID:26678747
A novel analysis strategy for integrating methylation and expression data reveals core pathways for thyroid cancer aetiology. PMID:26678064
High-throughput deep screening and identification of four peripheral leucocyte microRNAs as novel potential combination biomarkers for preeclampsia. PMID:26675000
Protein aggregation, structural disorder and RNA-binding ability: a new approach for physico-chemical and gene ontology classification of multiple datasets. PMID:26673865
Protein disorder reduced in Saccharomyces cerevisiae to survive heat shock. PMID:26673203
Quantitative proteomics reveals novel therapeutic and diagnostic markers in hypertension. PMID:26672470
Circadian rhythm influences genome-wide transcriptional responses to (131)I in a tissue-specific manner in mice. PMID:26669694
Physiological and Molecular Alterations Promoted by Schizotetranychus oryzae Mite Infestation in Rice Leaves. PMID:26667653
The administration of intranasal live attenuated influenza vaccine induces changes in the nasal microbiota and nasal epithelium gene expression profiles. PMID:26667497
IRES-dependent translated genes in fungi: computational prediction, phylogenetic conservation and functional association. PMID:26666532
Quantitative proteomics identifies 38 proteins that are differentially expressed in cucumber in response to cucumber green mottle mosaic virus infection. PMID:26666291
Genome sequence of Lysobacter dokdonensis DS-58(T), a gliding bacterium isolated from soil in Dokdo, Korea. PMID:26664701
Complete genome sequence of the molybdenum-resistant bacterium Bacillus subtilis strain LM 4-2. PMID:26664656
High-quality permanent draft genome sequence of Ensifer medicae strain WSM244, a microsymbiont isolated from Medicago polymorpha growing in alkaline soil. PMID:26664655
Genome sequences of two closely related strains of Escherichia coli K-12 GM4792. PMID:26664654
Draft genome sequence of Halopiger salifodinae KCY07-B2(T), an extremly halophilic archaeon isolated from a salt mine. PMID:26664653
Association of genetic and psychological factors with persistent pain after cosmetic thoracic surgery. PMID:26664154
In search of underlying mechanisms and potential drugs of melphalan-induced vascular toxicity through retinal endothelial cells using bioinformatics approach. PMID:26662105
Reproducible Analysis of Post-Translational Modifications in Proteomes--Application to Human Mutations. PMID:26659599
Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage. PMID:26658111
Gene Expression Analysis of Plum pox virus (Sharka) Susceptibility/Resistance in Apricot (Prunus armeniaca L.). PMID:26658051
MicroRNA 19a replacement partially rescues fin and cardiac defects in zebrafish model of Holt Oram syndrome. PMID:26657204
Kiwifruit Information Resource (KIR): a comparative platform for kiwifruit genomics. PMID:26656885
The Reactome pathway Knowledgebase. PMID:26656494
Noncontiguous finished genome sequence and description of Weeksella massiliensis sp. nov. PMID:26649182
Draft genome of Gemmata massiliana sp. nov, a water-borne Planctomycetes species exhibiting two variants. PMID:26649148
Global transcriptome profiling analysis reveals insight into saliva-responsive genes in alfalfa. PMID:26645698
Deep sequencing of Danish Holstein dairy cattle for variant detection and insight into potential loss-of-function variants in protein coding genes. PMID:26645365
A human 3'UTR clone collection to study post-transcriptional gene regulation. PMID:26645212
De novo transcriptome reconstruction and annotation of the Egyptian rousette bat. PMID:26643810
Gene expression changes triggered by end-of-day far-red light treatment on early developmental stages of Eustoma grandiflorum (Raf.) Shinn. PMID:26642764
Detecting Protein Complexes in Protein Interaction Networks Modeled as Gene Expression Biclusters. PMID:26641660
Transcription, Signaling Receptor Activity, Oxidative Phosphorylation, and Fatty Acid Metabolism Mediate the Presence of Closely Related Species in Distinct Intertidal and Cold-Seep Habitats. PMID:26637468
Lupus Nephritis IgG Induction of Calcium/Calmodulin-Dependent Protein Kinase IV Expression in Podocytes and Alteration of Their Function. PMID:26636664
RNA Sequence Analysis of Human Huntington Disease Brain Reveals an Extensive Increase in Inflammatory and Developmental Gene Expression. PMID:26636579
Time-Dependent Transcriptional Changes in Axenic Giardia duodenalis Trophozoites. PMID:26636323
AnGeLi: A Tool for the Analysis of Gene Lists from Fission Yeast. PMID:26635866
Genome sequence of a dissimilatory Fe(III)-reducing bacterium Geobacter soli type strain GSS01(T). PMID:26634019
Complete genome of Pseudomonas chlororaphis strain UFB2, a soil bacterium with antibacterial activity against bacterial canker pathogen of tomato. PMID:26634018
Complete genome sequence of Salinicoccus halodurans H3B36, isolated from the Qaidam Basin in China. PMID:26634017
An extracellular biochemical screen reveals that FLRTs and Unc5s mediate neuronal subtype recognition in the retina. PMID:26633812
Characterization of Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers in Two Species of Gynostemma (Cucurbitaceae). PMID:26633323
Overflow metabolism in Escherichia coli results from efficient proteome allocation. PMID:26632588
Recurrent Fusions in MYB and MYBL1 Define a Common, Transcription Factor-Driven Oncogenic Pathway in Salivary Gland Adenoid Cystic Carcinoma. PMID:26631070
Complete genome sequence and characterization of the haloacid-degrading Burkholderia caribensis MBA4. PMID:26629309
Genome sequence of Bradyrhizobium sp. WSM1253; a microsymbiont of Ornithopus compressus from the Greek Island of Sifnos. PMID:26629308
Genomic insights into the evolutionary origin of Myxozoa within Cnidaria. PMID:26627241
Suppression of transcriptional drift extends C. elegans lifespan by postponing the onset of mortality. PMID:26623667
Pathogenic mechanisms of lung adenocarcinoma in smokers and non-smokers determined by gene expression interrogation. PMID:26622675
PPIM: A Protein-Protein Interaction Database for Maize. PMID:26620522
Emerging tools, concepts and ideas to track the modulator genes underlying plant drought adaptive traits: An overview. PMID:26618613
Unbiased high-throughput characterization of mussel transcriptomic responses to sublethal concentrations of the biotoxin okadaic acid. PMID:26618092
RNA-seq de novo Assembly Reveals Differential Gene Expression in Glossina palpalis gambiensis Infected with Trypanosoma brucei gambiense vs. Non-Infected and Self-Cured Flies. PMID:26617594
The epigenomic landscape of African rainforest hunter-gatherers and farmers. PMID:26616214
Genome-wide expression analysis offers new insights into the origin and evolution of Physcomitrella patens stress response. PMID:26615914
ELM 2016--data update and new functionality of the eukaryotic linear motif resource. PMID:26615199
Database resources of the National Center for Biotechnology Information. PMID:26615191
Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. PMID:26615025
Dominance from the perspective of gene-gene and gene-chemical interactions. PMID:26613610
Large-scale transcriptome sequencing reveals novel expression patterns for key sex-related genes in a sex-changing fish. PMID:26613014
Data standards can boost metabolomics research, and if there is a will, there is a way. PMID:26612985
Advanced Applications of RNA Sequencing and Challenges. PMID:26609224
The sialyl-glycolipid stage-specific embryonic antigen 4 marks a subpopulation of chemotherapy-resistant breast cancer cells with mesenchymal features. PMID:26607327
Development and validation of a mixed-tissue oligonucleotide DNA microarray for Atlantic bluefin tuna, Thunnus thynnus (Linnaeus, 1758). PMID:26607231
Transcriptome Analysis Revealed Highly Expressed Genes Encoding Secondary Metabolite Pathways and Small Cysteine-Rich Proteins in the Sclerotium of Lignosus rhinocerotis. PMID:26606395
Complete genome sequence of bacteriophage P26218 infecting Rhodoferax sp. strain IMCC26218. PMID:26605005
Draft genome sequence of Janthinobacterium lividum strain MTR reveals its mechanism of capnophilic behavior. PMID:26605004
Global Profiling of Huntingtin-associated protein E (HYPE)-Mediated AMPylation through a Chemical Proteomic Approach. PMID:26604261
Systematic identification and correction of annotation errors in the genetic interaction map of Saccharomyces cerevisiae. PMID:26602688
From Single Variants to Protein Cascades: MULTISCALE MODELING OF SINGLE NUCLEOTIDE VARIANT SETS IN GENETIC DISORDERS. PMID:26601959
Identification of Putative Nuclear Receptors and Steroidogenic Enzymes in Murray-Darling Rainbowfish (Melanotaenia fluviatilis) Using RNA-Seq and De Novo Transcriptome Assembly. PMID:26599404
Gene-expression signature functional annotation of breast cancer tumours in function of age. PMID:26597277
Transcriptomics of diapause in an isogenic self-fertilizing vertebrate. PMID:26597228
Whole-Exome Sequencing in Familial Parkinson Disease. PMID:26595808
Complete genome sequence of Staphylococcus aureus, strain ILRI_Eymole1/1, isolated from a Kenyan dromedary camel. PMID:26594310
Complete genome sequence of Novosphingobium pentaromativorans US6-1(T). PMID:26594308
Genome sequence and description of the anaerobic lignin-degrading bacterium Tolumonas lignolytica sp. nov. PMID:26594307
Complete genome sequence of Thioalkalivibrio paradoxus type strain ARh 1(T), an obligately chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium isolated from a Kenyan soda lake. PMID:26594306
Engineering dynamic cell cycle control with synthetic small molecule-responsive RNA devices. PMID:26594238
High-throughput transcriptome sequencing of the cold seep mussel Bathymodiolus platifrons. PMID:26593439
Mitochondrial Involvement in Vertebrate Speciation? The Case of Mito-nuclear Genetic Divergence in Chameleons. PMID:26590214
Finding New Order in Biological Functions from the Network Structure of Gene Annotations. PMID:26588252
Transcriptome Analysis of Syringa oblata Lindl. Inflorescence Identifies Genes Associated with Pigment Biosynthesis and Scent Metabolism. PMID:26587670
Noncontiguous finished genome sequence and description of Necropsobacter massiliensis sp. nov. PMID:26587237
Draft genome sequence of Cellulomonas carbonis T26(T) and comparative analysis of six Cellulomonas genomes. PMID:26587181
An Overview of Biomolecular Event Extraction from Scientific Documents. PMID:26587051
The anatomical distribution of genetic associations. PMID:26586807
NSDF: Neuroscience Simulation Data Format. PMID:26585711
EBI metagenomics in 2016--an expanding and evolving resource for the analysis and archiving of metagenomic data. PMID:26582919
Investigating inter-chromosomal regulatory relationships through a comprehensive meta-analysis of matched copy number and transcriptomics data sets. PMID:26581858
Gonadal Transcriptome Analysis in Sterile Double Haploid Japanese Flounder. PMID:26580217
Changes in the nuclear proteome of developing wheat (Triticum aestivum L.) grain. PMID:26579155
Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities. PMID:26579098
Bioinformatic tools for microRNA dissection. PMID:26578605
Differential sialotranscriptomes of unfed and fed Rhipicephalus haemaphysaloides, with particular regard to differentially expressed genes of cysteine proteases. PMID:26577685
Massively parallel cis-regulatory analysis in the mammalian central nervous system. PMID:26576614
Beyond the E-Value: Stratified Statistics for Protein Domain Prediction. PMID:26575353
Identification of genes related to learning and memory in the brain transcriptome of the mollusc, Hermissenda crassicornis. PMID:26572652
A magnetic protein biocompass. PMID:26569474
Molecular Effects of Irradiation (Cobalt-60) on the Control of Panonychus citri (Acari: Tetranychidae). PMID:26569230
Genome sequence and description of Pantoea septica strain FF5. PMID:26568786
Complete genome sequencing of Dehalococcoides sp. strain UCH007 using a differential reads picking method. PMID:26568785
Complete genome sequence of the thermophilic Acidobacteria, Pyrinomonas methylaliphatogenes type strain K22(T). PMID:26568784
KMAD: knowledge-based multiple sequence alignment for intrinsically disordered proteins. PMID:26568635
MAPanalyzer: a novel online tool for analyzing microtubule-associated proteins. PMID:26568329
Type of in vitro cultivation influences cytoadhesion, knob structure, protein localization and transcriptome profile of Plasmodium falciparum. PMID:26568166
Transcriptional Dynamics Driving MAMP-Triggered Immunity and Pathogen Effector-Mediated Immunosuppression in Arabidopsis Leaves Following Infection with Pseudomonas syringae pv tomato DC3000. PMID:26566919
Genome sequence of Pedobacter glucosidilyticus DD6b, isolated from zooplankton Daphnia magna. PMID:26566425
Working draft genome sequence of the mesophilic acetate oxidizing bacterium Syntrophaceticus schinkii strain Sp3. PMID:26566424
High-quality draft genome sequence of Gracilimonas tropica CL-CB462(T) (DSM 19535(T)), isolated from a Synechococcus culture. PMID:26566423
Complete genome sequence of Bacillus cereus FORC_005, a food-borne pathogen from the soy sauce braised fish-cake with quail-egg. PMID:26566422
Complete genome sequence of bacteriophage P8625, the first lytic phage that infects Verrucomicrobia. PMID:26566421
High-quality draft genome sequence of a new phytase-producing microorganism Pantoea sp. 3.5.1. PMID:26566420
Bringing Down Cancer Aircraft: Searching for Essential Hypomutated Proteins in Skin Melanoma. PMID:26565620
From System-Wide Differential Gene Expression to Perturbed Regulatory Factors: A Combinatorial Approach. PMID:26562430
Complete genome sequence of Paracoccus marcusii phage vB_PmaS-R3 isolated from the South China Sea. PMID:26561517
High quality draft genome sequence of the moderately halophilic bacterium Pontibacillus yanchengensis Y32(T) and comparison among Pontibacillus genomes. PMID:26561516
High quality draft genomic sequence of Flavobacterium enshiense DK69(T) and comparison among Flavobacterium genomes. PMID:26561515
Effectiveness and Usability of Bioinformatics Tools to Analyze Pathways Associated with miRNA Expression. PMID:26560461
A network-based method to evaluate quality of reproducibility of differential expression in cancer genomics studies. PMID:26556852
Potential Role of lncRNAs in Contributing to Pathogenesis of Intervertebral Disc Degeneration Based on Microarray Data. PMID:26556537
Exosomes decrease sensitivity of breast cancer cells to adriamycin by delivering microRNAs. PMID:26555545
Molecular systems evaluation of oligomerogenic APP(E693Q) and fibrillogenic APP(KM670/671NL)/PSEN1(Δexon9) mouse models identifies shared features with human Alzheimer's brain molecular pathology. PMID:26552589
Sieve-based relation extraction of gene regulatory networks from biological literature. PMID:26551454
Corn Gluten Hydrolysate Affects the Time-Course of Metabolic Changes Through Appetite Control in High-Fat Diet-Induced Obese Rats. PMID:26549503
Pathway-based variant enrichment analysis on the example of dilated cardiomyopathy. PMID:26547721
Human TNF-α induces differential protein phosphorylation in Schistosoma mansoni adult male worms. PMID:26547565
Transcriptomic analysis of cobalt stress in the marine yeast Debaryomyces hansenii. PMID:26546454
A potential endophenotype for Alzheimer's disease: cerebrospinal fluid clusterin. PMID:26545630
Identification of Evening Complex Associated Proteins in Arabidopsis by Affinity Purification and Mass Spectrometry. PMID:26545401
Big Data in Caenorhabditis elegans: quo vadis? PMID:26543198
MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes. PMID:26541816
Umbilical cord gene expression reveals the molecular architecture of the fetal inflammatory response in extremely preterm newborns. PMID:26539667
An assessment of catalytic residue 3D ensembles for the prediction of enzyme function. PMID:26538500
Revisiting operons: an analysis of the landscape of transcriptional units in E. coli. PMID:26538447
Horizontal gene transfer in bdelloid rotifers is ancient, ongoing and more frequent in species from desiccating habitats. PMID:26537913
De Novo Assembly and Characterization of the Invasive Northern Pacific Seastar Transcriptome. PMID:26529321
Proteomic Analysis of Embryonic and Young Human Vitreous. PMID:26529037
Dynamic transcription profiles of "Qinguan" apple (Malus × domestica) leaves in response to Marssonina coronaria inoculation. PMID:26528306
Application of Functional Genomics for Bovine Respiratory Disease Diagnostics. PMID:26526746
Identification, Characterization, and Diel Pattern of Expression of Canonical Clock Genes in Nephrops norvegicus (Crustacea: Decapoda) Eyestalk. PMID:26524198
Genome sequence of Oceanobacillus picturae strain S1, an halophilic bacterium first isolated in human gut. PMID:26523201
Bayesian inference with historical data-based informative priors improves detection of differentially expressed genes. PMID:26519502
How to Use the Candida Genome Database. PMID:26519061
Increased hepatocellular protein carbonylation in human end-stage alcoholic cirrhosis. PMID:26518673
Early leukocyte gene expression associated with age, burn size, and inhalation injury in severely burned adults. PMID:26517785
Draft genome sequence of a nitrate-reducing, o-phthalate degrading bacterium, Azoarcus sp. strain PA01(T). PMID:26516406
High quality draft genomes of the Mycoplasma mycoides subsp. mycoides challenge strains Afadé and B237. PMID:26516405
Genomic information of the arsenic-resistant bacterium Lysobacter arseniciresistens type strain ZS79(T) and comparison of Lysobacter draft genomes. PMID:26516404
SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets. PMID:26516187
Avoiding abundance bias in the functional annotation of post-translationally modified proteins. PMID:26513550
High-quality permanent draft genome sequence of Bradyrhizobium sp. strain WSM1743 - an effective microsymbiont of an Indigofera sp. growing in Australia. PMID:26512312
Partial genome sequence of the haloalkaliphilic soda lake bacterium Thioalkalivibrio thiocyanoxidans ARh 2(T). PMID:26512310
Partial genome sequence of Thioalkalivibrio thiocyanodenitrificans ARhD 1(T), a chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium capable of complete denitrification. PMID:26512309
Deciphering the association between gene function and spatial gene-gene interactions in 3D human genome conformation. PMID:26511362
Novel gene sets improve set-level classification of prokaryotic gene expression data. PMID:26511329
GOTA: GO term annotation of biomedical literature. PMID:26511083
Blood transcriptomics of drug-naïve sporadic Parkinson's disease patients. PMID:26510930
A survey of computational tools for downstream analysis of proteomic and other omic datasets. PMID:26510531
Transcriptional and Linkage Analyses Identify Loci that Mediate the Differential Macrophage Response to Inflammatory Stimuli and Infection. PMID:26510153
Identification of Chemical Toxicity Using Ontology Information of Chemicals. PMID:26508991
A Systematic Evaluation of Feature Selection and Classification Algorithms Using Simulated and Real miRNA Sequencing Data. PMID:26508990
PhenoMiner: from text to a database of phenotypes associated with OMIM diseases. PMID:26507285
Transcriptional Profile of Bacillus subtilis sigF-Mutant during Vegetative Growth. PMID:26506528
Identification of Novel and Conserved miRNAs from Extreme Halophyte, Oryza coarctata, a Wild Relative of Rice. PMID:26506249
An acorn squash (Cucurbita pepo ssp. ovifera) fruit and seed transcriptome as a resource for the study of fruit traits in Cucurbita. PMID:26504561
Identification of SSRs and differentially expressed genes in two cultivars of celery (Apium graveolens L.) by deep transcriptome sequencing. PMID:26504532
Effect of summer daylight exposure and genetic background on growth in growth hormone-deficient children. PMID:26503811
Bioengineering Human Myocardium on Native Extracellular Matrix. PMID:26503464
Comparative analysis of molecular mechanism of spinal cord injury with time based on bioinformatics data. PMID:26503224
Networks' Characteristics Matter for Systems Biology. PMID:26500772
RDF2Graph a tool to recover, understand and validate the ontology of an RDF resource. PMID:26500754
Complete genome sequence of Propionibacterium freudenreichii DSM 20271(T). PMID:26500719
Complete genome sequences of bacteriophages P12002L and P12002S, two lytic phages that infect a marine Polaribacter strain. PMID:26500718
Target prediction utilising negative bioactivity data covering large chemical space. PMID:26500705
Characterization of whole-genome autosomal differences of DNA methylation between men and women. PMID:26500701
Moving from capstones toward cornerstones: successes and challenges in applying systems biology to identify mechanisms of autism spectrum disorders. PMID:26500678
Developing expressed sequence tag libraries and the discovery of simple sequence repeat markers for two species of raspberry (Rubus L.). PMID:26499487
GM3 ganglioside and phosphatidylethanolamine-containing lipids are adipose tissue markers of insulin resistance in obese women. PMID:26499445
Identification of key genes associated with the human abdominal aortic aneurysm based on the gene expression profile. PMID:26498477
Overexpression of mitochondrial uncoupling protein 1 (UCP1) induces a hypoxic response in Nicotiana tabacum leaves. PMID:26494730
DNA damage-induced ephrin-B2 reverse signaling promotes chemoresistance and drives EMT in colorectal carcinoma harboring mutant p53. PMID:26494468
Systems biology evaluation of cell-free amniotic fluid transcriptome of term and preterm infants to detect fetal maturity. PMID:26493725
The distribution and impact of common copy-number variation in the genome of the domesticated apple, Malus x domestica Borkh. PMID:26493398
GREM1 and POLE variants in hereditary colorectal cancer syndromes. PMID:26493165
Human Gene Expression in Uncomplicated Plasmodium falciparum Malaria. PMID:26491700
A Glimpse to Background and Characteristics of Major Molecular Biological Networks. PMID:26491677
Methods for biological data integration: perspectives and challenges. PMID:26490630
Identification of novel and conserved microRNAs in Panax notoginseng roots by high-throughput sequencing. PMID:26490136
HIV Tat controls RNA Polymerase II and the epigenetic landscape to transcriptionally reprogram target immune cells. PMID:26488441
LncRNA ontology: inferring lncRNA functions based on chromatin states and expression patterns. PMID:26485761
Ten Simple Rules for Experiments' Provenance. PMID:26485673
CD39 Expression Identifies Terminally Exhausted CD8+ T Cells. PMID:26485519
Identification of differentially methylated regions in new genes associated with knee osteoarthritis. PMID:26484395
Analyzing alternative splicing data of splice junction arrays from Parkinson patients' leukocytes before and after deep brain stimulation as compared with control donors. PMID:26484282
Kuwaiti population subgroup of nomadic Bedouin ancestry-Whole genome sequence and analysis. PMID:26484159
Transcriptome profiling of gene expression in fall dormant and nondormant alfalfa. PMID:26484109
Transcriptome profiling reveals differential gene expression in proanthocyanidin biosynthesis associated with red/green skin color mutant of pear (Pyrus communis L.). PMID:26483812
Protein Analysis of Sapienic Acid-Treated Porphyromonas gingivalis Suggests Differential Regulation of Multiple Metabolic Pathways. PMID:26483519
The human gene damage index as a gene-level approach to prioritizing exome variants. PMID:26483451
Reconstruction and Analysis of the Evolution of Modular Transcriptional Regulatory Programs Using Arboretum. PMID:26483033
Analysis of 5' gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals. PMID:26482678
Increased Transcript Complexity in Genes Associated with Chronic Obstructive Pulmonary Disease. PMID:26480348
High-quality permanent draft genome sequence of the Mimosa asperata - nodulating Cupriavidus sp. strain AMP6. PMID:26478786
High-quality permanent draft genome sequence of the Lebeckia ambigua-nodulating Burkholderia sp. strain WSM4176. PMID:26478785
Naturally Occurring Stilbenoid TSG Reverses Non-Alcoholic Fatty Liver Diseases via Gut-Liver Axis. PMID:26474417
Gene-Set Local Hierarchical Clustering (GSLHC)--A Gene Set-Based Approach for Characterizing Bioactive Compounds in Terms of Biological Functional Groups. PMID:26473729
Complete genome sequence of Mycobacterium tuberculosis K from a Korean high school outbreak, belonging to the Beijing family. PMID:26473025
Analysis of the Human Proteome in Subcutaneous and Visceral Fat Depots in Diabetic and Non-diabetic Patients with Morbid Obesity. PMID:26472921
An Integrated Multiomics Approach to Identify Candidate Antigens for Serodiagnosis of Human Onchocerciasis. PMID:26472727
Revealing crosstalk of plant and fungi in the symbiotic roots of sewage-cleaning Eichhornia crassipes using direct de novo metatranscriptomic analysis. PMID:26472343
Quantitative assessment of gene expression network module-validation methods. PMID:26470848
Estimating cumulative pathway effects on risk for age-related macular degeneration using mixed linear models. PMID:26467978
Virtual pathway explorer (viPEr) and pathway enrichment analysis tool (PEANuT): creating and analyzing focus networks to identify cross-talk between molecules and pathways. PMID:26467653
Gene expression profiling during adventitious root formation in carnation stem cuttings. PMID:26467528
FlyBase: establishing a Gene Group resource for Drosophila melanogaster. PMID:26467478
Jasmonate signalling drives time-of-day differences in susceptibility of Arabidopsis to the fungal pathogen Botrytis cinerea. PMID:26466558
Comparative Characterization of Cardiac Development Specific microRNAs: Fetal Regulators for Future. PMID:26465880
Gene Prioritization by Compressive Data Fusion and Chaining. PMID:26465776
Characterization of the Cardiac Overexpression of HSPB2 Reveals Mitochondrial and Myogenic Roles Supported by a Cardiac HspB2 Interactome. PMID:26465331
Draft genome sequence of Mesotoga strain PhosAC3, a mesophilic member of the bacterial order Thermotogales, isolated from a digestor treating phosphogypsum in Tunisia. PMID:26464750
Common variants in DRD2 are associated with sleep duration: the CARe consortium. PMID:26464489
The Effect of Statins on Blood Gene Expression in COPD. PMID:26462087
Sample size reassessment for a two-stage design controlling the false discovery rate. PMID:26461844
Proteomic Analysis of Anti-Cancerous Scopularide Production by a Marine Microascus brevicaulis Strain and Its UV Mutant. PMID:26460745
Genomic insight into Aquimarina longa SW024 T: its ultra-oligotrophic adapting mechanisms and biogeochemical functions. PMID:26459873
Prioritization Of Nonsynonymous Single Nucleotide Variants For Exome Sequencing Studies Via Integrative Learning On Multiple Genomic Data. PMID:26459872
Integrated ordination of miRNA and mRNA expression profiles. PMID:26459852
Gene expression profile analysis of ventilator-associated pneumonia. PMID:26459786
The complete genome sequence and emendation of the hyperthermophilic, obligate iron-reducing archaeon "Geoglobus ahangari" strain 234(T). PMID:26457129
Complete genome sequence of the thermophilic Thermus sp. CCB_US3_UF1 from a hot spring in Malaysia. PMID:26457128
Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology. PMID:26454094
WaspAtlas: a Nasonia vitripennis gene database and analysis platform. PMID:26452372
A Semi-Supervised Approach for Refining Transcriptional Signatures of Drug Response and Repositioning Predictions. PMID:26452147
Diversity in protein domain superfamilies. PMID:26451979
Comparative Transcriptome Analysis of the Less-Dormant Taiwanese Pear and the Dormant Japanese Pear during Winter Season. PMID:26451604
Draft genome sequence of Halomonas meridiana R1t3 isolated from the surface microbiota of the Caribbean Elkhorn coral Acropora palmata. PMID:26451236
Aberrant DNA methylation in non-small cell lung cancer-associated fibroblasts. PMID:26449251
An Ancient Yeast for Young Geneticists: A Primer on the Schizosaccharomyces pombe Model System. PMID:26447128
Ontology-based representation and analysis of host-Brucella interactions. PMID:26445639
Complete genome sequence of the chromate-reducing bacterium Thermoanaerobacter thermohydrosulfuricus strain BSB-33. PMID:26445627
Bioinformatics analyses of differentially expressed genes associated with bisphosphonate-related osteonecrosis of the jaw in patients with multiple myeloma. PMID:26445550
Protein and small non-coding RNA-enriched extracellular vesicles are released by the pathogenic blood fluke Schistosoma mansoni. PMID:26443722
The EcoCyc Database. PMID:26442933
Complete genome sequence of Geobacillus thermoglucosidasius C56-YS93, a novel biomass degrader isolated from obsidian hot spring in Yellowstone National Park. PMID:26442136
Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1. PMID:26441909
A FreeSurfer view of the cortical transcriptome generated from the Allen Human Brain Atlas. PMID:26441498
Identifying binary protein-protein interactions from affinity purification mass spectrometry data. PMID:26438428
Interlog protein network: an evolutionary benchmark of protein interaction networks for the evaluation of clustering algorithms. PMID:26437714
Genome-Wide Detection and Analysis of Multifunctional Genes. PMID:26436655
MitoMiner v3.1, an update on the mitochondrial proteomics database. PMID:26432830
MaizeGDB update: new tools, data and interface for the maize model organism database. PMID:26432828
Dynamics in Transcriptomics: Advancements in RNA-seq Time Course and Downstream Analysis. PMID:26430493
Transcriptomic Analysis of Ovaries from Pigs with High And Low Litter Size. PMID:26426260
The eNanoMapper database for nanomaterial safety information. PMID:26425413
miRSponge: a manually curated database for experimentally supported miRNA sponges and ceRNAs. PMID:26424084
Genome sequence of a native-feather degrading extremely thermophilic Eubacterium, Fervidobacterium islandicum AW-1. PMID:26421103
Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery. PMID:26420781
The digital revolution in phenotyping. PMID:26420780
Elucidation of the CHO Super-Ome (CHO-SO) by Proteoinformatics. PMID:26418914
A Survey of the ATP-Binding Cassette (ABC) Gene Superfamily in the Salmon Louse (Lepeophtheirus salmonis). PMID:26418738
LncRNA-Hh Strengthen Cancer Stem Cells Generation in Twist-Positive Breast Cancer via Activation of Hedgehog Signaling Pathway. PMID:26418365
Proteomic changes of the porcine small intestine in response to chronic heat stress. PMID:26416815
The decrease in histone methyltransferase EZH2 in response to fluid shear stress alters endothelial gene expression and promotes quiescence. PMID:26416763
Improved orthologous databases to ease protozoan targets inference. PMID:26416523
Genome sequence of Anoxybacillus ayderensis AB04(T) isolated from the Ayder hot spring in Turkey. PMID:26413199
The complete genome sequence of the rumen methanogen Methanosarcina barkeri CM1. PMID:26413197
Draft genome sequence of Bacillus azotoformans MEV2011, a (Co-) denitrifying strain unable to grow with oxygen. PMID:26413196
CLUSTERnGO: a user-defined modelling platform for two-stage clustering of time-series data. PMID:26411869
PanFP: pangenome-based functional profiles for microbial communities. PMID:26409790
The complete genome, structural proteome, comparative genomics and phylogenetic analysis of a broad host lytic bacteriophage ϕD3 infecting pectinolytic Dickeya spp. PMID:26405503
Label-Free LC-MS/MS Proteomic Analysis of Cerebrospinal Fluid Identifies Protein/Pathway Alterations and Candidate Biomarkers for Amyotrophic Lateral Sclerosis. PMID:26401960
Site-Specific Ser/Thr/Tyr Phosphoproteome of Sinorhizobium meliloti at Stationary Phase. PMID:26401955
Genomic alterations in BCL2L1 and DLC1 contribute to drug sensitivity in gastric cancer. PMID:26401016
Recent findings and technological advances in phosphoproteomics for cells and tissues. PMID:26400465
PathwaysWeb: a gene pathways API with directional interactions, expanded gene ontology, and versioning. PMID:26400039
Integrative analysis of human protein, function and disease networks. PMID:26399914
htsint: a Python library for sequencing pipelines that combines data through gene set generation. PMID:26399714
The role of breast-feeding in infant immune system: a systems perspective on the intestinal microbiome. PMID:26399409
Proteome-wide quantitative multiplexed profiling of protein expression: carbon-source dependency in Saccharomyces cerevisiae. PMID:26399295
De novo sequencing and assembly analysis of transcriptome in the Sodom apple (Calotropis gigantea). PMID:26395839
PDON: Parkinson's disease ontology for representation and modeling of the Parkinson's disease knowledge domain. PMID:26395080
TSS seq based core promoter architecture in blood feeding Tsetse fly (Glossina morsitans morsitans) vector of Trypanosomiasis. PMID:26394619
From Brain Maps to Cognitive Ontologies: Informatics and the Search for Mental Structure. PMID:26393866
Human pluripotent stem cell-derived neural constructs for predicting neural toxicity. PMID:26392547
High quality draft genomic sequence of Flavihumibacter solisilvae 3-3(T). PMID:26388970
High-quality permanent draft genome sequence of the Lebeckia - nodulating Burkholderia dilworthii strain WSM3556(T). PMID:26388968
Non-contiguous finished genome sequence and description of Clostridium ihumii sp. nov. PMID:26388967
Methylome profiling reveals functions and genes which are differentially methylated in serrated compared to conventional colorectal carcinoma. PMID:26388956
Reconstruction of novel transcription factor regulons through inference of their binding sites. PMID:26388177
Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology. PMID:26387907
Heimler Syndrome Is Caused by Hypomorphic Mutations in the Peroxisome-Biogenesis Genes PEX1 and PEX6. PMID:26387595
Computational functional genomics based analysis of pain-relevant micro-RNAs. PMID:26385553
De Novo Assembly and Characterization of Four Anthozoan (Phylum Cnidaria) Transcriptomes. PMID:26384772
Codon and Amino Acid Usage Are Shaped by Selection Across Divergent Model Organisms of the Pancrustacea. PMID:26384771
Deep Question Answering for protein annotation. PMID:26384372
SimiRa: A tool to identify coregulation between microRNAs and RNA-binding proteins. PMID:26383775
mapDIA: Preprocessing and statistical analysis of quantitative proteomics data from data independent acquisition mass spectrometry. PMID:26381204
Complete genome sequence of Bacillus thuringiensis strain HD521. PMID:26380647
Improved-high-quality draft genome sequence of Rhodococcus sp. JG-3, a eurypsychrophilic Actinobacteria from Antarctic Dry Valley permafrost. PMID:26380646
Complete genome sequence of Vibrio anguillarum strain NB10, a virulent isolate from the Gulf of Bothnia. PMID:26380645
High quality draft genomic sequence of Arenimonas donghaensis DSM 18148(T). PMID:26380644
Draft genome sequence of marine-derived Streptomyces sp. TP-A0598, a producer of anti-MRSA antibiotic lydicamycins. PMID:26380643
Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4. PMID:26380642
High-Quality draft genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain CJ3Sym. PMID:26380641
High-quality permanent draft genome sequence of the extremely osmotolerant diphenol degrading bacterium Halotalea alkalilenta AW-7(T), and emended description of the genus Halotalea. PMID:26380640
Genome sequence of the pink-pigmented marine bacterium Loktanella hongkongensis type strain (UST950701-009P(T)), a representative of the Roseobacter group. PMID:26380639
High quality draft genome sequence of Corynebacterium ulceribovis type strain IMMIB-L1395(T) (DSM 45146(T)). PMID:26380638
Genome sequence of the haloarchaeon Haloterrigena jeotgali type strain A29(T) isolated from salt-fermented food. PMID:26380637
High quality draft genome sequence of Bacteroides barnesiae type strain BL2(T) (DSM 18169(T)) from chicken caecum. PMID:26380636
Non contiguous-finished genome sequence and description of Bacillus jeddahensis sp. nov. PMID:26380635
High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2(T) (DSM 21788(T)), a valuable source of polysaccharide decomposing enzymes. PMID:26380634
High-quality permanent draft genome sequence of Rhizobium sullae strain WSM1592; a Hedysarum coronarium microsymbiont from Sassari, Italy. PMID:26380632
Draft-genome sequence of Shewanella algae strain C6G3. PMID:26380631
Complete genome sequence of Roseophage vB_DshP-R1, which infects Dinoroseobacter shibae DFL12. PMID:26380630
A close look at protein function prediction evaluation protocols. PMID:26380075
Permanent draft genome sequence of Acidiphilium sp. JA12-A1. PMID:26380040
Draft genome sequence of the extremely halophilic archaeon Haladaptatus cibarius type strain D43(T) isolated from fermented seafood. PMID:26380039
High-quality permanent draft genome sequence of Ensifer meliloti strain 4H41, an effective salt- and drought-tolerant microsymbiont of Phaseolus vulgaris. PMID:26380038
High-quality permanent draft genome sequence of Bradyrhizobium sp. Ai1a-2; a microsymbiont of Andira inermis discovered in Costa Rica. PMID:26380037
Gene activity in primary T cells infected with HIV89.6: intron retention and induction of genomic repeats. PMID:26377088
Identification of Gene-Expression Signatures and Protein Markers for Breast Cancer Grading and Staging. PMID:26375396
Comparative plasma proteomic studies of pulmonary TiO2 nanoparticle exposure in rats using liquid chromatography tandem mass spectrometry. PMID:26375203
Age-driven modulation of tRNA-derived fragments in Drosophila and their potential targets. PMID:26374501
Characterization of the Transcriptional Complexity of the Receptive and Pre-receptive Endometria of Dairy Goats. PMID:26373443
Global Identification of MicroRNAs and Their Targets in Barley under Salinity Stress. PMID:26372557
Integrated protein function prediction by mining function associations, sequences, and protein-protein and gene-gene interaction networks. PMID:26370280
Putative synaptic genes defined from a Drosophila whole body developmental transcriptome by a machine learning approach. PMID:26370122
A multilevel pan-cancer map links gene mutations to cancer hallmarks. PMID:26369414
Modeling the Regulatory Mechanisms by Which NLRX1 Modulates Innate Immune Responses to Helicobacter pylori Infection. PMID:26367386
Assessing the Metabolic Diversity of Streptococcus from a Protein Domain Point of View. PMID:26366735
Genome-wide association analyses based on whole-genome sequencing in Sardinia provide insights into regulation of hemoglobin levels. PMID:26366553
Quantitative Proteomic Analysis Reveals Molecular Adaptations in the Hippocampal Synaptic Active Zone of Chronic Mild Stress-Unsusceptible Rats. PMID:26364272
Bioinformatics-Based Identification of MicroRNA-Regulated and Rheumatoid Arthritis-Associated Genes. PMID:26359667
Prepatterning of differentiation-driven nuclear lamin A/C-associated chromatin domains by GlcNAcylated histone H2B. PMID:26359231
Optimization of next-generation sequencing transcriptome annotation for species lacking sequenced genomes. PMID:26358618
Parallel molecular routes to cold adaptation in eight genera of New Zealand stick insects. PMID:26355841
Draft genome of Brugia pahangi: high similarity between B. pahangi and B. malayi. PMID:26350613
Differential Expression of microRNAs in Thymic Epithelial Cells from Trypanosoma cruzi Acutely Infected Mice: Putative Role in Thymic Atrophy. PMID:26347748
Identification and comparative expression analysis of odorant binding protein genes in the tobacco cutworm Spodoptera litura. PMID:26346731
Multiple sources of bias confound functional enrichment analysis of global -omics data. PMID:26346307
The genetics of human autoimmune disease: A perspective on progress in the field and future directions. PMID:26343334
Genome-wide target analysis of NEUROD2 provides new insights into regulation of cortical projection neuron migration and differentiation. PMID:26341353
Transcriptomic Signatures Mirror the Lack of the Fecundity/Longevity Trade-Off in Ant Queens. PMID:26341296
Pervasive pleiotropy between psychiatric disorders and immune disorders revealed by integrative analysis of multiple GWAS. PMID:26340901
Negative Regulation of p21Waf1/Cip1 by Human INO80 Chromatin Remodeling Complex Is Implicated in Cell Cycle Phase G2/M Arrest and Abnormal Chromosome Stability. PMID:26340092
K-Profiles: A Nonlinear Clustering Method for Pattern Detection in High Dimensional Data. PMID:26339652
SwissPalm: Protein Palmitoylation database. PMID:26339475
Less pronounced response to exercise in healthy relatives to type 2 diabetic subjects compared with controls. PMID:26338460
Cross-tissue and cross-species analysis of gene expression in skeletal muscle and electric organ of African weakly-electric fish (Teleostei; Mormyridae). PMID:26335922
Implications of ethylene biosynthesis and signaling in soybean drought stress tolerance. PMID:26335593
A reverse-engineering approach to dissect post-translational modulators of transcription factor's activity from transcriptional data. PMID:26334955
A Large-Scale Functional Analysis of Putative Target Genes of Mating-Type Loci Provides Insight into the Regulation of Sexual Development of the Cereal Pathogen Fusarium graminearum. PMID:26334536
Genetic Analysis of Association Between Calcium Signaling and Hippocampal Activation, Memory Performance in the Young and Old, and Risk for Sporadic Alzheimer Disease. PMID:26332608
Integration of 'omics' data in aging research: from biomarkers to systems biology. PMID:26331998
A computational framework for the prioritization of disease-gene candidates. PMID:26330267
Prediction of high- and low-risk multiple myeloma based on gene expression and the International Staging System. PMID:26330243
Protein complex detection in PPI networks based on data integration and supervised learning method. PMID:26329886
CompGO: an R package for comparing and visualizing Gene Ontology enrichment differences between DNA binding experiments. PMID:26329719
Graded gene expression changes determine phenotype severity in mouse models of CRX-associated retinopathies. PMID:26324254
Network analysis reveals stage-specific changes in zebrafish embryo development using time course whole transcriptome profiling and prior biological knowledge. PMID:26322129
Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies. PMID:26320941
Proteomic and Biochemical Studies of Lysine Malonylation Suggest Its Malonic Aciduria-associated Regulatory Role in Mitochondrial Function and Fatty Acid Oxidation. PMID:26320211
Identifying Driver Genomic Alterations in Cancers by Searching Minimum-Weight, Mutually Exclusive Sets. PMID:26317392
Proteins with Intrinsically Disordered Domains Are Preferentially Recruited to Polyglutamine Aggregates. PMID:26317359
MGFM: a novel tool for detection of tissue and cell specific marker genes from microarray gene expression data. PMID:26314578
Genome-Wide Screen Reveals Valosin-Containing Protein Requirement for Coronavirus Exit from Endosomes. PMID:26311884
E2F1 controls germ cell apoptosis during the first wave of spermatogenesis. PMID:26311345
Predicting protein function via downward random walks on a gene ontology. PMID:26310806
RNA sequencing from human neutrophils reveals distinct transcriptional differences associated with chronic inflammatory states. PMID:26310571
Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. PMID:26309733
Harmonising and linking biomedical and clinical data across disparate data archives to enable integrative cross-biobank research. PMID:26306643
A Catalog of Proteins Expressed in the AG Secreted Fluid during the Mature Phase of the Chinese Mitten Crabs (Eriocheir sinensis). PMID:26305468
LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations. PMID:26304545
DNA-binding protein prediction using plant specific support vector machines: validation and application of a new genome annotation tool. PMID:26304539
Perivascular Mesenchymal Stem Cells From the Adult Human Brain Harbor No Instrinsic Neuroectodermal but High Mesodermal Differentiation Potential. PMID:26304036
Proteomic Analysis of Disease Stratified Human Pancreas Tissue Indicates Unique Signature of Type 1 Diabetes. PMID:26302420
Meta-analysis of shared genetic architecture across ten pediatric autoimmune diseases. PMID:26301688
Principal component gene set enrichment (PCGSE). PMID:26300978
Integrated inference and evaluation of host-fungi interaction networks. PMID:26300851
Gene expression profiling for human iPS-derived motor neurons from sporadic ALS patients reveals a strong association between mitochondrial functions and neurodegeneration. PMID:26300727
Aberrant RNA splicing in cancer; expression changes and driver mutations of splicing factor genes. PMID:26300000
Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis. PMID:26299571
Transcriptomic changes in the plant pathogenic fungus Rhizoctonia solani AG-3 in response to the antagonistic bacteria Serratia proteamaculans and Serratia plymuthica. PMID:26296338
YAP1 Exerts Its Transcriptional Control via TEAD-Mediated Activation of Enhancers. PMID:26295846
Persistent alterations of gene expression profiling of human peripheral blood mononuclear cells from smokers. PMID:26294040
Prediction of Causal Candidate Genes in Coronary Artery Disease Loci. PMID:26293461
De novo analysis of the transcriptome of Pratylenchus zeae to identify transcripts for proteins required for structural integrity, sensation, locomotion and parasitism. PMID:26292651
Impaired Cell Cycle Regulation in a Natural Equine Model of Asthma. PMID:26292153
Identification of Gene Biomarkers for Distinguishing Small-Cell Lung Cancer from Non-Small-Cell Lung Cancer Using a Network-Based Approach. PMID:26290870
The effect of antibiotic exposure on eicosanoid generation from arachidonic acid and gene expression in a primitive chordate, Branchiostoma belcheri. PMID:26288743
Gene Function Prediction from Functional Association Networks Using Kernel Partial Least Squares Regression. PMID:26288239
Gene expression during zombie ant biting behavior reflects the complexity underlying fungal parasitic behavioral manipulation. PMID:26285697
De Novo Transcriptome Analysis of Allium cepa L. (Onion) Bulb to Identify Allergens and Epitopes. PMID:26284934
Exome analysis of a family with Wolff-Parkinson-White syndrome identifies a novel disease locus. PMID:26284702
Diversified Control Paths: A Significant Way Disease Genes Perturb the Human Regulatory Network. PMID:26284649
Proteomic analysis and candidate allergenic proteins in Populus deltoides CL. "2KEN8" mature pollen. PMID:26284084
Identification of in vitro and in vivo disconnects using transcriptomic data. PMID:26282683
Moyamoya disease susceptibility gene RNF213 links inflammatory and angiogenic signals in endothelial cells. PMID:26278786
Identifying and characterising key alternative splicing events in Drosophila development. PMID:26275604
Curation of the Mammalian Palmitoylome Indicates a Pivotal Role for Palmitoylation in Diseases and Disorders of the Nervous System and Cancers. PMID:26275289
Differential mRNA expression profiling of oral squamous cell carcinoma by high-throughput RNA sequencing. PMID:26273018
OVA: integrating molecular and physical phenotype data from multiple biomedical domain ontologies with variant filtering for enhanced variant prioritization. PMID:26272982
Comparative analysis of anti-viral transcriptomics reveals novel effects of influenza immune antagonism. PMID:26272204
Transcriptome analysis of the Holly mangrove Acanthus ilicifolius and its terrestrial relative, Acanthus leucostachyus, provides insights into adaptation to intertidal zones. PMID:26272068
Cox4i2, Ifit2, and Prdm11 Mutant Mice: Effective Selection of Genes Predisposing to an Altered Airway Inflammatory Response from a Large Compendium of Mutant Mouse Lines. PMID:26263558
Acetylation of cell wall is required for structural integrity of the leaf surface and exerts a global impact on plant stress responses. PMID:26257757
Large-scale identification of membrane proteins with properties favorable for crystallization. PMID:26257393
Effects of subsampling on characteristics of RNA-seq data from triple-negative breast cancer patients. PMID:26253000
Draft De Novo Transcriptome of the Rat Kangaroo Potorous tridactylus as a Tool for Cell Biology. PMID:26252667
PhenomeCentral: a portal for phenotypic and genotypic matchmaking of patients with rare genetic diseases. PMID:26251998
Protective Effect of 2,4',5'-Trihydroxyl-5,2'-dibromo diphenylmethanone, a New Halophenol, against Hydrogen Peroxide-Induced EA.hy926 Cells Injury. PMID:26251890
Unique ability of pandemic influenza to downregulate the genes involved in neuronal disorders. PMID:26246405
Thalamic WNT3 Secretion Spatiotemporally Regulates the Neocortical Ribosome Signature and mRNA Translation to Specify Neocortical Cell Subtypes. PMID:26245956
FROG - Fingerprinting Genomic Variation Ontology. PMID:26244889
Prenatal Exposure to DEHP Affects Spermatogenesis and Sperm DNA Methylation in a Strain-Dependent Manner. PMID:26244509
RNA-seq for gene identification and transcript profiling in relation to root growth of bermudagrass (Cynodon dactylon) under salinity stress. PMID:26238595
Mouse Genome Informatics (MGI): reflecting on 25 years. PMID:26238262
Functional analysis of the nasopharyngeal carcinoma primary tumor‑associated gene interaction network. PMID:26238040
The deafness gene DFNA5 induces programmed cell death through mitochondria and MAPK-related pathways. PMID:26236191
The EGF receptor ligand amphiregulin controls cell division via FoxM1. PMID:26234682
Copy number variation-based genome wide association study reveals additional variants contributing to meat quality in Swine. PMID:26234186
Evidence of perturbations of the cytokine network in preterm labor. PMID:26232508
Prediction of problematic complexes from PPI networks: sparse, embedded, and small complexes. PMID:26231465
POTION: an end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes. PMID:26231214
Optimal Threshold Determination for Interpreting Semantic Similarity and Particularity: Application to the Comparison of Gene Sets and Metabolic Pathways Using GO and ChEBI. PMID:26230274
Identification of the key genes connected with plasma cells of multiple myeloma using expression profiles. PMID:26229487
Computer aided gene mining for gingerol biosynthesis. PMID:26229293
Genome-wide association study revealed a promising region and candidate genes for eggshell quality in an F2 resource population. PMID:26228268
Genome-Wide Analyses Suggest Mechanisms Involving Early B-Cell Development in Canine IgA Deficiency. PMID:26225558
BioModels: Content, Features, Functionality, and Use. PMID:26225232
Comparative Genomics of a Bacterivorous Green Alga Reveals Evolutionary Causalities and Consequences of Phago-Mixotrophic Mode of Nutrition. PMID:26224703
Effects of β-catenin on differentially expressed genes in multiple myeloma. PMID:26223925
Orthology for comparative genomics in the mouse genome database. PMID:26223881
An Integrative Approach for Mapping Differentially Expressed Genes and Network Components Using Novel Parameters to Elucidate Key Regulatory Genes in Colorectal Cancer. PMID:26222778
High-quality genome sequence and description of Bacillus dielmoensis strain FF4(T) sp. nov. PMID:26221422
Genome sequence of Clostridium sporogenes DSM 795(T), an amino acid-degrading, nontoxic surrogate of neurotoxin-producing Clostridium botulinum. PMID:26221421
Draft genome sequence of Methylibium sp. strain T29, a novel fuel oxygenate-degrading bacterial isolate from Hungary. PMID:26221420
Draft genomic sequence of a selenite-reducing bacterium, Paenirhodobacter enshiensis DW2-9(T). PMID:26221419
High-quality draft genome sequences of five anaerobic oral bacteria and description of Peptoanaerobacter stomatis gen. nov., sp. nov., a new member of the family Peptostreptococcaceae. PMID:26221418
High-quality permanent draft genome sequence of Rhizobium leguminosarum bv. viciae strain GB30; an effective microsymbiont of Pisum sativum growing in Poland. PMID:26221417
Longevity Genes Revealed by Integrative Analysis of Isoform-Specific daf-16/FoxO Mutants of Caenorhabditis elegans. PMID:26219299
A novel, dynamic pattern-based analysis of NF-κB binding during the priming phase of liver regeneration reveals switch-like functional regulation of target genes. PMID:26217230
Inter-Laboratory Variability in Array-Based RNA Quantification Methods. PMID:26217107
Whole transcriptome profiling of the vernalization process in Lilium longiflorum (cultivar White Heaven) bulbs. PMID:26216467
Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17 Human Proteome Project. PMID:26216192
Genes Caught In Flagranti: Integrating Renal Transcriptional Profiles With Genotypes and Phenotypes. PMID:26215861
Best behaviour? Ontologies and the formal description of animal behaviour. PMID:26215546
Representing virus-host interactions and other multi-organism processes in the Gene Ontology. PMID:26215368
Evolutionary insights from de novo transcriptome assembly and SNP discovery in California white oaks. PMID:26215102
Identification of neurodegenerative factors using translatome-regulatory network analysis. PMID:26214373
Differential DNA Methylation in Relation to Age and Health Risks of Obesity. PMID:26213922
A mutation profile for top-k patient search exploiting Gene-Ontology and orthogonal non-negative matrix factorization. PMID:26209432
Quantitative Trait Loci Associated with the Tocochromanol (Vitamin E) Pathway in Barley. PMID:26208213
A Methodology for the Development of RESTful Semantic Web Services for Gene Expression Analysis. PMID:26207740
Novel structural co-expression analysis linking the NPM1-associated ribosomal biogenesis network to chronic myelogenous leukemia. PMID:26205693
KnowEnG: a knowledge engine for genomics. PMID:26205246
Whole exome sequencing in extended families with autism spectrum disorder implicates four candidate genes. PMID:26204995
IMA Genome-F 4: Draft genome sequences of Chrysoporthe austroafricana, Diplodia scrobiculata, Fusarium nygamai, Leptographium lundbergii, Limonomyces culmigenus, Stagonosporopsis tanaceti, and Thielaviopsis punctulata. PMID:26203426
Genome sequences of copper resistant and sensitive Enterococcus faecalis strains isolated from copper-fed pigs in Denmark. PMID:26203344
Complete genome sequence of Actinobacillus equuli subspecies equuli ATCC 19392(T). PMID:26203343
High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Burkholderia sp. strain UYPR1.413. PMID:26203342
Complete genome sequence of Salmonella enterica subspecies arizonae str. RKS2983. PMID:26203341
High quality draft genome sequence of Brachymonas chironomi AIMA4(T) (DSM 19884(T)) isolated from a Chironomus sp. egg mass. PMID:26203340
Draft genome of Myxosarcina sp. strain GI1, a baeocytous cyanobacterium associated with the marine sponge Terpios hoshinota. PMID:26203339
High-quality permanent draft genome sequence of Bradyrhizobium sp. Tv2a.2, a microsymbiont of Tachigali versicolor discovered in Barro Colorado Island of Panama. PMID:26203338
High-quality permanent draft genome sequence of Bradyrhizobium sp. Th.b2, a microsymbiont of Amphicarpaea bracteata collected in Johnson City, New York. PMID:26203336
High quality draft genome sequence of Meganema perideroedes str. Gr1(T) and a proposal for its reclassification to the family Meganemaceae fam. nov. PMID:26203335
Complete genome sequence of endophytic nitrogen-fixing Klebsiella variicola strain DX120E. PMID:26203334
High quality draft genome sequence of Leucobacter chironomi strain MM2LB(T) (DSM 19883(T)) isolated from a Chironomus sp. egg mass. PMID:26203333
Genome sequence of the Roseovarius mucosus type strain (DSM 17069(T)), a bacteriochlorophyll a-containing representative of the marine Roseobacter group isolated from the dinoflagellate Alexandrium ostenfeldii. PMID:26203330
Draft genome sequence and characterization of Desulfitobacterium hafniense PCE-S. PMID:26203328
High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Cupriavidus sp. strain UYPR2.512. PMID:26203327
Draft genome sequences for the obligate bacterial predators Bacteriovorax spp. of four phylogenetic clusters. PMID:26203326
High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1(T) (DSM 17521(T)) isolated from muddy waters of a drainage system in Chandigarh, India. PMID:26203325
Complete genome sequence and description of Salinispira pacifica gen. nov., sp. nov., a novel spirochaete isolated form a hypersaline microbial mat. PMID:26203324
Genome sequence of the soil bacterium Corynebacterium callunae type strain DSM 20147(T). PMID:26203323
Genetic variation in insulin-induced kinase signaling. PMID:26202599
Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013. PMID:26202570
The Arabidopsis information resource: Making and mining the "gold standard" annotated reference plant genome. PMID:26201819
Kiwi genome provides insights into evolution of a nocturnal lifestyle. PMID:26201466
A P-Norm Robust Feature Extraction Method for Identifying Differentially Expressed Genes. PMID:26201006
Associations of SNPs located at candidate genes to bovine growth traits, prioritized with an interaction networks construction approach. PMID:26198337
A draft network of ligand-receptor-mediated multicellular signalling in human. PMID:26198319
Network-Based Analysis of Schizophrenia Genome-Wide Association Data to Detect the Joint Functional Association Signals. PMID:26193471
Proteomic Characterisation of the Salt Gland-Enriched Tissues of the Mangrove Tree Species Avicennia officinalis. PMID:26193361
Transcriptome Analysis and Discovery of Genes Involved in Immune Pathways from Coelomocytes of Sea Cucumber (Apostichopus japonicus) after Vibrio splendidus Challenge. PMID:26193268
Transcriptome sequencing of three Pseudo-nitzschia species reveals comparable gene sets and the presence of Nitric Oxide Synthase genes in diatoms. PMID:26189990
Identification and transcriptomic profiling of genes involved in increasing sugar content during salt stress in sweet sorghum leaves. PMID:26186930
Adaptation of a Bioinformatics Microarray Analysis Workflow for a Toxicogenomic Study in Rainbow Trout. PMID:26186543
Combined Analysis of SNP Array Data Identifies Novel CNV Candidates and Pathways in Ependymoma and Mesothelioma. PMID:26185765
A framework for ontology-based question answering with application to parasite immunology. PMID:26185615
Screening of potential diagnostic markers and therapeutic targets against colorectal cancer. PMID:26185457
Rice Xa21 primed genes and pathways that are critical for combating bacterial blight infection. PMID:26184504
Integrated network analysis and logistic regression modeling identify stage-specific genes in Oral Squamous Cell Carcinoma. PMID:26179909
Differentially expressed protein-coding genes and long noncoding RNA in early-stage lung cancer. PMID:26178480
Chronic ethanol consumption induces mitochondrial protein acetylation and oxidative stress in the kidney. PMID:26177469
Molecular Mechanisms Mediating Retinal Reactive Gliosis Following Bone Marrow Mesenchymal Stem Cell Transplantation. PMID:26175331
Identification of reproducible drug-resistance-related dysregulated genes in small-scale cancer cell line experiments. PMID:26173481
Genes Upregulated in Winter Wheat (Triticum aestivum L.) during Mild Freezing and Subsequent Thawing Suggest Sequential Activation of Multiple Response Mechanisms. PMID:26173115
RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway. PMID:26170170
Biomedical imaging ontologies: A survey and proposal for future work. PMID:26167381
Long non-coding RNAs in innate and adaptive immunity. PMID:26166759
GreedyPlus: An Algorithm for the Alignment of Interface Interaction Networks. PMID:26165520
Two Theobroma cacao genotypes with contrasting pathogen tolerance show aberrant transcriptional and ROS responses after salicylic acid treatment. PMID:26163705
Evolutionary Divergence of Gene and Protein Expression in the Brains of Humans and Chimpanzees. PMID:26163674
Identification of MicroRNAs in Response to Different Day Lengths in Soybean Using High-Throughput Sequencing and qRT-PCR. PMID:26162069
ErbB-3 activation by NRG-1β sustains growth and promotes vemurafenib resistance in BRAF-V600E colon cancer stem cells (CSCs). PMID:26160848
Extracellular protein analysis of activated sludge and their functions in wastewater treatment plant by shotgun proteomics. PMID:26160685
Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes. PMID:26158728
PAND: A Distribution to Identify Functional Linkage from Networks with Preferential Attachment Property. PMID:26158709
Genome Modeling System: A Knowledge Management Platform for Genomics. PMID:26158448
Bioinformatics and Moonlighting Proteins. PMID:26157797
Transcriptomic landscape of Pueraria lobata demonstrates potential for phytochemical study. PMID:26157443
Novel drug target identification for the treatment of dementia using multi-relational association mining. PMID:26154857
A genome-wide screening and SNPs-to-genes approach to identify novel genetic risk factors associated with frontotemporal dementia. PMID:26154020
Genome Scan for Selection in Structured Layer Chicken Populations Exploiting Linkage Disequilibrium Information. PMID:26151449
Mouse Genome Database: From sequence to phenotypes and disease models. PMID:26150326
Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders. PMID:26149713
Transcriptome analysis of the biofilm formed by methicillin-susceptible Staphylococcus aureus. PMID:26149474
The Medicago sativa gene index 1.2: a web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies. PMID:26149169
Lung Transcriptomics during Protective Ventilatory Support in Sepsis-Induced Acute Lung Injury. PMID:26147972
Application of comparative biology in GO functional annotation: the mouse model. PMID:26141960
Using prior knowledge from cellular pathways and molecular networks for diagnostic specimen classification. PMID:26141830
A genome-scale mining strategy for recovering novel rapidly-evolving nuclear single-copy genes for addressing shallow-scale phylogenetics in Hydrangea. PMID:26141718
Microarray profiling of long non-coding RNA (lncRNA) associated with hypertrophic cardiomyopathy. PMID:26141701
Transcriptional response of Atlantic salmon families to Piscirickettsia salmonis infection highlights the relevance of the iron-deprivation defence system. PMID:26141111
Development of an Ontology for Periodontitis. PMID:26140188
Functional classification of CATH superfamilies: a domain-based approach for protein function annotation. PMID:26139634
Integrative network analysis for survival-associated gene-gene interactions across multiple genomic profiles in ovarian cancer. PMID:26138921
Myeloid STAT3 promotes formation of colitis-associated colorectal cancer in mice. PMID:26137415
Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome. PMID:26137199
Integrated analysis of differentially expressed genes in breast cancer pathogenesis. PMID:26137106
Genome-wide analysis of androgen receptor binding sites in prostate cancer cells. PMID:26136980
Identification of Chemical Inhibitors of β-Catenin-Driven Liver Tumorigenesis in Zebrafish. PMID:26134322
Ambiguity and variability of database and software names in bioinformatics. PMID:26131352
toxoMine: an integrated omics data warehouse for Toxoplasma gondii systems biology research. PMID:26130662
Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis. PMID:26125937
MSL: A Measure to Evaluate Three-dimensional Patterns in Gene Expression Data. PMID:26124630
Gene Expression Changes Associated With the Developmental Plasticity of Sea Urchin Larvae in Response to Food Availability. PMID:26124444
Identification of enhanced hydrogen and ethanol Escherichia coli producer strains in a glycerol-based medium by screening in single-knock out mutant collections. PMID:26122736
A Comparative Transcriptome Analysis between Wild and Albino Yellow Catfish (Pelteobagrus fulvidraco). PMID:26114548
Time-Course Gene Set Analysis for Longitudinal Gene Expression Data. PMID:26111374
Self-Organizing Feature Maps Identify Proteins Critical to Learning in a Mouse Model of Down Syndrome. PMID:26111164
Conditional entropy in variation-adjusted windows detects selection signatures associated with expression quantitative trait loci (eQTLs). PMID:26111110
A de novo Assembly of the Common Frog (Rana temporaria) Transcriptome and Comparison of Transcription Following Exposure to Ranavirus and Batrachochytrium dendrobatidis. PMID:26111016
NET-GE: a novel NETwork-based Gene Enrichment for detecting biological processes associated to Mendelian diseases. PMID:26110971
Physical Features of Intracellular Proteins that Moonlight on the Cell Surface. PMID:26110848
Isolation, Characterization and Biological Properties of Membrane Vesicles Produced by the Swine Pathogen Streptococcus suis. PMID:26110524
Long noncoding RNAs in hepatitis B virus-related hepatocellular carcinoma. PMID:26109807
The human cardiac and skeletal muscle proteomes defined by transcriptomics and antibody-based profiling. PMID:26109061
Global Gene-Expression Analysis to Identify Differentially Expressed Genes Critical for the Heat Stress Response in Brassica rapa. PMID:26102990
A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics. PMID:26102527
Discovery and characterization of long intergenic non-coding RNAs (lincRNA) module biomarkers in prostate cancer: an integrative analysis of RNA-Seq data. PMID:26100580
Multiple signatures of a disease in potential biomarker space: Getting the signatures consensus and identification of novel biomarkers. PMID:26100469
Co-modulation analysis of gene regulation in breast cancer reveals complex interplay between ESR1 and ERBB2 genes. PMID:26100352
Systems analysis of gene ontology and biological pathways involved in post-myocardial infarction responses. PMID:26100218
Cross-organism analysis using InterMine. PMID:26097192
ZFIN, The zebrafish model organism database: Updates and new directions. PMID:26097180
Asian Citrus Psyllid Expression Profiles Suggest Candidatus Liberibacter Asiaticus-Mediated Alteration of Adult Nutrition and Metabolism, and of Nymphal Development and Immunity. PMID:26091106
Genome-Wide Gene Expression in relation to Age in Large Laboratory Cohorts of Drosophila melanogaster. PMID:26090231
PrOnto database : GO term functional dissimilarity inferred from biological data. PMID:26089836
Draft Genome Sequence of Gluconobacter oxydans NL71, a Strain That Efficiently Biocatalyzes Xylose to Xylonic Acid at a High Concentration. PMID:26089417
Characterization of the Tyrosine Kinase-Regulated Proteome in Breast Cancer by Combined use of RNA interference (RNAi) and Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) Quantitative Proteomics. PMID:26089344
Distal 10q trisomy with copy number gain in chromosome region 10q23.1-10q25.1: the Wnt signaling pathway is the most pertinent to the gene content in the region of copy number gain: a case report. PMID:26088875
Extensive rewiring of epithelial-stromal co-expression networks in breast cancer. PMID:26087699
Gene Expression Signature in Adipose Tissue of Acromegaly Patients. PMID:26087292
The Human Blood Metabolome-Transcriptome Interface. PMID:26086077
Revealing Pathway Dynamics in Heart Diseases by Analyzing Multiple Differential Networks. PMID:26083688
Tools for visualization and analysis of molecular networks, pathways, and -omics data. PMID:26082651
Confrontation of fibroblasts with cancer cells in vitro: gene network analysis of transcriptome changes and differential capacity to inhibit tumor growth. PMID:26081588
Targeting PBK/TOPK decreases growth and survival of glioma initiating cells in vitro and attenuates tumor growth in vivo. PMID:26081429
Association of Protein Translation and Extracellular Matrix Gene Sets with Breast Cancer Metastasis: Findings Uncovered on Analysis of Multiple Publicly Available Datasets Using Individual Patient Data Approach. PMID:26080057
Large-scale identification of encystment-related proteins and genes in Pseudourostyla cristata. PMID:26079518
ChemDIS: a chemical-disease inference system based on chemical-protein interactions. PMID:26078786
Defining the Human Brain Proteome Using Transcriptomics and Antibody-Based Profiling with a Focus on the Cerebral Cortex. PMID:26076492
Exploring Differentially Expressed Genes and Natural Antisense Transcripts in Sheep (Ovis aries) Skin with Different Wool Fiber Diameters by Digital Gene Expression Profiling. PMID:26076016
Multi-instance multilabel learning with weak-label for predicting protein function in electricigens. PMID:26075251
System-wide identification of wild-type SUMO-2 conjugation sites. PMID:26073453
Insights into the Transcriptional Architecture of Behavioral Plasticity in the Honey Bee Apis mellifera. PMID:26073445
Exploiting ontology graph for predicting sparsely annotated gene function. PMID:26072504
Dynamic changes of RNA-sequencing expression for precision medicine: N-of-1-pathways Mahalanobis distance within pathways of single subjects predicts breast cancer survival. PMID:26072495
PAGER: constructing PAGs and new PAG-PAG relationships for network biology. PMID:26072489
Gene network inference by fusing data from diverse distributions. PMID:26072487
Improving compound-protein interaction prediction by building up highly credible negative samples. PMID:26072486
Exploring the structure and function of temporal networks with dynamic graphlets. PMID:26072480
Regulation of flavonol content and composition in (Syrah×Pinot Noir) mature grapes: integration of transcriptional profiling and metabolic quantitative trait locus analyses. PMID:26071529
De novo deletions and duplications of 17q25.3 cause susceptibility to cardiovascular malformations. PMID:26070612
Genome-wide association study identifies novel genetic variants contributing to variation in blood metabolite levels. PMID:26068415
TCF12 is mutated in anaplastic oligodendroglioma. PMID:26068201
TRRUST: a reference database of human transcriptional regulatory interactions. PMID:26066708
Next-generation transcriptome analysis in transgenic birch overexpressing and suppressing APETALA1 sheds lights in reproduction development and diterpenoid biosynthesis. PMID:26063613
The IDA/IDA-LIKE and PIP/PIP-LIKE gene families in Arabidopsis: phylogenetic relationship, expression patterns, and transcriptional effect of the PIPL3 peptide. PMID:26062745
A survey on the computational approaches to identify drug targets in the postgenomic era. PMID:26060814
Fair evaluation of global network aligners. PMID:26060505
Gene set analysis: A step-by-step guide. PMID:26059482
Genome-wide identification of the Phaseolus vulgaris sRNAome using small RNA and degradome sequencing. PMID:26059339
Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae). PMID:26059236
PADPIN: protein-protein interaction networks of angiogenesis, arteriogenesis, and inflammation in peripheral arterial disease. PMID:26058837
Transcriptome Analysis of Minimal Residual Disease in Subtypes of Pediatric B Cell Acute Lymphoblastic Leukemia. PMID:26056509
Correspondence of DNA Methylation Between Blood and Brain Tissue and Its Application to Schizophrenia Research. PMID:26056378
Molecular transitions from papillomavirus infection to cervical precancer and cancer: Role of stromal estrogen receptor signaling. PMID:26056290
Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation. PMID:26056000
kpath: integration of metabolic pathway linked data. PMID:26055101
An Ebola virus-centered knowledge base. PMID:26055098
GeneStoryTeller: a mobile app for quick and comprehensive information retrieval of human genes. PMID:26055097
Angptl4 is upregulated under inflammatory conditions in the bone marrow of mice, expands myeloid progenitors, and accelerates reconstitution of platelets after myelosuppressive therapy. PMID:26054961
Comparative transcriptional profiling analysis of developing melon (Cucumis melo L.) fruit from climacteric and non-climacteric varieties. PMID:26054931
Extreme multifunctional proteins identified from a human protein interaction network. PMID:26054620
Transcriptomic Analysis Reveals Possible Influences of ABA on Secondary Metabolism of Pigments, Flavonoids and Antioxidants in Tomato Fruit during Ripening. PMID:26053166
Changes in Macrophage Gene Expression Associated with Leishmania (Viannia) braziliensis Infection. PMID:26052705
A bioinformatics approach to distinguish plant parasite and host transcriptomes in interface tissue by classifying RNA-Seq reads. PMID:26052341
E2F8 promotes hepatic steatosis through FABP3 expression in diet-induced obesity in zebrafish. PMID:26052340
Novel Findings from CNVs Implicate Inhibitory and Excitatory Signaling Complexes in Schizophrenia. PMID:26050040
Identification and characterization of long non-coding RNAs involved in osmotic and salt stress in Medicago truncatula using genome-wide high-throughput sequencing. PMID:26048392
Summarizing and visualizing structural changes during the evolution of biomedical ontologies using a Diff Abstraction Network. PMID:26048076
DeCoaD: determining correlations among diseases using protein interaction networks. PMID:26047952
Using Gene Ontology to describe the role of the neurexin-neuroligin-SHANK complex in human, mouse and rat and its relevance to autism. PMID:26047810
Visual annotation display (VLAD): a tool for finding functional themes in lists of genes. PMID:26047590
Quantitative Proteomics of an Amphibian Pathogen, Batrachochytrium dendrobatidis, following Exposure to Thyroid Hormone. PMID:26046527
FunPat: function-based pattern analysis on RNA-seq time series data. PMID:26046293
Biomarkers of erlotinib response in non-small cell lung cancer tumors that do not harbor the more common epidermal growth factor receptor mutations. PMID:26045797
Identification association of drug-disease by using functional gene module for breast cancer. PMID:26045063
Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication. PMID:26044654
The role of markup for enabling interoperability in health informatics. PMID:26042043
Epigenetic modulation of brain gene networks for cocaine and alcohol abuse. PMID:26041984
Partial depletion of yolk during zebrafish embryogenesis changes the dynamics of methionine cycle and metabolic genes. PMID:26040990
An application of MeSH enrichment analysis in livestock. PMID:26036323
Concept selection for phenotypes and diseases using learn to rank. PMID:26034558
An allelic series of miR-17 ∼ 92-mutant mice uncovers functional specialization and cooperation among members of a microRNA polycistron. PMID:26029871
Cosplicing network analysis of mammalian brain RNA-Seq data utilizing WGCNA and Mantel correlations. PMID:26029240
Hidden among the crowd: differential DNA methylation-expression correlations in cancer occur at important oncogenic pathways. PMID:26029238
DECODE: an integrated differential co-expression and differential expression analysis of gene expression data. PMID:26026612
Activation of the Nrf2 response by intrinsic hepatotoxic drugs correlates with suppression of NF-κB activation and sensitizes toward TNFα-induced cytotoxicity. PMID:26026609
A pipeline for the systematic identification of non-redundant full-ORF cDNAs for polymorphic and evolutionary divergent genomes: Application to the ascidian Ciona intestinalis. PMID:26025923
Dnmt1 is essential to maintain progenitors in the perinatal intestinal epithelium. PMID:26023099
Proteomic profile of KSR1-regulated signalling in response to genotoxic agents in breast cancer. PMID:26022350
Different Astrocytic Activation between Adult Gekko japonicus and Rats during Wound Healing In Vitro. PMID:26020931
Causal Modeling of Cancer-Stromal Communication Identifies PAPPA as a Novel Stroma-Secreted Factor Activating NFκB Signaling in Hepatocellular Carcinoma. PMID:26020769
GFVO: the Genomic Feature and Variation Ontology. PMID:26019997
sRNAtoolbox: an integrated collection of small RNA research tools. PMID:26019179
INGA: protein function prediction combining interaction networks, domain assignments and sequence similarity. PMID:26019177
Dynamic Proteome Response of Pseudomonas aeruginosa to Tobramycin Antibiotic Treatment. PMID:26018413
Unravelling the genome of Holy basil: an "incomparable" "elixir of life" of traditional Indian medicine. PMID:26017011
Transcriptome and venom proteome of the box jellyfish Chironex fleckeri. PMID:26014501
A density-based clustering approach for identifying overlapping protein complexes with functional preferences. PMID:26013799
Every Site Counts: Submitting Transcription Factor-Binding Site Information through the CollecTF Portal. PMID:26013488
Detection of composite communities in multiplex biological networks. PMID:26012716
A novel chitin binding crayfish molar tooth protein with elasticity properties. PMID:26010981
Gene target specificity of the Super Elongation Complex (SEC) family: how HIV-1 Tat employs selected SEC members to activate viral transcription. PMID:26007649
Evaluating a variety of text-mined features for automatic protein function prediction with GOstruct. PMID:26005564
BioMiner: Paving the Way for Personalized Medicine. PMID:26005322
Horsetails Are Ancient Polyploids: Evidence from Equisetum giganteum. PMID:26002871
From raw data to biological discoveries: a computational analysis pipeline for mass spectrometry-based proteomics. PMID:26002791
Haploinsufficiency predictions without study bias. PMID:26001969
High throughput profiling of the cotton bollworm Helicoverpa armigera immunotranscriptome during the fungal and bacterial infections. PMID:26001831
ProteINSIDE to Easily Investigate Proteomics Data from Ruminants: Application to Mine Proteome of Adipose and Muscle Tissues in Bovine Foetuses. PMID:26000831
Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints. PMID:26000633
An improved method for completely uncertain biological network alignment. PMID:26000284
The endogenous molecular clock orchestrates the temporal separation of substrate metabolism in skeletal muscle. PMID:26000164
Gene expression studies of a human monocyte cell line identify dissimilarities between differently manufactured glatiramoids. PMID:25998228
Biocuration at the Saccharomyces genome database. PMID:25997651
Label-Free Protein-RNA Interactome Analysis Identifies Khsrp Signaling Downstream of the p38/Mk2 Kinase Complex as a Critical Modulator of Cell Cycle Progression. PMID:25993413
Genetic variants and risk of gastric cancer: a pathway analysis of a genome-wide association study. PMID:25992311
A Combined Omics Approach to Generate the Surface Atlas of Human Naive CD4+ T Cells during Early T-Cell Receptor Activation. PMID:25991687
MyProteinNet: build up-to-date protein interaction networks for organisms, tissues and user-defined contexts. PMID:25990735
Multidimensional gene search with Genehopper. PMID:25990726
BET inhibitor OTX015 targets BRD2 and BRD4 and decreases c-MYC in acute leukemia cells. PMID:25989842
PALM-IST: Pathway Assembly from Literature Mining--an Information Search Tool. PMID:25989388
Human cell adhesion molecules: annotated functional subtypes and overrepresentation of addiction-associated genes. PMID:25988664
Heritability, SNP- and Gene-Based Analyses of Cannabis Use Initiation and Age at Onset. PMID:25987507
The Classification and Evolution of Enzyme Function. PMID:25986631
A BAYESIAN NONPARAMETRIC MIXTURE MODEL FOR SELECTING GENES AND GENE SUBNETWORKS. PMID:25984253
Herb Network Analysis for a Famous TCM Doctor's Prescriptions on Treatment of Rheumatoid Arthritis. PMID:25983850
Reverse enGENEering of Regulatory Networks from Big Data: A Roadmap for Biologists. PMID:25983554
Next generation distributed computing for cancer research. PMID:25983539
Comprehensively evaluating cis-regulatory variation in the human prostate transcriptome by using gene-level allele-specific expression. PMID:25983244
Acute myocardial infarction activates distinct inflammation and proliferation pathways in circulating monocytes, prior to recruitment, and identified through conserved transcriptional responses in mice and humans. PMID:25982896
Biology-Driven Gene-Gene Interaction Analysis of Age-Related Cataract in the eMERGE Network. PMID:25982363
Genetic alterations of JAK/STAT cascade and histone modification in extranodal NK/T-cell lymphoma nasal type. PMID:25980440
SIFTER search: a web server for accurate phylogeny-based protein function prediction. PMID:25979264
A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis. PMID:25977815
Comparative Meta-Analysis of Transcriptomics Data during Cellular Senescence and In Vivo Tissue Ageing. PMID:25977747
DIANA-miRPath v3.0: deciphering microRNA function with experimental support. PMID:25977294
Dissection of the style's response to pollination using transcriptome profiling in self-compatible (Solanum pimpinellifolium) and self-incompatible (Solanum chilense) tomato species. PMID:25976872
Quantitative proteomic analysis reveals that anti-cancer effects of selenium-binding protein 1 in vivo are associated with metabolic pathways. PMID:25974208
Different Temporal Effects of Ebola Virus VP35 and VP24 Proteins on Global Gene Expression in Human Dendritic Cells. PMID:25972536
AtmiRNET: a web-based resource for reconstructing regulatory networks of Arabidopsis microRNAs. PMID:25972521
Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data. PMID:25971253
A de novo floral transcriptome reveals clues into Phalaenopsis orchid flower development. PMID:25970572
Sharing and Specificity of Co-expression Networks across 35 Human Tissues. PMID:25970446
A novel method for identifying disease associated protein complexes based on functional similarity protein complex networks. PMID:25969691
IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. PMID:25969450
ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap. PMID:25969447
Transcriptome Analysis Comparison of Lipid Biosynthesis in the Leaves and Developing Seeds of Brassica napus. PMID:25965272
CATH FunFHMMer web server: protein functional annotations using functional family assignments. PMID:25964299
Screening of candidate genes in fibroblasts derived from patients with Dupuytren's contracture using bioinformatics analysis. PMID:25963801
Dynamic transcriptome profiles of skeletal muscle tissue across 11 developmental stages for both Tongcheng and Yorkshire pigs. PMID:25962502
Improving the Understanding of Pathogenesis of Human Papillomavirus 16 via Mapping Protein-Protein Interaction Network. PMID:25961044
Coexpression Pattern Analysis of NPM1-Associated Genes in Chronic Myelogenous Leukemia. PMID:25961029
An empirically derived taxonomy of errors in SNOMED CT. PMID:25954397
Evaluation of need for ontologies to manage domain content for the Reportable Conditions Knowledge Management System. PMID:25954354
Efficient exploration of pan-cancer networks by generalized covariance selection and interactive web content. PMID:25953855
CerebralWeb: a Cytoscape.js plug-in to visualize networks stratified by subcellular localization. PMID:25953080
Transcriptome profiling of trichome-less reveals genes associated with multicellular trichome development in Cucumis sativus. PMID:25952908
A method of searching for related literature on protein structure analysis by considering a user's intention. PMID:25952498
Gene Ontology and KEGG Pathway Enrichment Analysis of a Drug Target-Based Classification System. PMID:25951454
The Zinc-Finger Antiviral Protein ZAP Inhibits LINE and Alu Retrotransposition. PMID:25951186
Burden analysis of rare microdeletions suggests a strong impact of neurodevelopmental genes in genetic generalised epilepsies. PMID:25950944
piRNAs from Pig Testis Provide Evidence for a Conserved Role of the Piwi Pathway in Post-Transcriptional Gene Regulation in Mammals. PMID:25950437
Machine learning applications in genetics and genomics. PMID:25948244
Determining minimum set of driver nodes in protein-protein interaction networks. PMID:25947063
Assembly of a comprehensive regulatory network for the mammalian circadian clock: a bioinformatics approach. PMID:25945798
High quality draft genome sequence of the heavy metal resistant bacterium Halomonas zincidurans type strain B6(T). PMID:25945155
The proportion of genes in a functional category is linked to mass-specific metabolic rate and lifespan. PMID:25943793
Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance. PMID:25943316
FNTM: a server for predicting functional networks of tissues in mouse. PMID:25940632
Hierarchical ensemble methods for protein function prediction. PMID:25937954
Automatically exposing OpenLifeData via SADI semantic Web Services. PMID:25937881
Evaluating the Emotion Ontology through use in the self-reporting of emotional responses at an academic conference. PMID:25937879
HIGH-PRECISION BIOLOGICAL EVENT EXTRACTION: EFFECTS OF SYSTEM AND OF DATA. PMID:25937701
Identification of conserved drought-adaptive genes using a cross-species meta-analysis approach. PMID:25935420
Network-based Phenome-Genome Association Prediction by Bi-Random Walk. PMID:25933025
Key Role of Amino Acid Repeat Expansions in the Functional Diversification of Duplicated Transcription Factors. PMID:25931513
Moment based gene set tests. PMID:25928861
Capturing domain knowledge from multiple sources: the rare bone disorders use case. PMID:25926964
i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly. PMID:25925574
PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more. PMID:25925572
Visual analysis of biological data-knowledge networks. PMID:25925016
Sequence Analysis of Insecticide Action and Detoxification-Related Genes in the Insect Pest Natural Enemy Pardosa pseudoannulata. PMID:25923714
Metazoans evolved by taking domains from soluble proteins to expand intercellular communication network. PMID:25923201
Comparison of microarray expression profiles between follicular variant of papillary thyroid carcinomas and follicular adenomas of the thyroid. PMID:25923053
RNA-seq analysis of Macrobrachium rosenbergii hepatopancreas in response to Vibrio parahaemolyticus infection. PMID:25922623
Binary gene expression patterning of the molt cycle: the case of chitin metabolism. PMID:25919476
Computational algorithms to predict Gene Ontology annotations. PMID:25916950
MeDiA: Mean Distance Association and Its Applications in Nonlinear Gene Set Analysis. PMID:25915206
Multiset Statistics for Gene Set Analysis. PMID:25914887
Gene expression profile analysis of colorectal cancer to investigate potential mechanisms using bioinformatics. PMID:25914544
The genetic basis of peripheral arterial disease: current knowledge, challenges, and future directions. PMID:25908728
Long-range evolutionary constraints reveal cis-regulatory interactions on the human X chromosome. PMID:25908307
Bioinformatics analyses of significant prognostic risk markers for thyroid papillary carcinoma. PMID:25908172
Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities. PMID:25905672
Annotation-based feature extraction from sets of SBML models. PMID:25904997
Long non-coding RNA discovery across the genus anopheles reveals conserved secondary structures within and beyond the Gambiae complex. PMID:25903279
Hippocampal Pruning as a New Theory of Schizophrenia Etiopathogenesis. PMID:25902861
The resurrection genome of Boea hygrometrica: A blueprint for survival of dehydration. PMID:25902549
From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data. PMID:25902288
Linking gene expression to phenotypes via pathway information. PMID:25901272
De Novo Assembly and Transcriptome Analysis of Wheat with Male Sterility Induced by the Chemical Hybridizing Agent SQ-1. PMID:25898130
Babelomics 5.0: functional interpretation for new generations of genomic data. PMID:25897133
Toll-like receptor signaling in vertebrates: testing the integration of protein, complex, and pathway data in the protein ontology framework. PMID:25894391
Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. PMID:25893781
MicroRNA expression profiles and networks in mouse lung infected with H1N1 influenza virus. PMID:25893419
Epigenomic evolution in diffuse large B-cell lymphomas. PMID:25891015
Mimoza: web-based semantic zooming and navigation in metabolic networks. PMID:25889977
DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe. PMID:25888481
Interpolation based consensus clustering for gene expression time series. PMID:25888019
MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis. PMID:25887539
Transcriptomic analysis of hepatic responses to testosterone deficiency in miniature pigs fed a high-cholesterol diet. PMID:25887406
Measuring semantic similarities by combining gene ontology annotations and gene co-function networks. PMID:25886899
An atlas of mouse CD4(+) T cell transcriptomes. PMID:25886751
Recovering drug-induced apoptosis subnetwork from Connectivity Map data. PMID:25883971
Completing the is-a structure in light-weight ontologies. PMID:25883780
Novel primary immunodeficiency candidate genes predicted by the human gene connectome. PMID:25883595
CellWhere: graphical display of interaction networks organized on subcellular localizations. PMID:25883154
Integrative network analysis reveals molecular mechanisms of blood pressure regulation. PMID:25882670
Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions. PMID:25881257
Predicting response to multidrug regimens in cancer patients using cell line experiments and regularised regression models. PMID:25881228
Plasmodium knowlesi gene expression differs in ex vivo compared to in vitro blood-stage cultures. PMID:25880967
Spectral gene set enrichment (SGSE). PMID:25879888
ClusTrack: feature extraction and similarity measures for clustering of genome-wide data sets. PMID:25879845
BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontology. PMID:25879798
Identification of important interacting proteins (IIPs) in Plasmodium falciparum using large-scale interaction network analysis and in-silico knock-out studies. PMID:25879642
PheNetic: network-based interpretation of molecular profiling data. PMID:25878035
De novo transcriptome assembly of Ipomoea nil using Illumina sequencing for gene discovery and SSR marker identification. PMID:25877516
Mutation analysis in patients with total sperm immotility. PMID:25877373
Construction of an ortholog database using the semantic web technology for integrative analysis of genomic data. PMID:25875762
Tensor GSVD of patient- and platform-matched tumor and normal DNA copy-number profiles uncovers chromosome arm-wide patterns of tumor-exclusive platform-consistent alterations encoding for cell transformation and predicting ovarian cancer survival. PMID:25875127
Metaproteomics of complex microbial communities in biogas plants. PMID:25874383
RecRWR: a recursive random walk method for improved identification of diseases. PMID:25874227
Identification of subtype specific miRNA-mRNA functional regulatory modules in matched miRNA-mRNA expression data: multiple myeloma as a case. PMID:25874214
An Ontology-Based GIS for Genomic Data Management of Rumen Microbes. PMID:25873847
Quantitative Proteomics of Human Fibroblasts with I1061T Mutation in Niemann-Pick C1 (NPC1) Protein Provides Insights into the Disease Pathogenesis. PMID:25873482
GWAS for executive function and processing speed suggests involvement of the CADM2 gene. PMID:25869804
High-mobility group box 1 accelerates lipopolysaccharide-induced lung fibroblast proliferation in vitro: involvement of the NF-κB signaling pathway. PMID:25867768
Genome-wide Analysis of Body Proportion Classifies Height-Associated Variants by Mechanism of Action and Implicates Genes Important for Skeletal Development. PMID:25865494
The role of ontologies in biological and biomedical research: a functional perspective. PMID:25863278
Simultaneous Enrichment of Plasma Soluble and Extracellular Vesicular Glycoproteins Using Prolonged Ultracentrifugation-Electrostatic Repulsion-hydrophilic Interaction Chromatography (PUC-ERLIC) Approach. PMID:25862729
High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in Jute. PMID:25861616
Comparative transcriptome analysis of the petal degeneration mutant pdm in Chinese cabbage (Brassica campestris ssp. pekinensis) using RNA-Seq. PMID:25860116
Identifying overlapping mutated driver pathways by constructing gene networks in cancer. PMID:25859819
RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells. PMID:25858977
Rethinking the Niche of Upper-Atmosphere Bacteria: Draft Genome Sequences of Bacillus aryabhattai C765 and Bacillus aerophilus C772, Isolated from Rice Fields. PMID:25858824
Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature. PMID:25858285
Effect of vitrification on the microRNA transcriptome in mouse blastocysts. PMID:25853900
A DIseAse MOdule Detection (DIAMOnD) algorithm derived from a systematic analysis of connectivity patterns of disease proteins in the human interactome. PMID:25853560
Transcriptional response in normal mouse tissues after i.v. (211)At administration - response related to absorbed dose, dose rate, and time. PMID:25853007
Mapping the global mRNA transcriptome during development of the murine first molar. PMID:25852735
A scalable neuroinformatics data flow for electrophysiological signals using MapReduce. PMID:25852536
Concordant dysregulation of miR-5p and miR-3p arms of the same precursor microRNA may be a mechanism in inducing cell proliferation and tumorigenesis: a lung cancer study. PMID:25852169
Reduced expression of miRNA-1237-3p associated with poor survival of spinal chordoma patients. PMID:25850393
A new method for discovering disease-specific MiRNA-target regulatory networks. PMID:25848944
Genetic conflict reflected in tissue-specific maps of genomic imprinting in human and mouse. PMID:25848752
Biochemical functional predictions for protein structures of unknown or uncertain function. PMID:25848497
Disease gene prioritization using network and feature. PMID:25844670
