Gene Expression Omnibus
Names
More detailed information about this field from each metasource.
Gene Expression Omnibus
metasource: Fairsharing.org
version: FAIRsharing.org: GEO; Gene Expression Omnibus; DOI: https://doi.org/10.25504/FAIRsharing.5hc8vt; Last edited: April 26, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: re3data.org
version: re3data.org: Gene Expression Omnibus; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R33P44 last accessed: 2022-11-04
GEO
metasource: Fairsharing.org
version: FAIRsharing.org: GEO; Gene Expression Omnibus; DOI: https://doi.org/10.25504/FAIRsharing.5hc8vt; Last edited: April 26, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: re3data.org
version: re3data.org: Gene Expression Omnibus; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R33P44 last accessed: 2022-11-04
GEO - Gene Expression Omnibus
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
NCBI GEO
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:16.605798
ncbi_geo
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:16.605798
Names
More detailed information about this field from each metasource.
Gene Expression Omnibus
metasource: Fairsharing.orgversion: FAIRsharing.org: GEO; Gene Expression Omnibus; DOI: https://doi.org/10.25504/FAIRsharing.5hc8vt; Last edited: April 26, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: re3data.org
version: re3data.org: Gene Expression Omnibus; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R33P44 last accessed: 2022-11-04
GEO
metasource: Fairsharing.orgversion: FAIRsharing.org: GEO; Gene Expression Omnibus; DOI: https://doi.org/10.25504/FAIRsharing.5hc8vt; Last edited: April 26, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: re3data.org
version: re3data.org: Gene Expression Omnibus; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R33P44 last accessed: 2022-11-04
GEO - Gene Expression Omnibus
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
NCBI GEO
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:16.605798
ncbi_geo
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:16.605798
Other names: GEO, GEO - Gene Expression Omnibus, NCBI GEO, ncbi_geo
Names
More detailed information about this field from each metasource.
Gene Expression Omnibus
metasource: Fairsharing.orgversion: FAIRsharing.org: GEO; Gene Expression Omnibus; DOI: https://doi.org/10.25504/FAIRsharing.5hc8vt; Last edited: April 26, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: re3data.org
version: re3data.org: Gene Expression Omnibus; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R33P44 last accessed: 2022-11-04
GEO
metasource: Fairsharing.orgversion: FAIRsharing.org: GEO; Gene Expression Omnibus; DOI: https://doi.org/10.25504/FAIRsharing.5hc8vt; Last edited: April 26, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: re3data.org
version: re3data.org: Gene Expression Omnibus; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R33P44 last accessed: 2022-11-04
GEO - Gene Expression Omnibus
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
NCBI GEO
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:16.605798
ncbi_geo
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:16.605798
The Gene Expression Omnibus (GEO) is a public repository that archives and freely distributes microarray, next-generation sequencing, and other forms of high-throughput functional genomic data submitted by the scientific community. In addition to data storage, a collection of web-based interfaces and applications are available to help users query and download the studies and gene expression patterns stored in GEO.
Description
More detailed information about this field from each metasource.
The Gene Expression Omnibus (GEO) is a public repository that archives and freely distributes microarray, next-generation sequencing, and other forms of high-throughput functional genomic data submitted by the scientific community. In addition to data storage, a collection of web-based interfaces and applications are available to help users query and download the studies and gene expression patterns stored in GEO.
metasource: Fairsharing.orgversion: FAIRsharing.org: GEO; Gene Expression Omnibus; DOI: https://doi.org/10.25504/FAIRsharing.5hc8vt; Last edited: April 26, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
GEO serves as a public repository for a wide range of high-throughput experimental data. These data include single and dual channel microarray-based experiments, measuring the abundance of mRNA, genomic DNA and protein molecules. Data from non-array-based high-throughput functional genomics and proteomics technologies are also archived, including serial analysis of gene expression (SAGE) and protein identification technology. Several tools are provided to assist with the visualization and exploration of GEO data, including hierarchical cluster heat maps and searchable individual gene expression profiles. Suitable GEO records are assembled into biologically and statistically comparable datasets. These datasets are then indexed and loaded into Entrez GEO Profiles and Entrez GEO DataSets, which allows users to query and analyze the data using simple boolean queries, and provides links to other NCBI resources wherever possible (e.g. sequence, publication and genomic mapping). GEO is available on the World Wide Web at http://www.ncbi.nlm.nih.gov/geo/. GEO DataSets may be browsed at http://www.ncbi.nlm.nih.gov/geo/gds/gds_browse.cgi or searched by keywords at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gds . GEO Profiles are searchable at (3) http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=geo. All these tools are intralinked and accessible from the GEO home page.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Gene Expression Omnibus: a public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles.
metasource: re3data.orgversion: re3data.org: Gene Expression Omnibus; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R33P44 last accessed: 2022-11-04
Database that stores over 20,000 microarray- and sequence-based functional genomics studies, and continues to handle the majority of direct high-throughput data submissions from the research community. Multiple mechanisms are provided to help users effectively search, browse, download and visualize the data at the level of individual genes or entire studies.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:16.605798
Webpage:
http://www.ncbi.nlm.nih.gov/geo/Webpage
More detailed information about this field from each metasource.
http://www.ncbi.nlm.nih.gov/geo/
metasource: Fairsharing.orgversion: FAIRsharing.org: GEO; Gene Expression Omnibus; DOI: https://doi.org/10.25504/FAIRsharing.5hc8vt; Last edited: April 26, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: Gene Expression Omnibus; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R33P44 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:16.605798
Licence:
Name: GEO Attribution requiredLicence name
More detailed information about this field from each metasource.
GEO Attribution required
metasource: Fairsharing.orgversion: FAIRsharing.org: GEO; Gene Expression Omnibus; DOI: https://doi.org/10.25504/FAIRsharing.5hc8vt; Last edited: April 26, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
Copyrights
metasource: re3data.orgversion: re3data.org: Gene Expression Omnibus; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R33P44 last accessed: 2022-11-04
ODbL-1.0
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:16.605798
URL: https://www.ncbi.nlm.nih.gov/geo/info/linking.html
Licence URL
More detailed information about this field from each metasource.
https://www.ncbi.nlm.nih.gov/geo/info/linking.html
metasource: Fairsharing.orgversion: FAIRsharing.org: GEO; Gene Expression Omnibus; DOI: https://doi.org/10.25504/FAIRsharing.5hc8vt; Last edited: April 26, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html
metasource: re3data.orgversion: re3data.org: Gene Expression Omnibus; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R33P44 last accessed: 2022-11-04
Publications:
Publications
More detailed information about this field from each metasource.
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
PMID: 11752295
metasource: Fairsharing.org
version: FAIRsharing.org: GEO; Gene Expression Omnibus; DOI: https://doi.org/10.25504/FAIRsharing.5hc8vt; Last edited: April 26, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:16.605798
NCBI GEO: archive for functional genomics data sets--update
PMID: 23193258
metasource: Fairsharing.org
version: FAIRsharing.org: GEO; Gene Expression Omnibus; DOI: https://doi.org/10.25504/FAIRsharing.5hc8vt; Last edited: April 26, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
NCBI GEO: archive for functional genomics data sets--10 years on
PMID: 21097893
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:16.605798
Submission of microarray data to public repositories
PMID: 15340489
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:16.605798
http://dx.doi.org/10.1093/nar/gks1193
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 Expression Omnibus: NCBI gene expression and hybridization array data repository
PMID: 11752295
metasource: Fairsharing.org
version: FAIRsharing.org: GEO; Gene Expression Omnibus; DOI: https://doi.org/10.25504/FAIRsharing.5hc8vt; Last edited: April 26, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:16.605798
NCBI GEO: archive for functional genomics data sets--update
PMID: 23193258
metasource: Fairsharing.org
version: FAIRsharing.org: GEO; Gene Expression Omnibus; DOI: https://doi.org/10.25504/FAIRsharing.5hc8vt; Last edited: April 26, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
NCBI GEO: archive for functional genomics data sets--10 years on
PMID: 21097893
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:16.605798
Submission of microarray data to public repositories
PMID: 15340489
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:16.605798
http://dx.doi.org/10.1093/nar/gks1193
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
PubMed citations: 5825.
5825 articles citing: Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
Cogito: automated and generic comparison of annotated genomic intervals. PMID:35927614
METTL3 preferentially enhances non-m6A translation of epigenetic factors and promotes tumourigenesis. PMID:35927451
Cellular recovery after prolonged warm ischaemia of the whole body. PMID:35922506
Evolutionary Relationships Between Dysregulated Genes in Oral Squamous Cell Carcinoma and Oral Microbiota. PMID:35909962
Cancer-testis antigen KK-LC-1 is a potential biomarker associated with immune cell infiltration in lung adenocarcinoma. PMID:35907786
CC chemokine receptor 7 promotes macrophage recruitment and induces M2-polarization through CC chemokine ligand 19&21 in oral squamous cell carcinoma. PMID:35904690
The lupus susceptibility allele DRB1*03:01 encodes a disease-driving epitope. PMID:35902632
Overexpression of OAS1 Is Correlated With Poor Prognosis in Pancreatic Cancer. PMID:35898870
Global Profiling of Genes Expressed in the Silk Glands of Philippine-Reared Mulberry Silkworms (Bombyx mori). PMID:35893024
Immunomodulatory Responses of Subcapsular Sinus Floor Lymphatic Endothelial Cells in Tumor-Draining Lymph Nodes. PMID:35892863
Stemness Correlates Inversely with MHC Class I Expression in Pediatric Small Round Blue Cell Tumors. PMID:35892842
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
Transcriptional Profiling of Leishmania infantum Infected Dendritic Cells: Insights into the Role of Immunometabolism in Host-Parasite Interaction. PMID:35888991
Prenatal Detection of Novel Compound Heterozygous Splice Site Variants of the KIAA0825 Gene in a Fetus with Postaxial Polydactyly Type A. PMID:35886013
High Oxytocin Receptor Expression Linked to Increased Cell Migration and Reduced Survival in Patients with Triple-Negative Breast Cancer. PMID:35884900
Integrated Clinical and Genomic Models to Predict Optimal Cytoreduction in High-Grade Serous Ovarian Cancer. PMID:35884615
Large-Scale Profiling on lncRNAs in Human Platelets: Correlation with Platelet Reactivity. PMID:35883699
Induced Endothelial Cell-Integrated Liver Assembloids Promote Hepatic Maturation and Therapeutic Effect on Cholestatic Liver Fibrosis. PMID:35883684
In silico discovery of blood cell macromolecular associations. PMID:35879676
Identification of Metabolic Syndrome-Related miRNA-mRNA Regulatory Networks and Key Genes Based on Bioinformatics Analysis. PMID:35877019
Getting Started with LINCS Datasets and Tools. PMID:35876555
Longevity-Promoting Pathways and Transcription Factors Respond to and Control Extracellular Matrix Dynamics During Aging and Disease. PMID:35874275
Unveiling Co-Infection in Cystic Fibrosis Airways: Transcriptomic Analysis of Pseudomonas aeruginosa and Staphylococcus aureus Dual-Species Biofilms. PMID:35873457
The Lack of the TetR-Like Repressor Gene BCG_2177c (Rv2160A) May Help Mycobacteria Overcome Intracellular Redox Stress and Survive Longer Inside Macrophages When Surrounded by a Lipid Environment. PMID:35873160
In silico Identification of Immune Cell-Types and Pathways Involved in Chronic Spontaneous Urticaria. PMID:35872776
EpiVisR: exploratory data analysis and visualization in epigenome-wide association analyses. PMID:35870905
Increased Development of Th1, Th17, and Th1.17 Cells Under T1 Polarizing Conditions in Juvenile Idiopathic Arthritis. PMID:35860254
Un-biased housekeeping gene panel selection for high-validity gene expression analysis. PMID:35853974
An Immunity-Related Gene Model Predicts Prognosis in Cholangiocarcinoma. PMID:35847907
Predicting the Lung Adenocarcinoma and Its Biomarkers by Integrating Gene Expression and DNA Methylation Data. PMID:35846148
Senescent Tumor Cells in the Peritoneal Carcinomatosis Drive Immunosenescence in the Tumor Microenvironment. PMID:35844581
Single-Cell RNA Sequencing Unravels Upregulation of Immune Cell Crosstalk in Relapsed Pediatric Ependymoma. PMID:35844565
Uncovering a Genetic Polymorphism Located in Huntingtin Associated Protein 1 in Modulation of Central Pain Sensitization Signaling Pathways. PMID:35837121
Differential gene screening and bioinformatics analysis of epidermal stem cells and dermal fibroblasts during skin aging. PMID:35835980
Novel roles of luteinizing hormone (LH) in tissue regeneration-associated functions in endometrial stem cells. PMID:35831270
Multivariate competing endogenous RNA network characterization for cancer microRNA biomarker discovery: a novel bioinformatics model with application to prostate cancer metastasis. PMID:35821682
Network Pharmacology and Bioinformatics Methods Reveal the Mechanism of Berberine in the Treatment of Ischaemic Stroke. PMID:35815278
The clinical relevance of unfolded protein response signaling in breast cancer. PMID:35812054
miR-218-5p/RUNX2 Axis Positively Regulates Proliferation and Is Associated with Poor Prognosis in Cervical Cancer. PMID:35805994
DNA methylation fingerprint of hepatocellular carcinoma from tissue and liquid biopsies. PMID:35798798
Vitexin Mitigates Staphylococcus aureus-Induced Mastitis via Regulation of ROS/ER Stress/NF-κB/MAPK Pathway. PMID:35795861
Cytokinin and Its Key Role to Enrich the Plant Nutrients and Growth Under Adverse Conditions-An Update. PMID:35795201
Downregulation of LRRC19 Is Associated with Poor Prognosis in Colorectal Cancer. PMID:35794979
Highly perturbed genes and hub genes associated with type 2 diabetes in different tissues of adult humans: a bioinformatics analytic workflow. PMID:35788821
Integrated Analysis of Immune-Related circRNA-miRNA-mRNA Regulatory Network in Ischemic Stroke. PMID:35785353
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
SETDB1 acts as a topological accessory to Cohesin via an H3K9me3-independent, genomic shunt for regulating cell fates. PMID:35776115
The Bioinformatic Study Uncovers Probable Critical Genes Involved in the Pathophysiology of Biliary Atresia. PMID:35774294
FBXO38 Ubiquitin Ligase Controls Sertoli Cell Maturation. PMID:35769260
Methylome-wide analysis of IVF neonates that underwent embryo culture in different media revealed no significant differences. PMID:35768464
Farnesoid X receptor protects against cisplatin-induced acute kidney injury by regulating the transcription of ferroptosis-related genes. PMID:35767918
Network-based machine learning approach to predict immunotherapy response in cancer patients. PMID:35764641
Lymphangiogenesis requires Ang2/Tie/PI3K signaling for VEGFR3 cell-surface expression. PMID:35763346
Context-aware deconvolution of cell-cell communication with Tensor-cell2cell. PMID:35760817
Transcriptomic Profiling of Plaque Psoriasis and Cutaneous T-Cell Subsets during Treatment with Secukinumab. PMID:35757784
Driving innovation for rare skin cancers: utilizing common tumours and machine learning to predict immune checkpoint inhibitor response. PMID:35755000
Pathway importance by graph convolutional network and Shapley additive explanations in gene expression phenotype of diffuse large B-cell lymphoma. PMID:35749395
Model scenarios for cell cycle re-entry in Alzheimer's disease. PMID:35747391
Circulating miRNAs as Potential Biomarkers for Patient Stratification in Bipolar Disorder: A Combined Review and Data Mining Approach. PMID:35741801
Exploring the Core Genes of Schizophrenia Based on Bioinformatics Analysis. PMID:35741729
Identifying the Potential Roles of PBX4 in Human Cancers Based on Integrative Analysis. PMID:35740947
Murine Falcor/LL35 lncRNA Contributes to Glucose and Lipid Metabolism In Vitro and In Vivo. PMID:35740417
Single-cell transcriptome and accessible chromatin dynamics during endocrine pancreas development. PMID:35733248
Host CLIC4 expression in the tumor microenvironment is essential for breast cancer metastatic competence. PMID:35727842
An 8-Gene Signature for Classifying Major Subtypes of Non-Small-Cell Lung Cancer. PMID:35722224
C1QTNF3 is Upregulated During Subcutaneous Adipose Tissue Remodeling and Stimulates Macrophage Chemotaxis and M1-Like Polarization. PMID:35720277
Identification of Differentially Expressed Genes and miRNAs for Ulcerative Colitis Using Bioinformatics Analysis. PMID:35719390
Network Control Models With Personalized Genomics Data for Understanding Tumor Heterogeneity in Cancer. PMID:35712516
Identification of Prognosis-Related Molecular Subgroups and Construction of a Prognostic Prediction Model Using Immune-Related Genes in Pancreatic Cancer. PMID:35712127
Mechanical Strain Induces Transcriptomic Reprogramming of Saphenous Vein Progenitors. PMID:35711359
Integrated analysis reveals the pivotal interactions between immune cells in the melanoma tumor microenvironment. PMID:35710862
Identification of HOX signatures contributing to oral cancer phenotype. PMID:35710803
SFARI genes and where to find them; modelling Autism Spectrum Disorder specific gene expression dysregulation with RNA-seq data. PMID:35710789
T-cell trans-synaptic vesicles are distinct and carry greater effector content than constitutive extracellular vesicles. PMID:35710644
Premature Infants Have Normal Maturation of the T Cell Receptor Repertoire at Term. PMID:35707545
Elucidating gene expression patterns across multiple biological contexts through a large-scale investigation of transcriptomic datasets. PMID:35705903
Enhancing the REMBRANDT MRI collection with expert segmentation labels and quantitative radiomic features. PMID:35701399
Host protease activity classifies pneumonia etiology. PMID:35696579
The Olfactory Organ Is a Unique Site for Neutrophils in the Brain. PMID:35693773
Decoding the Mechanism behind the Pathogenesis of the Focal Segmental Glomerulosclerosis. PMID:35693262
SARS-CoV-2 infection impairs the insulin/IGF signaling pathway in the lung, liver, adipose tissue, and pancreatic cells via IRF1. PMID:35688210
Deriving time-concordant event cascades from gene expression data: A case study for Drug-Induced Liver Injury (DILI). PMID:35687583
Role of Nucleolin in Endometrial Precancerous Hyperplasia and Carcinogenesis: Ex Vivo and In Silico Study. PMID:35682908
The AKT1E17K Allele Promotes Breast Cancer in Mice. PMID:35681625
Chronic Chemogenetic Activation of the Superior Colliculus in Glaucomatous Mice: Local and Retrograde Molecular Signature. PMID:35681479
MicroRNAs and other small RNAs in Aedes aegypti saliva and salivary glands following chikungunya virus infection. PMID:35681077
Identification of biomarkers for immunotherapy response in prostate cancer and potential drugs to alleviate immunosuppression. PMID:35680563
An epigenome-wide view of osteoarthritis in primary tissues. PMID:35679866
Gut-derived short-chain fatty acids modulate skin barrier integrity by promoting keratinocyte metabolism and differentiation. PMID:35672452
STAT6 inhibits ferroptosis and alleviates acute lung injury via regulating P53/SLC7A11 pathway. PMID:35668064
Identification of Metabolic Pathways Differentially Regulated in Somatic and Zygotic Embryos of Maritime Pine. PMID:35665168
The DNA glycosylase NEIL2 plays a vital role in combating SARS-CoV-2 infection. PMID:35665009
Recapitulation of endogenous 4R tau expression and formation of insoluble tau in directly reprogrammed human neurons. PMID:35659876
Transcriptional profiling of transport mechanisms and regulatory pathways in rat choroid plexus. PMID:35659263
A gene prognostic index from cellular senescence predicting metastasis and radioresistance for prostate cancer. PMID:35658892
Integration of the Salmonella Typhimurium Methylome and Transcriptome Reveals That DNA Methylation and Transcriptional Regulation Are Largely Decoupled under Virulence-Related Conditions. PMID:35658533
The snoGloBe interaction predictor reveals a broad spectrum of C/D snoRNA RNA targets. PMID:35657102
Comprehensive competitive endogenous RNA network analysis reveals EZH2-related axes and prognostic biomarkers in hepatocellular carcinoma. PMID:35656182
JUN and PDGFRA as Crucial Candidate Genes for Childhood Autism Spectrum Disorder. PMID:35655651
Esrrb Regulates Specific Feed-Forward Loops to Transit From Pluripotency Into Early Stages of Differentiation. PMID:35652095
Persister state-directed transitioning and vulnerability in melanoma. PMID:35650266
Characterisation of a nucleo-adhesome. PMID:35650196
Transcriptomic datasets of cancer patients treated with immune-checkpoint inhibitors: a systematic review. PMID:35641998
Target and drug predictions for SARS-CoV-2 infection in hepatocellular carcinoma patients. PMID:35639708
Key gene network related to primary ciliary dyskinesia in hippocampus of patients with Alzheimer's disease revealed by weighted gene co-expression network analysis. PMID:35637434
Single-cell transcriptomics of adult macaque hippocampus reveals neural precursor cell populations. PMID:35637371
LIM Homeobox-2 Suppresses Hallmarks of Adult and Pediatric Liver Cancers by Inactivating MAPK/ERK and Wnt/Beta-Catenin Pathways. PMID:35634422
Chronic Exposure to the Food Additive tBHQ Modulates Expression of Genes Related to SARS-CoV-2 and Influenza Viruses. PMID:35629310
miR-486-5p and miR-22-3p Enable Megakaryocytic Differentiation of Hematopoietic Stem and Progenitor Cells without Thrombopoietin. PMID:35628168
The Circadian Clock in the Retinal Pigment Epithelium Controls the Diurnal Rhythm of Phagocytic Activity. PMID:35628111
miRNA Pattern in Hypoxic Microenvironment of Kidney Cancer-Role of PTEN. PMID:35625614
CDC25C is a prognostic biomarker and correlated with mitochondrial homeostasis in pancreatic adenocarcinoma. PMID:35615982
Identification of Differential Genes of DNA Methylation Associated With Alzheimer's Disease Based on Integrated Bioinformatics and Its Diagnostic Significance. PMID:35615586
Exploration of Potential Biomarker Genes and Pathways in Kawasaki Disease: An Integrated in-Silico Approach. PMID:35615376
Identification and validation of aging-related genes in COPD based on bioinformatics analysis. PMID:35609226
The Overexpression of Fibronectin 1 Promotes Cancer Progression and Associated with M2 Macrophages Polarization in Head and Neck Squamous Cell Carcinoma Patients. PMID:35607361
PqsE Expands and Differentially Modulates the RhlR Quorum Sensing Regulon in Pseudomonas aeruginosa. PMID:35604161
NUF2 Is a Potential Immunological and Prognostic Marker for Non-Small-Cell Lung Cancer. PMID:35600043
Dataset of differentially expressed genes in mouse P12 testes in response to the loss of ATRX in Sertoli cells. PMID:35592768
Adaptation of the gut pathobiont Enterococcus faecalis to deoxycholate and taurocholate bile acids. PMID:35590028
The impact of short-term confinement on human innate immunity. PMID:35589846
Interleukin-4 receptor signaling modulates neuronal network activity. PMID:35587822
Identification and validation of an eight-lncRNA signature that predicts prognosis in patients with esophageal squamous cell carcinoma. PMID:35578166
An Artificial Intelligence-guided signature reveals the shared host immune response in MIS-C and Kawasaki disease. PMID:35577777
Integrated Analysis of Transcriptome Data Revealed AURKA and KIF20A as Critical Genes in Medulloblastoma Progression. PMID:35574421
High intratumoral dihydrotestosterone is associated with antiandrogen resistance in VCaP prostate cancer xenografts in castrated mice. PMID:35573198
Endophenotype-based in silico network medicine discovery combined with insurance record data mining identifies sildenafil as a candidate drug for Alzheimer's disease. PMID:35572351
NMDA Receptor Antagonists Increase the Release of GLP-1 From Gut Endocrine Cells. PMID:35571112
Immunophenotyping of Acute Inflammatory Exacerbations of Lung Injury Driven by Mutant Surfactant Protein-C: A Role for Inflammatory Eosinophils. PMID:35571100
The Phytotoxin Myrigalone A Triggers a Phased Detoxification Programme and Inhibits Lepidium sativum Seed Germination via Multiple Mechanisms including Interference with Auxin Homeostasis. PMID:35563008
Systems-wide analysis revealed shared and unique responses to moderate and acute high temperatures in the green alga Chlamydomonas reinhardtii. PMID:35562408
Assessing the Potential Prognostic and Immunological Role of TK1 in Prostate Cancer. PMID:35559045
Identification of potential prognostic biomarkers for hepatocellular carcinoma. PMID:35557563
Enhancing Data Integration, Interoperability, and Reuse to Address Complex and Emerging Environmental Health Problems. PMID:35549252
Artificial intelligence in cancer target identification and drug discovery. PMID:35538061
Identification of key gene contributing to vitiligo by immune infiltration. PMID:35535201
Profiling senescent cells in human brains reveals neurons with CDKN2D/p19 and tau neuropathology. PMID:35531351
Recent Progress and Future Direction for the Application of Multiomics Data in Clinical Liver Transplantation. PMID:35528975
SigCom LINCS: data and metadata search engine for a million gene expression signatures. PMID:35524556
3'untranslated regions of tumor suppressor genes evolved specific features to favor cancer resistance. PMID:35523946
Elucidating Human Milk Oligosaccharide biosynthetic genes through network-based multi-omics integration. PMID:35508452
MTG16 regulates colonic epithelial differentiation, colitis, and tumorigenesis by repressing E protein transcription factors. PMID:35503250
Construction of a lncRNA-associated competing endogenous RNA regulatory network after traumatic brain injury in mouse. PMID:35501920
Low Level of PALMD Contributes to the Metastasis of Uveal Melanoma. PMID:35494064
RNA-seq profiling of tubulointerstitial tissue reveals a potential therapeutic role of dual anti-phosphatase 1 in glomerulonephritis. PMID:35488446
Fluorescent tracking identifies key migratory dendritic cells in the lymph node after radiotherapy. PMID:35487695
Temporal and sex-dependent gene expression patterns in a renal ischemia-reperfusion injury and recovery pig model. PMID:35484379
An Arabidopsis mutant deficient in phosphatidylinositol-4-phosphate kinases ß1 and ß2 displays altered auxin-related responses in roots. PMID:35484296
EBAG9 controls CD8+ T cell memory formation responding to tumor challenge in mice. PMID:35482418
lncRNA MALAT1 mediates osteogenic differentiation of bone mesenchymal stem cells by sponging miR-129-5p. PMID:35480561
Cancer Progression Gene Expression Profiling Identifies the Urokinase Plasminogen Activator Receptor as a Biomarker of Metastasis in Cutaneous Squamous Cell Carcinoma. PMID:35480116
Icariin: A Potential Molecule for Treatment of Knee Osteoarthritis. PMID:35479319
Human placental proteomics and exon variant studies link AAT/SERPINA1 with spontaneous preterm birth. PMID:35477570
Critical contribution of 3' non-seed base pairing to the in vivo function of the evolutionarily conserved let-7a microRNA. PMID:35476978
Alfalfa (Medicago sativa L.) pho2 mutant plants hyperaccumulate phosphate. PMID:35471600
Streptococcus pyogenes Hijacks Host Glutathione for Growth and Innate Immune Evasion. PMID:35467425
Pseudomonas aeruginosa Initiates a Rapid and Specific Transcriptional Response during Surface Attachment. PMID:35467391
Screening of Medications for Idiopathic Membranous Nephropathy Using Glomerular Whole-Genome Sequencing. PMID:35465008
Mitochondria Dysfunction-Mediated Molecular Subtypes and Gene Prognostic Index for Prostate Cancer Patients Undergoing Radical Prostatectomy or Radiotherapy. PMID:35463369
Characterization of transcriptome diversity and in vitro behavior of primary human high-risk breast cells. PMID:35459280
Recognition of a Novel Gene Signature for Human Glioblastoma. PMID:35456975
Transcriptional Profiling and Deriving a Seven-Gene Signature That Discriminates Active and Latent Tuberculosis: An Integrative Bioinformatics Approach. PMID:35456421
Prolonged Cadmium Exposure Alters Migration Dynamics and Increases Heterogeneity of Human Uterine Fibroid Cells-Insights from Time Lapse Analysis. PMID:35453667
Coexpression reveals conserved gene programs that co-vary with cell type across kingdoms. PMID:35451481
Global expression profiling of CD10 + /CD19 + pre-B lymphoblasts from Hispanic B-ALL patients correlates with comparative TARGET database analysis. PMID:35445848
CCNE1 amplification is synthetic lethal with PKMYT1 kinase inhibition. PMID:35444283
3JC48-3 (methyl 4'-methyl-5-(7-nitrobenzo[c][1,2,5]oxadiazol-4-yl)-[1,1'-biphenyl]-3-carboxylate): a novel MYC/MAX dimerization inhibitor reduces prostate cancer growth. PMID:35440696
Global ubiquitinome profiling identifies NEDD4 as a regulator of Profilin 1 and actin remodelling in neural crest cells. PMID:35440627
An evolutionarily conserved stop codon enrichment at the 5' ends of mammalian piRNAs. PMID:35440552
PELO facilitates PLK1-induced the ubiquitination and degradation of Smad4 and promotes the progression of prostate cancer. PMID:35437307
Genome-wide Identification and Expression Analysis of RcMYB Genes in Rhodiola crenulata. PMID:35432456
The human ion channel TRPM2 modulates cell survival in neuroblastoma through E2F1 and FOXM1. PMID:35428820
Systematic Characterization of the Clinical Relevance of KPNA4 in Pancreatic Ductal Adenocarcinoma. PMID:35425701
Construction of a Joint Prediction Model for the Occurrence of Ischemic Stroke and Acute Myocardial Infarction Based on Bioinformatic Analysis. PMID:35419117
The Arabidopsis F-box protein FBW2 targets AGO1 for degradation to prevent spurious loading of illegitimate small RNA. PMID:35417704
Angiopoietin-like 4 governs diurnal lipoprotein lipase activity in brown adipose tissue. PMID:35413480
Neural network modeling of differential binding between wild-type and mutant CTCF reveals putative binding preferences for zinc fingers 1-2. PMID:35410161
ENPP2 Promoter Methylation Correlates with Decreased Gene Expression in Breast Cancer: Implementation as a Liquid Biopsy Biomarker. PMID:35409077
ELK3 Controls Gastric Cancer Cell Migration and Invasion by Regulating ECM Remodeling-Related Genes. PMID:35409069
Construction of MicroRNA-mRNA Regulatory Network in the Molecular Mechanisms of Bleomycin-Induced Pulmonary Fibrosis. PMID:35402615
BTG2 as a tumor target for the treatment of luminal A breast cancer. PMID:35401805
Transcriptomic Analysis of Liver Indicates Novel Vaccine to Porcine Reproductive and Respiratory Virus Promotes Homeostasis in T-Cell and Inflammatory Immune Responses Compared to a Commercial Vaccine in Pigs. PMID:35400088
Molecular mechanisms underlying plasticity in a thermally varying environment. PMID:35397190
The interleukin-1 axis and the tumor immune microenvironment in pancreatic ductal adenocarcinoma. PMID:35395492
Predicted mouse interactome and network-based interpretation of differentially expressed genes. PMID:35390003
Predictive biomarkers for survival benefit with ramucirumab in urothelial cancer in the RANGE trial. PMID:35388003
Comparative functional genomics identifies an iron-limited bottleneck in a Saccharomyces cerevisiae strain with a cytosolic-localized isobutanol pathway. PMID:35387233
Purinergic Receptors in the Airways: Potential Therapeutic Targets for Asthma? PMID:35386996
Translational Analysis of Moderate to Severe Asthma GWAS Signals Into Candidate Causal Genes and Their Functional, Tissue-Dependent and Disease-Related Associations. PMID:35386986
Network-based stage-specific drug repurposing for Alzheimer's disease. PMID:35386099
Downregulation of KRAB zinc finger proteins in 5-fluorouracil resistant colorectal cancer cells. PMID:35379199
High-resolution Slide-seqV2 spatial transcriptomics enables discovery of disease-specific cell neighborhoods and pathways. PMID:35372810
Immunopeptidomic analyses of colorectal cancers with and without microsatellite instability. PMID:35367648
Computational analyses of mechanism of action (MoA): data, methods and integration. PMID:35360890
A Link Between Mitochondrial Dysfunction and the Immune Microenvironment of Salivary Glands in Primary Sjogren's Syndrome. PMID:35359935
Nuclear microRNA-466c regulates Vegfa expression in response to hypoxia. PMID:35358280
LKB1 acts as a critical brake for the glucagon-mediated fasting response. PMID:35357082
Transcript and blood-microbiome analysis towards a blood diagnostic tool for goats affected by Haemonchus contortus. PMID:35354850
Cardiac pericyte reprogramming by MEK inhibition promotes arteriologenesis and angiogenesis of the ischemic heart. PMID:35349488
Viral Mimicry of Interleukin-17A by SARS-CoV-2 ORF8. PMID:35343786
Single-Cell Analysis of Refractory Celiac Disease Demonstrates Inter- and Intra-Patient Aberrant Cell Heterogeneity. PMID:35338007
Machine Learning-Based Identification of Colon Cancer Candidate Diagnostics Genes. PMID:35336739
Transcriptomic Stress Response in Streptococcus mutans following Treatment with a Sublethal Concentration of Chlorhexidine Digluconate. PMID:35336136
Expression of cardiovascular-related microRNAs is altered in L-arginine:glycine amidinotransferase deficient mice. PMID:35332188
Tissue-Specific Methylation Biosignatures for Monitoring Diseases: An In Silico Approach. PMID:35328380
Screening the Significant Hub Genes by Comparing Tumor Cells, Normoxic and Hypoxic Glioblastoma Stem-like Cell Lines Using Co-Expression Analysis in Glioblastoma. PMID:35328072
Identification of the TF-miRNA-mRNA co-regulatory networks involved in sepsis. PMID:35322335
A flexible model-free prediction-based framework for feature ranking. PMID:35321091
Macrophage mitochondrial bioenergetics and tissue invasion are boosted by an Atossa-Porthos axis in Drosophila. PMID:35319107
Overexpression of CISD1 Predicts Worse Survival in Hepatocarcinoma Patients. PMID:35313629
Nucleoporin107 mediates female sexual differentiation via Dsx. PMID:35311642
Target-Dependent Coordinated Biogenesis of Secondary MicroRNAs by miR-146a Balances Macrophage Activation Processes. PMID:35311564
Blood SSR1: A Possible Biomarker for Early Prediction of Parkinson's Disease. PMID:35310885
Expression of AtWRI1 and AtDGAT1 during soybean embryo development influences oil and carbohydrate metabolism. PMID:35306726
Establishment of a Combined Diagnostic Model of Abdominal Aortic Aneurysm with Random Forest and Artificial Neural Network. PMID:35299890
Indisulam targets RNA splicing and metabolism to serve as a therapeutic strategy for high-risk neuroblastoma. PMID:35296644
Experimental evolution links post-transcriptional regulation to Leishmania fitness gain. PMID:35294501
Artificial intelligence-rationalized balanced PPARα/γ dual agonism resets dysregulated macrophage processes in inflammatory bowel disease. PMID:35288651
An integrated bioinformatic investigation of mitochondrial solute carrier family 25 (SLC25) in colon cancer followed by preliminary validation of member 5 (SLC25A5) in tumorigenesis. PMID:35288533
A mobile restriction-modification system provides phage defence and resolves an epigenetic conflict with an antagonistic endonuclease. PMID:35286398
The Key Genes Underlying Pathophysiology Correlation Between the Acute Myocardial Infarction and COVID-19. PMID:35282650
Exploring the Communal Pathogenesis, Ferroptosis Mechanism, and Potential Therapeutic Targets of Dilated Cardiomyopathy and Hypertrophic Cardiomyopathy via a Microarray Data Analysis. PMID:35282347
Identification of a seven-gene prognostic signature using the gene expression profile of osteosarcoma. PMID:35282067
Restoration of Default Blood Monocyte-Derived Macrophage Polarization With Adalimumab But Not Etanercept in Rheumatoid Arthritis. PMID:35281074
Energy Metabolism-Related Gene Prognostic Index Predicts Biochemical Recurrence for Patients With Prostate Cancer Undergoing Radical Prostatectomy. PMID:35280985
High-Calcium Microenvironment during the Development of Kidney Calculi Can Promote Phenotypic Transformation of NRK-52E Cells by Inhibiting the Expression of Stromal Interaction Molecule-1. PMID:35274024
Formation of the Mouse Internal Capsule and Cerebral Peduncle: A Pioneering Role for Striatonigral Axons as Revealed in Isl1 Conditional Mutants. PMID:35273083
Human Sex Matters: Y-Linked Lysine Demethylase 5D Drives Accelerated Male Craniofacial Osteogenic Differentiation. PMID:35269444
Diurnal and circadian rhythmicity of the human blood transcriptome overlaps with organ- and tissue-specific expression of a non-human primate. PMID:35264172
Melanoma-Secreted Amyloid Beta Suppresses Neuroinflammation and Promotes Brain Metastasis. PMID:35262173
The schizophrenia-associated variant in SLC39A8 alters protein glycosylation in the mouse brain. PMID:35260802
Regulation of chromatin accessibility by hypoxia and HIF. PMID:35258521
RNA transcription and degradation of Alu retrotransposons depends on sequence features and evolutionary history. PMID:35253846
A network-based computational and experimental framework for repurposing compounds toward the treatment of non-alcoholic fatty liver disease. PMID:35252807
Genome-Wide Methylation Profiling in the Thalamus of Scrapie Sheep. PMID:35252421
An Integrated Analysis of the Identified PRPF19 as an Onco-immunological Biomarker Encompassing the Tumor Microenvironment, Disease Progression, and Prognoses in Hepatocellular Carcinoma. PMID:35252202
Chromatin Changes in Phytochrome Interacting Factor-Regulated Genes Parallel Their Rapid Transcriptional Response to Light. PMID:35251080
High RAD51 gene expression is associated with aggressive biology and with poor survival in breast cancer. PMID:35249172
In PD-1+ human colon cancer cells NIVOLUMAB promotes survival and could protect tumor cells from conventional therapies. PMID:35246475