Abiotic stress and genome dynamics: specific genes and transposable elements response to iron excess in rice. PMID:25844118
Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis. PMID:25841438
Dietary nitrate is a modifier of vascular gene expression in old male mice. PMID:25838870
Molecular signatures of nicotinoid-pathogen synergy in the termite gut. PMID:25837376
Global genome and transcriptome analyses of Magnaporthe oryzae epidemic isolate 98-06 uncover novel effectors and pathogenicity-related genes, revealing gene gain and lose dynamics in genome evolution. PMID:25837042
Analysis of genomic regions of Trichoderma harzianum IOC-3844 related to biomass degradation. PMID:25836973
Identification of potential therapeutic target genes, key miRNAs and mechanisms in acute myeloid leukemia based on bioinformatics analysis. PMID:25832863
Plasmodium knowlesi genome sequences from clinical isolates reveal extensive genomic dimorphism. PMID:25830531
MicroRNA profiling of CD3+ CD56+ cytokine-induced killer cells. PMID:25826780
A comparative study of improvements Pre-filter methods bring on feature selection using microarray data. PMID:25825671
Identification of therapeutic targets for breast cancer using biological informatics methods. PMID:25824986
Autoantibodies targeting glomerular annexin A2 identify patients with proliferative lupus nephritis. PMID:25824007
Properties of protein drug target classes. PMID:25822509
Prediction of drug indications based on chemical interactions and chemical similarities. PMID:25821813
Key challenges for the creation and maintenance of specialist protein resources. PMID:25820941
Ligand-target prediction by structural network biology using nAnnoLyze. PMID:25816344
Gene expression changes in human mesenchymal stem cells from patients with osteoporosis. PMID:25815782
eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment. PMID:25815161
Biomarker-based classification of bacterial and fungal whole-blood infections in a genome-wide expression study. PMID:25814982
Genome Sequence of Phytophthora fragariae var. fragariae, a Quarantine Plant-Pathogenic Fungus. PMID:25814589
The Novel Ribonucleotide Reductase Inhibitor COH29 Inhibits DNA Repair In Vitro. PMID:25814515
Analysis of pharmacogenomic variants associated with population differentiation. PMID:25807276
Transcriptome sequencing and positive selected genes analysis of Bombyx mandarina. PMID:25806526
An epigenetic map of age-associated autosomal loci in northern European families at high risk for the metabolic syndrome. PMID:25806089
Survey of genome sequences in a wild sweet potato, Ipomoea trifida (H. B. K.) G. Don. PMID:25805887
Lessons learned from whole exome sequencing in multiplex families affected by a complex genetic disorder, intracranial aneurysm. PMID:25803036
Analysis of human upstream open reading frames and impact on gene expression. PMID:25800702
Alternative polyadenylation allows differential negative feedback of human miRNA miR-579 on its host gene ZFR. PMID:25799583
De novo characterization of fall dormant and nondormant alfalfa (Medicago sativa L.) leaf transcriptome and identification of candidate genes related to fall dormancy. PMID:25799491
Predicting protein interface residues using easily accessible on-line resources. PMID:25797794
Towards a PBMC "virogram assay" for precision medicine: Concordance between ex vivo and in vivo viral infection transcriptomes. PMID:25797143
GRYFUN: a web application for GO term annotation visualization and analysis in protein sets. PMID:25794277
Modes of interaction between individuals dominate the topologies of real world networks. PMID:25793969
Transcriptome assembly, gene annotation and tissue gene expression atlas of the rainbow trout. PMID:25793877
Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells. PMID:25792609
Differential gene expression in ovaries of Qira black sheep and Hetian sheep using RNA-Seq technique. PMID:25790350
Elevated levels of adaption in Helicobacter pylori genomes from Japan; a link to higher incidences of gastric cancer? PMID:25788149
Examining the evolution of the regulatory circuit controlling secondary metabolism and development in the fungal genus Aspergillus. PMID:25786130
A meta-analysis of gene expression signatures of blood pressure and hypertension. PMID:25785607
Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes. PMID:25785303
Comparative analysis of knowledge representation and reasoning requirements across a range of life sciences textbooks. PMID:25785183
Identification of B cells participated in the mechanism of postmenopausal women osteoporosis using microarray analysis. PMID:25785089
Analysis of protein expression changes of the Vero E6 cells infected with classic PEDV strain CV777 by using quantitative proteomic technique. PMID:25783682
Performance of case-control rare copy number variation annotation in classification of autism. PMID:25783485
Gene networks underlying convergent and pleiotropic phenotypes in a large and systematically-phenotyped cohort with heterogeneous developmental disorders. PMID:25781962
Complete genome sequence of Ornithobacterium rhinotracheale strain ORT-UMN 88. PMID:25780507
The complete genome sequence of the rumen methanogen Methanobacterium formicicum BRM9. PMID:25780506
Non-contiguous finished genome sequence of Ornithobacterium rhinotracheale strain H06-030791. PMID:25780505
Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305(T)), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae. PMID:25780503
High quality draft genome sequence and description of Occidentia massiliensis gen. nov., sp. nov., a new member of the family Rickettsiaceae. PMID:25780502
Non-contiguous finished genome sequence and description of Clostridium saudii sp. nov. PMID:25780501
Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain NZP2037. PMID:25780500
Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain R7A. PMID:25780499
Genome sequence of the dark pink pigmented Listia bainesii microsymbiont Methylobacterium sp. WSM2598. PMID:25780498
Genome sequence of Ensifer medicae Di28; an effective N2-fixing microsymbiont of Medicago murex and M. polymorpha. PMID:25780497
Genome sequence of the Lotus corniculatus microsymbiont Mesorhizobium loti strain R88B. PMID:25780496
Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. PMID:25780495
Analysis of expressed sequence tags from cDNA library of Fusarium culmorum infected barley (Hordeum vulgare L.) roots. PMID:25780278
High spatial resolution proteomic comparison of the brain in humans and chimpanzees. PMID:25779868
High-density genetic map construction and identification of a locus controlling weeping trait in an ornamental woody plant (Prunus mume Sieb. et Zucc). PMID:25776277
Ontology application and use at the ENCODE DCC. PMID:25776021
An ontology approach to comparative phenomics in plants. PMID:25774204
The pathway not taken: understanding 'omics data in the perinatal context. PMID:25772209
Structural and Functional Diversity of Peptide Toxins from Tarantula Haplopelma hainanum (Ornithoctonus hainana) Venom Revealed by Transcriptomic, Peptidomic, and Patch Clamp Approaches. PMID:25770214
Genome-Wide Localization Study of Yeast Pex11 Identifies Peroxisome-Mitochondria Interactions through the ERMES Complex. PMID:25769804
A hybrid computational method for the discovery of novel reproduction-related genes. PMID:25768094
The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release. PMID:25765701
A systems genetics study of swine illustrates mechanisms underlying human phenotypic traits. PMID:25765547
Quality measures for gene expression biclusters. PMID:25763839
Similarity-based search of model organism, disease and drug effect phenotypes. PMID:25763178
Transcriptome analysis reveals the potential mechanism of the albino skin development in pufferfish Takifugu obscurus. PMID:25761722
Integrated microRNA-mRNA analysis revealing the potential roles of microRNAs in tongue squamous cell cancer. PMID:25760063
Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative. PMID:25759811
Establishment and characterization of models of chemotherapy resistance in colorectal cancer: Towards a predictive signature of chemoresistance. PMID:25759163
Expression profile of mitrogen-activated protein kinase (MAPK) signaling genes in the skeletal muscle & liver of rat with type 2 diabetes: role in disease pathology. PMID:25758573
Segmentation of biological multivariate time-series data. PMID:25758050
Proteome exploration to provide a resource for the investigation of Ganoderma lucidum. PMID:25756518
Genomic analysis of drug resistant pancreatic cancer cell line by combining long non-coding RNA and mRNA expression profling. PMID:25755691
An LXR-NCOA5 gene regulatory complex directs inflammatory crosstalk-dependent repression of macrophage cholesterol efflux. PMID:25755249
Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST. PMID:25754993
mycoCLAP, the database for characterized lignocellulose-active proteins of fungal origin: resource and text mining curation support. PMID:25754864
Combining computational models, semantic annotations and simulation experiments in a graph database. PMID:25754863
Malleable nature of mRNA-protein compositional complementarity and its functional significance. PMID:25753660
Human primordial germ cell commitment in vitro associates with a unique PRDM14 expression profile. PMID:25750208
Mining host-pathogen protein interactions to characterize Burkholderia mallei infectivity mechanisms. PMID:25738731
Computational analysis of the LRRK2 interactome. PMID:25737818
Gram-positive and Gram-negative subcellular localization using rotation forest and physicochemical-based features. PMID:25734546
Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes. PMID:25733869
Gene expression profile predictive of response to chemotherapy in metastatic colorectal cancer. PMID:25730906
APOBEC3B expression in breast cancer reflects cellular proliferation, while a deletion polymorphism is associated with immune activation. PMID:25730878
Global analyses revealed age-related alterations in innate immune responses after stimulation of pathogen recognition receptors. PMID:25728020
Identification of hybrid node and link communities in complex networks. PMID:25728010
L-GRAAL: Lagrangian graphlet-based network aligner. PMID:25725498
SimSeq: a nonparametric approach to simulation of RNA-sequence datasets. PMID:25725090
Pathways associated with lignin biosynthesis in lignomaniac jute fibres. PMID:25724692
Evolution of an epigenetic gene ensemble within the genus Anopheles. PMID:25724208
Pathway-based analysis of genome-wide siRNA screens reveals the regulatory landscape of APP processing. PMID:25723573
An integrated approach to reconstructing genome-scale transcriptional regulatory networks. PMID:25723545
Analysis of long non-coding RNAs highlights tissue-specific expression patterns and epigenetic profiles in normal and psoriatic skin. PMID:25723451
Gateways to the FANTOM5 promoter level mammalian expression atlas. PMID:25723102
Transcriptional profiling defines dynamics of parasite tissue sequestration during malaria infection. PMID:25722744
Identifying microRNA-mRNA regulatory network in gemcitabine-resistant cells derived from human pancreatic cancer cells. PMID:25722110
Transcriptome analysis of feline infectious peritonitis virus infection. PMID:25720485
Randomized trial of glucosamine and chondroitin supplementation on inflammation and oxidative stress biomarkers and plasma proteomics profiles in healthy humans. PMID:25719429
Transcriptome sequencing of Codonopsis pilosula and identification of candidate genes involved in polysaccharide biosynthesis. PMID:25719364
Genome-Wide Profiling of TRACK Kidneys Shows Similarity to the Human ccRCC Transcriptome. PMID:25715653
New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing. PMID:25711827
Synergistic and antagonistic interplay between myostatin gene expression and physical activity levels on gene expression patterns in triceps Brachii muscles of C57/BL6 mice. PMID:25710176
Therapeutic opportunities within the DNA damage response. PMID:25709118
EXPath: a database of comparative expression analysis inferring metabolic pathways for plants. PMID:25708775
Integrating experimental and literature protein-protein interaction data for protein complex prediction. PMID:25708571
Pinpointing disease genes through phenomic and genomic data fusion. PMID:25708473
Analytical workflow profiling gene expression in murine macrophages. PMID:25708305
Investigating the utility of clinical outcome-guided mutual information network in network-based Cox regression. PMID:25708115
LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data. PMID:25707511
IIIDB: a database for isoform-isoform interactions and isoform network modules. PMID:25707505
Integrating multiple networks for protein function prediction. PMID:25707434
Phenotypic responses of differentiated asthmatic human airway epithelial cultures to rhinovirus. PMID:25706956
Bridging topological and functional information in protein interaction networks by short loops profiling. PMID:25703051
Techniques for transferring host-pathogen protein interactions knowledge to new tasks. PMID:25699028
Expression of ionotropic receptors in terrestrial hermit crab's olfactory sensory neurons. PMID:25698921
Gene co-expression network analysis provides novel insights into myostatin regulation at three different mouse developmental timepoints. PMID:25695797
Integrative analysis of 111 reference human epigenomes. PMID:25693563
Positive correlation between ADAR expression and its targets suggests a complex regulation mediated by RNA editing in the human brain. PMID:25692240
Protein complex discovery by interaction filtering from protein interaction networks using mutual rank coexpression and sequence similarity. PMID:25692131
Visualization of proteomics data using R and bioconductor. PMID:25690415
Phosphoproteomic analysis of the highly-metastatic hepatocellular carcinoma cell line, MHCC97-H. PMID:25690035
Mitofusin 2 is required to maintain mitochondrial coenzyme Q levels. PMID:25688136
Complete genome sequence of Roseophage vB_DshP-R1, which infects Dinoroseobacter shibae DFL12. PMID:25685262
Draft genome sequence of Bacillus azotoformans MEV2011, a (Co-) denitrifying strain unable to grow with oxygen. PMID:25685261
Complete genome sequence of Pseudomonas fluorescens strain PICF7, an indigenous root endophyte from olive (Olea europaea L.) and effective biocontrol agent against Verticillium dahliae. PMID:25685259
Complete genome sequence of the fish pathogen Flavobacterium psychrophilum ATCC 49418(T.). PMID:25685258
Genome sequence and description of the mosquitocidal and heavy metal tolerant strain Lysinibacillus sphaericus CBAM5. PMID:25685257
Alteration in abundance of specific membrane proteins of Aggregatibacter actinomycetemcomitans is attributed to deletion of the inner membrane protein MorC. PMID:25684173
Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii. PMID:25683379
Cross-talk between ER and HER2 regulates c-MYC-mediated glutamine metabolism in aromatase inhibitor resistant breast cancer cells. PMID:25683269
Crucial microRNAs and genes of human primary breast cancer explored by microRNA-mRNA integrated analysis. PMID:25680412
An ensemble method with hybrid features to identify extracellular matrix proteins. PMID:25680094
Phylogenetic profiling: how much input data is enough? PMID:25679783
Draft genome sequence of Halomonas lutea strain YIM 91125(T) (DSM 23508(T)) isolated from the alkaline Lake Ebinur in Northwest China. PMID:25678942
Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression. PMID:25677182
A statistically inferred microRNA network identifies breast cancer target miR-940 as an actin cytoskeleton regulator. PMID:25673565
New genetic loci link adipose and insulin biology to body fat distribution. PMID:25673412
Natural genetic variation for acclimation of photosynthetic light use efficiency to growth irradiance in Arabidopsis. PMID:25670817
Identification of a new Alcaligenes faecalis strain MOR02 and assessment of its toxicity and pathogenicity to insects. PMID:25667924
HPOSim: an R package for phenotypic similarity measure and enrichment analysis based on the human phenotype ontology. PMID:25664462
Biological mechanism analysis of acute renal allograft rejection: integrated of mRNA and microRNA expression profiles. PMID:25664019
Data Imputation in Epistatic MAPs by Network-Guided Matrix Completion. PMID:25658751
In Vivo Molecular Responses of Fast and Slow Muscle Fibers to Lipopolysaccharide in a Teleost Fish, the Rainbow Trout (Oncorhynchus mykiss). PMID:25658438
[FeFe]-hydrogenase maturation: insights into the role HydE plays in dithiomethylamine biosynthesis. PMID:25654171
A whole-genome microarray study of Arabidopsis thaliana semisolid callus cultures exposed to microgravity and nonmicrogravity related spaceflight conditions for 5 days on board of Shenzhou 8. PMID:25654111
Genome analysis of Flaviramulus ichthyoenteri Th78(T) in the family Flavobacteriaceae: insights into its quorum quenching property and potential roles in fish intestine. PMID:25652846
Characterization of tissue-specific differential DNA methylation suggests distinct modes of positive and negative gene expression regulation. PMID:25652663
De novo assembly, transcriptome characterization, lignin accumulation, and anatomic characteristics: novel insights into lignin biosynthesis during celery leaf development. PMID:25651889
A de novo transcriptome of the noble scallop, Chlamys nobilis, focusing on mining transcripts for carotenoid-based coloration. PMID:25651863
Methylomic trajectories across human fetal brain development. PMID:25650246
Identification of Target Genes Regulated by KSHV miRNAs in KSHV-Infected Lymphoma Cells. PMID:25648438
Identification and functional analysis of healing regulators in Drosophila. PMID:25647511
Describing the breakbone fever: IDODEN, an ontology for dengue fever. PMID:25646954
Fetal-adult cardiac transcriptome analysis in rats with contrasting left ventricular mass reveals new candidates for cardiac hypertrophy. PMID:25646840
A copy number variation map of the human genome. PMID:25645873
Genome-Wide Association Study of Behavioral Disinhibition in a Selected Adolescent Sample. PMID:25637581
The avian transcriptome response to malaria infection. PMID:25636457
Discovery of new candidate genes related to brain development using protein interaction information. PMID:25635857
Autophagy Regulatory Network - a systems-level bioinformatics resource for studying the mechanism and regulation of autophagy. PMID:25635527
Negative feedback buffers effects of regulatory variants. PMID:25634765
Functional organization of the genome may shape the species boundary in the house mouse. PMID:25631927
Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics. PMID:25631240
Upregulation of gingival tissue miR-200b in obese periodontitis subjects. PMID:25630869
Database of Gene Co-Regulation (dGCR): A Web Tool for Analysing Patterns of Gene Co-regulation across Publicly Available Expression Data. PMID:25628763
Aber-OWL: a framework for ontology-based data access in biology. PMID:25627673
Network analysis of gene expression in peripheral blood identifies mTOR and NF-κB pathways involved in antipsychotic-induced extrapyramidal symptoms. PMID:25623440
Berberine ameliorates nonalcoholic fatty liver disease by a global modulation of hepatic mRNA and lncRNA expression profiles. PMID:25623289
Deeper insight into chronic kidney disease-related atherosclerosis: comparative proteomic studies of blood plasma using 2DE and mass spectrometry. PMID:25622820
ASSIGN: context-specific genomic profiling of multiple heterogeneous biological pathways. PMID:25617415
Identification of key genes associated with colorectal cancer based on the transcriptional network. PMID:25613817
Fumarate induces redox-dependent senescence by modifying glutathione metabolism. PMID:25613188
Evolutionary constraint and disease associations of post-translational modification sites in human genomes. PMID:25611800
A computational approach to identifying gene-microRNA modules in cancer. PMID:25611546
Functional and phylogenetic characterization of proteins detected in various nematode intestinal compartments. PMID:25609831
Topology-function conservation in protein-protein interaction networks. PMID:25609797
Bias in microRNA functional enrichment analysis. PMID:25609791
Proteomic enrichment analysis of psychotic and affective disorders reveals common signatures in presynaptic glutamatergic signaling and energy metabolism. PMID:25609598
Genomes of the rice pest brown planthopper and its endosymbionts reveal complex complementary contributions for host adaptation. PMID:25609551
Chromatin decompaction by the nucleosomal binding protein HMGN5 impairs nuclear sturdiness. PMID:25609380
limma powers differential expression analyses for RNA-sequencing and microarray studies. PMID:25605792
p54nrb/NONO regulates cyclic AMP-dependent glucocorticoid production by modulating phosphodiesterase mRNA splicing and degradation. PMID:25605330
Comparative computational analysis of pluripotency in human and mouse stem cells. PMID:25604210
Robustness analysis on interspecies interaction network for iron and glucose competition between Candida albicans and zebrafish during infection. PMID:25603810
Reconstructing genome-wide protein-protein interaction networks using multiple strategies with homologous mapping. PMID:25602759
Genetic evidence that intratumoral T-cell proliferation and activation are associated with recurrence and survival in patients with resected colorectal liver metastases. PMID:25600439
Biological interpretation of genome-wide association studies using predicted gene functions. PMID:25597830
Chemokine-mediated inflammation in the degenerating retina is coordinated by Müller cells, activated microglia, and retinal pigment epithelium. PMID:25595590
Genome sequence of Coxiella burnetii strain Namibia. PMID:25593636
Fast and robust group-wise eQTL mapping using sparse graphical models. PMID:25593000
Identifying mutation specific cancer pathways using a structurally resolved protein interaction network. PMID:25592571
Predicting protein functions using incomplete hierarchical labels. PMID:25591917
Genome-wide association study of antibody level response to NDV and IBV in Jinghai yellow chicken based on SLAF-seq technology. PMID:25588649
MAPK feedback encodes a switch and timer for tunable stress adaptation in yeast. PMID:25587192
A disease module in the interactome explains disease heterogeneity, drug response and captures novel pathways and genes in asthma. PMID:25586491
Defining the transcriptomic landscape of Candida glabrata by RNA-Seq. PMID:25586221
Effects of copy number variable regions on local gene expression in white blood cells of Mexican Americans. PMID:25585699
Non-contiguous finished genome sequence and description of the gliding bacterium Flavobacterium seoulense sp. nov. PMID:25584140
The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau. PMID:25583503
Sparse expression bases in cancer reveal tumor drivers. PMID:25583238
The origin of CDR H3 structural diversity. PMID:25579815
ENViz: a Cytoscape App for integrated statistical analysis and visualization of sample-matched data with multiple data types. PMID:25577435
Insights on the evolution of mycoparasitism from the genome of Clonostachys rosea. PMID:25575496
POEAS: Automated Plant Phenomic Analysis Using Plant Ontology. PMID:25574136
Gene expression and fractionation resistance. PMID:25573431
A meta-approach for improving the prediction and the functional annotation of ortholog groups. PMID:25573073
Cabut/dTIEG associates with the transcription factor Yorkie for growth control. PMID:25572844
A co-culture genome-wide RNAi screen with mammary epithelial cells reveals transmembrane signals required for growth and differentiation. PMID:25572802
Orthology and paralogy constraints: satisfiability and consistency. PMID:25572629
Sex-related gene expression profiles in the adrenal cortex in the mature rat: microarray analysis with emphasis on genes involved in steroidogenesis. PMID:25572386
Integrative analysis of DNA methylation and gene expression data identifies EPAS1 as a key regulator of COPD. PMID:25569234
Myeloid decidual dendritic cells and immunoregulation of pregnancy: defective responsiveness to Coxiella burnetii and Brucella abortus. PMID:25566514
Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2. PMID:25566348
Genome-wide survey of the seagrass Zostera muelleri suggests modification of the ethylene signalling network. PMID:25563969
Genetic determinants of depression: recent findings and future directions. PMID:25563565
The enzymatic nature of an anonymous protein sequence cannot reliably be inferred from superfamily level structural information alone. PMID:25559918
Discovery of small protein complexes from PPI networks with size-specific supervised weighting. PMID:25559663
Identification of genes and pathways involved in kidney renal clear cell carcinoma. PMID:25559354
Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing. PMID:25553907
The kidney transcriptome and proteome defined by transcriptomics and antibody-based profiling. PMID:25551756
Environmentally selected aphid variants in clonality context display differential patterns of methylation in the genome. PMID:25551225
Expression of tumor necrosis factor-alpha-mediated genes predicts recurrence-free survival in lung cancer. PMID:25548907
The human pancreas proteome defined by transcriptomics and antibody-based profiling. PMID:25546435
Whole genome sequence analysis suggests intratumoral heterogeneity in dissemination of breast cancer to lymph nodes. PMID:25546409
A role for BMP-induced homeobox gene MIXL1 in acute myelogenous leukemia and identification of type I BMP receptor as a potential target for therapy. PMID:25544748
Genome-wide analysis of drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation. PMID:25544350
The transcriptomic and proteomic landscapes of bone marrow and secondary lymphoid tissues. PMID:25541736
Reproducibility enhancement and differential expression of non predefined functional gene sets in human genome. PMID:25539829
Systematic exploration of autonomous modules in noisy microRNA-target networks for testing the generality of the ceRNA hypothesis. PMID:25539629
Insights from systems pharmacology into cardiovascular drug discovery and therapy. PMID:25539592
Improving collaboration by standardization efforts in systems biology. PMID:25538939
Locus heterogeneity disease genes encode proteins with high interconnectivity in the human protein interaction network. PMID:25538735
The BRCA1/2-directed miRNA signature predicts a good prognosis in ovarian cancer patients with wild-type BRCA1/2. PMID:25537514
Enhanced cardiac Akt/protein kinase B signaling contributes to pathological cardiac hypertrophy in part by impairing mitochondrial function via transcriptional repression of mitochondrion-targeted nuclear genes. PMID:25535334
Role of lamin b1 in chromatin instability. PMID:25535332
Identification of low temperature stress regulated transcript sequences and gene families in Italian cypress. PMID:25534982
Sequence search and analysis of gene products containing RNA recognition motifs in the human genome. PMID:25534245
Comparative transcriptome analyses reveal core parasitism genes and suggest gene duplication and repurposing as sources of structural novelty. PMID:25534030
Div-BLAST: diversification of sequence search results. PMID:25531115
INTEGRATING COMPUTATIONAL PROTEIN FUNCTION PREDICTION INTO DRUG DISCOVERY INITIATIVES. PMID:25530654
Genetic contributions to urgency urinary incontinence in women. PMID:25524241
Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes. PMID:25523484
The application of the open pharmacological concepts triple store (open PHACTS) to support drug discovery research. PMID:25522365
Pilomyxoid Astrocytoma (PMA) Shows Significant Differences in Gene Expression vs. Pilocytic Astrocytoma (PA) and Variable Tendency Toward Maturation to PA. PMID:25521223
Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India. PMID:25520706
Genetic resources for methane production from biomass described with the Gene Ontology. PMID:25520705
Semantically linking in silico cancer models. PMID:25520553
Identifying causal regulatory SNPs in ChIP-seq enhancers. PMID:25520196
The genetics of colony form and function in Caribbean Acropora corals. PMID:25519925
Pedigree-based random effect tests to screen gene pathways. PMID:25519354
PROGgeneV2: enhancements on the existing database. PMID:25518851
Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation. PMID:25517091
Transcriptional profiling of adult neural stem-like cells from the human brain. PMID:25514637
TRPC3 channels critically regulate hippocampal excitability and contextual fear memory. PMID:25513972
Detection of alternative splice and gene duplication by RNA sequencing in Japanese flounder, Paralichthys olivaceus. PMID:25512620
Health information technology in oncology practice: a literature review. PMID:25506195
A chemical proteomics approach for global analysis of lysine monomethylome profiling. PMID:25505155
Evolutionary Dynamics of GLD-1-mRNA complexes in Caenorhabditis nematodes. PMID:25502909
Transcriptomic analysis of temperature responses of Aspergillus kawachii during barley koji production. PMID:25501485
Transcriptome profiles of the protoscoleces of Echinococcus granulosus reveal that excretory-secretory products are essential to metabolic adaptation. PMID:25500817
Genome-scale identification and characterization of moonlighting proteins. PMID:25497125
Kiwi: a tool for integration and visualization of network topology and gene-set analysis. PMID:25496126
Functional genomics and microbiome profiling of the Asian longhorned beetle (Anoplophora glabripennis) reveal insights into the digestive physiology and nutritional ecology of wood feeding beetles. PMID:25495900
Methodology for the inference of gene function from phenotype data. PMID:25495798
The ins and outs of metal homeostasis by the root nodule actinobacterium Frankia. PMID:25495525
Prioritization of candidate genes in QTL regions based on associations between traits and biological processes. PMID:25492368
chromoWIZ: a web tool to query and visualize chromosome-anchored genes from cereal and model genomes. PMID:25491094
Finding gene regulatory network candidates using the gene expression knowledge base. PMID:25490885
Predicting expression: the complementary power of histone modification and transcription factor binding data. PMID:25489339
In silico analysis of autoimmune diseases and genetic relationships to vaccination against infectious diseases. PMID:25486901
Gemcitabine resistant pancreatic cancer cell lines acquire an invasive phenotype with collateral hypersensitivity to histone deacetylase inhibitors. PMID:25485960
Temporal separation of replication and transcription during S-phase progression. PMID:25485504
Molecular effects of resistance elicitors from biological origin and their potential for crop protection. PMID:25484886
MicroRNA Dysregulation, Gene Networks, and Risk for Schizophrenia in 22q11.2 Deletion Syndrome. PMID:25484875
Inactivation of the budding yeast cohesin loader Scc2 alters gene expression both globally and in response to a single DNA double strand break. PMID:25483075
What helminth genomes have taught us about parasite evolution. PMID:25482650
Genomic characterisation of an endometrial pathogenic Escherichia coli strain reveals the acquisition of genetic elements associated with extra-intestinal pathogenicity. PMID:25481482
Graphical algorithm for integration of genetic and biological data: proof of principle using psoriasis as a model. PMID:25480373
LAILAPS: the plant science search engine. PMID:25480116
Accounting for eXentricities: analysis of the X chromosome in GWAS reveals X-linked genes implicated in autoimmune diseases. PMID:25479423
BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types. PMID:25477388
Evaluation and integration of functional annotation pipelines for newly sequenced organisms: the potato genome as a test case. PMID:25476999
Proteomic analysis and identification of cellular interactors of the giant ubiquitin ligase HERC2. PMID:25476789
Pathway activity inference for multiclass disease classification through a mathematical programming optimisation framework. PMID:25475756
Detection of pleiotropy through a Phenome-wide association study (PheWAS) of epidemiologic data as part of the Environmental Architecture for Genes Linked to Environment (EAGLE) study. PMID:25474351
The COPD Knowledge Base: enabling data analysis and computational simulation in translational COPD research. PMID:25471253
A-WINGS: an integrated genome database for Pleurocybella porrigens (Angel's wing oyster mushroom, Sugihiratake). PMID:25465051
De novo sequencing, assembly and characterization of antennal transcriptome of Anomala corpulenta Motschulsky (Coleoptera: Rutelidae). PMID:25461610
Mycofumigation by the volatile organic compound-producing Fungus Muscodor albus induces bacterial cell death through DNA damage. PMID:25452287
Contribution of bioinformatics prediction in microRNA-based cancer therapeutics. PMID:25450261
Determining microbial products and identifying molecular targets in the human microbiome. PMID:25440055
Comparison of potato and asian citrus psyllid adult and nymph transcriptomes identified vector transcripts with potential involvement in circulative, propagative liberibacter transmission. PMID:25436509
Impact of analytic provenance in genome analysis. PMID:25435180
Network-based modular latent structure analysis. PMID:25435002
Complete mitogenome of the edible sea urchin Loxechinus albus: genetic structure and comparative genomics within Echinozoa. PMID:25433433
Triticeae resources in Ensembl Plants. PMID:25432969
Nemertean toxin genes revealed through transcriptome sequencing. PMID:25432940
A model to investigate SNPs' interaction in GWAS studies. PMID:25432432
Predicting the potential ankylosing spondylitis-related genes utilizing bioinformatics approaches. PMID:25432079
A set-based association test identifies sex-specific gene sets associated with type 2 diabetes. PMID:25429300
Identification and molecular characterization of tissue-preferred rice genes and their upstream regularly sequences on a genome-wide level. PMID:25428432
The InterPro protein families database: the classification resource after 15 years. PMID:25428371
Gene Ontology Consortium: going forward. PMID:25428369
OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software. PMID:25428351
A robust data-driven approach for gene ontology annotation. PMID:25425037
microPIR2: a comprehensive database for human-mouse comparative study of microRNA-promoter interactions. PMID:25425035
Gene duplication of type-B ARR transcription factors systematically extends transcriptional regulatory structures in Arabidopsis. PMID:25425016
Transcriptional profiling of the spleen in progressive visceral leishmaniasis reveals mixed expression of type 1 and type 2 cytokine-responsive genes. PMID:25424735
System-level insights into the cellular interactome of a non-model organism: inferring, modelling and analysing functional gene network of soybean (Glycine max). PMID:25423109
Premorbid risk factors for major depressive disorder: are they associated with early onset and recurrent course? PMID:25422974
Sculpting the UMLS Refined Semantic Network. PMID:25422719
Using VisANT to Analyze Networks. PMID:25422679
Regulatory interplay between soybean root and soybean cyst nematode during a resistant and susceptible reaction. PMID:25421055
Synergy: a web resource for exploring gene regulation in Synechocystis sp. PCC6803. PMID:25420108
Proteomics-Based Identification of Differentially Abundant Proteins from Human Keratinocytes Exposed to Arsenic Trioxide. PMID:25419056
Key regulators in prostate cancer identified by co-expression module analysis. PMID:25418933
RNA-Seq reveals leaf cuticular wax-related genes in Welsh onion. PMID:25415343
Comparative transcriptomic analysis of male and female flowers of monoecious Quercus suber. PMID:25414713
Type I Interferon Regulates the Expression of Long Non-Coding RNAs. PMID:25414701
Identification by high-throughput imaging of the histone methyltransferase EHMT2 as an epigenetic regulator of VEGFA alternative splicing. PMID:25414343
Tree shrew database (TreeshrewDB): a genomic knowledge base for the Chinese tree shrew. PMID:25413576
Comparison of the transcriptional landscapes between human and mouse tissues. PMID:25413365
Community structure detection for overlapping modules through mathematical programming in protein interaction networks. PMID:25412367
Pathophysiologic and transcriptomic analyses of viscerotropic yellow fever in a rhesus macaque model. PMID:25412185
Expression of human skin-specific genes defined by transcriptomics and antibody-based profiling. PMID:25411189
Shift in GATA3 functions, and GATA3 mutations, control progression and clinical presentation in breast cancer. PMID:25410484
A comprehensive analysis of candidate genes and pathways in pancreatic cancer. PMID:25409614
Roles of intragenic and intergenic L1s in mouse and human. PMID:25409429
The genome of the generalist plant pathogen Fusarium avenaceum is enriched with genes involved in redox, signaling and secondary metabolism. PMID:25409087
Identification of differently expressed genes with specific SNP Loci for breast cancer by the integration of SNP and gene expression profiling analyses. PMID:25408372
Distance-based assessment of the localization of functional annotations in 3D genome reconstructions. PMID:25407917
I-GSEA4GWAS v2: a web server for functional analysis of SNPs in trait-associated pathways identified from genome-wide association study. PMID:25407412
Anatomo-proteomic characterization of human basal ganglia: focus on striatum and globus pallidus. PMID:25406675
CpG island-mediated global gene regulatory modes in mouse embryonic stem cells. PMID:25405324
What do all the (human) micro-RNAs do? PMID:25404408
Beyond protein expression, MOPED goes multi-omics. PMID:25404128
Rapid neurogenesis through transcriptional activation in human stem cells. PMID:25403753
RNA-sequencing reveals early, dynamic transcriptome changes in the corollas of pollinated petunias. PMID:25403317
In silico prediction of physical protein interactions and characterization of interactome orphans. PMID:25402006
Development and use of the Cytoscape app GFD-Net for measuring semantic dissimilarity of gene networks. PMID:25400907
Chitosan Degradation Products Promote Nerve Regeneration by Stimulating Schwann Cell Proliferation via miR-27a/FOXO1 Axis. PMID:25399953
A systems biology strategy to identify molecular mechanisms of action and protein indicators of traumatic brain injury. PMID:25399920
Computational characterization of moonlighting proteins. PMID:25399606
The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. PMID:25399418
Genome-wide identification and analysis of Catharanthus roseus RLK1-like kinases in rice. PMID:25399351
Database resources of the National Center for Biotechnology Information. PMID:25398906
UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. PMID:25398609
Behavioral and proteomic analysis of stress response in zebrafish (Danio rerio). PMID:25398274
Text mining in cancer gene and pathway prioritization. PMID:25392685
iPathCons and iPathDB: an improved insect pathway construction tool and the database. PMID:25388589
Exploring the genetic basis of adaptation to high elevations in reptiles: a comparative transcriptome analysis of two toad-headed agamas (genus Phrynocephalus). PMID:25386640
Identification of Cdca7 as a novel Notch transcriptional target involved in hematopoietic stem cell emergence. PMID:25385755
Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. PMID:25385592
A relative shift in cloacal location repositions external genitalia in amniote evolution. PMID:25383527
ProKinO: a unified resource for mining the cancer kinome. PMID:25382819
A deep transcriptomic analysis of pod development in the vanilla orchid (Vanilla planifolia). PMID:25380694
Systems biology as a comparative approach to understand complex gene expression in neurological diseases. PMID:25379238
Semi-automated literature mining to identify putative biomarkers of disease from multiple biofluids. PMID:25379168
Current advances in systems and integrative biology. PMID:25379142
Using biological networks to improve our understanding of infectious diseases. PMID:25379138
The nutritionally responsive transcriptome of the polyphenic beetle Onthophagus taurus and the importance of sexual dimorphism and body region. PMID:25377458
RNA-seq analysis and de novo transcriptome assembly of Jerusalem artichoke (Helianthus tuberosus Linne). PMID:25375764
Computational approaches for predicting biomedical research collaborations. PMID:25375164
Network based meta-analysis prediction of microenvironmental relays involved in stemness of human embryonic stem cells. PMID:25374775
A pan-cancer modular regulatory network analysis to identify common and cancer-specific network components. PMID:25374456
Profiling status epilepticus-induced changes in hippocampal RNA expression using high-throughput RNA sequencing. PMID:25373493
De-novo assembly of mango fruit peel transcriptome reveals mechanisms of mango response to hot water treatment. PMID:25373421
Identification of under-detected periodicity in time-series microarray data by using empirical mode decomposition. PMID:25372711
Covering complete proteomes with X-ray structures: a current snapshot. PMID:25372670
17β-estradiol modulates gene expression in the female mouse cerebral cortex. PMID:25372139
Systematic analysis of time-series gene expression data on tumor cell-selective apoptotic responses to HDAC inhibitors. PMID:25371703
Deep sequencing reveals important roles of microRNAs in response to drought and salinity stress in cotton. PMID:25371507
Comparative transcriptome analysis of two oysters, Crassostrea gigas and Crassostrea hongkongensis provides insights into adaptation to hypo-osmotic conditions. PMID:25369077
A shortcut for multiple testing on the directed acyclic graph of gene ontology. PMID:25366961
Identification of miRNAs involved in pear fruit development and quality. PMID:25366381
A census of human RNA-binding proteins. PMID:25365966
Transcriptional network analysis reveals that AT1 and AT2 angiotensin II receptors are both involved in the regulation of genes essential for glioma progression. PMID:25365520
From moderately severe to severe hypertriglyceridemia induced acute pancreatitis: circulating miRNAs play role as potential biomarkers. PMID:25365448
Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress. PMID:25362847
Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential. PMID:25362047
GeneFriends: a human RNA-seq-based gene and transcript co-expression database. PMID:25361971
PomBase 2015: updates to the fission yeast database. PMID:25361970
A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana. PMID:25361952
BiobankConnect: software to rapidly connect data elements for pooled analysis across biobanks using ontological and lexical indexing. PMID:25361575
Systems analysis reveals down-regulation of a network of pro-survival miRNAs drives the apoptotic response in dilated cardiomyopathy. PMID:25361207
Relating diseases by integrating gene associations and information flow through protein interaction network. PMID:25360770
Coordinated regulation of photosynthesis in rice increases yield and tolerance to environmental stress. PMID:25358745
dcGOR: an R package for analysing ontologies and protein domain annotations. PMID:25356683
Compartment-specific transcriptomics in a reef-building coral exposed to elevated temperatures. PMID:25354956
Genome-scale quantitative characterization of bacterial protein localization dynamics throughout the cell cycle. PMID:25353361
VariantDB: a flexible annotation and filtering portal for next generation sequencing data. PMID:25352915
Characterization of the rainbow trout spleen transcriptome and identification of immune-related genes. PMID:25352861
STRING v10: protein-protein interaction networks, integrated over the tree of life. PMID:25352553
The complex jujube genome provides insights into fruit tree biology. PMID:25350882
ComPPI: a cellular compartment-specific database for protein-protein interaction network analysis. PMID:25348397
MitProNet: A knowledgebase and analysis platform of proteome, interactome and diseases for mammalian mitochondria. PMID:25347823
Neisseria meningitidis elicits a pro-inflammatory response involving IκBζ in a human blood-cerebrospinal fluid barrier model. PMID:25347003
Genetic resources for advanced biofuel production described with the Gene Ontology. PMID:25346727
Identification and functional characterization of copy number variations in diverse chicken breeds. PMID:25344733
Understanding disease mechanisms with models of signaling pathway activities. PMID:25344409
Draft Genome Sequence of the Novel Exopolysaccharide-Producing Bacterium Altibacter lentus Strain JLT2010T, Isolated from Deep Seawater of the South China Sea. PMID:25342673
Comparative genome analysis of Wolbachia strain wAu. PMID:25341639
E2F1 induces miR-224/452 expression to drive EMT through TXNIP downregulation. PMID:25341426
Regression analysis of combined gene expression regulation in acute myeloid leukemia. PMID:25340776
The Comparative Genomics and Phylogenomics of Leishmania amazonensis Parasite. PMID:25336895
Genomic and transcriptomic analyses of the medicinal fungus Antrodia cinnamomea for its metabolite biosynthesis and sexual development. PMID:25336756
Expression profiling of mitochondrial voltage-dependent anion channel-1 associated genes predicts recurrence-free survival in human carcinomas. PMID:25333947
Association between DNA methylation and multidrug resistance in human glioma SHG-44 cells. PMID:25333456
Learning regulatory programs by threshold SVD regression. PMID:25331876
Systems biology studies of adult paragonimus lung flukes facilitate the identification of immunodominant parasite antigens. PMID:25329661
Angiogenesis interactome and time course microarray data reveal the distinct activation patterns in endothelial cells. PMID:25329517
Autosomal dominant immune dysregulation syndrome in humans with CTLA4 mutations. PMID:25329329
The Comparative Toxicogenomics Database's 10th year anniversary: update 2015. PMID:25326323
Impact of Amorphous SiO2 Nanoparticles on a Living Organism: Morphological, Behavioral, and Molecular Biology Implications. PMID:25325055
HSF-1-mediated cytoskeletal integrity determines thermotolerance and life span. PMID:25324391
Incorporating computational resources in a cancer research program. PMID:25324189
New tricks for "old" domains: how novel architectures and promiscuous hubs contributed to the organization and evolution of the ECM. PMID:25323955
Abundance, arrangement, and function of sequence motifs in the chicken promoters. PMID:25318583
Yeast systems biology: our best shot at modeling a cell. PMID:25316779
The transcriptomic profile of ovarian cancer grading. PMID:25314936
RNA sequencing and de novo assembly of the digestive gland transcriptome in Mytilus galloprovincialis fed with toxinogenic and non-toxic strains of Alexandrium minutum. PMID:25314922
Differential protein network analysis of the immune cell lineage. PMID:25309909
Comprehensive characterization of cancer subtype associated long non-coding RNAs and their clinical implications. PMID:25307233
Cortical spreading depression increases the phosphorylation of AMP-activated protein kinase in the cerebral cortex. PMID:25307110
Genome-wide DNA methylation profiles and their relationships with mRNA and the microRNA transcriptome in bovine muscle tissue (Bos taurine). PMID:25306978
Transcriptome analysis of the Trachinotus ovatus: identification of reproduction, growth and immune-related genes and microsatellite markers. PMID:25303650
'N-of-1-pathways' unveils personal deregulated mechanisms from a single pair of RNA-Seq samples: towards precision medicine. PMID:25301808
Copy number variants in short children born small for gestational age. PMID:25300501
Spotlite: web application and augmented algorithms for predicting co-complexed proteins from affinity purification--mass spectrometry data. PMID:25300367
Transcriptome analysis elucidates key developmental components of bryozoan lophophore development. PMID:25300304
Linear motif-mediated interactions have contributed to the evolution of modularity in complex protein interaction networks. PMID:25299147
FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species. PMID:25294921
Large-scale modeling of condition-specific gene regulatory networks by information integration and inference. PMID:25294834
Transcriptome Analysis of the Small Brown Planthopper, Laodelphax striatellus Carrying Rice stripe virus. PMID:25288960
Transcriptomic and proteomic analysis reveals mechanisms of embryo abortion during chrysanthemum cross breeding. PMID:25288482
Sequence specificity incompletely defines the genome-wide occupancy of Myc. PMID:25287278
Transcriptome sequencing of rhizome tissue of Sinopodophyllum hexandrum at two temperatures. PMID:25287271
A novel common variant in DCST2 is associated with length in early life and height in adulthood. PMID:25281659
Systematic identification of transcriptional and post-transcriptional regulations in human respiratory epithelial cells during influenza A virus infection. PMID:25281301
Joint genetic analysis of hippocampal size in mouse and human identifies a novel gene linked to neurodegenerative disease. PMID:25280473
Gene expression profiling of biological pathway alterations by radiation exposure. PMID:25276823
Structuring research methods and data with the research object model: genomics workflows as a case study. PMID:25276335
The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology. PMID:25276334
Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions. PMID:25275790
Enhancing the functional content of eukaryotic protein interaction networks. PMID:25275489
TGFβ receptor 1: an immune susceptibility gene in HPV-associated cancer. PMID:25273091
R-flurbiprofen attenuates experimental autoimmune encephalomyelitis in mice. PMID:25269445
De novo transcriptome sequence assembly and identification of AP2/ERF transcription factor related to abiotic stress in parsley (Petroselinum crispum). PMID:25268141
CarrotDB: a genomic and transcriptomic database for carrot. PMID:25267795
Genes and signaling networks regulated during zebrafish optic vesicle morphogenesis. PMID:25266257
Hippo signaling influences HNF4A and FOXA2 enhancer switching during hepatocyte differentiation. PMID:25263553
Widespread signals of convergent adaptation to high altitude in Asia and america. PMID:25262650
Maize and millet transcription factors annotated using comparative genomic and transcriptomic data. PMID:25261191
Begin at the beginning: A BAC-end view of the passion fruit (Passiflora) genome. PMID:25260959
FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus. PMID:25260589
Widespread intron retention in mammals functionally tunes transcriptomes. PMID:25258385
Identification of genomic regions associated with feed efficiency in Nelore cattle. PMID:25257854
A phylogenomic census of molecular functions identifies modern thermophilic archaea as the most ancient form of cellular life. PMID:25249790
Feature Screening via Distance Correlation Learning. PMID:25249709
The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome. PMID:25248950
Endometrial gene expression reveals compromised progesterone signaling in women refractory to embryo implantation. PMID:25248672
Identification of copy number variations in Qinchuan cattle using BovineHD Genotyping Beadchip array. PMID:25248638
Epigenomic profiling of men exposed to early-life stress reveals DNA methylation differences in association with current mental state. PMID:25247593
Overexpression of the soybean transcription factor GmDof4 significantly enhances the lipid content of Chlorella ellipsoidea. PMID:25246944
Population- and sex-biased gene expression in the excretion organs of Drosophila melanogaster. PMID:25246242
Leaf-, panel- and latex-expressed sequenced tags from the rubber tree (Hevea brasiliensis) under cold-stressed and suboptimal growing conditions: the development of gene-targeted functional markers for stress response. PMID:25242886
Genomic insights into processes driving the infection of Alexandrium tamarense by the Parasitoid Amoebophrya sp. PMID:25239978
New insights into the targeting of a subset of tail-anchored proteins to the outer mitochondrial membrane. PMID:25237314
Mechanosensitive kinases regulate stiffness-induced cardiomyocyte maturation. PMID:25236849
Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis. PMID:25236784
Single nucleotide variations: biological impact and theoretical interpretation. PMID:25234433
Draft genome sequence of eggplant (Solanum melongena L.): the representative solanum species indigenous to the old world. PMID:25233906
Allele-specific network reveals combinatorial interaction that transcends small effects in psoriasis GWAS. PMID:25233071
Antimicrobial targets localize to the extracellular vesicle-associated proteome of Pseudomonas aeruginosa grown in a biofilm. PMID:25232353
Cell-type-specific repression by methyl-CpG-binding protein 2 is biased toward long genes. PMID:25232122
A high-resolution network model for global gene regulation in Mycobacterium tuberculosis. PMID:25232098
A weighted multipath measurement based on gene ontology for estimating gene products similarity. PMID:25229994
Gene expression and pathway analysis of effects of the CMAH deactivation on mouse lung, kidney and heart. PMID:25229777
RADB: a database of rheumatoid arthritis-related polymorphisms. PMID:25228593
A root-expressed L-phenylalanine:4-hydroxyphenylpyruvate aminotransferase is required for tropane alkaloid biosynthesis in Atropa belladonna. PMID:25228340
Predicting disease associations via biological network analysis. PMID:25228247
Integrative quantitative proteomics unveils proteostasis imbalance in human hepatocellular carcinoma developed on nonfibrotic livers. PMID:25225353
Full-length enriched cDNA libraries and ORFeome analysis of sugarcane hybrid and ancestor genotypes. PMID:25222706
Organizing knowledge to enable personalization of medicine in cancer. PMID:25222080
The clinicopathological and gene expression patterns associated with ulceration of primary melanoma. PMID:25220403
Identification of gene expression profile in the rat brain resulting from acute alcohol intoxication. PMID:25218841
De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. PMID:25218520
Knowledge-driven genomic interactions: an application in ovarian cancer. PMID:25214892
Genomic analysis of the Pacific oyster (Crassostrea gigas) reveals possible conservation of vertebrate sex determination in a mollusc. PMID:25213692
SANTA: quantifying the functional content of molecular networks. PMID:25210953
Neighbor preferences of amino acids and context-dependent effects of amino acid substitutions in human, mouse, and dog. PMID:25210846
Co-regulated transcripts associated to cooperating eSNPs define Bi-fan motifs in human gene networks. PMID:25210734
Insights from the cold transcriptome of Physcomitrella patens: global specialization pattern of conserved transcriptional regulators and identification of orphan genes involved in cold acclimation. PMID:25209349
Genome-wide identification of housekeeping genes in maize. PMID:25209110
A semi-automated methodology for finding lipid-related GO terms. PMID:25209026
Unsupervised gene function extraction using semantic vectors. PMID:25209025
Human Tra2 proteins jointly control a CHEK1 splicing switch among alternative and constitutive target exons. PMID:25208576
Analysis of tumor suppressor genes based on gene ontology and the KEGG pathway. PMID:25207935
Insilico analysis of hypothetical proteins unveils putative metabolic pathways and essential genes in Leishmania donovani. PMID:25206363
Systems biology and brain activity in neuronal pathways by smart device and advanced signal processing. PMID:25206359
Pichia pastoris Aft1--a novel transcription factor, enhancing recombinant protein secretion. PMID:25205197
Annotation and re-sequencing of genes from de novo transcriptome assembly of Abies alba (Pinaceae). PMID:25202477
The sialotranscriptome of Amblyomma triste, Amblyomma parvum and Amblyomma cajennense ticks, uncovered by 454-based RNA-seq. PMID:25201527
Evolutionary conservation and expression of human RNA-binding proteins and their role in human genetic disease. PMID:25201102
Complexity of gene expression evolution after duplication: protein dosage rebalancing. PMID:25197576
Non-contiguous finished genome sequence and description of Paucisalibacillus algeriensis sp. nov. PMID:25197503
Non-contiguous finished genome sequence of Prevotella timonensis type strain 4401737(T.). PMID:25197502
Genome sequence of the exopolysaccharide-producing Salipiger mucosus type strain (DSM 16094(T)), a moderately halophilic member of the Roseobacter clade. PMID:25197501
Non-contiguous finished genome sequence and description of Kurthia senegalensis sp. nov. PMID:25197500
Non-contiguous finished genome sequence and description of Sulfurimonas hongkongensis sp. nov., a strictly anaerobic denitrifying, hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from marine sediment. PMID:25197498
Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California. PMID:25197496
Non-contiguous finished genome sequence and description of Alistipes ihumii sp. nov. PMID:25197494
Genomic analysis of Skermanella stibiiresistens type strain SB22 (T.). PMID:25197493
Non-contiguous finished genome sequence and description of Anaerococcus provenciensis sp. nov. PMID:25197492
Genome sequence and description of Bacteroides timonensis sp. nov. PMID:25197491
Genome sequence of Microvirga lupini strain LUT6(T), a novel Lupinus alphaproteobacterial microsymbiont from Texas. PMID:25197490
Non-contiguous finished genome sequence and description of Collinsella massiliensis sp. nov. PMID:25197489
Genome sequence and description of Corynebacterium ihumii sp. nov. PMID:25197488
Non-contiguous finished genome sequence of Staphylococcus capitis CR01 (pulsetype NRCS-A). PMID:25197487
Genome sequence of the Thermotoga thermarum type strain (LA3(T)) from an African solfataric spring. PMID:25197486
The complete genome sequence of Clostridium indolis DSM 755(T.). PMID:25197485
Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279(T)), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia. PMID:25197484
Complete genome sequence of the Radiation-Resistant bacterium Rubrobacter radiotolerans RSPS-4. PMID:25197483
Non-contiguous finished genome sequence and description of Bacillus massilioalgeriensis sp. nov. PMID:25197482
Non-contiguous finished genome sequence and description of Paenibacillus gorillae sp. nov. PMID:25197481
High quality draft genome sequence of the slightly halophilic bacterium Halomonas zhanjiangensis type strain JSM 078169(T) (DSM 21076(T)) from a sea urchin in southern China. PMID:25197480
Non contiguous-finished genome sequence and description of Clostridium jeddahense sp. nov. PMID:25197479
Non-contiguous finished genome sequence and description of Corynebacterium jeddahense sp. nov. PMID:25197478
Non contiguous-finished genome sequence and description of Enorma timonensis sp. nov. PMID:25197477
Non-contiguous finished genome sequence of Corynebacterium timonense type strain 5401744(T.). PMID:25197476
Complete genome sequence of invertebrate iridovirus IIV22A, a variant of IIV22, isolated originally from a blackfly larva. PMID:25197475
The Genome Sequence of a Type ST239 Methicillin-Resistant Staphylococcus aureus Isolate from a Malaysian Hospital. PMID:25197474
Complete genome sequence of the Phaeobacter gallaeciensis type strain CIP 105210(T) (= DSM 26640(T) = BS107(T)). PMID:25197473
Genome sequence of the pink to light reddish-pigmented Rubellimicrobium mesophilum type strain (DSM 19309(T)), a representative of the Roseobacter group isolated from soil, and emended description of the species. PMID:25197472
Complete genome sequence of Thalassolituus oleivorans R6-15, an obligate hydrocarbonoclastic marine bacterium from the Arctic Ocean. PMID:25197471
Draft genome sequence of Dyadobacter tibetensis type strain (Y620-1) isolated from glacial ice. PMID:25197470
Genome sequence and description of Nesterenkonia massiliensis sp. nov. strain NP1(T.). PMID:25197469
Genome sequence of the Wenxinia marina type strain (DSM 24838(T)), a representative of the Roseobacter group isolated from oilfield sediments. PMID:25197468
Complete genome sequence of the bacteriochlorophyll a-containing Roseibacterium elongatum type strain (DSM 19469(T)), a representative of the Roseobacter group isolated from Australian coast sand. PMID:25197467
Genome analysis of Desulfotomaculum gibsoniae strain Groll(T) a highly versatile Gram-positive sulfate-reducing bacterium. PMID:25197466
Non-contiguous finished genome sequence and description of Gorillibacterium massiliense gen. nov, sp. nov., a new member of the family Paenibacillaceae. PMID:25197465
Non-contiguous finished genome sequence and description of Bacteroides neonati sp. nov., a new species of anaerobic bacterium. PMID:25197464
High quality draft genome sequence of Olivibacter sitiensis type strain (AW-6(T)), a diphenol degrader with genes involved in the catechol pathway. PMID:25197463
Draft genome sequence of Bacillus amyloliquefaciens HB-26. PMID:25197462
Complete Genome sequence of Burkholderia phymatum STM815(T), a broad host range and efficient nitrogen-fixing symbiont of Mimosa species. PMID:25197461
High quality draft genome sequence of Staphylococcus cohnii subsp. cohnii strain hu-01. PMID:25197460
Draft genome sequences and description of Lactobacillus rhamnosus strains L31, L34, and L35. PMID:25197459
Non-contiguous finished genome sequence of Anoxybacillus flavithermus subsp. yunnanensis type strain (E13(T)), a strictly thermophilic and organic solvent-tolerant bacterium. PMID:25197458
Complete genome of the switchgrass endophyte Enterobacter clocace P101. PMID:25197457
Complete genome sequence of a plant associated bacterium Bacillus amyloliquefaciens subsp. plantarum UCMB5033. PMID:25197456
Non-contiguous finished genome sequence and description of Fenollaria massiliensis gen. nov., sp. nov., a new genus of anaerobic bacterium. PMID:25197455
Genome sequence and emended description of Leisingera nanhaiensis strain DSM 24252(T) isolated from marine sediment. PMID:25197454
High quality draft genome sequence of Streptomyces sp. strain AW19M42 isolated from a sea squirt in Northern Norway. PMID:25197453
Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans. PMID:25197452
Genome sequence of the anaerobic bacterium Bacillus sp. strain ZYK, a selenite and nitrate reducer from paddy soil. PMID:25197451
Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome. PMID:25197450
High-quality draft genome sequence of nematocidal Bacillus thuringiensis Sbt003. PMID:25197449
Draft genome sequence of Gluconobacter thailandicus NBRC 3257. PMID:25197448
Genome sequence of the Medicago-nodulating Ensifer meliloti commercial inoculant strain RRI128. PMID:25197447
Genomic analysis of Agrobacterium radiobacter DSM 30147(T) and emended description of A. radiobacter (Beijerinck and van Delden 1902) Conn 1942 (Approved Lists 1980) emend. Sawada et al. 1993. PMID:25197445
Complete genome sequence of Anabaena variabilis ATCC 29413. PMID:25197444
Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2232 from Karijini National Park, Australia. PMID:25197442
Non-contiguous finished genome sequence and description of Halopiger goleamassiliensis sp. nov. PMID:25197441
Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2230 from Karijini National Park, Australia. PMID:25197440
Genome sequence of the Listia angolensis microsymbiont Microvirga lotononidis strain WSM3557(T.). PMID:25197439
Genome sequence of Rhizobium leguminosarum bv trifolii strain WSM1689, the microsymbiont of the one flowered clover Trifolium uniflorum. PMID:25197438
Genome sequence of Ensifer medicae strain WSM1115; an acid-tolerant Medicago-nodulating microsymbiont from Samothraki, Greece. PMID:25197437
Genome sequence of the squalene-degrading bacterium Corynebacterium terpenotabidum type strain Y-11(T) (= DSM 44721(T)). PMID:25197436
Genome sequence of the chromate-resistant bacterium Leucobacter salsicius type strain M1-8(T.). PMID:25197435
Genome sequence of Burkholderia mimosarum strain LMG 23256(T), a Mimosa pigra microsymbiont from Anso, Taiwan. PMID:25197434
Genome sequence of Ensifer arboris strain LMG 14919(T); a microsymbiont of the legume Prosopis chilensis growing in Kosti, Sudan. PMID:25197433
Complete genome sequence of Mesorhizobium ciceri bv. biserrulae type strain (WSM1271(T)). PMID:25197432
Complete genome sequence of Granulicella tundricola type strain MP5ACTX9(T), an Acidobacteria from tundra soil. PMID:25197431
A sentinel protein assay for simultaneously quantifying cellular processes. PMID:25194849
Deep proteomic evaluation of primary and cell line motoneuron disease models delineates major differences in neuronal characteristics. PMID:25193168
Profiles of the auditory epithelia related microRNA expression in neonatal and adult rats. PMID:25192719
Discovering study-specific gene regulatory networks. PMID:25191999
Elucidating gene function and function evolution through comparison of co-expression networks of plants. PMID:25191328
A combined transgenic proteomic analysis and regulated trafficking of neuroligin-2. PMID:25190809
Global regulation of a differentiation MAPK pathway in yeast. PMID:25189875
MYCN repression of Lifeguard/FAIM2 enhances neuroblastoma aggressiveness. PMID:25188511
Research resources: comparative microRNA profiles in human corona radiata cells and cumulus oophorus cells detected by next-generation small RNA sequencing. PMID:25188034
Differentially-expressed genes in rice infected by Xanthomonas oryzae pv. oryzae relative to a flagellin-deficient mutant reveal potential functions of flagellin in host-pathogen interactions. PMID:25187853
Genetic analysis of DEFECTIVE KERNEL1 loop function in three-dimensional body patterning in Physcomitrella patens. PMID:25185121
Systematic screening reveals a role for BRCA1 in the response to transcription-associated DNA damage. PMID:25184681
FSim: a novel functional similarity search algorithm and tool for discovering functionally related gene products. PMID:25184141
Transcriptomic dissection of the rice-Burkholderia glumae interaction. PMID:25183458
BioModels linked dataset. PMID:25182954
Sequential transcriptional changes dictate safe and effective antigen-specific immunotherapy. PMID:25182274
A class-information-based penalized matrix decomposition for identifying plants core genes responding to abiotic stresses. PMID:25180509
Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities. PMID:25179155
Synergistic effects of combined DNA methyltransferase inhibition and MBD2 depletion on breast cancer cells; MBD2 depletion blocks 5-aza-2'-deoxycytidine-triggered invasiveness. PMID:25178277
An overview of the neurobiology of suicidal behaviors as one meta-system. PMID:25178164
PSEA-Quant: a protein set enrichment analysis on label-free and label-based protein quantification data. PMID:25177766
Systems-based analyses of brain regions functionally impacted in Parkinson's disease reveals underlying causal mechanisms. PMID:25170892
Global population-specific variation in miRNA associated with cancer risk and clinical biomarkers. PMID:25169894
Unbiased functional clustering of gene variants with a phenotypic-linkage network. PMID:25166029
Average oxidation state of carbon in proteins. PMID:25165594
The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective. PMID:25161254
Integration of molecular network data reconstructs Gene Ontology. PMID:25161252
Unveiling new biological relationships using shared hits of chemical screening assay pairs. PMID:25161250
HubAlign: an accurate and efficient method for global alignment of protein-protein interaction networks. PMID:25161231
Identifying transcription factor complexes and their roles. PMID:25161228
Broad-Enrich: functional interpretation of large sets of broad genomic regions. PMID:25161225
Making proteomics data accessible and reusable: current state of proteomics databases and repositories. PMID:25158685
Overview of the gene ontology task at BioCreative IV. PMID:25157073
Functional and genomic context in pathway analysis of GWAS data. PMID:25154796
A set of structural features defines the cis-regulatory modules of antenna-expressed genes in Drosophila melanogaster. PMID:25153327
Co-ordination and divergence of cell-specific transcription and translation of genes in arabidopsis root cells. PMID:25149544
Evaluating the Good Ontology Design Guideline (GoodOD) with the ontology quality requirements and evaluation method and metrics (OQuaRE). PMID:25148262
Genome-wide analysis of miRNA signature in the APPswe/PS1ΔE9 mouse model of alzheimer's disease. PMID:25148207
Phosphorylation site dynamics of early T-cell receptor signaling. PMID:25147952
Mining 3D patterns from gene expression temporal data: a new tricluster evaluation measure. PMID:25143987
De novo transcriptome of the desert beetle Microdera punctipennis (Coleoptera: Tenebrionidae) using Illumina RNA-seq technology. PMID:25142502
The genome of Eimeria falciformis--reduction and specialization in a single host apicomplexan parasite. PMID:25142335
From pathways to networks: connecting dots by establishing protein-protein interaction networks in signaling pathways using affinity purification and mass spectrometry. PMID:25137225
High atomic weight, high-energy radiation (HZE) induces transcriptional responses shared with conventional stresses in addition to a core "DSB" response specific to clastogenic treatments. PMID:25136344
Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers. PMID:25136101
A novel method for functional annotation prediction based on combination of classification methods. PMID:25133242
Identification of modules related to programmed cell death in CHD based on EHEN. PMID:25133163
A tree of cellular life inferred from a genomic census of molecular functions. PMID:25128982
Transcriptome sequencing and analysis of the zoonotic parasite Spirometra erinacei spargana (plerocercoids). PMID:25128015
Transcriptional landscape of glomerular parietal epithelial cells. PMID:25127402
PlantCAZyme: a database for plant carbohydrate-active enzymes. PMID:25125445
SNP identification by transcriptome sequencing and candidate gene-based association analysis for heat tolerance in the bay scallop Argopecten irradians. PMID:25121601
Identification of genes in HepG2 cells that respond to DNA methylation and histone deacetylation inhibitor treatment. PMID:25120605
Identifying a polymorphic 'switch' that influences miRNAs' regulation of a myasthenia gravis risk pathway. PMID:25118158
Heterosis in early maize ear inflorescence development: a genome-wide transcription analysis for two maize inbred lines and their hybrid. PMID:25116687
Grouping annotations on the subcellular layered interactome demonstrates enhanced autophagy activity in a recurrent experimental autoimmune uveitis T cell line. PMID:25116327
Modeling dynamic functional relationship networks and application to ex vivo human erythroid differentiation. PMID:25115705
Pathway analysis approaches for rare and common variants: insights from Genetic Analysis Workshop 18. PMID:25112195
Transcriptome instability as a molecular pan-cancer characteristic of carcinomas. PMID:25109687
Lean Big Data integration in systems biology and systems pharmacology. PMID:25109570
Global transcriptome-wide analysis of CIK cells identify distinct roles of IL-2 and IL-15 in acquisition of cytotoxic capacity against tumor. PMID:25108500
Genome-wide association analyses identify variants in developmental genes associated with hypospadias. PMID:25108383
A comprehensive proteomic view of responses of A549 type II alveolar epithelial cells to human respiratory syncytial virus infection. PMID:25106423
Protein localization analysis of essential genes in prokaryotes. PMID:25105358
A network-based approach to dissect the cilia/centrosome complex interactome. PMID:25102769
Modeling sequence and function similarity between proteins for protein functional annotation. PMID:25101328
Phenotypic profiling of ABC transporter coding genes in Myxococcus xanthus. PMID:25101061
Expression analysis of miRNA and target mRNAs in esophageal cancer. PMID:25098614
Serum miRNA signature in Moyamoya disease. PMID:25093848
Wnt pathway activation increases hypoxia tolerance during development. PMID:25093834
CSEO - the Cigarette Smoke Exposure Ontology. PMID:25093069
Generalising semantic category disambiguation with large lexical resources for fun and profit. PMID:25093067
Genome-wide analysis of gene expression in human embryonic tooth germ. PMID:25092397
Interactive transcriptome analysis of malaria patients and infecting Plasmodium falciparum. PMID:25091627
Concept mapping One-Carbon Metabolism to model future ontologies for nutrient-gene-phenotype interactions. PMID:25091042
Genome-wide association studies identify the loci for 5 exterior traits in a Large White × Minzhu pig population. PMID:25090094
Genome-wide screening and co-expression network analysis identify recurrence-specific biomarkers of esophageal squamous cell carcinoma. PMID:25087095
Gene set enrichment analysis for multiple continuous phenotypes. PMID:25086605
Phen-Gen: combining phenotype and genotype to analyze rare disorders. PMID:25086502
Does estrogen deficiency cause lacrimal gland inflammation and aqueous-deficient dry eye in mice? PMID:25084452
Molecular characterization and differential expression of olfactory genes in the antennae of the black cutworm moth Agrotis ipsilon. PMID:25083706
Integration of proteomic and transcriptomic profiles identifies a novel PDGF-MYC network in human smooth muscle cells. PMID:25080971
DNA-damage-induced differentiation of leukaemic cells as an anti-cancer barrier. PMID:25079327
Functional and genetic analysis of the colon cancer network. PMID:25079297
Concordance of deregulated mechanisms unveiled in underpowered experiments: PTBP1 knockdown case study. PMID:25079003
Furby: fuzzy force-directed bicluster visualization. PMID:25078951
Integrative genomics of chronic obstructive pulmonary disease. PMID:25078622
Hypoxia adaptations in the grey wolf (Canis lupus chanco) from Qinghai-Tibet Plateau. PMID:25078401
Profiling dose-dependent activation of p53-mediated signaling pathways by chemicals with distinct mechanisms of DNA damage. PMID:25078064
Fast and sensitive alignment of microbial whole genome sequencing reads to large sequence datasets on a desktop PC: application to metagenomic datasets and pathogen identification. PMID:25077800
Mapping Mental Function to Brain Structure: How Can Cognitive Neuroimaging Succeed? PMID:25076977
The genome of the Tiger Milk mushroom, Lignosus rhinocerotis, provides insights into the genetic basis of its medicinal properties. PMID:25073817
Role of Blimp-1 in programing Th effector cells into IL-10 producers. PMID:25073792
BC4GO: a full-text corpus for the BioCreative IV GO task. PMID:25070993
The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation. PMID:25068035
Integrative proteomic analysis of the NMDA NR1 knockdown mouse model reveals effects on central and peripheral pathways associated with schizophrenia and autism spectrum disorders. PMID:25061506
iRegulon: from a gene list to a gene regulatory network using large motif and track collections. PMID:25058159
Integrative genomic analysis for the discovery of biomarkers in prostate cancer. PMID:25057237
The cell envelope proteome of Aggregatibacter actinomycetemcomitans. PMID:25055881
A tri-component conservation strategy reveals highly confident microRNA-mRNA interactions and evolution of microRNA regulatory networks. PMID:25054916
A dedicated database system for handling multi-level data in systems biology. PMID:25053973
Systematic permutation testing in GWAS pathway analyses: identification of genetic networks in dilated cardiomyopathy and ulcerative colitis. PMID:25052024
Plasma proteomic changes during hypothermic and normothermic cardiopulmonary bypass in aortic surgeries. PMID:25050567
Paradigm of Time-sequence Development of the Intestine of Suckling Piglets with Microarray. PMID:25049506
biDCG: a new method for discovering global features of DNA microarray data via an iterative re-clustering procedure. PMID:25047553
Accurate in silico identification of species-specific acetylation sites by integrating protein sequence-derived and functional features. PMID:25042424
Genome-wide pathway analysis of a genome-wide association study on Alzheimer's disease. PMID:25037741
Genomic profiling of human Leishmania braziliensis lesions identifies transcriptional modules associated with cutaneous immunopathology. PMID:25036052
Copy number variable microRNAs in schizophrenia and their neurodevelopmental gene targets. PMID:25034949
Transcriptome sequencing and developmental regulation of gene expression in Anopheles aquasalis. PMID:25033462
Integrative omics analysis. A study based on Plasmodium falciparum mRNA and protein data. PMID:25033389
Bioinformatic analysis of proteomics data. PMID:25033288
The common ground of genomics and systems biology. PMID:25033072
Data integration in the era of omics: current and future challenges. PMID:25032990
Annexin V incorporated into influenza virus particles inhibits gamma interferon signaling and promotes viral replication. PMID:25031344
DBSecSys: a database of Burkholderia mallei secretion systems. PMID:25030112
Pathologic mechanical stress and endotoxin exposure increases lung endothelial microparticle shedding. PMID:25029266
OMIT: dynamic, semi-automated ontology development for the microRNA domain. PMID:25025130
De novo sequencing and comparative analysis of holy and sweet basil transcriptomes. PMID:25015319
A large number of nuclear genes in the human parasite blastocystis require mRNA polyadenylation to create functional termination codons. PMID:25015079
Transcriptome analysis of the differences in gene expression between testis and ovary in green mud crab (Scylla paramamosain). PMID:25015001
Modelling epigenetic regulation of gene expression in 12 human cell types reveals combinatorial patterns of cell-type-specific genes. PMID:25014377
Discovery and comparative profiling of microRNAs in representative monopodial bamboo (Phyllostachys edulis) and sympodial bamboo (Dendrocalamus latiflorus). PMID:25013900
Oil accumulation mechanisms of the oleaginous microalga Chlorella protothecoides revealed through its genome, transcriptomes, and proteomes. PMID:25012212
Genetic variation in DNA repair pathways and risk of non-Hodgkin's lymphoma. PMID:25010664
Fumaric acid esters can block pro-inflammatory actions of human CRP and ameliorate metabolic disturbances in transgenic spontaneously hypertensive rats. PMID:25010431
Why functions are not special dispositions: an improved classification of realizables for top-level ontologies. PMID:25009736
The ATXN2-SH2B3 locus is associated with peripheral arterial disease: an electronic medical record-based genome-wide association study. PMID:25009551
Abnormalities in human pluripotent cells due to reprogramming mechanisms. PMID:25008523
An integrative analysis of meningioma tumors reveals the determinant genes and pathways of malignant transformation. PMID:25003081
eXamine: exploring annotated modules in networks. PMID:25002203
Proteomic mapping of the human mitochondrial intermembrane space in live cells via ratiometric APEX tagging. PMID:25002142
Placental gene-expression profiles of intrahepatic cholestasis of pregnancy reveal involvement of multiple molecular pathways in blood vessel formation and inflammation. PMID:25001852
Expanding the computational toolbox for mining cancer genomes. PMID:25001846
Developmental cell fate and virulence are linked to trehalose homeostasis in Cryptococcus neoformans. PMID:25001408
RNA-Seq for gene identification and transcript profiling of three Stevia rebaudiana genotypes. PMID:25001368
Comparing reference-based RNA-Seq mapping methods for non-human primate data. PMID:25001289
Field-omics-understanding large-scale molecular data from field crops. PMID:24999347
Interdisciplinary perspectives on the development, integration, and application of cognitive ontologies. PMID:24999329
Proteomic analysis of solid pseudopapillary tumor of the pancreas reveals dysfunction of the endoplasmic reticulum protein processing pathway. PMID:24997997
Two-layer modular analysis of gene and protein networks in breast cancer. PMID:24997799
Partial least squares based gene expression analysis in renal failure. PMID:24997640
Expansion of biological pathways based on evolutionary inference. PMID:24995987
The domain landscape of virus-host interactomes. PMID:24991570
Analysis of gene expression changes in peach leaves in response to Plum pox virus infection using RNA-Seq. PMID:24989162
Inference of transcriptional networks in Arabidopsis through conserved noncoding sequence analysis. PMID:24989046
Archaea: the first domain of diversified life. PMID:24987307
Minimal metabolic pathway structure is consistent with associated biomolecular interactions. PMID:24987116
ChIP-seq analysis of androgen receptor in LNCaP cell line. PMID:24985976
Genome sequencing of four Aureobasidium pullulans varieties: biotechnological potential, stress tolerance, and description of new species. PMID:24984952
Characterization of transcriptional complexity during adipose tissue development in bovines of different ages and sexes. PMID:24983926
Brain Proteome Changes Induced by Olfactory Learning in Drosophila. PMID:24983411
Elucidation of the evolutionary expansion of phosphorylation signaling networks using comparative phosphomotif analysis. PMID:24981518
Ranking non-synonymous single nucleotide polymorphisms based on disease concepts. PMID:24980617
The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience. PMID:24980485
Identification of gene ontologies linked to prefrontal-hippocampal functional coupling in the human brain. PMID:24979789
Building a hierarchical organization of protein complexes out of protein association data. PMID:24978199
Differentially expressed plasma microRNAs and the potential regulatory function of Let-7b in chronic thromboembolic pulmonary hypertension. PMID:24978044
Genome sequence of Ensifer medicae strain WSM1369; an effective microsymbiont of the annual legume Medicago sphaerocarpos. PMID:24976897
Complete genome sequence of Mesorhizobium australicum type strain (WSM2073(T)). PMID:24976896
Non-contiguous finished genome sequence and description of Holdemania massiliensis sp. nov. PMID:24976895
Genome sequence of the Lebeckia ambigua-nodulating "Burkholderia sprentiae" strain WSM5005(T.). PMID:24976894
Non-contiguous finished genome sequence and description of Oceanobacillus massiliensis sp. nov. PMID:24976893
Complete genome sequence of Enterobacter sp. IIT-BT 08: A potential microbial strain for high rate hydrogen production. PMID:24976892
Non-contiguous finished genome sequence of Phocaeicola abscessus type strain 7401987(T.). PMID:24976891
Genome sequence of Phaeobacter inhibens type strain (T5(T)), a secondary metabolite producing representative of the marine Roseobacter clade, and emendation of the species description of Phaeobacter inhibens. PMID:24976890
Permanent draft genome sequences of the symbiotic nitrogen fixing Ensifer meliloti strains BO21CC and AK58. PMID:24976889
Genome sequence of Ensifer meliloti strain WSM1022; a highly effective microsymbiont of the model legume Medicago truncatula A17. PMID:24976888
Genome sequence of Ensifer sp. TW10; a Tephrosia wallichii (Biyani) microsymbiont native to the Indian Thar Desert. PMID:24976887
Complete genome sequence of Mesorhizobium opportunistum type strain WSM2075(T.). PMID:24976886
Genome sequence of the Trifolium rueppellianum -nodulating Rhizobium leguminosarum bv. trifolii strain WSM2012. PMID:24976885
Genome sequence of the lupin-nodulating Bradyrhizobium sp. strain WSM1417. PMID:24976884
Genome sequence of the South American clover-nodulating Rhizobium leguminosarum bv. trifolii strain WSM597. PMID:24976883
Genome sequence of the Ornithopus/Lupinus-nodulating Bradyrhizobium sp. strain WSM471. PMID:24976882
Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain TA1. PMID:24976881
Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI943. PMID:24976880
Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI565. PMID:24976879
ChIPseek, a web-based analysis tool for ChIP data. PMID:24974934
Exploring function prediction in protein interaction networks via clustering methods. PMID:24972109
Mutational analysis of primary central nervous system lymphoma. PMID:24970810
Chromosomal instability selects gene copy-number variants encoding core regulators of proliferation in ER+ breast cancer. PMID:24970479
Computational prediction of disease microRNAs in domestic animals. PMID:24970281
Exosomes from docetaxel-resistant breast cancer cells alter chemosensitivity by delivering microRNAs. PMID:24969560
A virulent strain of deformed wing virus (DWV) of honeybees (Apis mellifera) prevails after Varroa destructor-mediated, or in vitro, transmission. PMID:24968198
Genome-wide identification of transcription factors and transcription-factor binding sites in oleaginous microalgae Nannochloropsis. PMID:24965723
A vascular biology network model focused on inflammatory processes to investigate atherogenesis and plaque instability. PMID:24965703
Correlating information contents of gene ontology terms to infer semantic similarity of gene products. PMID:24963342
Detection of genome-wide copy number variations in two chicken lines divergently selected for abdominal fat content. PMID:24962627
Gene Set Enrichment Analysis (GSEA) of Toxoplasma gondii expression datasets links cell cycle progression and the bradyzoite developmental program. PMID:24962434
Cancer stem cells and cisplatin-resistant cells isolated from non-small-lung cancer cell lines constitute related cell populations. PMID:24961511
Novel insights into the regulatory architecture of CD4+ T cells in rheumatoid arthritis. PMID:24959711
Gene expression profile analysis in epilepsy by using the partial least squares method. PMID:24959624
Regulation of gene expression by the BLM helicase correlates with the presence of G-quadruplex DNA motifs. PMID:24958861
Metabolic Consequences of TGFb Stimulation in CulturedPrimary Mouse Hepatocytes Screened from Transcript Data with ModeScore . PMID:24957771
What mRNA Abundances Can Tell us about Metabolism. PMID:24957650
PubServer: literature searches by homology. PMID:24957597
Shared signatures of social stress and aging in peripheral blood mononuclear cell gene expression profiles. PMID:24956926
Transcriptome profiling of the theca interna from bovine ovarian follicles during atresia. PMID:24956388
Genomics: moving behavioural ecology beyond the phenotypic gambit. PMID:24954950
Controllability and observability analysis for vertex domination centrality in directed networks. PMID:24954137
Adolescent mouse takes on an active transcriptomic expression during postnatal cerebral development. PMID:24953867
Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators. PMID:24953126
The emerging era of genomic data integration for analyzing splice isoform function. PMID:24951248
Toxin diversity revealed by a transcriptomic study of Ornithoctonus huwena. PMID:24949878
Proteomics analysis of the non-muscle myosin heavy chain IIa-enriched actin-myosin complex reveals multiple functions within the podocyte. PMID:24949636
IIS--Integrated Interactome System: a web-based platform for the annotation, analysis and visualization of protein-metabolite-gene-drug interactions by integrating a variety of data sources and tools. PMID:24949626
Breast cancer prognosis risk estimation using integrated gene expression and clinical data. PMID:24949450
Sex- and tissue-specific profiles of chemosensory gene expression in a herbivorous gall-inducing fly (Diptera: Cecidomyiidae). PMID:24948464
Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast. PMID:24947676
Descending controls modulate inflammatory joint pain and regulate CXC chemokine and iNOS expression in the dorsal horn. PMID:24947159
Predicting targeted drug combinations based on Pareto optimal patterns of coexpression network connectivity. PMID:24944582
Fine-scale population epigenetic structure in relation to gastrointestinal parasite load in red grouse (Lagopus lagopus scotica). PMID:24943398
The genome of the white-rot fungus Pycnoporus cinnabarinus: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown. PMID:24942338
Comparison of the transcriptomes of ginger (Zingiber officinale Rosc.) and mango ginger (Curcuma amada Roxb.) in response to the bacterial wilt infection. PMID:24940878
Integration of partial least squares and Monte Carlo gene expression analysis in coronary artery disease. PMID:24940402
Exceptionally abundant exceptions: comprehensive characterization of intrinsic disorder in all domains of life. PMID:24939692
Harnessing natural sequence variation to dissect posttranscriptional regulatory networks in yeast. PMID:24938291
Fed state prior to hemorrhagic shock and polytrauma in a porcine model results in altered liver transcriptomic response. PMID:24937255
Genome-wide analysis of Sphingomonas wittichii RW1 behaviour during inoculation and growth in contaminated sand. PMID:24936762
A rare sequence variant in intron 1 of THAP1 is associated with primary dystonia. PMID:24936516
Comparative genomics of Riemerella anatipestifer reveals genetic diversity. PMID:24935762
SemFunSim: a new method for measuring disease similarity by integrating semantic and gene functional association. PMID:24932637
Robust clinical outcome prediction based on Bayesian analysis of transcriptional profiles and prior causal networks. PMID:24932007
Using association rule mining to determine promising secondary phenotyping hypotheses. PMID:24932005
Inferring gene ontologies from pairwise similarity data. PMID:24932003
New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence. PMID:24931987
Improving functional annotation for industrial microbes: a case study with Pichia pastoris. PMID:24929579
Detecting overlapping protein complexes based on a generative model with functional and topological properties. PMID:24928559
On the crucial cerebellar wound healing-related pathways and their cross-talks after traumatic brain injury in Danio rerio. PMID:24926785
Sequencing and characterization of the transcriptome of half-smooth tongue sole (Cynoglossus semilaevis). PMID:24924151
Egas: a collaborative and interactive document curation platform. PMID:24923820
Negative example selection for protein function prediction: the NoGO database. PMID:24922051
Inferring gene family histories in yeast identifies lineage specific expansions. PMID:24921666
Imatinib treatment causes substantial transcriptional changes in adult Schistosoma mansoni in vitro exhibiting pleiotropic effects. PMID:24921634
"Stop Ne(c)king around": How interactomics contributes to functionally characterize Nek family kinases. PMID:24921005
The genome of Eucalyptus grandis. PMID:24919147
Integrated pathway clusters with coherent biological themes for target prioritisation. PMID:24918583
dbCerEx: a web-based database for the analysis of cervical cancer transcriptomes. PMID:24918550
Increasing the precision of orthology-based complex prediction through network alignment. PMID:24918034
A biologist, a statistician, and a bioinformatician walk into a conference room… and walk out with a great metagenomics project plan. PMID:24917875
The global phosphoproteome of Chlamydomonas reinhardtii reveals complex organellar phosphorylation in the flagella and thylakoid membrane. PMID:24917610
A novel method for gathering and prioritizing disease candidate genes based on construction of a set of disease-related MeSH® terms. PMID:24917541
Kidney cancer is characterized by aberrant methylation of tissue-specific enhancers that are prognostic for overall survival. PMID:24916699
Multi-tissue transcriptomics of the black widow spider reveals expansions, co-options, and functional processes of the silk gland gene toolkit. PMID:24916340
Genetics: Pinpointing a hotspot in adrenal Cushing syndrome. PMID:24913521
Gene co-expression network analysis identifies porcine genes associated with variation in Salmonella shedding. PMID:24912583
CELLO2GO: a web server for protein subCELlular LOcalization prediction with functional gene ontology annotation. PMID:24911789
MOPED 2.5--an integrated multi-omics resource: multi-omics profiling expression database now includes transcriptomics data. PMID:24910945
Ontology-supported research on vaccine efficacy, safety and integrative biological networks. PMID:24909153
Event-based text mining for biology and functional genomics. PMID:24907365
Large-effect pleiotropic or closely linked QTL segregate within and across ten US cattle breeds. PMID:24906442
Quantitative temporal viromics: an approach to investigate host-pathogen interaction. PMID:24906157
Network Assessor: an automated method for quantitative assessment of a network's potential for gene function prediction. PMID:24904632
Using semantic web technologies to annotate and align microarray designs. PMID:24904201
Digital expression profiling of the compartmentalized translatome of Purkinje neurons. PMID:24904046
Primary sequence contribution to the optical function of the eye lens. PMID:24903231
Integrated pathway-based approach identifies association between genomic regions at CTCF and CACNB2 and schizophrenia. PMID:24901509
Coiled-coil proteins facilitated the functional expansion of the centrosome. PMID:24901223 -
The Gene Ontology (GO) database and informatics resource
PubMed citations: 1606.
1606 articles citing: The Gene Ontology (GO) database and informatics resource
Identification of Vesicle Transport Proteins via Hypergraph Regularized K-Local Hyperplane Distance Nearest Neighbour Model. PMID:35910197
Comparative Transcriptome Analysis Reveals Regulatory Factors Involved in Vibrio Parahaemolyticus Biofilm Formation. PMID:35899046
Comprehensive Analysis of Immune-Related Metabolic Genes in Lung Adenocarcinoma. PMID:35898471
Characterizing the extracellular matrix transcriptome of cervical, endometrial, and uterine cancers. PMID:35898192
Analyzing the Systems Biology Effects of COVID-19 mRNA Vaccines to Assess Their Safety and Putative Side Effects. PMID:35889989
Multi-Level Biological Network Analysis and Drug Repurposing Based on Leukocyte Transcriptomics in Severe COVID-19: In Silico Systems Biology to Precision Medicine. PMID:35887528
Integrative Analyses of Transcriptomes to Explore Common Molecular Effects of Antipsychotic Drugs. PMID:35886854
Transcriptome Approach Reveals the Response Mechanism of Heimia myrtifolia (Lythraceae, Myrtales) to Drought Stress. PMID:35874015
orsum: a Python package for filtering and comparing enrichment analyses using a simple principle. PMID:35870894
Correlation Between the RNA Methylation Genes and Immune Infiltration and Prognosis of Patients with Hepatocellular Carcinoma: A Pan-Cancer Analysis. PMID:35860228
Activity-based protein profiling identifies alternating activation of enzymes involved in the bifidobacterium shunt pathway or mucin degradation in the gut microbiome response to soluble dietary fiber. PMID:35858888
A Computational Framework to Characterize the Cancer Drug Induced Effect on Aging Using Transcriptomic Data. PMID:35847024
Sub-GOFA: A tool for Sub-Gene Ontology function analysis in clonal mosaicism using semantic (logical) similarity. PMID:35815201
Construction of a Novel circRNA/miRNA/mRNA Regulatory Network to Explore the Potential Pathogenesis of Wilson's Disease. PMID:35784724
An automatic integrative method for learning interpretable communities of biological pathways. PMID:35769343
PolarMorphism enables discovery of shared genetic variants across multiple traits from GWAS summary statistics. PMID:35758773
Bioinformatics Approach Predicts Candidate Targets for SARS-CoV-2 Infections to COPD Patients. PMID:35747501
Genomic and Biological Profile of a Novel Bacteriophage, Vibrio phage Virtus, Which Improves Survival of Sparus aurata Larvae Challenged with Vibrio harveyi. PMID:35745484
SIN-3 functions through multi-protein interaction to regulate apoptosis, autophagy, and longevity in Caenorhabditis elegans. PMID:35732652
Integrated Microbiome and Host Transcriptome Profiles Link Parkinson's Disease to Blautia Genus: Evidence From Feces, Blood, and Brain. PMID:35722294
Editorial: Advancement in Gene Set Analysis: Gaining Insight From High-Throughput Data. PMID:35711947
Identification of FCER1G related to Activated Memory CD4+ T Cells Infiltration by Gene Co-expression Network and Construction of a Risk Prediction Module in Diffuse Large B-Cell Lymphoma. PMID:35711924
Dynamic transcriptome landscape of pulmonary tissues of rats infected with Paragonimus proliferus. PMID:35702118
Tissue Sampling and Homogenization with NIRL Enables Spatially Resolved Cell Layer Specific Proteomic Analysis of the Murine Intestine. PMID:35682811
In Vitro Cell Density Determines the Sensitivity of Hepatocarcinoma Cells to Ascorbate. PMID:35677156
A semantics, energy-based approach to automate biomodel composition. PMID:35657966
The Construction and Analysis of Immune Infiltration and Competing Endogenous RNA Network in Acute Ischemic Stroke. PMID:35656537
Identification of Key Prognostic Genes of Triple Negative Breast Cancer by LASSO-Based Machine Learning and Bioinformatics Analysis. PMID:35627287
Gene Expression Meta-Analysis of Potential Shared and Unique Pathways between Autoimmune Diseases under Anti-TNFα Therapy. PMID:35627163
Inhaled Corticosteroids Selectively Alter the Microbiome and Host Transcriptome in the Small Airways of Patients with Chronic Obstructive Pulmonary Disease. PMID:35625847
Immune-Related Protein Interaction Network in Severe COVID-19 Patients toward the Identification of Key Proteins and Drug Repurposing. PMID:35625619
m7G Methylation-Related Genes as Biomarkers for Predicting Overall Survival Outcomes for Hepatocellular Carcinoma. PMID:35620469
An immune gene signature to predict prognosis and immunotherapeutic response in lung adenocarcinoma. PMID:35581376
RNA-Seq Based Toxicity Analysis of Mesoporous Polydopamine Nanoparticles in Mice Following Different Exposure Routes. PMID:35573233
Dynamic Interplay between Structural Variations and 3D Genome Organization in Pancreatic Cancer. PMID:35570408
Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation. PMID:35546409
SNAIL Induces EMT and Lung Metastasis of Tumours Secreting CXCL2 to Promote the Invasion of M2-Type Immunosuppressed Macrophages in Colorectal Cancer. PMID:35541899
Artificial intelligence in cancer target identification and drug discovery. PMID:35538061
Response of the Anaerobic Methanotrophic Archaeon Candidatus "Methanoperedens nitroreducens" to the Long-Term Ferrihydrite Amendment. PMID:35509320
Gene-SCOUT: identifying genes with similar continuous trait fingerprints from phenome-wide association analyses. PMID:35474393
Co-Expression Networks Unveiled Long Non-Coding RNAs as Molecular Targets of Drugs Used to Treat Bipolar Disorder. PMID:35462908
Novel Protein-Protein Interactions Highlighting the Crosstalk between Hypoplastic Left Heart Syndrome, Ciliopathies and Neurodevelopmental Delays. PMID:35456433
Darling: A Web Application for Detecting Disease-Related Biomedical Entity Associations with Literature Mining. PMID:35454109
Identification of Immune-Related Key Genes as Potential Diagnostic Biomarkers of Sepsis in Children. PMID:35444449
Gene expression profiles provide insights into the survival strategies in deep-sea mussel (Bathymodiolus platifrons) of different developmental stages. PMID:35439939
B3GNT3 as a prognostic biomarker and correlation with immune cell infiltration in lung adenocarcinoma. PMID:35434016
Polymyxin B1 and E2 From Paenibacillus polymyxa Y-1 for Controlling Rice Bacterial Disease. PMID:35419296
InfersentPPI: Prediction of Protein-Protein Interaction Using Protein Sentence Embedding With Gene Ontology Information. PMID:35419026
The State of Data in Healthcare: Path Towards Standardization. PMID:35415409
Computational and network pharmacology studies of Phyllanthus emblica to tackle SARS-CoV-2. PMID:35399824
Identification of microRNA-mRNA-TF regulatory networks in periodontitis by bioinformatics analysis. PMID:35397550
Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax. PMID:35393424
Genome Assembly and Genome Annotation of Leishmania martiniquensis Isolated from a Leishmaniasis Patient in Thailand. PMID:35371566
iAcety-SmRF: Identification of Acetylation Protein by Using Statistical Moments and Random Forest. PMID:35323738
Identification of the Ferroptosis-Related Long Non-Coding RNAs Signature to Improve the Prognosis Prediction in Papillary Renal Cell Carcinoma. PMID:35310430
Network Preservation Analysis Reveals Dysregulated Synaptic Modules and Regulatory Hubs Shared Between Alzheimer's Disease and Temporal Lobe Epilepsy. PMID:35309145
Identification of a DNA damage repair gene-related signature for lung squamous cell carcinoma prognosis. PMID:35293140
Intrinsically disordered signaling proteins: Essential hub players in the control of stress responses in Saccharomyces cerevisiae. PMID:35290420
Improving protein-ligand docking and screening accuracies by incorporating a scoring function correction term. PMID:35289359
Comparative analysis of the daily brain transcriptomes of Asian particolored bat. PMID:35264653
The Role of Intestinal Microbiota in Regulating the Metabolism of Bile Acids Is Conserved Across Vertebrates. PMID:35242120
Genome-wide transcriptome analysis of porcine epidemic diarrhea virus virulent or avirulent strain-infected porcine small intestinal epithelial cells. PMID:35234615
Transcriptomic Analysis of Fish Hosts Responses to Nervous Necrosis Virus. PMID:35215144
Identification of a new RNA-binding proteins-based signature for prognostic prediction in gastric cancer. PMID:35212295
Transcriptomics-Based Identification of Genes Related to Tapetum Degradation and Microspore Development in Lily. PMID:35205410
Weighted correlation network analysis revealed novel long non-coding RNAs for colorectal cancer. PMID:35194111
Targets and Potential Mechanism of Scutellaria baicalensis in Treatment of Primary Hepatocellular Carcinoma Based on Bioinformatics Analysis. PMID:35190740
Transcriptome Profiling During Muscadine Berry Development Reveals the Dynamic of Polyphenols Metabolism. PMID:35185966
Novel insight into pancreatic adenocarcinoma pathogenesis using liquid association analysis. PMID:35180880
Transcriptome-wide association study of coronary artery disease identifies novel susceptibility genes. PMID:35175464
Inferring Causation in Yeast Gene Association Networks With Kernel Logistic Regression. PMID:35173404
Transcription Factor Movement and Exercise-Induced Mitochondrial Biogenesis in Human Skeletal Muscle: Current Knowledge and Future Perspectives. PMID:35163441
Low-Level Laser Therapy Effects on Rat Blood Hemostasis Via Significant Alteration in Fibrinogen and Plasminogen Expression Level. PMID:35155144
Genomic Insights Into Cadmium Resistance of a Newly Isolated, Plasmid-Free Cellulomonas sp. Strain Y8. PMID:35154027
The Landscape of Aminoacyl-tRNA Synthetases Involved in Severe Acute Respiratory Syndrome Coronavirus 2 Infection. PMID:35153822
Data Integration Challenges for Machine Learning in Precision Medicine. PMID:35145977
Immune Infiltration of CD8+ T Cells in Patients With Diabetic Pancreatic Cancer Reduces the Malignancy of Cancer Tissues: An In Silico Study. PMID:35145483
PRDM paralogs antagonistically balance Wnt/β-catenin activity during craniofacial chondrocyte differentiation. PMID:35132438
A cluster of transcripts identifies a transition stage initiating leafy head growth in heading morphotypes of Brassica. PMID:35118736
Construction and Validation of a Newly Prognostic Signature for CRISPR-Cas9-Based Cancer Dependency Map Genes in Breast Cancer. PMID:35096059
Transcriptomic Insight into Underground Floral Differentiation in Erythronium japonicum. PMID:35087909
Host methylation predicts SARS-CoV-2 infection and clinical outcome. PMID:35072167
A novel gene functional similarity calculation model by utilizing the specificity of terms and relationships in gene ontology. PMID:35057740
Identification of the Key Immune-Related Genes in Chronic Obstructive Pulmonary Disease Based on Immune Infiltration Analysis. PMID:35018096
NETME: on-the-fly knowledge network construction from biomedical literature. PMID:35013714
Transcriptome Analysis Reveals Candidate Genes Involved in Light-Induced Primordium Differentiation in Pleurotus eryngii. PMID:35008859
N7-methylguanosine modification of lncRNAs in a rat model of hypoxic pulmonary hypertension: a comprehensive analysis. PMID:34996349
Absorbance or organization into ankylosis: a microarray analysis of haemarthrosis in a sheep model of temporomandibular joint trauma. PMID:34961493
A Novel Role for Histatin 5 in Combination with Zinc to Promote Commensalism in C. albicans Survivor Cells. PMID:34959564
Comprehensive analysis of chloroplast genome of Albizia julibrissin Durazz. (Leguminosae sp.). PMID:34940902
Amyloid-like aggregating proteins cause lysosomal defects in neurons via gain-of-function toxicity. PMID:34933920
Comprehensive analysis of the ceRNA network in coronary artery disease. PMID:34930980
Concept recognition as a machine translation problem. PMID:34920707
XDeathDB: a visualization platform for cell death molecular interactions. PMID:34907160
Computational modeling of human-nCoV protein-protein interaction network. PMID:34902553
Analysis of a circRNA-, miRNA-, and mRNA-associated ceRNA network reveals potential biomarkers in preeclampsia a ceRNA network in preeclampsia. PMID:34894939
S100A2 Is a Prognostic Biomarker Involved in Immune Infiltration and Predict Immunotherapy Response in Pancreatic Cancer. PMID:34887861
Identification of Galectin-3 as Potential Biomarkers for Renal Fibrosis by RNA-Sequencing and Clinicopathologic Findings of Kidney Biopsy. PMID:34869439
Artificial Intelligence in Functional Food Ingredient Discovery and Characterisation: A Focus on Bioactive Plant and Food Peptides. PMID:34868255
Building a reference transcriptome for Juniperus squamata (Cupressaceae) based on single-molecule real-time sequencing. PMID:34865616
RNAseq analysis of treatment-dependent signaling changes during inflammation in a mouse cutaneous wound healing model. PMID:34823472
RNA-Seq Reveals that Light and Darkness Are Different Stimuli in Freshwater Heterotrophic Actinobacteria. PMID:34790178
Rock inhibitor may compromise human induced pluripotent stem cells for cardiac differentiation in 3D. PMID:34786523
Chromosome-scale assembly reveals asymmetric paleo-subgenome evolution and targets for the acceleration of fungal resistance breeding in the nut crop, pecan. PMID:34778752
Transcriptomic Effects of Acute Ultraviolet Radiation Exposure on Two Syntrichia Mosses. PMID:34777431
Bioinformatics Analysis for Identifying Pertinent Pathways and Genes in Sepsis. PMID:34760021
A novel immune-related ceRNA network that predicts prognosis and immunotherapy response in lung adenocarcinoma. PMID:34734036
Characterization of Basal Transcriptomes Identifies Potential Metabolic and Virulence-Associated Adaptations Among Diverse Nontyphoidal Salmonella enterica Serovars. PMID:34721328
Whole transcriptome sequencing identifies key circRNAs, lncRNAs, and miRNAs regulating neurogenesis in developing mouse retina. PMID:34717547
Centrality of drug targets in protein networks. PMID:34715787
GFICLEE: ultrafast tree-based phylogenetic profile method inferring gene function at the genomic-wide level. PMID:34715785
Network-driven analysis of human-Plasmodium falciparum interactome: processes for malaria drug discovery and extracting in silico targets. PMID:34702263
Genomic Studies of White-Rot Fungus Cerrena unicolor SP02 Provide Insights into Food Safety Value-Added Utilization of Non-Food Lignocellulosic Biomass. PMID:34682256
Transcriptome and Metabolome Analysis Revealed the Freezing Resistance Mechanism in 60-Year-Old Overwintering Camellia sinensis. PMID:34681095
Association and Gene-Gene Interactions Study of Late-Onset Alzheimer's Disease in the Russian Population. PMID:34681041
Genomic Changes and Genetic Divergence of Vibrio alginolyticus Under Phage Infection Stress Revealed by Whole-Genome Sequencing and Resequencing. PMID:34671325
Experiment level curation of transcriptional regulatory interactions in neurodevelopment. PMID:34665801
Identification of a prognostic chemoresistance-related gene signature associated with immune microenvironment in breast cancer. PMID:34661511
RNA-Seq reveals different responses to drought in Neotropical trees from savannas and seasonally dry forests. PMID:34641780
Comparative Analysis of Unsupervised Protein Similarity Prediction Based on Graph Embedding. PMID:34630534
A Computational Framework to Identify Transcriptional and Network Differences between Hepatocellular Carcinoma and Normal Liver Tissue and Their Applications in Repositioning Drugs. PMID:34604388
A Combination of Genomics, Transcriptomics, and Genetics Provides Insights into the Mineral Weathering Phenotype of Pseudomonas azotoformans F77. PMID:34586903
Predicting metabolic pathway membership with deep neural networks by integrating sequential and ontology information. PMID:34579673
Analysis of PRX Gene Family and Its Function on Cell Lignification in Pears (Pyrus bretschneideri). PMID:34579408
In Silico Analysis to Explore Lineage-Independent and -Dependent Transcriptional Programs Associated with the Process of Endothelial and Neural Differentiation of Human Induced Pluripotent Stem Cells. PMID:34575270
Gene clusters based on OLIG2 and CD276 could distinguish molecular profiling in glioblastoma. PMID:34565408
Unveiling the transcriptomic complexity of Miscanthus sinensis using a combination of PacBio long read- and Illumina short read sequencing platforms. PMID:34551715
Deep GONet: self-explainable deep neural network based on Gene Ontology for phenotype prediction from gene expression data. PMID:34551707
Comprehensive Analysis of a Nine-Gene Signature Related to Tumor Microenvironment in Lung Adenocarcinoma. PMID:34540825
Comprehensive Analysis of circRNA Expression Profiles During Cervical Carcinogenesis. PMID:34532284
Identification of Novel Gene Signatures using Next-Generation Sequencing Data from COVID-19 Infection Models: Focus on Neuro-COVID and Potential Therapeutics. PMID:34531741
Can functional genomic diversity provide novel insights into mechanisms of community assembly? A pilot study from an invaded alpine streambed. PMID:34522362
RhoC Modulates Cell Junctions and Type I Interferon Response in Aggressive Breast Cancers. PMID:34513691
Full-length transcriptome analysis of Spodoptera frugiperda larval brain reveals detoxification genes. PMID:34513339
The chromosome-scale genome of Magnolia officinalis provides insight into the evolutionary position of magnoliids. PMID:34505009
Dermal Olfactory Receptor OR51B5 Is Essential for Survival and Collagen Synthesis in Human Dermal Fibroblast (Hs68 Cells). PMID:34502185
Air pollution-induced epigenetic changes: disease development and a possible link with hypersensitivity pneumonitis. PMID:34498177
Development of a defined medium for Corynebacterium glutamicum using urea as nitrogen source. PMID:34471588
ARMT: An automatic RNA-seq data mining tool based on comprehensive and integrative analysis in cancer research. PMID:34471489
Extracting Concepts for Precision Oncology from the Biomedical Literature. PMID:34457142
Drug repurposing for COVID-19 using computational screening: Is Fostamatinib/R406 a potential candidate? PMID:34455072
Epidermal PPARγ Is a Key Homeostatic Regulator of Cutaneous Inflammation and Barrier Function in Mouse Skin. PMID:34445339
Metatranscriptomic Analysis of Bacterial Communities on Laundered Textiles: A Pilot Case Study. PMID:34442670
Whole-Genome Differentially Hydroxymethylated DNA Regions among Twins Discordant for Cardiovascular Death. PMID:34440357
A convergent molecular network underlying autism and congenital heart disease. PMID:34411509
XOmiVAE: an interpretable deep learning model for cancer classification using high-dimensional omics data. PMID:34402865
Microarray Analysis of Differential Gene Expression Between Traumatic Temporomandibular Joint Fibrous and Bony Ankylosis in a Sheep Model. PMID:34400603
Bioinformatics Analysis of Potential Biomarkers and Pathway Identification for Major Depressive Disorder. PMID:34394704
Functional Analysis of Non-Genetic Resistance to Platinum in Epithelial Ovarian Cancer Reveals a Role for the MBD3-NuRD Complex in Resistance Development. PMID:34359703
FLAME: A Web Tool for Functional and Literature Enrichment Analysis of Multiple Gene Lists. PMID:34356520
Transcriptional Profiling During Neural Conversion. PMID:34324187
Exploiting the molecular basis of age and gender differences in outcomes of SARS-CoV-2 infections. PMID:34306570
The Compressed Vocabulary of Microbial Life. PMID:34305827
CD14 Involvement in Third-degree Skin Burn-induced Myocardial Injury via the MAPK Signaling Pathway. PMID:34297270
Dissecting the chromosome-level genome of the Asian Clam (Corbicula fluminea). PMID:34294825
Impact of Tenascin-C on Radiotherapy in a Novel Syngeneic Oral Squamous Cell Carcinoma Model With Spontaneous Dissemination to the Lymph Nodes. PMID:34290694
An integrative study of genetic variants with brain tissue expression identifies viral etiology and potential drug targets of multiple sclerosis. PMID:34284104
Transcriptome and proteome of the corm, leaf and flower of Hypoxis hemerocallidea (African potato). PMID:34283859
RNA sequencing indicates age-dependent shifts in the cardiac fibroblast transcriptome between fetal, neonatal, and adult developmental ages. PMID:34281425
Bioinformatic Analysis of Temporal and Spatial Proteome Alternations During Infections. PMID:34276775
Global Screening of LUBAC and OTULIN Interacting Proteins by Human Proteome Microarray. PMID:34262903
Thousands of induced germline mutations affecting immune cells identified by automated meiotic mapping coupled with machine learning. PMID:34260399
A Chromosome-Level Genome Assembly of the Mandarin Fish (Siniperca chuatsi). PMID:34249093
Screening of key biomarkers and immune infiltration in Pulmonary Arterial Hypertension via integrated bioinformatics analysis. PMID:34233597
Mitochondrial-Targeting Antioxidant SS-31 Suppresses Airway Inflammation and Oxidative Stress Induced by Cigarette Smoke. PMID:34221235
Genetic relationships and identification of core germplasm among rice photoperiod- and thermo-sensitive genic male sterile lines. PMID:34215178
Analysing Complex Oral Protein Samples: Complete Workflow and Case Analysis of Salivary Pellicles. PMID:34202147
Comparative transcriptome analysis of the hyperaccumulator plant Phytolacca americana in response to cadmium stress. PMID:34194911
A systems pharmacology approach based on oncogenic signalling pathways to determine the mechanisms of action of natural products in breast cancer from transcriptome data. PMID:34193143
Expression Profiling and Functional Analysis of Circular RNAs in Inner Mongolian Cashmere Goat Hair Follicles. PMID:34178035
Chromosome-Scale Genome Assembly of the Resurrection Plant Acanthochlamys bracteata (Velloziaceae). PMID:34165527
Robustification of GWAS to explore effective SNPs addressing the challenges of hidden population stratification and polygenic effects. PMID:34158546
Perinatal exposure to nicotine alters spermatozoal DNA methylation near genes controlling nicotine action. PMID:34153130
Bioinformatics Analysis of Differentially Expressed Rhythm Genes in Liver Hepatocellular Carcinoma. PMID:34149816
A Chromosome-Level Genome Assembly of the Spotted Scat (Scatophagus argus). PMID:34146395
Identification of Genes Related to Immune Infiltration in the Tumor Microenvironment of Cutaneous Melanoma. PMID:34136377
A novel algorithm for finding top-k weighted overlapping densest connected subgraphs in dual networks. PMID:34124340
Transcriptome Profile Analysis of Arabidopsis Reveals the Drought Stress-Induced Long Non-coding RNAs Associated With Photosynthesis, Chlorophyll Synthesis, Fatty Acid Synthesis and Degradation. PMID:34113361
Characterization of terminal-ileal and colonic Crohn's disease in treatment-naïve paediatric patients based on transcriptomic profile using logistic regression. PMID:34098982
PRoBE the cloud toolkit: finding the best biomarkers of drug response within a breast cancer clinical trial. PMID:34095775
Construction of a prognostic model with histone modification-related genes and identification of potential drugs in pancreatic cancer. PMID:34090418
The Quorum Sensing Auto-Inducer 2 (AI-2) Stimulates Nitrogen Fixation and Favors Ethanol Production over Biomass Accumulation in Zymomonas mobilis. PMID:34073173
Health monitoring in birds using bio-loggers and whole blood transcriptomics. PMID:34031452
Recovering Spatially-Varying Cell-Specific Gene Co-expression Networks for Single-Cell Spatial Expression Data. PMID:33981332
Hypericum perforatum L. Regulates Glutathione Redox Stress and Normalizes Ggt1/Anpep Signaling to Alleviate OVX-Induced Kidney Dysfunction. PMID:33981220
Deconvolution of sarcoma methylomes reveals varying degrees of immune cell infiltrates with association to genomic aberrations. PMID:33980253
Detecting Protein Communities in Native Cell Extracts by Machine Learning: A Structural Biologist's Perspective. PMID:33937337
Analysis of key genes and related transcription factors in liver fibrosis based on bioinformatic technology. PMID:33936366
Comparative Small RNA Profiling and Functional Exploration on Wheat With High- and Low-Cadmium Accumulation. PMID:33936166
Euler diagrams drawn with ellipses area-proportionally (Edeap). PMID:33902456
DNA methylation as the link between migration and the major noncommunicable diseases: the RODAM study. PMID:33890479
Arena3Dweb: interactive 3D visualization of multilayered networks. PMID:33885790
Molecular and Clinical Characterization of CCT2 Expression and Prognosis via Large-Scale Transcriptome Profile of Breast Cancer. PMID:33869000
Glioblastomas acquire myeloid-affiliated transcriptional programs via epigenetic immunoediting to elicit immune evasion. PMID:33857425
Screening of Hub Genes Associated with Pulmonary Arterial Hypertension by Integrated Bioinformatic Analysis. PMID:33816621
ON-bipolar cell gene expression during retinal degeneration: Implications for optogenetic visual restoration. PMID:33811915
Mitochondrial Mistranslation in Brain Provokes a Metabolic Response Which Mitigates the Age-Associated Decline in Mitochondrial Gene Expression. PMID:33803109
Prediction of LncRNA-encoded small peptides in glioma and oligomer channel functional analysis using in silico approaches. PMID:33735310
Identification and validation of a prognostic signature and combination drug therapy for immunotherapy of head and neck squamous cell carcinoma. PMID:33717423
De novo transcriptome assembly of transgenic tobacco (Nicotiana tabacum NC89) with early senescence characteristic. PMID:33707866
Stromal NRG1 in luminal breast cancer defines pro-fibrotic and migratory cancer-associated fibroblasts. PMID:33692466
The very early evolution of protein translocation across membranes. PMID:33684113
A De Novo Transcriptome Assembly of Ceratopteris richardii Provides Insights into the Evolutionary Dynamics of Complex Gene Families in Land Plants. PMID:33681974
Dysregulated Provision of Oxidisable Substrates to the Mitochondria in ME/CFS Lymphoblasts. PMID:33669532
Comparative analysis of Phytophthora genomes reveals oomycete pathogenesis in crops. PMID:33665461
Robust Physiological Metrics From Sparsely Sampled Networks. PMID:33643068
Systematic identification of key functional modules and genes in esophageal cancer. PMID:33632229
Regional identity of human neural stem cells determines oncogenic responses to histone H3.3 mutants. PMID:33631116
Identification of UBE2C as hub gene in driving prostate cancer by integrated bioinformatics analysis. PMID:33630978
Genetic diversity and population structure of Tibetan sheep breeds determined by whole genome resequencing. PMID:33611716
Identification of laminin γ2 as a prognostic and predictive biomarker for determining response to gemcitabine-based therapy in pancreatic ductal adenocarcinoma. PMID:33607476
Omics Playground: a comprehensive self-service platform for visualization, analytics and exploration of Big Omics Data. PMID:33575569
Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis. PMID:33574331
Alterations of 5-hydroxymethylation in circulating cell-free DNA reflect molecular distinctions of subtypes of non-Hodgkin lymphoma. PMID:33574286
A mixture model to detect edges in sparse co-expression graphs with an application for comparing breast cancer subtypes. PMID:33571253
Sequence characterisation and novel insights into bovine mastitis-associated Streptococcus uberis in dairy herds. PMID:33542314
Signalling pathways and mechanistic cues highlighted by transcriptomic analysis of primordial, primary, and secondary ovarian follicles in domestic cat. PMID:33514822
From Transcriptomics to Treatment in Inherited Optic Neuropathies. PMID:33499292
Computational Functional Genomics-Based AmpliSeq™ Panel for Next-Generation Sequencing of Key Genes of Pain. PMID:33467215
Comprehensive Analysis of Cardiac Xeno-Graft Unveils Rejection Mechanisms. PMID:33451076
Transcriptomic biomarkers for predicting response to neoadjuvant treatment in oesophageal cancer. PMID:33442473
Genome-Wide Analysis and the Expression Pattern of the ERF Gene Family in Hypericum perforatum. PMID:33440756
An Integrative Computational Approach for the Prediction of Human-Plasmodium Protein-Protein Interactions. PMID:33426052
Elucidating the network features and evolutionary attributes of intra- and interspecific protein-protein interactions between human and pathogenic bacteria. PMID:33420198
TriRNSC: triclustering of gene expression microarray data using restricted neighbourhood search. PMID:33399096
Survey and Sequence Characterization of Bovine Mastitis-Associated Escherichia coli in Dairy Herds. PMID:33365333
A Metagenome-Wide Association Study of Gut Microbiome in Patients With Multiple Sclerosis Revealed Novel Disease Pathology. PMID:33363050
Comparative genomics of Klebsiella michiganensis BD177 and related members of Klebsiella sp. reveal the symbiotic relationship with Bactrocera dorsalis. PMID:33339499
A biomimetic engineered bone platform for advanced testing of prosthetic implants. PMID:33335113
Biological and Genomic Characterization of a Novel Jumbo Bacteriophage, vB_VhaM_pir03 with Broad Host Lytic Activity against Vibrio harveyi. PMID:33333990
Graph embeddings on gene ontology annotations for protein-protein interaction prediction. PMID:33323115
Comparative transcriptome profiling of pomegranate genotypes having resistance and susceptible reaction to Xanthomonas axonopodis pv. punicae. PMID:33304163
Proteome size reduction in Apicomplexans is linked with loss of DNA repair and host redundant pathways. PMID:33296723
A self-consistent probabilistic formulation for inference of interactions. PMID:33293622
Statistical Approach for Biologically Relevant Gene Selection from High-Throughput Gene Expression Data. PMID:33286973
Pan-genome analysis and ancestral state reconstruction of class halobacteria: probability of a new super-order. PMID:33273480
SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery. PMID:33268350
Mitochondrial misreading in skeletal muscle accelerates metabolic aging and confers lipid accumulation and increased inflammation. PMID:33262249
Chemocentric Informatics Analysis: Dexamethasone Versus Combination Therapy for COVID-19. PMID:33251412
Aberrant (pro)renin receptor expression induces genomic instability in pancreatic ductal adenocarcinoma through upregulation of SMARCA5/SNF2H. PMID:33247206
Chromosomal genome of Triplophysa bleekeri provides insights into its evolution and environmental adaptation. PMID:33231676
The emergence and evolution of intron-poor and intronless genes in intron-rich plant gene families. PMID:33217085
Prediction of Burkholderia pseudomallei DsbA substrates identifies potential virulence factors and vaccine targets. PMID:33216758
Proteomic Analysis of Exosome-Like Vesicles Isolated From Saliva of the Tick Haemaphysalis longicornis. PMID:33194791
Integrative Network Analysis of Predicted miRNA-Targets Regulating Expression of Immune Response Genes in Bovine Coronavirus Infection. PMID:33193717
Transcriptome Analysis and Knockdown of the Juvenile Hormone Esterase Gene Reveal Abnormal Feeding Behavior in the Sugarcane Giant Borer. PMID:33192604
Exome Sequencing Identifies Abnormalities in Glycosylation and ANKRD36C in Patients with Immune-Mediated Thrombotic Thrombocytopenic Purpura. PMID:33184803
A haplotype-phased genome of wheat stripe rust pathogen Puccinia striiformis f. sp. tritici, race PST-130 from the Western USA. PMID:33175843
Molecular variation among virulent and avirulent strains of the quarantine nematode Bursaphelenchus xylophilus. PMID:33169231
Clustering of Alzheimer's and Parkinson's disease based on genetic burden of shared molecular mechanisms. PMID:33154531
Development of a novel immune-related genes prognostic signature for osteosarcoma. PMID:33110201
Chromatin accessibility dynamics of Chlamydia-infected epithelial cells. PMID:33109274
PresRAT: a server for identification of bacterial small-RNA sequences and their targets with probable binding region. PMID:33103602
Why All the Fuss about Oxidative Phosphorylation (OXPHOS)? PMID:33103432
A curated list of genes that affect the plant ionome. PMID:33103043
Learning gene networks underlying clinical phenotypes using SNP perturbation. PMID:33095769
Low expression of Talin1 is associated with advanced pathological features in colorectal cancer patients. PMID:33082414
Finding disease modules for cancer and COVID-19 in gene co-expression networks with the Core&Peel method. PMID:33077837
PIMD: An Integrative Approach for Drug Repositioning Using Multiple Characterization Fusion. PMID:33075523
The elephant grass (Cenchrus purpureus) genome provides insights into anthocyanidin accumulation and fast growth. PMID:33040437
Transcriptome Sequencing and Development of Novel Genic SSR Markers From Pistacia vera L. PMID:33033493
Genetic circuit characterization by inferring RNA polymerase movement and ribosome usage. PMID:33020480
The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering. PMID:33015004
Transcriptome characterization of BPG axis and expression profiles of ovarian steroidogenesis-related genes in the Japanese sardine. PMID:32993516
Named Entity Recognition and Relation Detection for Biomedical Information Extraction. PMID:32984300
Analysis of Metabolites and Gene Expression Changes Relative to Apricot (Prunus armeniaca L.) Fruit Quality During Development and Ripening. PMID:32973833
Machado: Open source genomics data integration framework. PMID:32930331
GFI1 functions to repress neuronal gene expression in the developing inner ear hair cells. PMID:32917668
Prognostic model of patients with liver cancer based on tumor stem cell content and immune process. PMID:32852285
Systems Biology Approaches to Understanding the Human Immune System. PMID:32849587
Chromosome-scale genome assembly of sweet cherry (Prunus avium L.) cv. Tieton obtained using long-read and Hi-C sequencing. PMID:32821405
Molecular insights into biochar-mediated plant growth promotion and systemic resistance in tomato against Fusarium crown and root rot disease. PMID:32811849
Genome-wide computational prediction of miRNAs in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) revealed target genes involved in pulmonary vasculature and antiviral innate immunity. PMID:32802902
Complete genome of a unicellular parasite (Antonospora locustae) and transcriptional interactions with its host locust. PMID:32783805
Comparative gut transcriptome analysis of Diatraea saccharalis in response to the dietary source. PMID:32745084
Complementary α-arrestin-ubiquitin ligase complexes control nutrient transporter endocytosis in response to amino acids. PMID:32744498
The Anatomy of the SARS-CoV-2 Biomedical Literature: Introducing the CovidX Network Algorithm for Drug Repurposing Recommendation. PMID:32735546
Salt stress induces endoplasmic reticulum stress-responsive genes in a grapevine rootstock. PMID:32730292
Microarray profiling and functional analysis of differentially expressed plasma exosomal circular RNAs in Graves' disease. PMID:32727578
Transcriptome analysis provides insights into the non-methylated lignin synthesis in Paphiopedilum armeniacum seed. PMID:32727352
BiPOm: a rule-based ontology to represent and infer molecule knowledge from a biological process-centered viewpoint. PMID:32703160
Reference Genome for the Highly Transformable Setaria viridis ME034V. PMID:32694197
Genetic Markers for Later Remission in Response to Early Improvement of Antidepressants. PMID:32664413
Glioma-derived exosomes drive the differentiation of neural stem cells to astrocytes. PMID:32649728
UFO: A tool for unifying biomedical ontology-based semantic similarity calculation, enrichment analysis and visualization. PMID:32645039
Dioxin-like compound exposures and DNA methylation in the Anniston Community Health Survey Phase II. PMID:32629249
Physiological blood-brain transport is impaired with age by a shift in transcytosis. PMID:32612231
Potential Molecular Mechanisms and Drugs for Aconitine-Induced Cardiotoxicity in Zebrafish through RNA Sequencing and Bioinformatics Analysis. PMID:32598336
Evolutionary History of the Globin Gene Family in Annelids. PMID:32597988
Identification of Known and Novel MicroRNAs in Raspberry Organs Through High-Throughput Sequencing. PMID:32582255
Baicalin Represses C/EBPβ via Its Antioxidative Effect in Parkinson's Disease. PMID:32566108
pyMeSHSim: an integrative python package for biomedical named entity recognition, normalization, and comparison of MeSH terms. PMID:32552728
Understanding Drug Repurposing From the Perspective of Biomedical Entities and Their Evolution: Bibliographic Research Using Aspirin. PMID:32543442
Genomic insights into a plant growth-promoting Pseudomonas koreensis strain with cyclic lipopeptide-mediated antifungal activity. PMID:32537904
Oak displays common local but specific distant gene regulation responses to different mycorrhizal fungi. PMID:32532205
Hybrid de novo genome assembly of red gromwell (Lithospermum erythrorhizon) reveals evolutionary insight into shikonin biosynthesis. PMID:32528694
Draft Genome Sequence of Streptomyces aureoverticillatus HN6, a Strain Antagonistic against Fusarium oxysporum f. sp. cubense Race 4. PMID:32499365
dBMHCC: A comprehensive hepatocellular carcinoma (HCC) biomarker database provides a reliable prediction system for novel HCC phosphorylated biomarkers. PMID:32497121
Longitudinal Analysis of Gene Expression Changes During Cervical Carcinogenesis Reveals Potential Therapeutic Targets. PMID:32489245
Computational Prediction of Ubiquitination Proteins Using Evolutionary Profiles and Functional Domain Annotation. PMID:32476995
MethGET: web-based bioinformatics software for correlating genome-wide DNA methylation and gene expression. PMID:32471342
The Possible Influence of Mediterranean Diet on Extracellular Vesicle miRNA Expression in Breast Cancer Survivors. PMID:32466456
MyomirDB: A unified database and server platform for muscle atrophy myomiRs, coregulatory networks and regulons. PMID:32451429
RNA Sequencing of Human Peripheral Nerve in Response to Injury: Distinctive Analysis of the Nerve Repair Pathways. PMID:32425114
MCM2 and NUSAP1 Are Potential Biomarkers for the Diagnosis and Prognosis of Pancreatic Cancer. PMID:32420375
Identification of a Gene-Related Risk Signature in Melanoma Patients Using Bioinformatic Profiling. PMID:32411243
Ewastools: Infinium Human Methylation BeadChip pipeline for population epigenetics integrated into Galaxy. PMID:32401319
Analysis of genes associated with prognosis of lung adenocarcinoma based on GEO and TCGA databases. PMID:32384511
Dark-rearing uncovers novel gene expression patterns in an obligate cave-dwelling fish. PMID:32372488
Comparative Genomic Analysis Provides Insights into the Phylogeny, Resistome, Virulome, and Host Adaptation in the Genus Ewingella. PMID:32354059
Identification of Key Genes Related to Lung Squamous Cell Carcinoma Using Bioinformatics Analysis. PMID:32340320
Comparative transcriptome analysis of the hippocampus from sleep-deprived and Alzheimer's disease mice. PMID:32338274
Comparative transcriptome analysis of differentially expressed genes between the fruit peel and flesh of the purple tomato cultivar 'Indigo Rose'. PMID:32338177
Temporal transcriptome change of Oncomelania hupensis revealed by Schistosoma japonicum invasion. PMID:32328235
Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis. PMID:32326049
High expression of CDCA7 predicts tumor progression and poor prognosis in human colorectal cancer. PMID:32319649
Genomic characterization of an emerging Enterobacteriaceae species: the first case of co-infection with a typical pathogen in a human patient. PMID:32293254
GOMCL: a toolkit to cluster, evaluate, and extract non-redundant associations of Gene Ontology-based functions. PMID:32272889
The First Genome Survey of the Antarctic Krill (Euphausia superba) Provides a Valuable Genetic Resource for Polar Biomedical Research. PMID:32244466
Dense module searching for gene networks associated with multiple sclerosis. PMID:32241259
RNA-seq data of soleus muscle tissue after spinal cord injury under conditions of inactivity and applied exercise. PMID:32226812
Comprehensive analysis of long non-coding RNA and mRNA expression profile in rectal cancer. PMID:32224706
Comparative Transcriptome Analysis Provides Insights Into Yellow Rind Formation and Preliminary Mapping of the Clyr (Yellow Rind) Gene in Watermelon. PMID:32218790
Comparative genomic analysis and mosquito larvicidal activity of four Bacillus thuringiensis serovar israelensis strains. PMID:32218451
Testing Proximity of Genomic Regions to Transcription Start Sites and Enhancers Complements Gene Set Enrichment Testing. PMID:32211031
Skewed X-Chromosome Inactivation and Compensatory Upregulation of Escape Genes Precludes Major Clinical Symptoms in a Female With a Large Xq Deletion. PMID:32194616
Identification of 13 Key Genes Correlated With Progression and Prognosis in Hepatocellular Carcinoma by Weighted Gene Co-expression Network Analysis. PMID:32180800
Learning supervised embeddings for large scale sequence comparisons. PMID:32168338
Identification of PTPRR and JAG1 as key genes in castration-resistant prostate cancer by integrated bioinformatics methods. PMID:32133801
Prediction of Alzheimer's disease using blood gene expression data. PMID:32103140
Comparative Transcriptome Analysis of Two Cucumber Cultivars with Different Sensitivity to Cucumber Mosaic Virus Infection. PMID:32098056
A Guide to Conquer the Biological Network Era Using Graph Theory. PMID:32083072
Systems biology-based approaches to summarize and identify novel genes and pathways associated with acute and chronic postsurgical pain. PMID:32058259
An Isolated Complex V Inefficiency and Dysregulated Mitochondrial Function in Immortalized Lymphocytes from ME/CFS Patients. PMID:32041178
Electrophysiology-based stratification of pancreatic tumorigenicity by label-free single-cell impedance cytometry. PMID:32029124
PlaPPISite: a comprehensive resource for plant protein-protein interaction sites. PMID:32028878
The high-quality genome of diploid strawberry (Fragaria nilgerrensis) provides new insights into anthocyanin accumulation. PMID:32003918
Chlamydomonas CHT7 Is Required for an Effective Quiescent State by Regulating Nutrient-Responsive Cell Cycle Gene Expression. PMID:32001503
TranCEP: Predicting the substrate class of transmembrane transport proteins using compositional, evolutionary, and positional information. PMID:31935244
More Agility to Semantic Similarities Algorithm Implementations. PMID:31905999
Expression profile-based screening for critical genes reveals S100A4, ACKR3 and CDH1 in docetaxel-resistant prostate cancer cells. PMID:31895690
Old drug repositioning and new drug discovery through similarity learning from drug-target joint feature spaces. PMID:31881829
Analysis of Differentially Expressed Genes in Coronary Artery Disease by Integrated Microarray Analysis. PMID:31881747
GO2Vec: transforming GO terms and proteins to vector representations via graph embeddings. PMID:31874639
Identifying Acetylation Protein by Fusing Its PseAAC and Functional Domain Annotation. PMID:31867311
Whole Genome Sequencing and Assembly of the Asian Honey Bee Apis dorsata. PMID:31860080
Transcriptome landscape of Rafflesia cantleyi floral buds reveals insights into the roles of transcription factors and phytohormones in flower development. PMID:31851702
Survival-Associated Alternative Splicing Events in Pan-Renal Cell Carcinoma. PMID:31850211
Evaluating the consistency of large-scale pharmacogenomic studies. PMID:31846027
Mice lacking uterine enhancer of zeste homolog 2 have transcriptomic changes associated with uterine epithelial proliferation. PMID:31841397
Chemogenomic profiling to understand the antifungal action of a bioactive aurone compound. PMID:31825988
Salinity stress-responsive transcription factors in the liverwort Marchantia polymorpha. PMID:31819734
Identification of key candidate genes and pathways in endometrial cancer: Evidence from bioinformatics analysis. PMID:31807178
Sequence-Derived Markers of Drug Targets and Potentially Druggable Human Proteins. PMID:31803227
A Novel Nitrite-Base Aerobic Denitrifying Bacterium Acinetobacter sp. YT03 and Its Transcriptome Analysis. PMID:31803151
CBNA: A control theory based method for identifying coding and non-coding cancer drivers. PMID:31790386
A comparative analysis of gene expression induced by the embryo in the caprine endometrium. PMID:31782264
Microbiome Multi-Omics Network Analysis: Statistical Considerations, Limitations, and Opportunities. PMID:31781153
TS-GOEA: a web tool for tissue-specific gene set enrichment analysis based on gene ontology. PMID:31760951
Integrated Analysis of mRNA and miRNA Expression Profiles in the Ovary of Oryctolagus cuniculus in Response to Gonadotrophic Stimulation. PMID:31736880
Complete Genome Sequence of Cellulomonas sp. Strain Y8, a High-GC-Content Plasmid-Free Heavy Metal-Resistant Bacterium Isolated from Farmland Soil. PMID:31727705
RNA sequencing of identical twins discordant for autism reveals blood-based signatures implicating immune and transcriptional dysregulation. PMID:31719968
Comparative Analysis of Whole-Genome and Methylome Profiles of a Smooth and a Rough Mycobacterium abscessus Clinical Strain. PMID:31719113
Measurement of Conditional Relatedness Between Genes Using Fully Convolutional Neural Network. PMID:31695723
RNA-seq analysis provides insights into cold stress responses of Xanthomonas citri pv. citri. PMID:31694530
Comparative gene expression analysis in melanocytes driven by tumor cell-derived exosomes. PMID:31678172
Accelerated evolution and diversifying selection drove the adaptation of cetacean bone microstructure. PMID:31651232
A chromosomal-level genome assembly for the giant African snail Achatina fulica. PMID:31634388
Gene Repositioning Is Under Constraints After Evolutionary Conserved Gene Neighborhood Separate. PMID:31632448
Data Integration in Poplar: 'Omics Layers and Integration Strategies. PMID:31608114
Common molecular markers between circulating tumor cells and blood exosomes in colorectal cancer: a systematic and analytical review. PMID:31576171
Isotopically Labeled Clickable Glutathione to Quantify Protein S-Glutathionylation. PMID:31560820
Reference gene and small RNA data from multiple tissues of Davidia involucrata Baill. PMID:31551451
Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars. PMID:31533702
Hibernation induces widespread transcriptional remodeling in metabolic tissues of the grizzly bear. PMID:31531397
Genome sequence of the Chinese white wax scale insect Ericerus pela: the first draft genome for the Coccidae family of scale insects. PMID:31518402
DIFFUSE: predicting isoform functions from sequences and expression profiles via deep learning. PMID:31510699
Identification of a Specific Gene Module for Predicting Prognosis in Glioblastoma Patients. PMID:31508371
Transcriptome and gene expression analysis of three developmental stages of the coffee berry borer, Hypothenemus hampei. PMID:31488852
Public Microbial Resource Centers: Key Hubs for Findable, Accessible, Interoperable, and Reusable (FAIR) Microorganisms and Genetic Materials. PMID:31471301
Eukaryote Genes Are More Likely than Prokaryote Genes to Be Composites. PMID:31466252
Nicotinamide mononucleotide (NMN) supplementation promotes anti-aging miRNA expression profile in the aorta of aged mice, predicting epigenetic rejuvenation and anti-atherogenic effects. PMID:31463647
An equivalence approach to the integrative analysis of feature lists. PMID:31455218
Insights into Early Recovery from Influenza Pneumonia by Spatial and Temporal Quantification of Putative Lung Regenerating Cells and by Lung Proteomics. PMID:31455003
DNA methylation profiling identifies potentially significant epigenetically-regulated genes in glioblastoma multiforme. PMID:31423235
RNA-Seq Analysis Reveals Genes Related to Photoreception, Nutrient Uptake, and Toxicity in a Noxious Red-Tide Raphidophyte Chattonella antiqua. PMID:31417538
The Methodological Trends of Traditional Herbal Medicine Employing Network Pharmacology. PMID:31412658
Transcriptomic analysis of Pacific white shrimp (Litopenaeus vannamei, Boone 1931) in response to acute hepatopancreatic necrosis disease caused by Vibrio parahaemolyticus. PMID:31408485
Endosome and Golgi-associated degradation (EGAD) of membrane proteins regulates sphingolipid metabolism. PMID:31368600
Phenome-wide Burden of Copy-Number Variation in the UK Biobank. PMID:31353025
Identification and Characterization of MiRNAs in Coccomyxa subellipsoidea C-169. PMID:31337051
Transcription Factors Indirectly Regulate Genes through Nuclear Colocalization. PMID:31330780
Exploring regulatory networks in plants: transcription factors of starch metabolism. PMID:31328026
Uncovering the molecular signature underlying the light intensity-dependent root development in Arabidopsis thaliana. PMID:31325959
Coordinate regulation of the expression of SdsR toxin and its downstream pphA gene by RyeA antitoxin in Escherichia coli. PMID:31270363
Biosynthetic Potential of a Novel Antarctic Actinobacterium Marisediminicola antarctica ZS314T Revealed by Genomic Data Mining and Pigment Characterization. PMID:31266176
De novo transcriptome analysis of Tibetan medicinal plant Dysphania schraderiana. PMID:31259355
Fold combinations in multi-domain proteins. PMID:31249437
Maize GO Annotation-Methods, Evaluation, and Review (maize-GAMER). PMID:31245718
Whole Genome Sequencing and Analysis of Chlorimuron-Ethyl Degrading Bacteria Klebsiella pneumoniae 2N3. PMID:31234527
MicroRNAs 145 and 148a Are Upregulated During Congenital Zika Virus Infection. PMID:31213064
Identification of co-evolving temporal networks. PMID:31189471
Deep expression analysis reveals distinct cold-response strategies in rubber tree (Hevea brasiliensis). PMID:31164105
Trait ontology analysis based on association mapping studies bridges the gap between crop genomics and Phenomics. PMID:31159731
Towards an Internet of Science. PMID:31145694
CODA-ML: context-specific biological knowledge representation for systemic physiology analysis. PMID:31138123
Identification of Crucial Candidate Genes and Pathways in Glioblastoma Multiform by Bioinformatics Analysis. PMID:31137733
Effects of Vitamin D Use on Outcomes of Psychotic Symptoms in Alzheimer Disease Patients. PMID:31126722
KEGG-expressed genes and pathways in intervertebral disc degeneration: Protocol for a systematic review and data mining. PMID:31124977
Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts. PMID:31112549
Pathway-based biomarker identification with crosstalk analysis for robust prognosis prediction in hepatocellular carcinoma. PMID:31101593
Using RNA-seq to characterize responses to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus). PMID:31060501
Analyses of circRNA profiling during the development from pre-receptive to receptive phases in the goat endometrium. PMID:31049198
m6Acomet: large-scale functional prediction of individual m6A RNA methylation sites from an RNA co-methylation network. PMID:31046660
Collembola interact with mycorrhizal fungi in modifying oak morphology, C and N incorporation and transcriptomics. PMID:31032040
The trihelix family of transcription factors: functional and evolutionary analysis in Moso bamboo (Phyllostachys edulis). PMID:31023225
Genome-wide analyses and expression patterns under abiotic stress of NAC transcription factors in white pear (Pyrus bretschneideri). PMID:31023218
The Draft Genome Sequence of Pseudomonas putida Strain TGRB4, an Aerobic Bacterium Capable of Producing Methylmercury. PMID:31004191
Interactive biomedical ontology matching. PMID:30995257
Identification of Important Invasion-Related Genes in Non-functional Pituitary Adenomas. PMID:30982163
isoTar: Consensus Target Prediction with Enrichment Analysis for MicroRNAs Harboring Editing Sites and Other Variations. PMID:30963495
Qualitative transcriptional signatures for evaluating the maturity degree of pluripotent stem cell-derived cardiomyocytes. PMID:30925936
Developing a vocabulary and ontology for modeling insect natural history data: example data, use cases, and competency questions. PMID:30918448
Identification of key proteins and lncRNAs in hypertrophic cardiomyopathy by integrated network analysis. PMID:30899302
The E. coli transcriptional regulatory network and its spatial embedding. PMID:30879159
Retinoic Acid Induces Hyperactivity, and Blocking Its Receptor Unmasks Light Responses and Augments Vision in Retinal Degeneration. PMID:30876849
Identifying miRNA-mRNA regulatory relationships in breast cancer with invariant causal prediction. PMID:30876399
Comparable Genomic Copy Number Aberrations Differ across Astrocytoma Malignancy Grades. PMID:30871102
DeepTACT: predicting 3D chromatin contacts via bootstrapping deep learning. PMID:30869141
Using Machine Learning to Measure Relatedness Between Genes: A Multi-Features Model. PMID:30862804
Evolutionary behaviour of bacterial prion-like proteins. PMID:30835736
Genetic and environmental perturbations lead to regulatory decoherence. PMID:30834892
Diversity and functional analysis of salivary microflora of Indian Antarctic expeditionaries. PMID:30834068
YESdb: integrative analysis of environmental stress in yeast. PMID:30821814
Prediction of itching diagnostic marker through RNA sequencing of contact hypersensitivity and skin scratching stimulation mice models. PMID:30820159
Elevated atmospheric CO2 concentrations alter grapevine (Vitis vinifera) systemic transcriptional response to European grapevine moth (Lobesia botrana) herbivory. PMID:30816321
Biomaterial Scaffolds Recruit an Aggressive Population of Metastatic Tumor Cells In Vivo. PMID:30808673
Modeling the Function of TATA Box Binding Protein in Transcriptional Changes Induced by HIV-1 Tat in Innate Immune Cells and the Effect of Methamphetamine Exposure. PMID:30778358
Integrated Bioinformatics Analysis of Hub Genes and Pathways in Anaplastic Thyroid Carcinomas. PMID:30774662
Analyzing a co-occurrence gene-interaction network to identify disease-gene association. PMID:30736752
Inverse similarity and reliable negative samples for drug side-effect prediction. PMID:30717666
Genome sequence of the barred knifejaw Oplegnathus fasciatus (Temminck & Schlegel, 1844): the first chromosome-level draft genome in the family Oplegnathidae. PMID:30715332
Identification of aberrant gene expression during breast ductal carcinoma in situ progression to invasive ductal carcinoma. PMID:30712460
Genome-wide analysis of circular RNAs in goat skin fibroblast cells in response to Orf virus infection. PMID:30697481
Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells. PMID:30696696
Transcriptome Analysis Clarified Genes Involved in Betalain Biosynthesis in the Fruit of Red Pitayas (Hylocereus costaricensis). PMID:30691184
Genome sequence of Malania oleifera, a tree with great value for nervonic acid production. PMID:30689848
Integrative Analyses of Genes Associated with Subcutaneous Insulin Resistance. PMID:30678306
Real world scenarios in rare variant association analysis: the impact of imbalance and sample size on the power in silico. PMID:30669967
Newly Discovered Occurrences and Gene Tree of the Extracellular Globins and Linker Chains from the Giant Hexagonal Bilayer Hemoglobin in Metazoans. PMID:30668717
A dynamic degradome landscape on miRNAs and their predicted targets in sugarcane caused by Sporisorium scitamineum stress. PMID:30658590
Network-Based Assessment of Adverse Drug Reaction Risk in Polypharmacy Using High-Throughput Screening Data. PMID:30658437
Comprehensive Analysis of Differentially Expressed Unigenes under NaCl Stress in Flax (Linum usitatissimum L.) Using RNA-Seq. PMID:30654562
Global gene expression analysis of cell-free RNA in amniotic fluid from women destined to develop preeclampsia. PMID:30653101
Uncoupling of transcriptomic and cytological differentiation in mouse spermatocytes with impaired meiosis. PMID:30649999
ACCBN: ant-Colony-clustering-based bipartite network method for predicting long non-coding RNA-protein interactions. PMID:30626319
A partially function-to-topic model for protein function prediction. PMID:30598098
Ischemia-reperfusion injury in a rat microvascular skin free flap model: A histological, genetic, and blood flow study. PMID:30589864
Harnessing formal concepts of biological mechanism to analyze human disease. PMID:30586388
Defining a Characteristic Gene Expression Set Responsible for Cancer Stem Cell-Like Features in a Sub-Population of Ewing Sarcoma Cells CADO-ES1. PMID:30563222
Induced Resistance Mechanism of Novel Curcumin Analogs Bearing a Quinazoline Moiety to Plant Virus. PMID:30558295
Identification of genes associated with cancer progression and prognosis in lung adenocarcinoma: Analyses based on microarray from Oncomine and The Cancer Genome Atlas databases. PMID:30556321
A novel lncRNA-mediated trans-regulatory mechanism in the development of cleft palate in mouse. PMID:30548829
Transcriptional profiling analysis predicts potential biomarkers for glaucoma: HGF, AKR1B10 and AKR1C3. PMID:30542465
Highlights on the Application of Genomics and Bioinformatics in the Fight Against Infectious Diseases: Challenges and Opportunities in Africa. PMID:30538723
Predicting protein targets for drug-like compounds using transcriptomics. PMID:30532261
Automatic gene annotation using GO terms from cellular component domain. PMID:30526566
The Chinese herbal formula Fuzheng Quxie Decoction attenuates cognitive impairment and protects cerebrovascular function in SAMP8 mice. PMID:30519025
Taxonomic and functional heterogeneity of the gill microbiome in a symbiotic coastal mangrove lucinid species. PMID:30518817
Circulating proteomic patterns in AF related left atrial remodeling indicate involvement of coagulation and complement cascade. PMID:30496173
Chi-miR-3031 regulates beta-casein via the PI3K/AKT-mTOR signaling pathway in goat mammary epithelial cells (GMECs). PMID:30482199
Transcriptome Analysis of Cinnamomum chago: A Revelation of Candidate Genes for Abiotic Stress Response and Terpenoid and Fatty Acid Biosyntheses. PMID:30455715
Computational prediction of miRNAs in Nipah virus genome reveals possible interaction with human genes involved in encephalitis. PMID:30426028
Comprehensive bioinformatics analysis identifies several potential diagnostic markers and potential roles of cyclin family members in lung adenocarcinoma. PMID:30425528
Integrating Coexpression Networks with GWAS to Prioritize Causal Genes in Maize. PMID:30413654
Genome-Scale Analysis of Perturbations in Translation Elongation Based on a Computational Model. PMID:30385856
Profiling Immune Escape in Hodgkin's and Diffuse large B-Cell Lymphomas Using the Transcriptome and Immunostaining. PMID:30384489
Comparative cochlear transcriptomics of echolocating bats provides new insights into different nervous activities of CF bat species. PMID:30374045
Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data. PMID:30372442
Transcriptomic analysis reveals critical genes for the hair follicle of Inner Mongolia cashmere goat from catagen to telogen. PMID:30356261
p53 modeling as a route to mesothelioma patients stratification and novel therapeutic identification. PMID:30316293
Plasticity of a holobiont: desiccation induces fasting-like metabolism within the lichen microbiota. PMID:30310167
Chromosomal-level assembly of yellow catfish genome using third-generation DNA sequencing and Hi-C analysis. PMID:30256939
Chromosome-level genome assembly of the spotted sea bass, Lateolabrax maculatus. PMID:30239684
ATD: a comprehensive bioinformatics resource for deciphering the association of autophagy and diseases. PMID:30239683
Wide-scope biomedical named entity recognition and normalization with CRFs, fuzzy matching and character level modeling. PMID:30239666
A draft genome assembly of the Chinese sillago (Sillago sinica), the first reference genome for Sillaginidae fishes. PMID:30202912
Introgression and gene family contraction drive the evolution of lifestyle and host shifts of hypocrealean fungi. PMID:30181924
CEA: Combination-based gene set functional enrichment analysis. PMID:30166636
Identification of key genes and pathways using bioinformatics analysis in septic shock children. PMID:30147344
Screening and identification of key biomarkers in bladder carcinoma: Evidence from bioinformatics analysis. PMID:30127900
High-density genetic map construction and quantitative trait loci analysis of the stony hard phenotype in peach based on restriction-site associated DNA sequencing. PMID:30107781
On entropy and information in gene interaction networks. PMID:30102349
The chromosome-level genome assemblies of two rattans (Calamus simplicifolius and Daemonorops jenkinsiana). PMID:30101322
Differential and Interactive Effects of Substrate Topography and Chemistry on Human Mesenchymal Stem Cell Gene Expression. PMID:30096912
siRNAs regulate DNA methylation and interfere with gene and lncRNA expression in the heterozygous polyploid switchgrass. PMID:30061930
Transcriptional profiling of two different physiological states of the yak mammary gland using RNA sequencing. PMID:30059556
In silico identification and computational characterization of endogenous small interfering RNAs from diverse grapevine tissues and stages. PMID:30047108
Chemogenomics Systems Pharmacology Mapping of Potential Drug Targets for Treatment of Traumatic Brain Injury. PMID:30014763
The Potential Correlation Between Bacterial Sporulation and the Characteristic Flavor of Chinese Maotai Liquor. PMID:30013536
CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata. PMID:30012108
Whole body transcriptomes and new insights into the biology of the tick Ixodes ricinus. PMID:29941016
High-quality assembly of the reference genome for scarlet sage, Salvia splendens, an economically important ornamental plant. PMID:29931210
Dysregulated genes targeted by microRNAs and metabolic pathways in bladder cancer revealed by bioinformatics methods. PMID:29928337
MptpB Promotes Mycobacteria Survival by Inhibiting the Expression of Inflammatory Mediators and Cell Apoptosis in Macrophages. PMID:29888212
Research Trend Visualization by MeSH Terms from PubMed. PMID:29848974
A physical model of cell metabolism. PMID:29844352
Transcriptomic response of breast cancer cells to anacardic acid. PMID:29795261
WEGO 2.0: a web tool for analyzing and plotting GO annotations, 2018 update. PMID:29788377
Synthesis and Insecticidal Activity of Mesoionic Pyrido[1,2-α]pyrimidinone Derivatives Containing a Neonicotinoid Moiety. PMID:29783735
Transcriptomic Analysis of Pseudoscorpion Venom Reveals a Unique Cocktail Dominated by Enzymes and Protease Inhibitors. PMID:29783636
Transcriptomic Profiling of Zebrafish Hair Cells Using RiboTag. PMID:29765956
Global assessment of its network dynamics reveals that the kinase Plk1 inhibits the phosphatase PP6 to promote Aurora A activity. PMID:29764989
How Artificial Intelligence Can Improve Our Understanding of the Genes Associated with Endometriosis: Natural Language Processing of the PubMed Database. PMID:29750165
Predicting high-risk endometrioid carcinomas using proteins. PMID:29731976
Innovative assembly strategy contributes to understanding the evolution and conservation genetics of the endangered Solenodon paradoxus from the island of Hispaniola. PMID:29718205
Draft genome sequence of Bosea sp. WAO an arsenite and sulfide oxidizer isolated from a pyrite rock outcrop in New Jersey. PMID:29682167
Cardiomyocytes have mosaic patterns of protein expression. PMID:29677652
Identification of Differentially Expressed Genes in Porcine Ovaries at Proestrus and Estrus Stages Using RNA-Seq Technique. PMID:29662904
Similarity in replication timing between polytene and diploid cells is associated with the organization of the Drosophila genome. PMID:29659604
Transcriptomic Analysis of Flower Bud Differentiation in Magnolia sinostellata. PMID:29659525
Effects of nicotine on the metabolism and gene expression profile of Sprague‑Dawley rat primary osteoblasts. PMID:29658611
Integrated analysis of the gene expression profile and DNA methylation profile of obese patients with type 2 diabetes. PMID:29620215
Identification of Streptococcus mitis321A vaccine antigens based on reverse vaccinology. PMID:29620181
Upregulated VEGFA and DLL4 act as potential prognostic genes for clear cell renal cell carcinoma. PMID:29618931
Cross-species multiple environmental stress responses: An integrated approach to identify candidate genes for multiple stress tolerance in sorghum (Sorghum bicolor (L.) Moench) and related model species. PMID:29590108
Feature selection with interactions in logistic regression models using multivariate synergies for a GWAS application. PMID:29589561
Systematic characterization of pan-cancer mutation clusters. PMID:29572294
Key Players of Cisplatin Resistance: Towards a Systems Pharmacology Approach. PMID:29518977
Screening for key lncRNAs in the progression of gallbladder cancer using bioinformatics analyses. PMID:29512694
Different Modes of Gene Duplication Show Divergent Evolutionary Patterns and Contribute Differently to the Expansion of Gene Families Involved in Important Fruit Traits in Pear (Pyrus bretschneideri). PMID:29487610
Construction of key signal regulatory network in metastatic colorectal cancer. PMID:29464057
Identification of a locus conferring dominant resistance to maize rough dwarf disease in maize. PMID:29459698
Integrating eQTL data with GWAS summary statistics in pathway-based analysis with application to schizophrenia. PMID:29411426
The regulatory network analysis of long noncoding RNAs in human colorectal cancer. PMID:29374362
DataMed - an open source discovery index for finding biomedical datasets. PMID:29346583
Systematic analysis of the molecular mechanism of microRNA-124 in hepatoblastoma cells. PMID:29344147
Bioinformatics analysis to screen key genes implicated in the differentiation of induced pluripotent stem cells to hepatocytes. PMID:29328449
Illumina-based de novo transcriptome sequencing and analysis of Chinese forest musk deer. PMID:29321364
Enriching Genomic Resources and Transcriptional Profile Analysis of Miscanthus sinensis under Drought Stress Based on RNA Sequencing. PMID:29318138
Lipopolysaccharide induces acute bursal atrophy in broiler chicks by activating TLR4-MAPK-NF-κB/AP-1 signaling. PMID:29312537
Identification and validation long non-coding RNAs of oral squamous cell carcinoma by bioinformatics method. PMID:29296179
Perturbation-response genes reveal signaling footprints in cancer gene expression. PMID:29295995
Effects of cell-cell crosstalk on gene expression patterns in a cell model of renal cell carcinoma lung metastasis. PMID:29286165
The integration of weighted gene association networks based on information entropy. PMID:29272314
The genomic study of an environmental isolate of Scedosporium apiospermum shows its metabolic potential to degrade hydrocarbons. PMID:29225727
Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community. PMID:29220441
LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis. PMID:29220437
Comparative genomics reveals the presence of putative toxin-antitoxin system in Wolbachia genomes. PMID:29214346
Repository corticotrophin injection exerts direct acute effects on human B cell gene expression distinct from the actions of glucocorticoids. PMID:29205315
Identification of key genes fluctuated induced by avian leukemia virus (ALV-J) infection in chicken cells. PMID:29197030
Complete Genome Sequence of Bacillus velezensis L-1, Which Has Antagonistic Activity against Pear Diseases. PMID:29192072
A network diffusion approach to inferring sample-specific function reveals functional changes associated with breast cancer. PMID:29190299
Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches. PMID:29186305
Computational systems biology approaches for Parkinson's disease. PMID:29185073
Whole transcriptome RNA-Seq analysis reveals extensive cell type-specific compartmentalization in Volvox carteri. PMID:29179763
An extracellular matrix-related prognostic and predictive indicator for early-stage non-small cell lung cancer. PMID:29170406
Functional diversity of topological modules in human protein-protein interaction networks. PMID:29170401
The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes. PMID:29169408
Selection for female traits of high fertility affects male reproductive performance and alters the testicular transcriptional profile. PMID:29157197
Protein-Specific Features Associated with Variability in Human Antibody Responses to Plasmodium falciparum Malaria Antigens. PMID:29141757
Target-Pathogen: a structural bioinformatic approach to prioritize drug targets in pathogens. PMID:29106651
Systems Study on the Antirheumatic Mechanism of Tibetan Medicated-Bath Therapy Using Wuwei-Ganlu-Yaoyu-Keli. PMID:29090217
Neuroinflammation and ALS: Transcriptomic Insights into Molecular Disease Mechanisms and Therapeutic Targets. PMID:29081603
A rank-based algorithm of differential expression analysis for small cell line data with statistical control. PMID:29040359
ThPP1 gene, encodes an inorganic pyrophosphatase in Thellungiella halophila, enhanced the tolerance of the transgenic rice to alkali stress. PMID:29030650
Review of computational methods for virus-host protein interaction prediction: a case study on novel Ebola-human interactions. PMID:29028879
The MicroRNA Interaction Network of Lipid Diseases. PMID:29018475
Broad Phylogenetic Occurrence of the Oxygen-Binding Hemerythrins in Bilaterians. PMID:29016798
Altered gene expression profiles in the lungs of benzo[a]pyrene-exposed mice in the presence of lipopolysaccharide-induced pulmonary inflammation. PMID:28987381
Sequence-Based Analysis of Thermal Adaptation and Protein Energy Landscapes in an Invasive Blue Mussel (Mytilus galloprovincialis). PMID:28985307
Whole genome microarray expression analysis in blood identifies pathways linked to signs and symptoms of a patient with hypercalprotectinaemia and hyperzincaemia. PMID:28984903
Towards refactoring the Molecular Function Ontology with a UML profile for function modeling. PMID:28978337
Whole genome gene expression changes and hematological effects of rikkunshito in patients with advanced non-small cell lung cancer receiving first line chemotherapy. PMID:28962123
iTRAQ protein profile analysis of developmental dynamics in soybean [Glycine max (L.) Merr.] leaves. PMID:28953898
NetGen: a novel network-based probabilistic generative model for gene set functional enrichment analysis. PMID:28950861
Differential expression of genes and differentially perturbed pathways associated with very high evening fatigue in oncology patients receiving chemotherapy. PMID:28944404
Screening critical genes associated with malignant glioma using bioinformatics analysis. PMID:28901452
Deep Sequencing Transcriptome Analysis of Murine Wound Healing: Effects of a Multicomponent, Multitarget Natural Product Therapy-Tr14. PMID:28879183
The transcriptional landscape of Rhizoctonia solani AG1-IA during infection of soybean as defined by RNA-seq. PMID:28877263
Virulence and transcriptome profile of multidrug-resistant Escherichia coli from chicken. PMID:28827616
Comparative Transcriptomics of Bacillus mycoides Strains in Response to Potato-Root Exudates Reveals Different Genetic Adaptation of Endophytic and Soil Isolates. PMID:28824604
Exploring Potential Germline-Associated Roles of the TRIM-NHL Protein NHL-2 Through RNAi Screening. PMID:28818867
A genome-wide transcriptome map of pistachio (Pistacia vera L.) provides novel insights into salinity-related genes and marker discovery. PMID:28814265
The mycobacterial phosphatase PtpA regulates the expression of host genes and promotes cell proliferation. PMID:28811474
Identification of breast cancer mechanism based on weighted gene coexpression network analysis. PMID:28799567
Time-series analysis in imatinib-resistant chronic myeloid leukemia K562-cells under different drug treatments. PMID:28786057
Large-scale identification of Gossypium hirsutum genes associated with Verticillium dahliae by comparative transcriptomic and reverse genetics analysis. PMID:28767675
Investigation of the molecular mechanisms underlying myotonic dystrophy types 1 and 2 cataracts using microRNA‑target gene networks. PMID:28731161
A Transcriptomic Survey of Ion Channel-Based Conotoxins in the Chinese Tubular Cone Snail (Conus betulinus). PMID:28718820
Developing a similarity searching module for patient safety event reporting system using semantic similarity measures. PMID:28699567
Reduced Circulating Levels of miR-433 and miR-133b Are Potential Biomarkers for Parkinson's Disease. PMID:28690499
Comparative genomic analysis of Mycobacterium neoaurum MN2 and MN4 substrate and product tolerance. PMID:28664368
A data analysis framework for biomedical big data: Application on mesoderm differentiation of human pluripotent stem cells. PMID:28654683
Using Coexpression Protein Interaction Network Analysis to Identify Mechanisms of Danshensu Affecting Patients with Coronary Heart Disease. PMID:28629174
Complexities of gene expression patterns in natural populations of an extremophile fish (Poecilia mexicana, Poeciliidae). PMID:28598519
Genome-Wide Transcriptome Analysis Reveals Extensive Alternative Splicing Events in the Protoscoleces of Echinococcus granulosus and Echinococcus multilocularis. PMID:28588571
Prediction of marker genes associated with hypertension by bioinformatics analyses. PMID:28560446
Effect of Necrosis on the miRNA-mRNA Regulatory Network in CRT-MG Human Astroglioma Cells. PMID:28546527
Large-scale transcriptome analysis reveals arabidopsis metabolic pathways are frequently influenced by different pathogens. PMID:28540497
Comparative transcriptome analyses of a late-maturing mandarin mutant and its original cultivar reveals gene expression profiling associated with citrus fruit maturation. PMID:28533983
Label-Free Quantitative Proteomic Analysis of Chitosan Oligosaccharide-Treated Rice Infected with Southern Rice Black-Streaked Dwarf Virus. PMID:28524115
Post-transcriptional regulation across human tissues. PMID:28481885
agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update. PMID:28472432
The natural history of molecular functions inferred from an extensive phylogenomic analysis of gene ontology data. PMID:28467492
A chromosome conformation capture ordered sequence of the barley genome. PMID:28447635
The draft genome of Ruellia speciosa (Beautiful Wild Petunia: Acanthaceae). PMID:28431014
Identification and analysis of mutational hotspots in oncogenes and tumour suppressors. PMID:28423505
Reduced changes in protein compared to mRNA levels across non-proliferating tissues. PMID:28420336
Transcriptome Sequencing of Dianthus spiculifolius and Analysis of the Genes Involved in Responses to Combined Cold and Drought Stress. PMID:28420173
Identification of miRNA biomarkers of pneumonia using RNA-sequencing and bioinformatics analysis. PMID:28413462
Identification of Biomarkers for Schistosoma-Associated Pulmonary Arterial Hypertension Based on RNA-Seq Data of Mouse Whole Lung Tissues. PMID:28393260
Genome sequence of a rice pest, the white-backed planthopper (Sogatella furcifera). PMID:28369349
In silico prediction of lncRNA function using tissue specific and evolutionary conserved expression. PMID:28361701
Comparative network stratification analysis for identifying functional interpretable network biomarkers. PMID:28361683
Spatial transcriptome analysis provides insights of key gene(s) involved in steroidal saponin biosynthesis in medicinally important herb Trillium govanianum. PMID:28349986
Gene Expression, Protein Function and Pathways of Arabidopsis thaliana Responding to Silver Nanoparticles in Comparison to Silver Ions, Cold, Salt, Drought, and Heat. PMID:28347022
Discovery and evolution of novel hemerythrin genes in annelid worms. PMID:28330441
TheCellMap.org: A Web-Accessible Database for Visualizing and Mining the Global Yeast Genetic Interaction Network. PMID:28325812
Extensive Copy Number Variation in Fermentation-Related Genes Among Saccharomyces cerevisiae Wine Strains. PMID:28292787
Development of Gene-Based SSR Markers in Winged Bean (Psophocarpus tetragonolobus (L.) DC.) for Diversity Assessment. PMID:28282950
A Novel Schema to Enhance Data Quality of Patient Safety Event Reports. PMID:28269943
Bioinformatics analysis on the differentiation of bone mesenchymal stem cells into osteoblasts and adipocytes. PMID:28260060
Notch signaling is significantly suppressed in basal cell carcinomas and activation induces basal cell carcinoma cell apoptosis. PMID:28259916
Unity in defence: honeybee workers exhibit conserved molecular responses to diverse pathogens. PMID:28249569
Transcriptome analysis of two recombinant inbred lines of common bean contrasting for symbiotic nitrogen fixation. PMID:28192540
Var2GO: a web-based tool for gene variants selection. PMID:28185576
Robust Inference of Genetic Exchange Communities from Microbial Genomes Using TF-IDF. PMID:28154557
Regulation of miR-29b-1/a transcription and identification of target mRNAs in CHO-K1 cells. PMID:28137615
Early Transcriptional Changes Induced by Wnt/β-Catenin Signaling in Hippocampal Neurons. PMID:28116168
A review of connectivity map and computational approaches in pharmacogenomics. PMID:28069634
De novo Sequencing and Comparative Transcriptomics of Floral Development of the Distylous Species Lithospermum multiflorum. PMID:28066486
Cloning and Characterization of TaTGW-7A Gene Associated with Grain Weight in Wheat via SLAF-seq-BSA. PMID:28066462
De novo transcriptome and expression profile analyses of the Asian corn borer (Ostrinia furnacalis) reveals relevant flubendiamide response genes. PMID:28056803
Analysis of molecular networks and targets mining of Chinese herbal medicines on anti-aging. PMID:28031022
Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency. PMID:27986076
Gene markers of fracture healing in early stage and the regulatory mechanism during the process using microarray analysis. PMID:27956081
Analysis of the molecular mechanism of osteosarcoma using a bioinformatics approach. PMID:27899966
Genome-wide analysis of miRNAs in the ovaries of Jining Grey and Laiwu Black goats to explore the regulation of fecundity. PMID:27897262
Differentiated regulation of immune-response related genes between LUAD and LUSC subtypes of lung cancers. PMID:27863400
HINT: a database of annotated protein-protein interactions and their homologs. PMID:27857549
Systematic analysis of mRNA expression profiles in NSCLC cell lines to screen metastasis-related genes. PMID:27840927
Transcriptome Profiling of the Phaseolus vulgaris - Colletotrichum lindemuthianum Pathosystem. PMID:27829044
ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions. PMID:27822512
Analysis of Gene Expression in an Inbred Line of Soft-Shell Clams (Mya arenaria) Displaying Growth Heterosis: Regulation of Structural Genes and the NOD2 Pathway. PMID:27822466
Discovery of the molecular mechanisms of the novel chalcone-based Magnaporthe oryzae inhibitor C1 using transcriptomic profiling and co-expression network analysis. PMID:27818889
snpGeneSets: An R Package for Genome-Wide Study Annotation. PMID:27807048
Transcriptome Analysis and Comparison of Marmota monax and Marmota himalayana. PMID:27806133
Natural Selection in the Great Apes. PMID:27795229
Identification of potential biomarkers and drugs for papillary thyroid cancer based on gene expression profile analysis. PMID:27779685
FEDRR: fast, exhaustive detection of redundant hierarchical relations for quality improvement of large biomedical ontologies. PMID:27777627
Integrating Candida albicans metabolism with biofilm heterogeneity by transcriptome mapping. PMID:27765942
Comparative virulence studies and transcriptome analysis of Staphylococcus aureus strains isolated from animals. PMID:27739497
Differential Coexpression Analysis Reveals Extensive Rewiring of Arabidopsis Gene Coexpression in Response to Pseudomonas syringae Infection. PMID:27721457
Mycobacteriophages as Incubators for Intein Dissemination and Evolution. PMID:27703073
Tooth agenesis and orofacial clefting: genetic brothers in arms? PMID:27699475
A machine-learned computational functional genomics-based approach to drug classification. PMID:27695919
Large-scale microarray profiling reveals four stages of immune escape in non-Hodgkin lymphomas. PMID:27622044
The Multivesicular Bodies (MVBs)-Localized AAA ATPase LRD6-6 Inhibits Immunity and Cell Death Likely through Regulating MVBs-Mediated Vesicular Trafficking in Rice. PMID:27618555
Positive Selection Linked with Generation of Novel Mammalian Dentition Patterns. PMID:27613398
Comparative Genomics of Acetobacterpasteurianus Ab3, an Acetic Acid Producing Strain Isolated from Chinese Traditional Rice Vinegar Meiguichu. PMID:27611790
Biochemical and transcriptomic analyses reveal different metabolite biosynthesis profiles among three color and developmental stages in 'Anji Baicha' (Camellia sinensis). PMID:27609021
Suppression of fat deposition in broiler chickens by (-)-hydroxycitric acid supplementation: A proteomics perspective. PMID:27586962
RNALocate: a resource for RNA subcellular localizations. PMID:27543076
The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation. PMID:27538448
Draft genome sequences of three Xanthomonas translucens pathovar reference strains (pv. arrhenatheri, pv. poae and pv. phlei) with different specificities for forage grasses. PMID:27536340
Supplements of vitamins B9 and B12 affect hepatic and mammary gland gene expression profiles in lactating dairy cows. PMID:27526683
Transcriptome analysis in oak uncovers a strong impact of endogenous rhythmic growth on the interaction with plant-parasitic nematodes. PMID:27520023
Regulatory complexity revealed by integrated cytological and RNA-seq analyses of meiotic substages in mouse spermatocytes. PMID:27519264
Analysis of ethanol fermentation mechanism of ethanol producing white-rot fungus Phlebia sp. MG-60 by RNA-seq. PMID:27515927
Transcriptome analysis of seed dormancy after rinsing and chilling in ornamental peaches (Prunus persica (L.) Batsch). PMID:27501791
IGDD: a database of intronless genes in dicots. PMID:27465544
Systems genetics identifies Hp1bp3 as a novel modulator of cognitive aging. PMID:27460150
RichMind: A Tool for Improved Inference from Large-Scale Neuroimaging Results. PMID:27455041
A method for exploring implicit concept relatedness in biomedical knowledge network. PMID:27454167
Reciprocal genomic evolution in the ant-fungus agricultural symbiosis. PMID:27436133
Nuclear import sequence identification in hOAS3 protein. PMID:27379722
Genome sequence of Candida versatilis and comparative analysis with other yeast. PMID:27234221
Predicting Subcellular Localization of Apoptosis Proteins Combining GO Features of Homologous Proteins and Distance Weighted KNN Classifier. PMID:27213149
Identification and Characterization of miRNAs in Chondrus crispus by High-Throughput Sequencing and Bioinformatics Analysis. PMID:27193824
Modular reorganization of the global network of gene regulatory interactions during perinatal human brain development. PMID:27175727
RNA-Seq of Huntington's disease patient myeloid cells reveals innate transcriptional dysregulation associated with proinflammatory pathway activation. PMID:27170315
De novo Transcriptome Analysis and Molecular Marker Development of Two Hemarthria Species. PMID:27148320
Whole-transcriptome analyses of the Sapsaree, a Korean natural monument, before and after exercise-induced stress. PMID:27087983
Microarray-Based Phospho-Proteomic Profiling of Complex Biological Systems. PMID:27084428
Data set for transcriptional response to depletion of the Shoc2 scaffolding protein. PMID:27077079
Genome-Wide Transcriptional Excavation of Dipsacus asperoides Unmasked both Cryptic Asperosaponin Biosynthetic Genes and SSR Markers. PMID:27066018
iTRAQ-based analysis of developmental dynamics in the soybean leaf proteome reveals pathways associated with leaf photosynthetic rate. PMID:27048574
Linking MedDRA(®)-Coded Clinical Phenotypes to Biological Mechanisms by the Ontology of Adverse Events: A Pilot Study on Tyrosine Kinase Inhibitors. PMID:27003817
The Transcript Profile of a Traditional Chinese Medicine, Atractylodes lancea, Revealing Its Sesquiterpenoid Biosynthesis of the Major Active Components. PMID:26990438
Utilizing a structural meta-ontology for family-based quality assurance of the BioPortal ontologies. PMID:26988001
RNA-seq analysis for plant carnivory gene discovery in Nepenthes × ventrata. PMID:26981352
RNA-seq analysis for secondary metabolite pathway gene discovery in Polygonum minus. PMID:26981350
Gene Expression Profiling of Evening Fatigue in Women Undergoing Chemotherapy for Breast Cancer. PMID:26957308
First Microsatellite Markers Developed from Cupuassu ESTs: Application in Diversity Analysis and Cross-Species Transferability to Cacao. PMID:26949967
De novo analysis of transcriptome reveals genes associated with leaf abscission in sugarcane (Saccharum officinarum L.). PMID:26946183
Identification and Analysis of the Porcine MicroRNA in Porcine Cytomegalovirus-Infected Macrophages Using Deep Sequencing. PMID:26943793
Pathway Analysis of Genome-wide Association Study in Childhood Leukemia among Hispanics. PMID:26941364
Human genetic variation database, a reference database of genetic variations in the Japanese population. PMID:26911352
Identification of Differentially Expressed Genes Related to Dehydration Resistance in a Highly Drought-Tolerant Pear, Pyrus betulaefolia, as through RNA-Seq. PMID:26900681
MicroRNA-1228(*) inhibit apoptosis in A549 cells exposed to fine particulate matter. PMID:26867688
Prediction of Genes Related to Positive Selection Using Whole-Genome Resequencing in Three Commercial Pig Breeds. PMID:26865845
Mechanisms Underlying Adaptation to Life in Hydrogen Sulfide-Rich Environments. PMID:26861137
Osteogenic Differentiation of MSC through Calcium Signaling Activation: Transcriptomics and Functional Analysis. PMID:26828589
Bioinformatics Resources for MicroRNA Discovery. PMID:26819547
Global analysis of human duplicated genes reveals the relative importance of whole-genome duplicates originated in the early vertebrate evolution. PMID:26801093
ConceptMetab: exploring relationships among metabolite sets to identify links among biomedical concepts. PMID:26794319
Prediction and characterization of protein-protein interaction network in Bacillus licheniformis WX-02. PMID:26782814
Transcriptomic Analysis Reveals Key Genes Related to Betalain Biosynthesis in Pulp Coloration of Hylocereus polyrhizus. PMID:26779215
COPD subtypes identified by network-based clustering of blood gene expression. PMID:26773458
Network-Based Comparative Analysis of Arabidopsis Immune Responses to Golovinomyces orontii and Botrytis cinerea Infections. PMID:26750561
A proteogenomic approach to understand splice isoform functions through sequence and expression-based computational modeling. PMID:26740460
The Proteomic Response of Arabidopsis thaliana to Cadmium Sulfide Quantum Dots, and Its Correlation with the Transcriptomic Response. PMID:26732871
Identification and characterization of microRNAs in Eucheuma denticulatum by high-throughput sequencing and bioinformatics analysis. PMID:26717154
Semantics-Based Composition of Integrated Cardiomyocyte Models Motivated by Real-World Use Cases. PMID:26716837
Genome-wide analysis of WRKY transcription factors in white pear (Pyrus bretschneideri) reveals evolution and patterns under drought stress. PMID:26704366
Method developments to extract proteins from oil palm chromoplast for proteomic analysis. PMID:26702380
Differential Expression of Hepatic Genes of the Greater Horseshoe Bat (Rhinolophus ferrumequinum) between the Summer Active and Winter Torpid States. PMID:26698122
Genome-wide analysis of microRNAs identifies the lipid metabolism pathway to be a defining factor in adipose tissue from different sheep. PMID:26690086
Draft Genome Sequence of Francisella tularensis Strain 410108 from Tibet, China. PMID:26679594
De novo dominant ASXL3 mutations alter H2A deubiquitination and transcription in Bainbridge-Ropers syndrome. PMID:26647312
Intein Clustering Suggests Functional Importance in Different Domains of Life. PMID:26609079
Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources. PMID:26589635
Psychiatric gene discoveries shape evidence on ADHD's biology. PMID:26573769
A potential endophenotype for Alzheimer's disease: cerebrospinal fluid clusterin. PMID:26545630
Effects of Controlled Cortical Impact on the Mouse Brain Vasculome. PMID:26528928
Genes with stable DNA methylation levels show higher evolutionary conservation than genes with fluctuant DNA methylation levels. PMID:26515589
Transcriptome Changes during the Life Cycle of the Red Sponge, Mycale phyllophila (Porifera, Demospongiae, Poecilosclerida). PMID:26492274
Genome-wide protein-protein interactions and protein function exploration in cyanobacteria. PMID:26490033
An overview of bioinformatics methods for modeling biological pathways in yeast. PMID:26476430
Differences in the Early Development of Human and Mouse Embryonic Stem Cells. PMID:26473594
Draft Genome Sequence of Burkholderia pseudomallei Strain 350105, Isolated in Hainan, China, in 1976. PMID:26472827
Quantitative phosphoproteomics reveals new roles for the protein phosphatase PP6 in mitotic cells. PMID:26462736
Proteomic Analysis of the Ubiquitin Landscape in the Drosophila Embryonic Nervous System and the Adult Photoreceptor Cells. PMID:26460970
Comparative genome analysis of the candidate functional starter culture strains Lactobacillus fermentum 222 and Lactobacillus plantarum 80 for controlled cocoa bean fermentation processes. PMID:26459565
Dynamic Changes in the Transcriptome and Methylome of Chlamydomonas reinhardtii throughout Its Life Cycle. PMID:26450704
The Nuclear Proteome of a Vertebrate. PMID:26441354
Prioritizing Clinically Relevant Copy Number Variation from Genetic Interactions and Gene Function Data. PMID:26437450
Genome-Wide Detection and Analysis of Multifunctional Genes. PMID:26436655
Transcriptome sequencing and analysis of major genes involved in calcium signaling pathways in pear plants (Pyrus calleryana Decne.). PMID:26424153
Characterization of the Transcriptional Complexity of the Receptive and Pre-receptive Endometria of Dairy Goats. PMID:26373443
Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases. PMID:26362267
De novo assembly of the Japanese lawngrass (Zoysia japonica Steud.) root transcriptome and identification of candidate unigenes related to early responses under salt stress. PMID:26347751
Large scale transcriptome analysis reveals interplay between development of forest trees and a beneficial mycorrhiza helper bacterium. PMID:26328611