Predicting molecular initiating events using chemical target annotations and gene expression. PMID:35246223
Identification of Crucial Genes and Key Functions in Type 2 Diabetic Hearts by Bioinformatic Analysis. PMID:35242109
Identification of novel therapeutic targets for Fuchs' endothelial corneal dystrophy based on gene bioinformatics analysis. PMID:35239706
Disruption of the circadian clock component BMAL1 elicits an endocrine adaption impacting on insulin sensitivity and liver disease. PMID:35238641
i6mA-Vote: Cross-Species Identification of DNA N6-Methyladenine Sites in Plant Genomes Based on Ensemble Learning With Voting. PMID:35237293
PLK1 inhibition selectively induces apoptosis in ARID1A deficient cells through uncoupling of oxygen consumption from ATP production. PMID:35236967
CASowary: CRISPR-Cas13 guide RNA predictor for transcript depletion. PMID:35236300
Summarizing internal dynamics boosts differential analysis and functional interpretation of super enhancers. PMID:35234924
CFIm-mediated alternative polyadenylation remodels cellular signaling and miRNA biogenesis. PMID:35234914
Contribution of Host miRNA-223-3p to SARS-CoV-Induced Lung Inflammatory Pathology. PMID:35229638
PUCHI represses early meristem formation in developing lateral roots of Arabidopsis thaliana. PMID:35224628
A Ferroptosis-Related Gene Prognostic Index Associated With Biochemical Recurrence and Radiation Resistance for Patients With Prostate Cancer Undergoing Radical Radiotherapy. PMID:35223835
Identification of NUTF2 as a Candidate Diagnostic and Prognostic Biomarker Associated with Immune Infiltration in Head and Neck Squamous Cell Carcinoma. PMID:35221694
Network meta-analysis of transcriptome expression changes in different manifestations of dengue virus infection. PMID:35220956
An in-frame deletion mutation in the degron tail of auxin coreceptor IAA2 confers resistance to the herbicide 2,4-D in Sisymbrium orientale. PMID:35217601
Identification of Nifurtimox and Chrysin as Anti-Influenza Virus Agents by Clinical Transcriptome Signature Reversion. PMID:35216485
Unlike Chloroquine, Mefloquine Inhibits SARS-CoV-2 Infection in Physiologically Relevant Cells. PMID:35215969
Analysing miRNA-Target Gene Networks in Inflammatory Bowel Disease and Other Complex Diseases Using Transcriptomic Data. PMID:35205414
DRPPM-EASY: A Web-Based Framework for Integrative Analysis of Multi-Omics Cancer Datasets. PMID:35205126
Tissular Genomic Responses to Oral FB1 Exposure in Pigs. PMID:35202111
Hsa-miR-183-5p Modulates Cell Adhesion by Repression of ITGB1 Expression in Prostate Cancer. PMID:35202085
Identification of Potential Cytokinin Responsive Key Genes in Rice Treated With Trans-Zeatin Through Systems Biology Approach. PMID:35198001
PI3K-regulated Glycine N-methyltransferase is required for the development of prostate cancer. PMID:35197445
Th1 cells are dispensable for primary clearance of Chlamydia from the female reproductive tract of mice. PMID:35196366
THRSP identified as a potential hepatocellular carcinoma marker by integrated bioinformatics analysis and experimental validation. PMID:35196258
tensorGSEA: Detecting Differential Pathways in Type 2 Diabetes via Tensor-Based Data Reconstruction. PMID:35195883
SEAseq: a portable and cloud-based chromatin occupancy analysis suite. PMID:35193506
FUS-DDIT3 Fusion Oncoprotein Expression Affects JAK-STAT Signaling in Myxoid Liposarcoma. PMID:35186752
Genotypic Variation of Nitrogen Use Efficiency and Amino Acid Metabolism in Barley. PMID:35185958
Elevated Detection of Dual Antibody B Cells Identifies Lupus Patients With B Cell-Reactive VH4-34 Autoantibodies. PMID:35185888
Identification of Transcriptional Pattern Related to Immune Cell Infiltration With Gene Co-Expression Network in Papillary Thyroid Cancer. PMID:35185791
FET fusion oncoproteins interact with BRD4 and SWI/SNF chromatin remodelling complex subtypes in sarcoma. PMID:35182012
Inferring Causation in Yeast Gene Association Networks With Kernel Logistic Regression. PMID:35173404
Placental methylome reveals a 22q13.33 brain regulatory gene locus associated with autism. PMID:35168652
Aureochromes maintain polyunsaturated fatty acid content in Nannochloropsis oceanica. PMID:35166829
Is Cadmium Toxicity Tissue-Specific? Toxicogenomics Studies Reveal Common and Specific Pathways in Pulmonary, Hepatic, and Neuronal Cell Models. PMID:35163690
Spheroid Culture Differentially Affects Cancer Cell Sensitivity to Drugs in Melanoma and RCC Models. PMID:35163092
Cellular and Gene Expression Response to the Combination of Genistein and Kaempferol in the Treatment of Mucopolysaccharidosis Type I. PMID:35162981
Aging Activates the Immune System and Alters the Regenerative Capacity in the Zebrafish Heart. PMID:35159152
gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit. PMID:35156023
In silico bioinformatics analysis for identification of differentially expressed genes and therapeutic drug molecules in Glucocorticoid-resistant Multiple myeloma. PMID:35150335
Osmotic stress induces long-term biofilm survival in Liberibacter crescens. PMID:35148684
From environmental adaptation to host survival: Attributes that mediate pathogenicity of Candida auris. PMID:35142597
USP25 Expression in Peripheral Blood Mononuclear Cells Is Associated With Bone Mineral Density in Women. PMID:35141233
A framework to predict the applicability of Oncotype DX, MammaPrint, and E2F4 gene signatures for improving breast cancer prognostic prediction. PMID:35140308
Translocated Legionella pneumophila small RNAs mimic eukaryotic microRNAs targeting the host immune response. PMID:35140216
Age-related long-term response in rat thyroid tissue and plasma after internal low dose exposure to 131I. PMID:35136135
Differential interferon-α subtype induced immune signatures are associated with suppression of SARS-CoV-2 infection. PMID:35131898
Identification of Potential Key Genes and Molecular Mechanisms of Medulloblastoma Based on Integrated Bioinformatics Approach. PMID:35127939
Immune Checkpoint Gene Expression Profiling Identifies Programmed Cell Death Ligand-1 Centered Immunologic Subtypes of Oral and Squamous Cell Carcinoma With Favorable Survival. PMID:35127742
Identification of Key Genes and Pathways Involved in Circulating Tumor Cells in Colorectal Cancer. PMID:35127345
Functional New Transcription Factors (TFs) Associated with Cervical Cancer. PMID:35126951
Estrogen modulation of the pronociceptive effects of serotonin on female rat trigeminal sensory neurons is timing dependent and dosage dependent and requires estrogen receptor alpha. PMID:35121697
Antigen cross-presentation in young tumor-bearing hosts promotes CD8+ T cell terminal differentiation. PMID:35119937
Anota2seq Analysis for Transcriptome-Wide Studies of mRNA Translation. PMID:35119670
Identification of biomarkers in colon cancer based on bioinformatic analysis. PMID:35117850
Construction and integrated analysis of a lncRNA-associated competing endogenous RNA network reveal functional lncRNAs in pancreatic cancer. PMID:35117727
Comprehensive analysis reveals a four-gene signature in colorectal cancer. PMID:35117487
Screening of hub genes associated with prognosis in non-small cell lung cancer by integrated bioinformatics analysis. PMID:35117319
Comprehensive analysis reveals novel gene signature in head and neck squamous cell carcinoma: predicting is associated with poor prognosis in patients. PMID:35117201
Bioinformatic analysis of long non-coding RNA-associated competing endogenous RNA network in adrenocortical carcinoma. PMID:35116967
Alternatively activated NUSAP1 promotes tumor growth and indicates poor prognosis in hepatocellular carcinoma. PMID:35116752
High expression of TXNDC11 indicated unfavorable prognosis of glioma. PMID:35116356
Surgical Trauma in Mice Modifies the Content of Circulating Extracellular Vesicles. PMID:35116043
Molecular Subtyping Resource: a user-friendly tool for rapid biological discovery from transcriptional data. PMID:35112706
Screening and identification of novel candidate biomarkers of focal cortical dysplasia type II via bioinformatics analysis. PMID:35112146
DDX10 promotes the proliferation and metastasis of colorectal cancer cells via splicing RPL35. PMID:35109823
Convergent clonal selection of donor- and recipient-derived CMV-specific T cells in hematopoietic stem cell transplant patients. PMID:35105810
Diagnostic Evidence GAuge of Single cells (DEGAS): a flexible deep transfer learning framework for prioritizing cells in relation to disease. PMID:35105355
Systems neuroimmunology: a review of multiomics methodologies to characterize neuroimmunological interactions in spinal and cranial diseases. PMID:35104798
Analytical kinetic model of native tandem promoters in E. coli. PMID:35100257
A Gene Prognostic Index Associated With Epithelial-Mesenchymal Transition Predicting Biochemical Recurrence and Tumor Chemoresistance for Prostate Cancer. PMID:35096608
Making sense of the linear genome, gene function and TADs. PMID:35090532
Early downregulation of hsa-miR-144-3p in serum from drug-naïve Parkinson's disease patients. PMID:35079043
Identification of key regulators in Sarcoidosis through multidimensional systems biological approach. PMID:35075176
Overexpression of chaperonin containing TCP1 subunit 7 has diagnostic and prognostic value for hepatocellular carcinoma. PMID:35073517
Identification of key genes associated with esophageal adenocarcinoma based on bioinformatics analysis. PMID:35071405
Immune response pathways enriched in breast cancer samples with brain metastasis. PMID:35070893
Establishment and characterization of NCC-DMM1-C1, a novel patient-derived cell line of desmoplastic malignant pleural mesothelioma. PMID:35069873
Identification of Characteristic Genes in Whole Blood of Intervertebral Disc Degeneration Patients by Weighted Gene Coexpression Network Analysis (WGCNA). PMID:35069789
Implication of Sphingolipid Metabolism Gene Dysregulation and Cardiac Sphingosine-1-Phosphate Accumulation in Heart Failure. PMID:35052814
MicroRNA-Enriched Exosomes from Different Sources of Mesenchymal Stem Cells Can Differentially Modulate Functions of Immune Cells and Neurogenesis. PMID:35052749
The Alzheimer's disease drug candidate J147 decreases blood plasma fatty acid levels via modulation of AMPK/ACC1 signaling in the liver. PMID:35051863
Identification of key genes and microRNAs for multiple sclerosis using bioinformatics analysis. PMID:35049167
Revealing potential diagnostic gene biomarkers of septic shock based on machine learning analysis. PMID:35045818
Identification of hub genes associated with COVID-19 and idiopathic pulmonary fibrosis by integrated bioinformatics analysis. PMID:35045126
Comparative analysis of protein-protein interaction networks in metastatic breast cancer. PMID:35045088
A cerebrospinal fluid microRNA analysis: Progressive supranuclear palsy. PMID:35039873
Identification of prognostic biomarkers in papillary renal cell carcinoma and PTTG1 may serve as a biomarker for predicting immunotherapy response. PMID:35037540
RiboReport - benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria. PMID:35037022
Transcriptomic identification of HBx-associated hub genes in hepatocellular carcinoma. PMID:35036167
Key genes associated with prognosis and metastasis of clear cell renal cell carcinoma. PMID:35036081
PD-L1 interacts with Frizzled 6 to activate β-catenin and form a positive feedback loop to promote cancer stem cell expansion. PMID:35034965
Dictionary learning allows model-free pseudotime estimation of transcriptomic data. PMID:35033004
APOE4 confers transcriptomic and functional alterations to primary mouse microglia. PMID:35031484
Multiomic analysis identifies CPT1A as a potential therapeutic target in platinum-refractory, high-grade serous ovarian cancer. PMID:35028612
A method for simultaneous detection of small and long RNA biotypes by ribodepleted RNA-Seq. PMID:35022475
Co-expression of cancer-testis antigens of MAGE-A6 and MAGE-A11 is associated with tumor aggressiveness in patients with bladder cancer. PMID:35022469
Mammalian brain glycoproteins exhibit diminished glycan complexity compared to other tissues. PMID:35022400
A lepidic gene signature predicts patient prognosis and sensitivity to immunotherapy in lung adenocarcinoma. PMID:35016696
[Identification of potential hub genes of Alzheimer's disease by weighted gene co-expression network analysis]. PMID:35012905
Enhancer RNA Expression in Response to Glucocorticoid Treatment in Murine Macrophages. PMID:35011590
The Antibiotic Fosfomycin Mimics the Effects of the Intermediate Metabolites Phosphoenolpyruvate and Glyceraldehyde-3-Phosphate on the Stenotrophomonas maltophilia Transcriptome. PMID:35008587
Anticancer Activities of 9-chloro-6-(piperazin-1-yl)-11H-indeno[1,2-c] quinolin-11-one (SJ10) in Glioblastoma Multiforme (GBM) Chemoradioresistant Cell Cycle-Related Oncogenic Signatures. PMID:35008426
IL-27 induces IFN/STAT1-dependent genes and enhances function of TIGIT+ HIVGag-specific T cells. PMID:35005538
ANXA9 as a novel prognostic biomarker associated with immune infiltrates in gastric cancer. PMID:35003923
Searching beyond the streetlight: Neonicotinoid exposure alters the neurogenomic state of worker honey bees. PMID:35003705
Acute sleep deprivation upregulates serotonin 2A receptors in the frontal cortex of mice via the immediate early gene Egr3. PMID:35001075
Human CD206+ macrophages associate with diabetes and adipose tissue lymphoid clusters. PMID:34990410
Integrative blood-derived epigenetic and transcriptomic analysis reveals the potential regulatory role of DNA methylation in ankylosing spondylitis. PMID:34986893
A versatile and robust cell purification system with an RNA-only circuit composed of microRNA-responsive ON and OFF switches. PMID:34985961
CREB1K292 and HINFPK330 as Putative Common Therapeutic Targets in Alzheimer's and Parkinson's Disease. PMID:34984308
Potential biomarkers and therapeutic targets of idiopathic pulmonary arterial hypertension. PMID:34981661
Fluctuating methylation clocks for cell lineage tracing at high temporal resolution in human tissues. PMID:34980912
CRISPR guides induce gene silencing in plants in the absence of Cas. PMID:34980227
The diagnostic and prognostic significance of small nuclear ribonucleoprotein Sm D1 aberrantly high expression in hepatocellular carcinoma. PMID:34976182
Expression profiling of lncRNAs and mRNAs in placental site trophoblastic tumor (PSTT) by microarray. PMID:34975294
Dysregulated BMP2 in the Placenta May Contribute to Early-Onset Preeclampsia by Regulating Human Trophoblast Expression of Extracellular Matrix and Adhesion Molecules. PMID:34970543
The interaction between the Spt6-tSH2 domain and Rpb1 affects multiple functions of RNA Polymerase II. PMID:34967414
High Expression of CEMIP Correlates Poor Prognosis and the Tumur Microenvironment in Breast Cancer as a Promisingly Prognostic Biomarker. PMID:34966410
Bioinformatics study on different gene expression profiles of fibroblasts and vascular endothelial cells in keloids. PMID:34964740
Sustained experimental activation of FGF8/ERK in the developing chicken spinal cord models early events in ERK-mediated tumorigenesis. PMID:34959031
Bacillus subtilis natto Derivatives Inhibit Enterococcal Biofilm Formation via Restructuring of the Cell Envelope. PMID:34956152
HPV16-LINC00393 Integration Alters Local 3D Genome Architecture in Cervical Cancer Cells. PMID:34950609
Autism-Related Transcription Factors Underlying the Sex-Specific Effects of Prenatal Bisphenol A Exposure on Transcriptome-Interactome Profiles in the Offspring Prefrontal Cortex. PMID:34947998
The Solvent Dimethyl Sulfoxide Affects Physiology, Transcriptome and Secondary Metabolism of Aspergillus flavus. PMID:34947037
hsa_circ_0001275 Is One of a Number of circRNAs Dysregulated in Enzalutamide Resistant Prostate Cancer and Confers Enzalutamide Resistance In Vitro. PMID:34945002
A Gene-Based Machine Learning Classifier Associated to the Colorectal Adenoma-Carcinoma Sequence. PMID:34944753
BET Proteins Regulate Expression of Osr1 in Early Kidney Development. PMID:34944697
C4d Deposition after Allogeneic Renal Transplantation in Rats Is Involved in Initial Apoptotic Cell Clearance. PMID:34944007
An episomal DNA vector platform for the persistent genetic modification of pluripotent stem cells and their differentiated progeny. PMID:34942088
Adipose Tissue Dysfunctions in Response to an Obesogenic Diet Are Reduced in Mice after Transgenerational Supplementation with Omega 3 Fatty Acids. PMID:34940596
TIPE polarity proteins are required for mucosal deployment of T lymphocytes and mucosal defense against bacterial infection. PMID:34939151
sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs. PMID:34937774
Identification of potential key genes and functional role of CENPF in osteosarcoma using bioinformatics and experimental analysis. PMID:34934449
Identification of Potential Genetic Biomarkers and Target Genes of Peri-Implantitis Using Bioinformatics Tools. PMID:34931168
Carbon nanotube biocompatibility in plants is determined by their surface chemistry. PMID:34930290
Comprehensive analysis identifies IFI16 as a novel signature associated with overall survival and immune infiltration of skin cutaneous melanoma. PMID:34930258
Characterization of Poldip2 knockout mice: Avoiding incorrect gene targeting. PMID:34928942
Parallel Single-Cell Multiomics Analysis of Neonatal Skin Reveals the Transitional Fibroblast States that Restrict Differentiation into Distinct Fates. PMID:34922949
B cell-related gene signature and cancer immunotherapy response. PMID:34921229
Identification of potential biomarkers for diagnosis of hepatocellular carcinoma. PMID:34917180
Mutations in LRRK2 linked to Parkinson disease sequester Rab8a to damaged lysosomes and regulate transferrin-mediated iron uptake in microglia. PMID:34914695
Col6a1+/CD201+ mesenchymal cells regulate intestinal morphogenesis and homeostasis. PMID:34910257
Deletion of TNFAIP6 Gene in Human Keratinocytes Demonstrates a Role for TSG-6 to Retain Hyaluronan Inside Epidermis. PMID:34909750
RANKL Blockade Reduces Cachexia and Bone Loss Induced by Non-Metastatic Ovarian Cancer in Mice. PMID:34904285
Relation Extraction of Protein Complexes from Dynamic Protein-Protein Interaction Network. PMID:34904064
Supervised Methods for Biomarker Detection from Microarray Experiments. PMID:34902125
Navigating Multi-Scale Cancer Systems Biology Towards Model-Driven Clinical Oncology and Its Applications in Personalized Therapeutics. PMID:34900668
Structural Equation Modeling of In silico Perturbations. PMID:34899830
CoRE-ATAC: A deep learning model for the functional classification of regulatory elements from single cell and bulk ATAC-seq data. PMID:34898596
Analysis of a circRNA-, miRNA-, and mRNA-associated ceRNA network reveals potential biomarkers in preeclampsia a ceRNA network in preeclampsia. PMID:34894939
Comparative transcriptomics of the Djungarian hamster hypothalamus during short photoperiod acclimation and spontaneous torpor. PMID:34894101
CAMML: Multi-Label Immune Cell-Typing and Stemness Analysis for Single-Cell RNA-sequencing. PMID:34890149
Canine DUXC: implications for DUX4 retrotransposition and preclinical models of FSHD. PMID:34888646
Organ Specific Copy Number Variations in Visceral Metastases of Human Melanoma. PMID:34885093
(20S) Ginsenoside Rh2 Exerts Its Anti-Tumor Effect by Disrupting the HSP90A-Cdc37 System in Human Liver Cancer Cells. PMID:34884975
Inference with Transposable Data: Modeling the Effects of Row and Column Correlations. PMID:34880705
Hirschsprung's disease: key microRNAs and target genes. PMID:34880446
Intrinsic Antiviral Activity of Optineurin Prevents Hyperproliferation of a Primary Herpes Simplex Virus Type 2 Infection. PMID:34880107
Identifying the temporal electrophysiological and molecular changes that contribute to TSC-associated epileptogenesis. PMID:34877936
Sparse Regression in Cancer Genomics: Comparing Variable Selection and Predictions in Real World Data. PMID:34866896
Epigenome-wide association studies: current knowledge, strategies and recommendations. PMID:34863305
Manganese transport by Streptococcus sanguinis in acidic conditions and its impact on growth in vitro and in vivo. PMID:34862691
Large Multicohort Study Reveals a Prostate Cancer Susceptibility Allele at 5p15 Regulating TERT via Androgen Signaling-Orchestrated Chromatin Binding of E2F1 and MYC. PMID:34858826
Predicting Bone Metastasis Using Gene Expression-Based Machine Learning Models. PMID:34858485
The impact of fine particulate matter (PM) on various beneficial functions of human endometrial stem cells through its key regulator SERPINB2. PMID:34857902
NEIL1 and NEIL2 DNA glycosylases modulate anxiety and learning in a cooperative manner in mice. PMID:34857879
Genomics and transcriptomics landscapes associated to changes in insulin sensitivity in response to endurance exercise training. PMID:34857871
A computational exploration of resilience and evolvability of protein-protein interaction networks. PMID:34857859
Why Environmental Biomarkers Work: Transcriptome-Proteome Correlations and Modeling of Multistressor Experiments in the Marine Bacterium Trichodesmium. PMID:34855411
JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. PMID:34850907
The SAGA and NuA4 component Tra1 regulates Candida albicans drug resistance and pathogenesis. PMID:34849885
The zinc cluster transcription factor Rha1 is a positive filamentation regulator in Candida albicans. PMID:34849863
Cross-species transcriptomic signatures predict response to MK2 inhibition in mouse models of chronic inflammation. PMID:34849469
Recurrent integration of human papillomavirus genomes at transcriptional regulatory hubs. PMID:34848725
Glutamine deprivation triggers NAGK-dependent hexosamine salvage. PMID:34844667
Diagnostic and Prognostic Implications of Caspase-1 and PD-L1 Co-Expression Patterns in Myelodysplastic Syndromes. PMID:34830867
Osteopontin Deficiency Ameliorates Prostatic Fibrosis and Inflammation. PMID:34830342
Circulatory Endothelin 1-Regulating RNAs Panel: Promising Biomarkers for Non-Invasive NAFLD/NASH Diagnosis and Stratification: Clinical and Molecular Pilot Study. PMID:34828420
The Identification of RNA Modification Gene PUS7 as a Potential Biomarker of Ovarian Cancer. PMID:34827123
Identification of Genes Potentially Associated with Melanoma Tumorigenesis Through Co-Expression Network Analysis. PMID:34824546
Genes and regulatory mechanisms associated with experimentally-induced bovine respiratory disease identified using supervised machine learning methodology. PMID:34824337
Effects of photodeoxygenation on cell biology using dibenzothiophene S-oxide derivatives as O(3P)-precursors. PMID:34822125
Establishment and characterization of prostate organoids from treatment-naïve patients with prostate cancer. PMID:34820005
Automatic cell type identification methods for single-cell RNA sequencing. PMID:34815832
Interleukin-4 and interleukin-13 induce different metabolic profiles in microglia and macrophages that relate with divergent outcomes after spinal cord injury. PMID:34815787
Functionally distinct roles for eEF2K in the control of ribosome availability and p-body abundance. PMID:34815424
Inheritance of gene expression throughout fruit development in chili pepper. PMID:34811443
A Single Human-Relevant Fast Food Meal Rapidly Reorganizes Metabolomic and Transcriptomic Signatures in a Gut Microbiota-Dependent Manner. PMID:34804604
The Macrophage Reprogramming Ability of Antifolates Reveals Soluble CD14 as a Potential Biomarker for Methotrexate Response in Rheumatoid Arthritis. PMID:34804067
Disruption of β-Catenin-Dependent Wnt Signaling in Colon Cancer Cells Remodels the Microenvironment to Promote Tumor Invasion. PMID:34799404
Identification of Immune-Related Genes for Establishment of Prognostic Index in Hepatocellular Carcinoma. PMID:34796177
CircleBase: an integrated resource and analysis platform for human eccDNAs. PMID:34792166
Identification of Cross-Pathway Connections via Protein-Protein Interactions Linked to Altered States of Metabolic Enzymes in Cervical Cancer. PMID:34790674
The Immune Infiltration in HNSCC and Its Clinical Value: A Comprehensive Study Based on the TCGA and GEO Databases. PMID:34790249
Sharing Biomedical Data Obtained Through Government-Funded Research and Development Projects in Korea. PMID:34788906
Human intestinal bitter taste receptors regulate innate immune responses and metabolic regulators in obesity. PMID:34784295
Peptide-YY3-36/glucagon-like peptide-1 combination treatment of obese diabetic mice improves insulin sensitivity associated with recovered pancreatic β-cell function and synergistic activation of discrete hypothalamic and brainstem neuronal circuitries. PMID:34781035
TRIB1 regulates LDL metabolism through CEBPα-mediated effects on the LDL receptor in hepatocytes. PMID:34779419
Machine learning and network medicine approaches for drug repositioning for COVID-19. PMID:34778851
Nanolipoprotein-Mediated Her2 Protein Transfection Induces Malignant Transformation in Human Breast Acinar Cultures. PMID:34778614
Expression Levels of RAD51 Inversely Correlate with Survival of Glioblastoma Patients. PMID:34771522
ENPP2 Methylation in Health and Cancer. PMID:34769391
Computationally Reconstructed Interactome of Bradyrhizobium diazoefficiens USDA110 Reveals Novel Functional Modules and Protein Hubs for Symbiotic Nitrogen Fixation. PMID:34769335
Classification and Functional Analysis between Cancer and Normal Tissues Using Explainable Pathway Deep Learning through RNA-Sequencing Gene Expression. PMID:34768960
TRPA1 Expression and Pathophysiology in Immune Cells. PMID:34768891
Histone lysine demethylase 4B regulates general and unique gene expression signatures in hypoxic cancer cells. PMID:34766154
Computational methods for protein localization prediction. PMID:34765098
Cigarette smoking-associated isoform switching and 3' UTR lengthening via alternative polyadenylation. PMID:34763026
The Identified Hub Gene GlcN in Osteoarthritis Progression and Treatment. PMID:34754325
Identification of key molecular markers of acute coronary syndrome using peripheral blood transcriptome sequencing analysis and mRNA-lncRNA co-expression network construction. PMID:34753383
Comparing the epigenetic landscape in myonuclei purified with a PCM1 antibody from a fast/glycolytic and a slow/oxidative muscle. PMID:34752468
Epigenetic signature of chronic low back pain in human T cells. PMID:34746619
Aberrant Methylation and Immune Microenvironment Are Associated With Overexpressed Fibronectin 1: A Diagnostic and Prognostic Target in Head and Neck Squamous Cell Carcinoma. PMID:34746236
Identification of an Autophagy-Related Risk Signature Correlates With Immunophenotype and Predicts Immune Checkpoint Blockade Efficacy of Neuroblastoma. PMID:34746127
Evaluation of ATAD2 as a Potential Target in Hepatocellular Carcinoma. PMID:34738187
Mucosal-Associated Invariant T (MAIT) Cell Dysfunction and PD-1 Expression in Prostate Cancer: Implications for Immunotherapy. PMID:34737749
β-caryophyllene enhances the transcriptional upregulation of cholesterol biosynthesis in breast cancer cells. PMID:34733015
Progenitor translatome changes coordinated by Tsc1 increase perception of Wnt signals to end nephrogenesis. PMID:34732708
Integrative genome-wide analysis of dopaminergic neuron-specific PARIS expression in Drosophila dissects recognition of multiple PPAR-γ associated gene regulation. PMID:34728675
Single-cell RNA-sequencing analysis of the ciliary epithelium and contiguous tissues in the mouse eye. PMID:34717927
Microenvironmental IL-6 inhibits anti-cancer immune responses generated by cytotoxic chemotherapy. PMID:34711820
A cis-regulatory element promoting increased transcription at low temperature in cultured ectothermic Drosophila cells. PMID:34711176
Molecular characterization of hematopoietic stem cells after in vitro amplification on biomimetic 3D PDMS cell culture scaffolds. PMID:34707135
Breast cancer dormancy is associated with a 4NG1 state and not senescence. PMID:34707097
Hypomethylation and downregulation of miR-23b-3p are associated with upregulated PLAU: a diagnostic and prognostic biomarker in head and neck squamous cell carcinoma. PMID:34702271
PIM1 phosphorylation of the androgen receptor and 14-3-3 ζ regulates gene transcription in prostate cancer. PMID:34697370
Colon Cancer Progression Is Reflected to Monotonic Differentiation in Gene Expression and Pathway Deregulation Facilitating Stage-specific Drug Repurposing. PMID:34697067
Identification of C3 and FN1 as potential biomarkers associated with progression and prognosis for clear cell renal cell carcinoma. PMID:34688260
Nkx3-1 and Fech genes might be switch genes involved in pituitary non-functioning adenoma invasiveness. PMID:34686726
Nanosecond Pulsed Electric Field Only Transiently Affects the Cellular and Molecular Processes of Leydig Cells. PMID:34681896
Trends in oligomannosylation and α1,2-mannosidase expression in human cancers. PMID:34676051
Construction and Investigation of Competing Endogenous RNA Networks and Candidate Genes Involved in SARS-CoV-2 Infection. PMID:34675627
Proteomic analysis of the host-pathogen interface in experimental cholera. PMID:34675415
Global Histone H3 Lysine 4 Trimethylation (H3K4me3) Landscape Changes in Response to TGFβ. PMID:34671716
Integrated computational analyses reveal novel insights into the stromal microenvironment of SHH-subtype medulloblastoma. PMID:34667228
Nrd1p identifies aberrant and natural exosomal target messages during the nuclear mRNA surveillance in Saccharomyces cerevisiae. PMID:34664673
Identification of key genes for HNSCC from public databases using bioinformatics analysis. PMID:34663338
Pleiotropic Effects of the P5-Type ATPase SpfA on Stress Response Networks Contribute to Virulence in the Pathogenic Mold Aspergillus fumigatus. PMID:34663092
IL-27 Derived From Macrophages Facilitates IL-15 Production and T Cell Maintenance Following Allergic Hypersensitivity Responses. PMID:34659203
Computational Interspecies Translation Between Alzheimer's Disease Mouse Models and Human Subjects Identifies Innate Immune Complement, TYROBP, and TAM Receptor Agonist Signatures, Distinct From Influences of Aging. PMID:34658769
A robust mean and variance test with application to high-dimensional phenotypes. PMID:34651232
Fasting-mimicking diet prevents high-fat diet effect on cardiometabolic risk and lifespan. PMID:34650272
GNG7 and ADCY1 as diagnostic and prognostic biomarkers for pancreatic adenocarcinoma through bioinformatic-based analyses. PMID:34650124
A brain-specific pgc1α fusion transcript affects gene expression and behavioural outcomes in mice. PMID:34649938
Meta-Analysis illustrates possible role of lipopolysaccharide (LPS)-induced tissue injury in nasopharyngeal carcinoma (NPC) pathogenesis. PMID:34648530
A novel m6A-related prognostic signature for predicting the overall survival of hepatocellular carcinoma patients. PMID:34647424
Oestrogen engages brain MC4R signalling to drive physical activity in female mice. PMID:34646010
The network interplay of interferon and Toll-like receptor signaling pathways in the anti-Candida immune response. PMID:34645905
A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development. PMID:34644528
Transcriptional Profiling of the Candida auris Response to Exogenous Farnesol Exposure. PMID:34643421
Comparison of the Metastasis Predictive Potential of mRNA and Long Non-Coding RNA Profiling in Systemically Untreated Breast Cancer. PMID:34638391
Evaluation of Comprehensive Gene Expression and NK Cell-Mediated Killing in Glioblastoma Cell Line-Derived Spheroids. PMID:34638384
The Role of miRNAs 340-5p, 92a-3p, and 381-3p in Patients with Endometriosis: A Plasma and Mesenchymal Stem-Like Cell Study. PMID:34631883
SPT6 loss permits the transdifferentiation of keratinocytes into an intestinal fate that resembles Barrett's metaplasia. PMID:34622168
Identification of immunization-related new prognostic biomarkers for papillary renal cell carcinoma by integrated bioinformatics analysis. PMID:34620162
Neuronal activity regulates the nuclear proteome to promote activity-dependent transcription. PMID:34617965
Lipocalin 2 Is a Regulator During Macrophage Polarization Induced by Soluble Worm Antigens. PMID:34616693
A dual-function RNA balances carbon uptake and central metabolism in Vibrio cholerae. PMID:34612526
Antimelanoma Effects of Concomitant Inhibition of SIRT1 and SIRT3 in BrafV600E/PtenNULL Mice. PMID:34597611
The profile analysis of circular RNAs in cervical cancer. PMID:34596168
A 41-Gene Pair Signature for Predicting the Pathological Response of Locally Advanced Rectal Cancer to Neoadjuvant Chemoradiation. PMID:34595195
The Interactions of Small Proline-Rich Proteins with Late Cornified Envelope Proteins are Involved in the Pathogenesis of Psoriasis. PMID:34594126
Transcriptional profiling of macaque microglia reveals an evolutionary preserved gene expression program. PMID:34589771
Protein Aggregation Is an Early Manifestation of Phospholamban p.(Arg14del)-Related Cardiomyopathy: Development of PLN-R14del-Related Cardiomyopathy. PMID:34587756
Transcriptome dataset of ethylene-treated Klutuk Wulung banana. PMID:34584916
Deep learning in cancer diagnosis, prognosis and treatment selection. PMID:34579788
Bioinformatic Analysis for Influential Core Gene Identification and Prognostic Significance in Advanced Serous Ovarian Carcinoma. PMID:34577856
RNA-Seq Provides New Insights into the Gene Expression Changes in Azoarcus olearius BH72 under Nitrogen-Deficient and Replete Conditions beyond the Nitrogen Fixation Process. PMID:34576783
Anaesthesia-Induced Transcriptomic Changes in the Context of Renal Ischemia Uncovered by the Use of a Novel Clamping Device. PMID:34576005
Searching for Biological Function of the Mysterious PA2504 Protein from Pseudomonas aeruginosa. PMID:34575996
Progression Risk Score Estimation Based on Immunostaining Data in Oral Cancer Using Unsupervised Hierarchical Clustering Analysis: A Retrospective Study in Taiwan. PMID:34575686
Dual-Specificity Phosphatase 1 (DUSP1) Has a Central Role in Redox Homeostasis and Inflammation in the Mouse Cochlea. PMID:34572983
The amino acid substitution affects cellular response to mistranslation. PMID:34568909
Position Specific Alternative Splicing and Gene Expression Profiles Along the Tonotopic Axis of Chick Cochlea. PMID:34568429
Limited Impact of Pivalate-Induced Secondary Carnitine Deficiency on Hepatic Transcriptome and Hepatic and Plasma Metabolome in Nursery Pigs. PMID:34564388
Smarca4 Inactivation Promotes Lineage-Specific Transformation and Early Metastatic Features in the Lung. PMID:34561242
Expression and prognosis of CDC45 in cervical cancer based on the GEO database. PMID:34557356
Reciprocal transcription factor networks govern tissue-resident ILC3 subset function and identity. PMID:34556884
ATP-competitive partial antagonists of the IRE1α RNase segregate outputs of the UPR. PMID:34556859
Association between chronic periodontitis and the risk of Alzheimer's disease: combination of text mining and GEO dataset. PMID:34556089
Polymorphic estrogen receptor binding site causes Cd2-dependent sex bias in the susceptibility to autoimmune diseases. PMID:34552089
Elevated Levels of the Escherichia coli nrdAB-Encoded Ribonucleotide Reductase Counteract the Toxicity Caused by an Increased Abundance of the β Clamp. PMID:34543109
The Mutant βE202K Sliding Clamp Protein Impairs DNA Polymerase III Replication Activity. PMID:34543108
Circular RNA repertoires are associated with evolutionarily young transposable elements. PMID:34542406
Programmed Cell Death Protein 1/Programmed Cell Death Ligand-1 Axis activates Intracellular ERK Signaling in Tumor Cells to Mediate Poor Prognosis in T-cell Lymphoma. PMID:34539885
High light and temperature reduce photosynthetic efficiency through different mechanisms in the C4 model Setaria viridis. PMID:34531541
Dynamin-related protein 1 regulates substrate oxidation in skeletal muscle by stabilizing cellular and mitochondrial calcium dynamics. PMID:34529976
Computational drug repositioning of atorvastatin for ulcerative colitis. PMID:34529084
Prognostic impact of a lymphocyte activation-associated gene signature in GBM based on transcriptome analysis. PMID:34527446
Understanding Competitive Endogenous RNA Network Mechanism in Type 1 Diabetes Mellitus Using Computational and Bioinformatics Approaches. PMID:34526791
Meta-analysis of gene expression disease signatures in colonic biopsy tissue from patients with ulcerative colitis. PMID:34521888
The Complex Transcriptional Landscape of Magnetosome Gene Clusters in Magnetospirillum gryphiswaldense. PMID:34519524
Comparative analysis of RNA enrichment methods for preparation of Cryptococcus neoformans RNA sequencing libraries. PMID:34518880
Tissue heterogeneity is prevalent in gene expression studies. PMID:34514392
RNA Sequence Profiling Reveals Unique Immune and Metabolic Features of Breast Cancer Brain Metastases. PMID:34513670
Prediction of the mechanism of miRNAs in laryngeal squamous cell carcinoma based on the miRNA-mRNA regulatory network. PMID:34513340
Identification of Genes Encoding Antimicrobial Proteins in Langerhans Cells. PMID:34512625
Single-Cell RNA Sequencing Reveals Cellular and Transcriptional Changes Associated With M1 Macrophage Polarization in Hidradenitis Suppurativa. PMID:34504848
Protein-gene Expression Nexus: Comprehensive characterization of human cancer cell lines with proteogenomic analysis. PMID:34504668
Mammalian and Invertebrate Models as Complementary Tools for Gaining Mechanistic Insight on Muscle Responses to Spaceflight. PMID:34502375
Investigating the Molecular Processes behind the Cell-Specific Toxicity Response to Titanium Dioxide Nanobelts. PMID:34502343
Herbaspirillum seropedicae expresses non-phosphorylative pathways for D-xylose catabolism. PMID:34499201
Identification of a novel six-gene signature with potential prognostic and therapeutic value in cervical cancer. PMID:34498424
Scanning mutagenesis of RNA-binding protein ProQ reveals a quality control role for the Lon protease. PMID:34497069
An ADAR1-dependent RNA editing event in the cyclin-dependent kinase CDK13 promotes thyroid cancer hallmarks. PMID:34496885
Functional characterization of a highly specific L-arabinose transporter from Trichoderma reesei. PMID:34496831
Dysregulation of KIF14 regulates the cell cycle and predicts poor prognosis in cervical cancer: a study based on integrated approaches. PMID:34495250
Two distinct Sertoli cell states are regulated via germ cell crosstalk†. PMID:34494084
Direct and Indirect Transcriptional Effects of Abiotic Stress in Zea mays Plants Defective in RNA-Directed DNA Methylation. PMID:34489998
Computational challenges and opportunities in spatially resolved transcriptomic data analysis. PMID:34489425
Disrupting biological sensors of force promotes tissue regeneration in large organisms. PMID:34489407
Carcinogenic effect of adenylosuccinate lyase (ADSL) in prostate cancer development and progression through the cell cycle pathway. PMID:34488772
Dataset for: Modeling chemotherapy induced neurotoxicity with human induced pluripotent stem cell (iPSC)-derived sensory neurons. PMID:34485650
Identification of a prognostic 4-mRNA signature in laryngeal squamous cell carcinoma. PMID:34475994
Loss of a 7q gene, CUX1, disrupts epigenetically driven DNA repair and drives therapy-related myeloid neoplasms. PMID:34473231
A computational approach for identification of core modules from a co-expression network and GWAS data. PMID:34467232
Adult stem cell-derived complete lung organoid models emulate lung disease in COVID-19. PMID:34463615
Reproducibility standards for machine learning in the life sciences. PMID:34462593
N6-methyladenosine (m6A) modification and its clinical relevance in cognitive dysfunctions. PMID:34461609
A multi-objective genetic algorithm to find active modules in multiplex biological networks. PMID:34460810
Annotating cell types in human single-cell RNA-seq data with CellO. PMID:34458864
Transcriptome Alterations of an in vitro-Selected, Moderately Resistant, Two-Row Malting Barley in Response to 3ADON, 15ADON, and NIV Chemotypes of Fusarium graminearum. PMID:34456945
New Insights Into Mitochondrial Dysfunction at Disease Susceptibility Loci in the Development of Type 2 Diabetes. PMID:34456865
PCA-based unsupervised feature extraction for gene expression analysis of COVID-19 patients. PMID:34456333
FluB-RAM and FluB-RANS: Genome Rearrangement as Safe and Efficacious Live Attenuated Influenza B Virus Vaccines. PMID:34452022
Screening and identification of NOTCH1, CDKN2A, and NOS3 as differentially expressed autophagy-related genes in erectile dysfunction. PMID:34447638
Exploring the role of monocyte chemoattractant protein-1 in fibroblast-like synovial cells in rheumatoid arthritis. PMID:34447637
HOXB8 Counteracts MAPK/ERK Oncogenic Signaling in a Chicken Embryo Model of Neoplasia. PMID:34445617
Epidermal PPARγ Is a Key Homeostatic Regulator of Cutaneous Inflammation and Barrier Function in Mouse Skin. PMID:34445339
A Novel Approach for the Discovery of Biomarkers of Radiotherapy Response in Breast Cancer. PMID:34442440
Artificial Intelligence for Alzheimer's Disease: Promise or Challenge? PMID:34441407
Two Auxinic Herbicides Affect Brassica napus Plant Hormone Levels and Induce Molecular Changes in Transcription. PMID:34439819
Transcriptome Analysis Identifies Doublesex and Mab-3 Related Transcription Factor (DMRT3) in Nasal Polyp Epithelial Cells of Patients Suffering from Non-Steroidal Anti-Inflammatory Drug-Exacerbated Respiratory Disease (AERD). PMID:34439758
CCL20/TNF/VEGFA Cytokine Secretory Phenotype of Tumor-Associated Macrophages Is a Negative Prognostic Factor in Cutaneous Melanoma. PMID:34439098
The autoimmune signature of hyperinflammatory multisystem inflammatory syndrome in children. PMID:34437303
The related coactivator complexes SAGA and ATAC control embryonic stem cell self-renewal through acetyltransferase-independent mechanisms. PMID:34433046
Perturbed transcriptional profiles after chronic low dose rate radiation in mice. PMID:34428250
Assessment of the Diagnostic Efficiency of a Liquid Biopsy Assay for Early Detection of Gastric Cancer. PMID:34427680
Genotypic Characteristics of Hepatoblastoma as Detected by Next Generation Sequencing and Their Correlation With Clinical Efficacy. PMID:34426785
INFIMA leverages multi-omics model organism data to identify effector genes of human GWAS variants. PMID:34425882
Loss of Mir146b with aging contributes to inflammation and mitochondrial dysfunction in thioglycollate-elicited peritoneal macrophages. PMID:34423778
Identification of JAK2 and FOXM1 expression as novel candidate biomarkers for predicting the benefit of immunotherapy in lung squamous cell carcinoma. PMID:34422993
Hypoxia-Inducible Factor 2-Alpha Mediated Gene Sets Differentiate Pulmonary Arterial Hypertension. PMID:34422822
CD86 Molecule Might Be a Novel Immune-Related Prognostic Biomarker for Patients With Bladder Cancer by Bioinformatics and Experimental Assays. PMID:34422632
Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients. PMID:34421903
Transcriptional Time Course After Rotator Cuff Tear. PMID:34421646
Histone H4 lysine 20 mono-methylation directly facilitates chromatin openness and promotes transcription of housekeeping genes. PMID:34417450
RHPN1‑AS1 promotes ovarian carcinogenesis by sponging miR‑6884‑5p thus releasing TOP2A mRNA. PMID:34414458
Large-scale transcriptome-wide profiling of microRNAs in human placenta and maternal plasma at early to mid gestation. PMID:34412547
Cerium Oxide Nanoparticle Administration to Skeletal Muscle Cells under Different Gravity and Radiation Conditions. PMID:34410709
Chronic social isolation signals starvation and reduces sleep in Drosophila. PMID:34408325
Key features of the environment promoting liver cancer in the absence of cirrhosis. PMID:34408183
Long non-coding RNA RP4-694A7.2 Promotes Hepatocellular Carcinoma Cell Proliferation and Metastasis through the Regulation of PSAT1. PMID:34405023
Transcriptomic analysis of the mouse retina after acute and chronic normobaric and hypobaric hypoxia. PMID:34404875
Human iPS-derived pre-epicardial cells direct cardiomyocyte aggregation expansion and organization in vitro. PMID:34404774
A primary cell wall cellulose-dependent defense mechanism against vascular pathogens revealed by time-resolved dual transcriptomics. PMID:34404410
The Rsm (Csr) post-transcriptional regulatory pathway coordinately controls multiple CRISPR-Cas immune systems. PMID:34403463
Metabolic preconditioning in CD4+ T cells restores inducible immune tolerance in lupus-prone mice. PMID:34403367
MiR-508-3p promotes proliferation and inhibits apoptosis of middle ear cholesteatoma cells by targeting PTEN/PI3K/AKT pathway. PMID:34400892
Integrated bioinformatics analysis reveals CDK1 and PLK1 as potential therapeutic targets of lung adenocarcinoma. PMID:34397869
Multi-omics network characterization reveals novel microRNA biomarkers and mechanisms for diagnosis and subtyping of kidney transplant rejection. PMID:34389032
ERK signaling controls productive HIF-1 binding to chromatin and cancer cell adaptation to hypoxia through HIF-1α interaction with NPM1. PMID:34388291
The epithelial potassium channel Kir7.1 is stimulated by progesterone. PMID:34387656
NOTUM promotes thermogenic capacity and protects against diet-induced obesity in male mice. PMID:34385484
Replacement of Nitrite in Meat Products by Natural Bioactive Compounds Results in Reduced Exposure to N-Nitroso Compounds: The PHYTOME Project. PMID:34382747
A merged microarray meta-dataset for transcriptionally profiling colorectal neoplasm formation and progression. PMID:34381057
KAT2A-mediated AR translocation into nucleus promotes abiraterone-resistance in castration-resistant prostate cancer. PMID:34381019
Lack of Interferon (IFN) Regulatory Factor 8 Associated with Restricted IFN-γ Response Augmented Japanese Encephalitis Virus Replication in the Mouse Brain. PMID:34379515
KITlow Cells Mediate Imatinib Resistance in Gastrointestinal Stromal Tumor. PMID:34376580
Human Placental Trophoblasts Infected by Listeria monocytogenes Undergo a Pro-Inflammatory Switch Associated With Poor Pregnancy Outcomes. PMID:34367171
Gene Expression Meta-Analysis Reveals Interferon-Induced Genes Associated With SARS Infection in Lungs. PMID:34367154
Volatile Compounds From Bacillus, Serratia, and Pseudomonas Promote Growth and Alter the Transcriptional Landscape of Solanum tuberosum in a Passively Ventilated Growth System. PMID:34367077
Distinct regulation of hippocampal neuroplasticity and ciliary genes by corticosteroid receptors. PMID:34362910
NAT10 as a potential prognostic biomarker and therapeutic target for HNSCC. PMID:34362389
mRNA Inventory of Extracellular Vesicles from Ustilago maydis. PMID:34356940
The Negative Effect of Protein Phosphatase Z1 Deletion on the Oxidative Stress Tolerance of Candida albicans Is Synergistic with Betamethasone Exposure. PMID:34356919
Delayed Contralateral Nephrectomy Halted Post-Ischemic Renal Fibrosis Progression and Inhibited the Ischemia-Induced Fibromir Upregulation in Mice. PMID:34356879
Yippee like 4 (Ypel4) is essential for normal mouse red blood cell membrane integrity. PMID:34354145
Personalized single-cell networks: a framework to predict the response of any gene to any drug for any patient. PMID:34353329
Tomato transcriptomic response to Tuta absoluta infestation. PMID:34348650
Long non-coding RNA profile study identifies a metabolism-related signature for colorectal cancer. PMID:34344319
Spatial transcriptomics analysis of uterine gene expression in enhancer of zeste homolog 2 conditional knockout mice†. PMID:34344022
The ALPK1 pathway drives the inflammatory response to Campylobacter jejuni in human intestinal epithelial cells. PMID:34339468
Does chronic dietary exposure to the mycotoxin deoxynivalenol affect the porcine hepatic transcriptome when an acute-phase response is initiated through first or second-pass LPS challenge of the liver? PMID:34338001
Identification of response signatures for tankyrase inhibitor treatment in tumor cell lines. PMID:34337362
Creation of a Single Cell RNASeq Meta-Atlas to Define Human Liver Immune Homeostasis. PMID:34335581
Epigenetic Analysis of the Chromatin Landscape Identifies a Repertoire of Murine Eosinophil-Specific PU.1-Bound Enhancers. PMID:34330753
Somatic cell hemoglobin modulates nitrogen oxide metabolism in the human airway epithelium. PMID:34326365
RNA sequencing identifies global transcriptional changes in peripheral CD4+ cells during active oesophagitis and following epicutaneous immunotherapy in eosinophilic oesophagitis. PMID:34322233
On the impact of batch effect correction in TCGA isomiR expression data. PMID:34316700
Transcriptional landscape of PTEN loss in primary prostate cancer. PMID:34311724
Identification of novel survival-related lncRNA-miRNA-mRNA competing endogenous RNA network associated with immune infiltration in colorectal cancer. PMID:34306328
Network Pharmacology-Based Mechanistic Investigation of Jinshui Huanxian Formula Acting on Idiopathic Pulmonary Fibrosis. PMID:34306156
A pH-eQTL Interaction at the RIT2-SYT4 Parkinson's Disease Risk Locus in the Substantia Nigra. PMID:34305570
Myeloid Cells Are Enriched in Tonsillar Crypts, Providing Insight into the Viral Tropism of Human Papillomavirus. PMID:34303699
Investigation of Fascin1, a Marker of Mature Dendritic Cells, Reveals a New Role for IL-6 Signaling in CCR7-Mediated Chemotaxis. PMID:34301846
Whole Blood Transcriptome Characterization of 3xTg-AD Mouse and Its Modulation by Transcranial Direct Current Stimulation (tDCS). PMID:34299250
Genomic and clinical characterization of early T-cell precursor lymphoblastic lymphoma. PMID:34297047
Screening of hub genes and evaluation of the growth regulatory role of CD44 in metastatic prostate cancer. PMID:34296309
IL-1B drives opposing responses in primary tumours and bone metastases; harnessing combination therapies to improve outcome in breast cancer. PMID:34290237
Transcriptomic changes in peripheral blood mononuclear cells with weight loss: systematic literature review and primary data synthesis. PMID:34281497
The methyl donor S-adenosyl methionine reverses the DNA methylation signature of chronic neuropathic pain in mouse frontal cortex. PMID:34278163
Effect of Protein O-Mannosyltransferase (MSMEG_5447) on M. smegmatis and Its Survival in Macrophages. PMID:34276591
Differential Packaging Into Outer Membrane Vesicles Upon Oxidative Stress Reveals a General Mechanism for Cargo Selectivity. PMID:34276573
The Progenetix oncogenomic resource in 2021. PMID:34272855
Analysis of the Prognostic Value and Gene Expression Mechanism of SHOX2 in Lung Adenocarcinoma. PMID:34262939
Identification of four key biomarkers and small molecule drugs in nasopharyngeal carcinoma by weighted gene co-expression network analysis. PMID:34261404
Deficiency of Antioxidative Paraoxonase 2 (Pon2) Leads to Increased Number of Phenotypic LT-HSCs and Disturbed Erythropoiesis. PMID:34257800
Linking genotype to phenotype in multi-omics data of small sample. PMID:34256701
CD40L modulates transcriptional signatures of neutrophils in the bone marrow associated with development and trafficking. PMID:34255742
Accurate transcriptome assembly by Nanopore RNA sequencing reveals novel functional transcripts in hepatocellular carcinoma. PMID:34255396
Targeting Bacterial Gyrase with Cystobactamid, Fluoroquinolone, and Aminocoumarin Antibiotics Induces Distinct Molecular Signatures in Pseudomonas aeruginosa. PMID:34254824
Predicting mechanism of action of novel compounds using compound structure and transcriptomic signature coembedding. PMID:34252937
'Single-subject studies'-derived analyses unveil altered biomechanisms between very small cohorts: implications for rare diseases. PMID:34252934
Loss of RND-Type Multidrug Efflux Pumps Triggers Iron Starvation and Lipid A Modifications in Pseudomonas aeruginosa. PMID:34252310
Detecting Differentially Methylated Promoters in Genes Related to Disease Phenotypes Using R. PMID:34250201
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
Role of NRP1 in Bladder Cancer Pathogenesis and Progression. PMID:34249735
Prolonged cadmium exposure alters benign uterine fibroid cell behavior, extracellular matrix components, and TGFB signaling. PMID:34245615
MicroRNA-378a-3p is overexpressed in psoriasis and modulates cell cycle arrest in keratinocytes via targeting BMP2 gene. PMID:34244572
Integrative analysis of key candidate genes and signaling pathways in acute coronary syndrome related to obstructive sleep apnea by bioinformatics. PMID:34239024
Identification of viral-mediated pathogenic mechanisms in neurodegenerative diseases using network-based approaches. PMID:34237135
Early inflammation precedes cardiac fibrosis and heart failure in desmoglein 2 murine model of arrhythmogenic cardiomyopathy. PMID:34236518
Combining multiomics and drug perturbation profiles to identify muscle-specific treatments for spinal muscular atrophy. PMID:34236053
DIMEimmune: Robust estimation of infiltrating lymphocytes in CNS tumors from DNA methylation profiles. PMID:34235002
Screening of key biomarkers and immune infiltration in Pulmonary Arterial Hypertension via integrated bioinformatics analysis. PMID:34233597
Active elimination of intestinal cells drives oncogenic growth in organoids. PMID:34233177
Identification of endometriosis-associated genes and pathways based on bioinformatic analysis. PMID:34232189
GNRH1 and LTB4R might be novel immune-related prognostic biomarkers in clear cell renal cell carcinoma (ccRCC). PMID:34229684
Identification of immune-infiltrating cell-related biomarkers in hepatocellular carcinoma based on gene co-expression network analysis. PMID:34218795
Regular football training down-regulates miR-1303 muscle expression in veterans. PMID:34212217
The Placental Response to Guinea Pig Cytomegalovirus Depends Upon the Timing of Maternal Infection. PMID:34211475
Profile of miR-23 Expression and Possible Role in Regulation of Glutamic Acid Decarboxylase during Postnatal Retinal Development. PMID:34209226
Diversity of Rainbow Trout Blood B Cells Revealed by Single Cell RNA Sequencing. PMID:34207643
Cleaning the Medicago Microarray Database to Improve Gene Function Analysis. PMID:34207216
Methylation Status of Corticotropin-Releasing Factor (CRF) Receptor Genes in Colorectal Cancer. PMID:34207031
Serine-Threonine Kinase Receptor-Associated Protein (STRAP) Knockout Decreases the Malignant Phenotype in Neuroblastoma Cell Lines. PMID:34206917
MIR29A Impedes Metastatic Behaviors in Hepatocellular Carcinoma via Targeting LOX, LOXL2, and VEGFA. PMID:34206143
Exploring the Metabolic Heterogeneity of Cancers: A Benchmark Study of Context-Specific Models. PMID:34205912
Statistical Integration of 'Omics Data Increases Biological Knowledge Extracted from Metabolomics Data: Application to Intestinal Exposure to the Mycotoxin Deoxynivalenol. PMID:34205708
Differential Regulation of Gonadotropins as Revealed by Transcriptomes of Distinct LH and FSH Cells of Fish Pituitary. PMID:34204216
TENT4A Non-Canonical Poly(A) Polymerase Regulates DNA-Damage Tolerance via Multiple Pathways That Are Mutated in Endometrial Cancer. PMID:34203408
mRNA-miRNA-lncRNA Regulatory Network in Nonalcoholic Fatty Liver Disease. PMID:34202571
Virus-Host Interaction Gets Curiouser and Curiouser. PART II: Functional Transcriptomics of the E. coli DksA-Deficient Cell upon Phage P1vir Infection. PMID:34200430
Biphasic α2β1 Integrin Expression in Breast Cancer Metastasis to Bone. PMID:34199096
Development of a Novel Live Attenuated Influenza A Virus Vaccine Encoding the IgA-Inducing Protein. PMID:34198994
Tribbles Pseudokinases in Colorectal Cancer. PMID:34198908
Towards a global investigation of transcriptomic signatures through co-expression networks and pathway knowledge for the identification of disease mechanisms. PMID:34197603
Genome of the Single Human Chromosome 18 as a "Gold Standard" for Its Transcriptome. PMID:34194472
Pars Pro Toto: Every Single Cell Matters. PMID:34194448
Toll-like receptor 2 induces pathogenicity in Th17 cells and reveals a role for IPCEF in regulating Th17 cell migration. PMID:34192530
Protocol for using heterologous spike-ins to normalize for technical variation in chromatin immunoprecipitation. PMID:34189474
Iron-dependent apoptosis causes embryotoxicity in inflamed and obese pregnancy. PMID:34188052
Conservation genomics reveals pesticide and pathogen exposure in the declining bumble bee Bombus terricola. PMID:34181797
Resistance to different anthracycline chemotherapeutics elicits distinct and actionable primary metabolic dependencies in breast cancer. PMID:34181531
Classifying Medulloblastoma Subgroups Based on Small, Clinically Achievable Gene Sets. PMID:34178626
Predicting Selective RNA Processing and Stabilization Operons in Clostridium spp. PMID:34177856
Bioinformatics analysis of differentially expressed genes and pathways in the development of cervical cancer. PMID:34174849
UniBind: maps of high-confidence direct TF-DNA interactions across nine species. PMID:34174819
Altered expression of SARS-CoV-2 entry and processing genes by Porphyromonas gingivalis-derived lipopolysaccharide, inflammatory cytokines and prostaglandin E2 in human gingival fibroblasts. PMID:34174588
A comprehensive database for integrated analysis of omics data in autoimmune diseases. PMID:34167460
Identification of Independent and Communal Differentially Expressed Genes as Well as Potential Therapeutic Targets in Ischemic Heart Failure and Non-Ischemic Heart Failure. PMID:34163213
Multiomic analysis of the Arabian camel (Camelus dromedarius) kidney reveals a role for cholesterol in water conservation. PMID:34163009
A method to analyze time expression profiles demonstrated in a database of chili pepper fruit development. PMID:34162966
Side effect prediction based on drug-induced gene expression profiles and random forest with iterative feature selection. PMID:34155353
A small RNA regulates pprM, a modulator of pleiotropic proteins promoting DNA repair, in Deinococcus radiodurans under ionizing radiation. PMID:34155239
Duplication and Functional Divergence of Branched-Chain Amino Acid Biosynthesis Genes in Aspergillus nidulans. PMID:34154419
Identification of NAA40 as a Potential Prognostic Marker for Aggressive Liver Cancer Subtypes. PMID:34150665
Identification of a Competing Endogenous RNA Network Related to Immune Signature in Lung Adenocarcinoma. PMID:34149807
Transcriptome Analysis Reveals Putative Target Genes of APETALA3-3 During Early Floral Development in Nigella damascena L. PMID:34149759
hsp-90 and unc-45 depletion induce characteristic transcriptional signatures in coexpression cliques of C. elegans. PMID:34145311
ATP/IL-33-triggered hyperactivation of mast cells results in an amplified production of pro-inflammatory cytokines and eicosanoids. PMID:34142370
Individual B cells transcribe multiple rearranged immunoglobulin light chains in teleost fish. PMID:34142062
DCBLD1 is associated with the integrin signaling pathway and has prognostic value in non-small cell lung and invasive breast carcinoma. PMID:34140574
Analysis of the transcriptome of bovine endometrial cells isolated by laser micro-dissection (1): specific signatures of stromal, glandular and luminal epithelial cells. PMID:34139994
Analysis of the transcriptome of bovine endometrial cells isolated by laser micro-dissection (2): impacts of post-partum negative energy balance on stromal, glandular and luminal epithelial cells. PMID:34139988
Transcriptional analysis of sweet corn hybrids in response to crowding stress. PMID:34138910
Endothelial SOCS3 maintains homeostasis and promotes survival in endotoxemic mice. PMID:34138760
The Immunology of Hormone Receptor Positive Breast Cancer. PMID:34135901
The Gene Expression Profile of the Song Control Nucleus HVC Shows Sex Specificity, Hormone Responsiveness, and Species Specificity Among Songbirds. PMID:34135731
Insulin Infusion Is Linked to Increased NPPC Expression in Muscle and Plasma C-type Natriuretic Peptide in Male Dogs. PMID:34131611
Capitalizing on transcriptome profiling to optimize and identify targets for promoting early murine folliculogenesis in vitro. PMID:34131220
Transcriptional drug repositioning and cheminformatics approach for differentiation therapy of leukaemia cells. PMID:34131166
IOAT: an interactive tool for statistical analysis of omics data and clinical data. PMID:34130622
Copy number alterations identify a smoking-associated expression signature predictive of poor outcome in head and neck squamous cell carcinoma. PMID:34130230
AI-guided discovery of the invariant host response to viral pandemics. PMID:34127431
TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data. PMID:34125906
Differences in the genome, methylome, and transcriptome do not differentiate isolates of Streptococcus equi subsp. equi from horses with acute clinical signs from isolates of inapparent carriers. PMID:34125848
The ChvG-ChvI and NtrY-NtrX Two-Component Systems Coordinately Regulate Growth of Caulobacter crescentus. PMID:34124942
Investigation of the Mechanism of Complement System in Diabetic Nephropathy via Bioinformatics Analysis. PMID:34124269
Murine Blastocysts Release Mature MicroRNAs Into Culture Media That Reflect Developmental Status. PMID:34122510
Exploring the Pathogenesis of Psoriasis Complicated With Atherosclerosis via Microarray Data Analysis. PMID:34122426
Transcriptome Analysis Reveals Cr(VI) Adaptation Mechanisms in Klebsiella sp. Strain AqSCr. PMID:34122372
Identification of Key Biomarkers and Immune Infiltration in Sciatic Nerve of Diabetic Neuropathy BKS-db/db Mice by Bioinformatics Analysis. PMID:34122109
Noncanonical functions of glucocorticoids: A novel role for glucocorticoids in performing multiple beneficial functions in endometrial stem cells. PMID:34120144
Identification of Disease-Specific Hub Biomarkers and Immune Infiltration in Osteoarthritis and Rheumatoid Arthritis Synovial Tissues by Bioinformatics Analysis. PMID:34113405
Exploration of Crucial Mediators for Carotid Atherosclerosis Pathogenesis Through Integration of Microbiome, Metabolome, and Transcriptome. PMID:34108883
Time trajectories in the transcriptomic response to exercise - a meta-analysis. PMID:34108459
Decoding empagliflozin's molecular mechanism of action in heart failure with preserved ejection fraction using artificial intelligence. PMID:34103605
Transcriptomic analysis of cork during seasonal growth highlights regulatory and developmental processes from phellogen to phellem formation. PMID:34103550
Gene expression changes and DNA damage after ex vivo exposure of peripheral blood cells to various CT photon spectra. PMID:34103547
Type II alveolar epithelial cell-specific loss of RhoA exacerbates allergic airway inflammation through SLC26A4. PMID:34101619
Molecular omics resources should require sex annotation: a call for action. PMID:34099934
A histone H3K4me1-specific binding protein is required for siRNA accumulation and DNA methylation at a subset of loci targeted by RNA-directed DNA methylation. PMID:34099688
HOXA13 in etiology and oncogenic potential of Barrett's esophagus. PMID:34099670
A Dynamic Transcription Factor Signature Along the Colorectal Adenoma-Carcinoma Sequence in Patients With Co-Occurrent Adenoma and Carcinoma. PMID:34094897
Differentially Expressed Genes and Enriched Signaling Pathways in the Adipose Tissue of Obese People. PMID:34093637
Mapping of m6A and Its Regulatory Targets in Prostate Cancer Reveals a METTL3-Low Induction of Therapy Resistance. PMID:34088870
Dynamics of alternative splicing during somatic cell reprogramming reveals functions for RNA-binding proteins CPSF3, hnRNP UL1, and TIA1. PMID:34082786
Continuous Inflammatory Stimulation Leads via Metabolic Plasticity to a Prometastatic Phenotype in Triple-Negative Breast Cancer Cells. PMID:34072893
Transcriptome Profiling of Embryonic Retinal Pigment Epithelium Reprogramming. PMID:34072522
Small RNA-Sequencing: Approaches and Considerations for miRNA Analysis. PMID:34071824
Pivotal Role for Cxcr2 in Regulating Tumor-Associated Neutrophil in Breast Cancer. PMID:34070438
Transcription Factor β-Catenin Plays a Key Role in Fluid Flow Shear Stress-Mediated Glomerular Injury in Solitary Kidney. PMID:34069476
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
Transcriptomic Profiling of Skeletal Muscle Reveals Candidate Genes Influencing Muscle Growth and Associated Lipid Composition in Portuguese Local Pig Breeds. PMID:34065673
Application of the Interaction between Tissue Immunohistochemistry Staining and Clinicopathological Factors for Evaluating the Risk of Oral Cancer Progression by Hierarchical Clustering Analysis: A Case-Control Study in a Taiwanese Population. PMID:34063938
Effect of Ecdysterone on the Hepatic Transcriptome and Lipid Metabolism in Lean and Obese Zucker Rats. PMID:34063487
Death Processes in Bovine Theca and Granulosa Cells Modelled and Analysed Using a Systems Biology Approach. PMID:34063056
GeromiRs Are Downregulated in the Tumor Microenvironment during Colon Cancer Colonization of the Liver in a Murine Metastasis Model. PMID:34062897
Deletion of Lats1/2 in adult kidney epithelia leads to renal cell carcinoma. PMID:34060480
GLEANER: a web server for GermLine cycle Expression ANalysis and Epigenetic Roadmap visualization. PMID:34058973
Pro-inflammatory Monocyte Phenotype During Acute Progression of Cerebral Small Vessel Disease. PMID:34055930
Prediction of clinical prognosis in cutaneous melanoma using an immune-related gene pair signature. PMID:34047683
MicroRNA-200c restoration reveals a cytokine profile to enhance M1 macrophage polarization in breast cancer. PMID:34045467
RNA Sequencing Reveals Key Metabolic Pathways Are Modified by Short-Term Whole Egg Consumption. PMID:34041258
In vivo stabilization of endogenous chloroplast RNAs by customized artificial pentatricopeptide repeat proteins. PMID:34037778
MicroRNA in combination with HER2-targeting drugs reduces breast cancer cell viability in vitro. PMID:34035375
Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods. PMID:34031612
NFAT5 Amplifies Antipathogen Responses by Enhancing Chromatin Accessibility, H3K27 Demethylation, and Transcription Factor Recruitment. PMID:34031145
Application of multi-omics data integration and machine learning approaches to identify epigenetic and transcriptomic differences between in vitro and in vivo produced bovine embryos. PMID:34029343
Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome. PMID:34029205
The relationship between cytokine and neutrophil gene network distinguishes SARS-CoV-2-infected patients by sex and age. PMID:34027897
Network-based analysis of key regulatory genes implicated in Type 2 Diabetes Mellitus and Recurrent Miscarriages in Turner Syndrome. PMID:34021221
eVITTA: a web-based visualization and inference toolbox for transcriptome analysis. PMID:34019643
Hub biomarkers for the diagnosis and treatment of glioblastoma based on microarray technology. PMID:34018447
Deep Large-Scale Multitask Learning Network for Gene Expression Inference. PMID:34014778
Identification of the EMT-Related Genes Signature for Predicting Occurrence and Progression in Thyroid Cancer. PMID:34012269
Genome-wide screening of SARS-CoV-2 infection-related genes based on the blood leukocytes sequencing data set of patients with COVID-19. PMID:34009691
Activated mast cells in skeletal muscle can be a potential mediator for cancer-associated cachexia. PMID:34008339
The ApiAP2 factor PfAP2-HC is an integral component of heterochromatin in the malaria parasite Plasmodium falciparum. PMID:33997710
Evaluating the Consistency of Gene Methylation in Liver Cancer Using Bisulfite Sequencing Data. PMID:33996828
Identification of Key Functional Gene Signatures Indicative of Dedifferentiation in Papillary Thyroid Cancer. PMID:33996555
Role of Flt4 in Skin Protection against UVB Radiation: A System Biology Approach. PMID:33995966
Genome-wide analysis of primary microRNA expression using H3K36me3 ChIP-seq data. PMID:33995896
Identifying the Potential Therapeutic Targets for Atopic Dermatitis Through the Immune Infiltration Analysis and Construction of a ceRNA Network. PMID:33994801
Centromere protein N may be a novel malignant prognostic biomarker for hepatocellular carcinoma. PMID:33987018
A surgical method for continuous intraportal infusion of gut microbial metabolites in mice. PMID:33986195
CD109-GP130 interaction drives glioblastoma stem cell plasticity and chemoresistance through STAT3 activity. PMID:33986188
Molecular Regulation of the Melatonin Biosynthesis Pathway in Unipolar and Bipolar Depression. PMID:33981243
Cbl-b deficiency prevents functional but not phenotypic T cell anergy. PMID:33974042
Levels and Characteristics of mRNAs in Spores of Firmicute Species. PMID:33972352
Knowledge bases and software support for variant interpretation in precision oncology. PMID:33971666
Interferon-induced degradation of the persistent hepatitis B virus cccDNA form depends on ISG20. PMID:33969602
Role of CCR2+ Myeloid Cells in Inflammation Responses Driven by Expression of a Surfactant Protein-C Mutant in the Alveolar Epithelium. PMID:33968067
Epigenetic dysregulation of immune-related pathways in cancer: bioinformatics tools and visualization. PMID:33963293
Intestinal mucosa-derived DNA methylation signatures in the penetrating intestinal mucosal lesions of Crohn's disease. PMID:33963246
Minimized combinatorial CRISPR screens identify genetic interactions in autophagy. PMID:33956155
Screening and identification of LMNB1 and DLGAP5, two key biomarkers in gliomas. PMID:33956061
Multiple roles of H2A.Z in regulating promoter chromatin architecture in human cells. PMID:33953180
A cloud-based bioinformatic analytic infrastructure and Data Management Core for the Expanded Program on Immunization Consortium. PMID:33948273
In vivo targets of Salmonella FinO include a FinP-like small RNA controlling copy number of a cohabitating plasmid. PMID:33939833
Human methylome variation across Infinium 450K data on the Gene Expression Omnibus. PMID:33937763
Enhancing Fatty Acid Catabolism of Macrophages Within Aberrant Breast Cancer Tumor Microenvironment Can Re-establish Antitumor Function. PMID:33937269
Transcriptome Based Estrogen Related Genes Biomarkers for Diagnosis and Prognosis in Non-small Cell Lung Cancer. PMID:33936178
Leonurine-Repressed miR-18a-5p/SOCS5/JAK2/STAT3 Axis Activity Disrupts CML malignancy. PMID:33935775
SNRPC promotes hepatocellular carcinoma cell motility by inducing epithelial-mesenchymal transition. PMID:33934562
A novel five-gene signature predicts overall survival of patients with hepatocellular carcinoma. PMID:33934539
Induction of stable human FOXP3+ Tregs by a parasite-derived TGF-β mimic. PMID:33929751
Reverse Engineering of Ewing Sarcoma Regulatory Network Uncovers PAX7 and RUNX3 as Master Regulators Associated with Good Prognosis. PMID:33924679
Maternal Heat Stress Alters Expression of Genes Associated with Nutrient Transport Activity and Metabolism in Female Placentae from Mid-Gestating Pigs. PMID:33923747
Hepatic Transcriptome Profiling Reveals Lack of Acsm3 Expression in Polydactylous Rats with High-Fat Diet-Induced Hypertriglyceridemia and Visceral Fat Accumulation. PMID:33923085
Muscle Proteomic and Transcriptomic Profiling of Healthy Aging and Metabolic Syndrome in Men. PMID:33921590
Deciphering the Methylation Landscape in Breast Cancer: Diagnostic and Prognostic Biosignatures through Automated Machine Learning. PMID:33918195
Multi-Layer Picture of Neurodegenerative Diseases: Lessons from the Use of Big Data through Artificial Intelligence. PMID:33917161
Expression Patterns in Reductive Iron Assimilation and Functional Consequences during Phagocytosis of Lichtheimia corymbifera, an Emerging Cause of Mucormycosis. PMID:33916756
Characterization of Type I Interferon-Associated Chemokines and Cytokines in Lacrimal Glands of Nonobese Diabetic Mice. PMID:33916486
Chronic interleukin-1 exposure triggers selection for Cebpa-knockout multipotent hematopoietic progenitors. PMID:33914855
Increasing metadata coverage of SRA BioSample entries using deep learning-based named entity recognition. PMID:33914028
Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia. PMID:33911178
Transcriptome profiles associated with selenium-deficiency-dependent oxidative stress identify potential diagnostic and therapeutic targets in liver cancer cells. PMID:33907497
VB10, a new blood biomarker for differential diagnosis and recovery monitoring of acute viral and bacterial infections. PMID:33906069
Expression analysis of progesterone‑regulated miRNAs in cells derived from human glioblastoma. PMID:33899118
Immune Subtyping in Latent Tuberculosis. PMID:33897680
eIF4E3 forms an active eIF4F complex during stresses (eIF4FS) targeting mTOR and re-programs the translatome. PMID:33893802
Differences in RNA and microRNA Expression Between PTCH1- and SUFU-mutated Medulloblastoma. PMID:33893086
BdERECTA controls vasculature patterning and phloem-xylem organization in Brachypodium distachyon. PMID:33892630
AGAP2-AS1 May Promote the Occurrence and Development of Glioblastoma by Sponging miR-9-5p: Evidence From a ceRNA Network. PMID:33889541
Identification of transcriptional subtypes in lung adenocarcinoma and squamous cell carcinoma through integrative analysis of microarray and RNA sequencing data. PMID:33888829
ARABIDOPSIS THALIANA HOMEOBOX GENE 1 controls plant architecture by locally restricting environmental responses. PMID:33888582
T cell self-reactivity during thymic development dictates the timing of positive selection. PMID:33884954
Nuclear receptors FXR and SHP regulate protein N-glycan modifications in the liver. PMID:33883138
Transcriptomic alterations in malignant pleural mesothelioma cells in response to long‑term treatment with bullfrog sialic acid‑binding lectin. PMID:33880588
Loss of α2-6 sialylation promotes the transformation of synovial fibroblasts into a pro-inflammatory phenotype in arthritis. PMID:33879788
The bone microenvironment increases phenotypic plasticity of ER+ breast cancer cells. PMID:33878299
A Case of Gene Fragmentation in Plant Mitochondria Fixed by the Selection of a Compensatory Restorer of Fertility-Like PPR Gene. PMID:33878189
Identification of a micropeptide and multiple secondary cell genes that modulate Drosophila male reproductive success. PMID:33876742
Fibroblast-Specific Proteotranscriptomes Reveal Distinct Fibrotic Signatures of Human Sinoatrial Node in Nonfailing and Failing Hearts. PMID:33874740
Prognostic Signature for Lung Adenocarcinoma Patients Based on Cell-Cycle-Related Genes. PMID:33869220
In silico Design for Systems-Based Metabolic Engineering for the Bioconversion of Valuable Compounds From Industrial By-Products. PMID:33868371
Artificial intelligence to deep learning: machine intelligence approach for drug discovery. PMID:33844136
Delta-like 4 is required for pulmonary vascular arborization and alveolarization in the developing lung. PMID:33830085
Altered Responsiveness to TGFβ and BMP and Increased CD45+ Cell Presence in Mitral Valves Are Unique Features of Ischemic Mitral Regurgitation. PMID:33827255
Fibrotic expression profile analysis reveals repurposed drugs with potential anti-fibrotic mode of action. PMID:33826640
The effect of calcium and magnesium on activity, immunogenicity, and efficacy of a recombinant N1/N2 neuraminidase vaccine. PMID:33824333
Sequencing error profiles of Illumina sequencing instruments. PMID:33817639
Screening of Hub Genes Associated with Pulmonary Arterial Hypertension by Integrated Bioinformatic Analysis. PMID:33816621
Different Expressions of Pericardial Fluid MicroRNAs in Patients With Arrhythmogenic Right Ventricular Cardiomyopathy and Ischemic Heart Disease Undergoing Ventricular Tachycardia Ablation. PMID:33816578
Spt4 Promotes Pol I Processivity and Transcription Elongation. PMID:33809333
Transcriptome Analyses Throughout Chili Pepper Fruit Development Reveal Novel Insights into the Domestication Process. PMID:33808668
Feature Selection Using Enhanced Particle Swarm Optimisation for Classification Models. PMID:33807806
TNMplot.com: A Web Tool for the Comparison of Gene Expression in Normal, Tumor and Metastatic Tissues. PMID:33807717
Persistent Inflammatory Stimulation Drives the Conversion of MSCs to Inflammatory CAFs That Promote Pro-Metastatic Characteristics in Breast Cancer Cells. PMID:33806906
Analysis of mir-9 Expression Pattern in Rat Retina during Postnatal Development. PMID:33806574
Voluntary Wheel Running Did Not Alter Gene Expression in 5xfad Mice, but in Wild-Type Animals Exclusively after One-Day of Physical Activity. PMID:33804749
Implication of EZH2 in the Pro-Proliferative and Apoptosis-Resistant Phenotype of Pulmonary Artery Smooth Muscle Cells in PAH: A Transcriptomic and Proteomic Approach. PMID:33803922
Identification of Hub Genes and Key Pathways Associated with Anti-VEGF Resistant Glioblastoma Using Gene Expression Data Analysis. PMID:33803224
The Role of Network Science in Glioblastoma. PMID:33801334
CRISPR-Cas9-Mediated TIM3 Knockout in Human Natural Killer Cells Enhances Growth Inhibitory Effects on Human Glioma Cells. PMID:33800561
Swine Inflammation and Necrosis Syndrome Is Associated with Plasma Metabolites and Liver Transcriptome in Affected Piglets. PMID:33799520
Signal-mediated localization of Candida albicans pheromone response pathway components. PMID:33793759
Effector and regulator: Diverse functions of C. elegans C-type lectin-like domain proteins. PMID:33793670
Proteomics study on the effect of silybin on cardiomyopathy in obese mice. PMID:33785854
Six genes involved in prognosis of hepatocellular carcinoma identified by Cox hazard regression. PMID:33784984
Large-scale labeling and assessment of sex bias in publicly available expression data. PMID:33784977
Randomized Controlled Trial of the Gastrin/CCK2 Receptor Antagonist Netazepide in Patients with Barrett's Esophagus. PMID:33782049
Gene Set Knowledge Discovery with Enrichr. PMID:33780170
Benefits of Airway Androgen Receptor Expression in Human Asthma. PMID:33779531
The Burkholderia pseudomallei intracellular 'TRANSITome'. PMID:33772012
Transcriptome analyses of 7-day-old zebrafish larvae possessing a familial Alzheimer's disease-like mutation in psen1 indicate effects on oxidative phosphorylation, ECM and MCM functions, and iron homeostasis. PMID:33761877
Colon epithelial cell TGFβ signaling modulates the expression of tight junction proteins and barrier function in mice. PMID:33759564
Transcriptomic insight into the translational value of two murine models in human atopic dermatitis. PMID:33758305
GAUGE-Annotated Microbial Transcriptomic Data Facilitate Parallel Mining and High-Throughput Reanalysis To Form Data-Driven Hypotheses. PMID:33758032