Deciphering Cis-Regulatory Element Mediated Combinatorial Regulation in Rice under Blast Infected Condition. PMID:26327607
Identification of Aberrant Chromosomal Regions in Human Breast Cancer Using Gene Expression Data and Related Gene Information. PMID:26319982
Protein-Protein Interactions Mediated by Helical Tertiary Structure Motifs. PMID:26302018
Non-immune immunoglobulins shield Schistosoma japonicum from host immunorecognition. PMID:26299686
Circadian systems biology: When time matters. PMID:26288701
Algorithms for modeling global and context-specific functional relationship networks. PMID:26254431
Unique ability of pandemic influenza to downregulate the genes involved in neuronal disorders. PMID:26246405
Unfoldome variation upon plant-pathogen interactions: strawberry infection by Colletotrichum acutatum. PMID:26245354
In-depth analysis of the critical genes and pathways in colorectal cancer. PMID:26239303
Rapastinel (GLYX-13) has therapeutic potential for the treatment of post-traumatic stress disorder: Characterization of a NMDA receptor-mediated metaplasticity process in the medial prefrontal cortex of rats. PMID:26210936
Reagent and Data Resources for Investigation of RNA Binding Protein Functions in Drosophila melanogaster Cultured Cells. PMID:26199285
Fitness Trade-Offs Determine the Role of the Molecular Chaperonin GroEL in Buffering Mutations. PMID:26116858
Co-modulation analysis of gene regulation in breast cancer reveals complex interplay between ESR1 and ERBB2 genes. PMID:26100352
Gene expression profiling analysis of osteosarcoma cell lines. PMID:26096802
Association of Protein Translation and Extracellular Matrix Gene Sets with Breast Cancer Metastasis: Findings Uncovered on Analysis of Multiple Publicly Available Datasets Using Individual Patient Data Approach. PMID:26080057
Systems biology of neurodegenerative diseases. PMID:26065845
Transcriptome sequencing and annotation of the polychaete Hermodice carunculata (Annelida, Amphinomidae). PMID:26059236
De Novo Assembly of Bitter Gourd Transcriptomes: Gene Expression and Sequence Variations in Gynoecious and Monoecious Lines. PMID:26047102
Detection of miRNA regulatory effect on triple negative breast cancer transcriptome. PMID:26046581
Identification association of drug-disease by using functional gene module for breast cancer. PMID:26045063
Maternal and zygotic transcriptomes in the appendicularian, Oikopleura dioica: novel protein-encoding genes, intra-species sequence variations, and trans-spliced RNA leader. PMID:26032664
De novo transcriptome characterization and gene expression profiling of the desiccation tolerant moss Bryum argenteum following rehydration. PMID:26016800
Identification and Expression Analysis of Candidate Genes Associated with Defense Responses to Phytophthora capsici in Pepper Line "PI 201234". PMID:25993303
De Novo Transcriptome Sequencing of Low Temperature-Treated Phlox subulata and Analysis of the Genes Involved in Cold Stress. PMID:25938968
The coordinated action of the MVB pathway and autophagy ensures cell survival during starvation. PMID:25902403
The uniform-score gene set analysis for identifying common pathways associated with different diabetes traits. PMID:25898945
Mongolian Almond (Prunus mongolica Maxim): The Morpho-Physiological, Biochemical and Transcriptomic Response to Drought Stress. PMID:25893685
REGULATOR: a database of metazoan transcription factors and maternal factors for developmental studies. PMID:25880930
Transcriptome responses to Ralstonia solanacearum infection in the roots of the wild potato Solanum commersonii. PMID:25880642
High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in Jute. PMID:25861616
Transcriptomic analysis revealed the mechanism of oil dynamic accumulation during developing Siberian apricot (Prunus sibirica L.) seed kernels for the development of woody biodiesel. PMID:25834637
Malleable nature of mRNA-protein compositional complementarity and its functional significance. PMID:25753660
Prediction of protein-protein interactions related to protein complexes based on protein interaction networks. PMID:25722972
Deep mRNA sequencing of the Tritonia diomedea brain transcriptome provides access to gene homologues for neuronal excitability, synaptic transmission and peptidergic signalling. PMID:25719197
De novo assembly and characterization of Oryza officinalis leaf transcriptome by using RNA-seq. PMID:25713814
Host proteome correlates of vaccine-mediated enhanced disease in a mouse model of respiratory syncytial virus infection. PMID:25694607
Enrichment of an intraspecific genetic map of upland cotton by developing markers using parental RAD sequencing. PMID:25656006
Genomic and transcriptomic analysis of the endophytic fungus Pestalotiopsis fici reveals its lifestyle and high potential for synthesis of natural products. PMID:25623211
Complete Genome Sequence of Bacillus pumilus Strain WP8, an Efficient Plant Growth-Promoting Rhizobacterium. PMID:25614565
RNA-Seq analysis and transcriptome assembly for blackberry (Rubus sp. Var. Lochness) fruit. PMID:25608670
De novo assembly and characterization of narrow-ridged finless porpoise renal transcriptome and identification of candidate genes involved in osmoregulation. PMID:25608655
Identification and characterization of microRNAs from Chinese pollination constant non-astringent persimmon using high-throughput sequencing. PMID:25604351
A field guide to whole-genome sequencing, assembly and annotation. PMID:25553065
Regulation of gene expression in HBV- and HCV-related hepatocellular carcinoma: integrated GWRS and GWGS analyses. PMID:25550913
Convergent genetic and expression data implicate immunity in Alzheimer's disease. PMID:25533204
The syntaxin 31-induced gene, LESION SIMULATING DISEASE1 (LSD1), functions in Glycine max defense to the root parasite Heterodera glycines. PMID:25530246
SCMHBP: prediction and analysis of heme binding proteins using propensity scores of dipeptides. PMID:25522279
Assessment of subnetwork detection methods for breast cancer. PMID:25520555
Comparison of whole blood and peripheral blood mononuclear cell gene expression for evaluation of the perioperative inflammatory response in patients with advanced heart failure. PMID:25517110
Transcriptomic analysis of temperature responses of Aspergillus kawachii during barley koji production. PMID:25501485
Categorizer: a tool to categorize genes into user-defined biological groups based on semantic similarity. PMID:25495442
Impact of analytic provenance in genome analysis. PMID:25435180
Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms. PMID:25431329
The evolution and adaptive potential of transcriptional variation in sticklebacks--signatures of selection and widespread heritability. PMID:25429004
From genes to behavior: placing cognitive models in the context of biological pathways. PMID:25414628
HIV-1, human interaction database: current status and new features. PMID:25378338
Transcriptomic analysis of the mussel Elliptio complanata identifies candidate stress-response genes and an abundance of novel or noncoding transcripts. PMID:25375103
Genetic resources for advanced biofuel production described with the Gene Ontology. PMID:25346727
Benzo pyrene-induced DNA adducts and gene expression profiles in target and non-target organs for carcinogenesis in mice. PMID:25297811
Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam. PMID:25293379
A reappraisal of how to build modular, reusable models of biological systems. PMID:25275523
Detecting SNPs underlying domestication-related traits in soybean. PMID:25258093
GeneMANIA: Fast gene network construction and function prediction for Cytoscape. PMID:25254104
A phylogenomic census of molecular functions identifies modern thermophilic archaea as the most ancient form of cellular life. PMID:25249790
Gene expression and pathway analysis of effects of the CMAH deactivation on mouse lung, kidney and heart. PMID:25229777
A root-expressed L-phenylalanine:4-hydroxyphenylpyruvate aminotransferase is required for tropane alkaloid biosynthesis in Atropa belladonna. PMID:25228340
The influence of mtDNA deletion on lung cancer cells under the conditions of hypoxia and irradiation. PMID:25218334
Adverse drug reaction prediction using scores produced by large-scale drug-protein target docking on high-performance computing machines. PMID:25191698
Interactome analysis of the influenza A virus transcription/replication machinery identifies protein phosphatase 6 as a cellular factor required for efficient virus replication. PMID:25187537
The temporal transcriptomic response of Pinus massoniana seedlings to phosphorus deficiency. PMID:25165828
Genome-wide transcriptome analysis shows extensive alternative RNA splicing in the zoonotic parasite Schistosoma japonicum. PMID:25156522
A pilot examination of the genome-wide DNA methylation signatures of subjects entering and exiting short-term alcohol dependence treatment programs. PMID:25147915
A feasibility study to identify proteins in the residual Pap test fluid of women with normal cytology by mass spectrometry-based proteomics. PMID:25097468
Prediction and functional analysis of the sweet orange protein-protein interaction network. PMID:25091279
Effect of histone deacetylase inhibitor JNJ-26481585 in pain. PMID:25085711
Gene loss rather than gene gain is associated with a host jump from monocots to dicots in the Smut Fungus Melanopsichium pennsylvanicum. PMID:25062916
Predicting disease-related proteins based on clique backbone in protein-protein interaction network. PMID:25013377
Transcriptomic landscape of prophase I sunflower male meiocytes. PMID:24982667
Interaction networks of prion, prionogenic and prion-like proteins in budding yeast, and their role in gene regulation. PMID:24972093
Computational prediction of disease microRNAs in domestic animals. PMID:24970281
Analysis of the transcriptome of Erigeron breviscapus uncovers putative scutellarin and chlorogenic acids biosynthetic genes and genetic markers. PMID:24956277
Biological overlap of attention-deficit/hyperactivity disorder and autism spectrum disorder: evidence from copy number variants. PMID:24954825
A controlled vocabulary for pathway entities and events. PMID:24951798
Genome-wide identification and characterization of long intergenic non-coding RNAs in Ganoderma lucidum. PMID:24932683
Genome and transcriptome of the porcine whipworm Trichuris suis. PMID:24929829
Discovering functional modules across diverse maize transcriptomes using COB, the Co-expression Browser. PMID:24922320
Identification and bioinformatics analysis of microRNAs associated with stress and immune response in serum of heat-stressed and normal Holstein cows. PMID:24917036
CELLO2GO: a web server for protein subCELlular LOcalization prediction with functional gene ontology annotation. PMID:24911789
Automated semantic annotation of rare disease cases: a case study. PMID:24903515
A systematic review of microRNA expression profiling studies in human gastric cancer. PMID:24902858
Regression hidden Markov modeling reveals heterogeneous gene expression regulation: a case study in mouse embryonic stem cells. PMID:24884369
OWL reasoning framework over big biological knowledge network. PMID:24877076
Predicting response to preoperative chemotherapy agents by identifying drug action on modeled microRNA regulation networks. PMID:24848634
Transduction motif analysis of gastric cancer based on a human signaling network. PMID:24838641
Biomarker gene signature discovery integrating network knowledge. PMID:24832044
Whole blood gene expression profile associated with spontaneous preterm birth in women with threatened preterm labor. PMID:24828675
Finding sequences for over 270 orphan enzymes. PMID:24826896
Ensemble positive unlabeled learning for disease gene identification. PMID:24816822
Profiling of microRNAs under wound treatment in Aquilaria sinensis to identify possible microRNAs involved in agarwood formation. PMID:24795531
Essential functional modules for pathogenic and defensive mechanisms in Candida albicans infections. PMID:24757665
Overrepresentation of glutamate signaling in Alzheimer's disease: network-based pathway enrichment using meta-analysis of genome-wide association studies. PMID:24755620
Transcriptome analysis of the Portunus trituberculatus: de novo assembly, growth-related gene identification and marker discovery. PMID:24722690
PSEA: Kinase-specific prediction and analysis of human phosphorylation substrates. PMID:24681538
miR-499 protects cardiomyocytes from H 2O 2-induced apoptosis via its effects on Pdcd4 and Pacs2. PMID:24646523
Evidence for contribution of epigenetic mechanisms in the pathogenesis of systemic mast cell activation disease. PMID:24622794
BambooGDB: a bamboo genome database with functional annotation and an analysis platform. PMID:24602877
Modulation of neuronal proteome profile in response to Japanese encephalitis virus infection. PMID:24599148
Hierarchical partitioning of metazoan protein conservation profiles provides new functional insights. PMID:24594619
Pathway analyses implicate glial cells in schizophrenia. PMID:24586781
Computational prediction of the human-microbial oral interactome. PMID:24576332
COMPARTMENTS: unification and visualization of protein subcellular localization evidence. PMID:24573882
Weighted set enrichment of gene expression data. PMID:24565001
Towards integrative gene functional similarity measurement. PMID:24564710
Classifying prion and prion-like phenomena. PMID:24549098
Polygenic inheritance of paclitaxel-induced sensory peripheral neuropathy driven by axon outgrowth gene sets in CALGB 40101 (Alliance). PMID:24513692
Genome-wide transcriptome analysis of Chinese pollination-constant nonastringent persimmon fruit treated with ethanol. PMID:24507483
Global patterns of protein domain gain and loss in superkingdoms. PMID:24499935
Comparative analysis of proteomes and functionomes provides insights into origins of cellular diversification. PMID:24492748
Citrus sinensis annotation project (CAP): a comprehensive database for sweet orange genome. PMID:24489955
A comparative study of Whi5 and retinoblastoma proteins: from sequence and structure analysis to intracellular networks. PMID:24478706
Construction of pancreatic cancer double-factor regulatory network based on chip data on the transcriptional level. PMID:24469724
PragmatiX: An Interactive Tool for Visualizing the Creation Process Behind Collaboratively Engineered Ontologies. PMID:24465189
Pathway-based analysis of the hidden genetic heterogeneities in cancers. PMID:24462714
Search for age-related macular degeneration risk variants in Alzheimer disease genes and pathways. PMID:24439028
DBM-DB: the diamondback moth genome database. PMID:24434032
Gene prioritization of resistant rice gene against Xanthomas oryzae pv. oryzae by using text mining technologies. PMID:24371834
Changes in gene expression within the extended amygdala following binge-like alcohol drinking by adolescent alcohol-preferring (P) rats. PMID:24355552
Comparison of ultra-conserved elements in drosophilids and vertebrates. PMID:24349264
Discrimination between adenocarcinoma and normal pancreatic ductal fluid by proteomic and glycomic analysis. PMID:24328148
Proteomic identification of novel plasma kallikrein substrates in the astrocyte secretome. PMID:24323554
Fermentation stage-dependent adaptations of Bacillus licheniformis during enzyme production. PMID:24313996
Multiplex cytological profiling assay to measure diverse cellular states. PMID:24312513
Transcriptome characterization and sequencing-based identification of drought-responsive genes in potato. PMID:24293150
De novo transcriptome sequencing of radish (Raphanus sativus L.) and analysis of major genes involved in glucosinolate metabolism. PMID:24279309
Discovery of genes related to witches broom disease in Paulownia tomentosa × Paulownia fortunei by a De Novo assembled transcriptome. PMID:24278262
Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data. PMID:24244129
Influence of differentially expressed genes from suicide post-mortem study on personality traits as endophenotypes on healthy subjects and suicide attempters. PMID:24241531
Quantitative network measures as biomarkers for classifying prostate cancer disease states: a systems approach to diagnostic biomarkers. PMID:24236006
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. PMID:24217912
Protein kinase C epsilon and genetic networks in osteosarcoma metastasis. PMID:24216982
Classification of α-helical membrane proteins using predicted helix architectures. PMID:24204844
Gene expression within the extended amygdala of 5 pairs of rat lines selectively bred for high or low ethanol consumption. PMID:24157127
Identifying the candidate genes involved in the calyx abscission process of 'Kuerlexiangli' (Pyrus sinkiangensis Yu) by digital transcript abundance measurements. PMID:24152304
Gleaning evolutionary insights from the genome sequence of a probiotic yeast Saccharomyces boulardii. PMID:24148866
Generation and analysis of a large-scale expressed sequence Tag database from a full-length enriched cDNA library of developing leaves of Gossypium hirsutum L. PMID:24146870
Dynamic expression of miR-132, miR-212, and miR-146 in the brain of different hosts infected with Angiostrongylus cantonensis. PMID:24142285
Genome-wide survey on genomic variation, expression divergence, and evolution in two contrasting rice genotypes under high salinity stress. PMID:24121498
Complete Genome Sequence of Encapsulated Haemophilus influenzae Type f KR494, an Invasive Isolate That Caused Necrotizing Myositis. PMID:24092777
Transcriptome sequencing and differential gene expression analysis of delayed gland morphogenesis in Gossypium australe during seed germination. PMID:24073262
Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data. PMID:24053776
Transcriptome profiling of Gossypium barbadense inoculated with Verticillium dahliae provides a resource for cotton improvement. PMID:24053558
Statistical properties on semiparametric regression for evaluating pathway effects. PMID:24014933
Extensive cooperation of immune master regulators IRF3 and NFκB in RNA Pol II recruitment and pause release in human innate antiviral transcription. PMID:23994473
Mesenchymal stem cells from human umbilical cord express preferentially secreted factors related to neuroprotection, neurogenesis, and angiogenesis. PMID:23991127
Genome-wide gene expression profiling of stress response in a spinal cord clip compression injury model. PMID:23984903
Predicting time to ovarian carcinoma recurrence using protein markers. PMID:23945238
Complete genome sequence and comparative analysis of Acetobacter pasteurianus 386B, a strain well-adapted to the cocoa bean fermentation ecosystem. PMID:23902333
Transcriptome of Atlantic cod (Gadus morhua L.) early embryos from farmed and wild broodstocks. PMID:23887676
Analysis of the genomic response of human prostate cancer cells to histone deacetylase inhibitors. PMID:23880963
Deep brain stimulation modulates nonsense-mediated RNA decay in Parkinson's patients leukocytes. PMID:23865419
Improved network community structure improves function prediction. PMID:23852097
Gene expression profiles of metabolic aggressiveness and tumor recurrence in benign meningioma. PMID:23840654
eFindSite: improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands. PMID:23838840
Boosting probabilistic graphical model inference by incorporating prior knowledge from multiple sources. PMID:23826291
Natural selection in a bangladeshi population from the cholera-endemic ganges river delta. PMID:23825302
Identification of salt treated proteins in sorghum using gene ontology linkage. PMID:23814435
Mining breast cancer genes with a network based noise-tolerant approach. PMID:23799982
Transcriptional response of honey bee larvae infected with the bacterial pathogen Paenibacillus larvae. PMID:23762370
Redundancy control in pathway databases (ReCiPa): an application for improving gene-set enrichment analysis in Omics studies and "Big data" biology. PMID:23758478
FIDEA: a server for the functional interpretation of differential expression analysis. PMID:23754850
Data integration through proximity-based networks provides biological principles of organization across scales. PMID:23749845
Proteomic analysis of schistosomiasis japonica vaccine candidate antigens recognized by UV-attenuated cercariae-immunized porcine serum IgG2. PMID:23715679
Changes in gene expression within the ventral tegmental area following repeated excessive binge-like alcohol drinking by alcohol-preferring (P) rats. PMID:23714385
Comparative genomic and transcriptomic analysis of tandemly and segmentally duplicated genes in rice. PMID:23696832
Rapid catalytic template searching as an enzyme function prediction procedure. PMID:23675414
Genome-wide patterns of codon bias are shaped by natural selection in the purple sea urchin, Strongylocentrotus purpuratus. PMID:23637123
Steiner tree methods for optimal sub-network identification: an empirical study. PMID:23627667
Investigating the concordance of Gene Ontology terms reveals the intra- and inter-platform reproducibility of enrichment analysis. PMID:23627640
High mobility group N proteins modulate the fidelity of the cellular transcriptional profile in a tissue- and variant-specific manner. PMID:23620591
Comprehensive annotation of secondary metabolite biosynthetic genes and gene clusters of Aspergillus nidulans, A. fumigatus, A. niger and A. oryzae. PMID:23617571
Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts. PMID:23599415
Function relaxation followed by diversifying selection after whole-genome duplication in flowering plants. PMID:23580595
Identification of genes related to agarwood formation: transcriptome analysis of healthy and wounded tissues of Aquilaria sinensis. PMID:23565705
Comparative GO: a web application for comparative gene ontology and gene ontology-based gene selection in bacteria. PMID:23536820
De-novo assembly and characterization of the transcriptome of Metschnikowia fructicola reveals differences in gene expression following interaction with Penicillium digitatum and grapefruit peel. PMID:23496978
Predictability of gene ontology slim-terms from primary structure information in Embryophyta plant proteins. PMID:23441934
Precise generation of systems biology models from KEGG pathways. PMID:23433509
Global transcriptome analysis and identification of a CONSTANS-like gene family in the orchid Erycina pusilla. PMID:23417646
Genome-wide analysis of protein disorder in Arabidopsis thaliana: implications for plant environmental adaptation. PMID:23408995
Visualization of protein interaction networks: problems and solutions. PMID:23368786
Transcription and redox enzyme activities: comparison of equilibrium and disequilibrium levels in the three-spined stickleback. PMID:23363636
Use of Gene Ontology Annotation to understand the peroxisome proteome in humans. PMID:23327938
Genetic variation and expression diversity between grain and sweet sorghum lines. PMID:23324212
Comparison of nanotube-protein corona composition in cell culture media. PMID:23322550
De-novo characterization of the soft-shelled turtle Pelodiscus sinensis transcriptome using Illumina RNA-Seq technology. PMID:23303632
Identification of MFS proteins in sorghum using semantic similarity. PMID:23299296
Novel features of a PIWI-like protein homolog in the parasitic protozoan Leishmania. PMID:23285111
Disease gene identification by random walk on multigraphs merging heterogeneous genomic and phenotype data. PMID:23282070
Computational analysis of transcriptome of Indian major carp, Labeo rohita (Hamilton-Buchanan, 1822) for functional annotation. PMID:23275698
OPTIMAS-DW: a comprehensive transcriptomics, metabolomics, ionomics, proteomics and phenomics data resource for maize. PMID:23272737
Systems biology, bioinformatics, and biomarkers in neuropsychiatry. PMID:23269912
Multiscale integration of -omic, imaging, and clinical data in biomedical informatics. PMID:23231990
A pathway-based analysis provides additional support for an immune-related genetic susceptibility to Parkinson's disease. PMID:23223016
Identification of pharmacological targets in amyotrophic lateral sclerosis through genomic analysis of deregulated genes and pathways. PMID:23204922
KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters. PMID:23193276
Predicting secretory proteins of malaria parasite by incorporating sequence evolution information into pseudo amino acid composition via grey system model. PMID:23189138
Transcriptome analysis of symptomatic and recovered leaves of geminivirus-infected pepper (Capsicum annuum). PMID:23185982
Genomic resources for a model in adaptation and speciation research: characterization of the Poecilia mexicana transcriptome. PMID:23170846
Building a statistical model for predicting cancer genes. PMID:23166609
Improved gene ontology annotation for biofilm formation, filamentous growth, and phenotypic switching in Candida albicans. PMID:23143685
Assessing the gain of biological data integration in gene networks inference. PMID:23134775
Non-gaussian distributions affect identification of expression patterns, functional annotation, and prospective classification in human cancer genomes. PMID:23118863
Comparative analysis of differentially expressed genes in Sika deer antler at different stages. PMID:23073784
Cross-Ontology multi-level association rule mining in the Gene Ontology. PMID:23071802
MetNet Online: a novel integrated resource for plant systems biology. PMID:23066841
A novel neural response algorithm for protein function prediction. PMID:23046521
Using rule-based natural language processing to improve disease normalization in biomedical text. PMID:23043124
Predicting the extension of biomedical ontologies. PMID:23028267
Convergent evolution of modularity in metabolic networks through different community structures. PMID:22974099
GO2PUB: Querying PubMed with semantic expansion of gene ontology terms. PMID:22958570
Reconstructing differentially co-expressed gene modules and regulatory networks of soybean cells. PMID:22938179
Positive-unlabeled learning for disease gene identification. PMID:22923290
Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya. PMID:22920653
The chordate proteome history database. PMID:22904610
Antagonism pattern detection between microRNA and target expression in Ewing's sarcoma. PMID:22848594
Fish lateral line innovation: insights into the evolutionary genomic dynamics of a unique mechanosensory organ. PMID:22844072
Identification of drought responsive proteins using gene ontology hierarchy. PMID:22829738
Gene expression signatures associated with the in vitro resistance to two tyrosine kinase inhibitors, nilotinib and imatinib. PMID:22829191
Beyond captions: linking figures with abstract sentences in biomedical articles. PMID:22815711
The genetics of addiction-a translational perspective. PMID:22806211
Multiscale modeling and data integration in the virtual physiological rat project. PMID:22805979
The Choice between MapMan and Gene Ontology for Automated Gene Function Prediction in Plant Science. PMID:22754563
Multiple genetic interaction experiments provide complementary information useful for gene function prediction. PMID:22737063
The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. PMID:22720753
A simple method for analyzing exome sequencing data shows distinct levels of nonsynonymous variation for human immune and nervous system genes. PMID:22701602
Insecticide resistance mechanisms in the green peach aphid Myzus persicae (Hemiptera: Aphididae) I: A transcriptomic survey. PMID:22685538
The language of gene ontology: a Zipf's law analysis. PMID:22676436
Widespread uncoupling between transcriptome and translatome variations after a stimulus in mammalian cells. PMID:22672192
Pyrosequencing-based comparative genome analysis of Vibrio vulnificus environmental isolates. PMID:22662170
Expressed sequence tags in cultivated peanut (Arachis hypogaea): discovery of genes in seed development and response to Ralstonia solanacearum challenge. PMID:22648474
Transcriptome profiling of the demosponge Amphimedon queenslandica reveals genome-wide events that accompany major life cycle transitions. PMID:22646746
Transcriptome profiling and in silico analysis of somatic embryos in Japanese larch (Larix leptolepis). PMID:22622308
Phosphosignature predicts dasatinib response in non-small cell lung cancer. PMID:22617229
Deficiency in nucleotide excision repair family gene activity, especially ERCC3, is associated with non-pigmented hair fiber growth. PMID:22615732
Cardiovascular genomics: a biomarker identification pipeline. PMID:22614726
Inferring carbon sources from gene expression profiles using metabolic flux models. PMID:22606312
Sequencing and analysis of the Mediterranean amphioxus (Branchiostoma lanceolatum) transcriptome. PMID:22590565
miRFANs: an integrated database for Arabidopsis thaliana microRNA function annotations. PMID:22583976
Gene expression in the ventral tegmental area of 5 pairs of rat lines selectively bred for high or low ethanol consumption. PMID:22579914
Open semantic annotation of scientific publications using DOMEO. PMID:22541592
PASSIOMA: Exploring Expressed Sequence Tags during Flower Development in Passiflora spp. PMID:22536117
Genome-wide DNA methylation scan in major depressive disorder. PMID:22511943
Characterization of domain-peptide interaction interface: prediction of SH3 domain-mediated protein-protein interaction network in yeast by generic structure-based models. PMID:22468754
Sample-level enrichment analysis unravels shared stress phenotypes among multiple cancer types. PMID:22458606
Bayesian semiparametric regression models for evaluating pathway effects on continuous and binary clinical outcomes. PMID:22438129
Correlation of Global MicroRNA Expression With Basal Cell Carcinoma Subtype. PMID:22384406
Bi-directional semantic similarity for gene ontology to optimize biological and clinical analyses. PMID:22374934
An ensemble classifier for eukaryotic protein subcellular location prediction using gene ontology categories and amino acid hydrophobicity. PMID:22303481
The diversity of cyanobacterial metabolism: genome analysis of multiple phototrophic microorganisms. PMID:22300633
Structure- and sequence-based function prediction for non-homologous proteins. PMID:22270458
The genetic control of growth rate: a systems biology study in yeast. PMID:22244311
Normalized Affymetrix expression data are biased by G-quadruplex formation. PMID:22199258
De novo characterization of the antler tip of Chinese Sika deer transcriptome and analysis of gene expression related to rapid growth. PMID:22198337
Computational identification of protein-protein interactions in rice based on the predicted rice interactome network. PMID:22196356
Structural measures for network biology using QuACN. PMID:22195644
Systematic identification of functional modules and cis-regulatory elements in Arabidopsis thaliana. PMID:22168340
Human proteome-scale structural modeling of E2-E3 interactions exploiting interface motifs. PMID:22149024
Identifying highly conserved and highly differentiated gene ontology categories in human populations. PMID:22140477
The entomopathogenic bacterial endosymbionts Xenorhabdus and Photorhabdus: convergent lifestyles from divergent genomes. PMID:22125637
Gene expression divergence is coupled to evolution of DNA structure in coding regions. PMID:22125484
An iterative network partition algorithm for accurate identification of dense network modules. PMID:22121225
Construction and EST sequencing of full-length, drought stress cDNA libraries for common beans (Phaseolus vulgaris L.). PMID:22118559
Computational prediction of host-parasite protein interactions between P. falciparum and H. sapiens. PMID:22114664
GONUTS: the Gene Ontology Normal Usage Tracking System. PMID:22110029
Defining the role of essential genes in human disease. PMID:22096564
Ascaris suum draft genome. PMID:22031327
Ebola virion attachment and entry into human macrophages profoundly effects early cellular gene expression. PMID:22028943
Mapping cell fate decisions that occur during soybean defense responses. PMID:21986905
Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris. PMID:21964414
Genomic basis of endosymbiont-conferred protection against an insect parasitoid. PMID:21948522
Bioinformatics and systems biology of the lipidome. PMID:21939287
Quantification of protein group coherence and pathway assignment using functional association. PMID:21929787
Systems biology and the future of medicine. PMID:21928407
MicroRNA-34a modulates genes involved in cellular motility and oxidative phosphorylation in neural precursors derived from human umbilical cord mesenchymal stem cells. PMID:21923954
Introduction to network analysis in systems biology. PMID:21917719
Distant cis-regulatory elements in human skeletal muscle differentiation. PMID:21907276
Disjunctive shared information between ontology concepts: application to Gene Ontology. PMID:21884591
Hypothesis-driven candidate genes for schizophrenia compared to genome-wide association results. PMID:21854684
Generation, annotation and analysis of first large-scale expressed sequence tags from developing fiber of Gossypium barbadense L. PMID:21829504
Why is there a lack of consensus on molecular subgroups of glioblastoma? Understanding the nature of biological and statistical variability in glioblastoma expression data. PMID:21829433
How the gene ontology evolves. PMID:21819553
Maps of protein structure space reveal a fundamental relationship between protein structure and function. PMID:21737750
The panorama of physiological responses and gene expression of whole plant of maize inbred line YQ7-96 at the three-leaf stage under water deficit and re-watering. PMID:21735236
Towards resolving the transcription factor network controlling myelin gene expression. PMID:21729871
Transcriptome sequencing and de novo analysis for Yesso scallop (Patinopecten yessoensis) using 454 GS FLX. PMID:21720557
DOSim: an R package for similarity between diseases based on Disease Ontology. PMID:21714896
On the origins of Mendelian disease genes in man: the impact of gene duplication. PMID:21705381
Computable visually observed phenotype ontological framework for plants. PMID:21702966
Comparative analysis of proteome and transcriptome variation in mouse. PMID:21695224
Applications of different weighting schemes to improve pathway-based analysis. PMID:21687588
Identification of SNP and SSR markers in eggplant using RAD tag sequencing. PMID:21663628
A transcriptome analysis of mitten crab testes (Eriocheir sinensis). PMID:21637557
Developing a kidney and urinary pathway knowledge base. PMID:21624162
An open annotation ontology for science on web 3.0. PMID:21624159
Genome-wide comparison of two poplar genotypes with different growth rates. PMID:21614644
Shared molecular strategies of the malaria parasite P. falciparum and the human virus HIV-1. PMID:21586753
CASCADE_SCAN: mining signal transduction network from high-throughput data based on steepest descent method. PMID:21575263
PRIN: a predicted rice interactome network. PMID:21575196
In vivo liver regeneration potential of human induced pluripotent stem cells from diverse origins. PMID:21562231
Signalogs: orthology-based identification of novel signaling pathway components in three metazoans. PMID:21559328
mirConnX: condition-specific mRNA-microRNA network integrator. PMID:21558324
BeeSpace Navigator: exploratory analysis of gene function using semantic indexing of biological literature. PMID:21558175
Mining the TRAF6/p62 interactome for a selective ubiquitination motif. PMID:21554762
Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88. PMID:21543515
Sequencing and characterization of the guppy (Poecilia reticulata) transcriptome. PMID:21507250
The human postsynaptic density shares conserved elements with proteomes of unicellular eukaryotes and prokaryotes. PMID:21503141
Analysis of coevolving gene families using mutually exclusive orthologous modules. PMID:21498882
Discordant and chameleon sequences: their distribution and implications for amyloidogenicity. PMID:21432934
GO-Module: functional synthesis and improved interpretation of Gene Ontology patterns. PMID:21421553
The expanded human disease network combining protein-protein interaction information. PMID:21386875
Evolutionary transients in the rice transcriptome. PMID:21382590
Identification of Parkinson's disease candidate genes using CAESAR and screening of MAPT and SNCAIP in South African Parkinson's disease patients. PMID:21344240
Genome-wide discovery of missing genes in biological pathways of prokaryotes. PMID:21342538
The what, where, how and why of gene ontology--a primer for bioinformaticians. PMID:21330331
Benefits of random-priming: exhaustive survey of a cDNA library from lung tissue of a SARS patient. PMID:21328370
Whole-genome resequencing shows numerous genes with nonsynonymous SNPs in the Japanese native cattle Kuchinoshima-Ushi. PMID:21310019
Time course of gene expression profiling in the liver of experimental mice infected with Echinococcus multilocularis. PMID:21283804
Gene expression profiling of connective tissue growth factor (CTGF) stimulated primary human tenon fibroblasts reveals an inflammatory and wound healing response in vitro. PMID:21245951
Gene Expression Signatures of Peripheral Blood Mononuclear Cells during the Early Post-Transplant Period in Patients Developing Cardiac Allograft Vasculopathy. PMID:21234308
Global proteomics analysis of testis and ovary in adult zebrafish (Danio rerio). PMID:21229308
A data mining approach for classifying DNA repair genes into ageing-related or non-ageing-related. PMID:21226956
OrthoInspector: comprehensive orthology analysis and visual exploration. PMID:21219603
LPS-annotate: complete annotation of compositionally biased regions in the protein knowledgebase. PMID:21216786
ONTO-ToolKit: enabling bio-ontology engineering via Galaxy. PMID:21210987
Prior knowledge based mining functional modules from Yeast PPI networks with gene ontology. PMID:21172053
Some remarks on protein attribute prediction and pseudo amino acid composition. PMID:21168420
Altered expression of miRNA-21 and its targets in the hippocampus after traumatic brain injury. PMID:21162128
Differences in gene expression amplitude overlie a conserved transcriptomic program occurring between the rapid and potent localized resistant reaction at the syncytium of the Glycine max genotype Peking (PI 548402) as compared to the prolonged and potent resistant reaction of PI 88788. PMID:21153862
Genes and biological processes commonly disrupted in rare and heterogeneous developmental delay syndromes. PMID:21147756
3D-interologs: an evolution database of physical protein- protein interactions across multiple genomes. PMID:21143789
GOAPhAR: An Integrative Discovery Tool for Annotation, Pathway Analysis. PMID:21132056
Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components. PMID:21124865
Unifying themes in microbial associations with animal and plant hosts described using the gene ontology. PMID:21119014
OMA 2011: orthology inference among 1000 complete genomes. PMID:21113020
Genetic evidence implicates the immune system and cholesterol metabolism in the aetiology of Alzheimer's disease. PMID:21085570
EMA - A R package for Easy Microarray data analysis. PMID:21047405
Uncovering genes and regulatory pathways related to urinary albumin excretion. PMID:21030601
Informatics in radiology: an information model of the DICOM standard. PMID:20980665
Length constraints of multi-domain proteins in metazoans. PMID:20975906
The potential for pathogenicity was present in the ancestor of the Ascomycete subphylum Pezizomycotina. PMID:20964831
An ordered EST catalogue and gene expression profiles of cassava (Manihot esculenta) at key growth stages. PMID:20957510
High-throughput screening of bacterial protein localization. PMID:20946849
Automatic, context-specific generation of Gene Ontology slims. PMID:20929524
Role of OsNPR1 in rice defense program as revealed by genome-wide expression analysis. PMID:20924648
Connections between alternative transcription and alternative splicing in mammals. PMID:20889654
Domain altering SNPs in the human proteome and their impact on signaling pathways. PMID:20886114
Computational analysis of candidate disease genes and variants for salt-sensitive hypertension in indigenous Southern Africans. PMID:20886000
The Renal Gene Ontology Annotation Initiative. PMID:20885853
Visual presentation as a welcome alternative to textual presentation of gene annotation information. PMID:20865558
A systems biology approach to identify effective cocktail drugs. PMID:20840734
Analyzing the regulation of metabolic pathways in human breast cancer. PMID:20831783
Identification of tumor-associated cassette exons in human cancer through EST-based computational prediction and experimental validation. PMID:20813049
Digital expression profiling of novel diatom transcripts provides insight into their biological functions. PMID:20738856
GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques. PMID:20689020
Large-scale evidence for conservation of NMD candidature across mammals. PMID:20657786
Locus category based analysis of a large genome-wide association study of rheumatoid arthritis. PMID:20639398
The role of nucleosome positioning in the evolution of gene regulation. PMID:20625544
Knowledge-based annotation of small molecule binding sites in proteins. PMID:20594344
Recursive expectation-maximization clustering: a method for identifying buffering mechanisms composed of phenomic modules. PMID:20590332
Modular composition predicts kinase/substrate interactions. PMID:20579376
mu-CS: an extension of the TM4 platform to manage Affymetrix binary data. PMID:20537149
Deciphering the Arabidopsis floral transition process by integrating a protein-protein interaction network and gene expression data. PMID:20530214
The biological context of HIV-1 host interactions reveals subtle insights into a system hijack. PMID:20529270
The hidden duplication past of the plant pathogen Phytophthora and its consequences for infection. PMID:20525264
Genome-wide identification of new Wnt/beta-catenin target genes in the human genome using CART method. PMID:20515496
Microarray Detection Call Methodology as a Means to Identify and Compare Transcripts Expressed within Syncytial Cells from Soybean (Glycine max) Roots Undergoing Resistant and Susceptible Reactions to the Soybean Cyst Nematode (Heterodera glycines). PMID:20508855
Maternal gene expression in Atlantic halibut (Hippoglossus hippoglossus L.) and its relation to egg quality. PMID:20497529
Discovering causal signaling pathways through gene-expression patterns. PMID:20494976
Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP. PMID:20482861
Touring Ensembl: a practical guide to genome browsing. PMID:20459808
Computing biological functions using BioPsi, a formal description of biological processes based on elementary bricks of actions. PMID:20448138
PANDORA: analysis of protein and peptide sets through the hierarchical integration of annotations. PMID:20444873
The Scottish Structural Proteomics Facility: targets, methods and outputs. PMID:20419351
Hsp90 inhibitor 17-allylamino-17-demethoxygeldanamycin inhibits the proliferation of ARPE-19 cells. PMID:20416086
Quantitative global studies of reactomes and metabolomes using a vectorial representation of reactions and chemical compounds. PMID:20406431
Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets. PMID:20385592
A set of ontologies to drive tools for the control of vector-borne diseases. PMID:20363364
An expression analysis of 57 transcription factors derived from ESTs of developing seeds in Maize (Zea mays). PMID:20336461
Natural selection drives the accumulation of amino acid tandem repeats in human proteins. PMID:20335526
Functional genomic identification of genes required for male gonadal differentiation in Caenorhabditis elegans. PMID:20308279
miRSel: automated extraction of associations between microRNAs and genes from the biomedical literature. PMID:20233441
High-fat diet leads to tissue-specific changes reflecting risk factors for diseases in DBA/2J mice. PMID:20215417
[Attenuation regulation of amino acid and amino acyl-tRNA biosynthetic operons in bacteria: comparative genomics analysis]. PMID:20198868
Pediatric primary central nervous system germ cell tumors of different prognosis groups show characteristic miRNome traits and chromosome copy number variations. PMID:20178649
Projection of gene-protein networks to the functional space of the proteome and its application to analysis of organism complexity. PMID:20158875
Lists2Networks: integrated analysis of gene/protein lists. PMID:20152038
Ontology engineering. PMID:20139945
Putting biomedical ontologies to work. PMID:20135080
Oral benzo[a]pyrene-induced cancer: two distinct types in different target organs depend on the mouse Cyp1 genotype. PMID:20127859
A general co-expression network-based approach to gene expression analysis: comparison and applications. PMID:20122284
BayesMotif: de novo protein sorting motif discovery from impure datasets. PMID:20122242
Integration of multiple data sources to prioritize candidate genes using discounted rating system. PMID:20122192
Changes in gene expression in regions of the extended amygdala of alcohol-preferring rats after binge-like alcohol drinking. PMID:20116196
The urine proteome for radiation biodosimetry: effect of total body vs. local kidney irradiation. PMID:20065682
CORNET: a user-friendly tool for data mining and integration. PMID:20053712
Effects of moderate drinking during pregnancy on placental gene expression. PMID:20053520
Disease gene characterization through large-scale co-expression analysis. PMID:20046828
Integration of gene ontology pathways with North American Rheumatoid Arthritis Consortium genome-wide association data via linear modeling. PMID:20018091
Increased epithelial stem cell traits in advanced endometrial endometrioid carcinoma. PMID:20015385
Human cancer protein-protein interaction network: a structural perspective. PMID:20011507
ConceptGen: a gene set enrichment and gene set relation mapping tool. PMID:20007254
Expansion of tandem repeats in sea anemone Nematostella vectensis proteome: A source for gene novelty? PMID:20003297
Composite annotations: requirements for mapping multiscale data and models to biomedical ontologies. PMID:19964601
MitoInteractome: mitochondrial protein interactome database, and its application in 'aging network' analysis. PMID:19958484
Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. PMID:19953085
Similarities and differences between smoking-related gene expression in nasal and bronchial epithelium. PMID:19952278
Phylogenetic Profiles Reveal Structural and Functional Determinants of Lipid-binding. PMID:19946567
Inclusion of a priori information in genome-wide association analysis. PMID:19924705
An expression database for roots of the model legume Medicago truncatula under salt stress. PMID:19906315
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. PMID:19900971
Edgetic perturbation models of human inherited disorders. PMID:19888216
Martini: using literature keywords to compare gene sets. PMID:19858102
Accounting for redundancy when integrating gene interaction databases. PMID:19847299
Angiotensin AT1 receptor antagonism ameliorates murine retinal proteome changes induced by diabetes. PMID:19845401
Text mining and manual curation of chemical-gene-disease networks for the comparative toxicogenomics database (CTD). PMID:19814812
Initial implementation of a comparative data analysis ontology. PMID:19812726
Facilitating functional annotation of chicken microarray data. PMID:19811685
Recombination and insertion events involving the botulinum neurotoxin complex genes in Clostridium botulinum types A, B, E and F and Clostridium butyricum type E strains. PMID:19804621
A gene expression analysis of syncytia laser microdissected from the roots of the Glycine max (soybean) genotype PI 548402 (Peking) undergoing a resistant reaction after infection by Heterodera glycines (soybean cyst nematode). PMID:19787434
Discovering cancer genes by integrating network and functional properties. PMID:19765316
Androgen-responsive gene database: integrated knowledge on androgen-responsive genes. PMID:19762544
GATA3 is a master regulator of the transcriptional response to low-dose ionizing radiation in human keratinocytes. PMID:19735555
Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network. PMID:19728866
Comparative analysis of gene regulation by the transcription factor PPARalpha between mouse and human. PMID:19710929
Extracting biologically significant patterns from short time series gene expression data. PMID:19695084
Microarray analysis of altered gene expression in ERbeta-overexpressing HEK293 cells. PMID:19680825
Gene expression changes in the nucleus accumbens of alcohol-preferring rats following chronic ethanol consumption. PMID:19666046
Knowledge based identification of essential signaling from genome-scale siRNA experiments. PMID:19653913
Semantic similarity in biomedical ontologies. PMID:19649320
Host sequence motifs shared by HIV predict response to antiretroviral therapy. PMID:19627600
Genomic evidence for non-random endemic populations of decaying exons from mammalian genes. PMID:19594905
Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression. PMID:19563678
Improving in vitro Sertoli cell/gonocyte co-culture model for assessing male reproductive toxicity: Lessons learned from comparisons of cytotoxicity versus genomic responses to phthalates. PMID:19560483
Forging links between human mental retardation-associated CNVs and mouse gene knockout models. PMID:19557186
Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: I. Method development. PMID:19543979
Gene ontology analysis of GWA study data sets provides insights into the biology of bipolar disorder. PMID:19539887
Adaptive prediction of environmental changes by microorganisms. PMID:19536156
Gene expression in peripheral blood leukocytes in monozygotic twins discordant for chronic fatigue: no evidence of a biomarker. PMID:19503787
The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process. PMID:19480664
From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations. PMID:19478018
New tools for functional genomic analysis. PMID:19477290
Integrative analysis of gene expression data including an assessment of pathway enrichment for predicting prostate cancer. PMID:19458772
Bioinformatics resources for cancer research with an emphasis on gene function and structure prediction tools. PMID:19458756
ESG: extended similarity group method for automated protein function prediction. PMID:19435743
Quantitative genome-scale analysis of protein localization in an asymmetric bacterium. PMID:19416866
Exploratory Visual Analysis of statistical results from microarray experiments comparing high and low grade glioma. PMID:19390666
Biological process linkage networks. PMID:19390589
A primary xenograft model of small-cell lung cancer reveals irreversible changes in gene expression imposed by culture in vitro. PMID:19351829
A correlation between host-mediated expression of parasite genes as tandem inverted repeats and abrogation of development of female Heterodera glycines cyst formation during infection of Glycine max. PMID:19347355
The carboxy-terminal domain of Dictyostelium C-module-binding factor is an independent gene regulatory entity. PMID:19343174
A comprehensive Plasmodium falciparum protein interaction map reveals a distinct architecture of a core interactome. PMID:19333996
Toward accurate reconstruction of functional protein networks. PMID:19293828
Population-specific gene expression in the plant pathogenic nematode Heterodera glycines exists prior to infection and during the onset of a resistant or susceptible reaction in the roots of the Glycine max genotype Peking. PMID:19291306
Genome-wide analysis of histidine repeats reveals their role in the localization of human proteins to the nuclear speckles compartment. PMID:19266028
Yin yang 1 modulates taxane response in epithelial ovarian cancer. PMID:19208743
Testing the accuracy of eukaryotic phylogenetic profiles for prediction of biological function. PMID:19204819
Gene expression patterns in hypoxic and post-hypoxic adult rat retina with special reference to the NMDA receptor and its interactome. PMID:19204789
Differential effects of ethanol in the nucleus accumbens shell of alcohol-preferring (P), alcohol-non-preferring (NP) and Wistar rats: a proteomics study. PMID:19166871
Functional dissection of drought-responsive gene expression patterns in Cynodon dactylon L. PMID:19152115
Phylogenetic and functional assessment of orthologs inference projects and methods. PMID:19148271
SIRT6 links histone H3 lysine 9 deacetylation to NF-kappaB-dependent gene expression and organismal life span. PMID:19135889
Microarray-based approach identifies microRNAs and their target functional patterns in polycystic kidney disease. PMID:19102782
GeneDistiller--distilling candidate genes from linkage intervals. PMID:19057649
Network integration and graph analysis in mammalian molecular systems biology. PMID:19045817
LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data. PMID:19038984
KEPE--a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors. PMID:19033273
ExDom: an integrated database for comparative analysis of the exon-intron structures of protein domains in eukaryotes. PMID:18984624
IFN-gamma-dependent regulatory circuits in immune inflammation highlighted in diabetes. PMID:18981116
The prediction of protein-protein interaction networks in rice blast fungus. PMID:18976500
The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience. PMID:18975148
Width of gene expression profile drives alternative splicing. PMID:18974852
Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa. PMID:18971307
Regulation of Cellular Metabolism and Cytokines by the Medicinal Herb Feverfew in the Human Monocytic THP-1 Cells. PMID:18955216
Issues in the design of a pilot concept-based query interface for the neuroinformatics information framework. PMID:18953674
InterPro: the integrative protein signature database. PMID:18940856
Insights into the organization of biochemical regulatory networks using graph theory analyses. PMID:18940806
easyExon--a Java-based GUI tool for processing and visualization of Affymetrix exon array data. PMID:18851762
Discovering functional novelty in metagenomes: examples from light-mediated processes. PMID:18849420
CPDB: a database of circular permutation in proteins. PMID:18842637
SchistoDB: a Schistosoma mansoni genome resource. PMID:18842636
Gene expression module-based chemical function similarity search. PMID:18842630
Application of new multi-resolution methods for the comparison of biomolecular electrostatic properties in the absence of global structural similarity. PMID:18841247
Gene expression changes in the course of normal brain aging are sexually dimorphic. PMID:18832152
The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae. PMID:18826580
PharmGKB: an integrated resource of pharmacogenomic data and knowledge. PMID:18819074
A bioinformatics tool for linking gene expression profiling results with public databases of microRNA target predictions. PMID:18812437
Clinical implication of recurrent copy number alterations in hepatocellular carcinoma and putative oncogenes in recurrent gains on 1q. PMID:18803288
NetGrep: fast network schema searches in interactomes. PMID:18801179
ExplorEnz: the primary source of the IUBMB enzyme list. PMID:18776214
Smoking-related genomic signatures in non-small cell lung cancer. PMID:18776155
Prioritization of candidate cancer genes--an aid to oncogenomic studies. PMID:18710882
Interpretation errors related to the GO annotation file format. PMID:18693894
RadiO: a prototype application ontology for radiology reporting tasks. PMID:18693889
Differential protein expression during aging in ventricular myocardium of Fischer 344 x Brown Norway hybrid rats. PMID:18682286
Comprehensive association study of type 2 diabetes and related quantitative traits with 222 candidate genes. PMID:18678618
Predicting pathway membership via domain signatures. PMID:18676972
Carcinogen-altered genes in rat esophagus positively modulated to normal levels of expression by both black raspberries and phenylethyl isothiocyanate. PMID:18676871
Structural similarity of genetically interacting proteins. PMID:18671848
The Cladosporium fulvum virulence protein Avr2 inhibits host proteases required for basal defense. PMID:18660430
Genomic analysis reveals age-dependent innate immune responses to severe acute respiratory syndrome coronavirus. PMID:18632870
The molecule role ontology: an ontology for annotation of signal transduction pathway molecules in the scientific literature. PMID:18629146
Obol: integrating language and meaning in bio-ontologies. PMID:18629143
Bioinformatic tools for inferring functional information from plant microarray data II: Analysis beyond single gene. PMID:18615189
Statistical analysis of interface similarity in crystals of homologous proteins. PMID:18599072
Automated analysis of viral integration sites in gene therapy research using the SeqMap web resource. PMID:18580967
Development and application of a framework for maintenance of medical terminological systems. PMID:18579838
Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence. PMID:18565990
Genome-wide transcriptional changes induced by phagocytosis or growth on bacteria in Dictyostelium. PMID:18559084
Whole genome assessment of the retinal response to diabetes reveals a progressive neurovascular inflammatory response. PMID:18554398
Genome-wide gene expression profiling analysis of Leishmania major and Leishmania infantum developmental stages reveals substantial differences between the two species. PMID:18510761
Calling on a million minds for community annotation in WikiProteins. PMID:18507872
Expansion of signaling genes for adaptive immune system evolution in early vertebrates. PMID:18479507
Domain-specific data sharing in neuroscience: what do we have to learn from each other? PMID:18473189
A novel Bayesian DNA motif comparison method for clustering and retrieval. PMID:18463706
Metrics for GO based protein semantic similarity: a systematic evaluation. PMID:18460186
Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse. PMID:18439302
Combining evidence, specificity, and proximity towards the normalization of Gene Ontology terms in text. PMID:18437221
The annotation of both human and mouse kinomes in UniProtKB/Swiss-Prot: one small step in manual annotation, one giant leap for full comprehension of genomes. PMID:18436524
Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network. PMID:18417725
Differential gene expression in the nucleus accumbens with ethanol self-administration in inbred alcohol-preferring rats. PMID:18405950
Rainbow smelt (Osmerus mordax) genomic library and EST resources. PMID:18386095
Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs. PMID:18384671
Protein networks in disease. PMID:18381899
Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens. PMID:18373860
Phenotype of the Cyp1a1/1a2/1b1-/- triple-knockout mouse. PMID:18372398
Predicting cancer involvement of genes from heterogeneous data. PMID:18371197
Functionally important segments in proteins dissected using Gene Ontology and geometric clustering of peptide fragments. PMID:18331637
ComPath: comparative enzyme analysis and annotation in pathway/subsystem contexts. PMID:18325116
Discovering gene annotations in biomedical text databases. PMID:18325104
Multivariate hierarchical Bayesian model for differential gene expression analysis in microarray experiments. PMID:18315862
GORouter: an RDF model for providing semantic query and inference services for Gene Ontology and its associations. PMID:18315859
Effect of synthetic dietary triglycerides: a novel research paradigm for nutrigenomics. PMID:18301758
Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species. PMID:18299576
VennMaster: area-proportional Euler diagrams for functional GO analysis of microarrays. PMID:18230172
Functional trends in structural classes of the DNA binding domains of regulatory transcription factors. PMID:18229706
Defining functional distances over gene ontology. PMID:18221506
Genome-wide demethylation during neural differentiation of P19 embryonal carcinoma cells. PMID:18200438
The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. PMID:18194960
Probing host pathogen cross-talk by transcriptional profiling of both Mycobacterium tuberculosis and infected human dendritic cells and macrophages. PMID:18167562
Sequencing analysis of 20,000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response. PMID:18096061
AphanoDB: a genomic resource for Aphanomyces pathogens. PMID:18096036
Maintenance of transposon-free regions throughout vertebrate evolution. PMID:18093339
Specific elements of the glyoxylate pathway play a significant role in the functional transition of the soybean cotyledon during seedling development. PMID:18093333
Denoising inferred functional association networks obtained by gene fusion analysis. PMID:18081932
PlantGDB: a resource for comparative plant genomics. PMID:18063570
Analysis of the neurotoxin complex genes in Clostridium botulinum A1-A4 and B1 strains: BoNT/A3, /Ba4 and /B1 clusters are located within plasmids. PMID:18060065
A new computational approach to analyze human protein complexes and predict novel protein interactions. PMID:18053208
Cloning, analysis and functional annotation of expressed sequence tags from the Earthworm Eisenia fetida. PMID:18047730
Towards validating the hypothesis of phylogenetic profiling. PMID:18047725
CancerLectinDB: a database of lectins relevant to cancer. PMID:18038206
Analysis of gene expression during neurite outgrowth and regeneration. PMID:18036227
Regulatory module network of basic/helix-loop-helix transcription factors in mouse brain. PMID:18021424
Inferring biological functions and associated transcriptional regulators using gene set expression coherence analysis. PMID:18021416
Genomic resources for Myzus persicae: EST sequencing, SNP identification, and microarray design. PMID:18021414
Making the most of high-throughput protein-interaction data. PMID:18001486
The BioGRID Interaction Database: 2008 update. PMID:18000002
Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria. PMID:17999997
Constraint and turnover in sex-biased gene expression in the genus Drosophila. PMID:17994089
Transcriptome profiling and functional analysis of Agrobacterium tumefaciens reveals a general conserved response to acidic conditions (pH 5.5) and a complex acid-mediated signaling involved in Agrobacterium-plant interactions. PMID:17993523
The Gene Ontology project in 2008. PMID:17984083
Construction, visualisation, and clustering of transcription networks from microarray expression data. PMID:17967053
Phospho.ELM: a database of phosphorylation sites--update 2008. PMID:17962309
Microarray analysis of gene expression of cancer to guide the use of chemotherapeutics. PMID:17962100
miRGator: an integrated system for functional annotation of microRNAs. PMID:17942429
Network-based classification of breast cancer metastasis. PMID:17940530
Multidimensional annotation of the Escherichia coli K-12 genome. PMID:17940092
Improved human disease candidate gene prioritization using mouse phenotype. PMID:17939863
The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. PMID:17933782
GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. PMID:17932055
All duplicates are not equal: the difference between small-scale and genome duplication. PMID:17916239
ARC: automated resource classifier for agglomerative functional classification of prokaryotic proteins using annotation texts. PMID:17914236
Linking microarray reporters with protein functions. PMID:17897448
Reversible and permanent effects of tobacco smoke exposure on airway epithelial gene expression. PMID:17894889
Creating and curating a terminology for radiology: ontology modeling and analysis. PMID:17874267
Identification of a peripheral blood transcriptional biomarker panel associated with operational renal allograft tolerance. PMID:17873064
Differential response of Mono Mac 6, BEAS-2B, and Jurkat cells to indoor dust. PMID:17805423
Gene analogue finder: a GRID solution for finding functionally analogous gene products. PMID:17767718
Analysis of the role of retrotransposition in gene evolution in vertebrates. PMID:17718914
The intracellular form of human MAGP1 elicits a complex and specific transcriptional response. PMID:17692555
Evolutionarily conserved optimization of amino acid biosynthesis. PMID:17684697
An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens. PMID:17683536
Network motif analysis of a multi-mode genetic-interaction network. PMID:17683534
Laser capture microdissection (LCM) and comparative microarray expression analysis of syncytial cells isolated from incompatible and compatible soybean (Glycine max) roots infected by the soybean cyst nematode (Heterodera glycines). PMID:17668236
ExplorEnz: a MySQL database of the IUBMB enzyme nomenclature. PMID:17662133
A time-course comparative microarray analysis of an incompatible and compatible response by Glycine max (soybean) to Heterodera glycines (soybean cyst nematode) infection. PMID:17653570
EasyGO: Gene Ontology-based annotation and functional enrichment analysis tool for agronomical species. PMID:17645808
Effects of phenylethyl isothiocyanate on early molecular events in N-nitrosomethylbenzylamine-induced cytotoxicity in rat esophagus. PMID:17616710
Using biomarker signature patterns for an mRNA molecular diagnostic of mouse embryonic stem cell differentiation state. PMID:17605829
Annotated expressed sequence tags (ESTs) from pre-smolt Atlantic salmon (Salmo salar) in a searchable data resource. PMID:17605782
Gene expression changes associated with Barrett's esophagus and Barrett's-associated adenocarcinoma cell lines after acid or bile salt exposure. PMID:17597535
DEEP--a tool for differential expression effector prediction. PMID:17584786
Comparative analysis of structured RNAs in S. cerevisiae indicates a multitude of different functions. PMID:17577407
Gene expression arrays as a tool to unravel mechanisms of normal tissue radiation injury and prediction of response. PMID:17569134
Transcription factor binding and modified histones in human bidirectional promoters. PMID:17568000
Systems developmental biology: the use of ontologies in annotating models and in identifying gene function within and across species. PMID:17566825
Comprehensive analysis of co-occurring domain sets in yeast proteins. PMID:17562021
Comparative analysis of expressed genes from cacao meristems infected by Moniliophthora perniciosa. PMID:17557832
Spatial preferences of microRNA targets in 3' untranslated regions. PMID:17555584
Characterization of an 18,166 EST dataset for cassava (Manihot esculenta Crantz) enriched for drought-responsive genes. PMID:17541599
Molecular concepts analysis links tumors, pathways, mechanisms, and drugs. PMID:17534450
Modular organization in the reductive evolution of protein-protein interaction networks. PMID:17532860
GOSim--an R-package for computation of information theoretic GO similarities between terms and gene products. PMID:17519018
3D-partner: a web server to infer interacting partners and binding models. PMID:17517763
Functional gene expression differences between inbred alcohol-preferring and -non-preferring rats in five brain regions. PMID:17517326
STATc is a key regulator of the transcriptional response to hyperosmotic shock. PMID:17517120
Network analysis of FDA approved drugs and their targets. PMID:17516560
Functional genomics analyses of differential macaque peripheral blood mononuclear cell infections by human immunodeficiency virus-1 and simian immunodeficiency virus. PMID:17507074
Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome. PMID:17506886
Analysis of gene expression in cotton fiber initials. PMID:17506877
Reconstruction of human protein interolog network using evolutionary conserved network. PMID:17493278
The conserved transcriptome in human and rodent male gametogenesis. PMID:17483452
Integrating epitope data into the emerging web of biomedical knowledge resources. PMID:17479127
Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation. PMID:17452354
Comparative genomics using Fugu reveals insights into regulatory subfunctionalization. PMID:17428329
Integrative content-driven concepts for bioinformatics "beyond the cell". PMID:17426389
Formal TCA cycle description based on elementary actions. PMID:17426387
Molecular defense mechanisms of Barrett's metaplasia estimated by an integrative genomics. PMID:17415542
ImmTree: database of evolutionary relationships of genes and proteins in the human immune system. PMID:17376226
Systematic genome instability screens in yeast and their potential relevance to cancer. PMID:17360454
Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. PMID:17356713
Microarray reveals complement components are regulated in the serum-deprived rat retinal ganglion cell line. PMID:17356516
Gene expression profiling of human mesenchymal stem cells derived from bone marrow during expansion and osteoblast differentiation. PMID:17352823
Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database. PMID:17335583
The (in)dependence of alternative splicing and gene duplication. PMID:17335345
Bioinformatic analysis of human CNS-expressed ion channels as candidates for episodic nervous system disorders. PMID:17333079
Supervised group Lasso with applications to microarray data analysis. PMID:17316436
Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363. PMID:17307855
Building an ontology-driven database for clinical immune research. PMID:17238637
Towards answering biological questions with experimental evidence: automatically identifying text that summarize image content in full-text articles. PMID:17238458
AffyMiner: mining differentially expressed genes and biological knowledge in GeneChip microarray data. PMID:17217519
Predicting tissue-specific enhancers in the human genome. PMID:17210927
DiscoverySpace: an interactive data analysis application. PMID:17210078
SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions. PMID:17202171
New developments in the InterPro database. PMID:17202162
GOAnnotator: linking protein GO annotations to evidence text. PMID:17181854
Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments. PMID:17177995
PATRIC: the VBI PathoSystems Resource Integration Center. PMID:17142235
CellCircuits: a database of protein network models. PMID:17135207
SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms. PMID:17135185
Analysis of the wheat endosperm transcriptome. PMID:17132893
Biological context networks: a mosaic view of the interactome. PMID:17130868
Rapid detection of similarity in protein structure and function through contact metric distances. PMID:17130161
Gene expression profiles distinguish the carcinogenic effects of aristolochic acid in target (kidney) and non-target (liver) tissues in rats. PMID:17118142
The transcription factors WRKY11 and WRKY17 act as negative regulators of basal resistance in Arabidopsis thaliana. PMID:17114354
Functional differentiation of SWI/SNF remodelers in transcription and cell cycle control. PMID:17101803
FlyBase: genomes by the dozen. PMID:17099233
GO PaD: the Gene Ontology Partition Database. PMID:17098937
KBERG: KnowledgeBase for Estrogen Responsive Genes. PMID:17090589
Assessing protein similarity with Gene Ontology and its use in subnuclear localization prediction. PMID:17090318
Patome: a database server for biological sequence annotation and analysis in issued patents and published patent applications. PMID:17085479
Mining housekeeping genes with a Naive Bayes classifier. PMID:17074078
ProtoBee: hierarchical classification and annotation of the honey bee proteome. PMID:17065614
Exhaustive assignment of compositional bias reveals universally prevalent biased regions: analysis of functional associations in human and Drosophila. PMID:17032452
PubFocus: semantic MEDLINE/PubMed citations analytics through integration of controlled biomedical dictionaries and ranking algorithm. PMID:17014720
Comparative assessment of performance and genome dependence among phylogenetic profiling methods. PMID:17005048
AgBase: a functional genomics resource for agriculture. PMID:16961921
Apoptosis resistance downstream of eIF4E: posttranscriptional activation of an anti-apoptotic transcript carrying a consensus hairpin structure. PMID:16936314
Integrated molecular signature of disease: analysis of influenza virus-infected macaques through functional genomics and proteomics. PMID:16928763
Transcriptional coordination of the metabolic network in Arabidopsis. PMID:16920875
Whole-plant growth stage ontology for angiosperms and its application in plant biology. PMID:16905665
The Comparative Toxicogenomics Database (CTD): a resource for comparative toxicological studies. PMID:16902965
Challenges and strategies of the Genetics Home Reference. PMID:16888669
Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. PMID:16878126
Analysis of cell-based RNAi screens. PMID:16869968
An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes. PMID:16855282
BiologicalNetworks: visualization and analysis tool for systems biology. PMID:16845051
YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms. PMID:16845020
WEGO: a web tool for plotting GO annotations. PMID:16845012
Systematic analysis of head-to-head gene organization: evolutionary conservation and potential biological relevance. PMID:16839196
Peeling off the hidden genetic heterogeneities of cancers based on disease-relevant functional modules. PMID:16838067
AMDA: an R package for the automated microarray data analysis. PMID:16824223
Genomic overview of mRNA 5'-leader trans-splicing in the ascidian Ciona intestinalis. PMID:16822859
One hundred years of high-throughput Drosophila research. PMID:16821132
Differences in the evolutionary history of disease genes affected by dominant or recessive mutations. PMID:16817963
Array2BIO: from microarray expression data to functional annotation of co-regulated genes. PMID:16780584
GenoCache: a Genomics and Cancer Chemoprevention portal. PMID:16779267
From components to regulatory motifs in signalling networks. PMID:16769680
An ontology for PACS integration. PMID:16763933
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. PMID:16762047
Automated interpretation of subcellular patterns in fluorescence microscope images for location proteomics. PMID:16752421
Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. PMID:16749936
Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations. PMID:16749918
Structure-based function inference using protein family-specific fingerprints. PMID:16731985
The gain and loss of genes during 600 million years of vertebrate evolution. PMID:16723033
The TREC 2004 genomics track categorization task: classifying full text biomedical documents. PMID:16722582
Enhancing access to the Bibliome: the TREC 2004 Genomics Track. PMID:16722581
Topology and weights in a protein domain interaction network--a novel way to predict protein interactions. PMID:16716232
Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. PMID:16685651
The comparative toxicogenomics database: a cross-species resource for building chemical-gene interaction networks. PMID:16675512
Enhanced automated function prediction using distantly related sequences and contextual association by PFP. PMID:16672240
A factor analysis model for functional genomics. PMID:16630343
Quality control for terms and definitions in ontologies and taxonomies. PMID:16623942
Toward understanding the genetics of alcohol drinking through transcriptome meta-analysis. PMID:16618939
Analysis of 10,000 ESTs from lymphocytes of the cynomolgus monkey to improve our understanding of its immune system. PMID:16618371
Benchmarking ortholog identification methods using functional genomics data. PMID:16613613
Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. PMID:16606704
Global gene expression analyses of hematopoietic stem cell-like cell lines with inducible Lhx2 expression. PMID:16600034
MIMAS: an innovative tool for network-based high density oligonucleotide microarray data management and annotation. PMID:16597336
Timecourse microarray analyses reveal global changes in gene expression of susceptible Glycine max (soybean) roots during infection by Heterodera glycines (soybean cyst nematode). PMID:16575592
Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions. PMID:16566817
Regions of extreme synonymous codon selection in mammalian genes. PMID:16556911
SNPs3D: candidate gene and SNP selection for association studies. PMID:16551372
Amplification of the Gene Ontology annotation of Affymetrix probe sets. PMID:16549014
Ensemble attribute profile clustering: discovering and characterizing groups of genes with similar patterns of biological features. PMID:16542449
Gene functional similarity search tool (GFSST). PMID:16536867
Ancient duplicated conserved noncoding elements in vertebrates: a genomic and functional analysis. PMID:16533910
Extraction of phylogenetic network modules from the metabolic network. PMID:16533389
Identification of similar regions of protein structures using integrated sequence and structure analysis tools. PMID:16526955
The proteome: structure, function and evolution. PMID:16524832
Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genome-wide scale. PMID:16520460
Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains. PMID:16493140
GO-Diff: mining functional differentiation between EST-based transcriptomes. PMID:16480524
Multistrain genetic comparisons reveal CCR5 as a receptor involved in airway hyperresponsiveness. PMID:16474097
Role of positive selection in the retention of duplicate genes in mammalian genomes. PMID:16461903
MitoRes: a resource of nuclear-encoded mitochondrial genes and their products in Metazoa. PMID:16433928
A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. PMID:16432200
LocustDB: a relational database for the transcriptome and biology of the migratory locust (Locusta migratoria). PMID:16426458
iVici: Interrelational Visualization and Correlation Interface. PMID:16420674
Primary and secondary transcriptional effects in the developing human Down syndrome brain and heart. PMID:16420667
Automatic discovery of cross-family sequence features associated with protein function. PMID:16409628
LTR retrotransposon-gene associations in Drosophila melanogaster. PMID:16408244
MaGe: a microbial genome annotation system supported by synteny results. PMID:16407324
Structural and functional properties of genes involved in human cancer. PMID:16405732
Gramene: a bird's eye view of cereal genomes. PMID:16381966
cisRED: a database system for genome-scale computational discovery of regulatory elements. PMID:16381958
PRIDE: a public repository of protein and peptide identifications for the proteomics community. PMID:16381953
HPtaa database-potential target genes for clinical diagnosis and immunotherapy of human carcinoma. PMID:16381942
The Mouse Genome Database (MGD): updates and enhancements. PMID:16381933
TRANSPATH: an information resource for storing and visualizing signaling pathways and their pathological aberrations. PMID:16381929
EndoNet: an information resource about endocrine networks. PMID:16381928
BioGRID: a general repository for interaction datasets. PMID:16381927
LMPD: LIPID MAPS proteome database. PMID:16381922
FlyBase: anatomical data, images and queries. PMID:16381917
FLIGHT: database and tools for the integration and cross-correlation of large-scale RNAi phenotypic datasets. PMID:16381916
dictyBase, the model organism database for Dictyostelium discoideum. PMID:16381903
ASAP: a resource for annotating, curating, comparing, and disseminating genomic data. PMID:16381899
PUMA2--grid-based high-throughput analysis of genomes and metabolic pathways. PMID:16381888
INVHOGEN: a database of homologous invertebrate genes. PMID:16381884
The integrated microbial genomes (IMG) system. PMID:16381883
PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees. PMID:16381879
The Gene Ontology (GO) project in 2006. PMID:16381878
SCOPPI: a structural classification of protein-protein interfaces. PMID:16381874
The Molecular Biology Database Collection: 2006 update. PMID:16381871
Gene3D: modelling protein structure, function and evolution. PMID:16381865
The Universal Protein Resource (UniProt): an expanding universe of protein information. PMID:16381842
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. PMID:16381831
Transposon-free regions in mammalian genomes. PMID:16365385
Ulysses - an application for the projection of molecular interactions across species. PMID:16356269
Folding free energies of 5'-UTRs impact post-transcriptional regulation on a genomic scale in yeast. PMID:16355254
ParPEST: a pipeline for EST data analysis based on parallel computing. PMID:16351758
HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. PMID:16351748
Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. PMID:16344560
PSE: a tool for browsing a large amount of MEDLINE/PubMed abstracts with gene names and common words as the keywords. PMID:16336692
Microarray analysis of androgen-regulated gene expression in testis: the use of the androgen-binding protein (ABP)-transgenic mouse as a model. PMID:16336681
Rapid and efficient cDNA library screening by self-ligation of inverse PCR products (SLIP). PMID:16326860
Profiling condition-specific, genome-wide regulation of mRNA stability in yeast. PMID:16317069
Laser capture microdissection (LCM) and expression analyses of Glycine max (soybean) syncytium containing root regions formed by the plant pathogen Heterodera glycines (soybean cyst nematode). PMID:16307369
An ontology for immune epitopes: application to the design of a broad scope database of immune reactivities. PMID:16305755
A data integration methodology for systems biology: experimental verification. PMID:16301536
Sequence features in regions of weak and strong linkage disequilibrium. PMID:16251462
Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence. PMID:16237009
Human promoter genomic composition demonstrates non-random groupings that reflect general cellular function. PMID:16232321
Human microRNAs target a functionally distinct population of genes with AT-rich 3' UTRs. PMID:16230613
Phydbac "Gene Function Predictor": a gene annotation tool based on genomic context analysis. PMID:16221304
A catalog of stability-associated sequence elements in 3' UTRs of yeast mRNAs. PMID:16207357
Human-zebrafish non-coding conserved elements act in vivo to regulate transcription. PMID:16179648
Dragon Plant Biology Explorer. A text-mining tool for integrating associations between genetic and biochemical entities with genome annotation and biochemical terms lists. PMID:16172098
Transcription factor families have much higher expansion rates in plants than in animals. PMID:16166257
Open reading frames provide a rich pool of potential natural antisense transcripts in fungal genomes. PMID:16147987
G2D: a tool for mining genes associated with disease. PMID:16115313
Dual activation of pathways regulated by steroid receptors and peptide growth factors in primary prostate cancer revealed by Factor Analysis of microarray data. PMID:16107210
Ab initio prediction of transcription factor targets using structural knowledge. PMID:16103898
DynGO: a tool for visualizing and mining of Gene Ontology and its associations. PMID:16091147
Plant genome resources at the national center for biotechnology information. PMID:16010002
It's all GO for plant scientists. PMID:16010001
Gene expression profile and synovial microcirculation at early stages of collagen-induced arthritis. PMID:15987489
Expressed sequence tags (ESTs) and simple sequence repeat (SSR) markers from octoploid strawberry (Fragaria x ananassa). PMID:15985176
GoPubMed: exploring PubMed with the Gene Ontology. PMID:15980585
RACE: Remote Analysis Computation for gene Expression data. PMID:15980552
VisANT: data-integrating visual framework for biological networks and modules. PMID:15980487
PhyloDome--visualization of taxonomic distributions of domains occurring in eukaryote protein sequence sets. PMID:15980439
An evaluation of GO annotation retrieval for BioCreAtIvE and GOA. PMID:15960829
Evaluation of BioCreAtIvE assessment of task 2. PMID:15960828
(TG/CA)n repeats in human gene families: abundance and selective patterns of distribution according to function and gene length. PMID:15935094
Considerations when using the significance analysis of microarrays (SAM) algorithm. PMID:15921534
Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing. PMID:15899965
Novel response to microtubule perturbation in meiosis. PMID:15899877
CAGER: classification analysis of gene expression regulation using multiple information sources. PMID:15890068
MetaCyc and AraCyc. Metabolic pathway databases for plant research. PMID:15888675
Integration of the Gene Ontology into an object-oriented architecture. PMID:15885145
Exploring relationships and mining data with the UCSC Gene Sorter. PMID:15867434
Conservation of regulatory sequences and gene expression patterns in the disintegrating Drosophila Hox gene complex. PMID:15867430
A proteomic survey of rat cerebral cortical synaptosomes. PMID:15852343
Filtering high-throughput protein-protein interaction data using a combination of genomic features. PMID:15833142
Promoter features related to tissue specificity as measured by Shannon entropy. PMID:15833120
Induction of the Candida albicans filamentous growth program by relief of transcriptional repression: a genome-wide analysis. PMID:15814840
Columba: an integrated database of proteins, structures, and annotations. PMID:15801979
Floral gene resources from basal angiosperms for comparative genomics research. PMID:15799777
Ranking the whole MEDLINE database according to a large training set using text indexing. PMID:15790421
GeneKeyDB: a lightweight, gene-centric, relational database to support data mining environments. PMID:15790402
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. PMID:15784138
The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data. PMID:15774030
Marine genomics: a clearing-house for genomic and transcriptomic data of marine organisms. PMID:15760464
Global transcriptome analysis of the C57BL/6J mouse testis by SAGE: evidence for nonrandom gene order. PMID:15748293
Differential expression of genes within the cochlea as defined by a custom mouse inner ear microarray. PMID:15735932
Atlas - a data warehouse for integrative bioinformatics. PMID:15723693
Ontological visualization of protein-protein interactions. PMID:15707487
Global mapping of the protein structure space and application in structure-based inference of protein function. PMID:15705717
Anatomics: the intersection of anatomy and bioinformatics. PMID:15679867
MILANO--custom annotation of microarray results using automatic literature searches. PMID:15661078
Using ontologies to describe mouse phenotypes. PMID:15642100
The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information. PMID:15642099
Full-length cDNAs from chicken bursal lymphocytes to facilitate gene function analysis. PMID:15642098
SpliceInfo: an information repository for mRNA alternative splicing in human genome. PMID:15608290
Brassica ASTRA: an integrated database for Brassica genomic research. PMID:15608282
Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics. PMID:15608281
openSputnik--a database to ESTablish comparative plant genomics using unsaturated sequence collections. PMID:15608275
Organelle DB: a cross-species database of protein localization and function. PMID:15608270
ArrayExpress--a public repository for microarray gene expression data at the EBI. PMID:15608260
SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs. PMID:15608254
The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology. PMID:15608240
The European Bioinformatics Institute's data resources: towards systems biology. PMID:15608238
ChickVD: a sequence variation database for the chicken genome. PMID:15608233
Reactome: a knowledgebase of biological pathways. PMID:15608231
The Biomolecular Interaction Network Database and related tools 2005 update. PMID:15608229
SilkDB: a knowledgebase for silkworm biology and genomics. PMID:15608225
FlyBase: genes and gene models. PMID:15608223
Poxvirus Bioinformatics Resource Center: a comprehensive Poxviridae informational and analytical resource. PMID:15608205
Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. PMID:15608201
The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. PMID:15608188
The SYSTERS Protein Family Database in 2005. PMID:15608183
InterPro, progress and status in 2005. PMID:15608177
UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. PMID:15608165
NONCODE: an integrated knowledge database of non-coding RNAs. PMID:15608158
Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags. PMID:15590942
Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information. PMID:15585062
Tumor taxonomy for the developmental lineage classification of neoplasms. PMID:15571625
GC/AT-content spikes as genomic punctuation marks. PMID:15548610
The Molecular Pages of the mesotelencephalic dopamine consortium (DopaNet). PMID:15518589
Automated prediction of protein function and detection of functional sites from structure. PMID:15456910
Genetic variation in radiation-induced expression phenotypes. PMID:15359380
Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions. PMID:15342556
Retrieving sequences of enzymes experimentally characterized but erroneously annotated : the case of the putrescine carbamoyltransferase. PMID:15287962
Global transcription profiling reveals multiple sugar signal transduction mechanisms in Arabidopsis. PMID:15273295
Nutritional homeostasis in batch and steady-state culture of yeast. PMID:15240820
GOAL: automated Gene Ontology analysis of expression profiles. PMID:15215435
GOblet: a platform for Gene Ontology annotation of anonymous sequence data. PMID:15215401
Dragon TF Association Miner: a system for exploring transcription factor associations through text-mining. PMID:15215386
Public web-based services from the European Bioinformatics Institute. PMID:15215339
Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins. PMID:15212693
Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data. PMID:14973197
The mouse Gene Expression Database (GXD): updates and enhancements. PMID:14681482 -
The Gene Ontology Resource: 20 years and still GOing strong
PubMed citations: 1480.