Overexpression of CCNE1 confers a poorer prognosis in triple-negative breast cancer identified by bioinformatic analysis. PMID:33757543
GPRC5A: An emerging prognostic biomarker for predicting malignancy of Pancreatic Cancer based on bioinformatics analysis. PMID:33753999
Blockade of IL-22 signaling reverses erythroid dysfunction in stress-induced anemias. PMID:33753942
Inducible mechanisms of disease tolerance provide an alternative strategy of acquired immunity to malaria. PMID:33752799
Transcriptomic analysis of feminizing somatic stem cells in the Drosophila testis reveals putative downstream effectors of the transcription factor Chinmo. PMID:33751104
Construction of competitive endogenous RNA network reveals regulatory role of long non-coding RNAs in intracranial aneurysm. PMID:33750300
Appyters: Turning Jupyter Notebooks into data-driven web apps. PMID:33748796
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
Spatiotemporal single-cell RNA sequencing of developing chicken hearts identifies interplay between cellular differentiation and morphogenesis. PMID:33741943
FTO-mediated cytoplasmic m6Am demethylation adjusts stem-like properties in colorectal cancer cell. PMID:33741917
Enhanced insulin signalling ameliorates C9orf72 hexanucleotide repeat expansion toxicity in Drosophila. PMID:33739284
Global miRNA/proteomic analyses identify miRNAs at 14q32 and 3p21, which contribute to features of chronic iron-exposed fallopian tube epithelial cells. PMID:33737539
Identification of New miRNA-mRNA Networks in the Development of Non-syndromic Cleft Lip With or Without Cleft Palate. PMID:33732700
Using Integrated Bioinformatics Analysis to Identify Abnormally Methylated Differentially Expressed Genes in Hepatocellular Carcinoma. PMID:33732011
Juxtapose: a gene-embedding approach for comparing co-expression networks. PMID:33726666
Modulation of the complex regulatory network for methionine biosynthesis in fungi. PMID:33724418
Stretch-activated ion channels identified in the touch-sensitive structures of carnivorous Droseraceae plants. PMID:33724187
Protein Biomarkers of Autism Spectrum Disorder Identified by Computational and Experimental Methods. PMID:33716802
Increased expression of MCM4 is associated with poor prognosis in patients with hepatocellular carcinoma. PMID:33708433
Correlation Between Immune Lymphoid Cells and Plasmacytoid Dendritic Cells in Human Colon Cancer. PMID:33708200
Burkholderia cenocepacia transcriptome during the early contacts with giant plasma membrane vesicles derived from live bronchial epithelial cells. PMID:33707642
Exovesicular-Shh confers Imatinib resistance by upregulating Bcl2 expression in chronic myeloid leukemia with variant chromosomes. PMID:33707419
Aging and pathological aging signatures of the brain: through the focusing lens of SIRT6. PMID:33690173
TDP-43 maximizes nerve conduction velocity by repressing a cryptic exon for paranodal junction assembly in Schwann cells. PMID:33689679
HIR V2: a human interactome resource for the biological interpretation of differentially expressed genes via gene set linkage analysis. PMID:33677507
Nerve Growth Factor Neutralization Promotes Oligodendrogenesis by Increasing miR-219a-5p Levels. PMID:33669304
Ccdc113/Ccdc96 complex, a novel regulator of ciliary beating that connects radial spoke 3 to dynein g and the nexin link. PMID:33661892
CD74 is a regulator of hematopoietic stem cell maintenance. PMID:33661886
Protein interacting with C-kinase 1 is involved in epithelial-mesenchymal transformation and suppresses progress of gastric cancer. PMID:33660148
Low expression of NLRP1 is associated with a poor prognosis and immune infiltration in lung adenocarcinoma patients. PMID:33658393
Fetal sex modulates placental microRNA expression, potential microRNA-mRNA interactions, and levels of amino acid transporter expression and substrates: INFAT study subpopulation analysis of n-3 LCPUFA intervention during pregnancy and associations with offspring body composition. PMID:33657992
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
Cancer-Associated Fibroblasts Positively Correlate with Dedifferentiation and Aggressiveness of Thyroid Cancer. PMID:33654411
ATF3-Induced Mammary Tumors Exhibit Molecular Features of Human Basal-Like Breast Cancer. PMID:33652981
SSRE: Cell Type Detection Based on Sparse Subspace Representation and Similarity Enhancement. PMID:33647482
Proximity-dependent Mapping of the Androgen Receptor Identifies Kruppel-like Factor 4 as a Functional Partner. PMID:33640491
The TUTase URT1 connects decapping activators and prevents the accumulation of excessively deadenylated mRNAs to avoid siRNA biogenesis. PMID:33637717
Computational screening of potential glioma-related genes and drugs based on analysis of GEO dataset and text mining. PMID:33635875
Transcriptional and Proteomic Characterization of Telomere-Induced Senescence in a Human Alveolar Epithelial Cell Line. PMID:33634147
Recursive ensemble feature selection provides a robust mRNA expression signature for myalgic encephalomyelitis/chronic fatigue syndrome. PMID:33633136
Identification BCL6 and miR-30 family associating with Ibrutinib resistance in activated B-cell-like diffuse large B-cell lymphoma. PMID:33629212
Identification of candidate repurposable drugs to combat COVID-19 using a signature-based approach. PMID:33627767
Dysregulated gene-associated biomarkers for Alzheimer's disease and aging. PMID:33623715
CHARTS: a web application for characterizing and comparing tumor subpopulations in publicly available single-cell RNA-seq data sets. PMID:33622236
High-throughput screening and validation of antibodies against synaptic proteins to explore opioid signaling dynamics. PMID:33619305
Bromodomain proteins regulate human cytomegalovirus latency and reactivation allowing epigenetic therapeutic intervention. PMID:33619107
Inferring perturbation profiles of cancer samples. PMID:33617647
Drought-Induced Root Pressure in Sorghum bicolor. PMID:33613594
Identification of biomarkers and pathways for the SARS-CoV-2 infections that make complexities in pulmonary arterial hypertension patients. PMID:33611340
Localized EMT reprograms glial progenitors to promote spinal cord repair. PMID:33609461
The one-carbon pool controls mitochondrial energy metabolism via complex I and iron-sulfur clusters. PMID:33608280
Complex pleiotropic genetic architecture of evolved heat stress and oxidative stress resistance in the nematode Caenorhabditis remanei. PMID:33605401
Peroxisomal Multifunctional Protein 2 Deficiency Perturbs Lipid Homeostasis in the Retina and Causes Visual Dysfunction in Mice. PMID:33604342
Identification of a non-coding RNA and its putative involvement in the regulation of tetanus toxin synthesis in Clostridium tetani. PMID:33603121
Virus infection of the CNS disrupts the immune-neural-synaptic axis via induction of pleiotropic gene regulation of host responses. PMID:33599611
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
Positioning of nucleosomes containing γ-H2AX precedes active DNA demethylation and transcription initiation. PMID:33594057
Joint probabilistic modeling of single-cell multi-omic data with totalVI. PMID:33589839
Decoding the protein composition of whole nucleosomes with Nuc-MS. PMID:33589837
Concordance of Immune-Related Markers in Lymphocytes and Prefrontal Cortex in Schizophrenia. PMID:33585819
Searching for a Putative Mechanism of RIZ2 Tumor-Promoting Function in Cancer Models. PMID:33585202
Identification of key biomarkers and functional pathways in osteosarcomas with lung metastasis: Evidence from bioinformatics analysis. PMID:33578541
Guidelines for biomarker discovery in endometrium: correcting for menstrual cycle bias reveals new genes associated with uterine disorders. PMID:33576824
Identification and analysis of consensus RNA motifs binding to the genome regulator CTCF. PMID:33575587
Functional networks of co-expressed genes to explore iron homeostasis processes in the pathogenic yeast Candida glabrata. PMID:33575583
Depletion of erythropoietic miR-486-5p and miR-451a improves detectability of rare microRNAs in peripheral blood-derived small RNA sequencing libraries. PMID:33575555
Screening and identification of hub genes in bladder cancer by bioinformatics analysis and KIF11 is a potential prognostic biomarker. PMID:33574944
Microarray Data Mining and Preliminary Bioinformatics Analysis of Hepatitis D Virus-Associated Hepatocellular Carcinoma. PMID:33564675
Knockdown of KIF15 promotes cell apoptosis by activating crosstalk of multiple pathways in ovarian cancer: bioinformatic and experimental analysis. PMID:33564360
Integrated bioinformatic analysis identifies COL4A3, COL4A4, and KCNJ1 as key biomarkers in Wilms tumor. PMID:33564352
Wolbachia and Virus Alter the Host Transcriptome at the Interface of Nucleotide Metabolism Pathways. PMID:33563832
A Grad-seq View of RNA and Protein Complexes in Pseudomonas aeruginosa under Standard and Bacteriophage Predation Conditions. PMID:33563827
Family-effects in the epigenomic response of red blood cells to a challenge test in the European sea bass (Dicentrarchus labrax, L.). PMID:33563212
Flow induces barrier and glycocalyx-related genes and negative surface charge in a lab-on-a-chip human blood-brain barrier model. PMID:33563079
Predicting therapeutic drugs for hepatocellular carcinoma based on tissue-specific pathways. PMID:33561121
Association of microbiota-derived propionic acid and Alzheimer's disease; bioinformatics analysis. PMID:33553012
High-Resolution Mapping of Transcription Initiation in the Asexual Stages of Toxoplasma gondii. PMID:33553008
Transcriptome from opaque cornea of Fanconi anemia patient uncovers fibrosis and two connected players. PMID:33552906
E-cadherin is regulated by GATA-2 and marks the early commitment of mouse hematopoietic progenitors to the basophil and mast cell fates. PMID:33547048
Arabidopsis Mitochondrial Transcription Termination Factor mTERF2 Promotes Splicing of Group IIB Introns. PMID:33546419
Development and verification of an immune-related gene pairs prognostic signature in ovarian cancer. PMID:33543590
Transgenerational supplementation with eicosapentaenoic acid reduced the metabolic consequences on the whole body and skeletal muscle in mice receiving an obesogenic diet. PMID:33543364
Identification of Genes Universally Differentially Expressed in Gastric Cancer. PMID:33542925
Metabolic Versatility of Mycobacterium tuberculosis during Infection and Dormancy. PMID:33540752
Sulfatase 2 Is Associated with Steroid Resistance in Childhood Nephrotic Syndrome. PMID:33540508
GEOlimma: differential expression analysis and feature selection using pre-existing microarray data. PMID:33535967
Identification of RCC Subtype-Specific microRNAs-Meta-Analysis of High-Throughput RCC Tumor microRNA Expression Data. PMID:33535553
ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways. PMID:33534793
P2X7 Receptor Induces Pyroptotic Inflammation and Cartilage Degradation in Osteoarthritis via NF-κB/NLRP3 Crosstalk. PMID:33532039
Identification of key miRNA-gene pairs in gastric cancer through integrated analysis of mRNA and miRNA microarray. PMID:33527022
Functional Signatures in Non-Small-Cell Lung Cancer: A Systematic Review and Meta-Analysis of Sex-Based Differences in Transcriptomic Studies. PMID:33526761
Acid pH Strategy Adaptation through NRG1 in Ustilago maydis. PMID:33525315
Identification of Key MicroRNAs and Mechanisms in Prostate Cancer Evolution Based on Biomarker Prioritization Model and Carcinogenic Survey. PMID:33519899
AtxA-Controlled Small RNAs of Bacillus anthracis Virulence Plasmid pXO1 Regulate Gene Expression in trans. PMID:33519762
High Throughput Sequencing of MicroRNA in Rainbow Trout Plasma, Mucus, and Surrounding Water Following Acute Stress. PMID:33519501
Role of an ancient light-harvesting protein of PSI in light absorption and photoprotection. PMID:33514722
Polycythemia Vera and Essential Thrombocythemia Patients Exhibit Unique Serum Metabolic Profiles Compared to Healthy Individuals and Secondary Thrombocytosis Patients. PMID:33513807
Identification of hub lncRNA ceRNAs in multiple sclerosis based on ceRNA mechanisms. PMID:33507382
Identification of Key Tissue-Specific, Biological Processes by Integrating Enhancer Information in Maize Gene Regulatory Networks. PMID:33505431
Identification of 37 Heterogeneous Drug Candidates for Treatment of COVID-19 via a Rational Transcriptomics-Based Drug Repurposing Approach. PMID:33504008
Genomic Adaption and Mutational Patterns in a HaCaT Subline Resistant to Alkylating Agents and Ionizing Radiation. PMID:33498964
Parallel in vivo analysis of large-effect autism genes implicates cortical neurogenesis and estrogen in risk and resilience. PMID:33497602
Chitosan modulates Pochonia chlamydosporia gene expression during nematode egg parasitism. PMID:33496078
AbaM Regulates Quorum Sensing, Biofilm Formation, and Virulence in Acinetobacter baumannii. PMID:33495249
Cancers in Agreement? Exploring the Cross-Talk of Cancer Metabolomic and Transcriptomic Landscapes Using Publicly Available Data. PMID:33494351
COL1A1 Is a Potential Prognostic Biomarker and Correlated with Immune Infiltration in Mesothelioma. PMID:33490271
Identification of IL10RA by Weighted Correlation Network Analysis and in vitro Validation of Its Association With Prognosis of Metastatic Melanoma. PMID:33490091
Challenge of Bovine Foot Skin Fibroblasts With Digital Dermatitis Treponemes Identifies Distinct Pathogenic Mechanisms. PMID:33489929
A meta-analysis of comorbidities in COVID-19: Which diseases increase the susceptibility of SARS-CoV-2 infection? PMID:33486379
Mining influential genes based on deep learning. PMID:33482718
CF monocyte-derived macrophages have an attenuated response to extracellular vesicles secreted by airway epithelial cells. PMID:33471607
Enrichment and Correlation Analysis of Serum miRNAs in Comorbidity Between Arnold-Chiari and Tourette Syndrome Contribute to Clarify Their Molecular Bases. PMID:33469418
Reiterative infusions of MSCs improve pediatric osteogenesis imperfecta eliciting a pro-osteogenic paracrine response: TERCELOI clinical trial. PMID:33463067
DNA methylome signatures of prenatal exposure to synthetic glucocorticoids in hippocampus and peripheral whole blood of female guinea pigs in early life. PMID:33462183
Significance of serglycin and its binding partners in autocrine promotion of metastasis in esophageal cancer. PMID:33456569
Computational methods for the prediction of chromatin interaction and organization using sequence and epigenomic profiles. PMID:33454752
Systematic analysis of differential rhythmic liver gene expression mediated by the circadian clock and feeding rhythms. PMID:33452134
Decreases in different Dnmt3b activities drive distinct development of hematologic malignancies in mice. PMID:33450231
The pioneer and differentiation factor FOXA2 is a key driver of yolk-sac tumour formation and a new biomarker for paediatric and adult yolk-sac tumours. PMID:33448076
SIX2 and SIX3 coordinately regulate functional maturity and fate of human pancreatic β cells. PMID:33446570
JAZF1, A Novel p400/TIP60/NuA4 Complex Member, Regulates H2A.Z Acetylation at Regulatory Regions. PMID:33445503
Endogenous membrane stress induces T6SS activity in Pseudomonas aeruginosa. PMID:33443205
Prognostic significance of KRT19 in Lung Squamous Cancer. PMID:33442422
AlzGPS: a genome-wide positioning systems platform to catalyze multi-omics for Alzheimer's drug discovery. PMID:33441136
Streamlining data-intensive biology with workflow systems. PMID:33438730
Prognosis Prediction for Colorectal Cancer Patients: A Risk Score Based on The Metabolic-Related Genes. PMID:33437216
Inhibition of microbiota-dependent TMAO production attenuates chronic kidney disease in mice. PMID:33436815
STIM1 Mediates Calcium-Dependent Epigenetic Reprogramming in Pancreatic Cancer. PMID:33436389
Exome-wide evaluation of rare coding variants using electronic health records identifies new gene-phenotype associations. PMID:33432171
Droplet-based mRNA sequencing of fixed and permeabilized cells by CLInt-seq allows for antigen-specific TCR cloning. PMID:33431692
Single-cell RNA sequencing reveals SARS-CoV-2 infection dynamics in lungs of African green monkeys. PMID:33431511
A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions. PMID:33431024
Whole Transcription Profile of Responders to Anti-TNF Drugs in Pediatric Inflammatory Bowel Disease. PMID:33429950
FAK regulates IL-33 expression by controlling chromatin accessibility at c-Jun motifs. PMID:33420223
Dnmt3b catalytic activity is critical for its tumour suppressor function in lymphomagenesis and is associated with c-Met oncogenic signalling. PMID:33418509
Metabolic reprogramming of the myeloid lineage by Schistosoma mansoni infection persists independently of antigen exposure. PMID:33417618
Transcriptomic analysis identifies organ-specific metastasis genes and pathways across different primary sites. PMID:33413400
Biomechanical Forces Regulate Gene Transcription During Stretch-Mediated Growth of Mammalian Neurons. PMID:33408609
STRA8 induces transcriptional changes in germ cells during spermatogonial development. PMID:33400349
Integrated molecular characterisation of the MAPK pathways in human cancers reveals pharmacologically vulnerable mutations and gene dependencies. PMID:33398072
microRNA Sequencing of CD34+ Sorted Adipose Stem Cells Undergoing Endotheliogenesis. PMID:33397204
Personalized beyond Precision: Designing Unbiased Gold Standards to Improve Single-Subject Studies of Personal Genome Dynamics from Gene Products. PMID:33396440
Pan-Cancer Molecular Patterns and Biological Implications Associated with a Tumor-Specific Molecular Signature. PMID:33396205
Specific MiRNAs in naïve T cells associated with Hepatitis C Virus-induced Hepatocellular Carcinoma. PMID:33391397
High-Pressure-Sprayed Double Stranded RNA Does Not Induce RNA Interference of a Reporter Gene. PMID:33391294
Predicting changes in renal metabolism after compound exposure with a genome-scale metabolic model. PMID:33387578
High Levels of Prebiotic Resistant Starch in Diet Modulate a Specific Pattern of miRNAs Expression Profile Associated to a Better Overall Survival in Pancreatic Cancer. PMID:33383727
HeartBioPortal2.0: new developments and updates for genetic ancestry and cardiometabolic quantitative traits in diverse human populations. PMID:33382884
Epstein-Barr virus LMP1 manipulates the content and functions of extracellular vesicles to enhance metastatic potential of recipient cells. PMID:33382850
Long-term transcriptomic and proteomic effects in Sprague Dawley rat thyroid and plasma after internal low dose 131I exposure. PMID:33382739
Adversarial deconfounding autoencoder for learning robust gene expression embeddings. PMID:33381842
A Multi-Pronged Computational Pipeline for Prioritizing Drug Target Strategies for Latent Tuberculosis. PMID:33381491
USP15 Deubiquitinase Safeguards Hematopoiesis and Genome Integrity in Hematopoietic Stem Cells and Leukemia Cells. PMID:33378683
Identifying biomolecules and constructing a prognostic risk prediction model for recurrence in osteosarcoma. PMID:33376666
Effect of let-7c on the PI3K/Akt/FoxO signaling pathway in hepatocellular carcinoma. PMID:33376529
Transcriptional profiling of the stringent response mutant strain E. coli SR reveals enhanced robustness to large-scale conditions. PMID:33369128
An Educational Bioinformatics Project to Improve Genome Annotation. PMID:33365016
Development and Validation of an Immune-Related Gene Pair Signature in Skin Cutaneous Melanoma. PMID:33364806
MiRNA-Mediated Subpathway Identification and Network Module Analysis to Reveal Prognostic Markers in Human Pancreatic Cancer. PMID:33362865
Acyl-CoA Thioesterase 8 and 11 as Novel Biomarkers for Clear Cell Renal Cell Carcinoma. PMID:33362855
Protein Synthesis in the Developing Neocortex at Near-Atomic Resolution Reveals Ebp1-Mediated Neuronal Proteostasis at the 60S Tunnel Exit. PMID:33357414
MS4A1 expression and function in T cells in the colorectal cancer tumor microenvironment. PMID:33352466
An Integrated Analysis of miRNA and Gene Expression Changes in Response to an Obesogenic Diet to Explore the Impact of Transgenerational Supplementation with Omega 3 Fatty Acids. PMID:33348802
Dynamics of transcriptional and post-transcriptional regulation. PMID:33348360
Denoising Autoencoder, A Deep Learning Algorithm, Aids the Identification of A Novel Molecular Signature of Lung Adenocarcinoma. PMID:33346087
Maternal antioxidant treatment prevents the adverse effects of prenatal stress on the offspring's brain and behavior. PMID:33344732
Benchmarking Computational Doublet-Detection Methods for Single-Cell RNA Sequencing Data. PMID:33338399
MuscleAtlasExplorer: a web service for studying gene expression in human skeletal muscle. PMID:33338203
Molecular patterns of isolated tubulitis differ from tubulitis with interstitial inflammation in early indication biopsies of kidney allografts. PMID:33335257
The mTOR regulated RNA-binding protein LARP1 requires PABPC1 for guided mRNA interaction. PMID:33332560
Riproximin Exhibits Diversity in Sugar Binding, and Modulates some Metastasis-Related Proteins with Lectin like Properties in Pancreatic Ductal Adenocarcinoma. PMID:33328982
Aortic Gene Expression Profiles Show How ApoA-I Levels Modulate Inflammation, Lysosomal Activity, and Sphingolipid Metabolism in Murine Atherosclerosis. PMID:33327742
Integrated Multichip Analysis Identifies Potential Key Genes in the Pathogenesis of Nonalcoholic Steatohepatitis. PMID:33324350
Cellular and Molecular Response of Macrophages THP-1 during Co-Culture with Inactive Trichophyton rubrum Conidia. PMID:33322794
Tensor-Decomposition-Based Unsupervised Feature Extraction Applied to Prostate Cancer Multiomics Data. PMID:33322492
Toll-Like Receptor 7 Is Required for Lacrimal Gland Autoimmunity and Type 1 Diabetes Development in Male Nonobese Diabetic Mice. PMID:33322152
Revealing Epigenetic Factors of circRNA Expression by Machine Learning in Various Cellular Contexts. PMID:33319172
Endometriosis Is Associated with a Significant Increase in hTERC and Altered Telomere/Telomerase Associated Genes in the Eutopic Endometrium, an Ex-Vivo and In Silico Study. PMID:33317189
Harmine and Piperlongumine Revert TRIB2-Mediated Drug Resistance. PMID:33316942
Sericin inhibits MDA‑MB‑468 cell proliferation via the PI3K/Akt pathway in triple‑negative breast cancer. PMID:33313947
A bioinformatics analysis on the potential role of ACE2 in cardiac impairment of patients with coronavirus disease 2019. PMID:33313148
Requirement of DNMT1 to orchestrate epigenomic reprogramming for NPM-ALK-driven lymphomagenesis. PMID:33310759
Run or Die in the Evolution of New MicroRNAs-Testing the Red Queen Hypothesis on De Novo New Genes. PMID:33306129
Coagulopathy in Malnourished Mice Is Sexually Dimorphic and Regulated by Nutrient-Sensing Nuclear Receptors. PMID:33305154
PDmethDB: A curated Parkinson's disease associated methylation information database. PMID:33304468
Genetic interaction mapping informs integrative structure determination of protein complexes. PMID:33303586
Tnfaip2/exoc3-driven lipid metabolism is essential for stem cell differentiation and organ homeostasis. PMID:33300287
Transmembrane Prolyl 4-Hydroxylase is a Novel Regulator of Calcium Signaling in Astrocytes. PMID:33298456
Transcriptome Remodeling in Gradual Development of Inverse Resistance between Paclitaxel and Cisplatin in Ovarian Cancer Cells. PMID:33287223
Identification of candidate biomarkers correlated with the pathogenesis and prognosis of breast cancer via integrated bioinformatics analysis. PMID:33285689
Differences in key genes in human alveolar macrophages between phenotypically normal smokers and nonsmokers: diagnostic and prognostic value in lung cancer. PMID:33284895
Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities. PMID:33279989
A review of COVID-19 biomarkers and drug targets: resources and tools. PMID:33279954
Detection of urinary miRNAs for diagnosis of clear cell renal cell carcinoma. PMID:33277569
MethHC 2.0: information repository of DNA methylation and gene expression in human cancer. PMID:33270889
The microRNA miR-29c-5p inhibits cell proliferation and migration by targeting TMEM98 in head and neck carcinoma. PMID:33257597
An Improved, Assay Platform Agnostic, Absolute Single Sample Breast Cancer Subtype Classifier. PMID:33255759
Manganese Depletion Leads to Multisystem Changes in the Transcriptome of the Opportunistic Pathogen Streptococcus sanguinis. PMID:33250881
PAGER-CoV: a comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies. PMID:33245774
Spontaneous intake of essential oils after a negative postnatal experience has long-term effects on blood transcriptome in chickens. PMID:33244117
Bioinformatics Analysis Identifies a Novel Role of GINS1 Gene in Colorectal Cancer. PMID:33235499
Investigation of drugs affecting hypertension in bevacizumab-treated patients and examination of the impact on the therapeutic effect. PMID:33231381
Active Transposition of Insertion Sequences by Oxidative Stress in Deinococcus geothermalis. PMID:33224109
FHOD formin and SRF promote post-embryonic striated muscle growth through separate pathways in C. elegans. PMID:33221314
Transcriptome profiling of laser-captured crown root primordia reveals new pathways activated during early stages of crown root formation in rice. PMID:33211715
Extracellular traps released by antimicrobial TH17 cells contribute to host defense. PMID:33211671
Biophysical and X-ray structural studies of the (GGGTT)3GGG G-quadruplex in complex with N-methyl mesoporphyrin IX. PMID:33206666
Patrolling monocytes inhibit osteosarcoma metastasis to the lung. PMID:33203789
Sarcolipin Exhibits Abundant RNA Transcription and Minimal Protein Expression in Horse Gluteal Muscle. PMID:33202832
Bile Ductal Transcriptome Identifies Key Pathways and Hub Genes in Clonorchis sinensis-Infected Sprague-Dawley Rats. PMID:33202503
ACVR2B antagonism as a countermeasure to multi-organ perturbations in metastatic colorectal cancer cachexia. PMID:33200567
Mutation bias within oncogene families is related to proliferation-specific codon usage. PMID:33199641
iCLIP analysis of RNA substrates of the archaeal exosome. PMID:33198623
Epidermal Growth Factor Is Essential for the Maintenance of Novel Prostate Epithelial Cells Isolated From Patient-Derived Organoids. PMID:33195205
A Novel Signature of 23 Immunity-Related Gene Pairs Is Prognostic of Cutaneous Melanoma. PMID:33193373
Data mining combined with experiments to validate CEP55 as a prognostic biomarker in colorectal cancer. PMID:33190424
Interleukin-6 (IL-6) deficiency enhances intramembranous osteogenesis following stress fracture in mice. PMID:33181349
Distinct regional ontogeny and activation of tumor associated macrophages in human glioblastoma. PMID:33177572
Co‑expression network analysis identified specific miRNAs and genes in association with slow‑transit constipation. PMID:33174045
Systematic Analysis of Protein-Protein and Gene-Environment Interactions to Decipher the Cognitive Mechanisms of Autism Spectrum Disorder. PMID:33165687
A single-cell atlas and lineage analysis of the adult Drosophila ovary. PMID:33159074
Maximizing the reusability of gene expression data by predicting missing metadata. PMID:33156882
Inhibition of inflammatory signaling in Pax5 mutant cells mitigates B-cell leukemogenesis. PMID:33154497
Unsupervised and supervised learning with neural network for human transcriptome analysis and cancer diagnosis. PMID:33154423
Widespread Traces of Lytic Kaposi Sarcoma-Associated Herpesvirus in Primary Effusion Lymphoma at Single-Cell Resolution. PMID:33154001
The RSC (Remodels the Structure of Chromatin) complex of Candida albicans shows compositional divergence with distinct roles in regulating pathogenic traits. PMID:33151931
Investigation of the potential regulator proteins associated with the expression of major surface protein and dentilisin in Treponema denticola. PMID:33149843
Integrative Analysis of miRNAs Identifies Clinically Relevant Epithelial and Stromal Subtypes of Head and Neck Squamous Cell Carcinoma. PMID:33148669
Expression of EMT-Related Genes in Hybrid E/M Colorectal Cancer Cells Determines Fibroblast Activation and Collagen Remodeling. PMID:33143259
The Antiviral Small-Interfering RNA Pathway Induces Zika Virus Resistance in Transgenic Aedes aegypti. PMID:33142991
Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L. PMID:33142722
Whole egg consumption increases gene expression within the glutathione pathway in the liver of Zucker Diabetic Fatty rats. PMID:33141822
Correcting for experiment-specific variability in expression compendia can remove underlying signals. PMID:33140829
Transcriptomic responses from improved murine sepsis models can better mimic human surgical sepsis. PMID:33140449
Functional module detection through integration of single-cell RNA sequencing data with protein-protein interaction networks. PMID:33138772
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 Novel Potential Type 2 Diabetes Genes Mediating β-Cell Loss and Hyperglycemia Using Positional Cloning. PMID:33133152
SINEUP long non-coding RNA acts via PTBP1 and HNRNPK to promote translational initiation assemblies. PMID:33130894
The birth of a bacterial tRNA gene by large-scale, tandem duplication events. PMID:33124983
Targeting 14-3-3ζ Overcomes Resistance to Epidermal Growth Factor Receptor-Tyrosine Kinase Inhibitors in Lung Adenocarcinoma via BMP2/Smad/ID1 Signaling. PMID:33123465
Changes in Northern Elephant Seal Skeletal Muscle Following Thirty Days of Fasting and Reduced Activity. PMID:33123026
A long noncoding RNA antisense to ICAM-1 is involved in allergic asthma associated hyperreactive response of airway epithelial cells. PMID:33122732
A CRISPR-Cas9 screen identifies mitochondrial translation as an essential process in latent KSHV infection of human endothelial cells. PMID:33122441
Screening and identification of key genes and pathways in metastatic uveal melanoma based on gene expression using bioinformatic analysis. PMID:33120861
Enzymatic Dissociation Induces Transcriptional and Proteotype Bias in Brain Cell Populations. PMID:33114694
Transcriptomic and Phenotypic Analyses of the Sigma B-Dependent Characteristics and the Synergism between Sigma B and Sigma L in Listeria monocytogenes EGD-e. PMID:33114171
Preparation of Multi-omics Grade Extracellular Vesicles by Density-Based Fractionation of Urine. PMID:33111109
Zeb1 modulates hematopoietic stem cell fates required for suppressing acute myeloid leukemia. PMID:33108352
ROS networks: designs, aging, Parkinson's disease and precision therapies. PMID:33106503
Genome-wide identification of accessible chromatin regions in bumblebee by ATAC-seq. PMID:33106500
Response of Pseudomonas aeruginosa to the Innate Immune System-Derived Oxidants Hypochlorous Acid and Hypothiocyanous Acid. PMID:33106346
Integrated Microarray to Identify the Hub miRNAs and Constructed miRNA-mRNA Network in Neuroblastoma Via Bioinformatics Analysis. PMID:33104965
Identification of a Twelve-Gene Signature and Establishment of a Prognostic Nomogram Predicting Overall Survival for Medulloblastoma. PMID:33101383
Derivation of Airway Basal Stem Cells from Human Pluripotent Stem Cells. PMID:33098807
Meta-analysis of Transcriptomic Data Reveals Pathophysiological Modules Involved with Atrial Fibrillation. PMID:33095430
Systems analysis of avascular necrosis of femoral head using integrative data analysis and literature mining delineates pathways associated with disease. PMID:33093559
A Semi-Automated Workflow for FAIR Maturity Indicators in the Life Sciences. PMID:33092028
Identification of a nomogram based on an 8-lncRNA signature as a novel diagnostic biomarker for head and neck squamous cell carcinoma. PMID:33091878
Tumor infiltrating immune cells (TIICs) as a biomarker for prognosis benefits in patients with osteosarcoma. PMID:33087099
Improved personalized survival prediction of patients with diffuse large B-cell Lymphoma using gene expression profiling. PMID:33087075
Comparative transcriptomics reveals hidden issues in the plant response to arthropod herbivores. PMID:33085192
Common gene signatures and key pathways in hypopharyngeal and esophageal squamous cell carcinoma: Evidence from bioinformatic analysis. PMID:33080677
Predicted functional interactome of Caenorhabditis elegans and a web tool for the functional interpretation of differentially expressed genes. PMID:33076954
A flexible, interpretable, and accurate approach for imputing the expression of unmeasured genes. PMID:33074331
Oxidative DNA Damage Accelerates Skin Inflammation in Pristane-Induced Lupus Model. PMID:33072095
Transcriptome analysis of Brucella abortus S19∆per immunized mouse spleen revealed activation of MHC-I and MHC-II pathways. PMID:33062939
Whole transcriptomic network analysis using Co-expression Differential Network Analysis (CoDiNA). PMID:33057419
Activation of the CARD8 Inflammasome Requires a Disordered Region. PMID:33053349
Identification of potential key genes and miRNAs involved in Hepatoblastoma pathogenesis and prognosis. PMID:33051830
Maintenance of Cell Fate by the Polycomb Group Gene Sex Combs Extra Enables a Partial Epithelial Mesenchymal Transition in Drosophila. PMID:33051260
Therapeutic Opportunities for Intestinal Angioectasia- Targeting PPARγ and Oxidative Stress. PMID:33048460
Machine learning approach to integrated endometrial transcriptomic datasets reveals biomarkers predicting uterine receptivity in cattle at seven days after estrous. PMID:33046742
Cell-free DNA Methylation and Transcriptomic Signature Prediction of Pregnancies with Adverse Outcomes. PMID:33045922
Silencing KIF18B enhances radiosensitivity: identification of a promising therapeutic target in sarcoma. PMID:33038765
Bioinformatic Identification of Potential Hub Genes in Muscle-Invasive Bladder Urothelial Carcinoma. PMID:33035117
Joint learning of multiple gene networks from single-cell gene expression data. PMID:33033579
Olfactory Stimulation Regulates the Birth of Neurons That Express Specific Odorant Receptors. PMID:33027656
Conditional expression of HGAL leads to the development of diffuse large B-cell lymphoma in mice. PMID:33024996
Network-based identification genetic effect of SARS-CoV-2 infections to Idiopathic pulmonary fibrosis (IPF) patients. PMID:33024988
Survival Strategies of Pathogenic Candida Species in Human Blood Show Independent and Specific Adaptations. PMID:33024045
H. pylori modulates DC functions via T4SS/TNFα/p38-dependent SOCS3 expression. PMID:33023610
Long-Term m5C Methylome Dynamics Parallel Phenotypic Adaptation in the Cyanobacterium Trichodesmium. PMID:33022053
Curated gene expression dataset of differentiating 3T3-L1 adipocytes under pharmacological and genetic perturbations. PMID:33016192
Investigating genetic drivers of dermatomyositis pathogenesis using meta-analysis. PMID:33015383
Screening and Identification of Key Biomarkers in Acquired Lapatinib-Resistant Breast Cancer. PMID:33013420
Database: web application for visualization of the cumulated RNAseq data against the salicylic acid (SA) and methyl jasmonate (MeJA) treatment of Arabidopsis thaliana. PMID:33008298
Reanalysis of Gene Expression Profiles of CD4+ T Cells Treated with HIV-1 Latency Reversal Agents. PMID:33007800
Integrative Analysis of Membrane Proteome and MicroRNA Reveals Novel Lung Cancer Metastasis Biomarkers. PMID:33005184
Transcriptional and Metabolic Profiling of Potato Plants Expressing a Plastid-Targeted Electron Shuttle Reveal Modulation of Genes Associated to Drought Tolerance by Chloroplast Redox Poise. PMID:33003500
The Cu(II) Reductase RclA Protects Escherichia coli against the Combination of Hypochlorous Acid and Intracellular Copper. PMID:32994322
Sex Steroids Induce Membrane Stress Responses and Virulence Properties in Pseudomonas aeruginosa. PMID:32994320
Reconstruction of lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveals functional lncRNAs in skin cutaneous melanoma. PMID:32993558
Inducible Deletion of YAP and TAZ in Adult Mouse Smooth Muscle Causes Rapid and Lethal Colonic Pseudo-Obstruction. PMID:32992050
Analysis of wild tomato introgression lines elucidates the genetic basis of transcriptome and metabolome variation underlying fruit traits and pathogen response. PMID:32989321
Tissue-specific usage of transposable element-derived promoters in mouse development. PMID:32988383
Multiple genetic programs contribute to CD4 T cell memory differentiation and longevity by maintaining T cell quiescence. PMID:32987276
A Prognostic Prediction Model Developed Based on Four CpG Sites and Weighted Correlation Network Analysis Identified DNAJB1 as a Novel Biomarker for Pancreatic Cancer. PMID:32984053
STAB: a spatio-temporal cell atlas of the human brain. PMID:32976581
Amphotericin B Specifically Induces the Two-Component System LnrJK: Development of a Novel Whole-Cell Biosensor for the Detection of Amphotericin-Like Polyenes. PMID:32973732
Landscape of Genome-Wide DNA Methylation of Colorectal Cancer Metastasis. PMID:32971738
MondoA regulates gene expression in cholesterol biosynthesis-associated pathways required for zebrafish epiboly. PMID:32969791
Genome Wide Analysis Points towards Subtype-Specific Diseases in Different Genetic Forms of Amyotrophic Lateral Sclerosis. PMID:32967368
Mining genetic and transcriptomic data using machine learning approaches in Parkinson's disease. PMID:32964109
Deconstructing Stepwise Fate Conversion of Human Fibroblasts to Neurons by MicroRNAs. PMID:32961143
Vitamin D3 receptor polymorphisms regulate T cells and T cell-dependent inflammatory diseases. PMID:32958661
Human G-MDSCs are neutrophils at distinct maturation stages promoting tumor growth in breast cancer. PMID:32958605
High dimensional model representation of log likelihood ratio: binary classification with SNP data. PMID:32957998
Integrated Bioinformatics analysis and clinical validation reveals that high expression of mucin 1 in intrahepatic cholangiocarcinoma predicts recurrence after curative resection. PMID:32952640
Molecular mechanisms underlying altered neurobehavioural development of female offspring of mothers with polycystic ovary syndrome: FOS-mediated regulation of neurotrophins in placenta. PMID:32949999
Cancer gene expression profiles associated with clinical outcomes to chemotherapy treatments. PMID:32948183
A Non-genetic Mechanism Involving the Integrin β4/Paxillin Axis Contributes to Chemoresistance in Lung Cancer. PMID:32947124
Quantitative mapping of transcriptome and proteome dynamics during polarization of human iPSC-derived neurons. PMID:32940601
Hypoxia inducible factor-2α importance for migration, proliferation, and self-renewal of trunk neural crest cells. PMID:32940375
Analyzing Gene Expression Profiles from Ataxia and Spasticity Phenotypes to Reveal Spastic Ataxia Related Pathways. PMID:32937819
Identification, Validation, and Functional Annotations of Genome-Wide Profile Variation between Melanocytic Nevus and Malignant Melanoma. PMID:32934956
Sterol regulatory element-binding protein Sre1 regulates carotenogenesis in the red yeast Xanthophyllomyces dendrorhous. PMID:32933952
The brlA Gene Deletion Reveals That Patulin Biosynthesis Is Not Related to Conidiation in Penicillium expansum. PMID:32932988
A crucial role for Jagunal homolog 1 in humoral immunity and antibody glycosylation in mice and humans. PMID:32930709
The tRNA pseudouridine synthase TruB1 regulates the maturation of let-7 miRNA. PMID:32926445
Are Antisense Proteins in Prokaryotes Functional? PMID:32923454
Identification and validation of novel metastasis-related signatures of clear cell renal cell carcinoma using gene expression databases. PMID:32913492
A gene prioritization method based on a swine multi-omics knowledgebase and a deep learning model. PMID:32913254
An intact gut microbiome protects genetically predisposed mice against leukemia. PMID:32911536
Network Pharmacology to Uncover the Biological Basis of Spleen Qi Deficiency Syndrome and Herbal Treatment. PMID:32908629
TRIM37 controls cancer-specific vulnerability to PLK4 inhibition. PMID:32908304
The neuromuscular junction is a focal point of mTORC1 signaling in sarcopenia. PMID:32908143
Integrated PPI- and WGCNA-Retrieval of Hub Gene Signatures Shared Between Barrett's Esophagus and Esophageal Adenocarcinoma. PMID:32903837
Nrf2 contributes to the weight gain of mice during space travel. PMID:32901092
The Utility of Resolving Asthma Molecular Signatures Using Tissue-Specific Transcriptome Data. PMID:32900903
Serial Passage of Cryptococcus neoformans in Galleria mellonella Results in Increased Capsule and Intracellular Replication in Hemocytes, but Not Increased Resistance to Hydrogen Peroxide. PMID:32899539
RnhP is a plasmid-borne RNase HI that contributes to genome maintenance in the ancestral strain Bacillus subtilis NCIB 3610. PMID:32896031
Bioinformatic analysis reveals hub genes and pathways that promote melanoma metastasis. PMID:32894090
FOXA1 Mutations Reveal Distinct Chromatin Profiles and Influence Therapeutic Response in Breast Cancer. PMID:32888433
Identification of circular RNA hsa_circ_0044556 and its effect on the progression of colorectal cancer. PMID:32884449
Integrative Analysis of MAPK14 as a Potential Biomarker for Cardioembolic Stroke. PMID:32879891
Transcriptomic analysis across liver diseases reveals disease-modulating activation of constitutive androstane receptor in cholestasis. PMID:32875282
Polar Infection of Echovirus-30 Causes Differential Barrier Affection and Gene Regulation at the Blood-Cerebrospinal Fluid Barrier. PMID:32872518
Dysregulated circulating SOCS3 and haptoglobin expression associated with stable coronary artery disease and acute coronary syndrome: An integrated study based on bioinformatics analysis and case-control validation. PMID:32870172
Dorsoventral inversion of the air-filled organ (lungs, gas bladder) in vertebrates: RNAsequencing of laser capture microdissected embryonic tissue. PMID:32864827
Comprehensive analysis of key genes associated with ceRNA networks in nasopharyngeal carcinoma based on bioinformatics analysis. PMID:32863767
Comparative Transcriptomic Analysis of Cerebral Organoids and Cortical Neuron Cultures Derived from Human Induced Pluripotent Stem Cells. PMID:32862797
Machine learning discriminates a movement disorder in a zebrafish model of Parkinson's disease. PMID:32859696
Identification of key differentially expressed mRNAs and microRNAs in non-small cell lung cancer using bioinformatics analysis. PMID:32855723
Comparative Analysis of the Development of Acquired Radioresistance in Canine and Human Mammary Cancer Cell Lines. PMID:32851022
Systematic Evaluation of the Diagnostic and Prognostic Significance of Competitive Endogenous RNA Networks in Prostate Cancer. PMID:32849794
Target Analysis and Mechanism of Podophyllotoxin in the Treatment of Triple-Negative Breast Cancer. PMID:32848800
Combined transcriptome and proteome profiling of the pancreatic β-cell response to palmitate unveils key pathways of β-cell lipotoxicity. PMID:32847508
Whole transcriptome analysis of bovine mammary progenitor cells by P-Cadherin enrichment as a marker in the mammary cell hierarchy. PMID:32843665
An Integrative Omics Approach Reveals Involvement of BRCA1 in Hepatic Metastatic Progression of Colorectal Cancer. PMID:32842712
SARS-CoV-2 infection dynamics in lungs of African green monkeys. PMID:32839775
Cytomegalovirus infection elicits a conserved chemokine response from human and guinea pig amnion cells. PMID:32838950
Microarray Normalization Revisited for Reproducible Breast Cancer Biomarkers. PMID:32832541
Analyzing the lncRNA, miRNA, and mRNA-associated ceRNA networks to reveal potential prognostic biomarkers for glioblastoma multiforme. PMID:32821246
Cancer-Derived Transforming Growth Factor-β Modulates Tumor-Associated Macrophages in Ampullary Cancer. PMID:32821120
Xylem systems genetics analysis reveals a key regulator of lignin biosynthesis in Populus deltoides. PMID:32817237
Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli. PMID:32813020
Human Tregs at the materno-fetal interface show site-specific adaptation reminiscent of tumor Tregs. PMID:32809975
Targeting Hypoxia Sensitizes TNBC to Cisplatin and Promotes Inhibition of Both Bulk and Cancer Stem Cells. PMID:32806648
Construction and Investigation of MicroRNA-mRNA Regulatory Network of Gastric Cancer with Helicobacter pylori Infection. PMID:32802507
The lysine demethylase KDM4A controls the cell-cycle expression of replicative canonical histone genes. PMID:32798738
Integrated Framework of the Immune-Defense Transcriptional Signatures in the Arabidopsis Shoot Apical Meristem. PMID:32796535
Transcriptome profiles acquired during cell expansion and licensing validate mesenchymal stromal cell lineage genes. PMID:32795342
Identification and Validation of Key Genes Associated With Systemic Sclerosis-Related Pulmonary Hypertension. PMID:32793290
Cysteine and Methionine Biosynthetic Enzymes Have Distinct Effects on Seed Nutritional Quality and on Molecular Phenotypes Associated With Accumulation of a Methionine-Rich Seed Storage Protein in Rice. PMID:32793268
Deregulated High Affinity Copper Transport Alters Iron Homeostasis in Arabidopsis. PMID:32793263
Elucidating the fundamental fibrotic processes driving abdominal adhesion formation. PMID:32792541
Interpretation of psychiatric genome-wide association studies with multispecies heterogeneous functional genomic data integration. PMID:32791514
Genome-wide gene expression analysis of a murine model of prostate cancer progression: Deciphering the roles of IL-6 and p38 MAPK as potential therapeutic targets. PMID:32790767
Gene Expression Network Analysis of Precursor Lesions in Familial Pancreatic Cancer. PMID:32783019
The oxytocin receptor signalling system and breast cancer: a critical review. PMID:32782397
Identification of common and divergent gene expression signatures in patients with venous and arterial thrombosis using data from public repositories. PMID:32780732
Identification of Players Controlling Meristem Arrest Downstream of the FRUITFULL-APETALA2 Pathway. PMID:32778534
Computational Identification of Tumor Suppressor Genes Based on Gene Expression Profiles in Normal and Cancerous Gastrointestinal Tissues. PMID:32774369
Molecular Signatures and Networks of Cardiomyocyte Differentiation in Humans and Mice. PMID:32769060
Transcriptional profiling of lung macrophages during pulmonary injury induced by nitrogen mustard. PMID:32767459
Bioinformatics analysis shows that TOP2A functions as a key candidate gene in the progression of cervical cancer. PMID:32765860
Systems Biology Will Direct Vascular-Targeted Therapy for Obesity. PMID:32760294
Characterization of peripheral blood mononuclear cells gene expression profiles of pediatric Staphylococcus aureus persistent and non-carriers using a targeted assay. PMID:32758644
Eight immune-related genes predict survival outcomes and immune characteristics in breast cancer. PMID:32756008
Escherichia coli Has a Unique Transcriptional Program in Long-Term Stationary Phase Allowing Identification of Genes Important for Survival. PMID:32753505
An interspecies translation model implicates integrin signaling in infliximab-resistant inflammatory bowel disease. PMID:32753478
Aberrant methylation and microRNA-target regulation are associated with downregulated NEURL1B: a diagnostic and prognostic target in colon cancer. PMID:32742189
Dynamical gene regulatory networks are tuned by transcriptional autoregulation with microRNA feedback. PMID:32737375
Absence of Plekhg5 Results in Myelin Infoldings Corresponding to an Impaired Schwann Cell Autophagy, and a Reduced T-Cell Infiltration Into Peripheral Nerves. PMID:32733205
The effect of compound kushen injection on cancer cells: Integrated identification of candidate molecular mechanisms. PMID:32730293
Human Nasal Turbinate Tissues in Organ Culture as a Model for Human Cytomegalovirus Infection at the Mucosal Entry Site. PMID:32727881
Time-Dependent miRNA Profile during Septic Acute Kidney Injury in Mice. PMID:32727087
Protamine-2 Deficiency Initiates a Reactive Oxygen Species (ROS)-Mediated Destruction Cascade during Epididymal Sperm Maturation in Mice. PMID:32727081
Insulin-Like Growth Factor 2 mRNA-Binding Protein 3 Modulates Aggressiveness of Ewing Sarcoma by Regulating the CD164-CXCR4 Axis. PMID:32719743
Inflammatory state of lymphatic vessels and miRNA profiles associated with relapse in ovarian cancer patients. PMID:32716937
Preeclamptic placentae release factors that damage neurons: implications for foetal programming of disease. PMID:32714596
Study on the Selection of the Targets of Esophageal Carcinoma and Interventions of Ginsenosides Based on Network Pharmacology and Bioinformatics. PMID:32714406
Integrative Network Biology Framework Elucidates Molecular Mechanisms of SARS-CoV-2 Pathogenesis. PMID:32714115
Absence of cGAS-mediated type I IFN responses in HIV-1-infected T cells. PMID:32709741
Loss of Tdp-43 disrupts the axonal transcriptome of motoneurons accompanied by impaired axonal translation and mitochondria function. PMID:32709255
Pre-Treatment Mutational and Transcriptomic Landscape of Responding Metastatic Melanoma Patients to Anti-PD1 Immunotherapy. PMID:32708981
Exploring Drug Treatment Patterns Based on the Action of Drug and Multilayer Network Model. PMID:32708644
Cell-Type Specificity of Genomic Imprinting in Cerebral Cortex. PMID:32707083
Membrane budding is a major mechanism of in vivo platelet biogenesis. PMID:32706855
A chemical biology approach to identifying molecular pathways associated with aging. PMID:32705410
Cross‑validation of genes potentially associated with neoadjuvant chemotherapy and platinum‑based chemoresistance in epithelial ovarian carcinoma. PMID:32705213
EGF-mediated reduced miR-92a-1-5p controls HTR-8/SVneo cell invasion through activation of MAPK8 and FAS which in turn increase MMP-2/-9 expression. PMID:32703964
Identification of key genes in calcific aortic valve disease by integrated bioinformatics analysis. PMID:32702920
Identification of new drug treatments to combat COVID19: A signature-based approach using iLINCS. PMID:32702077
Identifying the novel key genes in renal cell carcinoma by bioinformatics analysis and cell experiments. PMID:32699530
Cohesin-Dependent and -Independent Mechanisms Mediate Chromosomal Contacts between Promoters and Enhancers. PMID:32698000
An NMR-based approach reveals the core structure of the functional domain of SINEUP lncRNAs. PMID:32697302
Unique molecular signatures of microRNAs in ocular fluids and plasma in diabetic retinopathy. PMID:32692745
Developmental function and state transitions of a gene expression oscillator in Caenorhabditis elegans. PMID:32687264
Deep Proteomic Deconvolution of Interferons and HBV Transfection Effects on a Hepatoblastoma Cell Line. PMID:32685848
NRF2 is a key regulator of endothelial microRNA expression under proatherogenic stimuli. PMID:32683448
PfMAP-2 is essential for male gametogenesis in the malaria parasite Plasmodium falciparum. PMID:32681115
Reduced Brd1 expression leads to reversible depression-like behaviors and gene-expression changes in female mice. PMID:32681022
TH17 cells require ongoing classic IL-6 receptor signaling to retain transcriptional and functional identity. PMID:32680955
Fetal HLA-G mediated immune tolerance and interferon response in preeclampsia. PMID:32680723
Molecular and clinical characterization of PARP9 in gliomas: A potential immunotherapeutic target. PMID:32678519
Gene expression profiling identifies the role of Zac1 in cervical cancer metastasis. PMID:32678267
Chemical Priming by Isothiocyanates Protects Against Intoxication by Products of the Mustard Oil Bomb. PMID:32676087
Pathogenic Tau Causes a Toxic Depletion of Nuclear Calcium. PMID:32668249
Blueprint of human thymopoiesis reveals molecular mechanisms of stage-specific TCR enhancer activation. PMID:32667968
Bioinformatics-based analysis of the lncRNA-miRNA-mRNA and TF regulatory networks reveals functional genes in esophageal squamous cell carcinoma. PMID:32662828
Adenovirus-mediated ubiquitination alters protein-RNA binding and aids viral RNA processing. PMID:32661314
The circular RNA landscape in specific peripheral blood mononuclear cells of critically ill patients with sepsis. PMID:32660590
Extracellular vesicles from Heligmosomoides bakeri and Trichuris muris contain distinct microRNA families and small RNAs that could underpin different functions in the host. PMID:32659276
Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein. PMID:32646969
VviERF6Ls: an expanded clade in Vitis responds transcriptionally to abiotic and biotic stresses and berry development. PMID:32646368
Identification of key genes for esophageal squamous cell carcinoma via integrated bioinformatics analysis and experimental confirmation. PMID:32642240
Microinjection induces changes in the transcriptome of bovine oocytes. PMID:32641751
RAGE impairs murine diabetic atherosclerosis regression and implicates IRF7 in macrophage inflammation and cholesterol metabolism. PMID:32641587
Characterization of cell-free breast cancer patient-derived scaffolds using liquid chromatography-mass spectrometry/mass spectrometry data and RNA sequencing data. PMID:32637480
Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules. PMID:32636252
Machine Learning-Based Ensemble Recursive Feature Selection of Circulating miRNAs for Cancer Tumor Classification. PMID:32635415
A Single-Cell Transcriptomics CRISPR-Activation Screen Identifies Epigenetic Regulators of the Zygotic Genome Activation Program. PMID:32634384
Screening and identification of key gene in sepsis development: Evidence from bioinformatics analysis. PMID:32629654
Array Analysis Manager-An automated DNA microarray analysis tool simplifying microarray data filtering, bias recognition, normalization, and expression analysis. PMID:32624831
Rapid activation of distinct members of multigene families in Plasmodium spp. PMID:32620892
Quiescent stem cell marker genes in glioma gene networks are sufficient to distinguish between normal and glioblastoma (GBM) samples. PMID:32616845
Changes in gene expression in potato meristems treated with the sprout suppressor 1,4-dimethylnaphthalene are dependent on tuber age and dormancy status. PMID:32614863
cnd-1/NeuroD1 Functions with the Homeobox Gene ceh-5/Vax2 and Hox Gene ceh-13/labial To Specify Aspects of RME and DD Neuron Fate in Caenorhabditis elegans. PMID:32601060
Methylation data imputation performances under different representations and missingness patterns. PMID:32600298
Big behavior: challenges and opportunities in a new era of deep behavior profiling. PMID:32599604
PRC2-mediated H3K27me3 modulates shoot iron homeostasis in Arabidopsis thaliana. PMID:32594838
Hub genes and key pathways of traumatic brain injury: bioinformatics analysis and in vivo validation. PMID:32594047
Tryptophanyl-tRNA Synthetase, a Novel Damage-Induced Cytokine, Significantly Increases the Therapeutic Effects of Endometrial Stem Cells. PMID:32592690
An Insulin-Sensitive Circular RNA that Regulates Lifespan in Drosophila. PMID:32592682
Adipose tissue in health and disease through the lens of its building blocks. PMID:32591560
Identification of prognostic risk factors for pancreatic cancer using bioinformatics analysis. PMID:32587798
Minichromosome maintenance 6 complex component identified by bioinformatics analysis and experimental validation in esophageal squamous cell carcinoma. PMID:32583000
The Genetic Regulation of Alternative Splicing in Populus deltoides. PMID:32582229
Short-Term Magnesium Deficiency Triggers Nutrient Retranslocation in Arabidopsis thaliana. PMID:32582226
Adjuvanting Allergen Extracts for Sublingual Immunotherapy: Calcitriol Downregulates CXCL8 Production in Primary Sublingual Epithelial Cells. PMID:32582164
Deciphering the Novel Target Genes Involved in the Epigenetics of Hepatocellular Carcinoma Using Graph Theory Approach. PMID:32581643
Synergism between IL7R and CXCR4 drives BCR-ABL induced transformation in Philadelphia chromosome-positive acute lymphoblastic leukemia. PMID:32581241
Construction, analysis and validation of co-expression network to understand stress adaptation in Deinococcus radiodurans R1. PMID:32579573
Signature genes associated with immunological non-responsiveness to anti-retroviral therapy in HIV-1 subtype-c infection. PMID:32579550
The Tomato DELLA Protein PROCERA Promotes Abscisic Acid Responses in Guard Cells by Upregulating an Abscisic Acid Transporter. PMID:32576645
A circular RNA map for human induced pluripotent stem cells of foetal origin. PMID:32574961
Genome-wide transcriptome architecture in a mouse model of Gulf War Illness. PMID:32574576
Genome-wide Enrichment of De Novo Coding Mutations in Orofacial Cleft Trios. PMID:32574564
Infection cushions of Fusarium graminearum are fungal arsenals for wheat infection. PMID:32573086
Pervasive changes of mRNA splicing in upf1-deficient zebrafish identify rpl10a as a regulator of T cell development. PMID:32571908
Deletion of Glutathione S-Transferase Omega 1 Activates Type I Interferon Genes and Downregulates Tissue Factor. PMID:32571799
Sequentially induced motor neurons from human fibroblasts facilitate locomotor recovery in a rodent spinal cord injury model. PMID:32571478
Construction and analysis of a lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in oral cancer. PMID:32571304
Adaptation of the Marine Bacterium Shewanella baltica to Low Temperature Stress. PMID:32570789
Transcriptome analysis of a social caterpillar, Drepana arcuata: De novo assembly, functional annotation and developmental analysis. PMID:32569288
The acute effects of adjuvant radiation and chemotherapy on peripheral blood epigenetic age in early stage breast cancer patients. PMID:32566744
Downregulation of ST3GAL5 is associated with muscle invasion, high grade and a poor prognosis in patients with bladder cancer. PMID:32566010
Identification of key genes associated with the progression of intrahepatic cholangiocarcinoma using weighted gene co-expression network analysis. PMID:32565973
A novel prognostic signature of immune-related genes for patients with colorectal cancer. PMID:32564470
Prognostic characterization of OAS1/OAS2/OAS3/OASL in breast cancer. PMID:32560641
Engineered receptors for human cytomegalovirus that are orthogonal to normal human biology. PMID:32559251
Mitochondrial protein biogenesis in the synapse is supported by local translation. PMID:32558077
An analytical study of neocartilage from microtia and otoplasty surgical remnants: A possible application for BMP7 in microtia development and regeneration. PMID:32555733
Bone marrow adipose tissue is a unique adipose subtype with distinct roles in glucose homeostasis. PMID:32555194
LC-FACSeq is a method for detecting rare clones in leukemia. PMID:32554930
COnTORT: COmprehensive Transcriptomic ORganizational Tool for Simultaneously Retrieving and Organizing Numerous Gene Expression Data Sets from the NCBI Gene Expression Omnibus Database. PMID:32554783
An age-independent gene signature for monitoring acute rejection in kidney transplantation. PMID:32550916
Upregulation of Piezo1 Is a Novel Prognostic Indicator in Glioma Patients. PMID:32547190
Identification of Hub Genes in Type 2 Diabetes Mellitus Using Bioinformatics Analysis. PMID:32547141
The Leader Peptide peTrpL Forms Antibiotic-Containing Ribonucleoprotein Complexes for Posttranscriptional Regulation of Multiresistance Genes. PMID:32546623
The novel lncRNA PTTG3P is downregulated and predicts poor prognosis in non-small cell lung cancer. PMID:32542097
TGF-β1-Licensed Murine MSCs Show Superior Therapeutic Efficacy in Modulating Corneal Allograft Immune Rejection In Vivo. PMID:32531237
Bioinformatics analysis of the circRNA-miRNA-mRNA network for non-small cell lung cancer. PMID:32527185
metaRE R Package for Meta-Analysis of Transcriptome Data to Identify the cis-Regulatory Code behind the Transcriptional Reprogramming. PMID:32526881
CPPED1-targeting microRNA-371a-5p expression in human placenta associates with spontaneous delivery. PMID:32520951
KRT8 and KRT19, associated with EMT, are hypomethylated and overexpressed in lung adenocarcinoma and link to unfavorable prognosis. PMID:32519739
Transcriptome-Based Analysis of Tomato Genotypes Resistant to Bacterial Spot (Xanthomonas perforans) Race T4. PMID:32517212
Maternal high-fat diet during lactation reprograms the dopaminergic circuitry in mice. PMID:32510473
Comprehensive identification of a two-genesignature as a novel potential prognostic model for patients with medulloblastoma. PMID:32509164
How Do You Identify m6 A Methylation in Transcriptomes at High Resolution? A Comparison of Recent Datasets. PMID:32508872
Identification of immune-related biomarkers associated with tumorigenesis and prognosis in cutaneous melanoma patients. PMID:32508531
Can We Assume the Gene Expression Profile as a Proxy for Signaling Network Activity? PMID:32503292
Integrative analysis of key candidate genes and signaling pathways in autoimmune thyroid dysfunction related to anti-CTLA-4 therapy by bioinformatics. PMID:32500465
Circular RNA HIPK3: A Key Circular RNA in a Variety of Human Cancers. PMID:32500032
poly(UG)-tailed RNAs in genome protection and epigenetic inheritance. PMID:32499657
Expression profiling of small intestinal neuroendocrine tumors identified pathways and gene networks linked to tumorigenesis and metastasis. PMID:32496505
Immune landscapes predict chemotherapy resistance and immunotherapy response in acute myeloid leukemia. PMID:32493790
Analysis of FGF20-regulated genes in organ of Corti progenitors by translating ribosome affinity purification. PMID:32492250
Leaf tissue specific transcriptome sequence and de novo assembly datasets of Asiatic mangrove Rhizophora mucronata Lam. PMID:32490096
Mutually suppressive roles of KMT2A and KDM5C in behaviour, neuronal structure, and histone H3K4 methylation. PMID:32483278
Prognostic gene expression signature for high-grade serous ovarian cancer. PMID:32473302
Restoration of KMT2C/MLL3 in human colorectal cancer cells reinforces genome-wide H3K4me1 profiles and influences cell growth and gene expression. PMID:32471474
Tissue-specific angiogenic and invasive properties of human neonatal thymus and bone MSCs: Role of SLIT3-ROBO1. PMID:32470195
Interaction of YAP with the Myb-MuvB (MMB) complex defines a transcriptional program to promote the proliferation of cardiomyocytes. PMID:32469866
Computational analysis and verification of molecular genetic targets for glioblastoma. PMID:32469390
Drug screening and identification of key candidate genes and pathways of rheumatoid arthritis. PMID:32468016
UBR5 regulates proliferation and radiosensitivity in human laryngeal carcinoma via the p38/MAPK signaling pathway. PMID:32468011
Novel Discoveries Targeting Pathogenic Gut Microbes and New Therapies in Pancreatic Cancer: Does Pathogenic E. coli Infection Cause Pancreatic Cancer Progression Modulated by TUBB/Rho/ROCK Signaling Pathway? A Bioinformatic Analysis. PMID:32461969
Genes Involved in Energy Metabolism Are Differentially Expressed During the Day-Night Cycle in Murine Retinal Pigment Epithelium. PMID:32460311
Circular RNA circNRIP1 promotes migration and invasion in cervical cancer by sponging miR-629-3p and regulating the PTP4A1/ERK1/2 pathway. PMID:32457332
Rathke's cleft-like cysts arise from Isl1 deletion in murine pituitary progenitors. PMID:32453714
An up-to-date overview of computational polypharmacology in modern drug discovery. PMID:32452701
A novel risk score model based on eight genes and a nomogram for predicting overall survival of patients with osteosarcoma. PMID:32448271
Dyslexia Candidate Gene and Ciliary Gene Expression Dynamics During Human Neuronal Differentiation. PMID:32445086
Drought and plant litter chemistry alter microbial gene expression and metabolite production. PMID:32444813
Transcriptomic Evidence of Molecular Mechanisms Underlying the Response of Lactobacillus Plantarum WCFS1 to Hydroxytyrosol. PMID:32443873
Screening and identification of key biomarkers for retinoblastoma: Evidence from bioinformatics analysis. PMID:32443297
Elucidation of the RNA-granule inducing sodium azide stress response through transcriptome analysis. PMID:32437849
A meta-analysis of gene expression data highlights synaptic dysfunction in the hippocampus of brains with Alzheimer's disease. PMID:32433480
Functional Relevance of Citrulline in the Vegetative Tissues of Watermelon During Abiotic Stresses. PMID:32431723
The transition from acute to chronic pain: dynamic epigenetic reprogramming of the mouse prefrontal cortex up to 1 year after nerve injury. PMID:32427748
Dysregulation of Signaling Pathways Due to Differentially Expressed Genes From the B-Cell Transcriptomes of Systemic Lupus Erythematosus Patients - A Bioinformatics Approach. PMID:32426333
Cigarette Smoke Exposure and Inflammatory Signaling Increase the Expression of the SARS-CoV-2 Receptor ACE2 in the Respiratory Tract. PMID:32425701
An NMF-Based Methodology for Selecting Biomarkers in the Landscape of Genes of Heterogeneous Cancer-Associated Fibroblast Populations. PMID:32425511
Comprehensive analysis reveals a six-gene signature and associated drugs in mimic inguinal hernia model. PMID:32424728
TFEB regulates murine liver cell fate during development and regeneration. PMID:32424153
Detecting qualitative changes in biological systems. PMID:32424123
Novel Non-integrating DNA Nano-S/MAR Vectors Restore Gene Function in Isogenic Patient-Derived Pancreatic Tumor Models. PMID:32420409
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
Hepatotoxic pyrrolizidine alkaloids induce DNA damage response in rat liver in a 28-day feeding study. PMID:32419051
Myocardial micro-biopsy procedure for molecular characterization with increased precision and reduced trauma. PMID:32415191
CSN: unsupervised approach for inferring biological networks based on the genome alone. PMID:32414319
Global Transcriptional Profiling Reveals Novel Autocrine Functions of Interleukin 6 in Human Vascular Endothelial Cells. PMID:32410854
Endoplasmic reticulum stress actively suppresses hepatic molecular identity in damaged liver. PMID:32407006
An EGFR signature predicts cell line and patient sensitivity to multiple tyrosine kinase inhibitors. PMID:32406930
Identification of pathogenic TRAIL-expressing innate immune cells during HIV-1 infection in humanized mice by scRNA-Seq. PMID:32406872
Dietary lipids accumulate in macrophages and stromal cells and change the microarchitecture of mesenteric lymph nodes. PMID:32405435
Correlation-centred variable selection of a gene expression signature to predict breast cancer metastasis. PMID:32404965
MNase Profiling of Promoter Chromatin in Salmonella typhimurium-Stimulated GM12878 Cells Reveals Dynamic and Response-Specific Nucleosome Architecture. PMID:32404364
Alternative splicing of LSD1+8a in neuroendocrine prostate cancer is mediated by SRRM4. PMID:32403054
Neuronal activity increases translocator protein (TSPO) levels. PMID:32398717
Transcriptomics in Toxicogenomics, Part II: Preprocessing and Differential Expression Analysis for High Quality Data. PMID:32397130
PPARG Drives Molecular Networks as an Inhibitor for the Pathologic Development and Progression of Lung Adenocarcinoma. PMID:32395124
The Mnemiopsis Genome Project Portal: integrating new gene expression resources and improving data visualization. PMID:32386298
Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era. PMID:32384671
A putative competing endogenous RNA network in cisplatin-resistant lung adenocarcinoma cells identifying potentially rewarding research targets. PMID:32382346
Aberrant expression of two miRNAs promotes proliferation, hepatitis B virus amplification, migration and invasion of hepatocellular carcinoma cells: evidence from bioinformatic analysis and experimental validation. PMID:32377460
Kaposi's Sarcoma-Associated Herpesvirus Fine-Tunes the Temporal Expression of Late Genes by Manipulating a Host RNA Quality Control Pathway. PMID:32376621
Construction of an integrated human osteosarcoma database, HOsDb, based on literature mining, microarray analysis, and database retrieval. PMID:32375685
Hdac3 is an epigenetic inhibitor of the cytotoxicity program in CD8 T cells. PMID:32374402
Integrative Analysis for Elucidating Transcriptomics Landscapes of Glucocorticoid-Induced Osteoporosis. PMID:32373610
Mitral valve leaflet response to ischaemic mitral regurgitation: from gene expression to tissue remodelling. PMID:32370692
Differential B-Cell Receptor Signaling Requirement for Adhesion of Mantle Cell Lymphoma Cells to Stromal Cells. PMID:32370190
Multi-Gene Prognostic Signatures and Prediction of Pathological Complete Response to Neoadjuvant Chemotherapy in ER-positive, HER2-negative Breast Cancer Patients. PMID:32369904
The antibiotic bedaquiline activates host macrophage innate immune resistance to bacterial infection. PMID:32369020
Maintaining Myocardial Glucose Utilization in Diabetic Cardiomyopathy Accelerates Mitochondrial Dysfunction. PMID:32366681
CPS1 expression and its prognostic significance in lung adenocarcinoma. PMID:32355785
Promising diagnostic and prognostic value of six genes in human hepatocellular carcinoma. PMID:32355538
The Animal Lectin Galectin-8 Promotes Cytokine Expression and Metastatic Tumor Growth in Mice. PMID:32355198
JAK-STAT Activity in Peripheral Blood Cells and Kidney Tissue in IgA Nephropathy. PMID:32354727
Comparative proteogenomics profiling of non-small and small lung carcinoma cell lines using mass spectrometry. PMID:32351780
Polymorphisms in miRNA binding sites involved in metabolic diseases in mice and humans. PMID:32350386
Long-Term Aberrations To Cerebellar Endocannabinoids Induced By Early-Life Stress. PMID:32350298
EZH2-Deficient T-cell Acute Lymphoblastic Leukemia Is Sensitized to CHK1 Inhibition through Enhanced Replication Stress. PMID:32349972
Integrating SWATH-MS Proteomics and Transcriptome Analysis Identifies CHI3L1 as a Plasma Biomarker for Early Gastric Cancer. PMID:32346614
HMGA1-pseudogene7 transgenic mice develop B cell lymphomas. PMID:32341372
Interactions between DksA and Stress-Responsive Alternative Sigma Factors Control Inorganic Polyphosphate Accumulation in Escherichia coli. PMID:32341074
Identification of Key Genes Related to Lung Squamous Cell Carcinoma Using Bioinformatics Analysis. PMID:32340320
The Construction and Analysis of the Aberrant lncRNA-miRNA-mRNA Network in Adipose Tissue from Type 2 Diabetes Individuals with Obesity. PMID:32337289
GATA2 and Progesterone Receptor Interaction in Endometrial Stromal Cells Undergoing Decidualization. PMID:32335672
PHTF2 regulates lipids metabolism in gastric cancer. PMID:32335542
High dimensional model representation of log-likelihood ratio: binary classification with expression data. PMID:32334509
Differential Effects of the Hormonal and Copper Intrauterine Device on the Endometrial Transcriptome. PMID:32327684
Amyloid Precursor Protein (APP) Controls the Expression of the Transcriptional Activator Neuronal PAS Domain Protein 4 (NPAS4) and Synaptic GABA Release. PMID:32327470
Transcriptomics in Toxicogenomics, Part I: Experimental Design, Technologies, Publicly Available Data, and Regulatory Aspects. PMID:32326418
Comparative Transcriptomic Analysis of Subcutaneous Adipose Tissue from Local Pig Breeds. PMID:32326415
A Study of Gene Expression Changes in Human Spinal and Oculomotor Neurons; Identifying Potential Links to Sporadic ALS. PMID:32325953
Drought Stress Responses in Context-Specific Genome-Scale Metabolic Models of Arabidopsis thaliana. PMID:32325728
Computational Approach to Identifying Universal Macrophage Biomarkers. PMID:32322218
SPEED2: inferring upstream pathway activity from differential gene expression. PMID:32313938
Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis. PMID:32312741
Bioinformatics analysis and verification of gene targets for benign tracheal stenosis. PMID:32309912
Transcriptome analysis and functional characterization of cerebral organoids in bipolar disorder. PMID:32306996
The Molecular Processes in the Trabecular Meshwork After Exposure to Corticosteroids and in Corticosteroid-Induced Ocular Hypertension. PMID:32305042
Hepatocyte-specific deletion of Pparα promotes NAFLD in the context of obesity. PMID:32300166
Gene-Specific Control of tRNA Expression by RNA Polymerase II. PMID:32298650
Formation of colorectal liver metastases induces musculoskeletal and metabolic abnormalities consistent with exacerbated cachexia. PMID:32298240
20-Hydroxyecdysone Primes Innate Immune Responses That Limit Bacterial and Malarial Parasite Survival in Anopheles gambiae. PMID:32295874
Differences in the Transcriptomic Response of Campylobacter coli and Campylobacter lari to Heat Stress. PMID:32292399
An epigenetic map of malaria parasite development from host to vector. PMID:32286373
Altered Energy Metabolism During Early Optic Nerve Crush Injury: Implications of Warburg-Like Aerobic Glycolysis in Facilitating Retinal Ganglion Cell Survival. PMID:32277382
iMM1865: A New Reconstruction of Mouse Genome-Scale Metabolic Model. PMID:32277147
Whole-Genome DNA Methylation Profiling of CD14+ Monocytes Reveals Disease Status and Activity Differences in Crohn's Disease Patients. PMID:32276386
ngn-1/neurogenin Activates Transcription of Multiple Terminal Selector Transcription Factors in the Caenorhabditis elegans Nervous System. PMID:32273286
Molecular Fingerprints of Borderline Changes in Kidney Allografts Are Influenced by Donor Category. PMID:32269565
Autophosphorylation at serine 166 regulates RIP kinase 1-mediated cell death and inflammation. PMID:32269263
A Targeted Multi-omic Analysis Approach Measures Protein Expression and Low-Abundance Transcripts on the Single-Cell Level. PMID:32268080
Identification of core genes associated with prostate cancer progression and outcome via bioinformatics analysis in multiple databases. PMID:32266115
Impact of ex vivo Sample Handling on DNA Methylation Profiles in Human Cord Blood and Neonatal Dried Blood Spots. PMID:32265984
Defining the Design Principles of Skin Epidermis Postnatal Growth. PMID:32259486
Landscape of copy number aberrations in esophageal squamous cell carcinoma from a high endemic region of South Africa. PMID:32252688
Role of uL3 in the Crosstalk between Nucleolar Stress and Autophagy in Colon Cancer Cells. PMID:32244996
Wnt signaling regulates neural plate patterning in distinct temporal phases with dynamic transcriptional outputs. PMID:32243887
Chemotherapy exacerbates ovarian cancer cell migration and cancer stem cell-like characteristics through GLI1. PMID:32242101
Geographic assessment of cancer genome profiling studies. PMID:32239182
Endothelialization of arterial vascular grafts by circulating monocytes. PMID:32238801
Epigenetic inhibitors eliminate senescent melanoma BRAFV600E cells that survive long‑term BRAF inhibition. PMID:32236593
LAG3 (LAG-3, CD223) DNA methylation correlates with LAG3 expression by tumor and immune cells, immune cell infiltration, and overall survival in clear cell renal cell carcinoma. PMID:32234847
The immune infiltration in clear cell Renal Cell Carcinoma and their clinical implications: A study based on TCGA and GEO databases. PMID:32231726
Egyptian Rousette IFN-ω Subtypes Elicit Distinct Antiviral Effects and Transcriptional Responses in Conspecific Cells. PMID:32231668
A large-scale comparative study of isoform expressions measured on four platforms. PMID:32228441
Low-Dose Silver Nanoparticle Surface Chemistry and Temporal Effects on Gene Expression in Human Liver Cells. PMID:32227433
Decreased Expression of NUSAP1 Predicts Poor Overall Survival in Cervical Cancer. PMID:32226503
The CEDAR Workbench: An Ontology-Assisted Environment for Authoring Metadata that Describe Scientific Experiments. PMID:32219223
Valine-Induced Isoleucine Starvation in Escherichia coli K-12 Studied by Spike-In Normalized RNA Sequencing. PMID:32211022
Evidence of defined temporal expression patterns that lead a gram-negative cell out of dormancy. PMID:32203501
A novel stratification framework for predicting outcome in patients with prostate cancer. PMID:32203215
Fast tree aggregation for consensus hierarchical clustering. PMID:32197576
Tip of the iceberg: roles of circRNAs in hematological malignancies. PMID:32195014
Integrated bioinformatics analysis of the association between apolipoprotein E expression and patient prognosis in papillary thyroid carcinoma. PMID:32194729
IRF1 association with tumor immune microenvironment and use as a diagnostic biomarker for colorectal cancer recurrence. PMID:32194669
Arabidopsis Flippases Cooperate with ARF GTPase Exchange Factors to Regulate the Trafficking and Polarity of PIN Auxin Transporters. PMID:32193204
Neutrophil extracellular traps promote macrophage inflammation and impair atherosclerosis resolution in diabetic mice. PMID:32191637
Deletion of fatty acid transport protein 2 (FATP2) in the mouse liver changes the metabolic landscape by increasing the expression of PPARα-regulated genes. PMID:32188695
Alterations in the methylome of the stromal tumour microenvironment signal the presence and severity of prostate cancer. PMID:32188493
Transcriptomic Landscape and Functional Characterization of Induced Pluripotent Stem Cell-Derived Cerebral Organoids in Schizophrenia. PMID:32186681
Retinal endothelial cell phenotypic modifications during experimental autoimmune uveitis: a transcriptomic approach. PMID:32183784
Identification of key genes and pathways of diagnosis and prognosis in cervical cancer by bioinformatics analysis. PMID:32181600
Dataset of Cavendish banana transcriptome in response to chitosan coating application. PMID:32181300
Analysis of L-arginine:glycine amidinotransferase-, creatine- and homoarginine-dependent gene regulation in the murine heart. PMID:32179820
Enabling population assignment from cancer genomes with SNP2pop. PMID:32179800
Epigenetic Regulation of ABA-Induced Transcriptional Responses in Maize. PMID:32179621
The alarmones (p)ppGpp are part of the heat shock response of Bacillus subtilis. PMID:32176689
RNA-seq Analysis of Wild-Type vs. FOXC2-Deficient Melanoma Cells Reveals a Role for the FOXC2 Transcription Factor in the Regulation of Multiple Oncogenic Pathways. PMID:32175283
A transcriptional landscape of 28 porcine tissues obtained by super deepSAGE sequencing. PMID:32171242
Nitrosative Stress and Lipid Homeostasis as a Mechanism for Zileuton Hepatotoxicity and Resistance in Genetically Sensitive Mice. PMID:32170957
*-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments. PMID:32170312
Single-cell RNA sequencing reveals a heterogeneous response to Glucocorticoids in breast cancer cells. PMID:32170217
Cystic renal-epithelial derived induced pluripotent stem cells from polycystic kidney disease patients. PMID:32163234
Screening and identification of critical biomarkers in erectile dysfunction: evidence from bioinformatic analysis. PMID:32161689