1480 articles citing: The Gene Ontology Resource: 20 years and still GOing strong
Evolutionary Relationships Between Dysregulated Genes in Oral Squamous Cell Carcinoma and Oral Microbiota. PMID:35909962
Bioinformatics Analysis of the Mechanisms of Diabetic Nephropathy via Novel Biomarkers and Competing Endogenous RNA Network. PMID:35909518
Shared Genetics and Causality Between Decaffeinated Coffee Consumption and Neuropsychiatric Diseases: A Large-Scale Genome-Wide Cross-Trait Analysis and Mendelian Randomization Analysis. PMID:35898629
Challenges and Limitations of Biological Network Analysis. PMID:35892929
Computational modeling and analysis of the morphogenetic domain signaling networks regulating C. elegans embryogenesis. PMID:35891777
A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics. PMID:35888710
Large-Scale Multi-Omics Studies Provide New Insights into Blood Pressure Regulation. PMID:35886906
An Integrated Bioinformatics Analysis towards the Identification of Diagnostic, Prognostic, and Predictive Key Biomarkers for Urinary Bladder Cancer. PMID:35884419
Getting Started with LINCS Datasets and Tools. PMID:35876555
Venom composition of Trimeresurus albolabris, T. insularis, T. puniceus and T. purpureomaculatus from Indonesia. PMID:35875602
Identification of circRNA-miRNA-mRNA Regulatory Network and Crucial Signaling Pathway Axis Involved in Tetralogy of Fallot. PMID:35873466
Genetic Pathways Associated With Sleep Problems in Children With Autism Spectrum Disorder. PMID:35873241
orsum: a Python package for filtering and comparing enrichment analyses using a simple principle. PMID:35870894
Identification of Immune-Associated Genes in Diagnosing Aortic Valve Calcification With Metabolic Syndrome by Integrated Bioinformatics Analysis and Machine Learning. PMID:35865542
ORIGINS: A protein network-based approach to quantify cell pluripotency from scRNA-seq data. PMID:35855951
A genome-wide comparative evolutionary analysis of zinc finger-BED transcription factor genes in land plants. PMID:35853967
Integrated Analysis Revealing the Senescence-Mediated Immune Heterogeneity of HCC and Construction of a Prognostic Model Based on Senescence-Related Non-Coding RNA Network. PMID:35847928
Favoring Expression of Yak Alleles in Interspecies F1 Hybrids of Cattle and Yak Under High-Altitude Environments. PMID:35847643
Variations of SARS-CoV-2 in the Iranian population and candidate putative drug-like compounds to inhibit the mutated proteins. PMID:35847618
Excessive Sodium Intake Leads to Cardiovascular Disease by Promoting Sex-Specific Dysfunction of Murine Heart. PMID:35845798
The Mechanism of Wnt Pathway Regulated by Telocytes to Promote the Regeneration and Repair of Intrauterine Adhesions. PMID:35844454
A TP53 Related Immune Prognostic Model for the Prediction of Clinical Outcomes and Therapeutic Responses in Lung Adenocarcinoma. PMID:35837383
Selective expression of variant surface antigens enables Plasmodium falciparum to evade immune clearance in vivo. PMID:35831417
Identification of the shared gene signatures and pathways between polycystic ovary syndrome and endometrial cancer: An omics data based combined approach. PMID:35830453
Systems biology models to identify the influence of SARS-CoV-2 infections to the progression of human autoimmune diseases. PMID:35818398
Identification and Validation of Candidate Gene Module Along With Immune Cells Infiltration Patterns in Atherosclerosis Progression to Plaque Rupture via Transcriptome Analysis. PMID:35811739
Genetic variation associated with condensate dysregulation in disease. PMID:35809564
Lipolysis regulates major transcriptional programs in brown adipocytes. PMID:35803907
Identification of molecular mechanisms underlying the therapeutic effects of Xintong granule in coronary artery disease by a network pharmacology and molecular docking approach. PMID:35801781
A structural homology approach to identify potential cross-reactive antibody responses following SARS-CoV-2 infection. PMID:35794133
Increased CSF-decorin predicts brain pathological changes driven by Alzheimer's Aβ amyloidosis. PMID:35787306
A consensus view of the proteome of the last universal common ancestor. PMID:35784055
Bioinformatics Analysis Highlights Five Differentially Expressed Genes as Prognostic Biomarkers of Cervical Cancer and Novel Option for Anticancer Treatment. PMID:35782114
Identification of pyroptosis-related long non-coding RNAs with prognosis and therapy in lung squamous cell carcinoma. PMID:35778526
An automatic integrative method for learning interpretable communities of biological pathways. PMID:35769343
DeepGOZero: improving protein function prediction from sequence and zero-shot learning based on ontology axioms. PMID:35758802
Calculating genetic risk for dysfunction in pleiotropic biological processes using whole exome sequencing data. PMID:35751013
Metabolome and Transcriptome Analyses of Cucurbitacin Biosynthesis in Luffa (Luffa acutangula). PMID:35747880
Differences and Similarities between the Lung Transcriptomic Profiles of COVID-19, COPD, and IPF Patients: A Meta-Analysis Study of Pathophysiological Signaling Pathways. PMID:35743918
TCGA-My: A Systematic Repository for Systems Biology of Malaysian Colorectal Cancer. PMID:35743803
Molecular alterations in human milk in simulated maternal nasal mucosal infection with live attenuated influenza vaccination. PMID:35739193
Expression and prognosis analysis of mitochondrial ribosomal protein family in breast cancer. PMID:35739158
Many kinds of oxidized proteins are present more in the urine of the elderly. PMID:35733114
Human follicular mites: Ectoparasites becoming symbionts. PMID:35724423
Screening and Identification of Hub Genes in the Development of Early Diabetic Kidney Disease Based on Weighted Gene Co-Expression Network Analysis. PMID:35721731
Identification of a neural development gene expression signature in colon cancer stem cells reveals a role for EGR2 in tumorigenesis. PMID:35720265
Identification and Validation of Genomic Subtypes and a Prognostic Model Based on Antigen-Presenting Cells and Tumor Microenvironment Infiltration Characteristics in Hepatocellular Carcinoma. PMID:35720008
SFARI genes and where to find them; modelling Autism Spectrum Disorder specific gene expression dysregulation with RNA-seq data. PMID:35710789
A hexa-species transcriptome atlas of mammalian embryogenesis delineates metabolic regulation across three different implantation modes. PMID:35710749
The DNA methylation landscape of five pediatric-tumor types. PMID:35707123
Analysis and pharmacological modulation of senescence in human epithelial stem cells. PMID:35706382
Proteome analysis of urinary biomarkers in a cigarette smoke-induced COPD rat model. PMID:35705945
Nutrient Availability Does Not Affect Community Assembly in Root-Associated Fungi but Determines Fungal Effects on Plant Growth. PMID:35695510
Decoding the Mechanism behind the Pathogenesis of the Focal Segmental Glomerulosclerosis. PMID:35693262
Novel App knock-in mouse model shows key features of amyloid pathology and reveals profound metabolic dysregulation of microglia. PMID:35690868
Comparative transcriptome analysis reveals a rapid response to phosphorus deficiency in a phosphorus-efficient rice genotype. PMID:35676419
Neuropilin-1 is present on Foxp3+ T regulatory cell-derived small extracellular vesicles and mediates immunity against skin transplantation. PMID:35676234
Digital Cell Atlas of Mouse Uterus: From Regenerative Stage to Maturational Stage. PMID:35669188
The impact of genetic modifiers on variation in germline mutation rates within and among human populations. PMID:35666194
Gene Expression Profile Analysis of Human Epidermal Keratinocytes Expressing Human Papillomavirus Type 8 E7. PMID:35665406
SSRTool: A web tool for evaluating RNA secondary structure predictions based on species-specific functional interpretability. PMID:35664227
Brain proteome profiling implicates the complement and coagulation cascade in multiple system atrophy brain pathology. PMID:35657417
Exploring the Genetic Associations Between the Use of Statins and Alzheimer's Disease. PMID:35656152
A Novel lncRNA Panel for Risk Stratification and Immune Landscape in Breast Cancer Patients. PMID:35655656
Expediting knowledge acquisition by a web framework for Knowledge Graph Exploration and Visualization (KGEV): case studies on COVID-19 and Human Phenotype Ontology. PMID:35655307
Evolutionarily stable gene clusters shed light on the common grounds of pathogenicity in the Acinetobacter calcoaceticus-baumannii complex. PMID:35653398
Characterisation of a nucleo-adhesome. PMID:35650196
Potential biomarkers and molecular mechanisms in preeclampsia progression. PMID:35647297
Cystatin SN promotes epithelial-mesenchymal transition and serves as a prognostic biomarker in lung adenocarcinoma. PMID:35637432
Correlation Between Serum 25-Hydroxyvitamin D Levels in Albuminuria Progression of Diabetic Kidney Disease and Underlying Mechanisms By Bioinformatics Analysis. PMID:35634488
Flavivirus Capsid Proteins Inhibit the Interferon Response. PMID:35632712
Transcriptomics Integrated with Metabolomics Reveals 2-Methoxy-1, 4-Naphthoquinone-Based Carbon Dots Induced Molecular Shifts in Penicillium italicum. PMID:35628676
Epigenetic Silencing of PTEN and Epi-Transcriptional Silencing of MDM2 Underlied Progression to Secondary Acute Myeloid Leukemia in Myelodysplastic Syndrome Treated with Hypomethylating Agents. PMID:35628480
Trifluoperazine and Its Analog Suppressed the Tumorigenicity of Non-Small Cell Lung Cancer Cell; Applicability of Antipsychotic Drugs to Lung Cancer Treatment. PMID:35625784
CRISPR Library Screening in Cultured Cardiomyocytes. PMID:35618895
A preliminary, observational study using whole-blood RNA sequencing reveals differential expression of inflammatory and bone markers post-implantation of percutaneous osseointegrated prostheses. PMID:35617338
OncoboxPD: human 51 672 molecular pathways database with tools for activity calculating and visualization. PMID:35615022
An Myh11 single lysine deletion causes aortic dissection by reducing aortic structural integrity and contractility. PMID:35614093
Gene co-expression network based on part mutual information for gene-to-gene relationship and gene-cancer correlation analysis. PMID:35610556
Blood transcriptomics identifies immune signatures indicative of infectious complications in childhood cancer patients with febrile neutropenia. PMID:35602885
The ceRNA Crosstalk between mRNAs and lncRNAs in Diabetes Myocardial Infarction. PMID:35592708
DAB2IP down-regulates HSP90AA1 to inhibit the malignant biological behaviors of colorectal cancer. PMID:35590292
Local chromatin context regulates the genetic requirements of the heterochromatin spreading reaction. PMID:35584134
GenePlexus: a web-server for gene discovery using network-based machine learning. PMID:35580053
Transcription elongation is finely tuned by dozens of regulatory factors. PMID:35575476
Drosophila nicotinic acetylcholine receptor subunits and their native interactions with insecticidal peptide toxins. PMID:35575460
Identification of significant genes with a poor prognosis in skin cutaneous malignant melanoma based on a bioinformatics analysis. PMID:35571409
Pan-Cancer Bioinformatics Analysis of Gene UBE2C. PMID:35571064
Cancer Metabolic Subtypes and Their Association with Molecular and Clinical Features. PMID:35565274
Close Related Drug-Resistance Beijing Isolates of Mycobacterium tuberculosis Reveal a Different Transcriptomic Signature in a Murine Disease Progression Model. PMID:35563545
Identification of a novel lipid metabolism-related gene signature within the tumour immune microenvironment for breast cancer. PMID:35562758
CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation. PMID:35560159
Revealing the Mechanism of Huazhi Rougan Granule in the Treatment of Nonalcoholic Fatty Liver Through Intestinal Flora Based on 16S rRNA, Metagenomic Sequencing and Network Pharmacology. PMID:35559233
Role of tRNA derived fragments in renal ischemia-reperfusion injury. PMID:35546262
SubcellulaRVis: a web-based tool to simplify and visualise subcellular compartment enrichment. PMID:35536291
Transcriptomic profile of the predatory mite Amblyseius swirskii (Acari: Phytoseiidae) on different host plants. PMID:35534782
An approach for evaluating the effects of dietary fiber polysaccharides on the human gut microbiome and plasma proteome. PMID:35533274
SigCom LINCS: data and metadata search engine for a million gene expression signatures. PMID:35524556
The macrophage-associated microRNA-4715-3p / Gasdermin D axis potentially indicates fibrosis progression in nonalcoholic fatty liver disease: evidence from transcriptome and biological data. PMID:35521691
Signatures of selection in core and accessory genomes indicate different ecological drivers of diversification among Bacillus cereus clades. PMID:35510788
Survival-related genes are diversified across cancers but generally enriched in cancer hallmark pathways. PMID:35508961
Ox-LDL-mediated ILF3 overexpression in gastric cancer progression by activating the PI3K/AKT/mTOR signaling pathway. PMID:35507914
Analysis of host-pathogen gene association networks reveals patient-specific response to streptococcal and polymicrobial necrotising soft tissue infections. PMID:35505341
Identification of Inflammation-Related Biomarkers in Diabetes of the Exocrine Pancreas With the Use of Weighted Gene Co-Expression Network Analysis. PMID:35498402
Knowledge integration and decision support for accelerated discovery of antibiotic resistance genes. PMID:35487919
Identifying pleiotropic variants and candidate genes for fertility and reproduction traits in Holstein cattle via association studies based on imputed whole-genome sequence genotypes. PMID:35484513
Proteomic networks associated with tumor-educated macrophage polarization and cytotoxicity potentiated by heat-killed tuberculosis. PMID:35477732
Lupus Susceptibility Loci Predispose Mice to Clonal Lymphocytic Responses and Myeloid Expansion. PMID:35477687
Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data. PMID:35473573
Cell type and gene expression deconvolution with BayesPrism enables Bayesian integrative analysis across bulk and single-cell RNA sequencing in oncology. PMID:35469013
Bioinformatics and System Biology Approach to Identify the Influences of COVID-19 on Rheumatoid Arthritis. PMID:35464423
Identification of a Four-Gene Metabolic Signature to Evaluate the Prognosis of Colon Adenocarcinoma Patients. PMID:35462848
Estimating RNA dynamics using one time point for one sample in a single-pulse metabolic labeling experiment. PMID:35459101
A Bayesian framework to integrate multi-level genome-scale data for Autism risk gene prioritization. PMID:35459094
Identification of Novel Genes and Associated Drugs in Cervical Cancer by Bioinformatics Methods. PMID:35428744
Identification and Validation of Immune Cells and Hub Genes in Gastric Cancer Microenvironment. PMID:35422890
Research and experimental verification of the molecular mechanism of berberine in improving premature ovarian failure based on network pharmacology. PMID:35420511
An evidence-based lexical pattern approach for quality assurance of Gene Ontology relations. PMID:35419584
Analysis of human brain tissue derived from DBS surgery. PMID:35418104
A systematic review and functional bioinformatics analysis of genes associated with Crohn's disease identify more than 120 related genes. PMID:35418025
Transcriptional and Distributional Profiling of Microglia in Retinal Angiomatous Proliferation. PMID:35408803
An alternative UPF1 isoform drives conditional remodeling of nonsense-mediated mRNA decay. PMID:35403729
Multifaced regulator: RNA binding proteins and their roles in hematopoiesis. PMID:35402803
Machine learning-based screening of the diagnostic genes and their relationship with immune-cell infiltration in patients with lung adenocarcinoma. PMID:35399247
Deep whole-genome resequencing sheds light on the distribution and effect of amphioxus SNPs. PMID:35395709
Human pluripotent stem cell-derived myogenic progenitors undergo maturation to quiescent satellite cells upon engraftment. PMID:35395188
Predicted mouse interactome and network-based interpretation of differentially expressed genes. PMID:35390003
Hierarchical multi-label classification based on LSTM network and Bayesian decision theory for LncRNA function prediction. PMID:35388048
SuperDendrix algorithm integrates genetic dependencies and genomic alterations across pathways and cancer types. PMID:35382456
MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses. PMID:35380657
Transcriptome-wide association study for postpartum depression implicates altered B-cell activation and insulin resistance. PMID:35365803
NeuroSCORE is a genome-wide omics-based model that identifies candidate disease genes of the central nervous system. PMID:35361823
ALGAEFUN with MARACAS, microALGAE FUNctional enrichment tool for MicroAlgae RnA-seq and Chip-seq AnalysiS. PMID:35361110
Chicken Peripheral Blood Mononuclear Cells Response to Avian Leukosis Virus Subgroup J Infection Assessed by Single-Cell RNA Sequencing. PMID:35359721
Genomic heterogeneity underlies multidrug resistance in Pseudomonas aeruginosa: A population-level analysis beyond susceptibility testing. PMID:35358221
Computational methods, databases and tools for synthetic lethality prediction. PMID:35352098
Mechanism of Zhen Wu Decoction in the Treatment of Heart Failure Based on Network Pharmacology and Molecular Docking. PMID:35341142
Evolution of Protein Functional Annotation: Text Mining Study. PMID:35330478
Functional Enrichment Analysis of Regulatory Elements. PMID:35327392
GOing Forward With the Cardiac Conduction System Using Gene Ontology. PMID:35309148
Transcriptome Analyses of Senecavirus A-Infected PK-15 Cells: RIG-I and IRF7 Are the Important Factors in Inducing Type III Interferons. PMID:35308346
Machine Learning of All Mycobacterium tuberculosis H37Rv RNA-seq Data Reveals a Structured Interplay between Metabolism, Stress Response, and Infection. PMID:35306876
Transcriptomic analysis of human sensory neurons in painful diabetic neuropathy reveals inflammation and neuronal loss. PMID:35304484
Transcriptogram analysis reveals relationship between viral titer and gene sets responses during Corona-virus infection. PMID:35300459
Protocol for isolation and functional validation of label-retaining quiescent colorectal cancer stem cells from patient-derived organoids for RNA-seq. PMID:35300001
Contributions of Artificial Intelligence Reported in Obstetrics and Gynecology Journals: Systematic Review. PMID:35297766
Whole genome sequencing delineates regulatory, copy number, and cryptic splice variants in early onset cardiomyopathy. PMID:35288587
The Key Genes Underlying Pathophysiology Correlation Between the Acute Myocardial Infarction and COVID-19. PMID:35282650
HCK is a Potential Prognostic Biomarker that Correlates with Immune Cell Infiltration in Acute Myeloid Leukemia. PMID:35280440
GATA4/5/6 family transcription factors are conserved determinants of cardiac versus pharyngeal mesoderm fate. PMID:35275720
Proteome Analysis of Urinary Biomarkers in a Bovine IRBP-Induced Uveitis Rat Model via Data-Independent Acquisition and Parallel Reaction Monitoring Proteomics. PMID:35274006
Transcriptomics of Parental Care in the Hypothalamic-Septal Region of Female Zebra Finch Brain. PMID:35269661
A non-canonical tricarboxylic acid cycle underlies cellular identity. PMID:35264789
CRISPR/Cas9-Mediated Insertion of HIV Long Terminal Repeat within BACH2 Promotes Expansion of T Regulatory-like Cells. PMID:35264460
Broad domains of histone marks in the highly compact Paramecium macronuclear genome. PMID:35264449
E2F4 may be a core transcription factor in the lncRNA-TF regulatory network in cervical cancer. PMID:35262965
Expression and regulatory network of long noncoding RNA in rats after spinal cord hemisection injury. PMID:35259853
Human biliary epithelial cells from discarded donor livers rescue bile duct structure and function in a mouse model of biliary disease. PMID:35245467
Considerations for constructing a protein sequence database for metaproteomics. PMID:35242286
Upregulated YB-1 protein promotes glioblastoma growth through a YB-1/CCT4/mLST8/mTOR pathway. PMID:35239512
Multi-omic rejuvenation of naturally aged tissues by a single cycle of transient reprogramming. PMID:35235716
PSINDB: the postsynaptic protein-protein interaction database. PMID:35234850
LINC00665 regulates hepatocellular carcinoma by modulating mRNA via the m6A enzyme. PMID:35233461
Landscape genomics of the streamside salamander: Implications for species management in the face of environmental change. PMID:35233244
Growth-rate-dependent and nutrient-specific gene expression resource allocation in fission yeast. PMID:35228260
MHC-II Signature Correlates With Anti-Tumor Immunity and Predicts anti-PD-L1 Response of Bladder Cancer. PMID:35223828
Student biocuration projects as a learning environment. PMID:35211294
Differential Expression of RAD51AP1 in Ovarian Cancer: Effects of siRNA In Vitro. PMID:35207688
Development of Gene Expression-Based Random Forest Model for Predicting Neoadjuvant Chemotherapy Response in Triple-Negative Breast Cancer. PMID:35205629
The Transcription Factor FgAtrR Regulates Asexual and Sexual Development, Virulence, and DON Production and Contributes to Intrinsic Resistance to Azole Fungicides in Fusarium graminearum. PMID:35205191
A Review on Transcriptional Responses of Interactions between Insect Vectors and Plant Viruses. PMID:35203347
Identification of Potential Immune Checkpoint Inhibitor Targets in Gliomas via Bioinformatic Analyses. PMID:35198632
Proteome-defined changes in cellular pathways for decidua and trophoblast tissues associated with location and viability of early-stage pregnancy. PMID:35189928
Genomic characterization of the world's longest selection experiment in mouse reveals the complexity of polygenic traits. PMID:35189878
Cancer/Testis Antigen 55 is required for cancer cell proliferation and mitochondrial DNA maintenance. PMID:35189384
Wei2GO: weighted sequence similarity-based protein function prediction. PMID:35186498
DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules. PMID:35183110
Transcriptional changes in dendritic cells underlying allergen specific induced tolerance in a mouse model. PMID:35181694
Quantitative multiplexed proteomics analysis reveals reshaping of the lysine 2-hydroxyisobutyrylome in Fusarium graminearum by tebuconazole. PMID:35180840
Clinical and molecular characteristics of estrogen receptor-positive ultralow risk breast cancer tumors identified by the 70-gene signature. PMID:35179782
Insight Into Pituitary lncRNA and mRNA at Two Estrous Stages in Small Tail Han Sheep With Different FecB Genotypes. PMID:35178025
The m6A(m)-independent role of FTO in regulating WNT signaling pathways. PMID:35169043
Zebrafish information network, the knowledgebase for Danio rerio research. PMID:35166825
Transcriptomic Profile of Canine DH82 Macrophages Infected by Leishmania infantum Promastigotes with Different Virulence Behavior. PMID:35163386
Investigating changes of proteome in the bovine milk serum after retort processing using proteomics techniques. PMID:35154669
Gene-Interaction-Sensitive enrichment analysis in congenital heart disease. PMID:35151364
Multimodal reasoning based on knowledge graph embedding for specific diseases. PMID:35150235
Machine learning prediction and tau-based screening identifies potential Alzheimer's disease genes relevant to immunity. PMID:35149761
Identification of recurrent genetic patterns from targeted sequencing panels with advanced data science: a case-study on sporadic and genetic neurodegenerative diseases. PMID:35144616
blitzGSEA: Efficient computation of Gene Set Enrichment Analysis through Gamma distribution approximation. PMID:35143610
The Mechanism Study of Common Flavonoids on Antiglioma Based on Network Pharmacology and Molecular Docking. PMID:35140796
The DOMINO web-server for active module identification analysis. PMID:35139202
Evolutionary rewiring of regulatory networks contributes to phenotypic differences between human and mouse orthologous genes. PMID:35137181
Sperm acquire epididymis-derived proteins through epididymosomes. PMID:35137089
The genome of the Paleogene relic tree Bretschneidera sinensis: insights into trade-offs in gene family evolution, demographic history, and adaptive SNPs. PMID:35137004
PlantGF: an analysis and annotation platform for plant gene families. PMID:35134149
In silico prediction of HIV-1-host molecular interactions and their directionality. PMID:35134057
Role of mitochondrial genetic interactions in determining adaptation to high altitude human population. PMID:35132109
Common DNA methylation changes in biliary tract cancers identify subtypes with different immune characteristics and clinical outcomes. PMID:35130881
Shared Genetic Architecture and Causal Relationship Between Asthma and Cardiovascular Diseases: A Large-Scale Cross-Trait Analysis. PMID:35126453
Identification and validation of an autophagy-related gene signature for predicting prognosis in patients with esophageal squamous cell carcinoma. PMID:35121801
Genomic basis for skin phenotype and cold adaptation in the extinct Steller's sea cow. PMID:35119923
Identification of biomarkers for the diagnosis and treatment of primary colorectal cancer based on microarray technology. PMID:35117711
Comparison of confound adjustment methods in the construction of gene co-expression networks. PMID:35115012
Deep learning program to predict protein functions based on sequence information. PMID:35111575
Neuropeptidergic regulation of compulsive ethanol seeking in C. elegans. PMID:35110557
An in silico analysis identifies drugs potentially modulating the cytokine storm triggered by SARS-CoV-2 infection. PMID:35102208
Potential Clinical Value of Biomarker-Guided Emergency Triage for Thoracic Aortic Dissection. PMID:35096998
Making sense of the linear genome, gene function and TADs. PMID:35090532
A novel variant in SMG9 causes intellectual disability, confirming a role for nonsense-mediated decay components in neurocognitive development. PMID:35087184
Bioactive peptides from broccoli stems strongly enhance regenerative keratinocytes by stimulating controlled proliferation. PMID:35086428
Proteomic screen reveals diverse protein transport between connected neurons in the visual system. PMID:35081342
Haploidy in somatic cells is induced by mature oocytes in mice. PMID:35079104
NonLoss: a novel analytical method for differential biological module identification from single-cell transcriptome. PMID:35071482
A comprehensive characterization of the transcriptome in enzalutamide resistance prostate cancer. PMID:35071476
Cross-talk of pyroptosis and tumor immune landscape in lung adenocarcinoma. PMID:35070752
Comparison between Heat-Clearing Medicine and Antirheumatic Medicine in Treatment of Gastric Cancer Based on Network Pharmacology, Molecular Docking, and Tumor Immune Infiltration Analysis. PMID:35069767
Utilizing network pharmacology and experimental validation to explore the potential molecular mechanisms of BanXia-YiYiRen in treating insomnia. PMID:35067174
Tissue-specific multi-omics analysis of atrial fibrillation. PMID:35064145
Tumor microenvironment-related multigene prognostic prediction model for breast cancer. PMID:35060926
ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements. PMID:35058462
A novel gene functional similarity calculation model by utilizing the specificity of terms and relationships in gene ontology. PMID:35057740
Biallelic Variants in PYROXD2 Cause a Severe Infantile Metabolic Disorder Affecting Mitochondrial Function. PMID:35055180
Single-Cell Analysis of Aneurysmal Aortic Tissue in Patients with Marfan Syndrome Reveals Dysfunctional TGF-β Signaling. PMID:35052435
Capturing SNP Association across the NK Receptor and HLA Gene Regions in Multiple Sclerosis by Targeted Penalised Regression Models. PMID:35052430
Proteome-scale mapping of binding sites in the unstructured regions of the human proteome. PMID:35044719
Signatures of natural selection in a foundation tree along Mediterranean climatic gradients. PMID:35038378
The initial expression alterations occurring to transcription factors during the formation of breast cancer: Evidence from bioinformatics. PMID:35037412
Schisandrin B suppresses osteosarcoma lung metastasis in vivo by inhibiting the activation of the Wnt/β‑catenin and PI3K/Akt signaling pathways. PMID:35029287
Inferring early-life host and microbiome functions by mass spectrometry-based metaproteomics and metabolomics. PMID:35024099
RNAseq reveals extensive metabolic disruptions in the sensitive SF-295 cell line treated with schweinfurthins. PMID:35013404
Age-dependent pathogenic characteristics of SARS-CoV-2 infection in ferrets. PMID:35013229
Titanium with nanotopography attenuates the osteoclast-induced disruption of osteoblast differentiation by regulating histone methylation. PMID:35012895
Altered White Matter and microRNA Expression in a Murine Model Related to Williams Syndrome Suggests That miR-34b/c Affects Brain Development via Ptpru and Dcx Modulation. PMID:35011720
Searching beyond the streetlight: Neonicotinoid exposure alters the neurogenomic state of worker honey bees. PMID:35003705
Identification of the molecular subgroups in asthma by gene expression profiles: airway inflammation implications. PMID:35000593
Deep learning-based brain transcriptomic signatures associated with the neuropathological and clinical severity of Alzheimer's disease. PMID:34993477
HESML: a real-time semantic measures library for the biomedical domain with a reproducible survey. PMID:34991460
HMDB 5.0: the Human Metabolome Database for 2022. PMID:34986597
Prediction of lncRNA-disease association based on a Laplace normalized random walk with restart algorithm on heterogeneous networks. PMID:34983367
Systems Biology and Bioinformatics approach to Identify blood based signatures molecules and drug targets of patient with COVID-19. PMID:34981034
Structure-function relationships of the disease-linked A218T oxytocin receptor variant. PMID:34980886
Ultradian rhythms of AKT phosphorylation and gene expression emerge in the absence of the circadian clock components Per1 and Per2. PMID:34968386
Dichotomous Responses to Chronic Fetal Hypoxia Lead to a Predetermined Aging Phenotype. PMID:34958949
Unraveling Admixture, Inbreeding, and Recent Selection Signatures in West African Indigenous Cattle Populations in Benin. PMID:34956303
DeepSVP: Integration of genotype and phenotype for structural variant prioritization using deep learning. PMID:34951628
Immunosenescence in Choroidal Neovascularization (CNV)-Transcriptional Profiling of Naïve and CNV-Associated Retinal Myeloid Cells during Aging. PMID:34948115
MicroRNA Analysis of Human Stroke Brain Tissue Resected during Decompressive Craniectomy/Stroke-Ectomy Surgery. PMID:34946809
8-Hydroxydaidzein Downregulates JAK/STAT, MMP, Oxidative Phosphorylation, and PI3K/AKT Pathways in K562 Cells. PMID:34944720
Transcriptomic Profiles Reveal Downregulation of Low-Density Lipoprotein Particle Receptor Pathway Activity in Patients Surviving Severe COVID-19. PMID:34944005
Transcriptome Analysis of Induced Pluripotent Stem Cells and Neuronal Progenitor Cells, Derived from Discordant Monozygotic Twins with Parkinson's Disease. PMID:34943986
Genome-Wide RNAi Screening Identifies Novel Pathways/Genes Involved in Oxidative Stress and Repurposable Drugs to Preserve Cystic Fibrosis Airway Epithelial Cell Integrity. PMID:34943039
Co-existing TP53 and ARID1A mutations promote aggressive endometrial tumorigenesis. PMID:34941867
Proteomic profiling reveals engineered chitosan nanoparticles mediated cellular crosstalk and immunomodulation for therapeutic application in apical periodontitis. PMID:34938914
Extensive mitochondrial proteome disturbance occurs during the early stages of acute myocardial ischemia. PMID:34938367
Biosafety and Proteome Profiles of Different Heat Inactivation Methods for Mycobacterium tuberculosis. PMID:34937194
Druggable genetic targets in endometrial cancer✰,✰✰. PMID:34933203
Type I CRISPR-Cas provides robust immunity but incomplete attenuation of phage-induced cellular stress. PMID:34928385
exoRBase 2.0: an atlas of mRNA, lncRNA and circRNA in extracellular vesicles from human biofluids. PMID:34918744
GENPPI: standalone software for creating protein interaction networks from genomes. PMID:34915867
Identification of Potential circRNA-microRNA-mRNA Regulatory Network in Skeletal Muscle. PMID:34912845
Metabolic drug survey highlights cancer cell dependencies and vulnerabilities. PMID:34907165
Whole-transcriptome analysis of aluminum-exposed rat hippocampus and identification of ceRNA networks to investigate neurotoxicity of Al. PMID:34900398
A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data. PMID:34900140
Gene Ontology Enrichment Analysis of Renal Agenesis: Improving Prenatal Molecular Diagnosis. PMID:34899145
New data and collaborations at the Saccharomyces Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources. PMID:34897464
Integrated Analysis of Angiogenesis-Mediated Tumor Immune Microenvironment Pattern in Hepatocellular Carcinoma (HCC) and a Novel Prognostic Model Construction to Predict Patient Outcome. PMID:34897268
Integrative analysis of immune-related multi-omics profiles identifies distinct prognosis and tumor microenvironment patterns in osteosarcoma. PMID:34894177
Integrated genome and tissue engineering enables screening of cancer vulnerabilities in physiologically relevant perfusable ex vivo cultures. PMID:34890975
Meta-analyses identify DNA methylation associated with kidney function and damage. PMID:34887417
Epigenome-wide association study of serum urate reveals insights into urate co-regulation and the SLC2A9 locus. PMID:34887389
Splice-Variant Knock-Out of TGFβ Receptors Perturbates the Proteome of Ovarian Carcinoma Cells. PMID:34884451
The Power of Universal Contextualized Protein Embeddings in Cross-species Protein Function Prediction. PMID:34880594
Identifying the temporal electrophysiological and molecular changes that contribute to TSC-associated epileptogenesis. PMID:34877936
RYR2 mutation in non-small cell lung cancer prolongs survival via down-regulation of DKK1 and up-regulation of GS1-115G20.1: A weighted gene Co-expression network analysis and risk prognostic models. PMID:34877784
Identification and validation of cellular senescence patterns to predict clinical outcomes and immunotherapeutic responses in lung adenocarcinoma. PMID:34872577
Identification of Galectin-3 as Potential Biomarkers for Renal Fibrosis by RNA-Sequencing and Clinicopathologic Findings of Kidney Biopsy. PMID:34869439
Comprehensive Analysis Uncovers Prognostic and Immunogenic Characteristics of Cellular Senescence for Lung Adenocarcinoma. PMID:34869385
Multifaceted pathomolecular mechanism of a VWF large deletion involved in the pathogenesis of severe VWD. PMID:34861678
A Standardized Brain Molecular Atlas: A Resource for Systems Modeling and Simulation. PMID:34858137
Multiscale interactome analysis coupled with off-target drug predictions reveals drug repurposing candidates for human coronavirus disease. PMID:34857794
Identification of the Active Constituents and Significant Pathways of Shen-qi-Yi-zhu Decoction on Antigastric Cancer: A Network Pharmacology Research and Experimental Validation. PMID:34853601
Transcriptomic dataset for Sardina pilchardus: Assembly, annotation, and expression of nine tissues. PMID:34849383
Toll-Like Receptor (TLR) Signaling Enables Cyclic GMP-AMP Synthase (cGAS) Sensing of HIV-1 Infection in Macrophages. PMID:34844429
Knowledge-guided artificial intelligence technologies for decoding complex multiomics interactions in cells. PMID:34844399
Identification of copy number variation-driven molecular subtypes informative for prognosis and treatment in pancreatic adenocarcinoma of a Chinese cohort. PMID:34839264
The Aliment to Bodily Condition knowledgebase (ABCkb): a database connecting plants and human health. PMID:34838100
Transcriptome Analysis of Lolium temulentum Exposed to a Combination of Drought and Heat Stress. PMID:34834610
Multi-Omics Analysis Reveals Anti-Staphylococcus aureus Activity of Actinomycin D Originating from Streptomyces parvulus. PMID:34830114
Identification of Disease-Related Genes That Are Common between Alzheimer's and Cardiovascular Disease Using Blood Genome-Wide Transcriptome Analysis. PMID:34829754
Proteomics Profiling with SWATH-MS Quantitative Analysis of Changes in the Human Brain with HIV Infection Reveals a Differential Impact on the Frontal and Temporal Lobes. PMID:34827437
Single-cell analysis identifies dynamic gene expression networks that govern B cell development and transformation. PMID:34824268
A ROS-responsive, self-immolative and self-reporting hydrogen sulfide donor with multiple biological activities for the treatment of myocardial infarction. PMID:34820564
Quantitative dissection of multilocus pathogenic variation in an Egyptian infant with severe neurodevelopmental disorder resulting from multiple molecular diagnoses. PMID:34816580
Multiple regression analysis of a comprehensive transcriptomic data assembly elucidates mechanically- and biochemically-driven responses to focused ultrasound blood-brain barrier disruption. PMID:34815790
A Novel Autophagy-Related Long Non-Coding RNA Signature to Predict Prognosis and Therapeutic Response in Esophageal Squamous Cell Carcinoma. PMID:34815705
p300 or CBP is required for insulin-stimulated glucose uptake in skeletal muscle and adipocytes. PMID:34813504
Delayed DNA replication in haploid human embryonic stem cells. PMID:34810218
Hsa-mir-3163 and CCNB1 may be potential biomarkers and therapeutic targets for androgen receptor positive triple-negative breast cancer. PMID:34797837
Follicular T cells are clonally and transcriptionally distinct in B cell-driven mouse autoimmune disease. PMID:34795279
Altered cell and RNA isoform diversity in aging Down syndrome brains. PMID:34795060
APOBEC Mutagenesis Inhibits Breast Cancer Growth through Induction of T cell-Mediated Antitumor Immune Responses. PMID:34795033
Inferred expression regulator activities suggest genes mediating cardiometabolic genetic signals. PMID:34793442
The disease-associated proteins Drosophila Nab2 and Ataxin-2 interact with shared RNAs and coregulate neuronal morphology. PMID:34791182
Identification of Hub Genes and Potential ceRNA Networks of Diabetic Nephropathy by Weighted Gene Co-Expression Network Analysis. PMID:34790229
Dynamic Urinary Proteome Changes in Ovalbumin-Induced Asthma Mouse Model Using Data-Independent Acquisition Proteomics. PMID:34785909
The differentiation state of the Schwann cell progenitor drives phenotypic variation between two contagious cancers. PMID:34780568
Identification of discriminative gene-level and protein-level features associated with pathogenic gain-of-function and loss-of-function variants. PMID:34762822
Microarray profiling predicts early neurological and immune phenotypic traits in advance of CNS disease during disease progression in Trypanosoma. b. brucei infected CD1 mouse brains. PMID:34762691
Binge Ethanol Exposure in Mice Represses Expression of Genes Involved in Osteoblast Function and Induces Expression of Genes Involved in Osteoclast Differentiation Independently of Endogenous Catalase. PMID:34755883
BRAD V3.0: an upgraded Brassicaceae database. PMID:34755871
T2-DAG: a powerful test for differentially expressed gene pathways via graph-informed structural equation modeling. PMID:34755844
Regulatory network of miRNA, lncRNA, transcription factor and target immune response genes in bovine mastitis. PMID:34753991
Co-evolution based machine-learning for predicting functional interactions between human genes. PMID:34753957
The human telomeric proteome during telomere replication. PMID:34747482
International Prognostic Index-Based Immune Prognostic Model for Diffuse Large B-Cell Lymphoma. PMID:34745101
BCG vaccination and the risk of COVID 19: A possible correlation. PMID:34742127
Fibromine is a multi-omics database and mining tool for target discovery in pulmonary fibrosis. PMID:34741074
Prognostic and Immune-Infiltrate Significance of miR-222-3p and Its Target Genes in Thyroid Cancer. PMID:34737762
Cross-platform transcriptomic profiling of the response to recombinant human erythropoietin. PMID:34737331
Dysregulated expression levels of APH1B in peripheral blood are associated with brain atrophy and amyloid-β deposition in Alzheimer's disease. PMID:34732252
Genome-wide CRISPR interference screen identifies long non-coding RNA loci required for differentiation and pluripotency. PMID:34731163
Comparison of critical biomarkers in 2 erectile dysfunction models based on GEO and NOS-cGMP-PDE5 pathway. PMID:34731136
MCDB: A comprehensive curated mitotic catastrophe database for retrieval, protein sequence alignment, and target prediction. PMID:34729303
Weighted gene co-expression network analysis to identify key modules and hub genes associated with paucigranulocytic asthma. PMID:34727921
Spatially resolved transcriptomics reveals the architecture of the tumor-microenvironment interface. PMID:34725363
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. PMID:34718728
Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture. PMID:34716321
A human iPSC-astroglia neurodevelopmental model reveals divergent transcriptomic patterns in schizophrenia. PMID:34716291
Nanoencapsulation of sulforaphane in broccoli membrane vesicles and their in vitro antiproliferative activity. PMID:34714214
Cancer CRC: A Comprehensive Cancer Core Transcriptional Regulatory Circuit Resource and Analysis Platform. PMID:34712617
Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO). PMID:34710081
Identification of lncRNA-associated competing endogenous RNA networks for occurrence and prognosis of gastric carcinoma. PMID:34704289
Whole-exome analysis in Tunisian Imazighen and Arabs shows the impact of demography in functional variation. PMID:34702931
Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci. PMID:34699533
Mouse Genome Informatics (MGI): latest news from MGD and GXD. PMID:34698891
Gene Ontology curation of the blood-brain barrier to improve the analysis of Alzheimer's and other neurological diseases. PMID:34697638
Elucidate multidimensionality of type 1 diabetes mellitus heterogeneity by multifaceted information. PMID:34697343
Genome-Wide Association Studies for Growth Curves in Meat Rabbits Through the Single-Step Nonlinear Mixed Model. PMID:34691158
Recent innovations and in-depth aspects of post-genome wide association study (Post-GWAS) to understand the genetic basis of complex phenotypes. PMID:34689168
TAGOPSIN: collating taxa-specific gene and protein functional and structural information. PMID:34688246
Adaptive translational pausing is a hallmark of the cellular response to severe environmental stress. PMID:34686314
Microarray profile analysis identifies ETS1 as potential biomarker regulated by miR-23b and modulates TCF4 in gastric cancer. PMID:34686186
Investigations on the Degradation of the Bile Salt Cholate via the 9,10-Seco-Pathway Reveals the Formation of a Novel Recalcitrant Steroid Compound by a Side Reaction in Sphingobium sp. Strain Chol11. PMID:34683472
Entropy-Based Graph Clustering of PPI Networks for Predicting Overlapping Functional Modules of Proteins. PMID:34681995
Mining drug-target and drug-adverse drug reaction databases to identify target-adverse drug reaction relationships. PMID:34679164
Platelet proteome dynamics in hibernating 13-lined ground squirrels. PMID:34677084
Mechanisms of Rhizoma Coptidis against type 2 diabetes mellitus explored by network pharmacology combined with molecular docking and experimental validation. PMID:34675276
Lung proteomic biomarkers associated with chronic obstructive pulmonary disease. PMID:34668408
Screening of anti-chronic nonbacterial prostatitis activity of different extractions of the aerial part of Glycyrrhiza uralensis, and network pharmacology research. PMID:34667596
Antibiotics accelerate growth at the expense of immunity. PMID:34666517
Co-evolutionary Signals Identify Burkholderia pseudomallei Survival Strategies in a Hostile Environment. PMID:34662416
Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds. PMID:34659136
Comprehensive landscape and interference of clonal haematopoiesis mutations for liquid biopsy: A Chinese pan-cancer cohort. PMID:34658138
Combinatorial patterns of gene expression changes contribute to variable expressivity of the developmental delay-associated 16p12.1 deletion. PMID:34657631
Deep semi-supervised learning ensemble framework for classifying co-mentions of human proteins and phenotypes. PMID:34656098
Analyzing the whole-transcriptome profiles of ncRNAs and predicting the competing endogenous RNA networks in cervical cancer cell lines with cisplatin resistance. PMID:34641878
Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication. PMID:34635656
Disulfiram Alone Functions as a Radiosensitizer for Pancreatic Cancer Both In Vitro and In Vivo. PMID:34631519
Clustering Spatial Transcriptomics Data. PMID:34623423
A Taxon-Wise Insight Into Rock Weathering and Nitrogen Fixation Functional Profiles of Proglacial Systems. PMID:34621246
Phenotyping stomatal closure by thermal imaging for GWAS and TWAS of water use efficiency-related genes. PMID:34618072
Neuronal activity regulates the nuclear proteome to promote activity-dependent transcription. PMID:34617965
Host genetic factors associated with the range limit of a European hantavirus. PMID:34614264
A metric for evaluating biological information in gene sets and its application to identify co-expressed gene clusters in PBMC. PMID:34613979
An updated SYSCILIA gold standard (SCGSv2) of known ciliary genes, revealing the vast progress that has been made in the cilia research field. PMID:34613793
Genome-wide associations for immune traits in two maternal pig lines. PMID:34610786
High Throughput Transcriptome Data Analysis and Computational Verification Reveal Immunotherapy Biomarkers of Compound Kushen Injection for Treating Triple-Negative Breast Cancer. PMID:34604090
Bioinformatics and system biology approaches to identify pathophysiological impact of COVID-19 to the progression and severity of neurological diseases. PMID:34601390
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale. PMID:34597405
Dramatic transcriptomic differences in Macaca mulatta and Macaca fascicularis with Plasmodium knowlesi infections. PMID:34593836
Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19. PMID:34592166
Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels. PMID:34591957
Divergent patterns of selection on metabolite levels and gene expression. PMID:34587900
Identical twins carry a persistent epigenetic signature of early genome programming. PMID:34584077
Integrative proteome analysis implicates aberrant RNA splicing in impaired developmental potential of aged mouse oocytes. PMID:34582091
Predicting metabolic pathway membership with deep neural networks by integrating sequential and ontology information. PMID:34579673
Quantitative Proteomics and Phosphoproteomics Reveal TNF-α-Mediated Protein Functions in Hepatocytes. PMID:34576943
Isolation and Characterization of Outer Membrane Vesicles of Pectobacterium brasiliense 1692. PMID:34576813
Antioxidant and Antiproliferative Activity of Finasteride against Glioblastoma Cells. PMID:34575486
Comparative Transcriptome Analysis of the Expression of Antioxidant and Immunity Genes in the Spleen of a Cyanidin 3-O-Glucoside-Treated Alzheimer's Mouse Model. PMID:34573067
Promoter Hypermethylation Promotes the Binding of Transcription Factor NFATc1, Triggering Oncogenic Gene Activation in Pancreatic Cancer. PMID:34572796
Position Specific Alternative Splicing and Gene Expression Profiles Along the Tonotopic Axis of Chick Cochlea. PMID:34568429
Immune Mechanism, Gene Module, and Molecular Subtype Identification of Astragalus Membranaceus in the Treatment of Dilated Cardiomyopathy: An Integrated Bioinformatics Study. PMID:34567206
Viral suppressor of RNA silencing in vascular plants also interferes with the development of the bryophyte Physcomitrella patens. PMID:34564869
Challenges and opportunities in the study of extracellular vesicles: Global institutional context and national state of the art. PMID:34559503
clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. PMID:34557778
COVID19db: a comprehensive database platform to discover potential drugs and targets of COVID-19 at whole transcriptomic scale. PMID:34554255
Examination of Gene Loss in the DNA Mismatch Repair Pathway and Its Mutational Consequences in a Fungal Phylum. PMID:34554246
The role of metadata in reproducible computational research. PMID:34553169
A novel lncRNA Discn fine-tunes replication protein A (RPA) availability to promote genomic stability. PMID:34552092
RNALocate v2.0: an updated resource for RNA subcellular localization with increased coverage and annotation. PMID:34551440
Novel insights into the molecular mechanisms underlying risk of colorectal cancer from smoking and red/processed meat carcinogens by modeling exposure in normal colon organoids. PMID:34548904
Using informative features in machine learning based method for COVID-19 drug repurposing. PMID:34544500
Long Noncoding RNA AC007639.1 Promotes the Pathogenesis and Progression of Hepatocellular Carcinoma Through Inhibiting Apoptosis and Stimulating Chemotherapeutic Resistance. PMID:34540685
Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives. PMID:34540375
KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases. PMID:34537014
Transcriptome analysis reveals the mechanism of stromal cell-derived factor-1 and exendin-4 synergistically promoted periodontal ligament stem cells osteogenic differentiation. PMID:34532163
Identification of key genes and immune infiltration modulated by CPAP in obstructive sleep apnea by integrated bioinformatics analysis. PMID:34529670
Bioinformatic analysis for potential biological processes and key targets of heart failure-related stroke. PMID:34514752
Identifying Protein Complexes With Clear Module Structure Using Pairwise Constraints in Protein Interaction Networks. PMID:34512712
Chromosomal neighbourhoods allow identification of organ specific changes in gene expression. PMID:34506480
The Cancer Epitope Database and Analysis Resource: A Blueprint for the Establishment of a New Bioinformatics Resource for Use by the Cancer Immunology Community. PMID:34504503
Comprehensive Analysis of YTH Domain Family in Lung Adenocarcinoma: Expression Profile, Association with Prognostic Value, and Immune Infiltration. PMID:34497675
Single-cell analysis of a tumor-derived exosome signature correlates with prognosis and immunotherapy response. PMID:34496872
Vision, challenges and opportunities for a Plant Cell Atlas. PMID:34491200
Modelling the impact of decidual senescence on embryo implantation in human endometrial assembloids. PMID:34487490
Identification and Validation of a PPP1R12A-Related Five-Gene Signature Associated With Metabolism to Predict the Prognosis of Patients With Prostate Cancer. PMID:34484299
Effects of NaCl Concentrations on Growth Patterns, Phenotypes Associated With Virulence, and Energy Metabolism in Escherichia coli BW25113. PMID:34484145
Identification of anti-horn fly vaccine antigen candidates using a reverse vaccinology approach. PMID:34479607
The association of immunosurveillance and distant metastases in colorectal cancer. PMID:34476575
INHBA is a novel mediator regulating cellular senescence and immune evasion in colorectal cancer. PMID:34476008
Release of Notch activity coordinated by IL-1β signalling confers differentiation plasticity of airway progenitors via Fosl2 during alveolar regeneration. PMID:34475534
Human genetic analyses of organelles highlight the nucleus in age-related trait heritability. PMID:34467851
A novel missense variant in ACAA1 contributes to early-onset Alzheimer's disease, impairs lysosomal function, and facilitates amyloid-β pathology and cognitive decline. PMID:34465723
Predictability of polygenic risk score for progression to dementia and its interaction with APOE ε4 in mild cognitive impairment. PMID:34465370
Multitrait GWAS to connect disease variants and biological mechanisms. PMID:34460823
Comprehensive Analysis of the Systemic Transcriptomic Alternations and Inflammatory Response during the Occurrence and Progress of COVID-19. PMID:34457122
The blood transcriptome prior to ovarian cancer diagnosis: A case-control study in the NOWAC postgenome cohort. PMID:34449791
Identification of key proteins in the signaling crossroads between wound healing and cancer hallmark phenotypes. PMID:34446793
Pan-cancer analysis of longitudinal metastatic tumors reveals genomic alterations and immune landscape dynamics associated with pembrolizumab sensitivity. PMID:34446728
Promising Anticancer Activity of [Bis(1,8-quinolato)palladium (II)] Alone and in Combination. PMID:34445176
CANVS: an easy-to-use application for the analysis and visualization of mass spectrometry-based protein-protein interaction/association data. PMID:34432510
Depletion of TAX1BP1 Amplifies Innate Immune Responses during Respiratory Syncytial Virus Infection. PMID:34431698
Bacterial surface properties influence the activity of the TAT-RasGAP317-326 antimicrobial peptide. PMID:34430812
Transcriptional Analysis of Liver Tissue Identifies Distinct Phenotypes of Indeterminate Pediatric Acute Liver Failure. PMID:34430782
CeTF: an R/Bioconductor package for transcription factor co-expression networks using regulatory impact factors (RIF) and partial correlation and information (PCIT) analysis. PMID:34416858
Cadherin and Wnt signaling pathways as key regulators in diabetic nephropathy. PMID:34411124
Screening differentially expressed genes between endometriosis and ovarian cancer to find new biomarkers for endometriosis. PMID:34409913
Interferon stimulated binding of ISRE is cell type specific and is predicted by homeostatic chromatin state. PMID:34409284
Modeling the effects of EMT-immune dynamics on carcinoma disease progression. PMID:34408236
PhenoDB, GeneMatcher and VariantMatcher, tools for analysis and sharing of sequence data. PMID:34407837
A primary cell wall cellulose-dependent defense mechanism against vascular pathogens revealed by time-resolved dual transcriptomics. PMID:34404410
The Role of Long Noncoding RNA AL161431.1 in the Development and Progression of Pancreatic Cancer. PMID:34395245
Compressing deep graph convolution network with multi-staged knowledge distillation. PMID:34388224
Cortical Networks of Creative Ability Trace Gene Expression Profiles of Synaptic Plasticity in the Human Brain. PMID:34381343
Diffusion enables integration of heterogeneous data and user-driven learning in a desktop knowledge-base. PMID:34379637
Tumor microenvironment evaluation promotes precise checkpoint immunotherapy of advanced gastric cancer. PMID:34376552
From a genome assembly to full regulatory network prediction: the case study of Rhodotorula toruloides putative Haa1-regulon. PMID:34376148
Identification of m6A-Related Biomarkers Associated with Prognosis of Colorectal Cancer. PMID:34373442
Toward a systematic conflict resolution framework for ontologies. PMID:34372934
IRF7-Associated Immunophenotypes Have Dichotomous Responses to Virus/Allergen Coexposure and OM-85-Induced Reprogramming. PMID:34367159
Hanseniaspora smithiae sp. nov., a Novel Apiculate Yeast Species From Patagonian Forests That Lacks the Typical Genomic Domestication Signatures for Fermentative Environments. PMID:34367085
An Ontology-Based Framework for Psychological Monitoring in Education During the COVID-19 Pandemic. PMID:34366992
Collagen fiber orientation disorder from H&E images is prognostic for early stage breast cancer: clinical trial validation. PMID:34362928
Investigation of RNA metabolism through large-scale genetic interaction profiling in yeast. PMID:34358317
"Guilt by association" is not competitive with genetic association for identifying autism risk genes. PMID:34354131
Evaluating whole-genome expression differences in idiopathic and diabetic adhesive capsulitis. PMID:34352401
The 5-formyl-tetrahydrofolate proteome links folates with C/N metabolism and reveals feedback regulation of folate biosynthesis. PMID:34352110
Characterization of Five Transmembrane Proteins: With Focus on the Tweety, Sideroflexin, and YIP1 Domain Families. PMID:34350187
Myeloid-resident neuropilin-1 influences brown adipose tissue in obesity. PMID:34344941
Comprehensive Strain-Level Analysis of the Gut Microbe Faecalibacterium prausnitzii in Patients with Liver Cirrhosis. PMID:34342541
A systems-level study reveals host-targeted repurposable drugs against SARS-CoV-2 infection. PMID:34339582
Developmental lineage of human pluripotent stem cell-derived cardiac fibroblasts affects their functional phenotype. PMID:34339055
Computational identification of repurposed drugs against viruses causing epidemics and pandemics via drug-target network analysis. PMID:34332351
Epigenetic Analysis of the Chromatin Landscape Identifies a Repertoire of Murine Eosinophil-Specific PU.1-Bound Enhancers. PMID:34330753
Topological network based drug repurposing for coronavirus 2019. PMID:34324563
Proteomic analysis reveals dexamethasone rescues matrix breakdown but not anabolic dysregulation in a cartilage injury model. PMID:34322675
Molecular evaluation of five different isolation methods for extracellular vesicles reveals different clinical applicability and subcellular origin. PMID:34322205
Gene expression profile of the murine ischemic retina and its response to Aflibercept (VEGF-Trap). PMID:34321516
Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms. PMID:34318308
Characterization of a RAD51C-silenced high-grade serous ovarian cancer model during development of PARP inhibitor resistance. PMID:34316715
Mechanistic models of signaling pathways deconvolute the glioblastoma single-cell functional landscape. PMID:34316686
Recent ultra-rare inherited variants implicate new autism candidate risk genes. PMID:34312540
Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota. PMID:34312531
A new strategy to uncover fragile X proteomic biomarkers using the nascent proteome of peripheral blood mononuclear cells (PBMCs). PMID:34312401
Genomic signatures of the unjamming transition in compressed human bronchial epithelial cells. PMID:34301595
Proteomic analysis revealed the roles of YRR1 deletion in enhancing the vanillin resistance of Saccharomyces cerevisiae. PMID:34301255
Long-range linkage disequilibrium in French beef cattle breeds. PMID:34301193
Systematic review of human post-mortem immunohistochemical studies and bioinformatics analyses unveil the complexity of astrocyte reaction in Alzheimer's disease. PMID:34297416
Characterizing the Metabolic and Immune Landscape of Non-small Cell Lung Cancer Reveals Prognostic Biomarkers Through Omics Data Integration. PMID:34295900
Highly accurate protein structure prediction for the human proteome. PMID:34293799
Single-cell transcriptomic profile of human pulmonary artery endothelial cells in health and pulmonary arterial hypertension. PMID:34282213
Development of a Novel Immune Infiltration-Related ceRNA Network and Prognostic Model for Sarcoma. PMID:34277600
The Infectious Disease Ontology in the age of COVID-19. PMID:34275487
FOXC2 controls adult lymphatic endothelial specialization, function, and gut lymphatic barrier preventing multiorgan failure. PMID:34272244
Oxidation of Hemoglobin Drives a Proatherogenic Polarization of Macrophages in Human Atherosclerosis. PMID:34269613
Distinct mechanisms mediate X chromosome dosage compensation in Anopheles and Drosophila. PMID:34266874
Multimarker profiling identifies protective and harmful immune processes in heart failure: findings from BIOSTAT-CHF. PMID:34264317
A network-biology approach for identification of key genes and pathways involved in malignant peritoneal mesothelioma. PMID:34261301
Genome sequence of Apostasia ramifera provides insights into the adaptive evolution in orchids. PMID:34256691
Using Cell Type-Specific Genes to Identify Cell-Type Transitions Between Different in vitro Culture Conditions. PMID:34249906
IL-17 signaling pathway plays a key role in laryngeal squamous cell carcinoma with ethnic specificity. PMID:34249422
Stress Granules and Neurodegenerative Disorders: A Scoping Review. PMID:34248597
ANANSE: an enhancer network-based computational approach for predicting key transcription factors in cell fate determination. PMID:34244796
TIDB: a comprehensive database of trained immunity. PMID:34244719
Proteomic signatures for perioperative oxygen delivery in skin after major elective surgery: mechanistic sub-study of a randomised controlled trial. PMID:34238546
Whole-exome imputation within UK Biobank powers rare coding variant association and fine-mapping analyses. PMID:34226706
Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation. PMID:34225769
ReporterSeq reveals genome-wide dynamic modulators of the heat shock response across diverse stressors. PMID:34223816
Resident Kupffer cells and neutrophils drive liver toxicity in cancer immunotherapy. PMID:34215680
Fundamental limits on the rate of bacterial growth and their influence on proteomic composition. PMID:34214468
Machine Learning-Based Approach Highlights the Use of a Genomic Variant Profile for Precision Medicine in Ovarian Failure. PMID:34199109
Towards a global investigation of transcriptomic signatures through co-expression networks and pathway knowledge for the identification of disease mechanisms. PMID:34197603
A prognostic nomogram based on competing endogenous RNA network for clear-cell renal cell carcinoma. PMID:34196116
Extracellular matrix remodeling associated with bleomycin-induced lung injury supports pericyte-to-myofibroblast transition. PMID:34195593
Altered hypothalamic DNA methylation and stress-induced hyperactivity following early life stress. PMID:34193254
Epigenetic effects of parasites and pesticides on captive and wild nestling birds. PMID:34188846
Evolution of fibroblasts in the lung metastatic microenvironment is driven by stage-specific transcriptional plasticity. PMID:34169837
Long non-coding RNA ELFN1-AS1 in the pathogenesis of pancreatic cancer. PMID:34164511
Environmental enrichment preserves a young DNA methylation landscape in the aged mouse hippocampus. PMID:34162876
The brain transcriptome of the wolf spider, Schizocosa ocreata. PMID:34162407
Identification of Somatic Gene Signatures in Circulating Cell-Free DNA Associated with Disease Progression in Metastatic Prostate Cancer by a Novel Machine Learning Platform. PMID:34157173
MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses. PMID:34156446
A small RNA regulates pprM, a modulator of pleiotropic proteins promoting DNA repair, in Deinococcus radiodurans under ionizing radiation. PMID:34155239
ALKBH1-8 and FTO: Potential Therapeutic Targets and Prognostic Biomarkers in Lung Adenocarcinoma Pathogenesis. PMID:34150745
Effect of the Expression of ELOVL5 and IGFBP6 Genes on the Metastatic Potential of Breast Cancer Cells. PMID:34149804
Damage-Net: A program for DNA repair meta-analysis identifies a network of novel repair genes that facilitate cancer evolution. PMID:34147942
Systematic analysis of exonic germline and postzygotic de novo mutations in bipolar disorder. PMID:34145229
RNA sequencing of long-term label-retaining colon cancer stem cells identifies novel regulators of quiescence. PMID:34142064
Evolving Up-regulation of Biliary Fibrosis-Related Extracellular Matrix Molecules After Successful Portoenterostomy. PMID:34141988
Genotype-by-environment interactions for reproduction, body composition, and growth traits in maternal-line pigs based on single-step genomic reaction norms. PMID:34139991
Transcriptomic analyses of gastrulation-stage mouse embryos with differential susceptibility to alcohol. PMID:34137816
Genome-scale mechanistic modeling of signaling pathways made easy: A bioconductor/cytoscape/web server framework for the analysis of omic data. PMID:34136096
Transcriptomic Signature Differences Between SARS-CoV-2 and Influenza Virus Infected Patients. PMID:34135895
Transcriptomics of type 2 diabetic and healthy human neutrophils. PMID:34134627
Microglia RAGE exacerbates the progression of neurodegeneration within the SOD1G93A murine model of amyotrophic lateral sclerosis in a sex-dependent manner. PMID:34130712
Inter-individual body mass variations relate to fractionated functional brain hierarchies. PMID:34127795
A genetic interaction of NRXN2 with GABRE, SYT1 and CASK in migraine patients: a case-control study. PMID:34126933
Investigation of the Mechanism of Complement System in Diabetic Nephropathy via Bioinformatics Analysis. PMID:34124269
FGGA-lnc: automatic gene ontology annotation of lncRNA sequences based on secondary structures. PMID:34123354
Integrated Analyses Reveal the Multi-Omics and Prognostic Characteristics of ATP5B in Breast Cancer. PMID:34122507
Novel deep learning-based transcriptome data analysis for drug-drug interaction prediction with an application in diabetes. PMID:34116627
Integrating protein networks and machine learning for disease stratification in the Hereditary Spastic Paraplegias. PMID:34113825
Characterization of the small RNA transcriptomes of cell protrusions and cell bodies of highly metastatic hepatocellular carcinoma cells via RNA sequencing. PMID:34113396
Essential function and targets of BMP signaling during midbrain neural crest delamination. PMID:34102166
IL10RB as a key regulator of COVID-19 host susceptibility and severity. PMID:34100031
Transcriptome Analysis Reveals Differentially Expressed Genes and Long Non-coding RNAs Associated With Fecundity in Sheep Hypothalamus With Different FecB Genotypes. PMID:34095109
Differential expression of striatal proteins in a mouse model of DOPA-responsive dystonia reveals shared mechanisms among dystonic disorders. PMID:34092491
Chamber-enriched gene expression profiles in failing human hearts with reduced ejection fraction. PMID:34088950
Transmembrane adaptor protein PAG is a mediator of PD-1 inhibitory signaling in human T cells. PMID:34083754
Axonopathy precedes cell death in ocular damage mediated by blast exposure. PMID:34083587
A combination of Class-I fumarases and metabolites (α-ketoglutarate and fumarate) signal the DNA damage response in Escherichia coli. PMID:34083440
Patterns of recent natural selection on genetic loci associated with sexually differentiated human body size and shape phenotypes. PMID:34081690
Critical COVID-19 is associated with distinct leukocyte phenotypes and transcriptome patterns. PMID:34080738
Pan-Genome Analysis Reveals Host-Specific Functional Divergences in Burkholderia gladioli. PMID:34067383
Oncogenic Potential of the Dual-Function Protein MEX3A. PMID:34067172
Host Response of Atlantic Salmon (Salmo salar) Re-Inoculated with Paramoeba perurans. PMID:34062978
An in vitro model of tumor heterogeneity resolves genetic, epigenetic, and stochastic sources of cell state variability. PMID:34061819
The liver-clock coordinates rhythmicity of peripheral tissues in response to feeding. PMID:34059820
Model-based analysis uncovers mutations altering autophagy selectivity in human cancer. PMID:34059679
MicroRNA panel in serum reveals novel diagnostic biomarkers for prostate cancer. PMID:34055487
Identifying Subgroups of Patients With Autism by Gene Expression Profiles Using Machine Learning Algorithms. PMID:34054599
Multi-Omics Approach in the Identification of Potential Therapeutic Biomolecule for COVID-19. PMID:34054532
Synaptic proteins associated with cognitive performance and neuropathology in older humans revealed by multiplexed fractionated proteomics. PMID:34052751
Rapid evolution of mammalian APLP1 as a synaptic adhesion molecule. PMID:34050225
Proteotyping of knockout mouse strains reveals sex- and strain-specific signatures in blood plasma. PMID:34050187
Mergeomics 2.0: a web server for multi-omics data integration to elucidate disease networks and predict therapeutics. PMID:34048577
emiRIT: a text-mining-based resource for microRNA information. PMID:34048547
Transcriptomic analysis of atopic dermatitis in African Americans is characterized by Th2/Th17-centered cutaneous immune activation. PMID:34045476
Context-Dependent miR-21 Regulation of TLR7-Mediated Autoimmune and Foreign Antigen-Driven Antibody-Forming Cell and Germinal Center Responses. PMID:34039637
Adaptation to mitochondrial stress requires CHOP-directed tuning of ISR. PMID:34039602
Coordination of microbe-host homeostasis by crosstalk with plant innate immunity. PMID:34031541
Transcriptomic response of brain tissue to focused ultrasound-mediated blood-brain barrier disruption depends strongly on anesthesia. PMID:34027087
DNF: A differential network flow method to identify rewiring drivers for gene regulatory networks. PMID:34025035
MyCLADE: a multi-source domain annotation server for sequence functional exploration. PMID:34023906
Gene expression of intracortical bone demonstrates loading-induced increases in Wnt1 and Ngf and inhibition of bone remodeling processes. PMID:34023542
Chromatin-associated MRN complex protects highly transcribing genes from genomic instability. PMID:34020942
Genome-wide analysis identifies a novel LINC-PINT splice variant associated with vascular amyloid pathology in Alzheimer's disease. PMID:34020725
Defining the role of the polyasparagine repeat domain of the S. cerevisiae transcription factor Azf1p. PMID:34019539
A computational approach for detecting physiological homogeneity in the midst of genetic heterogeneity. PMID:34015270
Platelets orchestrate the resolution of pulmonary inflammation in mice by T reg cell repositioning and macrophage education. PMID:34014253
Characterization and comparison of gene-centered human interactomes. PMID:34010955
Chromosomal instability by mutations in the novel minor spliceosome component CENATAC. PMID:34009673
Activated mast cells in skeletal muscle can be a potential mediator for cancer-associated cachexia. PMID:34008339
Differential host circRNA expression profiles in human lung epithelial cells infected with SARS-CoV-2. PMID:34004360
Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis. PMID:34002013
A miR-375/YAP axis regulates neuroendocrine differentiation and tumorigenesis in lung carcinoid cells. PMID:34001972
The nuclear receptor HNF4 drives a brush border gene program conserved across murine intestine, kidney, and embryonic yolk sac. PMID:34001900
Primordial super-enhancers: heat shock-induced chromatin organization in yeast. PMID:34001402
Mutant PRPF8 Causes Widespread Splicing Changes in Spliceosome Components in Retinitis Pigmentosa Patient iPSC-Derived RPE Cells. PMID:33994920
Multimodality assessment of heart failure with preserved ejection fraction skeletal muscle reveals differences in the machinery of energy fuel metabolism. PMID:33991175
Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions. PMID:33988505
Mining TCGA database for gene expression in ovarian serous cystadenocarcinoma microenvironment. PMID:33987033
Identification of a five-gene signature in association with overall survival for hepatocellular carcinoma. PMID:33986994
ARTEMIS: A Novel Mass-Spec Platform for HLA-Restricted Self and Disease-Associated Peptide Discovery. PMID:33986749
IDSM ChemWebRDF: SPARQLing small-molecule datasets. PMID:33980298
Comparative Genome Analyses Highlight Transposon-Mediated Genome Expansion and the Evolutionary Architecture of 3D Genomic Folding in Cotton. PMID:33973633
Genoppi is an open-source software for robust and standardized integration of proteomic and genetic data. PMID:33972534
Collagen fiber regulation in human pediatric aortic valve development and disease. PMID:33963260
Updates to HCOP: the HGNC comparison of orthology predictions tool. PMID:33959747
Common genetic associations between age-related diseases. PMID:33959723
Identification of seven tumor-educated platelets RNAs for cancer diagnosis. PMID:33955587
Protective effects of Lycium barbarum polysaccharide on ovariectomy‑induced cognition reduction in aging mice. PMID:33955518
Evidence for phloem loading via the abaxial bundle sheath cells in maize leaves. PMID:33955497
Use of Network Pharmacology to Explore the Mechanism of Gegen (Puerariae lobatae Radix) in the Treatment of Type 2 Diabetes Mellitus Associated with Hyperlipidemia. PMID:33953784
Epigenetic silencing by SETDB1 suppresses tumour intrinsic immunogenicity. PMID:33953401
Activation of HERV-K(HML-2) disrupts cortical patterning and neuronal differentiation by increasing NTRK3. PMID:33951478
Characterization of Extracellular Vesicles Secreted in Lentiviral Producing HEK293SF Cell Cultures. PMID:33946875
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. PMID:33944776
Protein structure-based gene expression signatures. PMID:33941686
Bioinformatic identification of hub genes and related transcription factors in low shear stress treated endothelial cells. PMID:33941187
Experimental and natural evidence of SARS-CoV-2-infection-induced activation of type I interferon responses. PMID:33937724
A SARS-CoV-2 (COVID-19) biological network to find targets for drug repurposing. PMID:33931664
A clinical transcriptome approach to patient stratification and therapy selection in acute myeloid leukemia. PMID:33931648
Isolation and Characterization of Human Colon Adenocarcinoma Stem-Like Cells Based on the Endogenous Expression of the Stem Markers. PMID:33925224
Assessing Various Control Samples for Microarray Gene Expression Profiling of Laryngeal Squamous Cell Carcinoma. PMID:33923685
Characterization of the Survival Influential Genes in Carcinogenesis. PMID:33922264
Investigation of the Initial Host Response of Naïve Atlantic Salmon (Salmo salar) Inoculated with Paramoeba perurans. PMID:33918228
Altered microRNA Transcriptome in Cultured Human Liver Cells upon Infection with Ebola Virus. PMID:33917562
Single-Cell Atlas Reveals Fatty Acid Metabolites Regulate the Functional Heterogeneity of Mesenchymal Stem Cells. PMID:33912565
Reproductive Proteins Evolve Faster Than Non-reproductive Proteins Among Solanum Species. PMID:33912206
5-hydroxymethylcytosine is dynamically regulated during forebrain organoid development and aberrantly altered in Alzheimer's disease. PMID:33910000
Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator. PMID:33904398
The microRNA analysis portal is a next-generation tool for exploring and analyzing miRNA-focused data in the literature. PMID:33903708
Pathway analysis for genome-wide genetic variation data: Analytic principles, latest developments, and new opportunities. PMID:33896739
The VRNetzer platform enables interactive network analysis in Virtual Reality. PMID:33893283
Network-Based Analysis of Fatal Comorbidities of COVID-19 and Potential Therapeutics. PMID:33891554
System-Level Analysis of Alzheimer's Disease Prioritizes Candidate Genes for Neurodegeneration. PMID:33889174
Transcriptomic alterations in malignant pleural mesothelioma cells in response to long‑term treatment with bullfrog sialic acid‑binding lectin. PMID:33880588
An EPIC predictor of gestational age and its application to newborns conceived by assisted reproductive technologies. PMID:33875015
Ontology-Based Graphs of Research Communities: A Tool for Understanding Threat Reduction Networks. PMID:33870041
Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease. PMID:33864768
Conserved long-range base pairings are associated with pre-mRNA processing of human genes. PMID:33863890
Silencing SHMT2 inhibits the progression of tongue squamous cell carcinoma through cell cycle regulation. PMID:33863325
Disparate Interferon Signaling and Shared Aberrant Basaloid Cells in Single-Cell Profiling of Idiopathic Pulmonary Fibrosis and Systemic Sclerosis-Associated Interstitial Lung Disease. PMID:33859634
Multi-omic profiling of pituitary thyrotropic cells and progenitors. PMID:33858413
Interacting impact of maternal inflammatory response and stress on the amygdala transcriptome of pigs. PMID:33856433
Functional annotation of lung cancer‒associated genetic variants by cell type‒specific epigenome and long-range chromatin interactome. PMID:33840167
Dual-process brain mitochondria isolation preserves function and clarifies protein composition. PMID:33836587
MendelVar: gene prioritization at GWAS loci using phenotypic enrichment of Mendelian disease genes. PMID:33836063
MicroCellClust: mining rare and highly specific subpopulations from single-cell expression data. PMID:33830183
Gene expression evaluation of antioxidant enzymes in patients with hepatocellular carcinoma: RT-qPCR and bioinformatic analyses. PMID:33821873
Age-dependent pathogenic characteristics of SARS-CoV-2 infection in ferrets. PMID:33821260
Differential MicroRNA Expression Involved in Endometrial Receptivity of Goats. PMID:33810054
Distinct miRNA Signatures and Networks Discern Fetal from Adult Erythroid Differentiation and Primary from Immortalized Erythroid Cells. PMID:33807258
Chronic Alcohol Use Induces Molecular Genetic Changes in the Dorsomedial Thalamus of People with Alcohol-Related Disorders. PMID:33805312
Selective Activation of CNS and Reference PPARGC1A Promoters Is Associated with Distinct Gene Programs Relevant for Neurodegenerative Diseases. PMID:33804860
A Streamlined Approach to Pathway Analysis from RNA-Sequencing Data. PMID:33802642
Candidate Genes for the High-Altitude Adaptations of Two Mountain Pine Taxa. PMID:33801727
Transcriptional Regulatory Networks Associate with Early Stages of Potato Virus X Infection of Solanum tuberosum. PMID:33799566
Volume-constrained microcontainers enable myoepithelial functional differentiation in highly parallel mammary organoid culture. PMID:33796842
Building blocks and blueprints for bacterial autolysins. PMID:33793553
Investigations of Kidney Dysfunction-Related Gene Variants in Sickle Cell Disease Patients in Cameroon (Sub-Saharan Africa). PMID:33790942
Trans-acting genetic variation affects the expression of adjacent genes. PMID:33789351
Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning. PMID:33787872
Wormicloud: a new text summarization tool based on word clouds to explore the C. elegans literature. PMID:33787871
An expanding manifold in transmodal regions characterizes adolescent reconfiguration of structural connectome organization. PMID:33787489
USP42 protects ZNRF3/RNF43 from R-spondin-dependent clearance and inhibits Wnt signalling. PMID:33786993
Gene Set Knowledge Discovery with Enrichr. PMID:33780170
Gene Expression Analysis Suggests Immunological Changes of Peripheral Blood Monocytes in the Progression of Patients With Coronary Artery Disease. PMID:33777109
Regulatory Function of Sympathetic Innervation on the Endo/Lysosomal Trafficking of Acetylcholine Receptor. PMID:33776791
The deubiquitinase Usp9x regulates PRC2-mediated chromatin reprogramming during mouse development. PMID:33767158
In-Depth Analysis of the Hidradenitis Suppurativa Serum Proteome Identifies Distinct Inflammatory Subtypes. PMID:33766512
Piggybacking on Niche Adaptation Improves the Maintenance of Multidrug-Resistance Plasmids. PMID:33760032
SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks. PMID:33758926
G-quadruplexes originating from evolutionary conserved L1 elements interfere with neuronal gene expression in Alzheimer's disease. PMID:33758195
Novel ultra-rare exonic variants identified in a founder population implicate cadherins in schizophrenia. PMID:33756103
Cell-autonomous immune gene expression is repressed in pulmonary neuroendocrine cells and small cell lung cancer. PMID:33750914
Appyters: Turning Jupyter Notebooks into data-driven web apps. PMID:33748796
Noise regularization removes correlation artifacts in single-cell RNA-seq data preprocessing. PMID:33748795
Benchmark and Best Practices for Biomedical Knowledge Graph Embeddings. PMID:33746351
Expression and molecular profiles of the AlkB family in ovarian serous carcinoma. PMID:33744868
Identification of disease treatment mechanisms through the multiscale interactome. PMID:33741907
Differential microRNAs expression profiles in liver from three different lifestyle modification mice models. PMID:33740891
Natural variation in the regulation of neurodevelopmental genes modifies flight performance in Drosophila. PMID:33735180
Aberrant proteins expressed in skin fibroblasts of Parkinson's disease patients carrying heterozygous variants of glucocerebrosidase and parkin genes. PMID:33732455
Ultrafast functional profiling of RNA-seq data for nonmodel organisms. PMID:33731361
Chronic villitis of unknown etiology: Investigations into viral pathogenesis. PMID:33730616
A KDM5-Prospero transcriptional axis functions during early neurodevelopment to regulate mushroom body formation. PMID:33729157
Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics. PMID:33726670
COVID-19 patient transcriptomic and genomic profiling reveals comorbidity interactions with psychiatric disorders. PMID:33723208
Quantifying absolute gene expression profiles reveals distinct regulation of central carbon metabolism genes in yeast. PMID:33720010
Transcriptional analysis of islets of Langerhans from organ donors of different ages. PMID:33711030
Maternal Iron Deficiency Modulates Placental Transcriptome and Proteome in Mid-Gestation of Mouse Pregnancy. PMID:33693820
Copper Availability Influences the Transcriptomic Response of Candida albicans to Fluconazole Stress. PMID:33693623
Integrative network analyses of transcriptomics data reveal potential drug targets for acute radiation syndrome. PMID:33692493
Changes in protein expression due to metformin treatment and hyperinsulinemia in a human endometrial cancer cell line. PMID:33690729
Biodegradation of lignin monomers and bioconversion of ferulic acid to vanillic acid by Paraburkholderia aromaticivorans AR20-38 isolated from Alpine forest soil. PMID:33687503
Single cell transcriptomics of primate sensory neurons identifies cell types associated with chronic pain. PMID:33686078
Medication for Acromegaly Reduces Expression of MUC16, MACC1 and GRHL2 in Pituitary Neuroendocrine Tumour Tissue. PMID:33680922
Giant ankyrin-G regulates cardiac function. PMID:33675749
IFN signaling and neutrophil degranulation transcriptional signatures are induced during SARS-CoV-2 infection. PMID:33674719
Mitochondrial arginase-2 is essential for IL-10 metabolic reprogramming of inflammatory macrophages. PMID:33674584
Unique Human and Mouse β-Cell Senescence-Associated Secretory Phenotype (SASP) Reveal Conserved Signaling Pathways and Heterogeneous Factors. PMID:33674410
Next-Generation Sequencing in the Field of Primary Immunodeficiencies: Current Yield, Challenges, and Future Perspectives. PMID:33666867
The Changes of Leukocytes in Brain and Blood After Intracerebral Hemorrhage. PMID:33659003
RNA-Seq Implies Divergent Regulation Patterns of LincRNA on Spermatogenesis and Testis Growth in Goats. PMID:33653002
Dual DNA and protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia. PMID:33649590
Genomically Complex Human Angiosarcoma and Canine Hemangiosarcoma Establish Convergent Angiogenic Transcriptional Programs Driven by Novel Gene Fusions. PMID:33649193
Comprehensive analysis of cancer breakpoints reveals signatures of genetic and epigenetic contribution to cancer genome rearrangements. PMID:33647036
An update of KAIKObase, the silkworm genome database. PMID:33645624
Tumor-specific cytolytic CD4 T cells mediate immunity against human cancer. PMID:33637530
TOXPANEL: A Gene-Set Analysis Tool to Assess Liver and Kidney Injuries. PMID:33633572
RDmap: a map for exploring rare diseases. PMID:33632281
Genomic insight into diet adaptation in the biological control agent Cryptolaemus montrouzieri. PMID:33632122
Five key aspects of metaproteomics as a tool to understand functional interactions in host-associated microbiomes. PMID:33630960
Based on Network Pharmacology Tools to Investigate the Molecular Mechanism of Cordyceps sinensis on the Treatment of Diabetic Nephropathy. PMID:33628839
Automating parameter selection to avoid implausible biological pathway models. PMID:33623016
Hybrid semantic recommender system for chemical compounds in large-scale datasets. PMID:33622374
Discovery of molecular features underlying the morphological landscape by integrating spatial transcriptomic data with deep features of tissue images. PMID:33619564
Identifying molecular features that are associated with biological function of intrinsically disordered protein regions. PMID:33616531
Identification of biomarkers and pathways for the SARS-CoV-2 infections that make complexities in pulmonary arterial hypertension patients. PMID:33611340
Zinc transporter ZIP7 is a novel determinant of ferroptosis. PMID:33608508
A Functional Taxonomy of Tumor Suppression in Oncogenic KRAS-Driven Lung Cancer. PMID:33608386
Local adaptation contributes to gene expression divergence in maize. PMID:33604670
Curation of over 10 000 transcriptomic studies to enable data reuse. PMID:33599246
Comparative transcriptomics of spotted seatrout (Cynoscion nebulosus) populations to cold and heat stress. PMID:33598136
Limited effects of long-term daily cranberry consumption on the gut microbiome in a placebo-controlled study of women with recurrent urinary tract infections. PMID:33596852
Role of opiorphin genes in prostate cancer growth and progression. PMID:33593085
Converting disease maps into heavyweight ontologies: general methodology and application to Alzheimer's disease. PMID:33590873
Tonic Immobility Is Influenced by Starvation, Life Stage, and Body Mass in Ixodid Ticks. PMID:33590870
Cold Adaptation Mechanisms of a Snow Alga Chlamydomonas nivalis During Temperature Fluctuations. PMID:33584575
Identification of key biomarkers and functional pathways in osteosarcomas with lung metastasis: Evidence from bioinformatics analysis. PMID:33578541
Integration of single-cell datasets reveals novel transcriptomic signatures of β-cells in human type 2 diabetes. PMID:33575641
Family-specific analysis of variant pathogenicity prediction tools. PMID:33575576
Potential Drug Prediction of Glioblastoma Based on Drug Perturbation-Induced Gene Expression Signatures. PMID:33575336
A Semi-automated Organoid Screening Method Demonstrates Epigenetic Control of Intestinal Epithelial Differentiation. PMID:33575256
Transcriptomic and proteomic analysis of Hemidactylus frenatus during initial stages of tail regeneration. PMID:33574494
Human myelomeningocele risk and ultra-rare deleterious variants in genes associated with cilium, WNT-signaling, ECM, cytoskeleton and cell migration. PMID:33574475
Gene expression and epigenetics reveal species-specific mechanisms acting upon common molecular pathways in the evolution of task division in bees. PMID:33574391
A Molecular network approach reveals shared cellular and molecular signatures between chronic fatigue syndrome and other fatiguing illnesses. PMID:33564792
RIP-seq reveals LINE-1 ORF1p association with p-body enriched mRNAs. PMID:33563338
Modular Reorganization of Signaling Networks during the Development of Colon Adenoma and Carcinoma. PMID:33562960
Phosphoproteomic Landscape of AML Cells Treated with the ATP-Competitive CK2 Inhibitor CX-4945. PMID:33562780
Characterization of the Rhipicephalus (Boophilus) microplus Sialotranscriptome Profile in Response to Theileria equi Infection. PMID:33557100
Integrative Identification of Hub Genes Associated With Immune Cells in Atrial Fibrillation Using Weighted Gene Correlation Network Analysis. PMID:33553270
The functional analysis of ABCG transporters in the adaptation of pigeon pea (Cajanus cajan) to abiotic stresses. PMID:33552725
CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator. PMID:33547799
Multiomics-Identified Intervention to Restore Ethanol-Induced Dysregulated Proteostasis and Secondary Sarcopenia in Alcoholic Liver Disease. PMID:33543862
BSGatlas: a unified Bacillus subtilis genome and transcriptome annotation atlas with enhanced information access. PMID:33539279
Long non‑coding RNA LINC00491 promotes proliferation and inhibits apoptosis in esophageal squamous cell carcinoma. PMID:33537830
GEOlimma: differential expression analysis and feature selection using pre-existing microarray data. PMID:33535967
Independent component analysis recovers consistent regulatory signals from disparate datasets. PMID:33529205
Human keratinocyte-derived extracellular vesicles activate the MAPKinase pathway and promote cell migration and proliferation in vitro. PMID:33526070
Systematic Analysis of Functionally Related Gene Clusters in the Opportunistic Pathogen, Candida albicans. PMID:33525750
DeCompress: tissue compartment deconvolution of targeted mRNA expression panels using compressed sensing. PMID:33524140
From fuzziness to precision medicine: on the rapidly evolving proteomics with implications in mitochondrial connectivity to rare human disease. PMID:33521598
American lobster postlarvae alter gene regulation in response to ocean warming and acidification. PMID:33520168
An In-Silico Study on the Most Effective Growth Factors in Retinal Regeneration Utilizing Tissue Engineering Concepts. PMID:33520128
Identifying RBM47, HCK, CD53, TYROBP, and HAVCR2 as Hub Genes in Advanced Atherosclerotic Plaques by Network-Based Analysis and Validation. PMID:33519905
Computational resources for identifying and describing proteins driving liquid-liquid phase separation. PMID:33517364
Lipids, lysosomes and mitochondria: insights into Lewy body formation from rare monogenic disorders. PMID:33515275
Amynthas corticis genome reveals molecular mechanisms behind global distribution. PMID:33514865
The role of gene to gene interaction in the breast's genomic signature of pregnancy. PMID:33514799
Reporting on the Role of miRNAs and Affected Pathways on the Molecular Backbone of Ovarian Insufficiency: A Systematic Review and Critical Analysis Mapping of Future Research. PMID:33511114
Gene signature of children with severe respiratory syncytial virus infection. PMID:33510411
The Epstein-Barr virus deubiquitinase BPLF1 targets SQSTM1/p62 to inhibit selective autophagy. PMID:33509017
SinEx DB 2.0 update 2020: database for eukaryotic single-exon coding sequences. PMID:33507271
Genome-Wide Identification and Analysis of Chitinase GH18 Gene Family in Mycogone perniciosa. PMID:33505368
The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research. PMID:33494105
Short hairpin RNA attenuates liver fibrosis by regulating the PPAR‑γ and NF‑κB pathways in HBV‑induced liver fibrosis in mice. PMID:33491741
Inference of Intercellular Communications and Multilayer Gene-Regulations of Epithelial-Mesenchymal Transition From Single-Cell Transcriptomic Data. PMID:33488673
HELQ and EGR3 expression correlate with IGHV mutation status and prognosis in chronic lymphocytic leukemia. PMID:33485349
Integrative computational approach identifies drug targets in CD4+ T-cell-mediated immune disorders. PMID:33483502
Likelihood ratio statistics for gene set enrichment in Alzheimer's disease pathways. PMID:33480182
Potential interactions between the TBX4-FGF10 and SHH-FOXF1 signaling during human lung development revealed using ChIP-seq. PMID:33478486
Effect of Aging on Homeostasis in the Soft Tissue of the Periodontium: A Narrative Review. PMID:33477537
DOMINO: a network-based active module identification algorithm with reduced rate of false calls. PMID:33471440
Differentiation of Tracheary Elements in Sugarcane Suspension Cells Involves Changes in Secondary Wall Deposition and Extensive Transcriptional Reprogramming. PMID:33469464
Comprehensive computational target fishing approach to identify Xanthorrhizol putative targets. PMID:33452398
A systems-level gene regulatory network model for Plasmodium falciparum. PMID:33450011
A genome-wide strategy to identify causes and consequences of retrotransposon expression finds activation by BRCA1 in ovarian cancer. PMID:33447827
Late p65 nuclear translocation in glioblastoma cells indicates non-canonical TLR4 signaling and activation of DNA repair genes. PMID:33446690
An Integrative Transcriptomic Analysis of Systemic Juvenile Idiopathic Arthritis for Identifying Potential Genetic Markers and Drug Candidates. PMID:33445803
Knowledge Network Embedding of Transcriptomic Data from Spaceflown Mice Uncovers Signs and Symptoms Associated with Terrestrial Diseases. PMID:33445483
Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB. PMID:33445429
Genome-wide identification, characterization and transcriptional profiling of NHX-type (Na+/H+) antiporters under salinity stress in soybean. PMID:33442515
Embeddings from deep learning transfer GO annotations beyond homology. PMID:33441905
Signatures of conserved and unique molecular features in Afrotheria. PMID:33441654
Blood-derived mitochondrial DNA copy number is associated with gene expression across multiple tissues and is predictive for incident neurodegenerative disease. PMID:33441415
Ceruloplasmin Deamidation in Neurodegeneration: From Loss to Gain of Function. PMID:33440850
A modular master regulator landscape controls cancer transcriptional identity. PMID:33434495
Transcriptome profiling of insulin sensitive tissues from GH deficient mice following GH treatment. PMID:33433889
Ascending dorsal column sensory neurons respond to spinal cord injury and downregulate genes related to lipid metabolism. PMID:33431991
Absence of NLRP3 Inflammasome in Hematopoietic Cells Reduces Adverse Remodeling After Experimental Myocardial Infarction. PMID:33426377
The iPPI-DB initiative: A Community-centered database of Protein-Protein Interaction modulators. PMID:33416858
Plasma membrane vesicles from cauliflower meristematic tissue and their role in water passage. PMID:33413105
Evaluation of the potential of Pap test fluid and cervical swabs to serve as clinical diagnostic biospecimens for the detection of ovarian cancer by mass spectrometry-based proteomics. PMID:33413078
Shared Blood Transcriptomic Signatures between Alzheimer's Disease and Diabetes Mellitus. PMID:33406707
Mitochondrial bioenergetic deficits in C9orf72 amyotrophic lateral sclerosis motor neurons cause dysfunctional axonal homeostasis. PMID:33398403
Computationally predicted SARS-COV-2 encoded microRNAs target NFKB, JAK/STAT and TGFB signaling pathways. PMID:33398248
Spatiotemporal profiling of cytosolic signaling complexes in living cells by selective proximity proteomics. PMID:33397984
The Interactome of Cancer-Related Lysyl Oxidase and Lysyl Oxidase-Like Proteins. PMID:33383846
Effect of let-7c on the PI3K/Akt/FoxO signaling pathway in hepatocellular carcinoma. PMID:33376529
The m6A RNA Demethylase ALKBH5 Promotes Radioresistance and Invasion Capability of Glioma Stem Cells. PMID:33375621
Inflammatory Proteins HMGA2 and PRTN3 as Drivers of Vulvar Squamous Cell Carcinoma Progression. PMID:33374674
FIGNL1 promotes non‑small cell lung cancer cell proliferation. PMID:33367932
Comprehensive Profiling of Gene Expression in the Cerebral Cortex and Striatum of BTBRTF/ArtRbrc Mice Compared to C57BL/6J Mice. PMID:33362469
Salmonella enterica Serovars Dublin and Enteritidis Comparative Proteomics Reveals Differential Expression of Proteins Involved in Stress Resistance, Virulence, and Anaerobic Metabolism. PMID:33361201
A primer for generating and using transcriptome data and gene sets. PMID:33361089
Generation of an Interactome for the Tetratricopeptide Repeat Domain of O-GlcNAc Transferase Indicates a Role for the Enzyme in Intellectual Disability. PMID:33356293
Systematic review and meta-analysis of human transcriptomics reveals neuroinflammation, deficient energy metabolism, and proteostasis failure across neurodegeneration. PMID:33347974
A Novel Family of Acinetobacter Mega-Plasmids Are Disseminating Multi-Drug Resistance Across the Globe While Acquiring Location-Specific Accessory Genes. PMID:33343549
Episodic Decrease in Temperature Increases mcy Gene Transcription and Cellular Microcystin in Continuous Cultures of Microcystis aeruginosa PCC 7806. PMID:33343544
Transcriptional profiles of human islet and exocrine endothelial cells in subjects with or without impaired glucose metabolism. PMID:33339897
Competition between PRC2.1 and 2.2 subcomplexes regulates PRC2 chromatin occupancy in human stem cells. PMID:33338397
Modeling the human aging transcriptome across tissues, health status, and sex. PMID:33336875
Distinct Signatures in the Receptor Repertoire Discriminate CD56bright and CD56dim Natural Killer Cells. PMID:33335526
Upregulation of 5'-terminal oligopyrimidine mRNA translation upon loss of the ARF tumor suppressor. PMID:33335292
Cerina: systematic circRNA functional annotation based on integrative analysis of ceRNA interactions. PMID:33335165
Biological and physical approaches on the role of piplartine (piperlongumine) in cancer. PMID:33335138
The identification of co-expressed gene modules in Streptococcus pneumonia from colonization to infection to predict novel potential virulence genes. PMID:33334315
Gene expression profiling of SARS-CoV-2 infections reveal distinct primary lung cell and systemic immune infection responses that identify pathways relevant in COVID-19 disease. PMID:33333559
A Machine Learning Approach for Tracing Tumor Original Sites With Gene Expression Profiles. PMID:33330438
Comprehensive Transcriptomic Analysis Reveals Dysregulated Competing Endogenous RNA Network in Endocrine Resistant Breast Cancer Cells. PMID:33324567
Genetic Determinants of Gating Functions: Do We Get Closer to Understanding Schizophrenia Etiopathogenesis? PMID:33324248
PEREGRINE: A genome-wide prediction of enhancer to gene relationships supported by experimental evidence. PMID:33320871
Analysis of readability and structural accuracy in SNOMED CT. PMID:33319711
Quality assurance and enrichment of biological and biomedical ontologies and terminologies. PMID:33319696
Genome-wide correlation analysis to identify amplitude regulators of circadian transcriptome output. PMID:33318596
Hearing impairment due to Mir183/96/182 mutations suggests both loss and gain of function effects. PMID:33318051
Expression of PAWR predicts prognosis of ovarian cancer. PMID:33317551
Exostosin1 as a novel prognostic and predictive biomarker for squamous cell lung carcinoma: A study based on bioinformatics analysis. PMID:33314711
Hierarchical Canonical Correlation Analysis Reveals Phenotype, Genotype, and Geoclimate Associations in Plants. PMID:33313545
Comparative proteomic analysis highlights metabolic dysfunction in α-synucleinopathy. PMID:33311497
Transcriptomic Profiling of Human Pluripotent Stem Cell-derived Retinal Pigment Epithelium over Time. PMID:33307245
Applying graph database technology for analyzing perturbed co-expression networks in cancer. PMID:33306799
A Multi-Network Comparative Analysis of Transcriptome and Translatome Identifies Novel Hub Genes in Cardiac Remodeling. PMID:33304386
tRNA-Derived Fragments (tRFs) in Bladder Cancer: Increased 5'-tRF-LysCTT Results in Disease Early Progression and Patients' Poor Treatment Outcome. PMID:33291319
PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API. PMID:33290554
The Gene Ontology resource: enriching a GOld mine. PMID:33290552
Identification of Dysregulated Genes for Late-Onset Alzheimer's Disease Using Gene Expression Data in Brain. PMID:33282526
Network Pharmacology Identifies the Mechanisms of Action of Tongxie Anchang Decoction in the Treatment of Irritable Bowel Syndrome with Diarrhea Predominant. PMID:33281910
Machine Learning Based Network Analysis Determined Clinically Relevant miRNAs in Breast Cancer. PMID:33281885
A Novel Proximity Biotinylation Assay Based on the Self-Associating Split GFP1-10/11. PMID:33276494
Urinary vitronectin identifies patients with high levels of fibrosis in kidney grafts. PMID:33275196
CovMulNet19, Integrating Proteins, Diseases, Drugs, and Symptoms: A Network Medicine Approach to COVID-19. PMID:33274348
Reprogramming to recover youthful epigenetic information and restore vision. PMID:33268865
Humoral immune responses mediate the development of a restrictive phenotype of chronic lung allograft dysfunction. PMID:33268593
Comparative Analysis of the Global Transcriptomic Response to Oxidative Stress of Bacillus anthracis htrA-Disrupted and Parental Wild Type Strains. PMID:33265965
HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine. PMID:33264402
Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure. PMID:33262328
Adaptation Strategies of Halophytic Barley Hordeum marinum ssp. marinum to High Salinity and Osmotic Stress. PMID:33260985
Regulators of TNFα mediated insulin resistance elucidated by quantitative proteomics. PMID:33257747
MiR-215-5p Reduces Liver Metastasis in an Experimental Model of Colorectal Cancer through Regulation of ECM-Receptor Interactions and Focal Adhesion. PMID:33255928
TET2/IDH1/2/WT1 and NPM1 Mutations Influence the RUNX1 Expression Correlations in Acute Myeloid Leukemia. PMID:33255417
Essential gene prediction using limited gene essentiality information-An integrative semi-supervised machine learning strategy. PMID:33253254
Identifying longevity associated genes by integrating gene expression and curated annotations. PMID:33253142
Frequent Assembly of Chimeric Complexes in the Protein Interaction Network of an Interspecies Yeast Hybrid. PMID:33252673
Evolved bacterial resistance against fluoropyrimidines can lower chemotherapy impact in the Caenorhabditis elegans host. PMID:33252330
Spatial Proteomic Approach to Characterize Skeletal Muscle Myofibers. PMID:33251806
The Draft Genome of Red Lechwe, Kobus leche leche. PMID:33250921
A New Catalog of Structural Variants in 1,301 A. thaliana Lines from Africa, Eurasia, and North America Reveals a Signature of Balancing Selection at Defense Response Genes. PMID:33247723
Transcriptome and proteome profiling reveal complementary scavenger and immune features of rat liver sinusoidal endothelial cells and liver macrophages. PMID:33246411
In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes. PMID:33243861
Multiparametric Profiling of Engineered Nanomaterials: Unmasking the Surface Coating Effect. PMID:33240770
MutRank: an R shiny web-application for exploratory targeted mutual rank-based coexpression analyses integrated with user-provided supporting information. PMID:33240618
Identifying transcriptomic correlates of histology using deep learning. PMID:33237966
The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. PMID:33237311
UniProt: the universal protein knowledgebase in 2021. PMID:33237286
Integration of the Drug-Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts. PMID:33237278
Reduced lipolysis in lipoma phenocopies lipid accumulation in obesity. PMID:33235355
Is the Proteome of Bronchoalveolar Lavage Extracellular Vesicles a Marker of Advanced Lung Cancer? PMID:33233545
Physiological Changes in Barley mlo-11 Powdery Mildew Resistance Conditioned by Tandem Repeat Copy Number. PMID:33233522
Identification and analysis of immune-related subtypes of hepatocellular carcinoma. PMID:33231514
Phylostratic Shift of Whole-Genome Duplications in Normal Mammalian Tissues towards Unicellularity Is Driven by Developmental Bivalent Genes and Reveals a Link to Cancer. PMID:33228223
LnCeCell: a comprehensive database of predicted lncRNA-associated ceRNA networks at single-cell resolution. PMID:33219686
FlyBase: updates to the Drosophila melanogaster knowledge base. PMID:33219682
MolluscDB: an integrated functional and evolutionary genomics database for the hyper-diverse animal phylum Mollusca. PMID:33219670
RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. PMID:33211854
DEEPScreen: high performance drug-target interaction prediction with convolutional neural networks using 2-D structural compound representations. PMID:33209251
Whole exome sequencing and trio analysis to broaden the variant spectrum of genes in idiopathic hypogonadotropic hypogonadism. PMID:33208564
8-Hydroxydaidzein, an Isoflavone from Fermented Soybean, Induces Autophagy, Apoptosis, Differentiation, and Degradation of Oncoprotein BCR-ABL in K562 Cells. PMID:33207739
DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier. PMID:33206638
The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems. PMID:33205138
Epigenetic profiling of Italian patients identified methylation sites associated with hereditary transthyretin amyloidosis. PMID:33203445
Genome-Wide Functional Screen for Calcium Transients in Escherichia coli Identifies Increased Membrane Potential Adaptation to Persistent DNA Damage. PMID:33199283
OrthoDB in 2020: evolutionary and functional annotations of orthologs. PMID:33196836
RBP2GO: a comprehensive pan-species database on RNA-binding proteins, their interactions and functions. PMID:33196814
NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants. PMID:33196801
KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response. PMID:33196056
Integrated transcriptome meta-analysis of pancreatic ductal adenocarcinoma and matched adjacent pancreatic tissues. PMID:33194391
MaizeMine: A Data Mining Warehouse for the Maize Genetics and Genomics Database. PMID:33193550
Gene Expression Signatures in AML-12 Hepatocyte Cells upon Dengue virus Infection and Acetaminophen Treatment. PMID:33182673
FunRes: resolving tissue-specific functional cell states based on a cell-cell communication network model. PMID:33179736
Mesenchymal stem cells negatively regulate CD4<sup>+</sup> T cell activation in patients with primary Sjögren syndrome through the miRNA‑125b and miRNA‑155 TCR pathway. PMID:33179091
Prolonged Targeted Cardiovascular Epidural Stimulation Improves Immunological Molecular Profile: A Case Report in Chronic Severe Spinal Cord Injury. PMID:33177997
High SEMA4C expression promotes the epithelial-mesenchymal transition and predicts poor prognosis in colorectal carcinoma. PMID:33177246
PLK1 and NOTCH Positively Correlate in Melanoma and Their Combined Inhibition Results in Synergistic Modulations of Key Melanoma Pathways. PMID:33177155
Avian Immunome DB: an example of a user-friendly interface for extracting genetic information. PMID:33176685
Insulin-promoted mobilization of GLUT4 from a perinuclear storage site requires RAB10. PMID:33175605
Anti‑inflammatory mechanism of berberine on lipopolysaccharide‑induced IEC‑18 models based on comparative transcriptomics. PMID:33174609
MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations. PMID:33174596
Gene expression profile of lipopolysaccharide‑induced apoptosis of nucleus pulposus cells reversed by syringic acid. PMID:33174055
Identification of inflammation‑associated circulating long non‑coding RNAs and genes in intracranial aneurysm rupture‑induced subarachnoid hemorrhage. PMID:33174039
Using mRNA deep sequencing to analyze differentially expressed genes during Panax notoginseng saponin treatment of ischemic stroke. PMID:33173991
Integrated microarray analysis of key genes and a miRNA‑mRNA regulatory network of early‑onset preeclampsia. PMID:33173953
A compound downregulation of SRRM2 and miR-27a-3p with upregulation of miR-27b-3p in PBMCs of Parkinson's patients is associated with the early stage onset of disease. PMID:33171483
Survey of metaproteomics software tools for functional microbiome analysis. PMID:33170893
Genome Variation Map: a worldwide collection of genome variations across multiple species. PMID:33170268
The Zebrafish Information Network: major gene page and home page updates. PMID:33170210
LegumeIP V3: from models to crops-an integrative gene discovery platform for translational genomics in legumes. PMID:33166388
CSF1R inhibition depletes tumor-associated macrophages and attenuates tumor progression in a mouse sonic Hedgehog-Medulloblastoma model. PMID:33159168
CLAVATA Signaling Ensures Reproductive Development in Plants across Thermal Environments. PMID:33157018
Lipopolysaccharide triggers different transcriptional signatures in taurine and indicine cattle macrophages: Reactive oxygen species and potential outcomes to the development of immune response to infections. PMID:33156842
The InterPro protein families and domains database: 20 years on. PMID:33156333
Deep learning approach for predicting functional Z-DNA regions using omics data. PMID:33154517
DNMSO; an ontology for representing de novo sequencing results from Tandem-MS data. PMID:33150092
Constitution of a comprehensive phytochemical profile and network pharmacology based investigation to decipher molecular mechanisms of Teucrium polium L. in the treatment of type 2 diabetes mellitus. PMID:33150068
Loss of PHF6 leads to aberrant development of human neuron-like cells. PMID:33149206
Integrated Bioinformatics Analysis of Hub Genes and Pathways Associated with a Compression Model of Spinal Cord Injury in Rats. PMID:33149108
Dissecting Herpes Simplex Virus 1-Induced Host Shutoff at the RNA Level. PMID:33148793
Blocking IL1 Beta Promotes Tumor Regression and Remodeling of the Myeloid Compartment in a Renal Cell Carcinoma Model: Multidimensional Analyses. PMID:33148676
The Role of Salmonella Genomic Island 4 in Metal Tolerance of Salmonella enterica Serovar I 4,[5],12:i:- Pork Outbreak Isolate USDA15WA-1. PMID:33142960
Transcriptomic responses from improved murine sepsis models can better mimic human surgical sepsis. PMID:33140449
Bacterial-fungal interactions revealed by genome-wide analysis of bacterial mutant fitness. PMID:33139882
Ensembl 2021. PMID:33137190
Dual genome-wide CRISPR knockout and CRISPR activation screens identify mechanisms that regulate the resistance to multiple ATR inhibitors. PMID:33137164
Differential transcript usage in the Parkinson's disease brain. PMID:33137089
Many, but not all, lineage-specific genes can be explained by homology detection failure. PMID:33137085
A Systems Biology Approach to Identifying a Master Regulator That Can Transform the Fast Growing Cellular State to a Slowly Growing One in Early Colorectal Cancer Development Model. PMID:33133158
Plasma Proteomics Identify Biomarkers and Pathogenesis of COVID-19. PMID:33128875
Higher miR-543 levels correlate with lower STK31 expression and longer pancreatic cancer survival. PMID:33128354
Bufalin exerts antitumor effects in neuroblastoma via the induction of reactive oxygen species‑mediated apoptosis by targeting the electron transport chain. PMID:33125107
Paternal reprogramming-escape histone H3K4me3 marks located within promoters of RNA splicing genes. PMID:33119058
Common Adaptive Strategies Underlie Within-Host Evolution of Bacterial Pathogens. PMID:33118035
Murine interfollicular epidermal differentiation is gradualistic with GRHL3 controlling progression from stem to transition cell states. PMID:33116143
Analysing the meta-interaction between pathways by gene set topological impact analysis. PMID:33109101
Systematic Investigation of Resistance Evolution to Common Antibiotics Reveals Conserved Collateral Responses across Common Human Pathogens. PMID:33106260
Soluble Compounds Released by Hypoxic Stroma Confer Invasive Properties to Pancreatic Ductal Adenocarcinoma. PMID:33105540
PhycoCosm, a comparative algal genomics resource. PMID:33104790
The mouse Gene Expression Database (GXD): 2021 update. PMID:33104772
Genomic and transcriptomic landscapes and evolutionary dynamics of molluscan glycoside hydrolase families with implications for algae-feeding biology. PMID:33101612
DEG 15, an update of the Database of Essential Genes that includes built-in analysis tools. PMID:33095861
The efficacy of chemotherapeutic drug combinations may be predicted by concordance of gene response to the single agents. PMID:33093925
Maximized quantitative phosphoproteomics allows high confidence dissection of the DNA damage signaling network. PMID:33093574
Transcriptome analysis of Actinoplanes utahensis reveals molecular signature of saccharide impact on acarbose biosynthesis. PMID:33088668
Comprehensive Analysis of Differentially Expressed Circular RNAs in Patients with Senile Osteoporotic Vertebral Compression Fracture. PMID:33083467
Network-Based Coexpression Analysis Identifies Functional and Prognostic Long Noncoding RNAs in Hepatocellular Carcinoma. PMID:33083449
Transcriptome Analysis Identifies Novel Prognostic Genes in Osteosarcoma. PMID:33082842
Mitochondrial-Y chromosome epistasis in Drosophila melanogaster. PMID:33081607
Quantifying the distribution of protein oligomerization degree reflects cellular information capacity. PMID:33077848
Predicted functional interactome of Caenorhabditis elegans and a web tool for the functional interpretation of differentially expressed genes. PMID:33076954
Exploration of the sputum methylome and omics deconvolution by quadratic programming in molecular profiling of asthma and COPD: the road to sputum omics 2.0. PMID:33076907
SWI/SNF inactivation in the endometrial epithelium leads to loss of epithelial integrity. PMID:33075803
Differential Transcription and Alternative Splicing in Cotton Underly Specialized Defense Responses Against Pests. PMID:33072149
No Assembly Required: Using BTyper3 to Assess the Congruency of a Proposed Taxonomic Framework for the Bacillus cereus Group With Historical Typing Methods. PMID:33072050
mRNA and miRNA expression profile reveals the role of miR-31 overexpression in neural stem cell. PMID:33067542
Increased RNA editing in maternal immune activation model of neurodevelopmental disease. PMID:33067431
Divergent Resistance Mechanisms to Immunotherapy Explain Responses in Different Skin Cancers. PMID:33065980
ScatLay: utilizing transcriptome-wide noise for identifying and visualizing differentially expressed genes. PMID:33060728
Biomarker exploration of microRNA-203 as a promising substrate for predicting poor survival outcome in colorectal cancer. PMID:33059609
During bacteremia, Pseudomonas aeruginosa PAO1 adapts by altering the expression of numerous virulence genes including those involved in quorum sensing. PMID:33057423
smORFunction: a tool for predicting functions of small open reading frames and microproteins. PMID:33054771
Monosomy X in Female Mice Influences the Regional Formation and Augments the Severity of Angiotensin II-Induced Aortopathies. PMID:33054396
IurV, Encoded by ORF VCA0231, Is Involved in the Regulation of Iron Uptake Genes in Vibrio cholerae. PMID:33053678
A high-throughput CRISPR interference screen for dissecting functional regulators of GPCR/cAMP signaling. PMID:33052901
Semantic similarity and machine learning with ontologies. PMID:33049044
Maximizing cohesion and separation for detecting protein functional modules in protein-protein interaction networks. PMID:33048996
Electricity from lignocellulosic substrates by thermophilic Geobacillus species. PMID:33046790
Protein ontology on the semantic web for knowledge discovery. PMID:33046717
Transcriptome analysis revealed misregulated gene expression in blastoderms of interspecific chicken and Japanese quail F1 hybrids. PMID:33044996
The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals. PMID:33037820
In vivo mRNA display enables large-scale proteomics by next generation sequencing. PMID:33037152
Mitochondria under the spotlight: On the implications of mitochondrial dysfunction and its connectivity to neuropsychiatric disorders. PMID:33033576
A realism-based approach to an ontological representation of symbiotic interactions. PMID:33032576
Data mining of human plasma proteins generates a multitude of highly predictive aging clocks that reflect different aspects of aging. PMID:33031577
Graph-based exploitation of gene ontology using GOxploreR for scrutinizing biological significance. PMID:33028846
Root-Secreted Coumarins and the Microbiota Interact to Improve Iron Nutrition in Arabidopsis. PMID:33027611
Compartment-specific transcriptomics of ozone-exposed murine lungs reveals sex- and cell type-associated perturbations relevant to mucoinflammatory lung diseases. PMID:33026818
Development of a Cardiac Sarcomere Functional Genomics Platform to Enable Scalable Interrogation of Human TNNT2 Variants. PMID:33025817
A Novel Proteomic Method Reveals NLS Tagging of T-DM1 Contravenes Classical Nuclear Transport in a Model of HER2-Positive Breast Cancer. PMID:33024794
Transcript Isoforms of SLC7A11-AS1 Are Associated With Varicocele-Related Male Infertility. PMID:33024440
Long-Term m5C Methylome Dynamics Parallel Phenotypic Adaptation in the Cyanobacterium Trichodesmium. PMID:33022053
lncRNAKB, a knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA. PMID:33020484
Pseudo2GO: A Graph-Based Deep Learning Method for Pseudogene Function Prediction by Borrowing Information From Coding Genes. PMID:33014009
Human Pluripotent Stem Cell-Derived Neural Cells and Brain Organoids Reveal SARS-CoV-2 Neurotropism Predominates in Choroid Plexus Epithelium. PMID:33010822
Identification of NUF2 and FAM83D as potential biomarkers in triple-negative breast cancer. PMID:33005492
Transcriptomic signatures of cold adaptation and heat stress in the winter ant (Prenolepis imparis). PMID:33002025
Phenotype-genotype comorbidity analysis of patients with rare disorders provides insight into their pathological and molecular bases. PMID:33001999
Knockdown of SERPINE1 reverses resistance of triple‑negative breast cancer to paclitaxel via suppression of VEGFA. PMID:33000256
Uncovering potential differentially expressed miRNAs and targeted mRNAs in myocardial infarction based on integrating analysis. PMID:33000230
Implication of ZNF217 in Accelerating Tumor Development and Therapeutically Targeting ZNF217-Induced PI3K-AKT Signaling for the Treatment of Metastatic Osteosarcoma. PMID:32999043
SlFERL Interacts with S-Adenosylmethionine Synthetase to Regulate Fruit Ripening. PMID:32999005
Efficient Propagation of Circulating Tumor Cells: A First Step for Probing Tumor Metastasis. PMID:32998338
Identification of the significant pathways of Banxia Houpu decoction in the treatment of depression based on network pharmacology. PMID:32997725
Inducible Deletion of YAP and TAZ in Adult Mouse Smooth Muscle Causes Rapid and Lethal Colonic Pseudo-Obstruction. PMID:32992050
Functional signatures of evolutionarily young CTCF binding sites. PMID:32988407
Cancer-associated fibroblasts of the prostate promote a compliant and more invasive phenotype in benign prostate epithelial cells. PMID:32984808
Pharmacological and phosphoproteomic approaches to roles of protein kinase C in kappa opioid receptor-mediated effects in mice. PMID:32976891
TREND-DB-a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation. PMID:32976578
Burden of rare deleterious variants in WNT signaling genes among 511 myelomeningocele patients. PMID:32970752
Aldh inhibitor restores auditory function in a mouse model of human deafness. PMID:32970669
Thyroid hormone receptor α in skeletal muscle is essential for T3-mediated increase in energy expenditure. PMID:32969079
Unveiling Sex-Based Differences in the Effects of Alcohol Abuse: A Comprehensive Functional Meta-Analysis of Transcriptomic Studies. PMID:32967293
Circular RNAs associated with a mouse model of concanavalin A-induced autoimmune hepatitis: preliminary screening and comprehensive functional analysis. PMID:32965791
Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing. PMID:32962098
Identification of hub genes in colon cancer via bioinformatics analysis. PMID:32961078
Identification of novel candidate risk genes for myelomeningocele within the glucose homeostasis/oxidative stress and folate/one-carbon metabolism networks. PMID:32960507
Localized inhibition in the Drosophila mushroom body. PMID:32955437
Designing custom CRISPR libraries for hypothesis-driven drug target discovery. PMID:32952937
Knockdown of SAR1B suppresses proliferation and induces apoptosis of RKO colorectal cancer cells. PMID:32952655
An unanticipated tumor-suppressive role of the SUMO pathway in the intestine unveiled by Ubc9 haploinsufficiency. PMID:32948837
Bioinformatics Data Mining Repurposes the JAK2 (Janus Kinase 2) Inhibitor Fedratinib for Treating Pancreatic Ductal Adenocarcinoma by Reversing the KRAS (Kirsten Rat Sarcoma 2 Viral Oncogene Homolog)-Driven Gene Signature. PMID:32947833
Multi-layered Spatial Transcriptomics Identify Secretory Factors Promoting Human Hematopoietic Stem Cell Development. PMID:32946788
miR‑592 acts as an oncogene and promotes medullary thyroid cancer tumorigenesis by targeting cyclin‑dependent kinase 8. PMID:32945439
Small RNA deep sequencing reveals novel miRNAs in peripheral blood mononuclear cells from patients with IgA nephropathy. PMID:32945407
A clinical and multi‑omics study of Van der Woude syndrome in three generations of a Chinese family. PMID:32945398
Resveratrol modulates the apoptosis and autophagic death of human lung adenocarcinoma A549 cells via a p53‑dependent pathway: Integrated bioinformatics analysis and experimental validation. PMID:32945383
Enzyme-Constrained Models and Omics Analysis of Streptomyces coelicolor Reveal Metabolic Changes that Enhance Heterologous Production. PMID:32942174
IDDB: a comprehensive resource featuring genes, variants and characteristics associated with infertility. PMID:32941628
Chitinase 3-Like 1 Contributes to Food Allergy via M2 Macrophage Polarization. PMID:32935492
Cellular expression profiles of Epstein-Barr virus-transformed B-lymphoblastoid cell lines. PMID:32934816
TMEM206 is a potential prognostic marker of hepatocellular carcinoma. PMID:32934741
Immunotyping of tumor-infiltrating lymphocytes in triple-negative breast cancer and genetic characterization. PMID:32934708
Drosophila Voltage-Gated Sodium Channels Are Only Expressed in Active Neurons and Are Localized to Distal Axonal Initial Segment-like Domains. PMID:32928889
Deciphering the Plasma Proteome of Type 2 Diabetes. PMID:32928870
A Pilot Study on MicroRNA Profile in Tear Fluid to Predict Response to Anti-VEGF Treatments for Diabetic Macular Edema. PMID:32927780
Characterization and functional prediction of the microRNAs differentially expressed in a mouse model of concanavalin A-induced autoimmune hepatitis. PMID:32922197
Expression Profiles of Long Non-coding RNA and Messenger RNA in Human Traumatic Brain Injury. PMID:32919233
Comprehensive Characterization of Prognostic Long Noncoding RNAs in Osteosarcoma. PMID:32908905
Identification of Biomarkers to Construct a Competing Endogenous RNA Network and Establishment of a Genomic-Clinicopathologic Nomogram to Predict Survival for Children with Rhabdoid Tumors of the Kidney. PMID:32908900
Network Pharmacology to Uncover the Biological Basis of Spleen Qi Deficiency Syndrome and Herbal Treatment. PMID:32908629
ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. PMID:32907876
Differentially expressed genes on the growth of mouse Leydig cells treated with standardised Eurycoma longifolia extract. PMID:32901880
De novo transcriptome sequencing of Paecilomyces tenuipes revealed genes involved in adenosine biosynthesis. PMID:32901833
High-Resolution Mass Spectrometry-Based Approaches for the Detection and Quantification of Peptidase Activity in Plasma. PMID:32899982
In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age. PMID:32898168
Understanding microcephaly through the study of centrosome regulation in Drosophila neural stem cells. PMID:32897294
A long non-coding RNA (Lrap) modulates brain gene expression and levels of alcohol consumption in rats. PMID:32893479
Functional, Morphological, and Evolutionary Characterization of Hearing in Subterranean, Eusocial African Mole-Rats. PMID:32888484
Osteopontin Expression Identifies a Subset of Recruited Macrophages Distinct from Kupffer Cells in the Fatty Liver. PMID:32888418
Secretome Proteomic Approaches for Biomarker Discovery: An Update on Colorectal Cancer. PMID:32878319
Changes in MicroRNA Expression during Rabbit Hemorrhagic Disease Virus (RHDV) Infection. PMID:32878241
Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns. PMID:32875947
Differential contribution of bone marrow-derived infiltrating monocytes and resident macrophages to persistent lung inflammation in chronic air pollution exposure. PMID:32873817
Dissecting Transcription Factor-Target Interaction in Bovine Coronavirus Infection. PMID:32872640
Proteomics and Metabolomics Approaches towards a Functional Insight onto AUTISM Spectrum Disorders: Phenotype Stratification and Biomarker Discovery. PMID:32872562
Computational Methods and Software Tools for Functional Analysis of miRNA Data. PMID:32872205
Inference and multiscale model of epithelial-to-mesenchymal transition via single-cell transcriptomic data. PMID:32870263
Elucidation of remdesivir cytotoxicity pathways through genome-wide CRISPR-Cas9 screening and transcriptomics. PMID:32869031
Single-cell RNA expression profiling of SARS-CoV-2-related ACE2 and TMPRSS2 in human trophectoderm and placenta. PMID:32851697
Screening and Identification of Therapeutic Targets for Pulmonary Arterial Hypertension Through Microarray Technology. PMID:32849793
Newly identified Gon4l/Udu-interacting proteins implicate novel functions. PMID:32848183
Experimental Evolution of Bacillus subtilis Reveals the Evolutionary Dynamics of Horizontal Gene Transfer and Suggests Adaptive and Neutral Effects. PMID:32847815
KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response. PMID:32839776
Differential processing and localization of human Nocturnin controls metabolism of mRNA and nicotinamide adenine dinucleotide cofactors. PMID:32839274
Identification and classification of differentially expressed genes reveal potential molecular signature associated with SARS-CoV-2 infection in lung adenocarcinomal cells. PMID:32835074
Innate immune response in neuronopathic forms of Gaucher disease confers resistance against viral-induced encephalitis. PMID:32831144
Risuteganib Protects against Hydroquinone-induced Injury in Human RPE Cells. PMID:32818234
Experimental and Biological Insights from Proteomic Analyses of Extracellular Vesicle Cargos in Normalcy and Disease. PMID:32815324
Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli. PMID:32813020
The current landscape of coronavirus-host protein-protein interactions. PMID:32811513
Extreme Phenotype Approach Suggests Taste Transduction Pathway for Carotid Plaque in a Multi-Ethnic Cohort. PMID:32811377
Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment. PMID:32810438
CRISPR interference of nucleotide biosynthesis improves production of a single-domain antibody in Escherichia coli. PMID:32808670
Microarray-based transcriptional profiling of a mouse model of autoimmune hepatitis. PMID:32808463
Optic nerve coloboma as extension of the phenotype of 22q11.23 duplication syndrome: a case report. PMID:32807111
Integrated Framework of the Immune-Defense Transcriptional Signatures in the Arabidopsis Shoot Apical Meristem. PMID:32796535
IFN signaling and neutrophil degranulation transcriptional signatures are induced during SARS-CoV-2 infection. PMID:32793903
Discovery of small molecules that normalize the transcriptome and enhance cysteine cathepsin activity in progranulin-deficient microglia. PMID:32792571
An autophagy-related model of 4 key genes for predicting prognosis of patients with laryngeal cancer. PMID:32791689
Genetic Mutations That Drive Evolutionary Rescue to Lethal Temperature in Escherichia coli. PMID:32785667
Genomic Analysis of Localized High-Risk Prostate Cancer Circulating Tumor Cells at the Single-Cell Level. PMID:32784507
Mechanistic studies of cytotoxic activity of the mesoionic compound MIH 2.4Bl in MCF-7 breast cancer cells. PMID:32782546
Dissecting diagnostic heterogeneity in depression by integrating neuroimaging and genetics. PMID:32781460
Lack of TLR4 modifies the miRNAs profile and attenuates inflammatory signaling pathways. PMID:32780740
SOX10-regulated promoter use defines isoform-specific gene expression in Schwann cells. PMID:32770939
Mutant p53 induces Golgi tubulo-vesiculation driving a prometastatic secretome. PMID:32770028
Transcriptomic analysis reveals differential gene expression, alternative splicing, and novel exons during mouse trophoblast stem cell differentiation. PMID:32762732
FLUTE: Fast and reliable knowledge retrieval from biomedical literature. PMID:32761077
The effect of Jiedu Huoxue decoction on rat model of experimental nonbacterial prostatitis via regulation of miRNAs. PMID:32758035
Glycosaminoglycan-Protein Interactions: The First Draft of the Glycosaminoglycan Interactome. PMID:32757871
Circuits Regulating Superoxide and Nitric Oxide Production and Neutralization in Different Cell Types: Expression of Participating Genes and Changes Induced by Ionizing Radiation. PMID:32756515
Bioinformatics analysis of microRNA profiles and identification of microRNA-mRNA network and biological markers in intracranial aneurysm. PMID:32756097
COVID-19-Related Coagulopathy-Is Transferrin a Missing Link? PMID:32751741
iPS-Derived Early Oligodendrocyte Progenitor Cells from SPMS Patients Reveal Deficient In Vitro Cell Migration Stimulation. PMID:32751289
Metastasis of Uveal Melanoma with Monosomy-3 Is Associated with a Less Glycogenetic Gene Expression Profile and the Dysregulation of Glycogen Storage. PMID:32751097
A comprehensive rat transcriptome built from large scale RNA-seq-based annotation. PMID:32749457
Mapping the nucleolar proteome reveals a spatiotemporal organization related to intrinsic protein disorder. PMID:32744794
A human ESC-based screen identifies a role for the translated lncRNA LINC00261 in pancreatic endocrine differentiation. PMID:32744504
Single molecule poly(A) tail-seq shows LARP4 opposes deadenylation throughout mRNA lifespan with most impact on short tails. PMID:32744499
An Activity-Guided Map of Electrophile-Cysteine Interactions in Primary Human T Cells. PMID:32730809
Breed Differences in Dog Cognition Associated with Brain-Expressed Genes and Neurological Functions. PMID:32726413
GGCT promotes colorectal cancer migration and invasion via epithelial-mesenchymal transition. PMID:32724344
Single-cell transcriptome profiling reveals neutrophil heterogeneity in homeostasis and infection. PMID:32719519
A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer's Disease Through Expert Curation of Key Protein Targets. PMID:32716361
Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity. PMID:32711472
A Genome-Wide View of Transcriptional Responses during Aphis glycines Infestation in Soybean. PMID:32707968
Genome‑wide analysis of DNA methylation and gene expression changes in an ovalbumin‑induced asthma mouse model. PMID:32705270
Downregulation of miR‑193a‑3p via targeting cyclin D1 in thyroid cancer. PMID:32705210
Expression profiling of circular RNAs and their potential role in early‑stage diabetic cardiomyopathy. PMID:32705182
Expanded Phenotypic Definition Identifies Hundreds of Potential Causative Genes for Leukodystrophies and Leukoencephalopathies. PMID:32704519
A substrate-based ontology for human solute carriers. PMID:32697042
Meta-analysis of gene expression profiles of lean and obese PCOS to identify differentially regulated pathways and risk of comorbidities. PMID:32695266
DAZL mediates a broad translational program regulating expansion and differentiation of spermatogonial progenitors. PMID:32686646
Inhibition of the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs) stimulates osteoblastogenesis by potentiating bone morphogenetic protein 2 (BMP2) responses. PMID:32686190
The power and limitations of gene expression pathway analyses toward predicting population response to environmental stressors. PMID:32684953
Development and validation of an integrative methylation signature and nomogram for predicting survival in clear cell renal cell carcinoma. PMID:32676392
RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus. PMID:32673562
Black Soldier Fly Larvae Adapt to Different Food Substrates through Morphological and Functional Responses of the Midgut. PMID:32668813
Unified inference of missense variant effects and gene constraints in the human genome. PMID:32667917
Nonsense-Mediated RNA Decay Factor UPF1 Is Critical for Posttranscriptional and Translational Gene Regulation in Arabidopsis. PMID:32665305
Investigating higher-order interactions in single-cell data with scHOT. PMID:32661426
Sex- and Region-Specific Differences in the Transcriptomes of Rat Microglia from the Brainstem and Cervical Spinal Cord. PMID:32661056
A Bioinformatics Crash Course for Interpreting Genomics Data. PMID:32658646
Benchmarking gene ontology function predictions using negative annotations. PMID:32657372
Transcriptomic Analysis of Extracellular RNA Governed by the Endocytic Adaptor Protein Cin1 of Cryptococcus deneoformans. PMID:32656093
Transcriptomic and Ultrastructural Signatures of K+-Induced Aggregation in Phytophthora parasitica Zoospores. PMID:32645882
The Lyme disease bacterium, Borrelia burgdorferi, stimulates an inflammatory response in human choroid plexus epithelial cells. PMID:32645014
Protein-Protein Interactions Efficiently Modeled by Residue Cluster Classes. PMID:32640745
Phosphoproteomic quantitation and causal analysis reveal pathways in GPVI/ITAM-mediated platelet activation programs. PMID:32640021
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). PMID:32637990
A Comprehensive Coexpression Network Analysis in Vibrio cholerae. PMID:32636337
Low Oxygen Stress During Early Development Influences Regulation of Hypoxia-Response Genes in Farmed Atlantic Salmon (Salmo salar). PMID:32636218
Retinal pigment epithelium transcriptome analysis in chronic smoking reveals a suppressed innate immune response and activation of differentiation pathways. PMID:32634473
Transcriptome Analyses of Candida albicans Biofilms, Exposed to Arachidonic Acid and Fluconazole, Indicates Potential Drug Targets. PMID:32631950
Integrated microarray analysis to identify potential biomarkers and therapeutic targets in dilated cardiomyopathy. PMID:32626989
Placental exosomes isolated from urine of patients with gestational diabetes exhibit a differential profile expression of microRNAs across gestation. PMID:32626972
Transcriptome analysis of testis reveals the effects of developmental exposure to bisphenol a or 17α-ethinylestradiol in medaka (Oryzias latipes). PMID:32622090
Draft Genome Sequence of the Bacterium Paraburkholderia aromaticivorans AR20-38, a Gram-Negative, Cold-Adapted Degrader of Aromatic Compounds. PMID:32616634
Association study based on topological constraints of protein-protein interaction networks. PMID:32612246
Differences in Gene Expression Profile of Primary Tumors in Metastatic and Non-Metastatic Papillary Thyroid Carcinoma-Do They Exist? PMID:32610693
Mechanistic Models of Signaling Pathways Reveal the Drug Action Mechanisms behind Gender-Specific Gene Expression for Cancer Treatments. PMID:32610626
Cardiac Transcriptome Analysis Reveals Nr4a1 Mediated Glucose Metabolism Dysregulation in Response to High-Fat Diet. PMID:32610475
Identification of Novel microRNA Profiles Dysregulated in Plasma and Tissue of Abdominal Aortic Aneurysm Patients. PMID:32605321
Genetic relationship between Hashimoto`s thyroiditis and papillary thyroid carcinoma with coexisting Hashimoto`s thyroiditis. PMID:32603365
Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex. PMID:32602773
Chronic Hypersensitivity Pneumonitis, an Interstitial Lung Disease with Distinct Molecular Signatures. PMID:32602730
Experimentally Determined Long Intrinsically Disordered Protein Regions Are Now Abundant in the Protein Data Bank. PMID:32599863
Fulvic acid increases forage legume growth inducing preferential up-regulation of nodulation and signalling-related genes. PMID:32599619
Transcriptogram analysis reveals relationship between viral titer and gene sets responses during Corona-virus infection. PMID:32587961
Transcriptomic microRNA Profiling of Dendritic Cells in Response to Gut Microbiota-Secreted Vesicles. PMID:32585977
Phenotypic Responses to and Genetic Architecture of Sterility Following Exposure to Sub-Lethal Temperature During Development. PMID:32582294
Transcriptome Analysis of Wounding in the Model Grass Lolium temulentum. PMID:32580425
Identification of Conserved Proteomic Networks in Neurodegenerative Dementia. PMID:32579933
Drosophila models of pathogenic copy-number variant genes show global and non-neuronal defects during development. PMID:32579612
Predicting Functions of Uncharacterized Human Proteins: From Canonical to Proteoforms. PMID:32575886
A Knowledge-Based Machine Learning Approach to Gene Prioritisation in Amyotrophic Lateral Sclerosis. PMID:32575372
Skd3 (human ClpB) is a potent mitochondrial protein disaggregase that is inactivated by 3-methylglutaconic aciduria-linked mutations. PMID:32573439
Manumycin polyketides act as molecular glues between UBR7 and P53. PMID:32572277
TERT Promoter Mutations and Their Impact on Gene Expression Profile in Papillary Thyroid Carcinoma. PMID:32560331
Automated generation of gene summaries at the Alliance of Genome Resources. PMID:32559296
Transcriptome-Wide Regulation of Key Developmental Pathways in the Mouse Neural Tube by Prenatal Alcohol Exposure. PMID:32557641
Sequencing of RNA in single cells reveals a distinct transcriptome signature of hematopoiesis in GATA2 deficiency. PMID:32556286
The evolution of sex-biased gene expression in the Drosophila brain. PMID:32554780
Macrophage correlates with immunophenotype and predicts anti-PD-L1 response of urothelial cancer. PMID:32550918
An age-independent gene signature for monitoring acute rejection in kidney transplantation. PMID:32550916
RNA Binding Proteins as Drivers and Therapeutic Target Candidates in Pancreatic Ductal Adenocarcinoma. PMID:32545414
Expression of SARS-CoV-2 receptor ACE2 and coincident host response signature varies by asthma inflammatory phenotype. PMID:32531372
Pituispheres Contain Genetic Variants Characteristic to Pituitary Adenoma Tumor Tissue. PMID:32528411
PINOT: an intuitive resource for integrating protein-protein interactions. PMID:32527260
A selective inference approach for false discovery rate control using multiomics covariates yields insights into disease risk. PMID:32522875
A Photo-clickable ATP-Mimetic Reveals Nucleotide Interactors in the Membrane Proteome. PMID:32521230
PSIONplusm Server for Accurate Multi-Label Prediction of Ion Channels and Their Types. PMID:32517331
The core SWI/SNF catalytic subunit Brg1 regulates nephron progenitor cell proliferation and differentiation. PMID:32504627
Comparative Target Analysis of Chlorinated Biphenyl Antimicrobials Highlights MenG as a Molecular Target of Triclocarban. PMID:32503913
Identifying genetic variants and pathways associated with extreme levels of fetal hemoglobin in sickle cell disease in Tanzania. PMID:32503527
GC-AG Introns Features in Long Non-coding and Protein-Coding Genes Suggest Their Role in Gene Expression Regulation. PMID:32499820
Identification of prognostic gene biomarkers for metastatic skin cancer using data mining. PMID:32494360
A tissue level atlas of the healthy human virome. PMID:32493363
Biomarker roles identification of miR-106 family for predicting the risk and poor survival of colorectal cancer. PMID:32493303
A single-cell view on alga-virus interactions reveals sequential transcriptional programs and infection states. PMID:32490206
Ebstein anomaly associated with cri du chat (cat's cry) syndrome and 20q duplication. PMID:32487530
Urban air particulate matter induces mitochondrial dysfunction in human olfactory mucosal cells. PMID:32487172
Using Reactome to build an autophagy mechanism knowledgebase. PMID:32486891
Cadmium, Smoking, and Human Blood DNA Methylation Profiles in Adults from the Strong Heart Study. PMID:32484362
A-kinase-anchoring protein 1 (dAKAP1)-based signaling complexes coordinate local protein synthesis at the mitochondrial surface. PMID:32482893
dbPSP 2.0, an updated database of protein phosphorylation sites in prokaryotes. PMID:32472030
Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum. PMID:32471448
BEAVR: a browser-based tool for the exploration and visualization of RNA-seq data. PMID:32471392
Drug screening and identification of key candidate genes and pathways of rheumatoid arthritis. PMID:32468016
Regulatory Potential of bHLH-Type Transcription Factors on the Road to Rubber Biosynthesis in Hevea brasiliensis. PMID:32466493
A memory of eS25 loss drives resistance phenotypes. PMID:32463448
Itch attenuates CD4 T-cell proliferation in mice by limiting WBP2 protein stability. PMID:32459862
Inferring Virus-Host relationship between HPV and its host Homo sapiens using protein interaction network. PMID:32457456
Tumor Cell Associated Hyaluronan-CD44 Signaling Promotes Pro-Tumor Inflammation in Breast Cancer. PMID:32455980
Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago. PMID:32453742
Multipathway synergy promotes testicular transition from growth to spermatogenesis in early-puberty goats. PMID:32450814
Systematic identification of chicken type I, II and III interferon-stimulated genes. PMID:32448397
Discrete populations of isotype-switched memory B lymphocytes are maintained in murine spleen and bone marrow. PMID:32444631
Maternal Protein Restriction in Rats Alters the Expression of Genes Involved in Mitochondrial Metabolism and Epitranscriptomics in Fetal Hypothalamus. PMID:32438566
ThETA: transcriptome-driven efficacy estimates for gene-based TArget discovery. PMID:32437556
Effect of aging on the transcriptomic changes associated with the expression of the HERV-K (HML-2) provirus at 1q22. PMID:32435269
Bioinformatics Analysis Identifies the Estrogen Receptor 1 (ESR1) Gene and hsa-miR-26a-5p as Potential Prognostic Biomarkers in Patients with Intrahepatic Cholangiocarcinoma. PMID:32435051
Translational control of one-carbon metabolism underpins ribosomal protein phenotypes in cell division and longevity. PMID:32432546
A Single-Cell Transcriptional Roadmap of the Mouse and Human Lymph Node Lymphatic Vasculature. PMID:32426372
Tradeoff between metabolic i-proteasome addiction and immune evasion in triple-negative breast cancer. PMID:32423906
Molecular Signatures of Placentation and Secretion Uncovered in Poeciliopsis Maternal Follicles. PMID:32421768
Gene Ontology Curation of Neuroinflammation Biology Improves the Interpretation of Alzheimer's Disease Gene Expression Data. PMID:32417785
Large-scale network analysis captures biological features of bacterial plasmids. PMID:32415210
Myocardial micro-biopsy procedure for molecular characterization with increased precision and reduced trauma. PMID:32415191
3'-UTR Shortening Contributes to Subtype-Specific Cancer Growth by Breaking Stable ceRNA Crosstalk of Housekeeping Genes. PMID:32411683
Alternative splicing of LSD1+8a in neuroendocrine prostate cancer is mediated by SRRM4. PMID:32403054
Integrated urine proteomics and renal single-cell genomics identify an IFN-γ response gradient in lupus nephritis. PMID:32396533
Lower oxygen consumption and Complex I activity in mitochondria isolated from skeletal muscle of fetal sheep with intrauterine growth restriction. PMID:32396498
CoCoCoNet: conserved and comparative co-expression across a diverse set of species. PMID:32392296
CK14 Expression Identifies a Basal/Squamous-Like Type of Papillary Non-Muscle-Invasive Upper Tract Urothelial Carcinoma. PMID:32391279
Shared Regulatory Pathways Reveal Novel Genetic Correlations Between Grip Strength and Neuromuscular Disorders. PMID:32391060
Functional genomics analysis of human colon organoids identifies key transcription factors. PMID:32390556
Targeting PHGDH Upregulation Reduces Glutathione Levels and Resensitizes Resistant NRAS-Mutant Melanoma to MAPK Kinase Inhibition. PMID:32389536
Applying knowledge-driven mechanistic inference to toxicogenomics. PMID:32387679
Tomato Atypical Receptor Kinase1 Is Involved in the Regulation of Preinvasion Defense. PMID:32385090
The 15q11.2 BP1-BP2 Microdeletion (Burnside-Butler) Syndrome: In Silico Analyses of the Four Coding Genes Reveal Functional Associations with Neurodevelopmental Phenotypes. PMID:32384786
Proteomic Profiling of Small Extracellular Vesicles Secreted by Human Pancreatic Cancer Cells Implicated in Cellular Transformation. PMID:32382024
GeneTrail 3: advanced high-throughput enrichment analysis. PMID:32379325
Polygenic risk scores indicates genetic overlap between peripheral pain syndromes and chronic postsurgical pain. PMID:32377986
miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems. PMID:32374865
Towards the routine use of in silico screenings for drug discovery using metabolic modelling. PMID:32369553
Blast2Fish: a reference-based annotation web tool for transcriptome analysis of non-model teleost fish. PMID:32366294
In Vitro Evaluation of the Effects of Commercial Prebiotic GOS and FOS Products on Human Colonic Caco-2 Cells. PMID:32366023
Population-Specific Genetic and Expression Differentiation in Europeans. PMID:32365201
Genome-wide association study of MRI markers of cerebral small vessel disease in 42,310 participants. PMID:32358547
Community curation in PomBase: enabling fission yeast experts to provide detailed, standardized, sharable annotation from research publications. PMID:32353878
Comprehensive Immunoprofiling of Pediatric Zika Reveals Key Role for Monocytes in the Acute Phase and No Effect of Prior Dengue Virus Infection. PMID:32348760
Contribution of common and rare damaging variants in familial forms of bipolar disorder and phenotypic outcome. PMID:32345981
The phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia. PMID:32341346
Shared genetic architecture and casual relationship between leptin levels and type 2 diabetes: large-scale cross-trait meta-analysis and Mendelian randomization analysis. PMID:32341051
ABC Efflux Transporters and the Circuitry of miRNAs: Kinetics of Expression in Cancer Drug Resistance. PMID:32340269
Identification of Novel Targets of RBM5 in the Healthy and Injured Brain. PMID:32335213
Novel Apoptotic Mediators Identified by Conservation of Vertebrate Caspase Targets. PMID:32326640
Protein Synthesis by Day 16 Bovine Conceptuses during the Time of Maternal Recognition of Pregnancy. PMID:32325999
STAT3-dependent analysis reveals PDK4 as independent predictor of recurrence in prostate cancer. PMID:32323921
WIPI2 depletion inhibits the growth of hepatocellular carcinoma cells through the AMPK signaling pathway. PMID:32323845
Patient‑derived orthotopic xenograft glioma models fail to replicate the magnetic resonance imaging features of the original patient tumor. PMID:32323818
Application of weighted gene co‑expression network analysis to explore the potential diagnostic biomarkers for colorectal cancer. PMID:32323816
A novel plasma lncRNA ENST00000416361 is upregulated in coronary artery disease and is related to inflammation and lipid metabolism. PMID:32323776
Abnormal DNA methylation patterns in patients with infection‑caused leukocytopenia based on methylation microarrays. PMID:32323775
Pilot study and bioinformatics analysis of differentially expressed genes in adipose tissues of rats with excess dietary intake. PMID:32323762
CRISPR-mediated gene targeting of CK1δ/ε leads to enhanced understanding of their role in endocytosis via phosphoregulation of GAPVD1. PMID:32321936
ORF Ι of Mycovirus SsNSRV-1 is Associated with Debilitating Symptoms of Sclerotinia sclerotiorum. PMID:32316519
Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop. PMID:32313939
RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis. PMID:32311035
Pleiotropy-Based Decomposition of Genetic Risk Scores: Association and Interaction Analysis for Type 2 Diabetes and CAD. PMID:32302534
A Five-Genes-Based Prognostic Signature for Cervical Cancer Overall Survival Prediction. PMID:32300605
Transcriptomic diversity in seedling roots of European flint maize in response to cold. PMID:32293268
Stress-mediated convergence of splicing landscapes in male and female rock doves. PMID:32293250
Sporadic activation of an oxidative stress-dependent NRF2-p53 signaling network in breast epithelial spheroids and premalignancies. PMID:32291314
Cellular origins and genetic landscape of cutaneous gamma delta T cell lymphomas. PMID:32286303
Structured reviews for data and knowledge-driven research. PMID:32283553
Development of IFN-Stimulated Gene Expression from Embryogenesis through Adulthood, with and without Constitutive MDA5 Pathway Activation. PMID:32277054
Genome-Wide Analysis Reveals Mucociliary Remodeling of the Nasal Airway Epithelium Induced by Urban PM2.5. PMID:32275839
Hydra: A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures. PMID:32275708
GOMCL: a toolkit to cluster, evaluate, and extract non-redundant associations of Gene Ontology-based functions. PMID:32272889
Diversity of peripheral blood human NK cells identified by single-cell RNA sequencing. PMID:32271902
Loci associated with conception rate in crossbred beef heifers. PMID:32271764
In Silico Discovery of Candidate Drugs against Covid-19. PMID:32268515
Experimentally-driven protein structure modeling. PMID:32268219
Test of Arabidopsis Space Transcriptome: A Discovery Environment to Explore Multiple Plant Biology Spaceflight Experiments. PMID:32265943
Phospho-proteomic discovery of novel signal transducers including thioredoxin-interacting protein as mediators of erythropoietin-dependent human erythropoiesis. PMID:32259549
Expression profile analysis identifies key genes as prognostic markers for metastasis of osteosarcoma. PMID:32256213
Bayesian integrative analysis of epigenomic and transcriptomic data identifies Alzheimer's disease candidate genes and networks. PMID:32255787
Cell type-specific transcriptomics of esophageal adenocarcinoma as a scalable alternative for single cell transcriptomics. PMID:32255255
Cardiac miRNA Expression and their mRNA Targets in a Rat Model of Prediabetes. PMID:32244869
Adaptive Shifts in Gene Regulation Underlie a Developmental Delay in Thermogenesis in High-Altitude Deer Mice. PMID:32243546
Altered expression of glycoprotein non‑metastatic melanoma protein B in the distal sciatic nerve following injury. PMID:32236569
Uncovering Prognosis-Related Genes and Pathways by Multi-Omics Analysis in Lung Cancer. PMID:32235589
Transcriptome Ortholog Alignment Sequence Tools (TOAST) for phylogenomic dataset assembly. PMID:32228442
Effect of Ionizing Radiation on Transcriptome during Neural Differentiation of Human Embryonic Stem Cells. PMID:32216708
Chronic Ethanol Feeding in Mice Decreases Expression of Genes for Major Structural Bone Proteins in a Nox4-Independent Manner. PMID:32213546
Testing Proximity of Genomic Regions to Transcription Start Sites and Enhancers Complements Gene Set Enrichment Testing. PMID:32211031
Pharmacological target-focused transcriptomic analysis of native vs cultured human and mouse dorsal root ganglia. PMID:32197039
Portal of Juglandaceae: A comprehensive platform for Juglandaceae study. PMID:32194971
Identification of potential key genes in gastric cancer using bioinformatics analysis. PMID:32190306
PDGFD induces ibrutinib resistance of diffuse large B‑cell lymphoma through activation of EGFR. PMID:32186759
Absolute yeast mitochondrial proteome quantification reveals trade-off between biosynthesis and energy generation during diauxic shift. PMID:32184324
AllEnricher: a comprehensive gene set function enrichment tool for both model and non-model species. PMID:32183716
Genomic Landscape and Mutational Spectrum of ADAMTS Family Genes in Mendelian Disorders Based on Gene Evidence Review for Variant Interpretation. PMID:32183147
Identification of key genes and pathways of diagnosis and prognosis in cervical cancer by bioinformatics analysis. PMID:32181600
Integrated miRNA/mRNA Counter-Expression Analysis Highlights Oxidative Stress-Related Genes CCR7 and FOXO1 as Blood Markers of Coronary Arterial Disease. PMID:32178422
Systematical Analysis of the Cancer Genome Atlas Database Reveals EMCN/MUC15 Combination as a Prognostic Signature for Gastric Cancer. PMID:32175327
C-terminal binding proteins 1 and 2 in traumatic brain injury-induced inflammation and their inhibition as an approach for anti-inflammatory treatment. PMID:32174788
Global profile changes in transcripts induced with a phosphate analogue: implications for gene regulation. PMID:32172469
Enabling reusability of plant phenomic datasets with MIAPPE 1.1. PMID:32171029
Investigating global gene expression changes in a murine model of cherubism. PMID:32165349
Time-lapse single-cell transcriptomics reveals modulation of histone H3 for dormancy breaking in fission yeast. PMID:32152323
Temporal changes in the gene expression heterogeneity during brain development and aging. PMID:32139741
A pathway coordinated by DELE1 relays mitochondrial stress to the cytosol. PMID:32132706
Comparative genomic analysis reveals high intra-serovar plasticity within Salmonella Napoli isolated in 2005-2017. PMID:32131727
Supervised learning is an accurate method for network-based gene classification. PMID:32129827
Incorporation of a unified protein abundance dataset into the Saccharomyces genome database. PMID:32128557
Comparative proteomics analysis of Tibetan hull-less barley under osmotic stress via data-independent acquisition mass spectrometry. PMID:32126136
MicroRNA‑449a regulates the progression of brain aging by targeting SCN2B in SAMP8 mice. PMID:32124967
The Gossypium longicalyx Genome as a Resource for Cotton Breeding and Evolution. PMID:32122962
Alveolar Macrophage Chromatin Is Modified to Orchestrate Host Response to Mycobacterium bovis Infection. PMID:32117424
An Anti-inflammatory microRNA Signature Distinguishes Group 3 Innate Lymphoid Cells From Natural Killer Cells in Human Decidua. PMID:32117280
Genetic Modifiers and Rare Mendelian Disease. PMID:32106447
Integrative module analysis of HCC gene expression landscapes. PMID:32104233
Predicted Drosophila Interactome Resource and web tool for functional interpretation of differentially expressed genes. PMID:32103267
Data libraries - the missing element for modeling biological systems. PMID:32100391
Integrated characterization and validation of the prognostic significance of microRNA-200s in colorectal cancer. PMID:32099529
Detection and characterization of microRNA expression profiling and its target genes in response to canine parvovirus in Crandell Reese Feline Kidney cells. PMID:32095352
Toxicological response of the model fungus Saccharomyces cerevisiae to different concentrations of commercial graphene nanoplatelets. PMID:32094381
Imipridone Anticancer Compounds Ectopically Activate the ClpP Protease and Represent a New Scaffold for Antibiotic Development. PMID:32094149
Adaptation to Photooxidative Stress: Common and Special Strategies of the Alphaproteobacteria Rhodobacter sphaeroides and Rhodobacter capsulatus. PMID:32093084
In Vitro Zika Virus Infection of Human Neural Progenitor Cells: Meta-Analysis of RNA-Seq Assays. PMID:32079323
Endogenous Retrovirus Activation as a Key Mechanism of Anti-Tumor Immune Response in Radiotherapy. PMID:32074012
The MYCL and MXD1 transcription factors regulate the fitness of murine dendritic cells. PMID:32071205
Whole-exome sequencing of 81 individuals from 27 multiply affected bipolar disorder families. PMID:32066727
SSIF: Subsumption-based Sub-term Inference Framework to audit Gene Ontology. PMID:32065617
A systems approach to infectious disease. PMID:32060427
High-throughput quantification of protein structural change reveals potential mechanisms of temperature adaptation in Mytilus mussels. PMID:32054457
NCBP2 modulates neurodevelopmental defects of the 3q29 deletion in Drosophila and Xenopus laevis models. PMID:32053595
SurfaceGenie: a web-based application for prioritizing cell-type-specific marker candidates. PMID:32053146
Pilocytic astrocytoma demethylation and transcriptional landscapes link bZIP transcription factors to immune response. PMID:32052037
Probing Carbon Utilization of Cordyceps militaris by Sugar Transportome and Protein Structural Analysis. PMID:32050592
Selection in Australian Thoroughbred horses acts on a locus associated with early two-year old speed. PMID:32049967
Gene expression in immortalized versus primary isolated cardiac endothelial cells. PMID:32042042
Classification of Trispanins: A Diverse Group of Proteins That Function in Membrane Synthesis and Transport Mechanisms. PMID:32039202
Transcriptional and Functional Programming of Decidual Innate Lymphoid Cells. PMID:32038619
HAMAP as SPARQL rules-A portable annotation pipeline for genomes and proteomes. PMID:32034905
Exposure to the Florida red tide dinoflagellate, Karenia brevis, and its associated brevetoxins induces ecophysiological and proteomic alterations in Porites astreoides. PMID:32032360
iMTBGO: An Algorithm for Integrating Metabolic Networks with Transcriptomes Based on Gene Ontology Analysis. PMID:32030085
A rare subpopulation of melanoma cells with low expression of metastasis suppressor NME1 is highly metastatic in vivo. PMID:32029850
PANEV: an R package for a pathway-based network visualization. PMID:32028885
APOE genotype regulates pathology and disease progression in synucleinopathy. PMID:32024799
Establishment and Characterisation by Expression Microarray of Patient-Derived Xenograft Panel of Human Pancreatic Adenocarcinoma Patients. PMID:32024004
The IUPHAR Guide to Immunopharmacology: connecting immunology and pharmacology. PMID:32020584
Astrocyte-Derived Exosomal microRNA miR-200a-3p Prevents MPP+-Induced Apoptotic Cell Death Through Down-Regulation of MKK4. PMID:32016794
Quantitative analysis of protein crotonylation identifies its association with immunoglobulin A nephropathy. PMID:32016442
Proteomic Analysis of Brain Region and Sex-Specific Synaptic Protein Expression in the Adult Mouse Brain. PMID:32012899
BHi-Cect: a top-down algorithm for identifying the multi-scale hierarchical structure of chromosomes. PMID:32009153
Localized Inhibition of Protein Phosphatase 1 by NUAK1 Promotes Spliceosome Activity and Reveals a MYC-Sensitive Feedback Control of Transcription. PMID:32006464
miRgo: integrating various off-the-shelf tools for identification of microRNA-target interactions by heterogeneous features and a novel evaluation indicator. PMID:32001758
Highly multiplexed proteomic assessment of human bone marrow in acute myeloid leukemia. PMID:31985806
Biobtree: A tool to search, map and visualize bioinformatics identifiers and special keywords. PMID:31984130
Imputation of Gene Expression Data in Blood Cancer and Its Significance in Inferring Biological Pathways. PMID:31970084
Survival-Associated Metabolic Genes in Human Papillomavirus-Positive Head and Neck Cancers. PMID:31968678
A Similar Genetic Architecture Underlies the Convergent Evolution of the Selfing Syndrome in Capsella. PMID:31964802
The Developmental Transcriptome of Aedes albopictus, a Major Worldwide Human Disease Vector. PMID:31964684
Incorporating biological structure into machine learning models in biomedicine. PMID:31962244
Building a pipeline to solicit expert knowledge from the community to aid gene summary curation. PMID:31960022
A human ciliopathy reveals essential functions for NEK10 in airway mucociliary clearance. PMID:31959991
A Protein Interaction Information-based Generative Model for Enhancing Gene Clustering. PMID:31959782
Transcriptome signature of ventricular arrhythmia in dilated cardiomyopathy reveals increased fibrosis and activated TP53. PMID:31958463
Open Data for Differential Network Analysis in Glioma. PMID:31952211
The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences. PMID:31950984
Role of Secreted Frizzled-Related Protein 1 in Early Mammary Gland Tumorigenesis and Its Regulation in Breast Microenvironment. PMID:31947616
Combined network pharmacology and virtual reverse pharmacology approaches for identification of potential targets to treat vascular dementia. PMID:31937840
Parallel evolutionary paths to produce more than one Pseudomonas aeruginosa biofilm phenotype. PMID:31934344
The DNA polymerases of Drosophila melanogaster. PMID:31933406
Clonal kinetics and single-cell transcriptional profiling of CAR-T cells in patients undergoing CD19 CAR-T immunotherapy. PMID:31924795
Gambogenic acid exerts anticancer effects in cisplatin‑resistant non‑small cell lung cancer cells. PMID:31922223
The transcriptional correlates of divergent electric organ discharges in Paramormyrops electric fish. PMID:31918666
Analysis of HrpG regulons and HrpG-interacting proteins by ChIP-seq and affinity proteomics in Xanthomonas campestris. PMID:31916392
Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions. PMID:31913281
Integrative network analysis identifies cell-specific trans regulators of m6A. PMID:31912146
Differential Expression in Testis and Liver Transcriptomes from Four Species of Peromyscus (Rodentia: Cricetidae). PMID:31909812
Comparative and Functional Genomic Resource for Mechanistic Studies of Human Blood Pressure-Associated Single Nucleotide Polymorphisms. PMID:31902252
Mechanistic Dissection of RNA-Binding Proteins in Regulated Gene Expression at Chromatin Levels. PMID:31900328
Weighted gene co‑expression network analysis to identify key modules and hub genes associated with atrial fibrillation. PMID:31894294
Cyberinfrastructure and resources to enable an integrative approach to studying forest trees. PMID:31892954
Recommendations for application of the functional evidence PS3/BS3 criterion using the ACMG/AMP sequence variant interpretation framework. PMID:31892348
The Acute Phase Response Is a Prominent Renal Proteome Change in Sepsis in Mice. PMID:31892161
The essentiality landscape of cell cycle related genes in human pluripotent and cancer cells. PMID:31889988
Enhancer jungles establish robust tissue-specific regulatory control in the human genome. PMID:31887344
The Use of Whole Exome Sequencing in a Cohort of Transgender Individuals to Identify Rare Genetic Variants. PMID:31882810
Transcription factor regulatory modules provide the molecular mechanisms for functional redundancy observed among transcription factors in yeast. PMID:31881824
Single Nucleotide Polymorphism rs6942067 Is a Risk Factor in Young and in Non-Smoking Patients with HPV Negative Head and Neck Squamous Cell Carcinoma. PMID:31878157
The dynamics of DNA methylation during epigenetic reprogramming of primordial germ cells in medaka (Oryzias latipes). PMID:31851575
Multi-omics analysis of multiple missions to space reveal a theme of lipid dysregulation in mouse liver. PMID:31844325
dictyBase and the Dicty Stock Center (version 2.0) - a progress report. PMID:31840793
Predicting associations among drugs, targets and diseases by tensor decomposition for drug repositioning. PMID:31839008
Profiles of Long Non-Coding RNAs and mRNA Expression in Human Macrophages Regulated by Interleukin-27. PMID:31835347
TRANSNAP: a web database providing comprehensive information on Japanese pear transcriptome. PMID:31831861
Whole-Transcriptome Analysis of Dermal Fibroblasts, Derived from Three Pairs of Monozygotic Twins, Discordant for Parkinson's Disease. PMID:31823283
On the possible origin of protein homochirality, structure, and biochemical function. PMID:31822617
GenoSurf: metadata driven semantic search system for integrated genomic datasets. PMID:31820804
WormCat: An Online Tool for Annotation and Visualization of Caenorhabditis elegans Genome-Scale Data. PMID:31810987
Association between breast cancer cell migration and radiosensitivity in vitro. PMID:31807191
The distributions of protein coding genes within chromatin domains in relation to human disease. PMID:31805995
Reactome and ORCID-fine-grained credit attribution for community curation. PMID:31802127
Integrative Omics Approach to Identifying Genes Associated With Atrial Fibrillation. PMID:31801406
Network-Based Selection of Candidate Markers and Assays to Assess the Impact of Oral Immune Interventions on Gut Functions. PMID:31798593
Lithium alters expression of RNAs in a type-specific manner in differentiated human neuroblastoma neuronal cultures, including specific genes involved in Alzheimer's disease. PMID:31797941
Exploring Relationships between the Density of Charged Tracts within Disordered Regions and Phase Separation. PMID:31797598
The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases. PMID:31796553
Identification of hub genes and key pathways associated with the progression of gynecological cancer. PMID:31788113
Comparative analysis of functional assay evidence use by ClinGen Variant Curation Expert Panels. PMID:31783775
The JAX Synteny Browser for mouse-human comparative genomics. PMID:31776723
Evolution of placental invasion and cancer metastasis are causally linked. PMID:31768023
High content phenotypic screening identifies serotonin receptor modulators with selective activity upon breast cancer cell cycle and cytokine signaling pathways. PMID:31757681
LncRNA ROR1‑AS1 high expression and its prognostic significance in liver cancer. PMID:31746401
The Cyclic AMP Receptor Protein Regulates Quorum Sensing and Global Gene Expression in Yersinia pestis during Planktonic Growth and Growth in Biofilms. PMID:31744922
Genome-Scale Metabolic Networks Shed Light on the Carotenoid Biosynthesis Pathway in the Brown Algae Saccharina japonica and Cladosiphon okamuranus. PMID:31744163
Is MYND Domain-Mediated Assembly of SMYD3 Complexes Involved in Calcium Dependent Signaling? PMID:31737645
The neXtProt knowledgebase in 2020: data, tools and usability improvements. PMID:31724716
Mapping the perturbome network of cellular perturbations. PMID:31723137
The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform. PMID:31713623
New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. PMID:31713622
The Cytoscape BioGateway App: explorative network building from the BioGateway triple store. PMID:31710663
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. PMID:31701156
Hemagglutinin Stability Regulates H1N1 Influenza Virus Replication and Pathogenicity in Mice by Modulating Type I Interferon Responses in Dendritic Cells. PMID:31694942
The IUPHAR/BPS Guide to PHARMACOLOGY in 2020: extending immunopharmacology content and introducing the IUPHAR/MMV Guide to MALARIA PHARMACOLOGY. PMID:31691834
DrLLPS: a data resource of liquid-liquid phase separation in eukaryotes. PMID:31691822
miRPathDB 2.0: a novel release of the miRNA Pathway Dictionary Database. PMID:31691816
The reactome pathway knowledgebase. PMID:31691815
Enzyme annotation in UniProtKB using Rhea. PMID:31688925
Sequence and Structure Properties Uncover the Natural Classification of Protein Complexes Formed by Intrinsically Disordered Proteins via Mutual Synergistic Folding. PMID:31683980
Expression of Protein-Coding Gene Orthologs in Zebrafish and Mouse Inner Ear Non-sensory Supporting Cells. PMID:31680844
Immune Suppressive Extracellular Vesicle Proteins of Leptopilina heterotoma Are Encoded in the Wasp Genome. PMID:31676506
Phenome-wide association study of TTR and RBP4 genes in 361,194 individuals reveals novel insights in the genetics of hereditary and wildtype transthyretin amyloidoses. PMID:31659433
Chlamydia psittaci-Infected Dendritic Cells Communicate with NK Cells via Exosomes To Activate Antibacterial Immunity. PMID:31658957
Exploring lithium's transcriptional mechanisms of action in bipolar disorder: a multi-step study. PMID:31652432
Bovine Genome Database: new annotation tools for a new reference genome. PMID:31647100
Multi-tissue network analysis for drug prioritization in knee osteoarthritis. PMID:31645614
Network-Based Functional Prediction Augments Genetic Association To Predict Candidate Genes for Histamine Hypersensitivity in Mice. PMID:31645420
SilkDB 3.0: visualizing and exploring multiple levels of data for silkworm. PMID:31642484
Fermentation innovation through complex hybridization of wild and domesticated yeasts. PMID:31636426
GENAVi: a shiny web application for gene expression normalization, analysis and visualization. PMID:31619158
Challenges in the annotation of pseudoenzymes in databases: the UniProtKB approach. PMID:31618524
LnCeVar: a comprehensive database of genomic variations that disturb ceRNA network regulation. PMID:31617563
Biological Network Approaches and Applications in Rare Disease Studies. PMID:31614842
PhaSePro: the database of proteins driving liquid-liquid phase separation. PMID:31612960
DNAproDB: an expanded database and web-based tool for structural analysis of DNA-protein complexes. PMID:31612957
Transcriptome visualization and data availability at the Saccharomyces Genome Database. PMID:31612944
Exosome complex genes mediate RNA degradation and predict survival in mantle cell lymphoma. PMID:31612023
Four targeted genes for predicting the prognosis of colorectal cancer: A bioinformatics analysis case. PMID:31612015
Myo-REG: A Portal for Signaling Interactions in Muscle Regeneration. PMID:31611808
Loss of methionine sulfoxide reductases increases resistance to oxidative stress. PMID:31606431
KnockTF: a comprehensive human gene expression profile database with knockdown/knockout of transcription factors. PMID:31598675
Stereotyped transcriptomic transformation of somatosensory neurons in response to injury. PMID:31592768
YEASTRACT+: a portal for cross-species comparative genomics of transcription regulation in yeasts. PMID:31586406
CAGEfightR: analysis of 5'-end data using R/Bioconductor. PMID:31585526
The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics. PMID:31579570
Binding to medium and long chain fatty acyls is a common property of HEAT and ARM repeat modules. PMID:31578417
S‑allyl‑cysteine sulfoxide (alliin) alleviates myocardial infarction by modulating cardiomyocyte necroptosis and autophagy. PMID:31573046
Diesel exhaust particles dysregulate multiple immunological pathways in murine macrophages: Lessons from microarray and scRNA-seq technologies. PMID:31568751
Signatures of cell death and proliferation in perturbation transcriptomics data-from confounding factor to effective prediction. PMID:31552418
Alliance of Genome Resources Portal: unified model organism research platform. PMID:31552413
Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems. PMID:31548717
Reconstruction and analysis of competitive endogenous RNA network reveals regulatory role of long non‑coding RNAs in hepatic fibrosis. PMID:31545470
Comprehensive expression profiles and bioinformatics analysis reveal special circular RNA expression and potential predictability in the peripheral blood of humans with idiopathic membranous nephropathy. PMID:31545426
Druggable Transcriptional Networks in the Human Neurogenic Epigenome. PMID:31530573
Molecular Profiling of the Drosophila Antenna Reveals Conserved Genes Underlying Olfaction in Insects. PMID:31527046
Using MARRVEL v1.2 for Bioinformatics Analysis of Human Genes and Variant Pathogenicity. PMID:31524990
miRDB: an online database for prediction of functional microRNA targets. PMID:31504780
Migratory Neural Crest Cells Phagocytose Dead Cells in the Developing Nervous System. PMID:31495570
Voluntary exercise normalizes the proteomic landscape in muscle and brain and improves the phenotype of progeroid mice. PMID:31489782
Signaling pathways and gene co-expression modules associated with cytoskeleton and axon morphology in breast cancer survivors with chronic paclitaxel-induced peripheral neuropathy. PMID:31486345
A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition. PMID:31477929
Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information. PMID:31475990
Identification of modules and functional analysis in CRC subtypes by integrated bioinformatics analysis. PMID:31469863
A human endogenous retrovirus encoded protease potentially cleaves numerous cellular proteins. PMID:31462935
Identification of microRNA-181 as a promising biomarker for predicting the poor survival in colorectal cancer. PMID:31448575
Genome-Wide SNPs and InDels Characteristics of Three Chinese Cattle Breeds. PMID:31443466
Randomized trial of weight loss in primary breast cancer: Impact on body composition, circulating biomarkers and tumor characteristics. PMID:31442303
Synergistic Genetic Interactions between Pkhd1 and Pkd1 Result in an ARPKD-Like Phenotype in Murine Models. PMID:31427367
Dysregulation of DNA methylation patterns may identify patients with breast cancer resistant to endocrine therapy: A predictive classifier based on differentially methylated regions. PMID:31423189
Phellem Cell-Wall Components Are Discriminants of Cork Quality in Quercus suber. PMID:31417580
A network-based analysis for mining the risk pathways in glioblastoma. PMID:31402957
Omics Driven Understanding of the Intestines of Parasitic Nematodes. PMID:31402928
MEK inhibition remodels the active chromatin landscape and induces SOX10 genomic recruitment in BRAF(V600E) mutant melanoma cells. PMID:31399133
Integrated mRNA and miRNA profiling in NIH/3T3 cells in response to bovine papillomavirus E6 gene expression. PMID:31396463
Long Non-Coding RNA Expression Levels Modulate Cell-Type-Specific Splicing Patterns by Altering Their Interaction Landscape with RNA-Binding Proteins. PMID:31390792
Genetically diverse Pseudomonas aeruginosa populations display similar transcriptomic profiles in a cystic fibrosis explanted lung. PMID:31363089
Differential gene expression and gene ontologies associated with increasing water-stress in leaf and root transcriptomes of perennial ryegrass (Lolium perenne). PMID:31361773
Mammalian Annotation Database for improved annotation and functional classification of Omics datasets from less well-annotated organisms. PMID:31353404
Integrated identification of key genes and pathways in Alzheimer's disease via comprehensive bioinformatical analyses. PMID:31346329
Identification of differentially expressed genes in small and non-small cell lung cancer based on meta-analysis of mRNA. PMID:31338439
A step-by-step guide to analyzing CAGE data using R/Bioconductor. PMID:31327999
Estimating dispensable content in the human interactome. PMID:31324802
Identification and characterization of sexual dimorphism‑linked gene expression profile in hepatocellular carcinoma. PMID:31322260
Ligand Binding Site Structure Shapes Folding, Assembly and Degradation of Homomeric Protein Complexes. PMID:31306664
Comprehensive in vivo identification of the c-Myc mRNA protein interactome using HyPR-MS. PMID:31296583
Prediction of disease-associated mutations in the transmembrane regions of proteins with known 3D structure. PMID:31291347
A Cyclin A-Myb-MuvB-Aurora B network regulates the choice between mitotic cycles and polyploid endoreplication cycles. PMID:31291240
Cloudy with a Chance of Insights: Context Dependent Gene Regulation and Implications for Evolutionary Studies. PMID:31261769
PropaNet: Time-Varying Condition-Specific Transcriptional Network Construction by Network Propagation. PMID:31258543
Isatin inhibits the invasion of human neuroblastoma SH‑SY5Y cells, based on microarray analysis. PMID:31257543
Analysis of potential functional significance of microRNA‑3613‑3p in human umbilical vein endothelial cells affected by heat stress. PMID:31257536
Identification of key pathways and genes in different types of chronic kidney disease based on WGCNA. PMID:31257514
RNA polymerase II (RNAP II)-associated factors are recruited to tRNA loci, revealing that RNAP II- and RNAP III-mediated transcriptions overlap in yeast. PMID:31235518
Protein interactions and consensus clustering analysis uncover insights into herpesvirus virion structure and function relationships. PMID:31199794
Development of a Zebrafish S1500+ Sentinel Gene Set for High-Throughput Transcriptomics. PMID:31188086
Bioinformatics analysis of the regulatory lncRNA‑miRNA‑mRNA network and drug prediction in patients with hypertrophic cardiomyopathy. PMID:31180540
Culturing C2C12 myotubes on micromolded gelatin hydrogels accelerates myotube maturation. PMID:31174599
Screening key genes and signaling pathways in colorectal cancer by integrated bioinformatics analysis. PMID:31173250
Identification of diagnostic long non‑coding RNA biomarkers in patients with hepatocellular carcinoma. PMID:31173205
SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse. PMID:31171447
NetR and AttR, Two New Bioinformatic Tools to Integrate Diverse Datasets into Cytoscape Network and Attribute Files. PMID:31159440
LnCompare: gene set feature analysis for human long non-coding RNAs. PMID:31147707
Human pancreatic cancer cell exosomes, but not human normal cell exosomes, act as an initiator in cell transformation. PMID:31134894
INGA 2.0: improving protein function prediction for the dark proteome. PMID:31073595
Comparative transcriptome analysis of trout skin pigment cells. PMID:31072301
Ten quick tips for biocuration. PMID:31048830
A Multigene Assay Determines Risk of Recurrence in Patients with Triple-Negative Breast Cancer. PMID:31048497
Promiscuous Targeting of Cellular Proteins by Vpr Drives Systems-Level Proteomic Remodeling in HIV-1 Infection. PMID:31042482
The Promoter Regions of Intellectual Disability-Associated Genes Are Uniquely Enriched in LTR Sequences of the MER41 Primate-Specific Endogenous Retrovirus: An Evolutionary Connection Between Immunity and Cognition. PMID:31031802
The challenges of big data biology. PMID:30950793
Mutational spectrum and associations with clinical features in patients with acute myeloid leukaemia based on next‑generation sequencing. PMID:30942411
Proteomic profiling and integrated analysis with transcriptomic data bring new insights in the stress responses of Kluyveromyces marxianus after an arrest during high-temperature ethanol fermentation. PMID:30899329
Early Transcriptional Response to DNA Virus Infection in Sclerotinia sclerotiorum. PMID:30893849
Systematic analysis reveals the prevalence and principles of bypassable gene essentiality. PMID:30824696
Identification of Potential Genes Responsible for Thermotolerance in Wheat under High Temperature Stress. PMID:30823586
Integration of macromolecular complex data into the Saccharomyces Genome Database. PMID:30715277
Annotation of gene product function from high-throughput studies using the Gene Ontology. PMID:30715275
Mouse Genome Database (MGD) 2019. PMID:30407599
Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes. PMID:30357405 -
Gene Ontology Consortium: going forward
PubMed citations: 1343.
1343 articles citing: Gene Ontology Consortium: going forward
RNA-Seq Analysis Demonstrates Different Strategies Employed by Tiger Nuts (Cyperus esculentus L.) in Response to Drought Stress. PMID:35888139
STAT3 and NTRK2 Genes Predicted by the Bioinformatics Approach May Play Important Roles in the Pathogenesis of Multiple Sclerosis and Obsessive-Compulsive Disorder. PMID:35887540
A Census of Human Methionine-Rich Prion-like Domain-Containing Proteins. PMID:35883780
Comparative Analysis of Gene Correlation Networks of Breast Cancer Patients Based on Mutations in TP53. PMID:35883535
DES-Amyloidoses "Amyloidoses through the looking-glass": A knowledgebase developed for exploring and linking information related to human amyloid-related diseases. PMID:35877764
Computational analysis of potential candidate genes involved in the cold stress response of ten Rosaceae members. PMID:35842574
Prognostic role of NLGN2 and PTGDS in medulloblastoma based on gene expression omnibus. PMID:35836891
Seascape genomics of common dolphins (Delphinus delphis) reveals adaptive diversity linked to regional and local oceanography. PMID:35818031
Prognosis and Tumour Immune Microenvironment of Patients With Hepatocellular Carcinoma by a Novel Pyroptosis-Related lncRNA Signature. PMID:35812396
Identification of Hub Genes and Immune-Related Pathways for Membranous Nephropathy by Bioinformatics Analysis. PMID:35812314
Updated List of Transport Proteins in Plasmodium falciparum. PMID:35811673
The Genome of the Marine Alga Ulva compressa (Chlorophyta) Reveals Protein-Coding Genes with Similarity to Plants and Green Microalgae, but Also to Animal, Bacterial, and Fungal Genes. PMID:35806287
A novel signature derived from metabolism-related genes GPT and SMS to predict prognosis of laryngeal squamous cell carcinoma. PMID:35804447
Systemic approaches using single cell transcriptome reveal that C/EBPγ regulates autophagy under amino acid starved condition. PMID:35801910
hnRNP E1 Regulates HPV16 Oncogene Expression and Inhibits Cervical Cancerization. PMID:35800060
Analysis of Lymphoma-Related Genes with Gene Ontology and Kyoto Encyclopedia of Genes and Genomes Enrichment. PMID:35795312
Transcriptome Analysis Reveals the Regulatory Networks of Cytokinin in Promoting Floral Feminization in Castanea henryi. PMID:35742833
Rare Variants in Novel Candidate Genes Associated With Nonsyndromic Patent Ductus Arteriosus Identified With Whole-Exome Sequencing. PMID:35734438
Transcriptome study digs out BMP2 involved in adipogenesis in sheep tails. PMID:35725366
Identification of an Endoplasmic Reticulum Stress-Related Gene Signature to Evaluate the Immune Status and Predict the Prognosis of Hepatocellular Carcinoma. PMID:35711939
An Integrative Pan-Cancer Analysis Revealing MLN4924 (Pevonedistat) as a Potential Therapeutic Agent Targeting Skp2 in YAP-Driven Cancers. PMID:35685435
Identification of biomarkers for immunotherapy response in prostate cancer and potential drugs to alleviate immunosuppression. PMID:35680563
Comparative genomics reveals low levels of inter- and intraspecies diversity in the causal agents of dwarf and common bunt of wheat and hint at conspecificity of Tilletia caries and T. laevis. PMID:35672841
AnthraxKP: a knowledge graph-based, Anthrax Knowledge Portal mined from biomedical literature. PMID:35653350
Breaking the Immune Complexity of the Tumor Microenvironment Using Single-Cell Technologies. PMID:35651929
Three-Dimensional Organotypic Cultures Reshape the microRNAs Transcriptional Program in Breast Cancer Cells. PMID:35626094
TRP Family Genes Are Differently Expressed and Correlated with Immune Response in Glioma. PMID:35625048
Identification of AKIRIN2 as a potential biomarker and correlation with immunotherapy in gastric adenocarcinoma by integrated bioinformatics analysis. PMID:35589807
LncMIR181A1HG is a novel chromatin-bound epigenetic suppressor of early stage osteogenic lineage commitment. PMID:35546168
Computational Analysis of the Immune Infiltration Pattern and Candidate Diagnostic Biomarkers in Lumbar Disc Herniation. PMID:35531067
Proteomic and Antibody Profiles Reveal Antigenic Composition and Signatures of Bacterial Ghost Vaccine of Brucella abortus A19. PMID:35529865
Discovering Common Pathophysiological Processes between COVID-19 and Cystic Fibrosis by Differential Gene Expression Pattern Analysis. PMID:35528173
A game changer for bipolar disorder diagnosis using RNA editing-based biomarkers. PMID:35504874
Identification and validation of prognosis-associated DNA repair gene signatures in colorectal cancer. PMID:35484177
A Cancer Associated Fibroblasts-Related Six-Gene Panel for Anti-PD-1 Therapy in Melanoma Driven by Weighted Correlation Network Analysis and Supervised Machine Learning. PMID:35479936
Epigenetic Regulation of Immune and Inflammatory Responses in Rheumatoid Arthritis. PMID:35479077
Analysis of the Molecular Mechanism of Evodia rutaecarpa Fruit in the Treatment of Nasopharyngeal Carcinoma Using Network Pharmacology and Molecular Docking. PMID:35463684
SNARER: new molecular descriptors for SNARE proteins classification. PMID:35462533
Convergent evolution of polyploid genomes from across the eukaryotic tree of life. PMID:35451464
Integrated Bioinformatics Algorithms and Experimental Validation to Explore Robust Biomarkers and Landscape of Immune Cell Infiltration in Dilated Cardiomyopathy. PMID:35433865
Autophagy Induced by BCL2-Related ceRNA Network Participates in the Occurrence of COPD. PMID:35431545
Computed Tomography Imaging-Based Radiogenomics Analysis Reveals Hypoxia Patterns and Immunological Characteristics in Ovarian Cancer. PMID:35418998
Single-Cell RNA-Seq Analysis of Cells from Degenerating and Non-Degenerating Intervertebral Discs from the Same Individual Reveals New Biomarkers for Intervertebral Disc Degeneration. PMID:35409356
Investigation of the Effect of Curcumin on Protein Targets in NAFLD Using Bioinformatic Analysis. PMID:35405942
Comprehensive Analysis of Pyroptosis-Related Genes and Tumor Microenvironment Infiltration Characterization in Papillary Renal Cell Carcinoma. PMID:35402508
miR-589-3p promoted osteogenic differentiation of periodontal ligament stem cells through targeting ATF1. PMID:35399081
Predicted mouse interactome and network-based interpretation of differentially expressed genes. PMID:35390003
Screening and identification of potential biomarkers and therapeutic targets for systemic sclerosis-associated interstitial lung disease. PMID:35382367
Investigation of the mechanisms and experimental verification of Cuscuta-Salvia in the treatment of polycystic ovary syndrome (PCOS) via network pharmacology. PMID:35379295
OmicsView: Omics data analysis through interactive visual analytics. PMID:35356547
Inflammation and Brain Structure in Schizophrenia and Other Neuropsychiatric Disorders: A Mendelian Randomization Study. PMID:35353173
PLUS: Predicting cancer metastasis potential based on positive and unlabeled learning. PMID:35349572
Genome Sequence and Description of Paracoccus denitrificans Strain R-1, Isolated from Activated Sludge. PMID:35343764
Genomic signatures of high-altitude adaptation and chromosomal polymorphism in geladas. PMID:35332281
Integrated Bioinformatics Analysis and Validation of the Prognostic Value of RBM10 Expression in Hepatocellular Carcinoma. PMID:35283645
Comprehensive Analysis of the Effect of 20(R)-Ginsenoside Rg3 on Stroke Recovery in Rats via the Integrative miRNA-mRNA Regulatory Network. PMID:35268674
A Computational Text Mining-Guided Meta-Analysis Approach to Identify Potential Xerostomia Drug Targets. PMID:35268532
Smoking Status and Type 2 Diabetes, and Cardiovascular Disease: A Comprehensive Analysis of Shared Genetic Etiology and Causal Relationship. PMID:35250867
Prognostication of Pancreatic Cancer Using The Cancer Genome Atlas Based Ferroptosis-Related Long Non-Coding RNAs. PMID:35237306
Genetics and Brain Transcriptomics of Completed Suicide. PMID:35236118
Transcriptome sequencing and lncRNA-miRNA-mRNA network construction in cardiac fibrosis and heart failure. PMID:35235759
Multiomics Reveals the Effect of Root Rot on Polygonati Rhizome and Identifies Pathogens and Biocontrol Strain. PMID:35225655
MicroRNA-4722-5p and microRNA-615-3p serve as potential biomarkers for Alzheimer's disease. PMID:35222718
Construction and Verification of a Combined Hypoxia and Immune Index for Clear Cell Renal Cell Carcinoma. PMID:35222525
Weighted Co-Expression Network Analysis Identifies RNF181 as a Causal Gene of Coronary Artery Disease. PMID:35222523
Natural variation in Glume Coverage 1 causes naked grains in sorghum. PMID:35217660
STIL Acts as an Oncogenetic Driver in a Primary Cilia-Dependent Manner in Human Cancer. PMID:35155425
Syntenin Regulated by miR-216b Promotes Cancer Progression in Pancreatic Cancer. PMID:35155233
Differential gene expression associated with a floral scent polymorphism in the evening primrose Oenothera harringtonii (Onagraceae). PMID:35151274
PBK/TOPK Inhibitor Suppresses the Progression of Prolactinomas. PMID:35126305
Systems-based approaches to study immunometabolism. PMID:35121805
Comprehensive analysis reveals novel gene signature in head and neck squamous cell carcinoma: predicting is associated with poor prognosis in patients. PMID:35117201
KRAS, YWHAE, SP1 and MSRA as biomarkers in endometrial cancer. PMID:35116456
Identification of Novel Subtypes in Lung Adenocarcinoma: Evidence from Gene Set Variation Analysis in Tumor and Adjacent Nontumor Samples. PMID:35096200
NonLoss: a novel analytical method for differential biological module identification from single-cell transcriptome. PMID:35071482
Searching for New Z-DNA/Z-RNA Binding Proteins Based on Structural Similarity to Experimentally Validated Zα Domain. PMID:35054954
Toward Data-Driven Radiation Oncology Using Standardized Terminology as a Starting Point: Cross-sectional Study. PMID:35044315
Benchmark Evaluation of Protein-Protein Interaction Prediction Algorithms. PMID:35011283
Transcriptome Profiling Reveals Features of Immune Response and Metabolism of Acutely Infected, Dead and Asymptomatic Infection of African Swine Fever Virus in Pigs. PMID:34975923
Computational Prediction of Biomarkers, Pathways, and New Target Drugs in the Pathogenesis of Immune-Based Diseases Regarding Kidney Transplantation Rejection. PMID:34975915
Gene Expression Profiles Identify Biomarkers of Resistance to Decitabine in Myelodysplastic Syndromes. PMID:34944006
Amycolatopsis aidingensis sp. nov., a Halotolerant Actinobacterium, Produces New Secondary Metabolites. PMID:34938275
Different Regulatory Modes of Synechocystis sp. PCC 6803 in Response to Photosynthesis Inhibitory Conditions. PMID:34874777
Single cell sequencing analysis identifies genetics-modulated ORMDL3+ cholangiocytes having higher metabolic effects on primary biliary cholangitis. PMID:34872583
Tissue-specific transcriptomics reveal functional differences in floral development. PMID:34865134
Author-sourced capture of pathway knowledge in computable form using Biofactoid. PMID:34860157
Identification and Potential Mechanisms of a 7-MicroRNA Signature That Predicts Prognosis in Patients with Lower-Grade Glioma. PMID:34845420
Comprehensive analysis of miRNA-mRNA regulatory network and potential drugs in chronic chagasic cardiomyopathy across human and mouse. PMID:34844599
Multidimensional Single-Nuclei RNA-Seq Reconstruction of Adipose Tissue Reveals Adipocyte Plasticity Underlying Thermogenic Response. PMID:34831295
Gene expression analysis of human induced pluripotent stem cells cryopreserved by vitrification using StemCell Keep. PMID:34825070
Automatic consistency assurance for literature-based gene ontology annotation. PMID:34823464
Predicting Human Protein Subcellular Locations by Using a Combination of Network and Function Features. PMID:34804131
EP300 Selectively Controls the Enhancer Landscape of MYCN-Amplified Neuroblastoma. PMID:34772733
Cigarette smoking-associated isoform switching and 3' UTR lengthening via alternative polyadenylation. PMID:34763026
Down-regulation of EPB41L4A-AS1 mediated the brain aging and neurodegenerative diseases via damaging synthesis of NAD+ and ATP. PMID:34758883
PangenomeNet: a pan-genome-based network reveals functional modules on antimicrobial resistome for Escherichia coli strains. PMID:34758735
Web-based transcriptome analysis determines a sixteen-gene signature and associated drugs on hearing loss patients: A bioinformatics approach. PMID:34758154
Study on the Mechanism of Liuwei Dihuang Pills in Treating Parkinson's Disease Based on Network Pharmacology. PMID:34746302
Melatonin Alleviates Cardiac Function in Sepsis-Caused Myocarditis via Maintenance of Mitochondrial Function. PMID:34708067
Identification of Conserved Pappalysin 1-Derived Circular RNA-Mediated Competing Endogenous RNA in Osteosarcoma. PMID:34707339
Mouse Genome Informatics (MGI): latest news from MGD and GXD. PMID:34698891
TPSC: a module detection method based on topology potential and spectral clustering in weighted networks and its application in gene co-expression module discovery. PMID:34689740
The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley. PMID:34686763
UbiBrowser 2.0: a comprehensive resource for proteome-wide known and predicted ubiquitin ligase/deubiquitinase-substrate interactions in eukaryotic species. PMID:34669962
Pleiotropic Effects of the P5-Type ATPase SpfA on Stress Response Networks Contribute to Virulence in the Pathogenic Mold Aspergillus fumigatus. PMID:34663092
Transcriptomic and Metabolomic Analyses Reveals That Exogenous Methyl Jasmonate Regulates Galanthamine Biosynthesis in Lycoris longituba Seedlings. PMID:34659286
Genome-Wide DNA Methylation and Hydroxymethylation Changes Revealed Epigenetic Regulation of Neuromodulation and Myelination in Yak Hypothalamus. PMID:34646294
Risk Prediction of Cardiovascular Events by Exploration of Molecular Data with Explainable Artificial Intelligence. PMID:34638627
Getting to know each other: PPIMem, a novel approach for predicting transmembrane protein-protein complexes. PMID:34630938
Exploring Diagnostic Biomarkers and Comorbid Pathogenesis for Osteoarthritis and Metabolic Syndrome via Bioinformatics Approach. PMID:34616175
Overexpression of EWSR1 (Ewing sarcoma breakpoint region 1/EWS RNA binding protein 1) predicts poor survival in patients with hepatocellular carcinoma. PMID:34612781
Recurrence-associated gene signature in patients with stage I non-small-cell lung cancer. PMID:34599262
Transcriptomic profiling in canines and humans reveals cancer specific gene modules and biological mechanisms common to both species. PMID:34570764
Immune Mechanism, Gene Module, and Molecular Subtype Identification of Astragalus Membranaceus in the Treatment of Dilated Cardiomyopathy: An Integrated Bioinformatics Study. PMID:34567206
Malignant Tumor Purity Reveals the Driven and Prognostic Role of CD3E in Low-Grade Glioma Microenvironment. PMID:34557404
Experimental and computational investigation of enzyme functional annotations uncovers misannotation in the EC 1.1.3.15 enzyme class. PMID:34555022
A High-Throughput Method to Analyze the Interaction Proteins With p22 Protein of African Swine Fever Virus In Vitro. PMID:34552974
Evidence-based complementary and alternative medicine bioinformatics approach through network pharmacology and molecular docking to determine the molecular mechanisms of Erjing pill in Alzheimer's disease. PMID:34539848
Recurrence biomarkers of triple negative breast cancer treated with neoadjuvant chemotherapy and anti-EGFR antibodies. PMID:34535679
Identifying the dynamic gene regulatory network during latent HIV-1 reactivation using high-dimensional ordinary differential equations. PMID:34531927
Cell-specific gene association network construction from single-cell RNA sequence. PMID:34530677
Analysis of master transcription factors related to Parkinson's disease through the gene transcription regulatory network. PMID:34522247
Identification and Validation of a Five-Gene Signature Associated With Overall Survival in Breast Cancer Patients. PMID:34513664
Circulating microRNAs in Early Breast Cancer Patients and Its Association With Lymph Node Metastases. PMID:34513655
Protein function prediction with gene ontology: from traditional to deep learning models. PMID:34513334
Establishment of an Immune-Related Gene Signature for Risk Stratification for Patients with Glioma. PMID:34497663
Gene expression and prognosis of x-ray repair cross-complementing family members in non-small cell lung cancer. PMID:34486486
New Insights Into Mitochondrial Dysfunction at Disease Susceptibility Loci in the Development of Type 2 Diabetes. PMID:34456865
Exploring the Pharmacological Mechanisms of Tripterygium wilfordii Hook F against Cardiovascular Disease Using Network Pharmacology and Molecular Docking. PMID:34435046
Exploring new targets for the treatment of hepatitis-B virus and hepatitis-B virus-associated hepatocellular carcinoma: A new perspective in bioinformatics. PMID:34414947
Utilization of Transcriptome, Small RNA, and Degradome Sequencing to Provide Insights Into Drought Stress and Rewatering Treatment in Medicago ruthenica. PMID:34413864
Gentamicin-induced hearing loss: A retrospective study using the Food and Drug Administration Adverse Event Reporting System and a toxicological study using drug-gene network analysis. PMID:34401547
Male Infertility Knowledgebase: decoding the genetic and disease landscape. PMID:34363073
Identification of potential biomarkers in dengue via integrated bioinformatic analysis. PMID:34347790
Uncovering Potential lncRNAs and mRNAs in the Progression From Acute Myocardial Infarction to Myocardial Fibrosis to Heart Failure. PMID:34336943
Identification and Validation of Immune Molecular Subtypes in Pancreatic Ductal Adenocarcinoma: Implications for Prognosis and Immunotherapy. PMID:34335594
Mining a stroke knowledge graph from literature. PMID:34325669
Gene expression analysis method integration and co-expression module detection applied to rare glucide metabolism disorders using ExpHunterSuite. PMID:34301987
Seven key hub genes identified by gene co-expression network in cutaneous squamous cell carcinoma. PMID:34301206
Correlation between targeted RNAseq signature of breast cancer CTCs and onset of bone-only metastases. PMID:34272498
An ancestral recombination graph of human, Neanderthal, and Denisovan genomes. PMID:34272242
MSCFS: inferring circRNA functional similarity based on multiple data sources. PMID:34271851
The Taxus genome provides insights into paclitaxel biosynthesis. PMID:34267359
Thromboangiitis obliterans plasma-derived exosomal miR-223-5p inhibits cell viability and promotes cell apoptosis of human vascular smooth muscle cells by targeting VCAM1. PMID:34259105
DES-Tcell is a knowledgebase for exploring immunology-related literature. PMID:34253812
Comprehensive Bioinformatics Analysis of mRNA Expression Profiles and Identification of a miRNA-mRNA Network Associated with the Pathogenesis of Low-Grade Gliomas. PMID:34234557
Chaperone-like protein DAY plays critical roles in photomorphogenesis. PMID:34234144
Metabolomics and Network Pharmacology-Based Investigation into the Mechanisms Underlying the Therapeutic Effect of a New Chinese Traditional Medicine (Cui Nai Ling) on Bromocriptine-Induced Hypogalactia. PMID:34221092
Annotating the Insect Regulatory Genome. PMID:34209769
Gene Expression Profiles Associated with Radio-Responsiveness in Locally Advanced Rectal Cancer. PMID:34205090
Regulatory miRNA-mRNA Networks in Parkinson's Disease. PMID:34204164
Association Analysis of Chromosome X to Identify Genetic Modifiers of Huntington's Disease. PMID:34180418
An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia. PMID:34171302
RTP4 is a novel prognosis-related hub gene in cutaneous melanoma. PMID:34154655
Tankyrase regulates epithelial lumen formation via suppression of Rab11 GEFs. PMID:34128958
Identification of Ten Mitosis Genes Associated with Tamoxifen Resistance in Breast Cancer. PMID:34113127
Down-regulating Circular RNA Prkcsh suppresses the inflammatory response after spinal cord injury. PMID:34100450
The Synergistic Effects of 5-Aminosalicylic Acid and Vorinostat in the Treatment of Ulcerative Colitis. PMID:34093178
MicroRNA Profiles of Maternal and Neonatal Endothelial Progenitor Cells in Preeclampsia. PMID:34070163
Lantern: an integrative repository of functional annotations for lncRNAs in the human genome. PMID:34039271
DNA methylation signatures associated with prognosis of gastric cancer. PMID:34034702
An 8-gene DNA methylation signature predicts the recurrence risk of cervical cancer. PMID:34034542
Identification of differentially expressed genes in diabetic kidney disease by RNA-Seq analysis of venous blood platelets. PMID:34029013
Comparative transcriptome and histological analyses provide insights into the skin pigmentation in Minxian black fur sheep (Ovis aries). PMID:33986980
Circular RNA Plek promotes fibrogenic activation by regulating the miR-135b-5p/TGF-βR1 axis after spinal cord injury. PMID:33982670
Deciphering Pharmacological Mechanism of Buyang Huanwu Decoction for Spinal Cord Injury by Network Pharmacology Approach. PMID:33976706
CXCL1 Clone Evolution Induced by the HDAC Inhibitor Belinostat Might Be a Favorable Prognostic Indicator in Triple-Negative Breast Cancer. PMID:33959656
System biology and bioinformatics pipeline to identify comorbidities risk association: Neurodegenerative disorder case study. PMID:33956862
Sporulation is dispensable for the vegetable-associated life cycle of the human pathogen Bacillus cereus. PMID:33955675
Establishment of a prognostic model of four genes in gastric cancer based on multiple data sets. PMID:33934516
An Overview of Biological and Computational Methods for Designing Mechanism-Informed Anti-biofilm Agents. PMID:33927701
On the Unfounded Enthusiasm for Soft Selective Sweeps III: The Supervised Machine Learning Algorithm That Isn't. PMID:33916341
Genome-wide association study of antipsychotic-induced sinus bradycardia in Chinese schizophrenia patients. PMID:33914752
Research and Clinical Significance of the Differentially Expressed Genes TP63 and LMO4 in Human Immunodeficiency Virus-Related Penile Squamous Cell Carcinoma. PMID:33906487
Expression analysis of progesterone‑regulated miRNAs in cells derived from human glioblastoma. PMID:33899118
Exploring the Pharmacological Mechanism of Duhuo Jisheng Decoction in Treating Osteoporosis Based on Network Pharmacology. PMID:33880122
Potential targets identified in adenoid cystic carcinoma point out new directions for further research. PMID:33841642
Genetic Polymorphism Drives Susceptibility Between Bacteria and Bacteriophages. PMID:33841354
Tumor Microenvironment Proteomics: Lessons From Multiple Myeloma. PMID:33833982
The prognostic significance of tumor-infiltrating lymphocytes in cervical cancer. PMID:33825354
CRISPR-cas9 Screening Identified Lethal Genes Enriched in Cell Cycle Pathway and of Prognosis Significance in Breast Cancer. PMID:33816496
Immunogenomic Profiling Demonstrate AC003092.1 as an Immune-Related eRNA in Glioblastoma Multiforme. PMID:33815468
Identification of Decrease in TRiC Proteins as Novel Targets of Alpha-Amanitin-Derived Hepatotoxicity by Comparative Proteomic Analysis In Vitro. PMID:33803263
A Streamlined Approach to Pathway Analysis from RNA-Sequencing Data. PMID:33802642
Named Data Networking for Genomics Data Management and Integrated Workflows. PMID:33748749
STATegra: Multi-Omics Data Integration - A Conceptual Scheme With a Bioinformatics Pipeline. PMID:33747045
RNA-seq analysis and gene expression dynamics in the salivary glands of the argasid tick Ornithodoros erraticus along the trophogonic cycle. PMID:33743776
Identification of disease treatment mechanisms through the multiscale interactome. PMID:33741907
A multi-omic characterization of temperature stress in a halotolerant Scenedesmus strain for algal biotechnology. PMID:33712730
Unveiling the long non-coding RNA profile of porcine reproductive and respiratory syndrome virus-infected porcine alveolar macrophages. PMID:33711920
Short loop functional commonality identified in leukaemia proteome highlights crucial protein sub-networks. PMID:33709075
Analysing the yeast complexome-the Complex Portal rising to the challenge. PMID:33677561
The glycoconjugate ontology (GlycoCoO) for standardizing the annotation of glycoconjugate data and its application. PMID:33677548
HIR V2: a human interactome resource for the biological interpretation of differentially expressed genes via gene set linkage analysis. PMID:33677507
Putative Circulating MicroRNAs Are Able to Identify Patients with Mitral Valve Prolapse and Severe Regurgitation. PMID:33672625
Immune gene expression networks in sepsis: A network biology approach. PMID:33667236
Genome-wide association meta-analysis identifies pleiotropic risk loci for aerodigestive squamous cell cancers. PMID:33667223
Network pharmacology and RNA-sequencing reveal the molecular mechanism of Xuebijing injection on COVID-19-induced cardiac dysfunction. PMID:33662681
Structural and functional study of Legionella pneumophila effector RavA. PMID:33660322
HoSeIn: A Workflow for Integrating Various Homology Search Results from Metagenomic and Metatranscriptomic Sequence Datasets. PMID:33659350
Complete genome sequencing of Bacillus sp. TK-2, analysis of its cold evolution adaptability. PMID:33649356
Role of circular RNA expression in the pathological progression after spinal cord injury. PMID:33642393
The Paradoxical Behavior of microRNA-211 in Melanomas and Other Human Cancers. PMID:33628737
Genome-wide ancestry and introgression in a Zambian baboon hybrid zone. PMID:33624366
Ontology-guided segmentation and object identification for developmental mouse lung immunofluorescent images. PMID:33622235
Size changes in miR‑21 knockout mice: Geometric morphometrics on teeth, alveolar bone and mandible. PMID:33604680
Ferroptosis-related gene signature as a prognostic marker for lower-grade gliomas. PMID:33594759
A Meta-Analysis of the Effects of High-LET Ionizing Radiations in Human Gene Expression. PMID:33546472
Network mapping of primary CD34+ cells by Ampliseq based whole transcriptome targeted resequencing identifies unexplored differentiation regulatory relationships. PMID:33544756
Sialotranscriptomics of the argasid tick Ornithodoros moubata along the trophogonic cycle. PMID:33544727
Transcriptomic Analysis of the Anthocyanin Biosynthetic Pathway Reveals the Molecular Mechanism Associated with Purple Color Formation in Dendrobium Nestor. PMID:33540822
GeneWalk identifies relevant gene functions for a biological context using network representation learning. PMID:33526072
Genomics Reveals the Origins of Historical Specimens. PMID:33502509
Amino Acid Composition in Various Types of Nucleic Acid-Binding Proteins. PMID:33477647
Bioinformatics analysis of miRNA and mRNA expression profiles to reveal the key miRNAs and genes in osteoarthritis. PMID:33468167
Transcriptional regulation of alcohol induced liver fibrosis in a translational porcine hepatocellular carcinoma model. PMID:33444661
Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients. PMID:33441124
A novel Foxp3-related immune prognostic signature for glioblastoma multiforme based on immunogenomic profiling. PMID:33429364
Integrative Analysis Reveals Common and Unique Roles of Tetraspanins in Fibrosis and Emphysema. PMID:33424923
Automated Extraction of Information From Texts of Scientific Publications: Insights Into HIV Treatment Strategies. PMID:33414815
RGS2-mediated translational control mediates cancer cell dormancy and tumor relapse. PMID:33393490
Integrated Analysis of Key Pathways and Drug Targets Associated With Vogt-Koyanagi-Harada Disease. PMID:33384687
A Clinical Extensively-Drug Resistant (XDR) Escherichia coli and Role of Its β-Lactamase Genes. PMID:33362736
Predictive network modeling in human induced pluripotent stem cells identifies key driver genes for insulin responsiveness. PMID:33362275
Identify and Validate the Transcriptomic, Functional Network, and Predictive Validity of FBXL19-AS1 in Hepatocellular Carcinoma. PMID:33344260
The underlying molecular mechanism and identification of transcription factor markers for laryngeal squamous cell carcinoma. PMID:33315534
Immunogenetic and tolerance strategies against a novel parasitoid of wild field crickets. PMID:33304539
Identification of Key Genes and Potential New Biomarkers for Ovarian Aging: A Study Based on RNA-Sequencing Data. PMID:33304387
Common Factors in Neurodegeneration: A Meta-Study Revealing Shared Patterns on a Multi-Omics Scale. PMID:33302607
Comparative proteomics of common allergenic tree pollens of birch, alder, and hazel. PMID:33301602
Comprehensive gene expression profiling of human astrocytes treated with a hepatic encephalopathy-inducible factor, alpha 1-antichymotripsin. PMID:33299931
Proteomic Profiling Change and Its Implies in the Early Mycosis Fungoides (MF) Using Isobaric Tags for Relative and Absolute Quantification (iTRAQ). PMID:33299887
Characterization and validation of long noncoding RNAs as new candidates in prostate cancer. PMID:33292248
The Gene Ontology resource: enriching a GOld mine. PMID:33290552
multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data. PMID:33287694
Next Generation Sequencing Identify Rare Copy Number Variants in Non-syndromic Patent Ductus Arteriosus. PMID:33281884
An Automated Functional Annotation Pipeline That Rapidly Prioritizes Clinically Relevant Genes for Autism Spectrum Disorder. PMID:33261099
Comparative transcriptomic analysis of antimony resistant and susceptible Leishmania infantum lines. PMID:33256787
Transcriptional Remodeling Patterns in Murine Dendritic Cells Infected with Paracoccidioides brasiliensis: More Is Not Necessarily Better. PMID:33255176
scREAD: A Single-Cell RNA-Seq Database for Alzheimer's Disease. PMID:33241205
Genetic profiling for diffuse type and genomically stable subtypes in gastric cancer. PMID:33240471
Identification and analysis of immune-related subtypes of hepatocellular carcinoma. PMID:33231514
Identification and quantification of target metabolites combined with transcriptome of two rheum species focused on anthraquinone and flavonoids biosynthesis. PMID:33219248
Predicted rat interactome database and gene set linkage analysis. PMID:33216897
A fusion of CD63-BCAR4 identified in lung adenocarcinoma promotes tumorigenicity and metastasis. PMID:33204025
Treatment of keloids through Runx2 siRNA‑induced inhibition of the PI3K/AKT signaling pathway. PMID:33200804
Proteomic analysis of human cervical adenocarcinoma mucus to identify potential protein biomarkers. PMID:33194326
GelFAP: Gene Functional Analysis Platform for Gastrodia elata. PMID:33193491
A six-amino-acid motif is a major determinant in functional evolution of HOX1 proteins. PMID:33184220
A methodology for predicting tissue-specific metabolic roles of receptors applied to subcutaneous adipose. PMID:33177567
A novel method of high-purity extracellular vesicle enrichment from microliter-scale human serum for proteomic analysis. PMID:33169421
Genome-wide analysis of acute traumatic spinal cord injury-related RNA expression profiles and uncovering of a regulatory axis in spinal fibrotic scars. PMID:33150698
Stromal microenvironment promoted infiltration in esophageal adenocarcinoma and squamous cell carcinoma: a multi-cohort gene-based analysis. PMID:33122682
The Broad Transcription Factor Links Hormonal Signaling, Gene Expression, and Cellular Morphogenesis Events During Drosophila Imaginal Disc Development. PMID:33115752
Preclinical validation of therapeutic targets predicted by tensor factorization on heterogeneous graphs. PMID:33106501
A genome-wide association study of severe asthma exacerbations in Latino children and adolescents. PMID:33093117
Interferon-Mediated Long Non-Coding RNA Response in Macrophages in the Context of HIV. PMID:33086748
Coronavirus: proteomics analysis of chicken kidney tissue infected with variant 2 (IS-1494)-like avian infectious bronchitis virus. PMID:33083914
Genomic signatures of globally enhanced gene duplicate accumulation in the megadiverse higher Diptera fueling intralocus sexual conflict resolution. PMID:33083121
Predicted functional interactome of Caenorhabditis elegans and a web tool for the functional interpretation of differentially expressed genes. PMID:33076954
Neurogranin, Encoded by the Schizophrenia Risk Gene NRGN, Bidirectionally Modulates Synaptic Plasticity via Calmodulin-Dependent Regulation of the Neuronal Phosphoproteome. PMID:33032807
GeneSetCluster: a tool for summarizing and integrating gene-set analysis results. PMID:33028195
lncRNAKB, a knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA. PMID:33020484
Ancient RNA virus epidemics through the lens of recent adaptation in human genomes. PMID:33012231
Identification of putative master regulators in rheumatoid arthritis synovial fibroblasts using gene expression data and network inference. PMID:33004899
GNG5 is an unfavourable independent prognostic indicator of gliomas. PMID:33000557
Matrix Metallopeptidase 14: A Candidate Prognostic Biomarker for Diffuse Large B-Cell Lymphoma. PMID:32974187
The similarity of inherited diseases (II): clinical and biological similarity between the phenotypic series. PMID:32972400
Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing. PMID:32962098
Overexpression of novel long intergenic non‑coding RNA LINC02454 is associated with a poor prognosis in papillary thyroid cancer. PMID:32945494
A Quantitative Proteome Map of the Human Body. PMID:32916130
DNA methylation study of Huntington's disease and motor progression in patients and in animal models. PMID:32913184
PCOSKBR2: a database of genes, diseases, pathways, and networks associated with polycystic ovary syndrome. PMID:32895427
Mass spectrometry-based analysis of formalin-fixed, paraffin-embedded distal cholangiocarcinoma identifies stromal thrombospondin-2 as a potential prognostic marker. PMID:32887625
Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management. PMID:32883995
Dissecting Transcription Factor-Target Interaction in Bovine Coronavirus Infection. PMID:32872640
DEAD-Box Helicase 4 (Ddx4)+ Stem Cells Sustain Tumor Progression in Non-Serous Ovarian Cancers. PMID:32847044
Single-Cell Transcriptome Analysis of Colon Cancer Cell Response to 5-Fluorouracil-Induced DNA Damage. PMID:32846134
Mito-oncology agent: fermented extract suppresses the Warburg effect, restores oxidative mitochondrial activity, and inhibits in vivo tumor growth. PMID:32843660
HIF-1α and HIF-2α differently regulate tumour development and inflammation of clear cell renal cell carcinoma in mice. PMID:32807776
Deciphering serous ovarian carcinoma histopathology and platinum response by convolutional neural networks. PMID:32807164
Sex-Specific Transcriptome Differences in Human Adipose Mesenchymal Stem Cells. PMID:32784482
Molecular Signatures and Networks of Cardiomyocyte Differentiation in Humans and Mice. PMID:32769060
The regulatory genome constrains protein sequence evolution: implications for the search for disease-associated genes. PMID:32765967
Bioinformatic screening and identification of downregulated hub genes in adrenocortical carcinoma. PMID:32765768
An interspecies translation model implicates integrin signaling in infliximab-resistant inflammatory bowel disease. PMID:32753478
The Anatomy of the SARS-CoV-2 Biomedical Literature: Introducing the CovidX Network Algorithm for Drug Repurposing Recommendation. PMID:32735546
GADL1 is a multifunctional decarboxylase with tissue-specific roles in β-alanine and carnosine production. PMID:32733999
Network Pharmacology-Based Analysis of the Pharmacological Mechanisms of Aloperine on Cardiovascular Disease. PMID:32733582
Salt stress induces endoplasmic reticulum stress-responsive genes in a grapevine rootstock. PMID:32730292
Genome-wide effect of tetracycline, doxycycline and 4-epidoxycycline on gene expression in Saccharomyces cerevisiae. PMID:32726865
Tumorigenic effects of TLX overexpression in HEK 293T cells. PMID:32721119
Identification of Four Potential Biomarkers Associated With Coronary Artery Disease in Non-diabetic Patients by Gene Co-expression Network Analysis. PMID:32714363
Computational Analysis of the Global Effects of Ly6E in the Immune Response to Coronavirus Infection Using Gene Networks. PMID:32708319
Identification of potential markers for type 2 diabetes mellitus via bioinformatics analysis. PMID:32705173
Single-Cell Transcriptomic Profiling of Vascular Smooth Muscle Cell Phenotype Modulation in Marfan Syndrome Aortic Aneurysm. PMID:32698686
Identification of COVID-19 Infection-Related Human Genes Based on a Random Walk Model in a Virus-Human Protein Interaction Network. PMID:32685484
Identification of differentially expressed metastatic genes and their signatures to predict the overall survival of uveal melanoma patients by bioinformatics analysis. PMID:32685390
Integrative analysis of competitive endogenous RNA network reveals the regulatory role of non-coding RNAs in high-glucose-induced human retinal endothelial cells. PMID:32655995
Comparative proteomic analysis of human mesenchymal stromal cell behavior on calcium phosphate ceramics with different osteoinductive potential. PMID:32642640
Proteome analysis revealed the essential functions of protein phosphatase PP2A in the induction of Th9 cells. PMID:32620893
Adipose tissue in health and disease through the lens of its building blocks. PMID:32591560
Co-expression network analysis identifies a gene signature as a predictive biomarker for energy metabolism in osteosarcoma. PMID:32581649
Transcriptome profiling of venom gland from wasp species: de novo assembly, functional annotation, and discovery of molecular markers. PMID:32580761
Genome-wide transcriptome architecture in a mouse model of Gulf War Illness. PMID:32574576
Genome sequence of Kobresia littledalei, the first chromosome-level genome in the family Cyperaceae. PMID:32528014
GOcats: A tool for categorizing Gene Ontology into subgraphs of user-defined concepts. PMID:32525872
Gut-Brain Axis and Neurodegeneration: State-of-the-Art of Meta-Omics Sciences for Microbiota Characterization. PMID:32516966
Host-Virus Arms Races Drive Elevated Adaptive Evolution in Viral Receptors. PMID:32493827
A transcriptome-based approach to identify functional modules within and across primary human immune cells. PMID:32469933
Prognostic Value of a Stemness Index-Associated Signature in Primary Lower-Grade Glioma. PMID:32431729
Mining the role of angiopoietin-like protein family in gastric cancer and seeking potential therapeutic targets by integrative bioinformatics analysis. PMID:32410376
Galectin-3 modulates epithelial cell adaptation to stress at the ER-mitochondria interface. PMID:32398681
Comprehensive analysis of mutations of renal cell carcinoma in an autosomal dominant polycystic kidney disease patient. PMID:32384474
Genomic competition for noise reduction shaped evolutionary landscape of mir-4673. PMID:32376854
Tissue-selective regulation of protein homeostasis and unfolded protein response signalling in sporadic ALS. PMID:32324341
Identification of HO-1 as a novel biomarker for graft acute cellular rejection and prognosis prediction after liver transplantation. PMID:32309368
Impaired Metabolic Pathways Related to Colorectal Cancer Progression and Therapeutic Implications. PMID:32309224
DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases. PMID:32308806
Identification of Pan-Cancer Prognostic Biomarkers Through Integration of Multi-Omics Data. PMID:32300588
Modulation of stress and immune response by Amblyomin-X results in tumor cell death in a horse melanoma model. PMID:32286411
Investigation of miRNA and mRNA Co-expression Network in Ependymoma. PMID:32266223
Comprehensive gene and pathway analysis of cervical cancer progression. PMID:32256826
LncRNAs Predicted to Interfere With the Gene Regulation Activity of miR-637 and miR-196a-5p in GBM. PMID:32211330
Heterogeneity of chondrosarcomas response to irradiations with X-rays and carbon ions: A comparative study on five cell lines. PMID:32211283
Rewilding Nod2 and Atg16l1 Mutant Mice Uncovers Genetic and Environmental Contributions to Microbial Responses and Immune Cell Composition. PMID:32209431
Identification and validation of HELLS (Helicase, Lymphoid-Specific) and ICAM1 (Intercellular adhesion molecule 1) as potential diagnostic biomarkers of lung cancer. PMID:32195055
Effects of High-Dose Ionizing Radiation in Human Gene Expression: A Meta-Analysis. PMID:32178397
Identification of Biomarkers for Osteosarcoma Based on Integration Strategy. PMID:32173717
Loss of Cx43 in Murine Sertoli Cells Leads to Altered Prepubertal Sertoli Cell Maturation and Impairment of the Mitosis-Meiosis Switch. PMID:32164318
Screening and identification of critical biomarkers in erectile dysfunction: evidence from bioinformatic analysis. PMID:32161689
Systematic metadata analysis of brown rot fungi gene expression data reveals the genes involved in Fenton's reaction and wood decay process. PMID:32128279
An assessment of genome annotation coverage across the bacterial tree of life. PMID:32124724
ncRPheno: a comprehensive database platform for identification and validation of disease related noncoding RNAs. PMID:32122231
Stem Cell-Derived Endothelial Cell Model that Responds to Tobacco Smoke Like Primary Endothelial Cells. PMID:32119531
Genome sequence of the agarwood tree Aquilaria sinensis (Lour.) Spreng: the first chromosome-level draft genome in the Thymelaeceae family. PMID:32118265
Transcriptome differences in adipose stromal cells derived from pre- and postmenopausal women. PMID:32111240
Predicted Drosophila Interactome Resource and web tool for functional interpretation of differentially expressed genes. PMID:32103267
Enhancing reproducibility of gene expression analysis with known protein functional relationships: The concept of well-associated protein. PMID:32058996
Variations and expression features of CYP2D6 contribute to schizophrenia risk. PMID:32047265
A Network-Based Bioinformatics Approach to Identify Molecular Biomarkers for Type 2 Diabetes that Are Linked to the Progression of Neurological Diseases. PMID:32041280
Genomic characterization of Parengyodontium americanum sp. nov. PMID:32028048
Toward a gold standard for benchmarking gene set enrichment analysis. PMID:32026945
Genomic basis for RNA alterations in cancer. PMID:32025019
Clozapine-induced transcriptional changes in the zebrafish brain. PMID:32015324
Single-cell morphology encodes metastatic potential. PMID:32010778
Unveiling ncRNA regulatory axes in atherosclerosis progression. PMID:32009226
Machine Learning and Network Analyses Reveal Disease Subtypes of Pancreatic Cancer and their Molecular Characteristics. PMID:31988390