The Arabidopsis SAFEGUARD1 suppresses singlet oxygen-induced stress responses by protecting grana margins. PMID:32161131
Comprehensive evaluation of the metabolic effects of insect meal from Tenebrio molitor L. in growing pigs by transcriptomics, metabolomics and lipidomics. PMID:32158542
Evaluation of pre-processing on the meta-analysis of DNA methylation data from the Illumina HumanMethylation450 BeadChip platform. PMID:32155174
Whole-Transcriptome Analysis Unveils the Synchronized Activities of Genes for Fructans in Developing Tubers of the Jerusalem Artichoke. PMID:32153609
Deficiency in the endocytic adaptor proteins PHETA1/2 impairs renal and craniofacial development. PMID:32152089
The Application of Deep Learning in Cancer Prognosis Prediction. PMID:32150991
Biocomplexity and Fractality in the Search of Biomarkers of Aging and Pathology: Mitochondrial DNA Profiling of Parkinson's Disease. PMID:32143500
Understanding the Molecular Mechanisms of Asthma through Transcriptomics. PMID:32141255
Assessment of the Mode of Action Underlying the Effects of GenX in Mouse Liver and Implications for Assessing Human Health Risks. PMID:32138627
Evaluation of Seven Different RNA-Seq Alignment Tools Based on Experimental Data from the Model Plant Arabidopsis thaliana. PMID:32138290
Histone H4 dosage modulates DNA damage response in the pathogenic yeast Candida glabrata via homologous recombination pathway. PMID:32134928
Mitochondrial Pyruvate Carrier 1 Promotes Peripheral T Cell Homeostasis through Metabolic Regulation of Thymic Development. PMID:32130894
Supervised learning is an accurate method for network-based gene classification. PMID:32129827
Leptin and fractalkine: novel subcutaneous cytokines in burn injury. PMID:32127397
Hypoxia is regulating enzymatic wood decomposition and intracellular carbohydrate metabolism in filamentous white rot fungus. PMID:32123543
Cell Line-, Protein-, and Sialoglycosite-Specific Control of Flux-Based Sialylation in Human Breast Cells: Implications for Cancer Progression. PMID:32117864
Erratum: Identification of Breast Cancer Stem Cell Related Genes Using Functional Cellular Assays Combined With Single-Cell RNA Sequencing in MDA-MB-231 Cells. PMID:32117464
Evaluation of Pathway Activation for a Single Sample Toward Inflammatory Bowel Disease Classification. PMID:32117426
A TRANSPARENT TESTA Transcriptional Module Regulates Endothelium Polarity. PMID:32117351
The Epipeptide YydF Intrinsically Triggers the Cell Envelope Stress Response of Bacillus subtilis and Causes Severe Membrane Perturbations. PMID:32117169
Adaptive RSK-EphA2-GPRC5A signaling switch triggers chemotherapy resistance in ovarian cancer. PMID:32115889
A reference profile-free deconvolution method to infer cancer cell-intrinsic subtypes and tumor-type-specific stromal profiles. PMID:32111252
Empty SV40 capsids increase survival of septic rats by eliciting numerous host signaling networks that participate in a number of systemic functions. PMID:32110278
Restraining Lysosomal Activity Preserves Hematopoietic Stem Cell Quiescence and Potency. PMID:32109377
Investigation of the quorum-sensing regulon of the biocontrol bacterium Pseudomonas chlororaphis strain PA23. PMID:32109244
Molecular and genetic regulation of pig pancreatic islet cell development. PMID:32108026
Role of miRNA-542-5p in the tumorigenesis of osteosarcoma. PMID:32105410
Integrative module analysis of HCC gene expression landscapes. PMID:32104233
High-Throughput Fluorescence-Based Screen Identifies the Neuronal MicroRNA miR-124 as a Positive Regulator of Alphavirus Infection. PMID:32102877
Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation. PMID:32094412
Equivalent change enrichment analysis: assessing equivalent and inverse change in biological pathways between diverse experiments. PMID:32093613
Protein arginine methyltransferase 5 promotes cholesterol biosynthesis-mediated Th17 responses and autoimmunity. PMID:32091410
Transcriptional analysis of arogenate dehydratase genes identifies a link between phenylalanine biosynthesis and lignin biosynthesis. PMID:32090267
Circulating and tissue matricellular RNA and protein expression in calcific aortic valve disease. PMID:32089075
Transcriptomics at Maize Embryo/Endosperm Interfaces Identifies a Transcriptionally Distinct Endosperm Subdomain Adjacent to the Embryo Scutellum. PMID:32086366
RABL6A Is an Essential Driver of MPNSTs that Negatively Regulates the RB1 Pathway and Sensitizes Tumor Cells to CDK4/6 Inhibitors. PMID:32086342
Biosystem Analysis of the Hypoxia Inducible Domain Family Member 2A: Implications in Cancer Biology. PMID:32085461
Development of a four-gene prognostic model for pancreatic cancer based on transcriptome dysregulation. PMID:32081836
Disrupted Gene Networks in Subfertile Hybrid House Mice. PMID:32076722
Data on banana transcriptome in response to blood disease infection. PMID:32071957
Prognostic values of a novel multi-mRNA signature for predicting relapse of cholangiocarcinoma. PMID:32071556
Chromatin remodeling protein HELLS is critical for retinoblastoma tumor initiation and progression. PMID:32071286
Genome-Wide Analysis of Gene Expression Provides New Insights into Waterlogging Responses in Barley (Hordeum vulgare L.). PMID:32069892
Germ-free and microbiota-associated mice yield small intestinal epithelial organoids with equivalent and robust transcriptome/proteome expression phenotypes. PMID:32068945
IPF pathogenesis is dependent upon TGFβ induction of IGF-1. PMID:32067272
Identification of core biomarkers associated with pathogenesis and prognostic outcomes of laryngeal squamous-cell cancer using bioinformatics analysis. PMID:32067095
A Post-Processing Algorithm for miRNA Microarray Data. PMID:32059403
Computational discovery of therapeutic candidates for preventing preterm birth. PMID:32051340
Inhibition of methyltransferase activity of enhancer of zeste 2 leads to enhanced lipid accumulation and altered chromatin status in zebrafish. PMID:32051014
Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data. PMID:32051003
Differential Regulation of circRNA, miRNA, and piRNA during Early Osteogenic and Chondrogenic Differentiation of Human Mesenchymal Stromal Cells. PMID:32050423
Transcriptional Signatures of Tau and Amyloid Neuropathology. PMID:32049030
Using the Gibbs Function as a Measure of Human Brain Development Trends from Fetal Stage to Advanced Age. PMID:32046179
A Functional Landscape of CKD Entities From Public Transcriptomic Data. PMID:32043035
The health status alters the pituitary function and reproduction of mice in a Cxcr2-dependent manner. PMID:32041848
Gene Expression Signature Predictive of Neuroendocrine Transformation in Prostate Adenocarcinoma. PMID:32041153
Distinct cachexia profiles in response to human pancreatic tumours in mouse limb and respiratory muscle. PMID:32039571
Using SNP Weights Derived From Gene Expression Modules to Improve GWAS Power for Feed Efficiency in Pigs. PMID:32038708
APC-β-catenin-TCF signaling silences the intestinal guanylin-GUCY2C tumor suppressor axis. PMID:32037952
Assessing diagnostic value of microRNAs from peripheral blood mononuclear cells and extracellular vesicles in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome. PMID:32034172
Determining sequencing depth in a single-cell RNA-seq experiment. PMID:32034137
Combined Use of Three Machine Learning Modeling Methods to Develop a Ten-Gene Signature for the Diagnosis of Ventilator-Associated Pneumonia. PMID:32031163
Comprehensive analysis of tumor necrosis factor receptor TNFRSF9 (4-1BB) DNA methylation with regard to molecular and clinicopathological features, immune infiltrates, and response prediction to immunotherapy in melanoma. PMID:32028068
Synthetic analogues of 2-oxo acids discriminate metabolic contribution of the 2-oxoglutarate and 2-oxoadipate dehydrogenases in mammalian cells and tissues. PMID:32024885
PDGFRα and αSMA mark two distinct mesenchymal cell populations involved in parenchymal and vascular remodeling in pulmonary fibrosis. PMID:32023084
Construction of a prognosis‑associated long noncoding RNA‑mRNA network for multiple myeloma based on microarray and bioinformatics analysis. PMID:32016443
The molecular aetiology of tRNA synthetase depletion: induction of a GCN4 amino acid starvation response despite homeostatic maintenance of charged tRNA levels. PMID:32016368
Exploring the Key Genes and Pathways in the Formation of Corneal Scar Using Bioinformatics Analysis. PMID:32016117
Comparison of DNA methylation profiles from saliva in Coeliac disease and non-coeliac disease individuals. PMID:32014011
Limited utility of qPCR-based detection of tumor-specific circulating mRNAs in whole blood from clear cell renal cell carcinoma patients. PMID:32013938
Identification of differentially expressed protein-coding genes in lung adenocarcinomas. PMID:32010276
RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs for discerning baseline expression exclusivity of candidate biomarkers. PMID:32009518
Unveiling ncRNA regulatory axes in atherosclerosis progression. PMID:32009226
Reconstructed Single-Cell Fate Trajectories Define Lineage Plasticity Windows during Differentiation of Human PSC-Derived Distal Lung Progenitors. PMID:32004478
Knowledge-enhanced biomedical named entity recognition and normalization: application to proteins and genes. PMID:32000677
Changes in gene expression in human skeletal stem cells transduced with constitutively active Gsα correlates with hallmark histopathological changes seen in fibrous dysplastic bone. PMID:31999703
Triangular correlation (TrC) between cancer aggressiveness, cell uptake capability, and cell deformability. PMID:31998832
Identification of Key Genes and Prognostic Analysis between Chromophobe Renal Cell Carcinoma and Renal Oncocytoma by Bioinformatic Analysis. PMID:31998788
Interleukin-1 Beta-Mediated Sex Differences in Kawasaki Disease Vasculitis Development and Response to Treatment. PMID:31996019
Transcriptional responses of Candida glabrata biofilm cells to fluconazole are modulated by the carbon source. PMID:31993211
Identification of Key Biomarkers in Bladder Cancer: Evidence from a Bioinformatics Analysis. PMID:31991631
Clostridioides difficile-Associated Antibiotics Alter Human Mucosal Barrier Functions by Microbiome-Independent Mechanisms. PMID:31988098
Upregulation of Hallmark Muscle Genes Protects GneM743T/M743T Mutated Knock-In Mice From Kidney and Muscle Phenotype. PMID:31985472
Makorin 1 controls embryonic patterning by alleviating Bruno1-mediated repression of oskar translation. PMID:31978041
MicroRNA Biomarker hsa-miR-195-5p for Detecting the Risk of Lung Cancer. PMID:31976313
Integrated, multicohort analysis reveals unified signature of systemic lupus erythematosus. PMID:31971918
MicroRNAs and regulated interaction networks reveal differences between adult and pediatric acute myeloid leukemia. PMID:31966399
CRL4-Cereblon complex in Thalidomide Embryopathy: a translational investigation. PMID:31964914
A qualitative transcriptional signature for predicting the biochemical recurrence risk of prostate cancer patients after radical prostatectomy. PMID:31961962
Ontology-driven integrative analysis of omics data through Onassis. PMID:31959844
Manatee: detection and quantification of small non-coding RNAs from next-generation sequencing data. PMID:31959833
CeRNA regulatory network-based analysis to study the roles of noncoding RNAs in the pathogenesis of intrahepatic cholangiocellular carcinoma. PMID:31956102
Mining the proliferative diabetic retinopathy-associated genes and pathways by integrated bioinformatic analysis. PMID:31953631
Large-scale Analyses of Disease Biomarkers and Apremilast Pharmacodynamic Effects. PMID:31953524
Identification of biomarkers in common chronic lung diseases by co-expression networks and drug-target interactions analysis. PMID:31952466
Antiviral activity of interferon-stimulated gene 20, as a putative repressor binding to hepatitis B virus enhancer II and core promoter. PMID:31951295
tRNA 2'-O-methylation by a duo of TRM7/FTSJ1 proteins modulates small RNA silencing in Drosophila. PMID:31943105
Encapsulation boosts islet-cell signature in differentiating human induced pluripotent stem cells via integrin signalling. PMID:31942009
Targeting the Oncogenic Long Non-coding RNA SLNCR1 by Blocking Its Sequence-Specific Binding to the Androgen Receptor. PMID:31940495
The Arabidopsis Protein CGL20 Is Required for Plastid 50S Ribosome Biogenesis. PMID:31937683
Changes in the expression of genes encoding type IV pili-associated proteins are seen when Clostridium perfringens is grown in liquid or on surfaces. PMID:31937237
Comparing DNA methylation profiles across different tissues associated with the diagnosis of pediatric asthma. PMID:31932625
Future of Evidence Synthesis in Precision Oncology: Between Systematic Reviews and Biocuration. PMID:31930186
SCDC: bulk gene expression deconvolution by multiple single-cell RNA sequencing references. PMID:31925417
Array Comparative Genomic Hybridization Analysis Reveals Significantly Enriched Pathways in Canine Oral Melanoma. PMID:31921654
Rainbow Trout IgM+ B Cells Preferentially Respond to Thymus-Independent Antigens but Are Activated by CD40L. PMID:31921163
Scalable Prediction of Acute Myeloid Leukemia Using High-Dimensional Machine Learning and Blood Transcriptomics. PMID:31918046
A pantothenate kinase-deficient mouse model reveals a gene expression program associated with brain coenzyme a reduction. PMID:31918006
DNA hypermethylation associated with upregulated gene expression in prostate cancer demonstrates the diversity of epigenetic regulation. PMID:31914996
Pharmacological inhibition of CSF1R by GW2580 reduces microglial proliferation and is protective against neuroinflammation and dopaminergic neurodegeneration. PMID:31914683
PROP1-Dependent Retinoic Acid Signaling Regulates Developmental Pituitary Morphogenesis and Hormone Expression. PMID:31913463
Evaluation of the 12-Gene Molecular Score and the 21-Gene Recurrence Score as Predictors of Response to Neo-adjuvant Chemotherapy in Estrogen Receptor-Positive, HER2-Negative Breast Cancer. PMID:31907749
Identification and characterization of genes frequently responsive to Xanthomonas oryzae pv. oryzae and Magnaporthe oryzae infections in rice. PMID:31906847
MatchMixeR: a cross-platform normalization method for gene expression data integration. PMID:31904810
Bile and urine peptide marker profiles: access keys to molecular pathways and biological processes in cholangiocarcinoma. PMID:31900160
Differential Expression Gene Explorer (DrEdGE): a tool for generating interactive online visualizations of gene expression datasets. PMID:31899488
Insights into the Gene Expression Profiles of Active and Restricted Red/Green-HIV+ Human Astrocytes: Implications for Shock or Lock Therapies in the Brain. PMID:31896591
Robust hepatitis E virus infection and transcriptional response in human hepatocytes. PMID:31896581
Integrative Gene Expression Profiling Analysis to Investigate Potential Prognostic Biomarkers for Colorectal Cancer. PMID:31893510
A 6-Membrane Protein Gene score for prognostic prediction of cytogenetically normal acute myeloid leukemia in multiple cohorts. PMID:31892991
A systems biology approach uncovers a gene co-expression network associated with cell wall degradability in maize. PMID:31891625
Estrogen activates Alzheimer's disease genes. PMID:31890855
Integrative Analysis of Axolotl Gene Expression Data from Regenerative and Wound Healing Limb Tissues. PMID:31889169
CD4+ T Cell-Derived NGAL Modifies the Outcome of Ischemic Acute Kidney Injury. PMID:31889023
High-level integration of murine intestinal transcriptomics data highlights the importance of the complement system in mucosal homeostasis. PMID:31888466
Unique molecular signature in mucolipidosis type IV microglia. PMID:31883529
Increased HLA-DR expression and cortical demyelination in MS links with HLA-DR15. PMID:31882398
Venn-diaNet : venn diagram based network propagation analysis framework for comparing multiple biological experiments. PMID:31881980
PROMO: an interactive tool for analyzing clinically-labeled multi-omic cancer datasets. PMID:31878868
Habitat-Specific Clock Variation and Its Consequence on Reproductive Fitness. PMID:31878828
Arabidopsis EDR1 Protein Kinase Regulates the Association of EDS1 and PAD4 to Inhibit Cell Death. PMID:31876224
A robustness metric for biological data clustering algorithms. PMID:31874625
Syk degradation restrains plasma cell formation and promotes zonal transitions in germinal centers. PMID:31873727
Expression of Alpha-type Platelet-derived Growth Factor Receptor-influenced Genes Predicts Clinical Outcome in Glioma. PMID:31869747
Transcriptional regulation of a gonococcal gene encoding a virulence factor (L-lactate permease). PMID:31860664
StressGenePred: a twin prediction model architecture for classifying the stress types of samples and discovering stress-related genes in arabidopsis. PMID:31856731
Knowledge Base Commons (KBCommons) v1.1: a universal framework for multi-omics data integration and biological discoveries. PMID:31856718
Bioinformatic profiling identifies a platinum-resistant-related risk signature for ovarian cancer. PMID:31856408
Early cold stress responses in post-meiotic anthers from tolerant and sensitive rice cultivars. PMID:31853825
The InsP7 phosphatase Siw14 regulates inositol pyrophosphate levels to control localization of the general stress response transcription factor Msn2. PMID:31848224
Loss of ADAMTS19 causes progressive non-syndromic heart valve disease. PMID:31844321
Supplementation of live yeast based feed additive in early life promotes rumen microbial colonization and fibrolytic potential in lambs. PMID:31844130
Vascular PPARβ/δ Promotes Tumor Angiogenesis and Progression. PMID:31842402
Epigenetic Modifications in T Cells: The Role of DNA Methylation in Salt-Sensitive Hypertension. PMID:31838911
High-resolution chromosomal microarray analysis for copy-number variations in high-functioning autism reveals large aberration typical for intellectual disability. PMID:31838600
Transcriptomic and Proteomic Responses of the Organohalide-Respiring Bacterium Desulfoluna spongiiphila to Growth with 2,6-Dibromophenol as the Electron Acceptor. PMID:31836581
An Integrated Pan-Cancer Analysis and Structure-Based Virtual Screening of GPR15. PMID:31835584
Differences in the intrinsic spatial dynamics of the chromatin contribute to cell differentiation. PMID:31828312
Evolutionarily novel genes are expressed in transgenic fish tumors and their orthologs are involved in development of progressive traits in humans. PMID:31827597
PPP2R2A prostate cancer haploinsufficiency is associated with worse prognosis and a high vulnerability to B55α/PP2A reconstitution that triggers centrosome destabilization. PMID:31822657
Evolutionary transition from degenerate to nonredundant cytokine signaling networks supporting intrathymic T cell development. PMID:31822609
Longitudinal linear combination test for gene set analysis. PMID:31822265
The functional landscape of the human phosphoproteome. PMID:31819260
Distinct patterns of complex rearrangements and a mutational signature of microhomeology are frequently observed in PLP1 copy number gain structural variants. PMID:31818324
Identification of potential core genes in metastatic renal cell carcinoma using bioinformatics analysis. PMID:31814889
GliomaDB: A Web Server for Integrating Glioma Omics Data and Interactive Analysis. PMID:31811943
Comparative transcriptome analysis of hESC- and iPSC-derived lentoid bodies. PMID:31811247
Modelling the gene expression and the DNA-binding in the 3T3-L1 differentiating adipocytes. PMID:31809632
Clinical significance of the immune cell landscape in hepatocellular carcinoma patients with different degrees of fibrosis. PMID:31807510
Infectious stimuli promote malignant B-cell acute lymphoblastic leukemia in the absence of AID. PMID:31804490
Stress-induced changes in the expression of antioxidant system genes for rice (Oryza sativa L.) and bread wheat (Triticum aestivum L.). PMID:31803533
c-Jun overexpression in CAR T cells induces exhaustion resistance. PMID:31802004
mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations. PMID:31799603
Macrophage Coordination of the Interferon Lambda Immune Response. PMID:31798594
aTEMPO: Pathway-Specific Temporal Anomalies for Precision Therapeutics. PMID:31797638
The Transcriptional Profile of Trichophyton rubrum Co-Cultured with Human Keratinocytes Shows New Insights about Gene Modulation by Terbinafine. PMID:31795354
Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle. PMID:31794382
Identification of Susceptibility Genes to Allergic Rhinitis by Gene Expression Data Sets. PMID:31794148
Bioinformatics analysis of Ewing's sarcoma: Seeking key candidate genes and pathways. PMID:31788075
Identification of the lncRNA-miRNA-mRNA network associated with gastric cancer via integrated bioinformatics analysis. PMID:31788050
Microarray Gene Expression Dataset Re-analysis Reveals Variability in Influenza Infection and Vaccination. PMID:31787983
Biotin Supplementation Ameliorates Murine Colitis by Preventing NF-κB Activation. PMID:31786364
Gene Expression Value Prediction Based on XGBoost Algorithm. PMID:31781160
Dissection of gene expression datasets into clinically relevant interaction signatures via high-dimensional correlation maximization. PMID:31780653
Histone Lysine Methylation Dynamics Control EGFR DNA Copy-Number Amplification. PMID:31776131
IL-1β Induces SOCS2 Expression in Human Dendritic Cells. PMID:31775389
A comparative study of multi-omics integration tools for cancer driver gene identification and tumour subtyping. PMID:31774481
Commensal microbiota drive the functional diversification of colon macrophages. PMID:31772323
Network Modeling Approaches and Applications to Unravelling Non-Alcoholic Fatty Liver Disease. PMID:31771247
Screening and identification of key biomarkers in nasopharyngeal carcinoma: Evidence from bioinformatic analysis. PMID:31770211
Expression of the BAD pathway is a marker of triple-negative status and poor outcome. PMID:31767884
JASPer controls interphase histone H3S10 phosphorylation by chromosomal kinase JIL-1 in Drosophila. PMID:31767855
Deep Characterization of the Human Antibody Response to Natural Infection Using Longitudinal Immune Repertoire Sequencing. PMID:31767621
BNC1 regulates cell heterogeneity in human pluripotent stem cell-derived epicardium. PMID:31767620
Computational Inference of Gene Co-Expression Networks for the identification of Lung Carcinoma Biomarkers: An Ensemble Approach. PMID:31766738
Bioinformatics analyses of publicly available NEPCa datasets. PMID:31763364
Repurposing Drugs by In Silico Methods to Target BCR Kinase Domain in Chronic Myeloid Leukemia. PMID:31759365
Endothelial Cell-Specific Transcriptome Reveals Signature of Chronic Stress Related to Worse Outcome After Mild Transient Brain Ischemia in Mice. PMID:31758402
Bone marrow adipose tissue does not express UCP1 during development or adrenergic-induced remodeling. PMID:31758074
TACITuS: transcriptomic data collector, integrator, and selector on big data platform. PMID:31757212
The influence of PFK-II overexpression on neuroblastoma patients' survival may be dependent on the particular isoenzyme expressed, PFKFB3 or PFKFB4. PMID:31754349
Monocytes affect bone mineral density in pre- and postmenopausal women through ribonucleoprotein complex biogenesis by integrative bioinformatics analysis. PMID:31754224
iCrotoK-PseAAC: Identify lysine crotonylation sites by blending position relative statistical features according to the Chou's 5-step rule. PMID:31751380
Chaperone-mediated ordered assembly of the SAGA and NuA4 transcription co-activator complexes in yeast. PMID:31748520
Screening and identification of key biomarkers in prostate cancer using bioinformatics. PMID:31746380
A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons. PMID:31744472
Identification of a 6-lncRNA prognostic signature based on microarray re-annotation in gastric cancer. PMID:31743579
Elevating acetyl-CoA levels reduces aspects of brain aging. PMID:31742554
Differences in the importance of microcephaly, dysmorphism, and epilepsy in the detection of pathogenic CNVs in ID and ASD patients. PMID:31741789
The Microalga Nannochloropsis during Transition from Quiescence to Autotrophy in Response to Nitrogen Availability. PMID:31740503
Methylation of drug resistance-related genes in chemotherapy-sensitive Epstein-Barr virus-associated gastric cancer. PMID:31736281
The Gα-interacting vesicle-associated protein interacts with and promotes cell surface localization of GRP78 during endoplasmic reticulum stress. PMID:31736058
Gene expression microarray public dataset reanalysis in chronic obstructive pulmonary disease. PMID:31730674
Identification of key biomarkers associated with development and prognosis in patients with ovarian carcinoma: evidence from bioinformatic analysis. PMID:31729978
Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network. PMID:31726994
Proteomic and transcriptomic analyses of early and late-chronic Toxoplasma gondii infection shows novel and stage specific transcripts. PMID:31726967
Correlative evidence for co-regulation of phosphorus and carbon exchanges with symbiotic fungus in the arbuscular mycorrhizal Medicago truncatula. PMID:31710651
Assessing the Impact of Sample Heterogeneity on Transcriptome Analysis of Human Diseases Using MDP Webtool. PMID:31708960
Two Loci, RiAF3 and RiAF4, Contribute to the Annual-Fruiting Trait in Rubus. PMID:31708950
Collagen IV (COL4A1, COL4A2), a Component of the Viral Biofilm, Is Induced by the HTLV-1 Oncoprotein Tax and Impacts Virus Transmission. PMID:31708905
Mutation of the PTCH1 gene predicts recurrence of breast cancer. PMID:31704974
Defining the impact of exoribonucleases in the shift between exponential and stationary phases. PMID:31700028
Identification of Hub Genes and Pathways in a Rat Model of Renal Ischemia-Reperfusion Injury Using Bioinformatics Analysis of the Gene Expression Omnibus (GEO) Dataset and Integration of Gene Expression Profiles. PMID:31699960
DNA methylation profiles capturing breast cancer heterogeneity. PMID:31699026
Changes in Calcium Homeostasis and Gene Expression Implicated in Epilepsy in Hippocampi of Mice Overexpressing ORAI1. PMID:31698854
Salt-inducible kinase inhibition suppresses acute myeloid leukemia progression in vivo. PMID:31697837
Genetic Interactions Affect Lung Function in Patients with Systemic Sclerosis. PMID:31694854
The role of nitric oxide during embryonic wound healing. PMID:31694542
Rapid Discovery of Potential Drugs for Osteonecrosis of Femoral Head Based on Gene Expression Omnibus Database and Connectivity Map. PMID:31692295
Development of Tissue-Specific Age Predictors Using DNA Methylation Data. PMID:31690030
NK cell defects in X-linked pigmentary reticulate disorder. PMID:31672938
Non-Invasive Approach for Evaluation of Pulmonary Hypertension Using Extracellular Vesicle-Associated Small Non-Coding RNA. PMID:31671920
Complex Interactions between Cohesin and CTCF in Regulation of Kaposi's Sarcoma-Associated Herpesvirus Lytic Transcription. PMID:31666380
Synchronized replication of genes encoding the same protein complex in fast-proliferating cells. PMID:31662304
Proteasome inhibition preserves longitudinal growth of denervated muscle and prevents neonatal neuromuscular contractures. PMID:31661460
miR‑760 regulates skeletal muscle proliferation in rheumatoid arthritis by targeting Myo18b. PMID:31661144
The FOXC2 Transcription Factor Promotes Melanoma Outgrowth and Regulates Expression of Genes Associated With Drug Resistance and Interferon Responsiveness. PMID:31659103
High Expression of TTYH3 is Related to Poor Clinical Outcomes in Human Gastric Cancer. PMID:31652813
Identification of 15 T Cell Restricted Genes Evaluates T Cell Infiltration of Human Healthy Tissues and Cancers and Shows Prognostic and Predictive Potential. PMID:31652661
Generation and function of progenitor T cells from StemRegenin-1-expanded CD34+ human hematopoietic progenitor cells. PMID:31648315
Acute sprint exercise transcriptome in human skeletal muscle. PMID:31647849
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
Integrated bioinformatics analysis reveals role of the LINC01093/miR-96-5p/ZFAND5/NF-κB signaling axis in hepatocellular carcinoma. PMID:31641376
Size matters: how sample size affects the reproducibility and specificity of gene set analysis. PMID:31639047
ANLN and KDR Are Jointly Prognostic of Breast Cancer Survival and Can Be Modulated for Triple Negative Breast Cancer Control. PMID:31636652
Luteal Lipids Regulate Progesterone Production and May Modulate Immune Cell Function During the Estrous Cycle and Pregnancy. PMID:31636603
TFAP2C regulates carbonic anhydrase XII in human breast cancer. PMID:31636386
Different Pathways Mediate Amphotericin-Lactoferrin Drug Synergy in Cryptococcus and Saccharomyces. PMID:31632362
Global Transcriptional Response of Three Highly Acid-Tolerant Field Strains of Listeria monocytogenes to HCl Stress. PMID:31623206
Identification of prognostic biomarkers for malignant melanoma using microarray datasets. PMID:31620197
Oleuropein Transcriptionally Primes Lactobacillus plantarum to Interact With Plant Hosts. PMID:31620115
Cell Type- and Sex-Dependent Transcriptome Profiles of Rat Anterior Pituitary Cells. PMID:31620083
Long noncoding RNA GAS5 inhibits progression of colorectal cancer by interacting with and triggering YAP phosphorylation and degradation and is negatively regulated by the m6A reader YTHDF3. PMID:31619268
Variance-Preserving Estimation of Intensity Values Obtained From Omics Experiments. PMID:31616468
Peptidoglycan Recognition Protein 4 Limits Bacterial Clearance and Inflammation in Lungs by Control of the Gut Microbiota. PMID:31616404
D-GPM: A Deep Learning Method for Gene Promoter Methylation Inference. PMID:31615113
Electron transport chain biogenesis activated by a JNK-insulin-Myc relay primes mitochondrial inheritance in Drosophila. PMID:31612862
POPDC3 is a potential biomarker for prognosis and radioresistance in patients with head and neck squamous cell carcinoma. PMID:31612055
Screening and authentication of molecular markers in malignant glioblastoma based on gene expression profiles. PMID:31611967
Identification of key biomarkers and potential molecular mechanisms in lung cancer by bioinformatics analysis. PMID:31611952
Myo-REG: A Portal for Signaling Interactions in Muscle Regeneration. PMID:31611808
The PedBE clock accurately estimates DNA methylation age in pediatric buccal cells. PMID:31611402
Transcriptional activation of CBFβ by CDK11p110 is necessary to promote osteosarcoma cell proliferation. PMID:31610798
pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks. PMID:31608109
Gene expression profiling of whole blood: A comparative assessment of RNA-stabilizing collection methods. PMID:31600258
β-Catenin mutations as determinants of hepatoblastoma phenotypes in mice. PMID:31597698
Enhanced Ex Vivo Generation of Erythroid Cells from Human Induced Pluripotent Stem Cells in a Simplified Cell Culture System with Low Cytokine Support. PMID:31595840
Global gene expression analysis of Escherichia coli K-12 DH5α after exposure to 2.4 GHz wireless fidelity radiation. PMID:31595026
Functional Genomics of the Retina to Elucidate its Construction and Deconstruction. PMID:31590277
Identification of PIKfyve kinase as a target in multiple myeloma. PMID:31582538
Screening and Identification of Potential Prognostic Biomarkers in Adrenocortical Carcinoma. PMID:31572440
Maternal Obesity Alters Neurotrophin-Associated MAPK Signaling in the Hypothalamus of Male Mouse Offspring. PMID:31572115
Degradation of the transcription factors PIF4 and PIF5 under UV-B promotes UVR8-mediated inhibition of hypocotyl growth in Arabidopsis. PMID:31571300
Cytosolic Phospholipase A2 Alpha Regulates TLR Signaling and Migration in Metastatic 4T1 Cells. PMID:31569627
Delineating the role of MITF isoforms in pigmentation and tissue homeostasis. PMID:31562697
Comparison of Gene Expression Responses in the Small Intestine of Mice Following Exposure to 3 Carcinogens Using the S1500+ Gene Set Informs a Potential Common Adverse Outcome Pathway. PMID:31558096
A Caenorhabditis elegans ortholog of human selenium-binding protein 1 is a pro-aging factor protecting against selenite toxicity. PMID:31557719
ELTD1 facilitates glioma proliferation, migration and invasion by activating JAK/STAT3/HIF-1α signaling axis. PMID:31554859
Targeted transcriptional modulation with type I CRISPR-Cas systems in human cells. PMID:31548729
Screening and identification of biomarkers for systemic sclerosis via microarray technology. PMID:31545397
Mitochondrial Reprogramming Underlies Resistance to BCL-2 Inhibition in Lymphoid Malignancies. PMID:31543463
Similarities and differences in the biotransformation and transcriptomic responses of Caenorhabditis elegans and Haemonchus contortus to five different benzimidazole drugs. PMID:31542693
miR-511-3p protects against cockroach allergen-induced lung inflammation by antagonizing CCL2. PMID:31536479
Multi-omics profiling reveals key signaling pathways in ovarian cancer controlled by STAT3. PMID:31534498
Myceliophthora thermophila Xyr1 is predominantly involved in xylan degradation and xylose catabolism. PMID:31534479
FPR1 is the plague receptor on host immune cells. PMID:31534221
Comparative transcriptome analysis of the human endocervix and ectocervix during the proliferative and secretory phases of the menstrual cycle. PMID:31530865
Drivers of topoisomerase II poisoning mimic and complement cytotoxicity in AML cells. PMID:31523390
Rectal cancer sub-clones respond differentially to neoadjuvant therapy. PMID:31521947
Identification of differentially expressed genes between primary lung cancer and lymph node metastasis via bioinformatic analysis. PMID:31516588
Cross-disease analysis identified novel common genes for both lung adenocarcinoma and lung squamous cell carcinoma. PMID:31516564
Construction of gene causal regulatory networks using microarray data with the coefficient of intrinsic dependence. PMID:31512008
Off-target toxicity is a common mechanism of action of cancer drugs undergoing clinical trials. PMID:31511426
Weighted elastic net for unsupervised domain adaptation with application to age prediction from DNA methylation data. PMID:31510704
A statistical simulator scDesign for rational scRNA-seq experimental design. PMID:31510652
Model-based optimization of subgroup weights for survival analysis. PMID:31510644
Differences in blastomere totipotency in 2-cell mouse embryos are a maternal trait mediated by asymmetric mRNA distribution. PMID:31504820
SNV identification from single-cell RNA sequencing data. PMID:31504520
Genome-Scale Characterization of Toxicity-Induced Metabolic Alterations in Primary Hepatocytes. PMID:31501904
Seminal fluid compromises visual perception in honeybee queens reducing their survival during additional mating flights. PMID:31500699
Combination of Cannabinoids, Δ9- Tetrahydrocannabinol and Cannabidiol, Ameliorates Experimental Multiple Sclerosis by Suppressing Neuroinflammation Through Regulation of miRNA-Mediated Signaling Pathways. PMID:31497013
p13CMFA: Parsimonious 13C metabolic flux analysis. PMID:31490922
Bioinformatic evidences and analysis of putative biomarkers in pancreatic ductal adenocarcinoma. PMID:31489384
Single-Cell Transcriptome Analysis Reveals Gene Signatures Associated with T-cell Persistence Following Adoptive Cell Therapy. PMID:31484655
Interrogation of a live-attenuated enterotoxigenic Escherichia coli vaccine highlights features unique to wild-type infection. PMID:31482013
Complex Responses to Hydrogen Peroxide and Hypochlorous Acid by the Probiotic Bacterium Lactobacillus reuteri. PMID:31481604
Modulating Pathogenesis with Mobile-CRISPRi. PMID:31481541
Peripheral blood DNA methylation differences in twin pairs discordant for Alzheimer's disease. PMID:31477183
Dietary Effects on Dahl Salt-Sensitive Hypertension, Renal Damage, and the T Lymphocyte Transcriptome. PMID:31476910
Lymphatic vessels interact dynamically with the hair follicle stem cell niche during skin regeneration in vivo. PMID:31475747
Prospects of genomic resources available at the global databases for the flora of United Arab Emirates. PMID:31475085
A Tridimensional Model for NK Cell-Mediated ADCC of Follicular Lymphoma. PMID:31475004
Screening and identification of potential target genes in head and neck cancer using bioinformatics analysis. PMID:31452775
Identification of aberrantly methylated differentially expressed genes in glioblastoma multiforme and their association with patient survival. PMID:31452706
Calvarial osteoblast gene expression in patients with craniosynostosis leads to novel polygenic mouse model. PMID:31442251
The Inducible Response of the Nematode Caenorhabditis elegans to Members of Its Natural Microbiota Across Development and Adult Life. PMID:31440221
miR-30 Family miRNAs Mediate the Effect of Chronic Social Defeat Stress on Hippocampal Neurogenesis in Mouse Depression Model. PMID:31440139
An elastic-net logistic regression approach to generate classifiers and gene signatures for types of immune cells and T helper cell subsets. PMID:31438843
Statistical genomics in rare cancer. PMID:31437624
Identification of miRNAs involved in fruit ripening by deep sequencing of Olea europaea L. transcriptome. PMID:31437230
Gene networks underlying the early regulation of Paraburkholderia phytofirmans PsJN induced systemic resistance in Arabidopsis. PMID:31437216
FXYD5 (Dysadherin) upregulation predicts shorter survival and reveals platinum resistance in high-grade serous ovarian cancer patients. PMID:31434988
Inhibition of GATA2 restrains cell proliferation and enhances apoptosis and chemotherapy mediated apoptosis in human GATA2 overexpressing AML cells. PMID:31434974
Regulation of Macrophage Foam Cell Formation During Nitrogen Mustard (NM)-Induced Pulmonary Fibrosis by Lung Lipids. PMID:31428777
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
Microglia affect α-synuclein cell-to-cell transfer in a mouse model of Parkinson's disease. PMID:31419995
Moving from Empirical to Rational Vaccine Design in the 'Omics' Era. PMID:31416125
Assessing phenotype order in molecular data. PMID:31409831
Progress in data interoperability to support computational toxicology and chemical safety evaluation. PMID:31404555
Oct4 and Hnf4α-induced hepatic stem cells ameliorate chronic liver injury in liver fibrosis model. PMID:31404112
Nascent Polypeptide Domain Topology and Elongation Rate Direct the Cotranslational Hierarchy of Hsp70 and TRiC/CCT. PMID:31400849
Physiological and Transcriptional Responses of Candida parapsilosis to Exogenous Tyrosol. PMID:31399405
Accurate ethnicity prediction from placental DNA methylation data. PMID:31399127
Can Biofilm Be Reversed Through Quorum Sensing in Pseudomonas aeruginosa? PMID:31396166
Folate can promote the methionine-dependent reprogramming of glioblastoma cells towards pluripotency. PMID:31395852
Linker histones are fine-scale chromatin architects modulating developmental decisions in Arabidopsis. PMID:31391082
Long Non-Coding RNA Expression Levels Modulate Cell-Type-Specific Splicing Patterns by Altering Their Interaction Landscape with RNA-Binding Proteins. PMID:31390792
Tumour-infiltrating CD8+ lymphocytes and colorectal cancer recurrence by tumour and nodal stage. PMID:31388185
Interaction Among Sex, Aging, and Epigenetic Processes Concerning Visceral Fat, Insulin Resistance, and Dyslipidaemia. PMID:31379754
Epicardial cells derived from human embryonic stem cells augment cardiomyocyte-driven heart regeneration. PMID:31375810
Differential gene expression analysis reveals novel genes and pathways in pediatric septic shock patients. PMID:31375728
Gene Expression Profiling Reveals that PXR Activation Inhibits Hepatic PPARα Activity and Decreases FGF21 Secretion in Male C57Bl6/J Mice. PMID:31374856
Exploring induced pluripotency in human fibroblasts via construction, validation, and application of a gene regulatory network. PMID:31374103
Dysregulation of the histone demethylase KDM6B in alcohol dependence is associated with epigenetic regulation of inflammatory signaling pathways. PMID:31373129
RNA sequencing data of cultured primary rat Müller cells, the spontaneously immortalized rat Müller cell line, SIRMu-1, and the SV40-transformed rat Müller cell line, rMC-1. PMID:31372389
Disparity in Tumor Immune Microenvironment of Breast Cancer and Prognostic Impact: Asian Versus Western Populations. PMID:31371522
The prognostic value of JUNB-positive CTCs in metastatic breast cancer: from bioinformatics to phenotypic characterization. PMID:31370904
Cell-type-specific resolution epigenetics without the need for cell sorting or single-cell biology. PMID:31366909
Daphnia stressor database: Taking advantage of a decade of Daphnia '-omics' data for gene annotation. PMID:31366898
Evaluation of the Common Molecular Basis in Alzheimer's and Parkinson's Diseases. PMID:31366155
Mining of Self-Organizing Map Gene-Expression Portraits Reveals Prognostic Stratification of HPV-Positive Head and Neck Squamous Cell Carcinoma. PMID:31357501
Dramatic changes in gene expression in different forms of Crithidia fasciculata reveal potential mechanisms for insect-specific adhesion in kinetoplastid parasites. PMID:31356610
Identification and Application of Gene Expression Signatures Associated with Lifespan Extension. PMID:31353263
Circular RNAs are differentially expressed in prostate cancer and are potentially associated with resistance to enzalutamide. PMID:31341219
Anti-miRNA Oligonucleotide Therapy for Chondrosarcoma. PMID:31341031
L1TD1 - a prognostic marker for colon cancer. PMID:31337362
Discovery and Validation of Novel Biomarkers for Detection of Epithelial Ovarian Cancer. PMID:31336942
Cultivation and Transcriptional Analysis of a Canonical Nitrospira Under Stable Growth Conditions. PMID:31333593
The Pol IV largest subunit CTD quantitatively affects siRNA levels guiding RNA-directed DNA methylation. PMID:31329950
Data-driven characterization of molecular phenotypes across heterogeneous sample collections. PMID:31329928
AKAP6 and phospholamban colocalize and interact in HEK-293T cells and primary murine cardiomyocytes. PMID:31325238
Profiling microRNA expression in murine bone healing and non-union formation: Role of miR-140 during the early stage of bone healing. PMID:31323027
Identification and characterization of sexual dimorphism‑linked gene expression profile in hepatocellular carcinoma. PMID:31322260
mTORC1/AMPK responses define a core gene set for developmental cell fate switching. PMID:31319820
Transcriptional Regulation of the Glucose-6-Phosphate/Phosphate Translocator 2 Is Related to Carbon Exchange Across the Chloroplast Envelope. PMID:31316533
Changes in nuclear and cytoplasmic microRNA distribution in response to hypoxic stress. PMID:31316122
Density distribution of gene expression profiles and evaluation of using maximal information coefficient to identify differentially expressed genes. PMID:31314810
A Combined Transcriptomic and Genomic Analysis Identifies a Gene Signature Associated With the Response to Anti-TNF Therapy in Rheumatoid Arthritis. PMID:31312201
Regulation of the unfolded protein response through ATF4 and FAM129A in prostate cancer. PMID:31312022
Anti-tumor effects of PIM/PI3K/mTOR triple kinase inhibitor IBL-302 in neuroblastoma. PMID:31310053
Long Noncoding RNA Expression Profile in BV2 Microglial Cells Exposed to Lipopolysaccharide. PMID:31309106
Anti-inflammatory nutrition with high protein attenuates cardiac and skeletal muscle alterations in a pulmonary arterial hypertension model. PMID:31308383
Clinical update on head and neck cancer: molecular biology and ongoing challenges. PMID:31308358
PRPF40A as a potential diagnostic and prognostic marker is upregulated in pancreatic cancer tissues and cell lines: an integrated bioinformatics data analysis. PMID:31303762
Inferring Regulatory Programs Governing Region Specificity of Neuroepithelial Stem Cells during Early Hindbrain and Spinal Cord Development. PMID:31302154
Retention of paternal DNA methylome in the developing zebrafish germline. PMID:31296860
Evaluating single-subject study methods for personal transcriptomic interpretations to advance precision medicine. PMID:31296218
MCF-7 as a Model for Functional Analysis of Breast Cancer Risk Variants. PMID:31292138
Integration of probabilistic regulatory networks into constraint-based models of metabolism with applications to Alzheimer's disease. PMID:31291905
Septin 9 isoforms promote tumorigenesis in mammary epithelial cells by increasing migration and ECM degradation through metalloproteinase secretion at focal adhesions. PMID:31285548
Genome-scale metabolic model of the rat liver predicts effects of diet restriction. PMID:31285465
Surface PEGylation suppresses pulmonary effects of CuO in allergen-induced lung inflammation. PMID:31277695
Identification of diagnostic markers for major depressive disorder by cross-validation of data from whole blood samples. PMID:31275757
Gene coexpression network for trans-1,4-polyisoprene biosynthesis involving mevalonate and methylerythritol phosphate pathways in Eucommia ulmoides Oliver. PMID:31275023
Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics during Cardiac Reprogramming. PMID:31271750
Estimation of Transcription Factor Activity in Knockdown Studies. PMID:31270369
Identification of Genes With Enriched Expression in Early Developing Mouse Cone Photoreceptors. PMID:31260032
L1000 Viewer: A Search Engine and Web Interface for the LINCS Data Repository. PMID:31258549
Quantitative proteomics and single-nucleus transcriptomics of the sinus node elucidates the foundation of cardiac pacemaking. PMID:31253831
Ethylene-mediated improvement in sucrose accumulation in ripening sugarcane involves increased sink strength. PMID:31253103
Inferring Interaction Networks From Multi-Omics Data. PMID:31249591
Identification of gene expression logical invariants in Arabidopsis. PMID:31245766
Ethylene causes transcriptomic changes in Synechocystis during phototaxis. PMID:31245714
Dark period transcriptomic and metabolic profiling of two diverse Eutrema salsugineum accessions. PMID:31245703
Cross-species complementation reveals conserved functions for EARLY FLOWERING 3 between monocots and dicots. PMID:31245666
C/EBPβ-LIP induces cancer-type metabolic reprogramming by regulating the let-7/LIN28B circuit in mice. PMID:31240246
Genome-wide methylation in alcohol use disorder subjects: implications for an epigenetic regulation of the cortico-limbic glucocorticoid receptors (NR3C1). PMID:31239533
Pollination Type Recognition from a Distance by the Ovary Is Revealed Through a Global Transcriptomic Analysis. PMID:31238522
Integrative genomic analysis of matched primary and metastatic pediatric osteosarcoma. PMID:31236944
An Oncogenic Role for Four-Jointed Box 1 (FJX1) in Nasopharyngeal Carcinoma. PMID:31236144
Screening of Candida albicans GRACE library revealed a unique pattern of biofilm formation under repression of the essential gene ILS1. PMID:31235750
Axonal pathology in hPSC-based models of Parkinson's disease results from loss of Nrf2 transcriptional activity at the Map1b gene locus. PMID:31235589
miR-26a-5p is a Stable Reference Gene for miRNA Studies in Chondrocytes from Developing Human Cartilage. PMID:31234552
Core regulon of the global anaerobic regulator Anr targets central metabolism functions in Pseudomonas species. PMID:31227753
Polymorphisms of the cryptochrome 2 and mitoguardin 2 genes are associated with the variation of lipid-related traits in Duroc pigs. PMID:31227735
Next-Generation Sequencing Reveals Increased Anti-oxidant Response and Ecdysone Signaling in STAT Supercompetitors in Drosophila. PMID:31227525
Prophylactic inhibition of soluble epoxide hydrolase delays onset of nephritis and ameliorates kidney damage in NZB/W F1 mice. PMID:31222024
The glycan CA19-9 promotes pancreatitis and pancreatic cancer in mice. PMID:31221853
Genomic knockout of alms1 in zebrafish recapitulates Alström syndrome and provides insight into metabolic phenotypes. PMID:31220269
High similarity of IgG antibody profiles in blood and saliva opens opportunities for saliva based serology. PMID:31220138
BCScreen: A gene panel to test for breast carcinogenesis in chemical safety screening. PMID:31218268
MetaGxData: Clinically Annotated Breast, Ovarian and Pancreatic Cancer Datasets and their Use in Generating a Multi-Cancer Gene Signature. PMID:31217513
Pseudomonas donghuensis HYS virulence towards Caenorhabditis elegans is regulated by the Cbr/Crc system. PMID:31217473
Methylome-Wide Association Study in Peripheral White Blood Cells Focusing on Central Obesity and Inflammation. PMID:31212707
Carriage of Shiga toxin phage profoundly affects Escherichia coli gene expression and carbon source utilization. PMID:31208335
Insulin Sensitivity Is Associated with Lipoprotein Lipase (LPL) and Catenin Delta 2 (CTNND2) DNA Methylation in Peripheral White Blood Cells in Non-Diabetic Young Women. PMID:31208038
DNA methylation from a Type I restriction modification system influences gene expression and virulence in Streptococcus pyogenes. PMID:31206562
Multi omics analysis of fibrotic kidneys in two mouse models. PMID:31201317
SIMON, an Automated Machine Learning System, Reveals Immune Signatures of Influenza Vaccine Responses. PMID:31201239
Dissecting the Prognostic Significance and Functional Role of Progranulin in Chronic Lymphocytic Leukemia. PMID:31200555
Comprehensive bioinformatics analysis of trabecular meshwork gene expression data to unravel the molecular pathogenesis of primary open-angle glaucoma. PMID:31197946
Risk of spontaneous preterm birth and fetal growth associates with fetal SLIT2. PMID:31194736
Identification of Breast Cancer Stem Cell Related Genes Using Functional Cellular Assays Combined With Single-Cell RNA Sequencing in MDA-MB-231 Cells. PMID:31191614
Identification of novel biomarkers and candidate small molecule drugs in non-small-cell lung cancer by integrated microarray analysis. PMID:31190860
Overexpression of the MYB29 transcription factor affects aliphatic glucosinolate synthesis in Brassica oleracea. PMID:31190320
Cell Cycle-Dependent Regulation and Function of ARGONAUTE1 in Plants. PMID:31189739
Specialized eRpL22 paralogue-specific ribosomes regulate specific mRNA translation in spermatogenesis in Drosophila melanogaster. PMID:31188709
Molecular Signature of Asthma-Enhanced Sensitivity to CuO Nanoparticle Aerosols from 3D Cell Model. PMID:31188557
miR-17-92 and miR-106b-25 clusters regulate beta cell mitotic checkpoint and insulin secretion in mice. PMID:31187215
Dissecting the Stromal Signaling and Regulation of Myeloid Cells and Memory Effector T Cells in Pancreatic Cancer. PMID:31186314
Annotation and Expression of IDN2-like and FDM-like Genes in Sexual and Aposporous Hypericum perforatum L. accessions. PMID:31181659
Genetic resistance to DEHP-induced transgenerational endocrine disruption. PMID:31181066
Ovule Gene Expression Analysis in Sexual and Aposporous Apomictic Hypericum perforatum L. (Hypericaceae) Accessions. PMID:31178879
The role of TNF-α in chordoma progression and inflammatory pathways. PMID:31175552
Identification of microRNAs associated with the aggressiveness of prolactin pituitary tumors using bioinformatic analysis. PMID:31173251
Identification of key candidate genes involved in melanoma metastasis. PMID:31173190
Differentially expressed genes for atrial fibrillation identified by RNA sequencing from paired human left and right atrial appendages. PMID:31172864
Mitochondrial fusion is required for regulation of mitochondrial DNA replication. PMID:31170154
Tertiary lymphoid structures in the choroid plexus in neuropsychiatric lupus. PMID:31167973
Vitamin A Metabolism by Dendritic Cells Triggers an Antimicrobial Response against Mycobacterium tuberculosis. PMID:31167948
Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms. PMID:31165139
Toxicity mechanisms of ZnO UV-filters used in sunscreens toward the model cyanobacteria Synechococcus elongatus PCC 7942. PMID:31161548
RNA sequencing of isolated cell populations expressing human APOL1 G2 risk variant reveals molecular correlates of sickle cell nephropathy in zebrafish podocytes. PMID:31158233
PRC2-Mediated H3K27me3 Contributes to Transcriptional Regulation of FIT-Dependent Iron Deficiency Response. PMID:31156682
Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice. PMID:31150625
An overview of publicly available patient-centered prostate cancer datasets. PMID:31143673
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. PMID:31142855
Map and model-moving from observation to prediction in toxicogenomics. PMID:31140561
Cytochrome P450 Monooxygenase-Mediated Metabolic Utilization of Benzo[a]Pyrene by Aspergillus Species. PMID:31138742
Proton-irradiated breast cells: molecular points of view. PMID:31135901
Cannabinoid Receptor 1 Blockade Attenuates Obesity and Adipose Tissue Type 1 Inflammation Through miR-30e-5p Regulation of Delta-Like-4 in Macrophages and Consequently Downregulation of Th1 Cells. PMID:31134094
Microhomologies are prevalent at Cas9-induced larger deletions. PMID:31127293
Plasticity of intestinal gene expression profile signatures reflected by nutritional interventions in piglets. PMID:31122193
MultiPLIER: A Transfer Learning Framework for Transcriptomics Reveals Systemic Features of Rare Disease. PMID:31121115
Acid-Sensitive Ion Channels Are Expressed in Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes. PMID:31119982
Killer-like receptors and GPR56 progressive expression defines cytokine production of human CD4+ memory T cells. PMID:31118448
Transcriptomic responses to diet quality and viral infection in Apis mellifera. PMID:31117959
Cold acclimation triggers major transcriptional changes in Drosophila suzukii. PMID:31117947
The lncRNA SLNCR Recruits the Androgen Receptor to EGR1-Bound Genes in Melanoma and Inhibits Expression of Tumor Suppressor p21. PMID:31116991
ChEA3: transcription factor enrichment analysis by orthogonal omics integration. PMID:31114921
Differentially and Co-expressed Genes in Embryo, Germ-Line and Somatic Tissues of Tribolium castaneum. PMID:31113821
GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data. PMID:31110304
Inactivation of nuclear histone deacetylases by EP300 disrupts the MiCEE complex in idiopathic pulmonary fibrosis. PMID:31110176
The Placental Atlas Tool (PAT): A collaborative research and discovery platform for the placental research community. PMID:31103066
Hexameric NuMA:LGN structures promote multivalent interactions required for planar epithelial divisions. PMID:31101817
Identification of three subtypes of triple-negative breast cancer with potential therapeutic implications. PMID:31101122
CiliaCarta: An integrated and validated compendium of ciliary genes. PMID:31095607
Unbiased Boolean analysis of public gene expression data for cell cycle gene identification. PMID:31091168
GIDB: a knowledge database for the automated curation and multidimensional analysis of molecular signatures in gastrointestinal cancer. PMID:31089686
Differential Effects of Influenza Virus NA, HA Head, and HA Stalk Antibodies on Peripheral Blood Leukocyte Gene Expression during Human Infection. PMID:31088926
Hypoxia-Induced VISTA Promotes the Suppressive Function of Myeloid-Derived Suppressor Cells in the Tumor Microenvironment. PMID:31088847
A possible role for mitochondrial-derived peptides humanin and MOTS-c in patients with Q fever fatigue syndrome and chronic fatigue syndrome. PMID:31088495
Banana (Musa acuminata) transcriptome profiling in response to rhizobacteria: Bacillus amyloliquefaciens Bs006 and Pseudomonas fluorescens Ps006. PMID:31088352
Snf2 controls pulcherriminic acid biosynthesis and antifungal activity of the biocontrol yeast Metschnikowia pulcherrima. PMID:31081214
Strain-selective efficacy of sacubitril/valsartan on carotid fibrosis in response to injury in two inbred mouse strains. PMID:31077344
AKIRIN1: A Potential New Reference Gene in Human Natural Killer Cells and Granulocytes in Sepsis. PMID:31075840
Transcriptome and physiological analyses for revealing genes involved in wheat response to endoplasmic reticulum stress. PMID:31072347
Warburg Effects in Cancer and Normal Proliferating Cells: Two Tales of the Same Name. PMID:31071451
A miR-206 regulated gene landscape enhances mammary epithelial differentiation. PMID:31069797
Data-Driven Analysis of Age, Sex, and Tissue Effects on Gene Expression Variability in Alzheimer's Disease. PMID:31068785
scNPF: an integrative framework assisted by network propagation and network fusion for preprocessing of single-cell RNA-seq data. PMID:31068142
The Hippo Pathway Blocks Mammalian Retinal Müller Glial Cell Reprogramming. PMID:31067451
Integrative proteomics reveals an increase in non-degradative ubiquitylation in activated CD4+ T cells. PMID:31061531
The skin transcriptome in hidradenitis suppurativa uncovers an antimicrobial and sweat gland gene signature which has distinct overlap with wounded skin. PMID:31059533
Clonal evolution patterns in acute myeloid leukemia with NPM1 mutation. PMID:31048683
Mouse models and strain-dependency of Chédiak-Higashi syndrome-associated neurologic dysfunction. PMID:31043676
Characterizing novel olfactory receptors expressed in the murine renal cortex. PMID:31042061
Therapeutic discovery for marrow failure with MDS predisposition using pluripotent stem cells. PMID:31039138
Associations between Maternal Tobacco Smoke Exposure and the Cord Blood [Formula: see text] DNA Methylome. PMID:31039056
Specific chromatin changes mark lateral organ founder cells in the Arabidopsis inflorescence meristem. PMID:31037302
Cyclin C Regulated Oxidative Stress Responsive Transcriptome in Mus musculus Embryonic Fibroblasts. PMID:31036676
Robust pathway-based multi-omics data integration using directed random walks for survival prediction in multiple cancer studies. PMID:31036036
Tumor suppressor SMARCB1 suppresses super-enhancers to govern hESC lineage determination. PMID:31033435
A Novel Joint Gene Set Analysis Framework Improves Identification of Enriched Pathways in Cross Disease Transcriptomic Analysis. PMID:31031796
An Open Science Approach to Artificial Intelligence in Healthcare. PMID:31022753
Comparative Transcriptome Analysis Shows Conserved Metabolic Regulation during Production of Secondary Metabolites in Filamentous Fungi. PMID:31020039
Two putative MmpL homologs contribute to antimicrobial resistance and nephropathy of enterohemorrhagic E. coli O157:H7. PMID:31019555
Atlas of RNA sequencing profiles for normal human tissues. PMID:31015567
Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL. PMID:31015400
Ancestry patterns inferred from massive RNA-seq data. PMID:31010885
A Mobile Auxin Signal Connects Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls. PMID:31000634
OCT4 and PAX6 determine the dual function of SOX2 in human ESCs as a key pluripotent or neural factor. PMID:30999923
Comparison of multi-tissue aging between human and mouse. PMID:30996271
Development and characterisation of acquired radioresistant breast cancer cell lines. PMID:30987655
Variants in KIAA0825 underlie autosomal recessive postaxial polydactyly. PMID:30982135
Sensitive Quantitative Proteomics of Human Hematopoietic Stem and Progenitor Cells by Data-independent Acquisition Mass Spectrometry. PMID:30975897
Identification of Target Genes at Juvenile Idiopathic Arthritis GWAS Loci in Human Neutrophils. PMID:30972099
Gene expression shifts in yellow-bellied marmots prior to natal dispersal. PMID:30971856
Functioning of Mycobacterial Heat Shock Repressors Requires the Master Virulence Regulator PhoP. PMID:30962357
FET family fusion oncoproteins target the SWI/SNF chromatin remodeling complex. PMID:30962207
Downregulation of CENPF Remodels Prostate Cancer Cells and Alters Cellular Metabolism. PMID:30957416
Identification of common highly expressed genes of Salmonella Enteritidis by in silico prediction of gene expression and in vitro transcriptomic analysis. PMID:30953073
Influenza A Reinfection in Sequential Human Challenge: Implications for Protective Immunity and "Universal" Vaccine Development. PMID:30953061
exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids. PMID:30951672
PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data. PMID:30951143
Multi-omics Analysis Reveals Sequential Roles for ABA during Seed Maturation. PMID:30948555
The role of the GATA transcription factor AreB in regulation of nitrogen and carbon metabolism in Aspergillus nidulans. PMID:30939206
Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE). PMID:30939133
Transcriptome Sequence of Antibiotic-Treated Pseudomonas aeruginosa. PMID:30938705
Elevated Plasma microRNA-105-5p Level in Patients With Idiopathic Parkinson's Disease: A Potential Disease Biomarker. PMID:30936821
Progesterone Receptor Attenuates STAT1-Mediated IFN Signaling in Breast Cancer. PMID:30936295
Transcriptional and Chemical Changes in Soybean Leaves in Response to Long-Term Aphid Colonization. PMID:30930925
Accumulating Transcriptome Drift Precedes Cell Aging in Human Umbilical Cord-Derived Mesenchymal Stromal Cells Serially Cultured to Replicative Senescence. PMID:30924318
A Pathway-Based Strategy to Identify Biomarkers for Lung Cancer Diagnosis and Prognosis. PMID:30923439
Characterization of the European Sea Bass (Dicentrarchus labrax) Gonadal Transcriptome During Sexual Development. PMID:30919121
Transcriptional Analysis of the Human IgE-Expressing Plasma Cell Differentiation Pathway. PMID:30915071
let-7 coordinates the transition to adulthood through a single primary and four secondary targets. PMID:30910805
Repression of Germline Genes in Caenorhabditis elegans Somatic Tissues by H3K9 Dimethylation of Their Promoters. PMID:30910798
Advancing Computational Toxicology in the Big Data Era by Artificial Intelligence: Data-Driven and Mechanism-Driven Modeling for Chemical Toxicity. PMID:30907586
Integrated transcriptome interactome study of oncogenes and tumor suppressor genes in breast cancer. PMID:30906836
Inflammatory monocytes are detrimental to the host immune response during acute infection with Cryptococcus neoformans. PMID:30897162
Conformational Engineering of HIV-1 Env Based on Mutational Tolerance in the CD4 and PG16 Bound States. PMID:30894475
Metabolic Regulators Nampt and Sirt6 Serially Participate in the Macrophage Interferon Antiviral Cascade. PMID:30886604
A Systems Vaccinology Approach Reveals the Mechanisms of Immunogenic Responses to Hantavax Vaccination in Humans. PMID:30886186
Identification of Important Effector Proteins in the FOXJ1 Transcriptional Network Associated With Ciliogenesis and Ciliary Function. PMID:30881373
DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies. PMID:30878356
Copper transporter COPT5 participates in the crosstalk between vacuolar copper and iron pools mobilisation. PMID:30874615
Analysis of differential gene expression and alternative splicing is significantly influenced by choice of reference genome. PMID:30872414
Extracellular Vesicles as Diagnostics and Therapeutics for Structural Epilepsies. PMID:30871144
Clonal analyses of refractory testicular germ cell tumors. PMID:30870501
Herb Target Prediction Based on Representation Learning of Symptom related Heterogeneous Network. PMID:30867892
Bioinformatic exploration of OLFML2B overexpression in gastric cancer base on multiple analyzing tools. PMID:30866865
Glatiramer Acetate modulates ion channels expression and calcium homeostasis in B cell of patients with relapsing-remitting multiple sclerosis. PMID:30862866
Highly Resolved Systems Biology to Dissect the Etioplast-to-Chloroplast Transition in Tobacco Leaves. PMID:30862726
Regulatory network reconstruction of five essential microRNAs for survival analysis in breast cancer by integrating miRNA and mRNA expression datasets. PMID:30859354
Kaiso is required for MTG16-dependent effects on colitis-associated carcinoma. PMID:30858547
Transcriptional Analysis Shows a Robust Host Response to Toxoplasma gondii during Early and Late Chronic Infection in Both Male and Female Mice. PMID:30858341
Identification of Novel Interaction Partners of Ets-1: Focus on DNA Repair. PMID:30857266
The metabolic network coherence of human transcriptomes is associated with genetic variation at the cadherin 18 locus. PMID:30852652
Leveraging Big Data to Transform Drug Discovery. PMID:30848458
Automated exploration of gene ontology term and pathway networks with ClueGO-REST. PMID:30847467
Linking Terpene Synthases to Sesquiterpene Metabolism in Grapevine Flowers. PMID:30846994
A SIR-independent role for cohesin in subtelomeric silencing and organization. PMID:30842278
A new computational drug repurposing method using established disease-drug pair knowledge. PMID:30840053
Lifelong Football Training: Effects on Autophagy and Healthy Longevity Promotion. PMID:30837897
Folate Repletion after Deficiency Induces Irreversible Genomic and Transcriptional Changes in Human Papillomavirus Type 16 (HPV16)-Immortalized Human Keratinocytes. PMID:30836646
Minor Isozymes Tailor Yeast Metabolism to Carbon Availability. PMID:30834327
The Epstein-Barr virus EBNA1 protein modulates the alternative splicing of cellular genes. PMID:30832682
Direct reprogramming to human nephron progenitor-like cells using inducible piggyBac transposon expression of SNAI2-EYA1-SIX1. PMID:30827514
Targetome analysis of chaperone-mediated autophagy in cancer cells. PMID:30821613
Don't brush off buccal data heterogeneity. PMID:30821575
Silicon supply affects the root transcriptome of Brassica napus L. PMID:30820649
Comparing DNA methylation profiles in saliva and intestinal mucosa. PMID:30819108
Rapalog resistance is associated with mesenchymal-type changes in Tsc2-null cells. PMID:30816188
Clinical and research applications of a brain tumor tissue bank in the age of precision medicine. PMID:30816054
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
hsa-miR-301a- and SOX10-dependent miRNA-TF-mRNA regulatory circuits in breast cancer. PMID:30814872
Loss of Stromal Galectin-1 Enhances Multiple Myeloma Development: Emphasis on a Role in Osteoclasts. PMID:30813402
Podocyte-specific expression of Cre recombinase promotes glomerular basement membrane thickening. PMID:30810063
NADH Dehydrogenases in Pseudomonas aeruginosa Growth and Virulence. PMID:30804898
Circadian regulation in human white adipose tissue revealed by transcriptome and metabolic network analysis. PMID:30804433
Differential Gene Expression Patterns of Yersinia pestis and Yersinia pseudotuberculosis during Infection and Biofilm Formation in the Flea Digestive Tract. PMID:30801031
The prognostic landscape of interactive biological processes presents treatment responses in cancer. PMID:30799199
Circular RNAs are temporospatially regulated throughout development and ageing in the rat. PMID:30796328
Correlation-adjusted regression survival scores for high-dimensional variable selection. PMID:30793795
Epigenome-wide association study in peripheral white blood cells involving insulin resistance. PMID:30792424
Physiological and Transcriptional Responses in Weaned Piglets Fed Diets with Varying Phosphorus and Calcium Levels. PMID:30791512
Global transcriptional regulation of innate immunity by ATF-7 in C. elegans. PMID:30789901
Genetic programming of macrophages generates an in vitro model for the human erythroid island niche. PMID:30787325
Identification of Potential Key Genes and Pathways in Early-Onset Colorectal Cancer Through Bioinformatics Analysis. PMID:30786729
Analysis of the mRNAs in Spores of Bacillus subtilis. PMID:30782632
The Impact of the Wheat Rht-B1b Semi-Dwarfing Allele on Photosynthesis and Seed Development Under Field Conditions. PMID:30778362
Comparative Transcriptomics Between Zebrafish and Mammals: A Roadmap for Discovery of Conserved and Unique Signaling Pathways in Physiology and Disease. PMID:30775367
Unveiling the Link Between Inflammation and Adaptive Immunity in Breast Cancer. PMID:30761130
CD56dim CD16- Natural Killer Cell Profiling in Melanoma Patients Receiving a Cancer Vaccine and Interferon-α. PMID:30761123
Isoprene Acts as a Signaling Molecule in Gene Networks Important for Stress Responses and Plant Growth. PMID:30760638
Extrachloroplastic PP7L Functions in Chloroplast Development and Abiotic Stress Tolerance. PMID:30760637
Mapping Metabolic Events in the Cancer Cell Cycle Reveals Arginine Catabolism in the Committed SG2M Phase. PMID:30759381
IDO1 inhibition potentiates vaccine-induced immunity against pancreatic adenocarcinoma. PMID:30747725
Nuclear import of the DSCAM-cytoplasmic domain drives signaling capable of inhibiting synapse formation. PMID:30745319
Identification of potential blood biomarkers for Parkinson's disease by gene expression and DNA methylation data integration analysis. PMID:30744671
The genetic requirements of fatty acid import by Mycobacterium tuberculosis within macrophages. PMID:30735132
Analysis of long non-coding RNA and mRNA expression in bovine macrophages brings up novel aspects of Mycobacterium avium subspecies paratuberculosis infections. PMID:30733564
Sympathetic nervous system controls resolution of inflammation via regulation of repulsive guidance molecule A. PMID:30733433
Data mining for mutation-specific targets in acute myeloid leukemia. PMID:30728456
An experimental genetically attenuated live vaccine to prevent transmission of Toxoplasma gondii by cats. PMID:30728393
The bovine alveolar macrophage DNA methylome is resilient to infection with Mycobacterium bovis. PMID:30728374
Shambhala: a platform-agnostic data harmonizer for gene expression data. PMID:30727942
Boosting γδ T cell-mediated antibody-dependent cellular cytotoxicity by PD-1 blockade in follicular lymphoma. PMID:30723586
Comparison of RNA-Seq and Microarray Gene Expression Platforms for the Toxicogenomic Evaluation of Liver From Short-Term Rat Toxicity Studies. PMID:30723492
Amplified Host Defense by Toll-Like Receptor-Mediated Downregulation of the Glucocorticoid-Induced Leucine Zipper (GILZ) in Macrophages. PMID:30723476
Structural architecture of a dimeric class C GPCR based on co-trafficking of sweet taste receptor subunits. PMID:30723160
Mucor circinelloides Thrives inside the Phagosome through an Atf-Mediated Germination Pathway. PMID:30723131
Characterisation and validation of Mel38; A multi-tissue microRNA signature of cutaneous melanoma. PMID:30721246
Bioinformatic analysis of next‑generation sequencing data to identify dysregulated genes in fibroblasts of idiopathic pulmonary fibrosis. PMID:30720061
Combining data from TCGA and GEO databases and reverse transcription quantitative PCR validation to identify gene prognostic markers in lung cancer. PMID:30718962
Inferring Gene Regulatory Networks from a Population of Yeast Segregants. PMID:30718595
Mesoscale modeling reveals formation of an epigenetically driven HOXC gene hub. PMID:30718394
Latent network-based representations for large-scale gene expression data analysis. PMID:30717663
Temporal Change of Extracellular Matrix during Vein Arterialization Remodeling in Rats. PMID:30717394
Network-based identification of critical regulators as putative drivers of human cleft lip. PMID:30704473
SMAGEXP: a galaxy tool suite for transcriptomics data meta-analysis. PMID:30698691
Loss of CRWN Nuclear Proteins Induces Cell Death and Salicylic Acid Defense Signaling. PMID:30696746
Venous identity requires BMP signalling through ALK3. PMID:30692543
Assessment of weighted topological overlap (wTO) to improve fidelity of gene co-expression networks. PMID:30691386
X-ray irradiation induces subtle changes in the genome-wide distribution of DNA hydroxymethylation with opposing trends in genic and intergenic regions. PMID:30691379
Hypoxia Is Not a Main Stress When Mycobacterium tuberculosis Is in a Dormancy-Like Long-Chain Fatty Acid Environment. PMID:30687646
Drug repositioning for dengue haemorrhagic fever by integrating multiple omics analyses. PMID:30679503
Systems biology reveals how altered TGFβ signalling with age reduces protection against pro-inflammatory stimuli. PMID:30677026
Identification of Blood Biomarkers for Alzheimer's Disease Through Computational Prediction and Experimental Validation. PMID:30671019
Loss of miR-210 leads to progressive retinal degeneration in Drosophila melanogaster. PMID:30670478
CMEP: a database for circulating microRNA expression profiling. PMID:30668638
IRF4 and IRGs Delineate Clinically Relevant Gene Expression Signatures in Systemic Lupus Erythematosus and Rheumatoid Arthritis. PMID:30666255
Comparative transcriptomic analysis unveils interactions between the regulatory CarS protein and light response in Fusarium. PMID:30665350
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
Illuminating spatial A-to-I RNA editing signatures within the Drosophila brain. PMID:30659150
Homoharringtonine deregulates MYC transcriptional expression by directly binding NF-κB repressing factor. PMID:30659143
Oligodendrocyte Progenitor Cells Become Regionally Diverse and Heterogeneous with Age. PMID:30654924
Inhibition of Pannexin 1 Reduces the Tumorigenic Properties of Human Melanoma Cells. PMID:30654593
p.E95K mutation in Indian hedgehog causing brachydactyly type A1 impairs IHH/Gli1 downstream transcriptional regulation. PMID:30651074
Restructured GEO: restructuring Gene Expression Omnibus metadata for genome dynamics analysis. PMID:30649296
MLPA is a practical and complementary alternative to CMA for diagnostic testing in patients with autism spectrum disorders and identifying new candidate CNVs associated with autism. PMID:30647996
Systems Biology Approach to Identify Novel Genomic Determinants for Pancreatic Cancer Pathogenesis. PMID:30644396
ALS-implicated protein TDP-43 sustains levels of STMN2, a mediator of motor neuron growth and repair. PMID:30643292
TULP3: A potential biomarker in colorectal cancer? PMID:30640939
HSP90 inhibitor geldanamycin reverts IL-13- and IL-17-induced airway goblet cell metaplasia. PMID:30640172
Circulating Tumor Cell Clustering Shapes DNA Methylation to Enable Metastasis Seeding. PMID:30633912
Computational translation of genomic responses from experimental model systems to humans. PMID:30629591
Meta-analysis of gene expression profiles in long-term non-progressors infected with HIV-1. PMID:30626383
Transcriptomic profiles of tissues from rats treated with anticancer drug combinations. PMID:30620345
Reciprocal control of motility and biofilm formation by the PdhS2 two-component sensor kinase of Agrobacterium tumefaciens. PMID:30620265
HMGN1 and R848 Synergistically Activate Dendritic Cells Using Multiple Signaling Pathways. PMID:30619338
Iron Regulation in Clostridioides difficile. PMID:30619231
A Longitudinal Study of the Association between Mammographic Density and Gene Expression in Normal Breast Tissue. PMID:30613869
lncRNA-based study of epigenetic regulations in diabetic peripheral neuropathy. PMID:30607320
Re-annotation of eight Drosophila genomes. PMID:30599046
An internal ribosome entry site in the coding region of tyrosyl-DNA phosphodiesterase 2 drives alternative translation start. PMID:30593505
Modeling human prostate cancer progression in vitro. PMID:30590461
Low STYK1 expression indicates poor prognosis in gastric cancer. PMID:30584361
Camphor white oil induces tumor regression through cytotoxic T cell-dependent mechanisms. PMID:30582219
MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data. PMID:30577750
Impaired immune surveillance accelerates accumulation of senescent cells and aging. PMID:30575733
Downregulation of the Vitamin D Receptor Regulated Gene Set in the Hippocampus After MDMA Treatment. PMID:30559663
RNA⁻Protein Interactions Prevent Long RNA Duplex Formation: Implications for the Design of RNA-Based Therapeutics. PMID:30558267
Factor cooperation for chromosome discrimination in Drosophila. PMID:30541149
Identification of molecular signatures of cystic fibrosis disease status with plasma-based functional genomics. PMID:30540547
Aberrantly expressed long noncoding RNAs and genes in Parkinson's disease. PMID:30538480
A transcriptomics analysis of the Tbx5 paralogues in zebrafish. PMID:30532148
LCE: an open web portal to explore gene expression and clinical associations in lung cancer. PMID:30532070
CNOT3 targets negative cell cycle regulators in non-small cell lung cancer development. PMID:30531840
A Serum-Induced Transcriptome and Serum Cytokine Signature Obtained at Diagnosis Correlates with the Development of Early Pancreatic Ductal Adenocarcinoma Metastasis. PMID:30530849
Mms21: A Putative SUMO E3 Ligase in Candida albicans That Negatively Regulates Invasiveness and Filamentation, and Is Required for the Genotoxic and Cellular Stress Response. PMID:30530734
SerpinA3N is a novel hypothalamic gene upregulated by a high-fat diet and leptin in mice. PMID:30519364
Danger signals activate a putative innate immune system during regeneration in a filamentous fungus. PMID:30500812
Genome-wide identification of RETINOBLASTOMA RELATED 1 binding sites in Arabidopsis reveals novel DNA damage regulators. PMID:30500810
Tracking microRNA Processing Signals by Degradome Sequencing Data Analysis. PMID:30487815
Two functionally redundant sources of retinoic acid secure spermatogonia differentiation in the seminiferous epithelium. PMID:30487180
PNPase is involved in the coordination of mRNA degradation and expression in stationary phase cells of Escherichia coli. PMID:30486791
Relation between Biofilm and Virulence in Vibrio tapetis: A Transcriptomic Study. PMID:30486310
SkeletalVis: an exploration and meta-analysis data portal of cross-species skeletal transcriptomics data. PMID:30481257
Genetic, Transcriptome, Proteomic, and Epidemiological Evidence for Blood-Brain Barrier Disruption and Polymicrobial Brain Invasion as Determinant Factors in Alzheimer's Disease. PMID:30480234
Prediction of plant-derived xenomiRs from plant miRNA sequences using random forest and one-dimensional convolutional neural network models. PMID:30477446
Identifying cancer-related microRNAs based on subpathways. PMID:30472691
Network Pharmacology to Unveil the Biological Basis of Health-Strengthening Herbal Medicine in Cancer Treatment. PMID:30469422
Differential expression of heat shock and floral regulatory genes in pseudocarpel initials of mantled female inflorescences from Elaeis guineensis Jacq. PMID:30467592
Human Prolactinoma: A View of Protein-Protein Interaction Pattern. PMID:30464775
STE20/PAKA Protein Kinase Gene Releases an Autoinhibitory Domain through Pre-mRNA Alternative Splicing in the Dermatophyte Trichophyton rubrum. PMID:30463281
From sequencing data to gene functions: co-functional network approaches. PMID:30460054
A data citation roadmap for scientific publishers. PMID:30457573