Lymphatic endothelial cells prime naïve CD8+ T cells into memory cells under steady-state conditions. PMID:31988323
ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets. PMID:31978042
Genome-wide meta-analysis associates GPSM1 with type 2 diabetes, a plausible gene involved in skeletal muscle function. PMID:31959871
Domain-mediated interactions for protein subfamily identification. PMID:31937869
Proteomics and Bioinformatics Analysis of Cartilage in Post-Traumatic Osteoarthritis in a Mini-Pig Model of Anterior Cruciate Ligament Repair. PMID:31916546
Local adaptation of a dominant coastal tree to freshwater availability and solar radiation suggested by genomic and ecophysiological approaches. PMID:31882752
Acute pancreatitis promotes the generation of two different exosome populations. PMID:31882721
A novel algorithm for alignment of multiple PPI networks based on simulated annealing. PMID:31881842
Identification of Regulatory Modules That Stratify Lupus Disease Mechanism through Integrating Multi-Omics Data. PMID:31877408
LePrimAlign: local entropy-based alignment of PPI networks to predict conserved modules. PMID:31874635
Translational Knowledge Discovery Between Drug Interactions and Pharmacogenetics. PMID:31863452
Transcriptional network dynamics during the progression of pluripotency revealed by integrative statistical learning. PMID:31853542
Next-generation hypomethylating agent SGI-110 primes acute myeloid leukemia cells to IAP antagonist by activating extrinsic and intrinsic apoptosis pathways. PMID:31831875
Identification of distinct blood-based biomarkers in early stage of Parkinson's disease. PMID:31828678
Epigenome-wide association of father's smoking with offspring DNA methylation: a hypothesis-generating study. PMID:31827900
Formal axioms in biomedical ontologies improve analysis and interpretation of associated data. PMID:31821406
Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization. PMID:31804475
Multivariable regulation of gene expression plasticity in metazoans. PMID:31795914
Prognostic genes of melanoma identified by weighted gene co-expression network analysis and drug repositioning using a network-based method. PMID:31788081
NNTox: Gene Ontology-Based Protein Toxicity Prediction Using Neural Network. PMID:31784686
Expression and potential prognostic value of histone family gene signature in breast cancer. PMID:31772649
Phylostratigraphic Analysis Shows the Earliest Origination of the Abiotic Stress Associated Genes in A. thaliana. PMID:31766757
TS-GOEA: a web tool for tissue-specific gene set enrichment analysis based on gene ontology. PMID:31760951
Metabolic gene alterations impact the clinical aggressiveness and drug responses of 32 human cancers. PMID:31754644
Gene Regulatory Network of Dorsolateral Prefrontal Cortex: a Master Regulator Analysis of Major Psychiatric Disorders. PMID:31728928
PCOSBase: a manually curated database of polycystic ovarian syndrome. PMID:31725861
A transcriptome-wide association study implicates specific pre- and post-synaptic abnormalities in schizophrenia. PMID:31691811
Melittin inhibits proliferation, migration and invasion of bladder cancer cells by regulating key genes based on bioinformatics and experimental assays. PMID:31691530
Astrovirus replication in human intestinal enteroids reveals multi-cellular tropism and an intricate host innate immune landscape. PMID:31671153
SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update. PMID:31665520
Rewiring of Cancer Cell Metabolism by Mitochondrial VDAC1 Depletion Results in Time-Dependent Tumor Reprogramming: Glioblastoma as a Proof of Concept. PMID:31661894
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. PMID:31647099
Elevated serum alpha-1 antitrypsin is a major component of GlycA-associated risk for future morbidity and mortality. PMID:31644575
An in silico Approach for Integrating Phenotypic and Target-based Approaches in Drug Discovery. PMID:31638744
Transcriptional Regulator TonEBP Mediates Oxidative Damages in Ischemic Kidney Injury. PMID:31635160
Druggable genome in attention deficit/hyperactivity disorder and its co-morbid conditions. New avenues for treatment. PMID:31628418
Chromatin profiling of cortical neurons identifies individual epigenetic signatures in schizophrenia. PMID:31624234
Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives. PMID:31614509
Changing expression profiles of lncRNAs, circRNAs and mRNAs in esophageal squamous carcinoma. PMID:31612046
KnockTF: a comprehensive human gene expression profile database with knockdown/knockout of transcription factors. PMID:31598675
Changes of Gene Expression in Euglena gracilis Obtained During the 29th DLR Parabolic Flight Campaign. PMID:31582787
Genomics Analysis of L-DOPA Exposure in Drosophila sechellia. PMID:31575638
Quantitative Proteomics of Uukuniemi Virus-host Cell Interactions Reveals GBF1 as Proviral Host Factor for Phleboviruses. PMID:31570497
Translational offsetting as a mode of estrogen receptor α-dependent regulation of gene expression. PMID:31556460
LINC00461 affects the survival of patients with renal cell carcinoma by acting as a competing endogenous RNA for microRNA‑942. PMID:31545458
Lossless Compression of Binary Trees with Correlated Vertex Names. PMID:31537945
Exploring the Pathological Mechanism of Bladder Cancer Based on Tumor Mutational Burden Analysis. PMID:31534952
RCSB Protein Data Bank: Enabling biomedical research and drug discovery. PMID:31531901
Enabling Web-scale data integration in biomedicine through Linked Open Data. PMID:31531395
Exosomal miR-1246 in serum as a potential biomarker for early diagnosis of gastric cancer. PMID:31506750
Gene-diet interactions associated with complex trait variation in an advanced intercross outbred mouse line. PMID:31506438
Low complexity regions in the proteins of prokaryotes perform important functional roles and are highly conserved. PMID:31504783
Gene Cascade Finder: A tool for identification of gene cascades and its application in Caenorhabditis elegans. PMID:31504044
SamPler - a novel method for selecting parameters for gene functional annotation routines. PMID:31488049
Extensive Thioautotrophic Gill Endosymbiont Diversity within a Single Ctena orbiculata (Bivalvia: Lucinidae) Population and Implications for Defining Host-Symbiont Specificity and Species Recognition. PMID:31455638
Toward understanding the origin and evolution of cellular organisms. PMID:31441146
Replication timing networks reveal a link between transcription regulatory circuits and replication timing control. PMID:31434679
Five genes may predict metastasis in non-small cell lung cancer using bioinformatics analysis. PMID:31423239
A Nutrigenomics Approach Using RNA Sequencing Technology to Study Nutrient-Gene Interactions in Agricultural Animals. PMID:31414073
CAG Repeat Not Polyglutamine Length Determines Timing of Huntington's Disease Onset. PMID:31398342
Analysis of Protein-Protein Functional Associations by Using Gene Ontology and KEGG Pathway. PMID:31396531
Head Start Immunity: Characterizing the Early Protection of C Strain Vaccine Against Subsequent Classical Swine Fever Virus Infection. PMID:31396205
GRAPHICAL MODELS FOR ZERO-INFLATED SINGLE CELL GENE EXPRESSION. PMID:31388390
Avian Binocularity and Adaptation to Nocturnal Environments: Genomic Insights from a Highly Derived Visual Phenotype. PMID:31386143
Cholestatic liver disease results increased production of reactive aldehydes and an atypical periportal hepatic antioxidant response. PMID:31377417
The Evolution of Gene Duplicates in Angiosperms and the Impact of Protein-Protein Interactions and the Mechanism of Duplication. PMID:31364708
Precise and systematic survey of the efficacy of multicomponent drugs against functional dyspepsia. PMID:31341240
Identification of Gene Changes Induced by Dexamethasone in the Anterior Segment of the Human Eye Using Bioinformatics Analysis. PMID:31339875
SMAC, a computational system to link literature, biomedical and expression data. PMID:31324861
Improved detection of common variants in coronary artery disease and blood pressure using a pleiotropy cFDR method. PMID:31316127
A gene expression network analysis of the pancreatic islets from lean and obese mice identifies complement 1q like-3 secreted protein as a regulator of β-cell function. PMID:31300714
Simultaneous Enrichment Analysis of all Possible Gene-sets: Unifying Self-Contained and Competitive Methods. PMID:31297505
Inhibiting ubiquitination causes an accumulation of SUMOylated newly synthesized nuclear proteins at PML bodies. PMID:31285264
Integrating proteomics and transcriptomics for the identification of potential targets in early colorectal cancer. PMID:31268166
A systems biology pipeline identifies regulatory networks for stem cell engineering. PMID:31267104
GAIL: An interactive webserver for inference and dynamic visualization of gene-gene associations based on gene ontology guided mining of biomedical literature. PMID:31260503
Experimental Acute Exposure to Thirdhand Smoke and Changes in the Human Nasal Epithelial Transcriptome: A Randomized Clinical Trial. PMID:31251375
metaQuantome: An Integrated, Quantitative Metaproteomics Approach Reveals Connections Between Taxonomy and Protein Function in Complex Microbiomes. PMID:31235611
T cell receptor signaling pathway and cytokine-cytokine receptor interaction affect the rehabilitation process after respiratory syncytial virus infection. PMID:31223533
Literature-Based Enrichment Insights into Redox Control of Vascular Biology. PMID:31223421
Microhomology-mediated end joining drives complex rearrangements and overexpression of MYC and PVT1 in multiple myeloma. PMID:31221783
Computational identification of protein-protein interactions in model plant proteomes. PMID:31217453
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. PMID:31209238
Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution. PMID:31206013
Expanding Alternative Splicing Identification by Integrating Multiple Sources of Transcription Data in Tomato. PMID:31191588
Characterization of a prognostic four‑gene methylation signature associated with radiotherapy for head and neck squamous cell carcinoma. PMID:31180552
RNA‑seq analyses of antibiotic resistance mechanisms in Serratia marcescens. PMID:31180518
Using a Multi-Stage hESC Model to Characterize BDE-47 Toxicity during Neurogenesis. PMID:31173147
Recent trends in molecular diagnostics of yeast infections: from PCR to NGS. PMID:31158289
Maize transcriptomic repertoires respond to gibberellin stimulation. PMID:31144186
Transcriptomics Analysis Reveals New Insights into the Roles of Notch1 Signaling on Macrophage Polarization. PMID:31142802
Integrating yeast chemical genomics and mammalian cell pathway analysis. PMID:31138898
Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk. PMID:31133750
Immunological Molecular Responses of Human Retinal Pigment Epithelial Cells to Infection With Toxoplasma gondii. PMID:31118929
A hypergraph-based method for large-scale dynamic correlation study at the transcriptomic scale. PMID:31117943
Metabolic Remodeling during Biofilm Development of Bacillus subtilis. PMID:31113899
Retinal Gene Distribution and Functionality Implicated in Inherited Retinal Degenerations Can Reveal Disease-Relevant Pathways for Pharmacologic Intervention. PMID:31108889
Identification of an early cell fate regulator by detecting dynamics in transcriptional heterogeneity and co-regulation during astrocyte differentiation. PMID:31098297
DEEPred: Automated Protein Function Prediction with Multi-task Feed-forward Deep Neural Networks. PMID:31089211
Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity. PMID:31080084
Multi-omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency. PMID:31078527
Pathway-specific protein domains are predictive for human diseases. PMID:31075101
GScluster: network-weighted gene-set clustering analysis. PMID:31072324
Return to the Sea, Get Huge, Beat Cancer: An Analysis of Cetacean Genomes Including an Assembly for the Humpback Whale (Megaptera novaeangliae). PMID:31070747
Genetic mechanism underlying sexual plasticity and its association with colour patterning in zebrafish (Danio rerio). PMID:31060508
What Changed on the Folliculogenesis in the Process of Mouse Ovarian Aging? PMID:31058188
Autism risk genes are evolutionarily ancient and maintain a unique feature landscape that echoes their function. PMID:31025836
EDAR, LYPLAL1, PRDM16, PAX3, DKK1, TNFSF12, CACNA2D3, and SUPT3H gene variants influence facial morphology in a Eurasian population. PMID:31025105
Postovulatory maternal transcriptome in Atlantic salmon and its relation to developmental potential of embryos. PMID:31014241
Integration of Multiple Data Sources for Gene Network Inference Using Genetic Perturbation Data. PMID:31009236
AXL knockdown gene signature reveals a drug repurposing opportunity for a class of antipsychotics to reduce growth and metastasis of triple-negative breast cancer. PMID:31007848
Prediction of seed gene function in progressive diabetic neuropathy by a network-based inference method. PMID:31007748
Identification of noncoding RNA expression profiles and regulatory interaction networks following traumatic spinal cord injury by sequence analysis. PMID:30998503
Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation. PMID:30976019
In silico Characterization of Human Prion-Like Proteins: Beyond Neurological Diseases. PMID:30971948
Genome sequence analysis of the fairy ring-forming fungus Lepista sordida and gene candidates for interaction with plants. PMID:30971747
New Zealand Tree and Giant Wētā (Orthoptera) Transcriptomics Reveal Divergent Selection Patterns in Metabolic Loci. PMID:30957857
Preeclampsia-Associated Alteration of DNA Methylation in Fetal Endothelial Progenitor Cells. PMID:30949477
Transcriptome-wide analysis of the difference of alternative splicing in susceptible and resistant silkworm strains after BmNPV infection. PMID:30944799
miR‑146a‑5p expression is upregulated by the CXCR4 antagonist TN14003 and attenuates SDF‑1‑induced cartilage degradation. PMID:30942441
MSTD: an efficient method for detecting multi-scale topological domains from symmetric and asymmetric 3D genomic maps. PMID:30941409
Identification of SERPINE1, PLAU and ACTA1 as biomarkers of head and neck squamous cell carcinoma based on integrated bioinformatics analysis. PMID:30937621
A Network Module for the Perseus Software for Computational Proteomics Facilitates Proteome Interaction Graph Analysis. PMID:30931570
GO functional similarity clustering depends on similarity measure, clustering method, and annotation completeness. PMID:30917779
Compositional epistasis detection using a few prototype disease models. PMID:30917131
Genomic Variants Among Threatened Acropora Corals. PMID:30914426
Gene expression imputation across multiple brain regions provides insights into schizophrenia risk. PMID:30911161
Prediction of key gene function in spinal muscular atrophy using guilt by association method based on network and gene ontology. PMID:30906446
Identification of Candidate Genes and MicroRNAs for Acute Myocardial Infarction by Weighted Gene Coexpression Network Analysis. PMID:30886860
PRISMA: Protein Interaction Screen on Peptide Matrix Reveals Interaction Footprints and Modifications- Dependent Interactome of Intrinsically Disordered C/EBPβ. PMID:30884312
RNAi-based small molecule repositioning reveals clinically approved urea-based kinase inhibitors as broadly active antivirals. PMID:30883607
Precision drug repurposing via convergent eQTL-based molecules and pathway targeting independent disease-associated polymorphisms. PMID:30864332
Identification of co-expression modules and pathways correlated with osteosarcoma and its metastasis. PMID:30849987
How to Develop a Drug Target Ontology: KNowledge Acquisition and Representation Methodology (KNARM). PMID:30848456
Investigating the role of Osiris genes in Drosophila sechellia larval resistance to a host plant toxin. PMID:30847082
Regulation of Intronic Polyadenylation by PCF11 Impacts mRNA Expression of Long Genes. PMID:30840896
CSgator: an integrated web platform for compound set analysis. PMID:30830479
Isoform-specific GSK3A activity is negatively correlated with human sperm motility. PMID:30824926
Identification of Essential Proteins Based on Improved HITS Algorithm. PMID:30823614
Genetic meta-analysis of diagnosed Alzheimer's disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing. PMID:30820047
The evolution of gene regulatory networks controlling Arabidopsis thaliana L. trichome development. PMID:30813891
JNK modifies neuronal metabolism to promote proteostasis and longevity. PMID:30810280
Handling Big Data Scalability in Biological Domain Using Parallel and Distributed Processing: A Case of Three Biological Semantic Similarity Measures. PMID:30809545
Identification of common genetic risk variants for autism spectrum disorder. PMID:30804558
Repository of Enriched Structures of Proteins Involved in the Red Blood Cell Environment (RESPIRE). PMID:30794542
SuCComBase: a manually curated repository of plant sulfur-containing compounds. PMID:30793170
Identification of Potential Key Genes and Pathways in Early-Onset Colorectal Cancer Through Bioinformatics Analysis. PMID:30786729
Indoxyl Sulfate Induces Apoptosis Through Oxidative Stress and Mitogen-Activated Protein Kinase Signaling Pathway Inhibition in Human Astrocytes. PMID:30764571
A Genome-Scale Co-Functional Network of Xanthomonas Genes Can Accurately Reconstruct Regulatory Circuits Controlled by Two-Component Signaling Systems. PMID:30759970
Enhanced Growth of Pilin-Deficient Geobacter sulfurreducens Mutants in Carbon Poor and Electron Donor Limiting Conditions. PMID:30759269
Longitudinal investigation of DNA methylation changes preceding adolescent psychotic experiences. PMID:30718501
Identification of the targets of hematoporphyrin derivative in lung adenocarcinoma using integrated network analysis. PMID:30717818
CircFunBase: a database for functional circular RNAs. PMID:30715276
Transcriptome Analysis of Mesenchymal Stem Cells from Multiple Myeloma Patients Reveals Downregulation of Genes Involved in Cell Cycle Progression, Immune Response, and Bone Metabolism. PMID:30705326
Conserved regulation of RNA processing in somatic cell reprogramming. PMID:30704403
The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function. PMID:30698741
Deterministic column subset selection for single-cell RNA-Seq. PMID:30682053
The Genetic Structures of an Extensively Drug Resistant (XDR) Klebsiella pneumoniae and Its Plasmids. PMID:30662878
Proteomic analysis of the rice (Oryza officinalis) provides clues on molecular tagging of proteins for brown planthopper resistance. PMID:30658570
Identification of Prognostic Biomarker Signatures and Candidate Drugs in Colorectal Cancer: Insights from Systems Biology Analysis. PMID:30658502
Single cell functional genomics reveals the importance of mitochondria in cell-to-cell phenotypic variation. PMID:30638445
GOTrapper: a tool to navigate through branches of gene ontology hierarchy. PMID:30634902
Computational translation of genomic responses from experimental model systems to humans. PMID:30629591
Epigallocatechin‑3‑gallate modulates long non‑coding RNA and mRNA expression profiles in lung cancer cells. PMID:30628683
The transcriptome landscape of the carcinogenic treatment response in the blind mole rat: insights into cancer resistance mechanisms. PMID:30621584
Quantitative Proteomics of Potato Leaves Infected with Phytophthora infestans Provides Insights into Coordinated and Altered Protein Expression during Early and Late Disease Stages. PMID:30609684
Low Expression of the Androgen-Induced Tumor Suppressor Gene PLZF and Lethal Prostate Cancer. PMID:30602500
Optimizing gene set annotations combining GO structure and gene expression data. PMID:30598093
Classification of Widely and Rarely Expressed Genes with Recurrent Neural Network. PMID:30595815
Arabidopsis thaliana responds to colonisation of Piriformospora indica by secretion of symbiosis-specific proteins. PMID:30589877
FELLA: an R package to enrich metabolomics data. PMID:30577788
Dosage Compensation of the X Chromosomes in Bovine Germline, Early Embryos, and Somatic Tissues. PMID:30566637
Bone Marrow-Derived Proangiogenic Cells Mediate Pulmonary Arteriole Stiffening via Serotonin 2B Receptor Dependent Mechanism. PMID:30566041
Identification of genes associated with cancer progression and prognosis in lung adenocarcinoma: Analyses based on microarray from Oncomine and The Cancer Genome Atlas databases. PMID:30556321
Genome survey sequencing for the characterization of genetic background of Dracaena cambodiana and its defense response during dragon's blood formation. PMID:30550595
Identification of key genes and pathways in diabetic nephropathy by bioinformatics analysis. PMID:30536626
Gene ontology improves template selection in comparative protein docking. PMID:30520123
Comprehensive Analysis of BAP1 Somatic Mutation in Clear Cell Renal Cell Carcinoma to Explore Potential Mechanisms in Silico. PMID:30519310
The subcellular organisation of Saccharomyces cerevisiae. PMID:30503867
Impact of human milk on the transcriptomic response of fetal intestinal epithelial cells reveals expression changes of immune-related genes. PMID:30499575
Genomics of neonatal sepsis: has-miR-150 targeting BCL11B functions in disease progression. PMID:30497506
Selective expansion of myeloid and NK cells in humanized mice yields human-like vaccine responses. PMID:30487575
A new method for evaluating the impacts of semantic similarity measures on the annotation of gene sets. PMID:30481204
Discovery of the first genome-wide significant risk loci for attention deficit/hyperactivity disorder. PMID:30478444
Adipocyte-secreted BMP8b mediates adrenergic-induced remodeling of the neuro-vascular network in adipose tissue. PMID:30478315
From sequencing data to gene functions: co-functional network approaches. PMID:30460054
BioGraph: a web application and a graph database for querying and analyzing bioinformatics resources. PMID:30458802
Assembly of a parts list of the human mitotic cell cycle machinery. PMID:30452682
Elevation in Cell Cycle and Protein Metabolism Gene Transcription in Inactive Colonic Tissue From Icelandic Patients With Ulcerative Colitis. PMID:30452647
Detection of correlated hidden factors from single cell transcriptomes using Iteratively Adjusted-SVA (IA-SVA). PMID:30451954
funcExplorer: a tool for fast data-driven functional characterisation of high-throughput expression data. PMID:30428831
Dynamics of the Phanerochaete carnosa transcriptome during growth on aspen and spruce. PMID:30424733
Higher-order molecular organization as a source of biological function. PMID:30423061
Born to Cry: A Genetic Dissection of Infant Vocalization. PMID:30420800
Lung fibroblasts express a miR-19a-19b-20a sub-cluster to suppress TGF-β-associated fibroblast activation in murine pulmonary fibrosis. PMID:30413725
Identification of critically carcinogenesis-related genes in basal cell carcinoma. PMID:30410353
Human Disease Ontology 2018 update: classification, content and workflow expansion. PMID:30407550
Identification of key differentially expressed MicroRNAs in cancer patients through pan-cancer analysis. PMID:30384176
Comparative Gene Expression Analysis in WM164 Melanoma Cells Revealed That β-β-Dimethylacrylshikonin Leads to ROS Generation, Loss of Mitochondrial Membrane Potential, and Autophagy Induction. PMID:30380804
OrthoInspector 3.0: open portal for comparative genomics. PMID:30380106
Species-level functional profiling of metagenomes and metatranscriptomes. PMID:30377376
Predicting bioprocess targets of chemical compounds through integration of chemical-genetic and genetic interactions. PMID:30376562
Cytogenetic and Transcriptomic Analysis of Human Endometrial MSC Retaining Proliferative Activity after Sublethal Heat Shock. PMID:30366433
ETCM: an encyclopaedia of traditional Chinese medicine. PMID:30365030
Overlapping Patterns of Gene Expression Between Gametophyte and Sporophyte Phases in the Fern Polypodium amorphum (Polypodiales). PMID:30356815
The biological embedding of early-life socioeconomic status and family adversity in children's genome-wide DNA methylation. PMID:30351206
An integrative tissue-network approach to identify and test human disease genes. PMID:30346941
Unveiling gibberellin-responsive coding and long noncoding RNAs in maize. PMID:30341662
Trendy: segmented regression analysis of expression dynamics in high-throughput ordered profiling experiments. PMID:30326833
EWASdb: epigenome-wide association study database. PMID:30321400
Targeting the endoplasmic reticulum-mitochondria interface sensitizes leukemia cells to cytostatics. PMID:30309851
Sequence Alterations of Cortical Genes Linked to Individual Connectivity of the Human Brain. PMID:30307489
Global identification and characterization of lncRNAs that control inflammation in malignant cholangiocytes. PMID:30305026
Classification, Ontology, and Precision Medicine. PMID:30304648
Overlapping clustering of gene expression data using penalized weighted normalized cut. PMID:30302823
The jPOST environment: an integrated proteomics data repository and database. PMID:30295851
Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes. PMID:30290830
Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties. PMID:30286077
Reprogramming of regulatory network using expression uncovers sex-specific gene regulation in Drosophila. PMID:30283019
Cardiac recovery via extended cell-free delivery of extracellular vesicles secreted by cardiomyocytes derived from induced pluripotent stem cells. PMID:30271672
Additional common variants associated with type 2 diabetes and coronary artery disease detected using a pleiotropic cFDR method. PMID:30270018
WEADE: A workflow for enrichment analysis and data exploration. PMID:30265728
Identification of Moonlighting Proteins in Genomes Using Text Mining Techniques. PMID:30260564
Topological alternate centrality measure capturing drug targets in the network of MAPK pathways. PMID:30259868
Single cell molecular alterations reveal target cells and pathways of concussive brain injury. PMID:30254269
Identification of a 3'-Untranslated Genetic Variant of RARB Associated With Carotid Intima-Media Thickness in Rheumatoid Arthritis: A Genome-Wide Association Study. PMID:30251476
MaxMIF: A New Method for Identifying Cancer Driver Genes through Effective Data Integration. PMID:30250803
Fenretinide targeting of human colon cancer sphere cells through cell cycle regulation and stress-responsive activities. PMID:30250604
Neurogenetic profiles delineate large-scale connectivity dynamics of the human brain. PMID:30250030
Genome-scale analysis of Acetobacterium bakii reveals the cold adaptation of psychrotolerant acetogens by post-transcriptional regulation. PMID:30249742
PGD: Pineapple Genomics Database. PMID:30245835
PalmXplore: oil palm gene database. PMID:30239681
Identification of tRNA-derived small noncoding RNAs as potential biomarkers for prediction of recurrence in triple-negative breast cancer. PMID:30239174
The FAK inhibitor BI 853520 exerts anti-tumor effects in breast cancer. PMID:30237500
Analysis of porcine body size variation using re-sequencing data of miniature and large pigs. PMID:30231878
Model organism data evolving in support of translational medicine. PMID:30224793
Conditional and interaction gene-set analysis reveals novel functional pathways for blood pressure. PMID:30218068
DNA methylation in adolescents with anxiety disorder: a longitudinal study. PMID:30218003
Discovery and characterization of conserved binding of eIF4E 1 (CBE1), a eukaryotic translation initiation factor 4E-binding plant protein. PMID:30213859
Genomic Profiling of BDE-47 Effects on Human Placental Cytotrophoblasts. PMID:30202865
An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures. PMID:30202034
Nuclear Factor I Represses the Notch Effector HEY1 in Glioblastoma. PMID:30195713
DES-Mutation: System for Exploring Links of Mutations and Diseases. PMID:30190574
Comparison of gene expression profiles between human erythroid cells derived from fetal liver and adult peripheral blood. PMID:30186694
ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes. PMID:30169674
Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences. PMID:30165572
Developing reduced SNP assays from whole-genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Apis mellifera iberiensis). PMID:30151039
Comprehensive innate immune profiling of chikungunya virus infection in pediatric cases. PMID:30150281
Numerous recursive sites contribute to accuracy of splicing in long introns in flies. PMID:30148878
Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation. PMID:30143032
The inconsistent regulation of HOXC13 on different keratins and the regulation mechanism on HOXC13 in cashmere goat (Capra hircus). PMID:30139327
Divergent brain gene expression patterns associate with distinct cell-specific tau neuropathology traits in progressive supranuclear palsy. PMID:30136084
Discovering Putative Prion-Like Proteins in Plasmodium falciparum: A Computational and Experimental Analysis. PMID:30131778
Developmental effects of maternal smoking during pregnancy on the human frontal cortex transcriptome. PMID:30131587
LncRNAs KB-1836B5, LINC00566 and FAM27L are associated with the survival time of patients with ovarian cancer. PMID:30127984
Selective gene dependencies in MYCN-amplified neuroblastoma include the core transcriptional regulatory circuitry. PMID:30127528
Efficient proximity labeling in living cells and organisms with TurboID. PMID:30125270
Approaches to target tractability assessment - a practical perspective. PMID:30108951
Impulse model-based differential expression analysis of time course sequencing data. PMID:30102402
CellBIC: bimodality-based top-down clustering of single-cell RNA sequencing data reveals hierarchical structure of the cell type. PMID:30102368
Computational resources associating diseases with genotypes, phenotypes and exposures. PMID:30102366
A multi-objective gene clustering algorithm guided by apriori biological knowledge with intensification and diversification strategies. PMID:30100924
Proteomic distinction of renal oncocytomas and chromophobe renal cell carcinomas. PMID:30087584
Examination of the shared genetic basis of anorexia nervosa and obsessive-compulsive disorder. PMID:30087453
HPO2GO: prediction of human phenotype ontology term associations for proteins using cross ontology annotation co-occurrences. PMID:30083448
An automated identification and analysis of ontological terms in gastrointestinal diseases and nutrition-related literature provides useful insights. PMID:30065857
Application of Transcriptomics to Compare the Carbohydrate Active Enzymes That Are Expressed by Diverse Genera of Anaerobic Fungi to Degrade Plant Cell Wall Carbohydrates. PMID:30061875
Creating a Structured AOP Knowledgebase via Ontology-Based Annotations. PMID:30057931
Epigenetic Variability Confounds Transcriptome but Not Proteome Profiling for Coexpression-based Gene Function Prediction. PMID:30042154
Using RegulonDB, the Escherichia coli K-12 Gene Regulatory Transcriptional Network Database. PMID:30040192
Differential aging of growth plate cartilage underlies differences in bone length and thus helps determine skeletal proportions. PMID:30036371
Potential biomarkers and therapeutic targets in cervical cancer: Insights from the meta-analysis of transcriptomics data within network biomedicine perspective. PMID:30020984
Integrative analysis of promising molecular biomarkers and pathways for coronary artery disease using WGCNA and MetaDE methods. PMID:30015926
Comprehensive analysis of gene expression profiles provides insight into the pathogenesis of Crohn's disease. PMID:30015893
Decoding the chromatin proteome of a single genomic locus by DNA sequencing. PMID:30005073
Genome-wide association meta-analysis of age at first cannabis use. PMID:30003630
E47 Governs the MYC-CDKN1B/p27KIP1-RB Network to Growth Arrest PDA Cells Independent of CDKN2A/p16INK4A and Wild-Type p53. PMID:30003124
The Complex Interaction of Mitochondrial Genetics and Mitochondrial Pathways in Psychiatric Disease. PMID:29998118
A new bioinformatics tool to help assess the significance of BRCA1 variants. PMID:29996917
Bioinformatics analysis to reveal the key genes related to obstructive sleep apnea. PMID:29992456
Phenotype-driven gene prioritization for rare diseases using graph convolution on heterogeneous networks. PMID:29980210
Quantifying compartment-associated variations of protein abundance in proteomics data. PMID:29967062
Clustering huge protein sequence sets in linear time. PMID:29959318
Genome-scale analysis identifies paralog lethality as a vulnerability of chromosome 1p loss in cancer. PMID:29955178
Gene prioritization using Bayesian matrix factorization with genomic and phenotypic side information. PMID:29949967
PrimAlign: PageRank-inspired Markovian alignment for large biological networks. PMID:29949962
PanACEA: a bioinformatics tool for the exploration and visualization of bacterial pan-chromosomes. PMID:29945570
dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments. PMID:29921301
Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data. PMID:29917034
Regular aspirin use and gene expression profiles in prostate cancer patients. PMID:29915914
Gene Discovery of Characteristic Metabolic Pathways in the Tea Plant (Camellia sinensis) Using 'Omics'-Based Network Approaches: A Future Perspective. PMID:29915604
Proteomic Architecture of Human Coronary and Aortic Atherosclerosis. PMID:29915101
Identification of the potential oncogenes in glioblastoma based on bioinformatic analysis and elucidation of the underlying mechanisms. PMID:29901201
Secretome Screening Reveals Fibroblast Growth Factors as Novel Inhibitors of Viral Replication. PMID:29899088
Identification of common coexpression modules based on quantitative network comparison. PMID:29897320
Cellular stress alters 3'UTR landscape through alternative polyadenylation and isoform-specific degradation. PMID:29891946
MU-LOC: A Machine-Learning Method for Predicting Mitochondrially Localized Proteins in Plants. PMID:29875778
MGOGP: a gene module-based heuristic algorithm for cancer-related gene prioritization. PMID:29871590
The SS18-SSX Fusion Oncoprotein Hijacks BAF Complex Targeting and Function to Drive Synovial Sarcoma. PMID:29861296
VarAFT: a variant annotation and filtration system for human next generation sequencing data. PMID:29860484
Benefit of Apabetalone on Plasma Proteins in Renal Disease. PMID:29854980
Word-of-Mouth Innovation: Hypothesis Generation for Supplement Repurposing based on Consumer Reviews. PMID:29854134
Computational Approach to Investigating Key GO Terms and KEGG Pathways Associated with CNV. PMID:29850576
A Domain-Specific Terminology for Retinopathy of Prematurity and Its Applications in Clinical Settings. PMID:29850007
Clinical Correlations of Transcriptional Profile in Patients Infected With Avian Influenza H7N9 Virus. PMID:29846612
Oxidative stress in female cancers. PMID:29805775
Identification and bioinformatics analysis of overlapping differentially expressed genes in depression, papillary thyroid cancer and uterine fibroids. PMID:29805500
Elevated Nrf-2 responses are insufficient to mitigate protein carbonylation in hepatospecific PTEN deletion mice. PMID:29799837
Sex-Specific Transcriptome Differences in Substantia Nigra Tissue: A Meta-Analysis of Parkinson's Disease Data. PMID:29799491
The combined effects of FADS gene variation and dietary fats in obesity-related traits in a population from the far north of Sweden: the GLACIER Study. PMID:29795460
Elevated histone H3 acetylation is associated with genes involved in T lymphocyte activation and glutamate decarboxylase antibody production in patients with type 1 diabetes. PMID:29791073
WEGO 2.0: a web tool for analyzing and plotting GO annotations, 2018 update. PMID:29788377
A genome-wide cross-trait analysis from UK Biobank highlights the shared genetic architecture of asthma and allergic diseases. PMID:29785011
Altered mitochondrial acetylation profiles in a kainic acid model of temporal lobe epilepsy. PMID:29778462
TelNet - a database for human and yeast genes involved in telomere maintenance. PMID:29776332
CoNVaQ: a web tool for copy number variation-based association studies. PMID:29776329
Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes. PMID:29761466
EuPathDB: The Eukaryotic Pathogen Genomics Database Resource. PMID:29761457
PomBase: The Scientific Resource for Fission Yeast. PMID:29761456
Structural biology data archiving - where we are and what lies ahead. PMID:29749603
Regulation of osteogenesis by long noncoding RNAs: An epigenetic mechanism contributing to bone formation. PMID:29745821
A Strategy for Discovery of Endocrine Interactions with Application to Whole-Body Metabolism. PMID:29719227
Sensing the cilium, digital capture of ciliary data for comparative genomics investigations. PMID:29713460
Functional and structural characterization of osteocytic MLO-Y4 cell proteins encoded by genes differentially expressed in response to mechanical signals in vitro. PMID:29712973
Knockout of the Gsta4 Gene in Male Mice Leads to an Altered Pattern of Hepatic Protein Carbonylation and Enhanced Inflammation Following Chronic Consumption of an Ethanol Diet. PMID:29708596
Germline pathogenic variants in PALB2 and other cancer-predisposing genes in families with hereditary diffuse gastric cancer without CDH1 mutation: a whole-exome sequencing study. PMID:29706558
Adaptations in energy metabolism and gene family expansions revealed by comparative transcriptomics of three Chagas disease triatomine vectors. PMID:29699489
Tumor-Independent Host Secretomes Induced By Angiogenesis and Immune-Checkpoint Inhibitors. PMID:29695634
Exploration of gene functions for esophageal squamous cell carcinoma using network-based guilt by association principle. PMID:29694510
Improved ontology-based similarity calculations using a study-wise annotation model. PMID:29688377
An epistatic effect of KRT25 on SP6 is involved in curly coat in horses. PMID:29686323
Bioinformatics challenges and perspectives when studying the effect of epigenetic modifications on alternative splicing. PMID:29685977
Comparative transcriptome analysis to investigate the potential role of miRNAs in milk protein/fat quality. PMID:29674689
Multiple large-scale gene and genome duplications during the evolution of hexapods. PMID:29674453
Menin regulates the serine biosynthetic pathway in Ewing sarcoma. PMID:29672864
Annotating activation/inhibition relationships to protein-protein interactions using gene ontology relations. PMID:29671402
WNT ligands control initiation and progression of human papillomavirus-driven squamous cell carcinoma. PMID:29662191
Detecting Disease Specific Pathway Substructures through an Integrated Systems Biology Approach. PMID:29657291
Gene-level differential analysis at transcript-level resolution. PMID:29650040
Reduction of Proliferating Olfactory Cells and Low Expression of Extracellular Matrix Genes Are Hallmarks of the Aged Olfactory Mucosa. PMID:29636678
Highly parallel genome variant engineering with CRISPR-Cas9. PMID:29632376
Cross-talk between monocyte invasion and astrocyte proliferation regulates scarring in brain injury. PMID:29632244
Open chromatin dynamics reveals stage-specific transcriptional networks in hiPSC-based neurodevelopmental model. PMID:29631039
Identification of PP1-Gadd34 substrates involved in the unfolded protein response using K-BIPS, a method for phosphatase substrate identification. PMID:29623310
Integrating images from multiple microscopy screens reveals diverse patterns of change in the subcellular localization of proteins. PMID:29620521
The Use of CRISPR/Cas9 Gene Editing to Confirm Congenic Contaminations in Host-Pathogen Interaction Studies. PMID:29616197
A comparative analysis of rod bipolar cell transcriptomes identifies novel genes implicated in night vision. PMID:29615777
Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss. PMID:29608732
Analyzing AbrB-Knockout Effects through Genome and Transcriptome Sequencing of Bacillus licheniformis DW2. PMID:29599755
Metazoan Parasite Vaccines: Present Status and Future Prospects. PMID:29594064
GENEASE: real time bioinformatics tool for multi-omics and disease ontology exploration, analysis and visualization. PMID:29590301
Systematic Characterization of Stress-Induced RNA Granulation. PMID:29576526
Systematic characterization of pan-cancer mutation clusters. PMID:29572294
Long non-coding RNAs RP5-821D11.7, APCDD1L-AS1 and RP11-277P12.9 were associated with the prognosis of lung squamous cell carcinoma. PMID:29568882
An LaeA- and BrlA-Dependent Cellular Network Governs Tissue-Specific Secondary Metabolism in the Human Pathogen Aspergillus fumigatus. PMID:29564395
QSurface: fast identification of surface expression markers in cancers. PMID:29560830
System analysis of the regulation of the immune response by CD147 and FOXC1 in cancer cell lines. PMID:29560120
Molecular Networks of Postia placenta Involved in Degradation of Lignocellulosic Biomass Revealed from Metadata Analysis of Open Access Gene Expression Data. PMID:29559843
Baseline mRNA expression differs widely between common laboratory strains of zebrafish. PMID:29555936
Identification of lncRNAs by microarray analysis reveals the potential role of lncRNAs in cervical cancer pathogenesis. PMID:29552195
Differential Phagocytic Properties of CD45low Microglia and CD45high Brain Mononuclear Phagocytes-Activation and Age-Related Effects. PMID:29552013
Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness. PMID:29549885
A comprehensive evaluation of module detection methods for gene expression data. PMID:29545622
PRR4: A novel downregulated gene in laryngeal cancer. PMID:29541239
Insulin resistance causes inflammation in adipose tissue. PMID:29528335
A Novel Five-Node Feed-Forward Loop Unravels miRNA-Gene-TF Regulatory Relationships in Ischemic Stroke. PMID:29524052
Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides. PMID:29521624
Proteomic analyses identify prognostic biomarkers for pancreatic ductal adenocarcinoma. PMID:29515771
Epistasis analysis of microRNAs on pathological stages in colon cancer based on an Empirical Bayesian Elastic Net method. PMID:29513198
Semantic biclustering for finding local, interpretable and predictive expression patterns. PMID:29513193
Identification of key genes and long non‑coding RNAs in celecoxib‑treated lung squamous cell carcinoma cell line by RNA‑sequencing. PMID:29512696
Prediction and characterization of human ageing-related proteins by using machine learning. PMID:29511309
Hereditary cancer genes are highly susceptible to splicing mutations. PMID:29505604
Using deep learning to model the hierarchical structure and function of a cell. PMID:29505029
FunGeneNet: a web tool to estimate enrichment of functional interactions in experimental gene sets. PMID:29504895
Gene expression in retinal ischemic post-conditioning. PMID:29504043
Phosphatidylserine-Liposomes Promote Tolerogenic Features on Dendritic Cells in Human Type 1 Diabetes by Apoptotic Mimicry. PMID:29491866
Gene expression models based on a reference laboratory strain are poor predictors of Mycobacterium tuberculosis complex transcriptional diversity. PMID:29491462
It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data. PMID:29490019
Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection. PMID:29483656
Codominant grasses differ in gene expression under experimental climate extremes in native tallgrass prairie. PMID:29473008
Network analysis of coronary artery disease risk genes elucidates disease mechanisms and druggable targets. PMID:29467471
Exploring autophagy with Gene Ontology. PMID:29455577
AOP-DB: A database resource for the exploration of Adverse Outcome Pathways through integrated association networks. PMID:29454060
Transcriptomics reveals a cross-modulatory effect between riboflavin and iron and outlines responses to riboflavin biosynthesis and uptake in Vibrio cholerae. PMID:29453341
A community approach to mortality prediction in sepsis via gene expression analysis. PMID:29449546
The BioCyc collection of microbial genomes and metabolic pathways. PMID:29447345
Diverse Regulators of Human Ribosome Biogenesis Discovered by Changes in Nucleolar Number. PMID:29444442
araGWAB: Network-based boosting of genome-wide association studies in Arabidopsis thaliana. PMID:29440686
Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology. PMID:29440116
Atomic structures of low-complexity protein segments reveal kinked β sheets that assemble networks. PMID:29439243
Identification and analysis of key genes in osteosarcoma using bioinformatics. PMID:29435005
Molecular Correlates of In Vitro Responses to Dacomitinib and Afatinib in Bladder Cancer. PMID:29430509
Differential gene expression induced by anti-cancer agent plumbagin is mediated by androgen receptor in prostate cancer cells. PMID:29426892
Comparative genomics reveals new single-nucleotide polymorphisms that can assist in identification of adherent-invasive Escherichia coli. PMID:29426864
Differences in MWCNT- and SWCNT-induced DNA methylation alterations in association with the nuclear deposition. PMID:29426343
Genome-Wide Association Study in African Americans with Acute Respiratory Distress Syndrome Identifies the Selectin P Ligand Gene as a Risk Factor. PMID:29425463
Human Cervical Mucus Plugs Exhibit Insufficiencies in Antimicrobial Activity Towards Group B Streptococcus. PMID:29425317
Enhancer redundancy provides phenotypic robustness in mammalian development. PMID:29420474
Region-Specific Methylation Profiling in Acute Myeloid Leukemia. PMID:29405013
Bio-SimVerb and Bio-SimLex: wide-coverage evaluation sets of word similarity in biomedicine. PMID:29402212
Decellularization and Solubilization of Porcine Liver for Use as a Substrate for Porcine Hepatocyte Culture: Method Optimization and Comparison. PMID:29390876
DIBS: a repository of disordered binding sites mediating interactions with ordered proteins. PMID:29385418
Translation Stress Positively Regulates MscL-Dependent Excretion of Cytoplasmic Proteins. PMID:29382730
Integrated multi-omic analysis of host-microbiota interactions in acute oak decline. PMID:29378627
Interleukins and their signaling pathways in the Reactome biological pathway database. PMID:29378288
Molecular Genetic Analysis of Human Endometrial Mesenchymal Stem Cells That Survived Sublethal Heat Shock. PMID:29375621
Proteomic analysis reveals distinctive protein profiles involved in CD8+ T cell-mediated murine autoimmune cholangitis. PMID:29375127
Ribosome Incorporation into Somatic Cells Promotes Lineage Transdifferentiation towards Multipotency. PMID:29374279
miR-29 contributes to normal endothelial function and can restore it in cardiometabolic disorders. PMID:29374012
Cell-surface marker discovery for lung cancer. PMID:29371917
Revealing the action mechanisms of dexamethasone on the birth weight of infant using RNA-sequencing data of trophoblast cells. PMID:29369181
Construction of Pará rubber tree genome and multi-transcriptome database accelerates rubber researches. PMID:29363422
Comparative Genomics Reveals Accelerated Evolution in Conserved Pathways during the Diversification of Anole Lizards. PMID:29360978
Dynamic genome wide expression profiling of Drosophila head development reveals a novel role of Hunchback in retinal glia cell development and blood-brain barrier integrity. PMID:29360820
Identification of 22q13 genes most likely to contribute to Phelan McDermid syndrome. PMID:29358616
Sphingolipid Metabolism Is Dysregulated at Transcriptomic and Metabolic Levels in the Spinal Cord of an Animal Model of Amyotrophic Lateral Sclerosis. PMID:29354030
Systematic Gene-to-Phenotype Arrays: A High-Throughput Technique for Molecular Phenotyping. PMID:29351850
Transcriptomic signatures of cellular and humoral immune responses in older adults after seasonal influenza vaccination identified by data-driven clustering. PMID:29335477
Large-scale aggregation analysis of eukaryotic proteins reveals an involvement of intrinsically disordered regions in protein folding. PMID:29330519
Systematic target function annotation of human transcription factors. PMID:29325558
ASGDB: a specialised genomic resource for interpreting Anopheles sinensis insecticide resistance. PMID:29321052
Update on 13 Syndromes Affecting Craniofacial and Dental Structures. PMID:29311971
Identification of epigenetically altered genes and potential gene targets in melanoma using bioinformatic methods. PMID:29302192
Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins. PMID:29302007
A novel gene signature based on five glioblastoma stem-like cell relevant genes predicts the survival of primary glioblastoma. PMID:29299749
Identifying term relations cross different gene ontology categories. PMID:29297309
CUFID-query: accurate network querying through random walk based network flow estimation. PMID:29297279
Semantic Relations in Compound Nouns: Perspectives from Inter-Annotator Agreement. PMID:29295175
Whole genome sequencing of the monomorphic pathogen Mycobacterium bovis reveals local differentiation of cattle clinical isolates. PMID:29291727
About miRNAs, miRNA seeds, target genes and target pathways. PMID:29291020
EZH2 Represses the B Cell Transcriptional Program and Regulates Antibody-Secreting Cell Metabolism and Antibody Production. PMID:29288200
A molecular signature of lung cancer: potential biomarkers for adenocarcinoma and squamous cell carcinoma. PMID:29285267
Restoration of type 1 iodothyronine deiodinase expression in renal cancer cells downregulates oncoproteins and affects key metabolic pathways as well as anti-oxidative system. PMID:29272308
Cell Cycle Model System for Advancing Cancer Biomarker Research. PMID:29269772
Identification of differential protein-coding gene expressions in early phase lung adenocarcinoma. PMID:29266838
Integrated Bayesian analysis of rare exonic variants to identify risk genes for schizophrenia and neurodevelopmental disorders. PMID:29262854
Prioritizing chronic obstructive pulmonary disease (COPD) candidate genes in COPD-related networks. PMID:29262568
A flexible ontology for inference of emergent whole cell function from relationships between subcellular processes. PMID:29255142
cFLIP critically modulates apoptotic resistance in epithelial-to-mesenchymal transition. PMID:29254146
Proteome profiling of clear cell renal cell carcinoma in von Hippel-Lindau patients highlights upregulation of Xaa-Pro aminopeptidase-1, an anti-proliferative and anti-migratory exoprotease. PMID:29245961
Loci and pathways associated with uterine capacity for pregnancy and fertility in beef cattle. PMID:29228019
Vulvar squamous cell carcinoma aggressiveness is associated with differential expression of collagen and STAT1. PMID:29225558
Association of Rare Predicted Loss-of-Function Variants in Cellular Pathways with Sub-Phenotypes in Age-Related Macular Degeneration. PMID:29224928
Exploring digenic inheritance in arrhythmogenic cardiomyopathy. PMID:29221435
MPK1/SLT2 Links Multiple Stress Responses with Gene Expression in Budding Yeast by Phosphorylating Tyr1 of the RNAP II CTD. PMID:29220656
Emergence of pathway-level composite biomarkers from converging gene set signals of heterogeneous transcriptomic responses. PMID:29218907
Single subject transcriptome analysis to identify functionally signed gene set or pathway activity. PMID:29218900
Chemical reaction vector embeddings: towards predicting drug metabolism in the human gut microbiome. PMID:29218869
Expanding horizons: new roles for non-canonical RNA-binding proteins in cancer. PMID:29216518
ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of the Statistical Property of the Mutual Rank Index. PMID:29216398
Integrative gene network analysis identifies key signatures, intrinsic networks and host factors for influenza virus A infections. PMID:29214055
Know Me! Unraveling the Riddle of Calcific Aortic Valve Disease by Bioinformatics. PMID:29212966
Identification of potential pathogenic genes associated with osteoporosis. PMID:29203636
Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists. PMID:29202807
Transcriptomics reveal an integrative role for maternal thyroid hormones during zebrafish embryogenesis. PMID:29192226
Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells. PMID:29191787
Subchronic olanzapine exposure leads to increased expression of myelination-related genes in rat fronto-medial cortex. PMID:29187753
Novel Common Variants Associated with Obesity and Type 2 Diabetes Detected Using a cFDR Method. PMID:29180724
A Workflow Guide to RNA-seq Analysis of Chaperone Function and Beyond. PMID:29177664
The Gene Ontology of eukaryotic cilia and flagella. PMID:29177046
Phosphoproteomics of cAMP signaling of Bordetella adenylate cyclase toxin in mouse dendritic cells. PMID:29176673
The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes. PMID:29169408
ADAGE signature analysis: differential expression analysis with data-defined gene sets. PMID:29166858
FunCoup 4: new species, data, and visualization. PMID:29165593
Identification of diverse target RNAs that are functionally regulated by human Pumilio proteins. PMID:29165587
Comparative Pan-Genome Analysis of Piscirickettsia salmonis Reveals Genomic Divergences within Genogroups. PMID:29164068
Whole-Genome Characterization of Bacillus cereus Associated with Specific Disease Manifestations. PMID:29158433
DGIdb 3.0: a redesign and expansion of the drug-gene interaction database. PMID:29156001
Investigation of common, low-frequency and rare genome-wide variation in anorexia nervosa. PMID:29155802
GFAPδ/GFAPα ratio directs astrocytoma gene expression towards a more malignant profile. PMID:29152145
ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets. PMID:29149270
Minimotif Miner 4: a million peptide minimotifs and counting. PMID:29140456
Transcriptome dynamics along axolotl regenerative development are consistent with an extensive reduction in gene expression heterogeneity in dedifferentiated cells. PMID:29134148
Proteomics in non-human primates: utilizing RNA-Seq data to improve protein identification by mass spectrometry in vervet monkeys. PMID:29132314
PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology. PMID:29126216
Identification of New Features from Known Bacterial Protective Vaccine Antigens Enhances Rational Vaccine Design. PMID:29123525
Guanylate-binding protein-1 is a potential new therapeutic target for triple-negative breast cancer. PMID:29115931
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families. PMID:29112718
Bacterial colonization stimulates a complex physiological response in the immature human intestinal epithelium. PMID:29110754
The UCSC Genome Browser database: 2018 update. PMID:29106570
GRAFENE: Graphlet-based alignment-free network approach integrates 3D structural and sequence (residue order) data to improve protein structural comparison. PMID:29097661
Mouse Genome Database (MGD)-2018: knowledgebase for the laboratory mouse. PMID:29092072
MARK3-mediated phosphorylation of ARHGEF2 couples microtubules to the actin cytoskeleton to establish cell polarity. PMID:29089450
eQTLs Regulating Transcript Variations Associated with Rapid Internode Elongation in Deepwater Rice. PMID:29081784
Hsp90-downregulation influences the heat-shock response, innate immune response and onset of oocyte development in nematodes. PMID:29078207
Reactome enhanced pathway visualization. PMID:29077811
Group spike-and-slab lasso generalized linear models for disease prediction and associated genes detection by incorporating pathway information. PMID:29077795
Metabolic responses to ethanol and butanol in Chlamydomonas reinhardtii. PMID:29075323
Expanded and updated data and a query pipeline for iBeetle-Base. PMID:29069517
Polysome-profiling in small tissue samples. PMID:29069469
A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE). PMID:29061110
Hemodynamic Forces Sculpt Developing Heart Valves through a KLF2-WNT9B Paracrine Signaling Axis. PMID:29056552
BioPlex Display: An Interactive Suite for Large-Scale AP-MS Protein-Protein Interaction Data. PMID:29054129
Epigenome-wide association study of asthma and wheeze in childhood and adolescence. PMID:29046734
Epigenetic mechanisms underlying maternal diabetes-associated risk of congenital heart disease. PMID:29046480
Modulation of Global Transcriptional Regulatory Networks as a Strategy for Increasing Kanamycin Resistance of the Translational Elongation Factor-G Mutants in Escherichia coli. PMID:29046437
Widespread Post-transcriptional Attenuation of Genomic Copy-Number Variation in Cancer. PMID:29032074
Transcriptomic Analysis of Octanoic Acid Response in Drosophila sechellia Using RNA-Sequencing. PMID:29021218
Molecular architecture underlying fluid absorption by the developing inner ear. PMID:28994389
RNA sequencing identifies novel non-coding RNA and exon-specific effects associated with cigarette smoking. PMID:28985737
Congenic mice demonstrate the presence of QTLs conferring obesity and hypercholesterolemia on chromosome 1 in the TALLYHO mouse. PMID:28983685
Early Life Exposure to Low Levels of AHR Agonist PCB126 (3,3',4,4',5-Pentachlorobiphenyl) Reprograms Gene Expression in Adult Brain. PMID:28973690
Meta-analysis of transcriptomic datasets identifies genes enriched in the mammalian circadian pacemaker. PMID:28973476
A composite network of conserved and tissue specific gene interactions reveals possible genetic interactions in glioma. PMID:28957313
Inflammasome-driven catecholamine catabolism in macrophages blunts lipolysis during ageing. PMID:28953873
Stable Gene Regulatory Network Modeling From Steady-State Data. PMID:28952574
The Arabidopsis MOS4-Associated Complex Promotes MicroRNA Biogenesis and Precursor Messenger RNA Splicing. PMID:28947490
Relating protein functional diversity to cell type number identifies genes that determine dynamic aspects of chromatin organisation as potential contributors to organismal complexity. PMID:28945800
SMARCB1 is required for widespread BAF complex-mediated activation of enhancers and bivalent promoters. PMID:28945250
Integrated network analysis to explore the key genes regulated by parathyroid hormone receptor 1 in osteosarcoma. PMID:28934958
A computational method using the random walk with restart algorithm for identifying novel epigenetic factors. PMID:28932904
APE1/Ref-1 knockdown in pancreatic ductal adenocarcinoma - characterizing gene expression changes and identifying novel pathways using single-cell RNA sequencing. PMID:28922540
The DREAM complex through its subunit Lin37 cooperates with Rb to initiate quiescence. PMID:28920576
Digoxin-induced anemia among patients with atrial fibrillation and heart failure: clinical data analysis and drug-gene interaction network. PMID:28915649
Microbial diversity in the hypersaline Lake Meyghan, Iran. PMID:28912589
Global organization of a binding site network gives insight into evolution and structure-function relationships of proteins. PMID:28912495
Data Analysis Pipeline for RNA-seq Experiments: From Differential Expression to Cryptic Splicing. PMID:28902396
Analysis of dermal fibroblasts isolated from neonatal and child cleft lip and adult skin: Developmental implications on reconstructive surgery. PMID:28901389
Unravelling the biology of chromatin in health and cancer using proteomic approaches. PMID:28895440
A Preliminary List of Horizontally Transferred Genes in Prokaryotes Determined by Tree Reconstruction and Reconciliation. PMID:28894459
A meta-analysis of genome-wide association studies identifies 17 new Parkinson's disease risk loci. PMID:28892059
Global Analysis of Membrane-associated Protein Oligomerization Using Protein Correlation Profiling. PMID:28887381
Mapping the STK4/Hippo signaling network in prostate cancer cell. PMID:28880957
Transcriptomic profiling in muscle and adipose tissue identifies genes related to growth and lipid deposition. PMID:28877211
FunctionAnnotator, a versatile and efficient web tool for non-model organism annotation. PMID:28874813
Transcriptome analysis of inflammation-related gene expression in endothelial cells activated by complement MASP-1. PMID:28874747
Chronic obstructive pulmonary disease candidate gene prioritization based on metabolic networks and functional information. PMID:28873096
Trichostatin A Sensitizes Hepatocellular Carcinoma Cells to Enhanced NK Cell-mediated Killing by Regulating Immune-related Genes. PMID:28871002
Development of an Efficient Protein Extraction Method Compatible with LC-MS/MS for Proteome Mapping in Two Australian Seagrasses Zostera muelleri and Posidonia australis. PMID:28861098
Ancient human miRNAs are more likely to have broad functions and disease associations than young miRNAs. PMID:28859623
Conserved Transcription Factors Steer Growth-Related Genomic Programs in Daphnia. PMID:28854641
Multiplexed quantification of proteins and transcripts in single cells. PMID:28854175
A proteomic portrait of dinoflagellate chromatin reveals abundant RNA-binding proteins. PMID:28852823
Identification of prognostic markers of high grade prostate cancer through an integrated bioinformatics approach. PMID:28849390
Analysis of gene expression profiling variations induced by hsa‑miR‑145‑5p‑overexpression in laryngeal squamous cell carcinoma cell line Tu‑177. PMID:28849105
Rat Genome and Model Resources. PMID:28838068
Single-Nucleotide Polymorphisms in Vitamin D-Related Genes May Modify Vitamin D-Breast Cancer Associations. PMID:28830874
GeNET: a web application to explore and share Gene Co-expression Network Analysis data. PMID:28828272
Assisted clustering of gene expression data using ANCut. PMID:28814280
Proteomic comparison by iTRAQ combined with mass spectrometry of egg white proteins in laying hens (Gallus gallus) fed with soybean meal and cottonseed meal. PMID:28813468
Sex differences in microRNA-mRNA networks: examination of novel epigenetic programming mechanisms in the sexually dimorphic neonatal hypothalamus. PMID:28810930
Strategies and tools to improve crop productivity by targeting photosynthesis. PMID:28808096
Inhibition of β-Catenin Signaling in the Skin Rescues Cutaneous Adipogenesis in Systemic Sclerosis: A Randomized, Double-Blind, Placebo-Controlled Trial of C-82. PMID:28807667
A network-based method using a random walk with restart algorithm and screening tests to identify novel genes associated with Menière's disease. PMID:28787010
Genome-wide signatures of complex introgression and adaptive evolution in the big cats. PMID:28776029
Complete Genome Sequence of Achromobacter denitrificans PR1. PMID:28774990
High-Coverage Whole-Exome Sequencing Identifies Candidate Genes for Suicide in Victims with Major Depressive Disorder. PMID:28769055
Quantitative Temporal in Vivo Proteomics Deciphers the Transition of Virus-Driven Myeloid Cells into M2 Macrophages. PMID:28768414
De novo assembly and annotation of the retinal transcriptome for the Nile grass rat (Arvicanthis ansorgei). PMID:28759564
Active nuclear transcriptome analysis reveals inflammasome-dependent mechanism for early neutrophil response to Mycobacterium marinum. PMID:28747644
Histological and transcriptomic effects of 17α-methyltestosterone on zebrafish gonad development. PMID:28738802
iTRAQ-based Proteomic Analysis of APPSw,Ind Mice Provides Insights into the Early Changes in Alzheimer's Disease. PMID:28730955
The Functional Genetics of Handedness and Language Lateralization: Insights from Gene Ontology, Pathway and Disease Association Analyses. PMID:28729848
DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species. PMID:28729549
MINERVA-a platform for visualization and curation of molecular interaction networks. PMID:28725475
Pediatric dilated cardiomyopathy hearts display a unique gene expression profile. PMID:28724804
Mutation intolerant genes and targets of FMRP are enriched for nonsynonymous alleles in schizophrenia. PMID:28719003
The human cytoplasmic dynein interactome reveals novel activators of motility. PMID:28718761
Genome reconstruction in Cynara cardunculus taxa gains access to chromosome-scale DNA variation. PMID:28717205
Microarray analysis reveals key genes and pathways in Tetralogy of Fallot. PMID:28713939
Assessing glycolytic flux alterations resulting from genetic perturbations in E. coli using a biosensor. PMID:28709932
The yeast noncoding RNA interaction network. PMID:28701522
Activating transcription factor 3 promotes loss of the acinar cell phenotype in response to cerulein-induced pancreatitis in mice. PMID:28701342
Dynamic regulation of lysine acetylation: the balance between acetyltransferase and deacetylase activities. PMID:28701313
Fish Oil Feeding Modulates the Expression of Hepatic MicroRNAs in a Western-Style Diet-Induced Nonalcoholic Fatty Liver Disease Rat Model. PMID:28691019
Energy metabolism and whole-exome sequencing-based analysis of Sasang constitution: a pilot study. PMID:28664140
RBM10 promotes transformation-associated processes in small cell lung cancer and is directly regulated by RBM5. PMID:28662214
Detecting similar binding pockets to enable systems polypharmacology. PMID:28662117
A Poly(Lactic-co-Glycolic) Acid Nanovaccine Based on Chimeric Peptides from Different Leishmania infantum Proteins Induces Dendritic Cells Maturation and Promotes Peptide-Specific IFNγ-Producing CD8+ T Cells Essential for the Protection against Experimental Visceral Leishmaniasis. PMID:28659922
Ontological interpretation of biomedical database content. PMID:28651575
Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction. PMID:28651538
Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium. PMID:28650483
Exploring Wound-Healing Genomic Machinery with a Network-Based Approach. PMID:28635674
The constitutive protease release by primary human acute myeloid leukemia cells. PMID:28631213
Temperature-responsive miRNAs in Drosophila orchestrate adaptation to different ambient temperatures. PMID:28630141
DUSP1 and KCNJ2 mRNA upregulation can serve as a biomarker of mechanical asphyxia-induced death in cardiac tissue. PMID:28624985
Transcriptome modulation by hydrocortisone in severe burn shock: ancillary analysis of a prospective randomized trial. PMID:28623938
MyGeneFriends: A Social Network Linking Genes, Genetic Diseases, and Researchers. PMID:28623182
ELIXIR pilot action: Marine metagenomics - towards a domain specific set of sustainable services. PMID:28620454
Plasticity in gene transcription explains the differential performance of two invasive fish species. PMID:28616064
RNAseq based transcriptomics study of SMCs from carotid atherosclerotic plaque: BMP2 and IDs proteins are crucial regulators of plaque stability. PMID:28615715
Cognitive Characterization of Schizophrenia Risk Variants Involved in Synaptic Transmission: Evidence of CACNA1C's Role in Working Memory. PMID:28607492
Transcriptional Changes in the Mouse Retina after Ocular Blast Injury: A Role for the Immune System. PMID:28599600
CottonFGD: an integrated functional genomics database for cotton. PMID:28595571
N-of-1-pathways MixEnrich: advancing precision medicine via single-subject analysis in discovering dynamic changes of transcriptomes. PMID:28589853
Identification of Proteases and Protease Inhibitors in Allergenic and Non-Allergenic Pollen. PMID:28587253
Fast and general tests of genetic interaction for genome-wide association studies. PMID:28586362
Dynamic changes in murine forebrain miR-211 expression associate with cholinergic imbalances and epileptiform activity. PMID:28584127
Dynamic regulation of Nanog and stem cell-signaling pathways by Hoxa1 during early neuro-ectodermal differentiation of ES cells. PMID:28584089
Catch and Release of Cytokines Mediated by Tumor Phosphatidylserine Converts Transient Exposure into Long-Lived Inflammation. PMID:28575659
Monitoring of the spatial and temporal dynamics of BER/SSBR pathway proteins, including MYH, UNG2, MPG, NTH1 and NEIL1-3, during DNA replication. PMID:28575236
Genetic subclone architecture of tumor clone-initiating cells in colorectal cancer. PMID:28572216
Histone H3 lysine 36 methylation affects temperature-induced alternative splicing and flowering in plants. PMID:28566089
GLADIATOR: a global approach for elucidating disease modules. PMID:28549478
Genomic adaptation to agricultural environments: cabbage white butterflies (Pieris rapae) as a case study. PMID:28549454
A resource of potential drug targets and strategic decision-making for obstructive sleep apnoea pharmacotherapy. PMID:28544082
Ebola virus glycoprotein directly triggers T lymphocyte death despite of the lack of infection. PMID:28542576
The long non-coding RNA LINC00152 is essential for cell cycle progression through mitosis in HeLa cells. PMID:28536419
Protein charge distribution in proteomes and its impact on translation. PMID:28531225
Identification of breast cancer prognostic modules based on weighted protein-protein interaction networks. PMID:28529601
Protein-RNA interactions: structural biology and computational modeling techniques. PMID:28510023
MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome. PMID:28502612
Specific MicroRNA Pattern in Colon Tissue of Young Children with Eosinophilic Colitis. PMID:28498330
DDX11-AS1 as potential therapy targets for human hepatocellular carcinoma. PMID:28496001
A new two-stage method for revealing missing parts of edges in protein-protein interaction networks. PMID:28493910
Bioinformatics in translational drug discovery. PMID:28487472
BioMake: a GNU make-compatible utility for declarative workflow management. PMID:28486579
Altered interactions between unicellular and multicellular genes drive hallmarks of transformation in a diverse range of solid tumors. PMID:28484005
Constructing Networks of Organelle Functional Modules in Arabidopsis. PMID:28479871
CHARGE and Kabuki Syndromes: Gene-Specific DNA Methylation Signatures Identify Epigenetic Mechanisms Linking These Clinically Overlapping Conditions. PMID:28475860
Tradict enables accurate prediction of eukaryotic transcriptional states from 100 marker genes. PMID:28474674
WebGIVI: a web-based gene enrichment analysis and visualization tool. PMID:28472919
Identifying novel fruit-related genes in Arabidopsis thaliana based on the random walk with restart algorithm. PMID:28472169
Interactive Toxicogenomics: Gene set discovery, clustering and analysis in Toxygates. PMID:28469246
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper. PMID:28460117
Insights into Ciliary Genes and Evolution from Multi-Level Phylogenetic Profiling. PMID:28460059
QueryOR: a comprehensive web platform for genetic variant analysis and prioritization. PMID:28454514
Identification of molecular characteristics induced by radiotherapy in rectal cancer based on microarray data. PMID:28454466
CHK2 is involved in the p53-independent radiosensitizing effects of valproic acid. PMID:28454438
The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation. PMID:28453653
Neuro-symbolic representation learning on biological knowledge graphs. PMID:28449114
PARP3 is a promoter of chromosomal rearrangements and limits G4 DNA. PMID:28447610
Mps1 Regulates Kinetochore-Microtubule Attachment Stability via the Ska Complex to Ensure Error-Free Chromosome Segregation. PMID:28441529
KLRG1 impairs regulatory T-cell competitive fitness in the gut. PMID:28437578
Tumour-associated changes in intestinal epithelial cells cause local accumulation of KLRG1+ GATA3+ regulatory T cells in mice. PMID:28437001
Oncodomains: A protein domain-centric framework for analyzing rare variants in tumor samples. PMID:28426665
Transcriptome Analysis of Mango (Mangifera indica L.) Fruit Epidermal Peel to Identify Putative Cuticle-Associated Genes. PMID:28425468
CDCA2 promotes lung adenocarcinoma cell proliferation and predicts poor survival in lung adenocarcinoma patients. PMID:28423619
Transcriptome and proteome responses in RNAlater preserved tissue of Arabidopsis thaliana. PMID:28423006
Identification of protein features encoded by alternative exons using Exon Ontology. PMID:28420690
goSTAG: gene ontology subtrees to tag and annotate genes within a set. PMID:28413437
An additional k-means clustering step improves the biological features of WGCNA gene co-expression networks. PMID:28403906
IGF2BP3 functions as a potential oncogene and is a crucial target of miR-34a in gastric carcinogenesis. PMID:28399871
Matrix Metalloproteinase-28 Is a Key Contributor to Emphysema Pathogenesis. PMID:28399390
A Circadian Genomic Signature Common to Ketamine and Sleep Deprivation in the Anterior Cingulate Cortex. PMID:28395871
The integrative omics of white-rot fungus Pycnoporus coccineus reveals co-regulated CAZymes for orchestrated lignocellulose breakdown. PMID:28394946
eTumorType, An Algorithm of Discriminating Cancer Types for Circulating Tumor Cells or Cell-free DNAs in Blood. PMID:28389380
Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells. PMID:28388430
An Approach to Spatiotemporally Resolve Protein Interaction Networks in Living Cells. PMID:28388416
DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining. PMID:28387604
Transcriptome-based investigation of cirrus development and identifying microsatellite markers in rattan (Daemonorops jenkinsiana). PMID:28383053
Connecting myelin-related and synaptic dysfunction in schizophrenia with SNP-rich gene expression hubs. PMID:28382934
Comparative Genomics Analysis of a New Exiguobacterium Strain from Salar de Huasco Reveals a Repertoire of Stress-Related Genes and Arsenic Resistance. PMID:28377753
Inferring Genes and Biological Functions That Are Sensitive to the Severity of Toxicity Symptoms. PMID:28368331
Genetic variation in the exome: Associations with alcohol and tobacco co-use. PMID:28368157
Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation. PMID:28365736
SEQUOIA: significance enhanced network querying through context-sensitive random walk and minimization of network conductance. PMID:28361708
Prior knowledge guided active modules identification: an integrated multi-objective approach. PMID:28361699
DIGNiFI: Discovering causative genes for orphan diseases using protein-protein interaction networks. PMID:28361678
Construction and evaluation of yeast expression networks by database-guided predictions. PMID:28357360
Identification of genes associated with tongue cancer in patients with a history of tobacco and/or alcohol use. PMID:28356939
Identification of Key Candidate Genes and Pathways in Colorectal Cancer by Integrated Bioinformatical Analysis. PMID:28350360
Time-matched analysis of DNA adduct formation and early gene expression as predictive tool for renal carcinogenesis in methylazoxymethanol acetate treated Eker rats. PMID:28349193
Epigenetic silencing of V(D)J recombination is a major determinant for selective differentiation of mucosal-associated invariant t cells from induced pluripotent stem cells. PMID:28346544
Genomic Comparison of Indigenous African and Northern European Chickens Reveals Putative Mechanisms of Stress Tolerance Related to Environmental Selection Pressure. PMID:28341699
RCAS: an RNA centric annotation system for transcriptome-wide regions of interest. PMID:28334930
Structure of the Transcriptional Regulatory Network Correlates with Regulatory Divergence in Drosophila. PMID:28333240
The Transcriptome of the Zebrafish Embryo After Chemical Exposure: A Meta-Analysis. PMID:28329862
The genome sequence of the wisent (Bison bonasus). PMID:28327911
Comparative transcriptome analyses of flower development in four species of Achimenes (Gesneriaceae). PMID:28320315
Bioinformatics identification of new targets for improving low temperature stress tolerance in spring and winter wheat. PMID:28302069
Systematic protein-protein interaction mapping for clinically relevant human GPCRs. PMID:28298427
Mitochondrial chaperone HSP-60 regulates anti-bacterial immunity via p38 MAP kinase signaling. PMID:28283579
Gene Expression Profiling with Cre-Conditional Pseudorabies Virus Reveals a Subset of Midbrain Neurons That Participate in Reward Circuitry. PMID:28283558
Gene expression metadata analysis reveals molecular mechanisms employed by Phanerochaete chrysosporium during lignin degradation and detoxification of plant extractives. PMID:28275822
Characterization of TPP-binding proteins in Methanococci archaeal species. PMID:28275290
Exploring biomedical ontology mappings with graph theory methods. PMID:28265499
Two-way learning with one-way supervision for gene expression data. PMID:28257645
Splicing-related genes are alternatively spliced upon changes in ambient temperatures in plants. PMID:28257507
Identifying and Analyzing Novel Epilepsy-Related Genes Using Random Walk with Restart Algorithm. PMID:28255556
Therapeutic indications and other use-case-driven updates in the drug ontology: anti-malarials, anti-hypertensives, opioid analgesics, and a large term request. PMID:28253937
De novo transcriptome assembly reveals high transcriptional complexity in Pisum sativum axillary buds and shows rapid changes in expression of diurnally regulated genes. PMID:28253862
Evolution of complexity in the zebrafish synapse proteome. PMID:28252024
Genome content analysis yields new insights into the relationship between the human malaria parasite Plasmodium falciparum and its anopheline vectors. PMID:28241792
A three-way approach for protein function classification. PMID:28234929
Identification of novel cancer therapeutic targets using a designed and pooled shRNA library screen. PMID:28223711
Plasmodium falciparum CRK4 directs continuous rounds of DNA replication during schizogony. PMID:28211852
Resolving host-pathogen interactions by dual RNA-seq. PMID:28207848
Exploring targeted therapy of osteosarcoma using proteomics data. PMID:28203090
Predicting disease-related genes using integrated biomedical networks. PMID:28198675
Overcoming the divide between ataxias and spastic paraplegias: Shared phenotypes, genes, and pathways. PMID:28195350
From comorbidities of chronic obstructive pulmonary disease to identification of shared molecular mechanisms by data integration. PMID:28185567
Large-scale bioactivity analysis of the small-molecule assayed proteome. PMID:28178331
Transcriptome analysis reveals rod/cone photoreceptor specific signatures across mammalian retinas. PMID:28172828
Annotation of functional impact of voltage-gated sodium channel mutations. PMID:28168870
Hypoxia-induced HIF1α targets in melanocytes reveal a molecular profile associated with poor melanoma prognosis. PMID:28168807
A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma. PMID:28166733
Genetic loci associated with chronic obstructive pulmonary disease overlap with loci for lung function and pulmonary fibrosis. PMID:28166215
From the research laboratory to the database: the Caenorhabditis elegans kinome in UniProtKB. PMID:28159896
Bridging Chromosomal Architecture and Pathophysiology of Streptococcus pneumoniae. PMID:28158485
TrypsNetDB: An integrated framework for the functional characterization of trypanosomatid proteins. PMID:28158179
Tutorial on Protein Ontology Resources. PMID:28150233
Protein Bioinformatics Databases and Resources. PMID:28150231
Dendritic Cell-Mediated Mechanisms Triggered by LT-IIa-B5, a Mucosal Adjuvant Derived from a Type II Heat-Labile Enterotoxin of Escherichia coli. PMID:28144014
Metabox: A Toolbox for Metabolomic Data Analysis, Interpretation and Integrative Exploration. PMID:28141874
Identifying the Metabolic Differences of a Fast-Growth Phenotype in Synechococcus UTEX 2973. PMID:28139686
TP53 Modulates Oxidative Stress in Gata1+ Erythroid Cells. PMID:28132886
Brief exposure to small molecules allows induction of mouse embryonic fibroblasts into neural crest-like precursors. PMID:28129669
Extensive cargo identification reveals distinct biological roles of the 12 importin pathways. PMID:28117667
TOMATOMICS: A Web Database for Integrated Omics Information in Tomato. PMID:28111364
Integrity of Induced Pluripotent Stem Cell (iPSC) Derived Megakaryocytes as Assessed by Genetic and Transcriptomic Analysis. PMID:28107356
Phenotype-Specific Association of Single-Nucleotide Polymorphisms with Heart Failure and Preserved Ejection Fraction: a Genome-Wide Association Analysis of the Cardiovascular Health Study. PMID:28105587
The antineoplastic drug, trastuzumab, dysregulates metabolism in iPSC-derived cardiomyocytes. PMID:28101782
Screening and analysis of breast cancer genes regulated by the human mammary microenvironment in a humanized mouse model. PMID:28101242
Primary Cell Culture of Live Neurosurgically Resected Aged Adult Human Brain Cells and Single Cell Transcriptomics. PMID:28099855
Comparative analysis of the root transcriptomes of cultivated sweetpotato (Ipomoea batatas [L.] Lam) and its wild ancestor (Ipomoea trifida [Kunth] G. Don). PMID:28086804
Human Lacrimal Gland Gene Expression. PMID:28081151
Suppression of C9orf72 RNA repeat-induced neurotoxicity by the ALS-associated RNA-binding protein Zfp106. PMID:28072389
Embryonic origin of adult stem cells required for tissue homeostasis and regeneration. PMID:28072387
Genetic evidence that Nkx2.2 acts primarily downstream of Neurog3 in pancreatic endocrine lineage development. PMID:28071588
Alga-PrAS (Algal Protein Annotation Suite): A Database of Comprehensive Annotation in Algal Proteomes. PMID:28069893
Toward a comprehensive drug ontology: extraction of drug-indication relations from diverse information sources. PMID:28069052
Supra-operonic clusters of functionally related genes (SOCs) are a source of horizontal gene co-transfers. PMID:28067311
Comparative Characterization of the Leaf Tissue of Physalis alkekengi and Physalis peruviana Using RNA-seq and Metabolite Profiling. PMID:28066454
ontologyX: a suite of R packages for working with ontological data. PMID:28062448
Integrated Approaches to Drug Discovery for Oxidative Stress-Related Retinal Diseases. PMID:28053689
ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium. PMID:28053168
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
Functional Transcriptomics in Diverse Intestinal Epithelial Cell Types Reveals Robust MicroRNA Sensitivity in Intestinal Stem Cells to Microbial Status. PMID:28053090
A Genome-wide Association Study Identifies Risk Alleles in Plasminogen and P4HA2 Associated with Giant Cell Arteritis. PMID:28041642
Developing integrated crop knowledge networks to advance candidate gene discovery. PMID:28018846
Driver gene classification reveals a substantial overrepresentation of tumor suppressors among very large chromatin-regulating proteins. PMID:28008934
Complex systems analysis of bladder cancer susceptibility reveals a role for decarboxylase activity in two genome-wide association studies. PMID:27999618
The BioGRID interaction database: 2017 update. PMID:27980099
Nitric Oxide Modulates Histone Acetylation at Stress Genes by Inhibition of Histone Deacetylases. PMID:27980017
Landscape of Pleiotropic Proteins Causing Human Disease: Structural and System Biology Insights. PMID:27957775
A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells. PMID:27939218
Utility and Limitations of Using Gene Expression Data to Identify Functional Associations. PMID:27935950
Exploring FlyBase Data Using QuickSearch. PMID:27930807
Tribbles ortholog NIPI-3 and bZIP transcription factor CEBP-1 regulate a Caenorhabditis elegans intestinal immune surveillance pathway. PMID:27927200
FARNA: knowledgebase of inferred functions of non-coding RNA transcripts. PMID:27924038
BRENDA in 2017: new perspectives and new tools in BRENDA. PMID:27924025
Identification of critical paralog groups with indispensable roles in the regulation of signaling flow. PMID:27922122
Human Intervention Study to Assess the Effects of Supplementation with Olive Leaf Extract on Peripheral Blood Mononuclear Cell Gene Expression. PMID:27918443
Piecemeal Buildup of the Genetic Code, Ribosomes, and Genomes from Primordial tRNA Building Blocks. PMID:27918435
Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes. PMID:27903897
Open Targets: a platform for therapeutic target identification and validation. PMID:27899665
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. PMID:27899636
The neXtProt knowledgebase on human proteins: 2017 update. PMID:27899619
SUBA4: the interactive data analysis centre for Arabidopsis subcellular protein locations. PMID:27899614
MalaCards: an amalgamated human disease compendium with diverse clinical and genetic annotation and structured search. PMID:27899610
DisProt 7.0: a major update of the database of disordered proteins. PMID:27899601
Modulation of nonsense mediated decay by rapamycin. PMID:27899591
The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching. PMID:27899582
Uniclust databases of clustered and deeply annotated protein sequences and alignments. PMID:27899574
Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse. PMID:27899570
Expansion of the Gene Ontology knowledgebase and resources. PMID:27899567
The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize. PMID:27899149
ToxReporter: viewing the genome through the eyes of a toxicologist. PMID:27888230
Microarray Expression Profiling of Long Non-Coding RNAs Involved in Nasopharyngeal Carcinoma Metastasis. PMID:27886062
Genome-wide transcriptome analysis revealed organelle specific responses to temperature variations in algae. PMID:27883062
MathIOmica: An Integrative Platform for Dynamic Omics. PMID:27883025
Inhibition of mTOR induces a paused pluripotent state. PMID:27880763
Draft genome of the living fossil Ginkgo biloba. PMID:27871309
The genome of Onchocerca volvulus, agent of river blindness. PMID:27869790
De-novo protein function prediction using DNA binding and RNA binding proteins as a test case. PMID:27869118
Multiparameter functional diversity of human C2H2 zinc finger proteins. PMID:27852650
Systems analysis identifies miR-29b regulation of invasiveness in melanoma. PMID:27852308
Local Cellular and Cytokine Cues in the Spleen Regulate In Situ T Cell Receptor Affinity, Function, and Fate of CD8+ T Cells. PMID:27851926
Knowledge Representation and Management: a Linked Data Perspective. PMID:27830248
CASTIN: a system for comprehensive analysis of cancer-stromal interactome. PMID:27829362
Primer on the Gene Ontology. PMID:27812933
omicsNPC: Applying the Non-Parametric Combination Methodology to the Integrative Analysis of Heterogeneous Omics Data. PMID:27812137
A transcription factor hierarchy defines an environmental stress response network. PMID:27811239
Large-scale gene co-expression network as a source of functional annotation for cattle genes. PMID:27806696
mirDNMR: a gene-centered database of background de novo mutation rates in human. PMID:27799474
Plant Reactome: a resource for plant pathways and comparative analysis. PMID:27799469
Proteome-pI: proteome isoelectric point database. PMID:27789699
TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions. PMID:27789689
Changes to the Aqueous Humor Proteome during Glaucoma. PMID:27788204
Mapping wild-type and R345W fibulin-3 intracellular interactomes. PMID:27777122
Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns. PMID:27774140
Proteomic Analysis, Immune Dysregulation, and Pathway Interconnections with Obesity. PMID:27769113
Name-calling in the hippocampus (and beyond): coming to terms with neuron types and properties. PMID:27747821
Progress Towards Computational 3-D Multicellular Systems Biology. PMID:27739051
Differences in reproductive toxicology between alopecia drugs: an analysis on adverse events among female and male cases. PMID:27738338
Exploring human disease using the Rat Genome Database. PMID:27736745
Microarray data analysis to identify crucial genes regulated by CEBPB in human SNB19 glioma cells. PMID:27716259
Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli. PMID:27713404
Cancer-associated fibroblast-derived annexin A6+ extracellular vesicles support pancreatic cancer aggressiveness. PMID:27701147
Regulation of Secondary Metabolism by the Velvet Complex Is Temperature-Responsive in Aspergillus. PMID:27694115
NUCLEAR FACTOR Y, Subunit C (NF-YC) Transcription Factors Are Positive Regulators of Photomorphogenesis in Arabidopsis thaliana. PMID:27685091
Immunoproteomic analysis of house dust mite antigens reveals distinct classes of dominant T cell antigens according to function and serological reactivity. PMID:27684489
COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH). PMID:27679477
Identifying and removing the cell-cycle effect from single-cell RNA-Sequencing data. PMID:27670849
Somatic polyploidy is associated with the upregulation of c-MYC interacting genes and EMT-like signature. PMID:27655693
Head regeneration in hemichordates is not a strict recapitulation of development. PMID:27649280
Translational Advances in the Field of Pulmonary Hypertension. Translating MicroRNA Biology in Pulmonary Hypertension. It Will Take More Than "miR" Words. PMID:27648944
The PathoYeastract database: an information system for the analysis of gene and genomic transcription regulation in pathogenic yeasts. PMID:27625390
Zinc finger protein 407 overexpression upregulates PPAR target gene expression and improves glucose homeostasis in mice. PMID:27624101
An intestinal microRNA modulates the homeostatic adaptation to chronic oxidative stress in C. elegans. PMID:27623524
GeneSCF: a real-time based functional enrichment tool with support for multiple organisms. PMID:27618934
Tissue enrichment analysis for C. elegans genomics. PMID:27618863
Bipartite Community Structure of eQTLs. PMID:27618581
GenToS: Use of Orthologous Gene Information to Prioritize Signals from Human GWAS. PMID:27612175
Analyzing and interpreting genome data at the network level with ConsensusPathDB. PMID:27606777
Temporal dynamics of the developing lung transcriptome in three common inbred strains of laboratory mice reveals multiple stages of postnatal alveolar development. PMID:27602285
Modeling biochemical pathways in the gene ontology. PMID:27589964
Complex Sources of Variation in Tissue Expression Data: Analysis of the GTEx Lung Transcriptome. PMID:27588449
Arthrogryposis as a Syndrome: Gene Ontology Analysis. PMID:27587986
InteGO2: a web tool for measuring and visualizing gene semantic similarities using Gene Ontology. PMID:27586009
Transcriptome sequencing reveals genome-wide variation in molecular evolutionary rate among ferns. PMID:27577050
Rapid evolutionary response to a transmissible cancer in Tasmanian devils. PMID:27575253
Global phylogeography and evolutionary history of Shigella dysenteriae type 1. PMID:27572446
Systems-level effects of ectopic galectin-7 reconstitution in cervical cancer and its microenvironment. PMID:27558259
Dynamic DNA methylation regulates neuronal intrinsic membrane excitability. PMID:27555660
Training and evaluation corpora for the extraction of causal relationships encoded in biological expression language (BEL). PMID:27554092
Order, Disorder, and Everything in Between. PMID:27548131
A protein network descriptor server and its use in studying protein, disease, metabolic and drug targeted networks. PMID:27542402
Increased Intestinal Microbial Diversity Following Fecal Microbiota Transplant for Active Crohn's Disease. PMID:27542133
Differential Biphasic Transcriptional Host Response Associated with Coevolution of Hemagglutinin Quasispecies of Influenza A Virus. PMID:27536272
Identification of compound-protein interactions through the analysis of gene ontology, KEGG enrichment for proteins and molecular fragments of compounds. PMID:27530612
ExSurv: A Web Resource for Prognostic Analyses of Exons Across Human Cancers Using Clinical Transcriptomes. PMID:27528797
SVM-Prot 2016: A Web-Server for Machine Learning Prediction of Protein Functional Families from Sequence Irrespective of Similarity. PMID:27525735
PDZD7-MYO7A complex identified in enriched stereocilia membranes. PMID:27525485
Identification of crucial microRNAs and genes in hypoxia-induced human lung adenocarcinoma cells. PMID:27524914
Highlighting the Need for Systems-Level Experimental Characterization of Plant Metabolic Enzymes. PMID:27516767
Coding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle. PMID:27516620
Time-course gene expression data on the transcriptional effects of Aminaphtone on ECV304 endothelial cells. PMID:27508230
The Role of Retrotransposons in Gene Family Expansions in the Human and Mouse Genomes. PMID:27503295
Prediction of scaffold proteins based on protein interaction and domain architectures. PMID:27490120
Genetic analysis of variation in lifespan using a multiparental advanced intercross Drosophila mapping population. PMID:27485207
Behavior change interventions: the potential of ontologies for advancing science and practice. PMID:27481101
eSNPO: An eQTL-based SNP Ontology and SNP functional enrichment analysis platform. PMID:27470167
The effects of lymph node status on predicting outcome in ER+ /HER2- tamoxifen treated breast cancer patients using gene signatures. PMID:27469239
Computational assessment of feature combinations for pathogenic variant prediction. PMID:27468419
Representing and querying disease networks using graph databases. PMID:27462371
Whole-Transcriptome Analysis of Verocytotoxigenic Escherichia coli O157:H7 (Sakai) Suggests Plant-Species-Specific Metabolic Responses on Exposure to Spinach and Lettuce Extracts. PMID:27462311
Seven protective miRNA signatures for prognosis of cervical cancer. PMID:27447860
Identification of Key Proteins and Networks Related to Grain Development in Wheat (Triticum aestivum L.) by Comparative Transcription and Proteomic Analysis of Allelic Variants in TaGW2-6A. PMID:27446152
Identification of biomarkers for pseudo and true progression of GBM based on radiogenomics study. PMID:27421136
Obtaining Human Ischemic Stroke Gene Expression Biomarkers from Animal Models: A Cross-species Validation Study. PMID:27407070
High-throughput sequencing and de novo transcriptome assembly of Swertia japonica to identify genes involved in the biosynthesis of therapeutic metabolites. PMID:27378356
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. PMID:27377652
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
N(6)-methyladenosine of HIV-1 RNA regulates viral infection and HIV-1 Gag protein expression. PMID:27371828
bioassayR: Cross-Target Analysis of Small Molecule Bioactivity. PMID:27367556
Regions of variable DNA methylation in human placenta associated with newborn neurobehavior. PMID:27366929
Genetic variants determining survival and fertility in an adverse African environment: a population-based large-scale candidate gene association study. PMID:27356285
Isofunctional Protein Subfamily Detection Using Data Integration and Spectral Clustering. PMID:27348631
Model organism databases: essential resources that need the support of both funders and users. PMID:27334346
Generalized enrichment analysis improves the detection of adverse drug events from the biomedical literature. PMID:27333889
MUFFINN: cancer gene discovery via network analysis of somatic mutation data. PMID:27333808
Convergent evidence from systematic analysis of GWAS revealed genetic basis of esophageal cancer. PMID:27331408
Molecular serum signature of treatment resistant depression. PMID:27325393
TBR1 regulates autism risk genes in the developing neocortex. PMID:27325115
Epidermal growth factor receptor inhibitors trigger a type I interferon response in human skin. PMID:27322144
Differential RNA-seq, Multi-Network Analysis and Metabolic Regulation Analysis of Kluyveromyces marxianus Reveals a Compartmentalised Response to Xylose. PMID:27315089
Learning mixed graphical models with separate sparsity parameters and stability-based model selection. PMID:27294886
Comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database. PMID:27287925
Identification of differentially expressed genes from multipotent epithelia at the onset of an asexual development. PMID:27264734
miR-30 Family Controls Proliferation and Differentiation of Intestinal Epithelial Cell Models by Directing a Broad Gene Expression Program That Includes SOX9 and the Ubiquitin Ligase Pathway. PMID:27261459
Differential burden of rare protein truncating variants in Alzheimer's disease patients compared to centenarians. PMID:27260402
The Proteasix Ontology. PMID:27259807
Differentially Expressed miRNAs in Tumor, Adjacent, and Normal Tissues of Lung Adenocarcinoma. PMID:27247934
Differences in somatic mutation landscape of hepatocellular carcinoma in Asian American and European American populations. PMID:27246981
VESPUCCI: Exploring Patterns of Gene Expression in Grapevine. PMID:27242836
EP300 Protects from Light-Induced Retinopathy in Zebrafish. PMID:27242532
Genome-wide functional annotation of Phomopsis longicolla isolate MSPL 10-6. PMID:27222801
Transcriptome analysis of cortical tissue reveals shared sets of downregulated genes in autism and schizophrenia. PMID:27219343
Altered gene expression in the lower respiratory tract of Car6 (-/-) mice. PMID:27209317
Effects of hibernation on bone marrow transcriptome in thirteen-lined ground squirrels. PMID:27207617
Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis. PMID:27199545
A flexible method for estimating the fraction of fitness influencing mutations from large sequencing data sets. PMID:27197222
Network-assisted investigation of virulence and antibiotic-resistance systems in Pseudomonas aeruginosa. PMID:27194047
Viruses are a dominant driver of protein adaptation in mammals. PMID:27187613
Interconnections Between RNA-Processing Pathways Revealed by a Sequencing-Based Genetic Screen for Pre-mRNA Splicing Mutants in Fission Yeast. PMID:27172183
Targeted Sequencing and Meta-Analysis of Preterm Birth. PMID:27163930
ToxEvaluator: an integrated computational platform to aid the interpretation of toxicology study-related findings. PMID:27161010
UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB. PMID:27153729
Molecular characterization of Gleason patterns 3 and 4 prostate cancer using reverse Warburg effect-associated genes. PMID:27152194
Complete genome sequence of an agr-dysfunctional variant of the ST239 lineage of the methicillin-resistant Staphylococcus aureus strain GV69 from Brazil. PMID:27152133
PathwAX: a web server for network crosstalk based pathway annotation. PMID:27151197
Whole organism transcriptome analysis of zebrafish models of Bardet-Biedl Syndrome and Alström Syndrome provides mechanistic insight into shared and divergent phenotypes. PMID:27142762
Candidate gene prioritization with Endeavour. PMID:27131783
The omic approach to parasitic trematode research-a review of techniques and developments within the past 5 years. PMID:27126082
Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. PMID:27126040
Network-driven plasma proteomics expose molecular changes in the Alzheimer's brain. PMID:27112350
Companion: a web server for annotation and analysis of parasite genomes. PMID:27105845
g:Profiler-a web server for functional interpretation of gene lists (2016 update). PMID:27098042
Analysis of microRNA expression during the torpor-arousal cycle of a mammalian hibernator, the 13-lined ground squirrel. PMID:27084747
Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. PMID:27082250
Novel Biomarker Proteins in Chronic Lymphocytic Leukemia: Impact on Diagnosis, Prognosis and Treatment. PMID:27078856
FAM46 proteins are novel eukaryotic non-canonical poly(A) polymerases. PMID:27060136
ATtRACT-a database of RNA-binding proteins and associated motifs. PMID:27055826
ICEPO: the ion channel electrophysiology ontology. PMID:27055825
The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable. PMID:27051515
Standardized benchmarking in the quest for orthologs. PMID:27043882
GAMDB: a web resource to connect microRNAs with autophagy in gerontology. PMID:27037912
Contextualizing the Genes Altered in Bladder Neoplasms in Pediatric andTeen Patients Allows Identifying Two Main Classes of Biological ProcessesInvolved and New Potential Therapeutic Targets. PMID:27013923
Utilization of HPASubC for the Identification of Sinusoid-Specific Proteins in the Liver. PMID:27005832
Activation of Myenteric Glia during Acute Inflammation In Vitro and In Vivo. PMID:26964064
A systematic study on drug-response associated genes using baseline gene expressions of the Cancer Cell Line Encyclopedia. PMID:26960563
Gene regulatory mechanisms underpinning prostate cancer susceptibility. PMID:26950096
Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems. PMID:26949740
Stable engineered vascular networks from human induced pluripotent stem cell-derived endothelial cells cultured in synthetic hydrogels. PMID:26945632
Multidimensional Screening Platform for Simultaneously Targeting Oncogenic KRAS and Hypoxia-Inducible Factors Pathways in Colorectal Cancer. PMID:26938486
Guidelines for the functional annotation of microRNAs using the Gene Ontology. PMID:26917558
Epigenome-wide profiling of DNA methylation in paired samples of adipose tissue and blood. PMID:26891033
Leaf apoplastic proteome composition in UV-B treated Arabidopsis thaliana mutants impaired in extracellular glutathione degradation. PMID:26862584
Long-noncoding RNAs in basal cell carcinoma. PMID:26861560
Quorum sensing activity of Citrobacter amalonaticus L8A, a bacterium isolated from dental plaque. PMID:26860259
A review of the new HGNC gene family resource. PMID:26842383
The Arabidopsis transcriptional regulator DPB3-1 enhances heat stress tolerance without growth retardation in rice. PMID:26841113
The genomic basis of parasitism in the Strongyloides clade of nematodes. PMID:26829753
Using the Gene Ontology to Annotate Key Players in Parkinson's Disease. PMID:26825309
Epigenome overlap measure (EPOM) for comparing tissue/cell types based on chromatin states. PMID:26817822
Accelerating Adverse Outcome Pathway Development Using Publicly Available Data Sources. PMID:26809562
Expression Profiles and Biological Roles of miR-196a in Swine. PMID:26805888
Multi-task consensus clustering of genome-wide transcriptomes from related biological conditions. PMID:26801959
Assembly, Assessment, and Availability of De novo Generated Eukaryotic Transcriptomes. PMID:26793234
Insight into the Salivary Gland Transcriptome of Lygus lineolaris (Palisot de Beauvois). PMID:26789269
Lamina Associated Polypeptide 1 (LAP1) Interactome and Its Functional Features. PMID:26784240
QuickRNASeq lifts large-scale RNA-seq data analyses to the next level of automation and interactive visualization. PMID:26747388
Exome arrays capture polygenic rare variant contributions to schizophrenia. PMID:26740555
Systems Genomics Support for Immune and Inflammation Hypothesis of Depression. PMID:26733279
Constraint methods that accelerate free-energy simulations of biomolecules. PMID:26723628
HitPredict version 4: comprehensive reliability scoring of physical protein-protein interactions from more than 100 species. PMID:26708988
Mathematical models of cancer metabolism. PMID:26702357
Building accurate sequence-to-affinity models from high-throughput in vitro protein-DNA binding data using FeatureREDUCE. PMID:26701911
Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods. PMID:26694353
Prediction of tissue-specific effects of gene knockout on apoptosis in different anatomical structures of human brain. PMID:26693857
The administration of intranasal live attenuated influenza vaccine induces changes in the nasal microbiota and nasal epithelium gene expression profiles. PMID:26667497
IRES-dependent translated genes in fungi: computational prediction, phylogenetic conservation and functional association. PMID:26666532
GeneWeaver: data driven alignment of cross-species genomics in biology and disease. PMID:26656951
The Reactome pathway Knowledgebase. PMID:26656494
TAF1 Variants Are Associated with Dysmorphic Features, Intellectual Disability, and Neurological Manifestations. PMID:26637982
COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps. PMID:26635392
Transcriptional program for nitrogen starvation-induced lipid accumulation in Chlamydomonas reinhardtii. PMID:26633994
Recurrent Fusions in MYB and MYBL1 Define a Common, Transcription Factor-Driven Oncogenic Pathway in Salivary Gland Adenoid Cystic Carcinoma. PMID:26631070
Representation and inference of cellular architecture for metabolic reconstruction and modeling. PMID:26628588
orthoFind Facilitates the Discovery of Homologous and Orthologous Proteins. PMID:26624019
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. PMID:26615188
Whole-Exome Sequencing in Familial Parkinson Disease. PMID:26595808
Complete genome sequence of Staphylococcus aureus, strain ILRI_Eymole1/1, isolated from a Kenyan dromedary camel. PMID:26594310
FunTree: advances in a resource for exploring and contextualising protein function evolution. PMID:26590404
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. PMID:26582926
Mouse genome database 2016. PMID:26578600
Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database. PMID:26578582
Ensembl Genomes 2016: more genomes, more complexity. PMID:26578574
WormBase 2016: expanding to enable helminth genomic research. PMID:26578572
PlanMine--a mineable resource of planarian biology and biodiversity. PMID:26578570
PCOSKB: A KnowledgeBase on genes, diseases, ontology terms and biochemical pathways associated with PolyCystic Ovary Syndrome. PMID:26578565
Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine. PMID:26578564
LegumeIP 2.0--a platform for the study of gene function and genome evolution in legumes. PMID:26578557
GEneSTATION 1.0: a synthetic resource of diverse evolutionary and functional genomic data for studying the evolution of pregnancy-associated tissues and phenotypes. PMID:26567549
Next-generation diagnostics and disease-gene discovery with the Exomiser. PMID:26562621
Union Exon Based Approach for RNA-Seq Gene Quantification: To Be or Not to Be? PMID:26559532
An Antifungal Combination Matrix Identifies a Rich Pool of Adjuvant Molecules that Enhance Drug Activity against Diverse Fungal Pathogens. PMID:26549450
The Transporter Classification Database (TCDB): recent advances. PMID:26546518
DESM: portal for microbial knowledge exploration systems. PMID:26546514
DGIdb 2.0: mining clinically relevant drug-gene interactions. PMID:26531824
Application of Functional Genomics for Bovine Respiratory Disease Diagnostics. PMID:26526746
Multiclassifier combinatorial proteomics of organelle shadows at the example of mitochondria in chromatin data. PMID:26510496
Bioinformatics Knowledge Map for Analysis of Beta-Catenin Function in Cancer. PMID:26509276
Bovine Genome Database: new tools for gleaning function from the Bos taurus genome. PMID:26481361
PhytoPath: an integrative resource for plant pathogen genomics. PMID:26476449
SIGNOR: a database of causal relationships between biological entities. PMID:26467481
CAMPR3: a database on sequences, structures and signatures of antimicrobial peptides. PMID:26467475
Egr-5 is a post-mitotic regulator of planarian epidermal differentiation. PMID:26457503
MitoMiner v3.1, an update on the mitochondrial proteomics database. PMID:26432830
Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery. PMID:26420781
Genome-Wide Assessment of Outer Membrane Vesicle Production in Escherichia coli. PMID:26406465
Allorecognition, via TgrB1 and TgrC1, mediates the transition from unicellularity to multicellularity in the social amoeba Dictyostelium discoideum. PMID:26395484
Modeling the Regulatory Mechanisms by Which NLRX1 Modulates Innate Immune Responses to Helicobacter pylori Infection. PMID:26367386
Small RNAs and Gene Network in a Durable Disease Resistance Gene--Mediated Defense Responses in Rice. PMID:26335702
Genetic, epigenetic, and molecular landscapes of multifocal and multicentric glioblastoma. PMID:26323991
In Silico Analysis of Correlations between Protein Disorder and Post-Translational Modifications in Algae. PMID:26307970
Integrated inference and evaluation of host-fungi interaction networks. PMID:26300851
Prediction of Causal Candidate Genes in Coronary Artery Disease Loci. PMID:26293461
Characterization of genome-wide H3K27ac profiles reveals a distinct PM2.5-associated histone modification signature. PMID:26276146
The history of the CATH structural classification of protein domains. PMID:26253692
Phenotype-driven strategies for exome prioritization of human Mendelian disease genes. PMID:26229552
Orthology for comparative genomics in the mouse genome database. PMID:26223881
The Esg Gene Is Involved in Nicotine Sensitivity in Drosophila melanogaster. PMID:26222315
High-quality draft genome sequences of five anaerobic oral bacteria and description of Peptoanaerobacter stomatis gen. nov., sp. nov., a new member of the family Peptostreptococcaceae. PMID:26221418
GESearch: An Interactive GUI Tool for Identifying Gene Expression Signature. PMID:26199946
A large-scale crop protection bioassay data set. PMID:26175909
MicroRNA Expression Profile in Penile Cancer Revealed by Next-Generation Small RNA Sequencing. PMID:26158897
Mouse Genome Database: From sequence to phenotypes and disease models. PMID:26150326
Application of comparative biology in GO functional annotation: the mouse model. PMID:26141960
SmedGD 2.0: The Schmidtea mediterranea genome database. PMID:26138588
Disease insights through cross-species phenotype comparisons. PMID:26092691
dictyBase 2015: Expanding data and annotations in a new software environment. PMID:26088819
Stress-induced DNA damage biomarkers: applications and limitations. PMID:26082923
High-Throughput Sequencing and De Novo Assembly of Red and Green Forms of the Perilla frutescens var. crispa Transcriptome. PMID:26070213
Visual annotation display (VLAD): a tool for finding functional themes in lists of genes. PMID:26047590
FAST: FAST Analysis of Sequences Toolbox. PMID:26042145
Databases for Microbiologists. PMID:26013493
Global alterations of the transcriptional landscape during yeast growth and development in the absence of Ume6-dependent chromatin modification. PMID:25957495
ProtPhylo: identification of protein-phenotype and protein-protein functional associations via phylogenetic profiling. PMID:25956654
GXD: a community resource of mouse Gene Expression Data. PMID:25939429
Toll-like receptor signaling in vertebrates: testing the integration of protein, complex, and pathway data in the protein ontology framework. PMID:25894391
Biological databases for human research. PMID:25712261 -
Gene Ontology annotations and resources
PubMed citations: 292.
292 articles citing: Gene Ontology annotations and resources
Downregulation of PGM5 expression correlates with tumor progression and poor prognosis in human prostate cancer. PMID:35819729
Transcriptome Analysis Reveals Crosstalk between the Abscisic Acid and Jasmonic Acid Signaling Pathways in Rice-Mediated Defense against Nilaparvata lugens. PMID:35682997
METTL3 Is Associated With the Malignancy of Esophageal Squamous Cell Carcinoma and Serves as a Potential Immunotherapy Biomarker. PMID:35574315
Transcriptomic Analysis of Fumarate Compounds Identifies Unique Effects of Isosorbide Di-(Methyl Fumarate) on NRF2, NF-kappaB and IRF1 Pathway Genes. PMID:35455458
The Prognostic Signature of Head and Neck Squamous Cell Carcinoma Constructed by Immune-Related RNA-Binding Proteins. PMID:35449571
Genetic Modeling and Genomic Analyses of Yearling Temperament in American Angus Cattle and Its Relationship With Productive Efficiency and Resilience Traits. PMID:35444687
PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe. PMID:35411388
GOntoSim: a semantic similarity measure based on LCA and common descendants. PMID:35264663
Tumor ENPP1 (CD203a)/Haptoglobin Axis Exploits Myeloid-Derived Suppressor Cells to Promote Post-Radiotherapy Local Recurrence in Breast Cancer. PMID:35191482
NonLoss: a novel analytical method for differential biological module identification from single-cell transcriptome. PMID:35071482
A novel gene functional similarity calculation model by utilizing the specificity of terms and relationships in gene ontology. PMID:35057740
A Sensitization-Free Dimethyl Fumarate Prodrug, Isosorbide Di-(Methyl Fumarate), Provides a Topical Treatment Candidate for Psoriasis. PMID:34909741
Prognostic characterization of immune molecular subtypes in non-small cell lung cancer to immunotherapy. PMID:34844602
Homozygous duplication identified by whole genome sequencing causes LRBA deficiency. PMID:34795304
PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions. PMID:34788826
Neuroprotective effects of long noncoding RNAs involved in ischemic postconditioning after ischemic stroke. PMID:34782575
Tomato leaves under stress: a comparison of stress response to mild abiotic stress between a cultivated and a wild tomato species. PMID:34677706
A differential DNA methylome signature of pulmonary immune cells from individuals converting to latent tuberculosis infection. PMID:34593857
Transcriptome Adaptation of the Ovine Mammary Gland to Dietary Supplementation of Extruded Linseed. PMID:34573673
Utilization of Transcriptome, Small RNA, and Degradome Sequencing to Provide Insights Into Drought Stress and Rewatering Treatment in Medicago ruthenica. PMID:34413864
The Prognostic Value of the DNA Repair Gene Signature in Head and Neck Squamous Cell Carcinoma. PMID:34395285
The brain transcriptome of the wolf spider, Schizocosa ocreata. PMID:34162407
Interplay between SARS-CoV-2-derived miRNAs, immune system, vitamin D pathway and respiratory system. PMID:34159729
Multi Locus View: an extensible web-based tool for the analysis of genomic data. PMID:34035422
A five-gene signature for predicting overall survival of esophagus adenocarcinoma. PMID:33832101
De novo Prediction of Moonlighting Proteins Using Multimodal Deep Ensemble Learning. PMID:33828582
Combined Genome, Transcriptome and Metabolome Analysis in the Diagnosis of Childhood Cerebellar Ataxia. PMID:33804237
A Systematic Review of Genomic Regions and Candidate Genes Underlying Behavioral Traits in Farmed Mammals and Their Link with Human Disorders. PMID:33800722
Enhanced anti-inflammatory effects of mesenchymal stromal cells mediated by the transient ectopic expression of CXCR4 and IL10. PMID:33579367
System Pharmacology-Based Strategy to Decode the Synergistic Mechanism of GanDouLing for Wilson's Disease. PMID:33564316
Comparing the hippocampal miRNA expression profiles of wild and domesticated Chinese tree shrews (Tupaia belangeri chinensis). PMID:33514308
Transcriptome Remodeling in Gradual Development of Inverse Resistance between Paclitaxel and Cisplatin in Ovarian Cancer Cells. PMID:33287223
The Zebrafish Perivitelline Fluid Provides Maternally-Inherited Defensive Immunity. PMID:32899417
Identifying disease-associated signaling pathways through a novel effector gene analysis. PMID:32864216
The Biological Significance of Multi-copy Regions and Their Impact on Variant Discovery. PMID:32827758
Salt stress induces endoplasmic reticulum stress-responsive genes in a grapevine rootstock. PMID:32730292
RNA Sequencing for Gene Expression Profiles in Peripheral Blood Mononuclear Cells with Ankylosing Spondylitis RNA. PMID:32596323
Chromosome-level reference genome of the jellyfish Rhopilema esculentum. PMID:32315029
Association of a Reproducible Epigenetic Risk Profile for Schizophrenia With Brain Methylation and Function. PMID:32049268
Evaluating liquid biopsies for methylomic profiling of prostate cancer. PMID:32000564
Transcriptome analysis reveals an important candidate gene involved in both nodal metastasis and prognosis in lung adenocarcinoma. PMID:31827762
A novel miRNA-4484 is up-regulated on microarray and associated with increased MMP-21 expression in serum of systemic sclerosis patients. PMID:31582779
Integrated analysis of quantitative proteome and transcriptional profiles reveals abnormal gene expression and signal pathway in bladder cancer. PMID:31576517
Co-culture With Human Breast Adipocytes Differentially Regulates Protein Abundance in Breast Cancer Cells. PMID:31467226
UNIPred-Web: a web tool for the integration and visualization of biomolecular networks for protein function prediction. PMID:31412768
Integrated analyses of microRNA-29 family and the related combination biomarkers demonstrate their widespread influence on risk, recurrence, metastasis and survival outcome in colorectal cancer. PMID:31346316
RNA-seq reveals outcome-specific gene expression of MMP7 and PCK1 in biliary atresia. PMID:31342296
Bioinformatics analysis of a long non‑coding RNA and mRNA regulation network in rats with middle cerebral artery occlusion based on RNA sequencing. PMID:31180537
Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms. PMID:31165139
ALS blood expression profiling identifies new biomarkers, patient subgroups, and evidence for neutrophilia and hypoxia. PMID:31118040
EcRBPome: a comprehensive database of all known E. coli RNA-binding proteins. PMID:31117939
Reversal of Vocal Fold Mucosal Fibrosis Using siRNA against the Collagen-Specific Chaperone Serpinh1. PMID:31100613
Whole genome sequencing reveals the impact of recent artificial selection on red sea bream reared in fish farms. PMID:31019228
Identification and functional analysis of microRNAs in rats following focal cerebral ischemia injury. PMID:30896823
PASS2 version 6: a database of structure-based sequence alignments of protein domain superfamilies in accordance with SCOPe. PMID:30820573
Functional annotation of putative QTL associated with black tea quality and drought tolerance traits. PMID:30728388
Extracellular vesicles from Kaposi Sarcoma-associated herpesvirus lymphoma induce long-term endothelial cell reprogramming. PMID:30716130
Biological Interpretation of Complex Genomic Data. PMID:30649721
Functional genomics of the digestive tract in broilers. PMID:30545300
GM604 regulates developmental neurogenesis pathways and the expression of genes associated with amyotrophic lateral sclerosis. PMID:30524706
Gene ontology improves template selection in comparative protein docking. PMID:30520123
ECO, the Evidence & Conclusion Ontology: community standard for evidence information. PMID:30407590
Gene ontology concept recognition using named concept: understanding the various presentations of the gene functions in biomedical literature. PMID:30376045
Aberrant splicing in B-cell acute lymphoblastic leukemia. PMID:30357359
Genome-wide identification and characterization of CONSTANS-like gene family in radish (Raphanus sativus). PMID:30248137
Comprehensive analysis of the whole coding and non-coding RNA transcriptome expression profiles and construction of the circRNA-lncRNA co-regulated ceRNA network in laryngeal squamous cell carcinoma. PMID:30128795
Unraveling the Plasmodium vivax sporozoite transcriptional journey from mosquito vector to human host. PMID:30111801
"Super Gene Set" Causal Relationship Discovery from Functional Genomics Data. PMID:30040650
RNA Sequencing and Pathway Analysis Identify Important Pathways Involved in Hypertrichosis and Intellectual Disability in Patients with Wiedemann-Steiner Syndrome. PMID:30014449
Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations. PMID:29949999
Elevated histone H3 acetylation is associated with genes involved in T lymphocyte activation and glutamate decarboxylase antibody production in patients with type 1 diabetes. PMID:29791073
WEGO 2.0: a web tool for analyzing and plotting GO annotations, 2018 update. PMID:29788377
A Multi-Omics Database for Parasitic Nematodes and Trematodes. PMID:29761465
CircRNAs in the tree shrew (Tupaia belangeri) brain during postnatal development and aging. PMID:29723158
The draft genome sequence of forest musk deer (Moschus berezovskii). PMID:29635287
Comparative transcriptome profiling of the human and mouse dorsal root ganglia: an RNA-seq-based resource for pain and sensory neuroscience research. PMID:29561359
Hydrogen sulfide mediates athero-protection against oxidative stress via S-sulfhydration. PMID:29518145
Comparative transcriptome analysis reveals molecular response to salinity stress of salt-tolerant and sensitive genotypes of indica rice at seedling stage. PMID:29391416
Transcriptome profiling of lentil (Lens culinaris) through the first 24 hours of Ascochyta lentis infection reveals key defence response genes. PMID:29385986
Identification of differentially expressed molecular functions associated with breast cancer using Gibbs sampling. PMID:29344193
Genome-Wide Methylation Patterns in Androgen-Independent Prostate Cancer Cells: A Comprehensive Analysis Combining MeDIP-Bisulfite, RNA, and microRNA Sequencing Data. PMID:29324665
Reversible dual inhibitor against G9a and DNMT1 improves human iPSC derivation enhancing MET and facilitating transcription factor engagement to the genome. PMID:29281720
Ten quick tips for machine learning in computational biology. PMID:29234465
Genomic characterization of a new endophytic Streptomyces kebangsaanensis identifies biosynthetic pathway gene clusters for novel phenazine antibiotic production. PMID:29201559
Identification of key genes in glioma CpG island methylator phenotype via network analysis of gene expression data. PMID:29152649
Fusing multiple protein-protein similarity networks to effectively predict lncRNA-protein interactions. PMID:29072138
Establishing multiple omics baselines for three Southeast Asian populations in the Singapore Integrative Omics Study. PMID:28935855
Unravelling the biology of chromatin in health and cancer using proteomic approaches. PMID:28895440
Comparative proteomic analysis of autotetraploid and diploid Paulownia tomentosa reveals proteins associated with superior photosynthetic characteristics and stress adaptability in autotetraploid Paulownia. PMID:28878499
Identification of the SOX2 Interactome by BioID Reveals EP300 as a Mediator of SOX2-dependent Squamous Differentiation and Lung Squamous Cell Carcinoma Growth. PMID:28794006
A neurogenetic model for the study of schizophrenia spectrum disorders: the International 22q11.2 Deletion Syndrome Brain Behavior Consortium. PMID:28761081
Identification of key genes in Gram‑positive and Gram‑negative sepsis using stochastic perturbation. PMID:28714002
A genome-wide association scan of biological processes involved in oral lichen planus and oral squamous cell carcinoma. PMID:28640079
Bioinformatics analysis of dysregulated microRNAs in the nipple discharge of patients with breast cancer. PMID:28521415
Large-scale detection of drug off-targets: hypotheses for drug repurposing and understanding side-effects. PMID:28449705
Large-scale collection of full-length cDNA and transcriptome analysis in Hevea brasiliensis. PMID:28431015
Whole-genome sequencing suggests mechanisms for 22q11.2 deletion-associated Parkinson's disease. PMID:28430790
Bioinformatics analysis of gene expression alterations in microRNA‑122 knockout mice with hepatocellular carcinoma. PMID:28393247
The anatomy of phenotype ontologies: principles, properties and applications. PMID:28387809
Selecting high-quality negative samples for effectively predicting protein-RNA interactions. PMID:28361676
Genome-wide identification of conserved intronic non-coding sequences using a Bayesian segmentation approach. PMID:28347272
NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology. PMID:28320317
Differential Transcriptional Regulation in Roots of Tomato Near-Isogenic Lines in Response to Rapid-Onset Water Stress. PMID:28270818
Medical Subject Heading (MeSH) annotations illuminate maize genetics and evolution. PMID:28250803
Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants. PMID:28228535
Direct experimental manipulation of intestinal cells in Ascaris suum, with minor influences on the global transcriptome. PMID:28223178
An integrative approach unveils FOSL1 as an oncogene vulnerability in KRAS-driven lung and pancreatic cancer. PMID:28220783
HAPPI-2: a Comprehensive and High-quality Map of Human Annotated and Predicted Protein Interactions. PMID:28212602
SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases. PMID:28178937
Genome Sequence of Christensenella minuta DSM 22607T. PMID:28082495
Cancer Progression Prediction Using Gene Interaction Regularized Elastic Net. PMID:28055897
Semaphorin 4C: A Novel Component of B-Cell Polarization in Th2-Driven Immune Responses. PMID:28003812
Datasets for the validation of the "in vivo" siRNA-silencing of CD40 and for the detection of new markers of atherosclerosis progression in ApoE-deficient mice. PMID:27924297
Function-driven discovery of disease genes in zebrafish using an integrated genomics big data resource. PMID:27903883
Transcriptome Dynamics in Mango Fruit Peel Reveals Mechanisms of Chilling Stress. PMID:27812364
Cluster Analysis of p53 Binding Site Sequences Reveals Subsets with Different Functions. PMID:27812278
Introducing the Big Knowledge to Use (BK2U) challenge. PMID:27750400
RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information. PMID:27717309
MiR-125a-3p timely inhibits oligodendroglial maturation and is pathologically up-regulated in human multiple sclerosis. PMID:27698367
A drug target slim: using gene ontology and gene ontology annotations to navigate protein-ligand target space in ChEMBL. PMID:27678076
The Tetraodon nigroviridis reference transcriptome: developmental transition, length retention and microsynteny of long non-coding RNAs in a compact vertebrate genome. PMID:27628538
Comparative analysis of transcriptomes in aerial stems and roots of Ephedra sinica based on high-throughput mRNA sequencing. PMID:27625990
Comparative proteomic analysis reveals alterations in development and photosynthesis-related proteins in diploid and triploid rice. PMID:27619227
Head Transcriptomes of Two Closely Related Species of Fruit Flies of the Anastrepha fraterculus Group Reveals Divergent Genes in Species with Extensive Gene Flow. PMID:27558666
Systems-level effects of ectopic galectin-7 reconstitution in cervical cancer and its microenvironment. PMID:27558259
Network analysis and juvenile idiopathic arthritis (JIA): a new horizon for the understanding of disease pathogenesis and therapeutic target identification. PMID:27411317
Reannotation of Yersinia pestis Strain 91001 Based on Omics Data. PMID:27382076
Gene regulation knowledge commons: community action takes care of DNA binding transcription factors. PMID:27270715
Weighted mutual information analysis substantially improves domain-based functional network models. PMID:27207946
Single-cell-type quantitative proteomic and ionomic analysis of epidermal bladder cells from the halophyte model plant Mesembryanthemum crystallinum to identify salt-responsive proteins. PMID:27160145
ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information. PMID:27153652
Genome-scale prediction of moonlighting proteins using diverse protein association information. PMID:27153604
Fungal and host transcriptome analysis of pH-regulated genes during colonization of apple fruits by Penicillium expansum. PMID:27146851
An examination of the regulatory mechanism of Pxdn mutation-induced eye disorders using microarray analysis. PMID:27121343
From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF. PMID:27114493
UbiNet: an online resource for exploring the functional associations and regulatory networks of protein ubiquitylation. PMID:27114492
Modeling fibrosis using fibroblasts isolated from scarred rat vocal folds. PMID:27111284
Requirements for the formal representation of pathophysiology mechanisms by clinicians. PMID:27051514
CTCF-mediated chromatin loops enclose inducible gene regulatory domains. PMID:27004515
Utilizing a structural meta-ontology for family-based quality assurance of the BioPortal ontologies. PMID:26988001
Transcriptome analysis reveals differentially expressed genes associated with germ cell and gonad development in the Southern bluefin tuna (Thunnus maccoyii). PMID:26965070
RNA sequencing to characterize transcriptional changes of sexual maturation and mating in the female oriental fruit fly Bactrocera dorsalis. PMID:26946038
Low Dose Iron Treatments Induce a DNA Damage Response in Human Endothelial Cells within Minutes. PMID:26866805
The Arabidopsis transcriptional regulator DPB3-1 enhances heat stress tolerance without growth retardation in rice. PMID:26841113
A new scheme to discover functional associations and regulatory networks of E3 ubiquitin ligases. PMID:26818115
Advanced Running Performance by Genetic Predisposition in Male Dummerstorf Marathon Mice (DUhTP) Reveals Higher Sterol Regulatory Element-Binding Protein (SREBP) Related mRNA Expression in the Liver and Higher Serum Levels of Progesterone. PMID:26799318
Diverse Hormone Response Networks in 41 Independent Drosophila Cell Lines. PMID:26772746
Mitochondrial iron chelation ameliorates cigarette smoke-induced bronchitis and emphysema in mice. PMID:26752519
LEGO: a novel method for gene set over-representation analysis by incorporating network-based gene weights. PMID:26750448
Bioinformatics identification of potentially involved microRNAs in Tibetan with gastric cancer based on microRNA profiling. PMID:26692821
Dynamic Proteomic Analysis of Pancreatic Mesenchyme Reveals Novel Factors That Enhance Human Embryonic Stem Cell to Pancreatic Cell Differentiation. PMID:26681951
Expressed Sequence Tags Analysis and Design of Simple Sequence Repeats Markers from a Full-Length cDNA Library in Perilla frutescens (L.). PMID:26664999
ALCOdb: Gene Coexpression Database for Microalgae. PMID:26644461
The Saccharomyces Genome Database: A Tool for Discovery. PMID:26631132
The Saccharomyces Genome Database: Gene Product Annotation of Function, Process, and Component. PMID:26631125
Identification of minimal eukaryotic introns through GeneBase, a user-friendly tool for parsing the NCBI Gene databank. PMID:26581719
PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features. PMID:26553811
Application of Functional Genomics for Bovine Respiratory Disease Diagnostics. PMID:26526746
CompGO: an R package for comparing and visualizing Gene Ontology enrichment differences between DNA binding experiments. PMID:26329719
Inntags: small self-structured epitopes for innocuous protein tagging. PMID:26322837
In Vivo Effects of Mesenchymal Stromal Cells in Two Patients With Severe Acute Respiratory Distress Syndrome. PMID:26285659
Evaluating the Hypoxia Response of Ruffe and Flounder Gills by a Combined Proteome and Transcriptome Approach. PMID:26273839
Potential anti-cancer effect of curcumin in human lung squamous cell carcinoma. PMID:26273408
Differential Proteomic Analysis Using iTRAQ Reveals Alterations in Hull Development in Rice (Oryza sativa L.). PMID:26230730
Biological processes and pathway changes in isoflurane-induced anesthesia revealed by bioinformatics analysis of gene expression profiles. PMID:26223573
The Arabidopsis information resource: Making and mining the "gold standard" annotated reference plant genome. PMID:26201819
Three-dimensional immersive virtual reality for studying cellular compartments in 3D models from EM preparations of neural tissues. PMID:26179415
Comparison of Gene Coexpression Profiles and Construction of Conserved Gene Networks to Find Functional Modules. PMID:26147120
Transcriptome response signatures associated with the overexpression of a mitochondrial uncoupling protein (AtUCP1) in tobacco. PMID:26106890
The Disease Ontology: fostering interoperability between biological and clinical human disease-related data. PMID:26093607
Comparative genomic and phenomic analysis of Clostridium difficile and Clostridium sordellii, two related pathogens with differing host tissue preference. PMID:26059449
Summarizing and visualizing structural changes during the evolution of biomedical ontologies using a Diff Abstraction Network. PMID:26048076
The mouse gene expression database: New features and how to use them effectively. PMID:26045019
A novel software architecture for the provision of context-aware semantic transport information. PMID:26016915
Differential Gene Expression Profiling of Dystrophic Dog Muscle after MuStem Cell Transplantation. PMID:25955839
FlyNet: a versatile network prioritization server for the Drosophila community. PMID:25943544
The SwissLipids knowledgebase for lipid biology. PMID:25943471
Hierarchical ensemble methods for protein function prediction. PMID:25937954
Pathway reporter genes define molecular phenotypes of human cells. PMID:25903797
Iterative carotenogenic screens identify combinations of yeast gene deletions that enhance sclareol production. PMID:25903744
The role of ontologies in biological and biomedical research: a functional perspective. PMID:25863278
Shared resources, shared costs--leveraging biocuration resources. PMID:25776020
The Open Physiology workflow: modeling processes over physiology circuitboards of interoperable tissue units. PMID:25759670
Transcription factor and microRNA-regulated network motifs for cancer and signal transduction networks. PMID:25707690
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study. PMID:25652942
EcoliNet: a database of cofunctional gene network for Escherichia coli. PMID:25650278
Annotation of proteins of unknown function: initial enzyme results. PMID:25630330
Using comparative genomics to drive new discoveries in microbiology. PMID:25617609
Microarray-based characterization of differential gene expression during vocal fold wound healing in rats. PMID:25592437
POEAS: Automated Plant Phenomic Analysis Using Plant Ontology. PMID:25574136
Exhaustive data mining comparison of the effects of low doses of ionizing radiation, formaldehyde and dioxins. PMID:25563934
An integrative approach for measuring semantic similarities using gene ontology. PMID:25559943
MOROKOSHI: transcriptome database in Sorghum bicolor. PMID:25505007
Genome-scale identification and characterization of moonlighting proteins. PMID:25497125
Methodology for the inference of gene function from phenotype data. PMID:25495798
Transcriptome sequencing reveals the virulence and environmental genetic programs of Vibrio vulnificus exposed to host and estuarine conditions. PMID:25489854
The conserved histone deacetylase Rpd3 and its DNA binding subunit Ume6 control dynamic transcript architecture during mitotic growth and meiotic development. PMID:25477386
Parallel profiling of fission yeast deletion mutants for proliferation and for lifespan during long-term quiescence. PMID:25452419
Estrogen receptor alpha drives proliferation in PTEN-deficient prostate carcinoma by stimulating survival signaling, MYC expression and altering glucose sensitivity. PMID:25436982
An ontology for microbial phenotypes. PMID:25433798
Genes regulating lipid and protein metabolism are highly expressed in mammary gland of lactating dairy goats. PMID:25433708
Gene Ontology Consortium: going forward. PMID:25428369
The BioGRID interaction database: 2015 update. PMID:25428363
Proteomics-Based Identification of Differentially Abundant Proteins from Human Keratinocytes Exposed to Arsenic Trioxide. PMID:25419056
BioModels: ten-year anniversary. PMID:25414348
The Pathogen-Host Interactions database (PHI-base): additions and future developments. PMID:25414340
ProteomeScout: a repository and analysis resource for post-translational modifications and proteins. PMID:25414335
Araport: the Arabidopsis information portal. PMID:25414324
PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs. PMID:25404129
dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S-nitrosylation. PMID:25399423
Helminth.net: expansions to Nematode.net and an introduction to Trematode.net. PMID:25392426
Rfam 12.0: updates to the RNA families database. PMID:25392425
Whole-genome sequencing of the world's oldest people. PMID:25390934
Proteomics for systems toxicology. PMID:25379146
Europe PMC: a full-text literature database for the life sciences and platform for innovation. PMID:25378340
Genome-wide patterns of polymorphism in an inbred line of the African malaria mosquito Anopheles gambiae. PMID:25377942
De-novo assembly of mango fruit peel transcriptome reveals mechanisms of mango response to hot water treatment. PMID:25373421
Human cancer databases (review). PMID:25369839
Transcriptome profiling of the UV-B stress response in the desert shrub Lycium ruthenicum. PMID:25366177
PomBase 2015: updates to the fission yeast database. PMID:25361970
The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease. PMID:25355511
AraNet v2: an improved database of co-functional gene networks for the study of Arabidopsis thaliana and 27 other nonmodel plant species. PMID:25355510
The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease. PMID:25348401
HAMAP in 2015: updates to the protein family classification and annotation system. PMID:25348399
The human DEPhOsphorylation database DEPOD: a 2015 update. PMID:25332398
Neuregulin-1β induces mature ventricular cardiac differentiation from induced pluripotent stem cells contributing to cardiac tissue repair. PMID:25329043
ImmuCo: a database of gene co-expression in immune cells. PMID:25326331
EpilepsyGene: a genetic resource for genes and mutations related to epilepsy. PMID:25324312
MoonProt: a database for proteins that are known to moonlight. PMID:25324305
The complex portal--an encyclopaedia of macromolecular complexes. PMID:25313161
Human germline and pan-cancer variomes and their distinct functional profiles. PMID:25232094
VirusMentha: a new resource for virus-host protein interactions. PMID:25217587
Proteome-wide subcellular topologies of E. coli polypeptides database (STEPdb). PMID:25210196
Transcriptome profiling of biliary atresia from new born infants by deep sequencing. PMID:25192893
Entropy-driven partitioning of the hierarchical protein space. PMID:25161256
Overview of the gene ontology task at BioCreative IV. PMID:25157073
Composition and applications of focus libraries to phenotypic assays. PMID:25104937
Selective clearance of aberrant tau proteins and rescue of neurotoxicity by transcription factor EB. PMID:25069841
Nonlinear quantitative radiation sensitivity prediction model based on NCI-60 cancer cell lines. PMID:25032244
Identification and characterization of long intergenic non-coding RNAs related to mouse liver development. PMID:25012394
Biophysical constraints on the evolution of tissue structure and function. PMID:24882821
What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins. PMID:24723265
Biblio-MetReS for user-friendly mining of genes and biological processes in scientific documents. PMID:24688854
Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt. PMID:24641996
Genomics and bioinformatics resources for translational science in Rosaceae. PMID:24634697
NCG 4.0: the network of cancer genes in the era of massive mutational screenings of cancer genomes. PMID:24608173
Protein-protein interactions prediction based on iterative clique extension with gene ontology filtering. PMID:24578640
Canto: an online tool for community literature curation. PMID:24574118
Genome-wide SNP calling using next generation sequencing data in tomato. PMID:24552708
Minimum information about a biofilm experiment (MIABiE): standards for reporting experiments and data on sessile microbial communities living at interfaces. PMID:24478124
Mining gene expression data for pollutants (dioxin, toluene, formaldehyde) and low dose of gamma-irradiation. PMID:24475070
Systems toxicology: from basic research to risk assessment. PMID:24446777
DBM-DB: the diamondback moth genome database. PMID:24434032
Galaxy tools to study genome diversity. PMID:24377391
Draft Genome Sequences of Human Pathogenic Fungus Geomyces pannorum Sensu Lato and Bat White Nose Syndrome Pathogen Geomyces (Pseudogymnoascus) destructans. PMID:24356829
The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. PMID:24319146
BacMet: antibacterial biocide and metal resistance genes database. PMID:24304895
topPTM: a new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins. PMID:24302577
MycoCosm portal: gearing up for 1000 fungal genomes. PMID:24297253
The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse. PMID:24285300
The Structure-Function Linkage Database. PMID:24271399
The European Bioinformatics Institute's data resources 2014. PMID:24271396
CentrosomeDB: a new generation of the centrosomal proteins database for Human and Drosophila melanogaster. PMID:24270791
Saccharomyces genome database provides new regulation data. PMID:24265222
Modulation of epidermal transcription circuits in psoriasis: new links between inflammation and hyperproliferation. PMID:24260178
MultitaskProtDB: a database of multitasking proteins. PMID:24253302
Ten quick tips for using the gene ontology. PMID:24244145
P³DB 3.0: From plant phosphorylation sites to protein networks. PMID:24243849
Mouse phenome database. PMID:24243846
The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. PMID:24234451
COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia. PMID:24214998
CottonGen: a genomics, genetics and breeding database for cotton research. PMID:24203703
GoMapMan: integration, consolidation and visualization of plant gene annotations within the MapMan ontology. PMID:24194592
FunCoup 3.0: database of genome-wide functional coupling networks. PMID:24185702
HRaP: database of occurrence of HomoRepeats and patterns in proteomes. PMID:24150944
Measuring the evolution of ontology complexity: the gene ontology case study. PMID:24146805
HoPaCI-DB: host-Pseudomonas and Coxiella interaction database. PMID:24137008
Selective anticancer agents suppress aging in Drosophila. PMID:24096697
3did: a catalog of domain-based interactions of known three-dimensional structure. PMID:24081580
Rebelling for a reason: protein structural "outliers". PMID:24073209
Manteia, a predictive data mining system for vertebrate genes and its applications to human genetic diseases. PMID:24038354
IDOMAL: the malaria ontology revisited. PMID:24034841
Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort. PMID:23981286
metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research. PMID:23935057
Bioinformatics for spermatogenesis: annotation of male reproduction based on proteomics. PMID:23852026
A guide to best practices for Gene Ontology (GO) manual annotation. PMID:23842463
FIDEA: a server for the functional interpretation of differential expression analysis. PMID:23754850
The banana genome hub. PMID:23707967
Comprehensive annotation of secondary metabolite biosynthetic genes and gene clusters of Aspergillus nidulans, A. fumigatus, A. niger and A. oryzae. PMID:23617571
Models incorporating chromatin modification data identify functionally important p53 binding sites. PMID:23599002
Transcriptome analyses reveal protein and domain families that delineate stage-related development in the economically important parasitic nematodes, Ostertagia ostertagi and Cooperia oncophora. PMID:23432754
Orchidstra: an integrated orchid functional genomics database. PMID:23324169 -
The Gene Ontology in 2010: extensions and refinements
PubMed citations: 252.
252 articles citing: The Gene Ontology in 2010: extensions and refinements
Comprehensive Identification of Human Cell Type Chromatin Activity-Specific and Cell Type Expression-Specific MicroRNAs. PMID:35806329
Eigenvectors from Eigenvalues Sparse Principal Component Analysis (EESPCA). PMID:35693984
Comprehensive genome wide identification and expression analysis of MTP gene family in tomato (Solanum lycopersicum) under multiple heavy metal stress. PMID:34866994
An Emiliania huxleyi pan-transcriptome reveals basal strain specificity in gene expression patterns. PMID:34675226
Genome-Wide Identification and Expression Analysis of Metal Tolerance Protein Gene Family in Medicago truncatula Under a Broad Range of Heavy Metal Stress. PMID:34603378
Identification of disease treatment mechanisms through the multiscale interactome. PMID:33741907
Predicting functions of maize proteins using graph convolutional network. PMID:33323113
Exploring Drug Treatment Patterns Based on the Action of Drug and Multilayer Network Model. PMID:32708644
Automated generation of gene summaries at the Alliance of Genome Resources. PMID:32559296
Arsenic Disulfide Promoted Hypomethylation by Increasing DNA Methyltransferases Expression in Myelodysplastic Syndrome. PMID:32431489
Traditional Chinese Medicine Containing Arsenic Treated MDS Patients Effectively through Regulating Aberrant Hypomethylation. PMID:32215045
A region-based gene association study combined with a leave-one-out sensitivity analysis identifies SMG1 as a pancreatic cancer susceptibility gene. PMID:31469826
Augmenting subnetwork inference with information extracted from the scientific literature. PMID:31246951
RNA sequencing uncovers the key long non-coding RNAs and potential molecular mechanism contributing to XAV939-mediated inhibition of non-small cell lung cancer. PMID:31186710
Analytical Validation of Clinical Whole-Genome and Transcriptome Sequencing of Patient-Derived Tumors for Reporting Targetable Variants in Cancer. PMID:30138725
Candidate gene and mechanism investigations in congenital obstructive nephropathy based on bioinformatics analysis. PMID:30015886
Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources. PMID:29931155
WEGO 2.0: a web tool for analyzing and plotting GO annotations, 2018 update. PMID:29788377
Effects of Zhizi Chuanxiong Capsule () on the Abnormal Methylation in Rabbits with Atherosclerosis. PMID:29752693
Computation and application of tissue-specific gene set weights. PMID:29659714
Effect of Qinghuang Powder () Combined with Bupi Yishen Decoction () in Treating Patients with Refractory Cytopenia with Multilineage Dysplasia through Regulating DNA Methylation. PMID:29500545
Convergent downstream candidate mechanisms of independent intergenic polymorphisms between co-classified diseases implicate epistasis among noncoding elements. PMID:29218911
A post-gene silencing bioinformatics protocol for plant-defence gene validation and underlying process identification: case study of the Arabidopsis thaliana NPR1. PMID:29169324
A genome-by-environment interaction classifier for precision medicine: personal transcriptome response to rhinovirus identifies children prone to asthma exacerbations. PMID:29016970
Extending XNAT Platform with an Incremental Semantic Framework. PMID:28912709
Perturbed human sub-networks by Fusobacterium nucleatum candidate virulence proteins. PMID:28793925
Comparing sequencing assays and human-machine analyses in actionable genomics for glioblastoma. PMID:28740869
Quality assurance of chemical ingredient classification for the National Drug File - Reference Terminology. PMID:28723580
E3 Ubiquitin ligase ZNRF4 negatively regulates NOD2 signalling and induces tolerance to MDP. PMID:28656966
Bacterial Virus Ontology; Coordinating across Databases. PMID:28545254
Gene set selection via LASSO penalized regression (SLPR). PMID:28472344
The physical characteristics of human proteins in different biological functions. PMID:28459865
Identifying key genes associated with Hirschsprung's disease based on bioinformatics analysis of RNA-sequencing data. PMID:28120235
Unsupervised gene set testing based on random matrix theory. PMID:27809777
Molecular mechanisms underlying COPD-muscle dysfunction unveiled through a systems medicine approach. PMID:27794560
Systematically characterizing dysfunctional long intergenic non-coding RNAs in multiple brain regions of major psychosis. PMID:27661005
Modeling biochemical pathways in the gene ontology. PMID:27589964
Integrative genomics analyses unveil downstream biological effectors of disease-specific polymorphisms buried in intergenic regions. PMID:27482468
Entropy-based divergent and convergent modular pattern reveals additive and synergistic anticerebral ischemia mechanisms. PMID:27480252
Exploring lateral genetic transfer among microbial genomes using TF-IDF. PMID:27452976
Statin Intensity or Achieved LDL? Practice-based Evidence for the Evaluation of New Cholesterol Treatment Guidelines. PMID:27227451
GCGene: a gene resource for gastric cancer with literature evidence. PMID:27127885
GeneAnalytics: An Integrative Gene Set Analysis Tool for Next Generation Sequencing, RNAseq and Microarray Data. PMID:26983021
Long-noncoding RNAs in basal cell carcinoma. PMID:26861560
Multi-tissue transcriptomics for construction of a comprehensive gene resource for the terrestrial snail Theba pisana. PMID:26852673
CSGene: a literature-based database for cell senescence genes and its application to identify critical cell aging pathways and associated diseases. PMID:26775705
CancerNet: a database for decoding multilevel molecular interactions across diverse cancer types. PMID:26690544
An evidence-based knowledgebase of metastasis suppressors to identify key pathways relevant to cancer metastasis. PMID:26486520
An Independent Filter for Gene Set Testing Based on Spectral Enrichment. PMID:26451820
Connectivity Homology Enables Inter-Species Network Models of Synthetic Lethality. PMID:26451775
ExoCarta: A Web-Based Compendium of Exosomal Cargo. PMID:26434508
My Corporis Fabrica Embryo: An ontology-based 3D spatio-temporal modeling of human embryo development. PMID:26413258
Host genetic variation impacts microbiome composition across human body sites. PMID:26374288
Mouse anatomy ontologies: enhancements and tools for exploring and integrating biomedical data. PMID:26208972
Pathway and network analysis of cancer genomes. PMID:26125594
dbEMT: an epithelial-mesenchymal transition associated gene resource. PMID:26099468
Pedican: an online gene resource for pediatric cancers with literature evidence. PMID:26073932
Dynamic changes of RNA-sequencing expression for precision medicine: N-of-1-pathways Mahalanobis distance within pathways of single subjects predicts breast cancer survival. PMID:26072495
Gene set analysis: A step-by-step guide. PMID:26059482
Towards a PBMC "virogram assay" for precision medicine: Concordance between ex vivo and in vivo viral infection transcriptomes. PMID:25797143
The Internet as a new tool in the rehabilitation process of patients--education in focus. PMID:25711359
Identification of Yellow Pigmentation Genes in Brassica rapa ssp. pekinensis Using Br300 Microarray. PMID:25629030
New mode of energy metabolism in the seventh order of methanogens as revealed by comparative genome analysis of “Candidatus methanoplasma termitum”. PMID:25501486
Information content-based Gene Ontology functional similarity measures: which one to use for a given biological data type? PMID:25474538
CMPD: cancer mutant proteome database. PMID:25398898
CATH: comprehensive structural and functional annotations for genome sequences. PMID:25348408
'N-of-1-pathways' unveils personal deregulated mechanisms from a single pair of RNA-Seq samples: towards precision medicine. PMID:25301808
Vitamin D prevents cognitive decline and enhances hippocampal synaptic function in aging rats. PMID:25267625
An integrated ontology resource to explore and study host-virus relationships. PMID:25233094
A semi-automated methodology for finding lipid-related GO terms. PMID:25209026
Systems-based analyses of brain regions functionally impacted in Parkinson's disease reveals underlying causal mechanisms. PMID:25170892
Concordance of deregulated mechanisms unveiled in underpowered experiments: PTBP1 knockdown case study. PMID:25079003
Building a hierarchical organization of protein complexes out of protein association data. PMID:24978199
The gene expression database for mouse development (GXD): putting developmental expression information at your fingertips. PMID:24958384
Structuring osteosarcoma knowledge: an osteosarcoma-gene association database based on literature mining and manual annotation. PMID:24865352
The DNA methylome and transcriptome of different brain regions in schizophrenia and bipolar disorder. PMID:24776767
Phenotype ontologies and cross-species analysis for translational research. PMID:24699242
High-throughput transcriptome sequencing and preliminary functional analysis in four Neotropical tree species. PMID:24673733
HybridGO-Loc: mining hybrid features on gene ontology for predicting subcellular localization of multi-location proteins. PMID:24647341
Annotation enrichment analysis: an alternative method for evaluating the functional properties of gene sets. PMID:24569707
Improving transcriptome construction in non-model organisms: integrating manual and automated gene definition in Emiliania huxleyi. PMID:24559402
DFLAT: functional annotation for human development. PMID:24507166
A Bayesian Hierarchical Model for Relating Multiple SNPs within Multiple Genes to Disease Risk. PMID:24490143
Insights into the maize pan-genome and pan-transcriptome. PMID:24488960
Comparative transcriptional profiling analysis of olive ripe-fruit pericarp and abscission zone tissues shows expression differences and distinct patterns of transcriptional regulation. PMID:24320622
Novel insights into embryonic stem cell self-renewal revealed through comparative human and mouse systems biology networks. PMID:24307629
HuPSON: the human physiology simulation ontology. PMID:24267822
The Reactome pathway knowledgebase. PMID:24243840
Annotating cancer variants and anti-cancer therapeutics in reactome. PMID:24213504
The mouse Gene Expression Database (GXD): 2014 update. PMID:24163257
The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments. PMID:24093723
Information content-based gene ontology semantic similarity approaches: toward a unified framework theory. PMID:24078912
DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures. PMID:24067102
The mouse pathology ontology, MPATH; structure and applications. PMID:24033988
IQdb: an intelligence quotient score-associated gene resource for human intelligence. PMID:24030781
EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update. PMID:23972281
Predicting and analyzing interactions between Mycobacterium tuberculosis and its human host. PMID:23844013
A guide to best practices for Gene Ontology (GO) manual annotation. PMID:23842463
Mining breast cancer genes with a network based noise-tolerant approach. PMID:23799982
Pathway databases: making chemical and biological sense of the genomic data flood. PMID:23706629
Similar properties of chondrocytes from osteoarthritis joints and mesenchymal stem cells from healthy donors for tissue engineering of articular cartilage. PMID:23671648
Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts. PMID:23599415
Computational analyses of transcriptomic data reveal the dynamic organization of the Escherichia coli chromosome under different conditions. PMID:23599001
Shotgun proteomic analysis on the diapause and non-diapause eggs of domesticated silkworm Bombyx mori. PMID:23580252
Endometrial receptivity: a revisit to functional genomics studies on human endometrium and creation of HGEx-ERdb. PMID:23555582
Suppression subtractive hybridization (SSH) combined with bioinformatics method: an integrated functional annotation approach for analysis of differentially expressed immune-genes in insects. PMID:23519487
In-depth performance evaluation of PFP and ESG sequence-based function prediction methods in CAFA 2011 experiment. PMID:23514353
Using nanoinformatics methods for automatically identifying relevant nanotoxicology entities from the literature. PMID:23509721
Transcriptomic events involved in melon mature-fruit abscission comprise the sequential induction of cell-wall degrading genes coupled to a stimulation of endo and exocytosis. PMID:23484021
Cell-type-specific predictive network yields novel insights into mouse embryonic stem cell self-renewal and cell fate. PMID:23468881
The repertoires of ubiquitinating and deubiquitinating enzymes in eukaryotic genomes. PMID:23393154
DNA damage and transcriptional changes in the gills of mytilus galloprovincialis exposed to nanomolar doses of combined metal salts (Cd, Cu, Hg). PMID:23355883
Phyletic profiling with cliques of orthologs is enhanced by signatures of paralogy relationships. PMID:23308060
Chapter 5: Network biology approach to complex diseases. PMID:23300411
Building an efficient curation workflow for the Arabidopsis literature corpus. PMID:23221298
BioCreative-2012 virtual issue. PMID:23221175
Karyotype and DNA-Methylation Responses in Myelodysplastic Syndromes following Treatment with Traditional Chinese Formula Containing Arsenic. PMID:23118798
Bio-crude transcriptomics: gene discovery and metabolic network reconstruction for the biosynthesis of the terpenome of the hydrocarbon oil-producing green alga, Botryococcus braunii race B (Showa). PMID:23110428
Cross-Ontology multi-level association rule mining in the Gene Ontology. PMID:23071802
MetNet Online: a novel integrated resource for plant systems biology. PMID:23066841
Metagenomic analysis: the challenge of the data bonanza. PMID:22962339
Analysis of functional pathways altered after mild traumatic brain injury. PMID:22913729
Schizophrenia shows a unique metabolomics signature in plasma. PMID:22892715
Assessment of community-submitted ontology annotations from a novel database-journal partnership. PMID:22859749
Ontologies as integrative tools for plant science. PMID:22847540
Function prediction and analysis of mycobacterium tuberculosis hypothetical proteins. PMID:22837694
Cell type specificity of signaling: view from membrane receptors distribution and their downstream transduction networks. PMID:22802048
Protein interactions with piALU RNA indicates putative participation of retroRNA in the cell cycle, DNA repair and chromatin assembly. PMID:22754750
Quality of computationally inferred gene ontology annotations. PMID:22693439
A topology-based metric for measuring term similarity in the gene ontology. PMID:22666244
Cis-acting polymorphisms affect complex traits through modifications of microRNA regulation pathways. PMID:22606281
BRCT domains: A little more than kin, and less than kind. PMID:22584059
GPSy: a cross-species gene prioritization system for conserved biological processes--application in male gamete development. PMID:22570409
Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing. PMID:22558305
Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL. PMID:22541594
Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology. PMID:22539675
Nprl3 is required for normal development of the cardiovascular system. PMID:22538705
Candidate pathway based analysis for cleft lip with or without cleft palate. PMID:22499695
Multiple apical plasma membrane constituents are associated with susceptibility to meconium ileus in individuals with cystic fibrosis. PMID:22466613
Ontology searching and browsing at the Rat Genome Database. PMID:22434847
CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. PMID:22434836
The mouse-human anatomy ontology mapping project. PMID:22434834
Functional roles for redox genes in ethanol sensitivity in Drosophila. PMID:22430022
An update on the strategies in multicomponent activity monitoring within the phytopharmaceutical field. PMID:22417247
QServer: a biclustering server for prediction and assessment of co-expressed gene clusters. PMID:22403692
On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report. PMID:22359495
CytoSaddleSum: a functional enrichment analysis plugin for Cytoscape based on sum-of-weights scores. PMID:22345616
Implications of functional similarity for gene regulatory interactions. PMID:22298814
vHOG, a multispecies vertebrate ontology of homologous organs groups. PMID:22285560
Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison. PMID:22275074
Transcriptome-based differentiation of closely-related Miscanthus lines. PMID:22253803
Solving the Problem: Genome Annotation Standards before the Data Deluge. PMID:22180819
The impact of focused Gene Ontology curation of specific mammalian systems. PMID:22174742
Using the gene ontology to scan multilevel gene sets for associations in genome wide association studies. PMID:22161999
Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences. PMID:22146221
Idiopathic and heritable PAH perturb common molecular pathways, correlated with increased MSX1 expression. PMID:22140629
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. PMID:22140109
CharProtDB: a database of experimentally characterized protein annotations. PMID:22140108
ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species. PMID:22140105
MetaBase--the wiki-database of biological databases. PMID:22139927
Nematode.net update 2011: addition of data sets and tools featuring next-generation sequencing data. PMID:22139919
neXtProt: a knowledge platform for human proteins. PMID:22139911
The UniProt-GO Annotation database in 2011. PMID:22123736
UniPathway: a resource for the exploration and annotation of metabolic pathways. PMID:22102589
The Gene Ontology: enhancements for 2011. PMID:22102568
dbDEPC 2.0: updated database of differentially expressed proteins in human cancers. PMID:22096234
Repercussion of Mitochondria Deformity Induced by Anti-Hsp90 Drug 17AAG in Human Tumor Cells. PMID:22087060
Disease Ontology: a backbone for disease semantic integration. PMID:22080554
GeneWeaver: a web-based system for integrative functional genomics. PMID:22080549
Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers. PMID:22080467
The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse. PMID:22075990
FungiDB: an integrated functional genomics database for fungi. PMID:22064857
PomBase: a comprehensive online resource for fission yeast. PMID:22039153
Heat shock partially dissociates the overlapping modules of the yeast protein-protein interaction network: a systems level model of adaptation. PMID:22022244
BioPAX support in CellDesigner. PMID:22021903
The transcriptome of the novel dinoflagellate Oxyrrhis marina (Alveolata: Dinophyceae): response to salinity examined by 454 sequencing. PMID:22014029
The Reactome BioMart. PMID:22012987
Direct iterative protein profiling (DIPP) - an innovative method for large-scale protein detection applied to budding yeast mitosis. PMID:21997732
Genes2WordCloud: a quick way to identify biological themes from gene lists and free text. PMID:21995939
Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop. PMID:21994619
Prioritizing human cancer microRNAs based on genes' functional consistency between microRNA and cancer. PMID:21976726
Functional analysis beyond enrichment: non-redundant reciprocal linkage of genes and biological terms. PMID:21949701
Quantification of protein group coherence and pathway assignment using functional association. PMID:21929787
Oxidative injury is a common consequence of BMPR2 mutations. PMID:21904662
Minimum information about a bioactive entity (MIABE). PMID:21878981
Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. PMID:21873635
Integrating systems biology models and biomedical ontologies. PMID:21835028
How the gene ontology evolves. PMID:21819553
Dynamics of nuclear matrix proteome during embryonic development in Drosophila melanogaster. PMID:21799256
Genome-scale phylogenetic function annotation of large and diverse protein families. PMID:21784873
COLOMBOS: access port for cross-platform bacterial expression compendia. PMID:21779320
Transcriptome profiling and insilico analysis of Gynostemma pentaphyllum using a next generation sequencer. PMID:21769605
Reactome pathway analysis to enrich biological discovery in proteomics data sets. PMID:21751369
Systematic approaches towards the development of host-directed antiviral therapeutics. PMID:21747723
Therapy-, gender- and race-specific microRNA markers, target genes and networks related to glioblastoma recurrence and survival. PMID:21737610
Generation and analysis of expressed sequence tags from the bone marrow of Chinese Sika deer. PMID:21681423
MarkUs: a server to navigate sequence-structure-function space. PMID:21672961
The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences. PMID:21646335
A protein network-guided screen for cell cycle regulators in Drosophila. PMID:21548953
Ontologies and standards in bioscience research: for machine or for human. PMID:21519400
UniProt Knowledgebase: a hub of integrated protein data. PMID:21447597
Exploration of plant genomes in the FLAGdb++ environment. PMID:21447150
The representation of heart development in the gene ontology. PMID:21419760
Gene discovery in Triatoma infestans. PMID:21418565
Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. PMID:21411447
Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches. PMID:21408204
Disease and phenotype data at Ensembl. PMID:21400687
Autism candidate genes via mouse phenomics. PMID:21397722
GOChase-II: correcting semantic inconsistencies from Gene Ontology-based annotations for gene products. PMID:21342572
The what, where, how and why of gene ontology--a primer for bioinformaticians. PMID:21330331
Quantifying protein function specificity in the gene ontology. PMID:21304708
Dr. PIAS: an integrative system for assessing the druggability of protein-protein interactions. PMID:21303559
The Mouse Tumor Biology Database (MTB): a central electronic resource for locating and integrating mouse tumor pathology data. PMID:21282667
Ubiquitin-proteasome genes as targets for modulation of cisplatin sensitivity in fission yeast. PMID:21247416
Logical development of the cell ontology. PMID:21208450
Execution of the meiotic noncoding RNA expression program and the onset of gametogenesis in yeast require the conserved exosome subunit Rrp6. PMID:21149693
Correlating traits of gene retention, sequence divergence, duplicability and essentiality in vertebrates, arthropods, and fungi. PMID:21148284
Gerontome: a web-based database server for aging-related genes and analysis pipelines. PMID:21143804
IntelliGO: a new vector-based semantic similarity measure including annotation origin. PMID:21122125
Computational biology for ageing. PMID:21115530
Entrez Gene: gene-centered information at NCBI. PMID:21115458
EcoCyc: a comprehensive database of Escherichia coli biology. PMID:21097882
Chondrogenic differentiation of human bone marrow-derived mesenchymal stem cells in self-gelling alginate discs reveals novel chondrogenic signature gene clusters. PMID:21087199
AgBase: supporting functional modeling in agricultural organisms. PMID:21075795
Molecular and physiological responses to juvenile traumatic brain injury: focus on growth and metabolism. PMID:21071915
ConsensusPathDB: toward a more complete picture of cell biology. PMID:21071422
CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality. PMID:21071393
Reactome: a database of reactions, pathways and biological processes. PMID:21067998
The mouse Gene Expression Database (GXD): 2011 update. PMID:21062809
Human and chicken TLR pathways: manual curation and computer-based orthology analysis. PMID:21052677
The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics. PMID:21051359
Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. PMID:21045053
DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila. PMID:21036869
ZFIN: enhancements and updates to the Zebrafish Model Organism Database. PMID:21036866
The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources. PMID:21030441
OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011. PMID:20972218
TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins. PMID:20965969
ProFITS of maize: a database of protein families involved in the transduction of signalling in the maize genome. PMID:20955618
KUPS: constructing datasets of interacting and non-interacting protein pairs with associated attributions. PMID:20952400
ViralZone: a knowledge resource to understand virus diversity. PMID:20947564
The Protein Ontology: a structured representation of protein forms and complexes. PMID:20935045
MatrixDB, the extracellular matrix interaction database. PMID:20852260
IDOMAL: an ontology for malaria. PMID:20698959
Protein kinase target discovery from genome-wide messenger RNA expression profiling. PMID:20687179
The systematic annotation of the three main GPCR families in Reactome. PMID:20671204
Somatic polyploidy promotes cell function under stress and energy depletion: evidence from tissue-specific mammal transcriptome. PMID:20625914
TabSQL: a MySQL tool to facilitate mapping user data to public databases. PMID:20573251
Nuclear matrix proteome analysis of Drosophila melanogaster. PMID:20530634
Ontologies in quantitative biology: a basis for comparison, integration, and discovery. PMID:20520843
A MOD(ern) perspective on literature curation. PMID:20221640
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. PMID:20015972
The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources. PMID:19965766 -
The Gene Ontology: enhancements for 2011
PubMed citations: 117.
117 articles citing: The Gene Ontology: enhancements for 2011
Transcriptome Remodeling in Gradual Development of Inverse Resistance between Paclitaxel and Cisplatin in Ovarian Cancer Cells. PMID:33287223
YEASTRACT+: a portal for cross-species comparative genomics of transcription regulation in yeasts. PMID:31586406
The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species. PMID:31214208
The Gene Ontology Resource: 20 years and still GOing strong. PMID:30395331
Identification of ceRNA network based on a RNA-seq shows prognostic lncRNA biomarkers in human lung adenocarcinoma. PMID:30344725
Predicting human protein function with multi-task deep neural networks. PMID:29889900
WEGO 2.0: a web tool for analyzing and plotting GO annotations, 2018 update. PMID:29788377
Cross-species multiple environmental stress responses: An integrated approach to identify candidate genes for multiple stress tolerance in sorghum (Sorghum bicolor (L.) Moench) and related model species. PMID:29590108
Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework. PMID:29385081
The ins and outs of eukaryotic viruses: Knowledge base and ontology of a viral infection. PMID:28207819
Datasets for the validation of the "in vivo" siRNA-silencing of CD40 and for the detection of new markers of atherosclerosis progression in ApoE-deficient mice. PMID:27924297
Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder. PMID:27479844
Pathway and network-based strategies to translate genetic discoveries into effective therapies. PMID:27340225
Dysfunctional miRNA-Mediated Regulation in Chromophobe Renal Cell Carcinoma. PMID:27258182
The genome of the miiuy croaker reveals well-developed innate immune and sensory systems. PMID:26902509
SOHSite: incorporating evolutionary information and physicochemical properties to identify protein S-sulfenylation sites. PMID:26819243
Identification of novel genes and pathways in carotid atheroma using integrated bioinformatic methods. PMID:26742467
Extensive Transcriptome Changes During Natural Onset and Release of Vegetative Bud Dormancy in Populus. PMID:26734012
A-DaGO-Fun: an adaptable Gene Ontology semantic similarity-based functional analysis tool. PMID:26476781
Global transcriptome and gene regulation network for secondary metabolite biosynthesis of tea plant (Camellia sinensis). PMID:26220550
Representing virus-host interactions and other multi-organism processes in the Gene Ontology. PMID:26215368
Genome Sequence of Acidovorax citrulli Group 1 Strain pslb65 Causing Bacterial Fruit Blotch of Melons. PMID:25908136
Genome Sequence of a Copper-Resistant Strain of Acidovorax citrulli Causing Bacterial Fruit Blotch of Melons. PMID:25908132
KaBOB: ontology-based semantic integration of biomedical databases. PMID:25903923
Exploring triacylglycerol biosynthetic pathway in developing seeds of Chia (Salvia hispanica L.): a transcriptomic approach. PMID:25875809
Genome Sequence of a Pseudomonas syringae pv. tabaci Strain, yuexi-1, Causing Wildfire Disease in Tobacco. PMID:25858831
Discovery of molecular markers to discriminate corneal endothelial cells in the human body. PMID:25807145
Ontology application and use at the ENCODE DCC. PMID:25776021
An ontology approach to comparative phenomics in plants. PMID:25774204
CSAX: Characterizing Systematic Anomalies in eXpression Data. PMID:25651392
Identification of retinopathy of prematurity related miRNAs in hyperoxia-induced neonatal rats by deep sequencing. PMID:25561234
A regulatory similarity measure using the location information of transcription factor binding sites in Saccharomyces cerevisiae. PMID:25560196
Metazoan remaining genes for essential amino acid biosynthesis: sequence conservation and evolutionary analyses. PMID:25545100
Gene Ontology Consortium: going forward. PMID:25428369
The draft genome of the large yellow croaker reveals well-developed innate immunity. PMID:25407894
The use of semantic similarity measures for optimally integrating heterogeneous Gene Ontology data from large scale annotation pipelines. PMID:25147557
Standardized description of scientific evidence using the Evidence Ontology (ECO). PMID:25052702
Transcriptional targets of the schizophrenia risk gene MIR137. PMID:24984191
BioCreative-IV virtual issue. PMID:24852177
Copy number variation in schizophrenia in Sweden. PMID:24776740
Identification of functional modules by integration of multiple data sources using a Bayesian network classifier. PMID:24736851
A rule-based ontological framework for the classification of molecules. PMID:24735706
RNA editome in rhesus macaque shaped by purifying selection. PMID:24722121
HybridGO-Loc: mining hybrid features on gene ontology for predicting subcellular localization of multi-location proteins. PMID:24647341
Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies. PMID:24595056
M-Finder: Uncovering functionally associated proteins from interactome data integrated with GO annotations. PMID:24565382
Identification of core T cell network based on immunome interactome. PMID:24528953
DFLAT: functional annotation for human development. PMID:24507166
Functional categorization of transcriptome in the species Symphysodon aequifasciatus Pellegrin 1904 (Perciformes: Cichlidae) exposed to benzo[a]pyrene and phenanthrene. PMID:24312524
NeXO Web: the NeXO ontology database and visualization platform. PMID:24271398
The European Bioinformatics Institute's data resources 2014. PMID:24271396
Representing annotation compositionality and provenance for the Semantic Web. PMID:24268021
De novo characterization of the Anthurium transcriptome and analysis of its digital gene expression under cold stress. PMID:24267953
ArchDB 2014: structural classification of loops in proteins. PMID:24265221
Ten quick tips for using the gene ontology. PMID:24244145
Ontology based molecular signatures for immune cell types via gene expression analysis. PMID:24004649
TCW: transcriptome computational workbench. PMID:23874959
Large-scale gene function analysis with the PANTHER classification system. PMID:23868073
Prioritizing Potentially Druggable Mutations with dGene: An Annotation Tool for Cancer Genome Sequencing Data. PMID:23826350
Biochemical Characterization of Hypothetical Proteins from Helicobacter pylori. PMID:23825549
GoSynthetic database tool to analyse natural and engineered molecular processes. PMID:23813641
Optimization criteria and biological process enrichment in homologous multiprotein modules. PMID:23757502
FIDEA: a server for the functional interpretation of differential expression analysis. PMID:23754850
FYPO: the fission yeast phenotype ontology. PMID:23658422
PhenoMiner: quantitative phenotype curation at the rat genome database. PMID:23603846
Genome-wide identification of bone metastasis-related microRNAs in lung adenocarcinoma by high-throughput sequencing. PMID:23593434
Systematic curation of protein and genetic interaction data for computable biology. PMID:23587305
Comparative GO: a web application for comparative gene ontology and gene ontology-based gene selection in bacteria. PMID:23536820
ORFcor: identifying and accommodating ORF prediction inconsistencies for phylogenetic analysis. PMID:23484025
A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation. PMID:23445355
Defining the extracellular matrix using proteomics. PMID:23419153
The YeastGenome app: the Saccharomyces Genome Database at your fingertips. PMID:23396302
Use of Gene Ontology Annotation to understand the peroxisome proteome in humans. PMID:23327938
RamiGO: an R/Bioconductor package providing an AmiGO visualize interface. PMID:23297033
The plant ontology as a tool for comparative plant anatomy and genomic analyses. PMID:23220694
The ortholog conjecture is untestable by the current gene ontology but is supported by RNA sequencing data. PMID:23209392
BSRD: a repository for bacterial small regulatory RNA. PMID:23203879
New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures. PMID:23203873
COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals. PMID:23203868
NetwoRx: connecting drugs to networks and phenotypes in Saccharomyces cerevisiae. PMID:23203867
Virus pathogen database and analysis resource (ViPR): a comprehensive bioinformatics database and analysis resource for the coronavirus research community. PMID:23202522
H-InvDB in 2013: an omics study platform for human functional gene and transcript discovery. PMID:23197657
DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications. PMID:23193290
PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. PMID:23193289
GenColors-based comparative genome databases for small eukaryotic genomes. PMID:23193285
The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology. PMID:23193278
HAMAP in 2013, new developments in the protein family classification and annotation system. PMID:23193261
The RCSB Protein Data Bank: new resources for research and education. PMID:23193259
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs. PMID:23180791
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. PMID:23180789
The mouse genome database: genotypes, phenotypes, and models of human disease. PMID:23175610
eProS--a database and toolbox for investigating protein sequence-structure-function relationships through energy profiles. PMID:23161695
SchistoDB: an updated genome resource for the three key schistosomes of humans. PMID:23161692
Gene Ontology annotations and resources. PMID:23161678
Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR. PMID:23160413
Opportunities for text mining in the FlyBase genetic literature curation workflow. PMID:23160412
Text-mining solutions for biomedical research: enabling integrative biology. PMID:23150036
Genome sequences of wild and domestic bactrian camels. PMID:23149746
MonarchBase: the monarch butterfly genome database. PMID:23143105
CellLineNavigator: a workbench for cancer cell line analysis. PMID:23118487
Linkers of cell polarity and cell cycle regulation in the fission yeast protein interaction network. PMID:23093924
BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions. PMID:23087378
Cross-Ontology multi-level association rule mining in the Gene Ontology. PMID:23071802
AbsIDconvert: an absolute approach for converting genetic identifiers at different granularities. PMID:22967011
Human more complex than mouse at cellular level. PMID:22911852
Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data. PMID:22898448
Endosomal crosstalk: meeting points for signaling pathways. PMID:22796207
Genetic architectures of psychiatric disorders: the emerging picture and its implications. PMID:22777127
Concept annotation in the CRAFT corpus. PMID:22776079
From classification to epilepsy ontology and informatics. PMID:22765502
ProteinHistorian: tools for the comparative analysis of eukaryote protein origin. PMID:22761559
Grand Challenges in Plant Systems Biology: Closing the Circle(s). PMID:22639645
Functional and topological characterization of transcriptional cooperativity in yeast. PMID:22574744
OREMPdb: a semantic dictionary of computational pathway models. PMID:22536973
Accelerating discovery for complex neurological and behavioral disorders through systems genetics and integrative genomics in the laboratory mouse. PMID:22422471
The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. PMID:22144685
The UniProt-GO Annotation database in 2011. PMID:22123736 -
The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species
PubMed citations: 101.
101 articles citing: The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species
Contributions of Artificial Intelligence Reported in Obstetrics and Gynecology Journals: Systematic Review. PMID:35297766
PANTHER: Making genome-scale phylogenetics accessible to all. PMID:34717010
Structure-based protein function prediction using graph convolutional networks. PMID:34039967
Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylation in the Phytopathogenic Fungus Botrytis cinerea. PMID:33329453
Predicting functions of maize proteins using graph convolutional network. PMID:33323113
Development and validation of prognostic gene signature for basal-like breast cancer and high-grade serous ovarian cancer. PMID:32880016
Molecular genotyping, diversity studies and high-resolution molecular markers unveiled by microsatellites in Giardia duodenalis. PMID:30500829
The evolutionary signal in metagenome phyletic profiles predicts many gene functions. PMID:29991352
A descriptive marker gene approach to single-cell pseudotime inference. PMID:29939207
OmicsNet: a web-based tool for creation and visual analysis of biological networks in 3D space. PMID:29878180
Integrative genomics identifies new genes associated with severe COPD and emphysema. PMID:29566699
Metagenomic Analysis of Microbial Diversity in Landfill Lysimeter Soil of Ghazipur Landfill Site, New Delhi, India. PMID:29051248
Metagenomic Sequencing of Microbial Communities from Brackish Water of Pangong Lake of the Northwest Indian Himalayas. PMID:28982995
Global transcriptome analysis of the maize (Zea mays L.) inbred line 08LF during leaf senescence initiated by pollination-prevention. PMID:28973044
NoGOA: predicting noisy GO annotations using evidences and sparse representation. PMID:28732468
RNA target profiles direct the discovery of virulence functions for the cold-shock proteins CspC and CspE. PMID:28611217
The Biomphalaria glabrata DNA methylation machinery displays spatial tissue expression, is differentially active in distinct snail populations and is modulated by interactions with Schistosoma mansoni. PMID:28510608
Combined Administration of ASCs and BMP-12 Promotes an M2 Macrophage Phenotype and Enhances Tendon Healing. PMID:28462460
Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae. PMID:28446171
Genomic responses to the socio-sexual environment in male Drosophila melanogaster exposed to conspecific rivals. PMID:28428330
Neuropilin-1 Is Expressed on Lymphoid Tissue Residing LTi-like Group 3 Innate Lymphoid Cells and Associated with Ectopic Lymphoid Aggregates. PMID:28199847
Interspecies gene function prediction using semantic similarity. PMID:28155711
LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells. PMID:28056766
Expansion of the Gene Ontology knowledgebase and resources. PMID:27899567
The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations. PMID:27812948
Primer on the Gene Ontology. PMID:27812933
Behavioral, morphometric, and gene expression effects in adult zebrafish (Danio rerio) embryonically exposed to PFOA, PFOS, and PFNA. PMID:27710860
Functional Annotations of Paralogs: A Blessing and a Curse. PMID:27618105
MicroRNAs as biomarkers for major depression: a role for let-7b and let-7c. PMID:27483380
A draft map of the mouse pluripotent stem cell spatial proteome. PMID:26754106
COGNIZER: A Framework for Functional Annotation of Metagenomic Datasets. PMID:26561344
Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells. PMID:26430063
Mouse Genome Database: From sequence to phenotypes and disease models. PMID:26150326
Using Gene Ontology to describe the role of the neurexin-neuroligin-SHANK complex in human, mouse and rat and its relevance to autism. PMID:26047810
Combination of inflammation-related cytokines promotes long-term muscle stem cell expansion. PMID:25976405
Community challenges in biomedical text mining over 10 years: success, failure and the future. PMID:25935162
Transcript and protein expression decoupling reveals RNA binding proteins and miRNAs as potential modulators of human aging. PMID:25853883
INTEGRATING COMPUTATIONAL PROTEIN FUNCTION PREDICTION INTO DRUG DISCOVERY INITIATIVES. PMID:25530654
Expression profiles of long non-coding RNAs located in autoimmune disease-associated regions reveal immune cell-type specificity. PMID:25419237
UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. PMID:25398609
PLAZA 3.0: an access point for plant comparative genomics. PMID:25324309
Managing, analysing, and integrating big data in medical bioinformatics: open problems and future perspectives. PMID:25254202
The use of semantic similarity measures for optimally integrating heterogeneous Gene Ontology data from large scale annotation pipelines. PMID:25147557
Standardized description of scientific evidence using the Evidence Ontology (ECO). PMID:25052702
OMIT: dynamic, semi-automated ontology development for the microRNA domain. PMID:25025130
A Gpr120-selective agonist improves insulin resistance and chronic inflammation in obese mice. PMID:24997608
Protein Ontology: a controlled structured network of protein entities. PMID:24270789
Large-scale gene function analysis with the PANTHER classification system. PMID:23868073
A genome-wide integrative study of microRNAs in human liver. PMID:23758991
A semi-automated genome annotation comparison and integration scheme. PMID:23725374
A protein prioritization approach tailored for the FA/BRCA pathway. PMID:23620800
SNPranker 2.0: a gene-centric data mining tool for diseases associated SNP prioritization in GWAS. PMID:23369106
Phyletic profiling with cliques of orthologs is enhanced by signatures of paralogy relationships. PMID:23308060
PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. PMID:23193289
ProteinHistorian: tools for the comparative analysis of eukaryote protein origin. PMID:22761559
Quality of computationally inferred gene ontology annotations. PMID:22693439
Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs. PMID:22615551
Mining Gene Ontology Data with AGENDA. PMID:22553422
Toward community standards in the quest for orthologs. PMID:22332236
Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. PMID:22301074
Accurate evaluation and analysis of functional genomics data and methods. PMID:22268703
The impact of focused Gene Ontology curation of specific mammalian systems. PMID:22174742
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. PMID:22140109
Proteomics plus genomics approaches in primary immunodeficiency: the case of immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome. PMID:22132891
GeneSigDB: a manually curated database and resource for analysis of gene expression signatures. PMID:22110038
Saccharomyces Genome Database: the genomics resource of budding yeast. PMID:22110037
GONUTS: the Gene Ontology Normal Usage Tracking System. PMID:22110029
The Gene Ontology: enhancements for 2011. PMID:22102568
The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse. PMID:22075990
AIGO: towards a unified framework for the analysis and the inter-comparison of GO functional annotations. PMID:22054122
The dynamics and evolutionary potential of domain loss and emergence. PMID:22016574
The Reactome BioMart. PMID:22012987
New resources for functional analysis of omics data for the genus Aspergillus. PMID:21974739
Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. PMID:21873635
Reactome pathway analysis to enrich biological discovery in proteomics data sets. PMID:21751369
Systematic approaches towards the development of host-directed antiviral therapeutics. PMID:21747723
PILGRM: an interactive data-driven discovery platform for expert biologists. PMID:21653547
Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation. PMID:21556138
Ontologies and standards in bioscience research: for machine or for human. PMID:21519400
Inferring protein function from homology using the Princeton Protein Orthology Database (P-POD). PMID:21400696
The what, where, how and why of gene ontology--a primer for bioinformaticians. PMID:21330331
Combining modularity, conservation, and interactions of proteins significantly increases precision and coverage of protein function prediction. PMID:21171995
AgBase: supporting functional modeling in agricultural organisms. PMID:21075795
The BioGRID Interaction Database: 2011 update. PMID:21071413
Reactome: a database of reactions, pathways and biological processes. PMID:21067998
Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development. PMID:20973947
Gene regulatory network reveals oxidative stress as the underlying molecular mechanism of type 2 diabetes and hypertension. PMID:20942928
The Protein Ontology: a structured representation of protein forms and complexes. PMID:20935045
The Renal Gene Ontology Annotation Initiative. PMID:20885853
Improving disease gene prioritization using the semantic similarity of Gene Ontology terms. PMID:20823322
GIGA: a simple, efficient algorithm for gene tree inference in the genomic age. PMID:20534164
A multilevel data integration resource for breast cancer study. PMID:20525248
A MOD(ern) perspective on literature curation. PMID:20221640
Visualization of multiple alignments, phylogenies and gene family evolution. PMID:20195253
PLAZA: a comparative genomics resource to study gene and genome evolution in plants. PMID:20040540
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. PMID:20015972
Representing ontogeny through ontology: a developmental biologist's guide to the gene ontology. PMID:19921742
The Gene Ontology in 2010: extensions and refinements. PMID:19920128
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. PMID:19892828
Computational resources in infectious disease: limitations and challenges. PMID:19855825
Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation. PMID:19622167 -
Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology
PubMed citations: 20.
20 articles citing: Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology
Improved characterisation of clinical text through ontology-based vocabulary expansion. PMID:33845909
Learning chemistry: exploring the suitability of machine learning for the task of structure-based chemical ontology classification. PMID:33726837
BiPOm: a rule-based ontology to represent and infer molecule knowledge from a biological process-centered viewpoint. PMID:32703160
Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems. PMID:31548717
ROBOT: A Tool for Automating Ontology Workflows. PMID:31357927
From Affective Science to Psychiatric Disorder: Ontology as a Semantic Bridge. PMID:30349491
Using OWL reasoning to support the generation of novel gene sets for enrichment analysis. PMID:29444698
The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes. PMID:29169408
Modeling biochemical pathways in the gene ontology. PMID:27589964
Functional Profiling of Human MeCP2 by Automated Data Comparison Analysis and Computerized Expression Pathway Modeling. PMID:27200222
Using the Gene Ontology to Annotate Key Players in Parkinson's Disease. PMID:26825309
ChEBI in 2016: Improved services and an expanding collection of metabolites. PMID:26467479
TermGenie - a web-application for pattern-based ontology class generation. PMID:25937883
Genetic resources for advanced biofuel production described with the Gene Ontology. PMID:25346727
Updates in Rhea--a manually curated resource of biochemical reactions. PMID:25332395
A semi-automated methodology for finding lipid-related GO terms. PMID:25209026
My Corporis Fabrica: an ontology-based tool for reasoning and querying on complex anatomical models. PMID:24936286
A method for increasing expressivity of Gene Ontology annotations using a compositional approach. PMID:24885854
The European Bioinformatics Institute's data resources 2014. PMID:24271396
Ten quick tips for using the gene ontology. PMID:24244145 - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3037419/
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323945/
- https://doi.org/10.1093/nar/gkaa1113
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annotation
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
biocuration
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
biological process
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
cellular component
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
data model
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
gene
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
gene ontology enrichment
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
gene expression data
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
gene functional annotation
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
knowledge representation
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
molecular function
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
sequence annotation
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
transcript
metasource: Fairsharing.org
version: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
genomics databases (non-vertebrate)
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
genome annotation terms, ontologies and nomenclature
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
ontology and terminology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:12.564649
zoology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:12.564649
gene expression
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:12.564649
small molecules
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:12.564649
gene structure
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:12.564649
Tags
More detailed information about this field from each metasource.
annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
biocuration
metasource: Fairsharing.orgversion: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
biological process
metasource: Fairsharing.orgversion: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
cellular component
metasource: Fairsharing.orgversion: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
data model
metasource: Fairsharing.orgversion: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
gene
metasource: Fairsharing.orgversion: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
gene ontology enrichment
metasource: Fairsharing.orgversion: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
gene expression data
metasource: Fairsharing.orgversion: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
gene functional annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
knowledge representation
metasource: Fairsharing.orgversion: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
molecular function
metasource: Fairsharing.orgversion: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
sequence annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
transcript
metasource: Fairsharing.orgversion: FAIRsharing.org: GO; Gene Ontology; DOI: https://doi.org/10.25504/FAIRsharing.6xq0ee; Last edited: Nov. 22, 2020, 3:16 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
genomics databases (non-vertebrate)
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
genome annotation terms, ontologies and nomenclature
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
ontology and terminology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.564649
zoology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.564649
gene expression
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.564649
small molecules
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.564649
gene structure
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:12.564649
biocuration biological process cellular component data model gene gene ontology enrichment gene expression gene functional annotation knowledge representation molecular function protein sequence annotation transcript genomics genome annotation terms, ontologies and nomenclature ontology and terminology zoology gene expression small molecule gene structure
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