RNase E cleavage shapes the transcriptome of Rhodobacter sphaeroides and strongly impacts phototrophic growth. PMID:30456366
RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs database. PMID:30453895
BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud. PMID:30447998
Screening and clinical significance of tumor markers in head and neck squamous cell carcinoma through bioinformatics analysis. PMID:30431092
Identification of hub genes with diagnostic values in pancreatic cancer by bioinformatics analyses and supervised learning methods. PMID:30428899
Comprehensive bioinformatics analysis identifies several potential diagnostic markers and potential roles of cyclin family members in lung adenocarcinoma. PMID:30425528
Deoxynivalenol Affects Cell Metabolism and Increases Protein Biosynthesis in Intestinal Porcine Epithelial Cells (IPEC-J2): DON Increases Protein Biosynthesis. PMID:30423940
Single cell network analysis with a mixture of Nested Effects Models. PMID:30423100
Conditional generative adversarial network for gene expression inference. PMID:30423066
A Comparison of the TempO-Seq S1500+ Platform to RNA-Seq and Microarray Using Rat Liver Mode of Action Samples. PMID:30420870
Increased sporulation underpins adaptation of Clostridium difficile strain 630 to a biologically-relevant faecal environment, with implications for pathogenicity. PMID:30420658
C/VDdb: A multi-omics expression profiling database for a knowledge-driven approach in cardiovascular disease (CVD). PMID:30419069
Stemformatics: visualize and download curated stem cell data. PMID:30407577
Azithromycin treatment modifies airway and blood gene expression networks in neutrophilic COPD. PMID:30406125
The metabolite BH4 controls T cell proliferation in autoimmunity and cancer. PMID:30405245
LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells. PMID:30404662
Bayesian variable selection for parametric survival model with applications to cancer omics data. PMID:30400837
Enabling precision medicine in neonatology, an integrated repository for preterm birth research. PMID:30398470
Effects of simulated microgravity on the expression profiles of RNA during osteogenic differentiation of human bone marrow mesenchymal stem cells. PMID:30397970
FAM92A Underlies Nonsyndromic Postaxial Polydactyly in Humans and an Abnormal Limb and Digit Skeletal Phenotype in Mice. PMID:30395363
Haemopedia RNA-seq: a database of gene expression during haematopoiesis in mice and humans. PMID:30395284
PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants. PMID:30395277
Profiling Immune Escape in Hodgkin's and Diffuse large B-Cell Lymphomas Using the Transcriptome and Immunostaining. PMID:30384489
Identification of grade and origin specific cell populations in serous epithelial ovarian cancer by single cell RNA-seq. PMID:30383866
New miRNA Signature Heralds Human NK Cell Subsets at Different Maturation Steps: Involvement of miR-146a-5p in the Regulation of KIR Expression. PMID:30374356
Deep sequencing and miRNA profiles in alcohol-induced neuroinflammation and the TLR4 response in mice cerebral cortex. PMID:30374194
ViBrism DB: an interactive search and viewer platform for 2D/3D anatomical images of gene expression and co-expression networks. PMID:30371824
Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data. PMID:30371680
RNA-Seq-Based Analysis Reveals Heterogeneity in Mature 16S rRNA 3' Termini and Extended Anti-Shine-Dalgarno Motifs in Bacterial Species. PMID:30355764
wTO: an R package for computing weighted topological overlap and a consensus network with integrated visualization tool. PMID:30355288
Regulation of human glioma cell migration, tumor growth, and stemness gene expression using a Lck targeted inhibitor. PMID:30353164
Expression of calcium pumps is differentially regulated by histone deacetylase inhibitors and estrogen receptor alpha in breast cancer cells. PMID:30352569
Dietary fibers inhibit obesity in mice, but host responses in the cecum and liver appear unrelated to fiber-specific changes in cecal bacterial taxonomic composition. PMID:30349136
Gene expression profiling in a mouse model of Dravet syndrome. PMID:30347190
Prediction of Target Genes and Pathways Associated With Cetuximab Insensitivity in Colorectal Cancer. PMID:30336768
Single-Cell RNA Sequencing Reveals Novel Markers of Male Pituitary Stem Cells and Hormone-Producing Cell Types. PMID:30335147
A proteasome-resistant fragment of NIK mediates oncogenic NF-κB signaling in schwannomas. PMID:30335132
Comparative Study on Alternative Splicing in Human Fungal Pathogens Suggests Its Involvement During Host Invasion. PMID:30333805
Genome organization and DNA accessibility control antigenic variation in trypanosomes. PMID:30333624
Essential roles of mitochondrial biogenesis regulator Nrf1 in retinal development and homeostasis. PMID:30333037
PWWP2A binds distinct chromatin moieties and interacts with an MTA1-specific core NuRD complex. PMID:30327463
sEst: Accurate Sex-Estimation and Abnormality Detection in Methylation Microarray Data. PMID:30326623
Effects of rheumatoid arthritis associated transcriptional changes on osteoclast differentiation network in the synovium. PMID:30324023
A comparative study of endoderm differentiation in humans and chimpanzees. PMID:30322406
Early IL-10 producing B-cells and coinciding Th/Tr17 shifts during three year grass-pollen AIT. PMID:30318182
WNT signaling memory is required for ACTIVIN to function as a morphogen in human gastruloids. PMID:30311909
Translocated duplication of a targeted chromosomal segment enhances gene expression at the duplicated site and results in phenotypic changes in Aspergillus oryzae. PMID:30305913
Combining Developmental and Perturbation-Seq Uncovers Transcriptional Modules Orchestrating Neuronal Remodeling. PMID:30300589
Identification of gene expression predictors of occupational benzene exposure. PMID:30300410
Multiomics approach reveals metabolic changes in the heart at birth. PMID:30300011
Two Regulators, PA3898 and PA2100, Modulate the Pseudomonas aeruginosa Multidrug Resistance MexAB-OprM and EmrAB Efflux Pumps and Biofilm Formation. PMID:30297364
Proteome and transcriptome profiling of equine myofibrillar myopathy identifies diminished peroxiredoxin 6 and altered cysteine metabolic pathways. PMID:30289745
Early isolated V-lesion may not truly represent rejection of the kidney allograft. PMID:30287520
Identification of key genes involved in the phenotypic alterations of res (restored cell structure by salinity) tomato mutant and its recovery induced by salt stress through transcriptomic analysis. PMID:30285698
Exposure to childhood abuse is associated with human sperm DNA methylation. PMID:30279435
Increased EXT1 gene copy number correlates with increased mRNA level predicts short disease-free survival in hepatocellular carcinoma without vascular invasion. PMID:30278583
New insights into the cellular temporal response to proteostatic stress. PMID:30272558
Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease. PMID:30270042
Divergent Matrix-Remodeling Strategies Distinguish Developmental from Neoplastic Mammary Epithelial Cell Invasion Programs. PMID:30269950
Innate and adaptive signals enhance differentiation and expansion of dual-antibody autoreactive B cells in lupus. PMID:30266981
Glucocorticoid deficiency causes transcriptional and post-transcriptional reprogramming of glutamine metabolism. PMID:30266295
Candida albicans Sfl1/Sfl2 regulatory network drives the formation of pathogenic microcolonies. PMID:30252918
Synergistic combination of flavopiridol and carfilzomib targets commonly dysregulated pathways in adrenocortical carcinoma and has biomarkers of response. PMID:30250647
Fenretinide targeting of human colon cancer sphere cells through cell cycle regulation and stress-responsive activities. PMID:30250604
Comprehensive analysis of gene expression profiles associated with proliferative diabetic retinopathy. PMID:30250524
Robustness by intrinsically disordered C-termini and translational readthrough. PMID:30247639
Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations. PMID:30241495
Zingerone Suppresses Tumor Development through Decreasing Cyclin D1 Expression and Inducing Mitotic Arrest. PMID:30235818
Overexpression of an auxin receptor OsAFB6 significantly enhanced grain yield by increasing cytokinin and decreasing auxin concentrations in rice panicle. PMID:30232356
Mannose Alters Gut Microbiome, Prevents Diet-Induced Obesity, and Improves Host Metabolism. PMID:30231992
Subgroup-specific immune and stromal microenvironment in medulloblastoma. PMID:30228931
Integrated Genome-Wide Analysis of Gene Expression and DNA Copy Number Variations Highlights Stem Cell-Related Pathways in Small Cell Esophageal Carcinoma. PMID:30228821
Genome-Wide Association Study Reveals Genetic Link between Diarrhea-Associated Entamoeba histolytica Infection and Inflammatory Bowel Disease. PMID:30228239
Longitudinal transcriptomic characterization of the immune response to acute hepatitis C virus infection in patients with spontaneous viral clearance. PMID:30222771
The topoisomerase 3α zinc-finger domain T1 of Arabidopsis thaliana is required for targeting the enzyme activity to Holliday junction-like DNA repair intermediates. PMID:30222730
Inhibition of neogenin fosters resolution of inflammation and tissue regeneration. PMID:30222138
Effects of hydroxyurea on CNV induction in the mouse germline. PMID:30218578
Assortment of Flowering Time and Immunity Alleles in Natural Arabidopsis thaliana Populations Suggests Immunity and Vegetative Lifespan Strategies Coevolve. PMID:30215800
Systematic Analysis of Gene Expression Profiles Controlled by hnRNP Q and hnRNP R, Two Closely Related Human RNA Binding Proteins Implicated in mRNA Processing Mechanisms. PMID:30214903
Identification of a novel gene fusion in ALT positive osteosarcoma. PMID:30214690
PAX5A and PAX5B isoforms are both efficient to drive B cell differentiation. PMID:30214688
Distinct prognostic values of mRNA expression of glutathione peroxidases in non-small cell lung cancer. PMID:30214294
Whole genome sequencing identifies high-impact variants in well-known pharmacogenomic genes. PMID:30214008
Polarized Entry of Human Parechoviruses in the Airway Epithelium. PMID:30211126
Regional Differences in Airway Epithelial Cells Reveal Tradeoff between Defense against Oxidative Stress and Defense against Rhinovirus. PMID:30208323
Computational prediction of changes in brain metabolic fluxes during Parkinson's disease from mRNA expression. PMID:30208076
Knockout of the Hmt1p Arginine Methyltransferase in Saccharomyces cerevisiae Leads to the Dysregulation of Phosphate-associated Genes and Processes. PMID:30206180
Genotoxic, Metabolic, and Oxidative Stresses Regulate the RNA Repair Operon of Salmonella enterica Serovar Typhimurium. PMID:30201777
An admixture mapping meta-analysis implicates genetic variation at 18q21 with asthma susceptibility in Latinos. PMID:30201514
Elevated expression of NFE2L3 predicts the poor prognosis of pancreatic cancer patients. PMID:30196752
Characterization of Spleen Transcriptome and Immunity Against Avian Colibacillosis After Immunization With Recombinant Attenuated Salmonella Vaccine Strains. PMID:30186843
A Microarray Study of Articular Cartilage in Relation to Obesity and Severity of Knee Osteoarthritis. PMID:30173558
Feasibility of developing reliable gene expression modules from FFPE derived RNA profiled on Affymetrix arrays. PMID:30169535
Transforming growth factor beta1 targets estrogen receptor signaling in bronchial epithelial cells. PMID:30165855
Post-transcriptional gene regulation by an Hfq-independent small RNA in Caulobacter crescentus. PMID:30165530
Quantitative RNA-seq Analysis Unveils Osmotic and Thermal Adaptation Mechanisms Relevant for Ectoine Production in Chromohalobacter salexigens. PMID:30158907
Differentially expressed proteins in positive versus negative HNSCC lymph nodes. PMID:30157864
Harnessing the biological complexity of Big Data from LINCS gene expression signatures. PMID:30157183
A Chromatin Basis for Cell Lineage and Disease Risk in the Human Pancreas. PMID:30145115
Fate-restricted retinal progenitor cells adopt a molecular profile and spatial position distinct from multipotent progenitor cells. PMID:30145104
Construction and analysis of mRNA, miRNA, lncRNA, and TF regulatory networks reveal the key genes associated with prostate cancer. PMID:30138363
Effects of bone marrow-derived mesenchymal stromal cells on gene expression in human alveolar type II cells exposed to TNF-α, IL-1β, and IFN-γ. PMID:30136410
Plasma microRNA markers of upper limb recovery following human stroke. PMID:30135469
Transcriptional targeting of oncogene addiction in medullary thyroid cancer. PMID:30135308
Prediction of key genes and pathways involved in trastuzumab-resistant gastric cancer. PMID:30134903
Identification of protein complexes associated with myocardial infarction using a bioinformatics approach. PMID:30132549
Dissecting the expression landscape of mitochondrial genes in lung squamous cell carcinoma and lung adenocarcinoma. PMID:30128019
Identification of genes that predict the biochemical recurrence of prostate cancer. PMID:30127947
Screening and identification of key biomarkers in bladder carcinoma: Evidence from bioinformatics analysis. PMID:30127900
Profiles of immune infiltration in colorectal cancer and their clinical significant: A gene expression-based study. PMID:30117315
Detecting Differentially Variable MicroRNAs via Model-Based Clustering. PMID:30116730
A Spatiotemporal DNA Endoploidy Map of the Arabidopsis Root Reveals Roles for the Endocycle in Root Development and Stress Adaptation. PMID:30115738
Comprehensive integrated analysis of gene expression datasets identifies key anti-cancer targets in different stages of breast cancer. PMID:30112036
QsRNA-seq: a method for high-throughput profiling and quantifying small RNAs. PMID:30107842
Revealing a human p53 universe. PMID:30107566
Machine Learning Based Toxicity Prediction: From Chemical Structural Description to Transcriptome Analysis. PMID:30103448
The effect of Tmem135 overexpression on the mouse heart. PMID:30102730
AMPK activation negatively regulates GDAP1, which influences metabolic processes and circadian gene expression in skeletal muscle. PMID:30093355
JAK-STAT signaling is activated in the kidney and peripheral blood cells of patients with focal segmental glomerulosclerosis. PMID:30093081
Marked disparity of microRNA modulation by cGMP-selective PDE5 versus PDE9 inhibitors in heart disease. PMID:30089721
BART: bioinformatics array research tool. PMID:30089462
Reconstruction of the Protein-Protein Interaction Network for Protein Complexes Identification by Walking on the Protein Pair Fingerprints Similarity Network. PMID:30087694
Myc and ChREBP transcription factors cooperatively regulate normal and neoplastic hepatocyte proliferation in mice. PMID:30087120
Consensus on Molecular Subtypes of High-Grade Serous Ovarian Carcinoma. PMID:30084834
Diagnosis of Kawasaki Disease Using a Minimal Whole-Blood Gene Expression Signature. PMID:30083721
Sensory Neuron Diversity in the Inner Ear Is Shaped by Activity. PMID:30078709
Improving knowledge on the activation of bone marrow fibroblasts in MGUS and MM disease through the automatic extraction of genes via a nonnegative matrix factorization approach on gene expression profiles. PMID:30075788
Douglas-Fir ( Pseudotsuga menziesii (Mirb.) Franco) Transcriptome Profile Changes Induced by Diesel Emissions Generated with CeO2 Nanoparticle Fuel Borne Catalyst. PMID:30075627
Combinatorial Approaches to Viral Attenuation. PMID:30073203
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
Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish (Danio rerio) progeny. PMID:30070994
Male increase in brain gene expression variability is linked to genetic risk for schizophrenia. PMID:30068996
PAK2-c-Myc-PKM2 axis plays an essential role in head and neck oncogenesis via regulating Warburg effect. PMID:30068946
Cardiovascular progenitor cells cultured aboard the International Space Station exhibit altered developmental and functional properties. PMID:30062101
Pattern of DNA Methylation in Daphnia: Evolutionary Perspective. PMID:30060190
The CRISPR/Cas system in Neisseria meningitidis affects bacterial adhesion to human nasopharyngeal epithelial cells. PMID:30059276
Mud2 functions in transcription by recruiting the Prp19 and TREX complexes to transcribed genes. PMID:30053068
A New Bioactive Compound From the Marine Sponge-Derived Streptomyces sp. SBT348 Inhibits Staphylococcal Growth and Biofilm Formation. PMID:30050506
Co-inhibition of mTORC1, HDAC and ESR1α retards the growth of triple-negative breast cancer and suppresses cancer stem cells. PMID:30050079
Requirements for Neurogenin2 during mouse postnatal retinal neurogenesis. PMID:30048641
Automatic extraction of gene-disease associations from literature using joint ensemble learning. PMID:30048465
Analysis of public RNA-sequencing data reveals biological consequences of genetic heterogeneity in cell line populations. PMID:30046134
Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks. PMID:30046115
Network Rewiring in Cancer: Applications to Melanoma Cell Lines and the Cancer Genome Atlas Patients. PMID:30042785
Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data. PMID:30041657
Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity. PMID:30039798
Construction of Discrete Model of Human Pluripotency in Predicting Lineage-Specific Outcomes and Targeted Knockdowns of Essential Genes. PMID:30038409
The Trithorax group protein dMLL3/4 instructs the assembly of the zygotic genome at fertilization. PMID:30037897
Investigation of epigenetic regulatory networks associated with autism spectrum disorder (ASD) by integrated global LINE-1 methylation and gene expression profiling analyses. PMID:30036398
Using Transcriptomes as Mutant Phenotypes Reveals Functional Regions of a Mediator Subunit in Caenorhabditis elegans. PMID:30030292
Dual RNA-Seq Analysis of Trichophyton rubrum and HaCat Keratinocyte Co-Culture Highlights Important Genes for Fungal-Host Interaction. PMID:30029541
The lincRNA MIRAT binds to IQGAP1 and modulates the MAPK pathway in NRAS mutant melanoma. PMID:30026510
Transcriptional Profiling of Immune-Related Genes in Leishmania infantum-Infected Mice: Identification of Potential Biomarkers of Infection and Progression of Disease. PMID:30013952
Altered Gene Expression in Prefrontal Cortex of a Fabry Disease Mouse Model. PMID:30013462
Dynamics of the Pollen Sequestrome Defined by Subcellular Coupled Omics. PMID:30007911
Integrated Analysis of Quantitative Proteome and Transcriptional Profiles Reveals the Dynamic Function of Maternally Expressed Proteins After Parthenogenetic Activation of Buffalo Oocyte. PMID:30002204
Gene expression profiles in neurological tissues during West Nile virus infection: a critical meta-analysis. PMID:30001706
Alternative empirical Bayes models for adjusting for batch effects in genomic studies. PMID:30001694
Transcriptional Alterations in the Trigeminal Ganglia, Nucleus and Peripheral Blood Mononuclear Cells in a Rat Orofacial Pain Model. PMID:29997476
The association of genomic lesions and PD-1/PD-L1 expression in resected triple-negative breast cancers. PMID:29996881
Novel dual regulators of Pseudomonas aeruginosa essential for productive biofilms and virulence. PMID:29995308
Translational Bioinformatics for Cholangiocarcinoma: Opportunities and Challenges. PMID:29989102
Expression of Adhesive Pili and the Collagen-Binding Adhesin Ace Is Activated by ArgR Family Transcription Factors in Enterococcus faecalis. PMID:29986940
MicroRNAs mediate the senescence-associated decline of NRF2 in endothelial cells. PMID:29986211
Germline DNA replication timing shapes mammalian genome composition. PMID:29986092
Predicting Risk of Postoperative Disease Recurrence in Crohn's Disease: Patients With Indolent Crohn's Disease Have Distinct Whole Transcriptome Profiles at the Time of First Surgery. PMID:29982468
Deletion of Nkx2-5 in trabecular myocardium reveals the developmental origins of pathological heterogeneity associated with ventricular non-compaction cardiomyopathy. PMID:29979676
Arsenic Reduces Gene Expression Response to Changing Salinity in Killifish. PMID:29979584
Dosage compensation and DNA methylation landscape of the X chromosome in mouse liver. PMID:29973619
Maternal obesity has sex-dependent effects on insulin, glucose and lipid metabolism and the liver transcriptome in young adult rat offspring. PMID:29972240
Pirfenidone decreases mesothelioma cell proliferation and migration via inhibition of ERK and AKT and regulates mesothelioma tumor microenvironment in vivo. PMID:29968778
Inhibition of integrin αVβ6 changes fibril thickness of stromal collagen in experimental carcinomas. PMID:29966518
Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species. PMID:29958539
Histology and Transcriptome Profiles of the Mammary Gland across Critical Windows of Development in Sprague Dawley Rats. PMID:29956080
Metabolic Effects of a Chronic Dietary Exposure to a Low-Dose Pesticide Cocktail in Mice: Sexual Dimorphism and Role of the Constitutive Androstane Receptor. PMID:29950287
LONGO: an R package for interactive gene length dependent analysis for neuronal identity. PMID:29950021
GSEA-InContext: identifying novel and common patterns in expression experiments. PMID:29950010
SigMat: a classification scheme for gene signature matching. PMID:29950002
Quantifying and Localizing the Mitochondrial Proteome Across Five Tissues in A Mouse Population. PMID:29945935
aaquetzalli is required for epithelial cell polarity and neural tissue formation in Drosophila. PMID:29942698
Stable STIM1 Knockdown in Self-Renewing Human Neural Precursors Promotes Premature Neural Differentiation. PMID:29942250
Temporal transcriptomic analysis of metabolic genes in maternal organs and placenta during murine pregnancy. PMID:29939228
Use of Haploid Model of Candida albicans to Uncover Mechanism of Action of a Novel Antifungal Agent. PMID:29938200
Regulatory RNA binding proteins contribute to the transcriptome-wide splicing alterations in human cellular senescence. PMID:29936497
Investigation of Islet2a function in zebrafish embryos: Mutants and morphants differ in morphologic phenotypes and gene expression. PMID:29927984
Co-Expression Network Analysis of AMPK and Autophagy Gene Products during Adipocyte Differentiation. PMID:29921805
Mammary molecular portraits reveal lineage-specific features and progenitor cell vulnerabilities. PMID:29921600
Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data. PMID:29917034
Presymptomatic change in microRNAs modulates Tau pathology. PMID:29915328
GeNets: a unified web platform for network-based genomic analyses. PMID:29915188
SAMHD1 modulates in vitro proliferation of acute myeloid leukemia-derived THP-1 cells through the PI3K-Akt-p27 axis. PMID:29911928
Damage-associated molecular pattern recognition is required for induction of retinal neuroprotective pathways in a sex-dependent manner. PMID:29904087
MicroRNA-30 modulates metabolic inflammation by regulating Notch signaling in adipose tissue macrophages. PMID:29899524
A data mining paradigm for identifying key factors in biological processes using gene expression data. PMID:29899432
Dietary Intake of Curcumin Improves eIF2 Signaling and Reduces Lipid Levels in the White Adipose Tissue of Obese Mice. PMID:29899429
Transcriptomic immune profiling of ovarian cancers in paraneoplastic cerebellar degeneration associated with anti-Yo antibodies. PMID:29899393
KLRD1-expressing natural killer cells predict influenza susceptibility. PMID:29898768
The Probiotic Escherichia coli Strain Nissle 1917 Combats Lambdoid Bacteriophages stx and λ. PMID:29896160
SSMART: sequence-structure motif identification for RNA-binding proteins. PMID:29893814
Transcriptome analysis highlights nuclear control of chloroplast development in the shoot apex. PMID:29892011
Lmo2 expression defines tumor cell identity during T-cell leukemogenesis. PMID:29880602
The Kinase Complex mTOR Complex 2 Promotes the Follicular Migration and Functional Maturation of Differentiated Follicular Helper CD4+ T Cells During Viral Infection. PMID:29875775
Group A Streptococcus M1T1 Intracellular Infection of Primary Tonsil Epithelial Cells Dampens Levels of Secreted IL-8 Through the Action of SpyCEP. PMID:29868516
Meta-Analysis of Maternal and Fetal Transcriptomic Data Elucidates the Role of Adaptive and Innate Immunity in Preterm Birth. PMID:29867970
SV-BR-1-GM, a Clinically Effective GM-CSF-Secreting Breast Cancer Cell Line, Expresses an Immune Signature and Directly Activates CD4+ T Lymphocytes. PMID:29867922
Strong correlation of downregulated genes related to synaptic transmission and mitochondria in post-mortem autism cerebral cortex. PMID:29859039
Targeted Transcriptional Profiling of Kidney Transplant Biopsies. PMID:29854981
Disease-Specific Integration of Omics Data to Guide Functional Validation of Genetic Associations. PMID:29854229
Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations. PMID:29854196
A big data pipeline: Identifying dynamic gene regulatory networks from time-course Gene Expression Omnibus data with applications to influenza infection. PMID:29846143
Identification of candidate biomarkers and pathways associated with SCLC by bioinformatics analysis. PMID:29845250
Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data. PMID:29843593
Social interaction-induced activation of RNA splicing in the amygdala of microbiome-deficient mice. PMID:29809134
Supplementation of fructooligosaccharides to suckling piglets affects intestinal microbiota colonization and immune development. PMID:29800418
Identification of genes involved in metabolism and signalling of abscisic acid and gibberellins during Epimedium pseudowushanense B.L.Guo seed morphophysiological dormancy. PMID:29796945
A 2-transcript host cell signature distinguishes viral from bacterial diarrhea and it is influenced by the severity of symptoms. PMID:29795312
BRG1 governs glucocorticoid receptor interactions with chromatin and pioneer factors across the genome. PMID:29792595
Combining NGN2 Programming with Developmental Patterning Generates Human Excitatory Neurons with NMDAR-Mediated Synaptic Transmission. PMID:29791859
Targetable vulnerabilities in T- and NK-cell lymphomas identified through preclinical models. PMID:29789628
CellAtlasSearch: a scalable search engine for single cells. PMID:29788498
Sphingosine-1-Phosphate Signaling and Metabolism Gene Signature in Pediatric Inflammatory Bowel Disease: A Matched-case Control Pilot Study. PMID:29788359
High-fructose diet during adolescent development increases neuroinflammation and depressive-like behavior without exacerbating outcomes after stroke. PMID:29787857
Reversal of siRNA-mediated gene silencing in vivo. PMID:29786096
Identification of brain metastasis genes and therapeutic evaluation of histone deacetylase inhibitors in a clinically relevant model of breast cancer brain metastasis. PMID:29784888
Biomarker microRNAs for prostate cancer metastasis: screened with a network vulnerability analysis model. PMID:29784056
Human plasma and serum extracellular small RNA reference profiles and their clinical utility. PMID:29777089
Targeting invadopodia-mediated breast cancer metastasis by using ABL kinase inhibitors. PMID:29774130
Methylation guide RNA evolution in archaea: structure, function and genomic organization of 110 C/D box sRNA families across six Pyrobaculum species. PMID:29771354
Maternal folate genes and aberrant DNA hypermethylation in pediatric acute lymphoblastic leukemia. PMID:29763473
Immunization Elicits Antigen-Specific Antibody Sequestration in Dorsal Root Ganglia Sensory Neurons. PMID:29755449
Decoding Common Features of Neurodegenerative Disorders: From Differentially Expressed Genes to Pathways. PMID:29755292
Multiclass classification for skin cancer profiling based on the integration of heterogeneous gene expression series. PMID:29750795
Identification of novel drug targets for diamond-blackfan anemia based on RPS19 gene mutation using protein-protein interaction network. PMID:29745857
Automated transition analysis of activated gene regulation during diauxic nutrient shift in Escherichia coli and adipocyte differentiation in mouse cells. PMID:29745848
An integrated view of the role of miR-130b/301b miRNA cluster in prostate cancer. PMID:29744254
UFD1 contributes to MYC-mediated leukemia aggressiveness through suppression of the proapoptotic unfolded protein response. PMID:29743725
Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia. PMID:29743478
Paternal developmental toxicant exposure is associated with epigenetic modulation of sperm and placental Pgr and Igf2 in a mouse model. PMID:29741588
MAPK Reliance via Acquired CDK4/6 Inhibitor Resistance in Cancer. PMID:29739788
Time-evolving genetic networks reveal a NAC troika that negatively regulates leaf senescence in Arabidopsis. PMID:29735710
Transcriptome profiling of the interconnection of pathways involved in malignant transformation and response to hypoxia. PMID:29731978
Human serum and platelet lysate are appropriate xeno-free alternatives for clinical-grade production of human MuStem cell batches. PMID:29720259
Identification and characterization of the Komagataella phaffii mating pheromone genes. PMID:29718186
Low-level laser irradiation induces a transcriptional myotube-like profile in C2C12 myoblasts. PMID:29717386
Structural and functional dissection of differentially expressed tomato WRKY transcripts in host defense response against the vascular wilt pathogen (Fusarium oxysporum f. sp. lycopersici). PMID:29709017
DANUBE: Data-driven meta-ANalysis using UnBiased Empirical distributions-applied to biological pathway analysis. PMID:29706661
New perspectives: systems medicine in cardiovascular disease. PMID:29699591
IncGraph: Incremental graphlet counting for topology optimisation. PMID:29698494
Epithelial-Mesenchymal Transition during Metastasis of HPV-Negative Pharyngeal Squamous Cell Carcinoma. PMID:29693014
CellExpress: a comprehensive microarray-based cancer cell line and clinical sample gene expression analysis online system. PMID:29688349
Community-driven roadmap for integrated disease maps. PMID:29688273
Genome-wide analyses of late pollen-preferred genes conserved in various rice cultivars and functional identification of a gene involved in the key processes of late pollen development. PMID:29687350
Integrated genome-wide Alu methylation and transcriptome profiling analyses reveal novel epigenetic regulatory networks associated with autism spectrum disorder. PMID:29686828
Domains within RbpA Serve Specific Functional Roles That Regulate the Expression of Distinct Mycobacterial Gene Subsets. PMID:29686140
The TLR4 Agonist Monophosphoryl Lipid A Drives Broad Resistance to Infection via Dynamic Reprogramming of Macrophage Metabolism. PMID:29686054
Mapping Interaction Sites on Human Chemokine Receptors by Deep Mutational Scanning. PMID:29678950
Specific breast cancer prognosis-subtype distinctions based on DNA methylation patterns. PMID:29675884
Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition. PMID:29674686
BBS9 gene in nonsyndromic craniosynostosis: Role of the primary cilium in the aberrant ossification of the suture osteogenic niche. PMID:29674126
ANLN functions as a key candidate gene in cervical cancer as determined by integrated bioinformatic analysis. PMID:29670400
Global H3.3 dynamic deposition defines its bimodal role in cell fate transition. PMID:29670118
ASB1 differential methylation in ischaemic cardiomyopathy: relationship with left ventricular performance in end-stage heart failure patients. PMID:29667349
Arsenic trioxide-mediated suppression of miR-182-5p is associated with potent anti-oxidant effects through up-regulation of SESN2. PMID:29662624
Activation of TRPV3 by Wood Smoke Particles and Roles in Pneumotoxicity. PMID:29658714
Sponge Long Non-Coding RNAs Are Expressed in Specific Cell Types and Conserved Networks. PMID:29657303
FAR2 is associated with kidney disease in mice and humans. PMID:29652635
Bioinformatic analysis reveals the key pathways and genes in early-onset breast cancer. PMID:29644522
Targeting Sphingosine Kinase Isoforms Effectively Reduces Growth and Survival of Neoplastic Mast Cells With D816V-KIT. PMID:29643855
A systematic and prospectively validated approach for identifying synergistic drug combinations against malaria. PMID:29642892
Condition-Specific Modeling of Biophysical Parameters Advances Inference of Regulatory Networks. PMID:29641998
A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors. PMID:29638227
Massive mining of publicly available RNA-seq data from human and mouse. PMID:29636450
Dietary and Endocrine Regulation of Endogenous Hydrogen Sulfide Production: Implications for Longevity. PMID:29634343
Topical application of aminoglycoside antibiotics enhances host resistance to viral infections in a microbiota-independent manner. PMID:29632368
Identification of Prognostic Biomarkers by Combined mRNA and miRNA Expression Microarray Analysis in Pancreatic Cancer. PMID:29631214
TRPM2 promotes the proliferation and invasion of pancreatic ductal adenocarcinoma. PMID:29620272
Identification of key genes in non‑alcoholic fatty liver disease progression based on bioinformatics analysis. PMID:29620197
Rudhira/BCAS3 is essential for mouse development and cardiovascular patterning. PMID:29618843
Differential expression of microRNAs and other small RNAs in muscle tissue of patients with ALS and healthy age-matched controls. PMID:29618798
Global dynamics of stage-specific transcription factor binding during thymocyte development. PMID:29618724
Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas. PMID:29617658
Radiation-Induced Gene Expression Changes in High and Low Grade Breast Cancer Cell Types. PMID:29617354
Expression of the microRNA-143/145 cluster is decreased in hepatitis B virus-associated hepatocellular carcinoma and may serve as a biomarker for tumorigenesis in patients with chronic hepatitis B. PMID:29616093
Adjusting for Batch Effects in DNA Methylation Microarray Data, a Lesson Learned. PMID:29616078
Pairwise gene GO-based measures for biclustering of high-dimensional expression data. PMID:29610579
Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In Vivo Binding. PMID:29605182
Identification of the key transcription factors in esophageal squamous cell carcinoma. PMID:29600044
Neurogenomic Profiling Reveals Distinct Gene Expression Profiles Between Brain Parts That Are Consistent in Ophthalmotilapia Cichlids. PMID:29593484
GDV1 induces sexual commitment of malaria parasites by antagonizing HP1-dependent gene silencing. PMID:29590075
Heuristic algorithms for feature selection under Bayesian models with block-diagonal covariance structure. PMID:29589558
Methylation-to-Expression Feature Models of Breast Cancer Accurately Predict Overall Survival, Distant-Recurrence Free Survival, and Pathologic Complete Response in Multiple Cohorts. PMID:29581450
Comprehensive analysis of Helicobacter pylori infection-associated diseases based on miRNA-mRNA interaction network. PMID:29579224
Burden-driven feedback control of gene expression. PMID:29578536
IRF8 Regulates Transcription of Naips for NLRC4 Inflammasome Activation. PMID:29576451
Induction of Genes Encoding Plant Cell Wall-Degrading Carbohydrate-Active Enzymes by Lignocellulose-Derived Monosaccharides and Cellobiose in the White-Rot Fungus Dichomitus squalens. PMID:29572208
Lysosomal acid lipase promotes cholesterol ester metabolism and drives clear cell renal cell carcinoma progression. PMID:29569766
Blocking hexose entry into glycolysis activates alternative metabolic conversion of these sugars and upregulates pentose metabolism in Aspergillus nidulans. PMID:29566661
No evidence for association of MTHFR 677C>T and 1298A>C variants with placental DNA methylation. PMID:29564022
A switch in transcription and cell fate governs the onset of an epigenetically-deregulated tumor in Drosophila. PMID:29560857
Bordetella pertussis pertactin knock-out strains reveal immunomodulatory properties of this virulence factor. PMID:29559630
New drug candidates for treatment of atypical meningiomas: An integrated approach using gene expression signatures for drug repurposing. PMID:29558515
Characterization of human dental pulp cells grown in chemically defined serum-free medium. PMID:29556382
Lowered dietary phosphorus affects intestinal and renal gene expression to maintain mineral homeostasis with immunomodulatory implications in weaned piglets. PMID:29554878
Could ALDH2*2 be the reason for low incidence and mortality of ovarian cancer for East Asia women? PMID:29552329
Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness. PMID:29549885
Allopregnanolone Alters the Gene Expression Profile of Human Glioblastoma Cells. PMID:29543748
A novel computational approach for drug repurposing using systems biology. PMID:29534151
A regulatory RNA is involved in RNA duplex formation and biofilm regulation in Sulfolobus acidocaldarius. PMID:29529252
p38-MK2 signaling axis regulates RNA metabolism after UV-light-induced DNA damage. PMID:29523821
EAF2 and p53 Co-Regulate STAT3 Activation in Prostate Cancer. PMID:29518696
TRAP-seq identifies cystine/glutamate antiporter as a driver of recovery from liver injury. PMID:29517978
Extracellular vesicle RNAs reflect placenta dysfunction and are a biomarker source for preterm labour. PMID:29516617
Genome-wide transcriptome analysis identifies alternative splicing regulatory network and key splicing factors in mouse and human psoriasis. PMID:29515135
Spatiotemporal compartmentalization of hepatic NADH and NADPH metabolism. PMID:29514978
The mRNA, miRNA and lncRNA networks in hepatocellular carcinoma: An integrative transcriptomic analysis from Gene Expression Omnibus. PMID:29512731
A standardized fold change method for microarray differential expression analysis used to reveal genes involved in acute rejection in murine allograft models. PMID:29511625
Protein interaction mapping interpretation of none alcoholic fatty liver disease model of rats after fat diet feeding. PMID:29511485
Association of miR-548c-5p, miR-7-5p, miR-210-3p, miR-128-3p with recurrence in systemically untreated breast cancer. PMID:29507672
Zc3h10 is a novel mitochondrial regulator. PMID:29507079
CRISPR RNA-Dependent Binding and Cleavage of Endogenous RNAs by the Campylobacter jejuni Cas9. PMID:29499139
Computational de novo discovery of distinguishing genes for biological processes and cell types in complex tissues. PMID:29494600
A minimal RNA ligand for potent RIG-I activation in living mice. PMID:29492454
Loss of Pax5 Exploits Sca1-BCR-ABLp190 Susceptibility to Confer the Metabolic Shift Essential for pB-ALL. PMID:29490943
Modulation of the peripheral blood transcriptome by the ingestion of probiotic yoghurt and acidified milk in healthy, young men. PMID:29489876
Functional Genomics and Phylogenetic Evidence Suggest Genus-Wide Cobalamin Production by the Globally Distributed Marine Nitrogen Fixer Trichodesmium. PMID:29487583
Evidence that DNA polymerase δ contributes to initiating leading strand DNA replication in Saccharomyces cerevisiae. PMID:29487291
Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses. PMID:29485625
Transcription factors Tp73, Cebpd, Pax6, and Spi1 rather than DNA methylation regulate chronic transcriptomics changes after experimental traumatic brain injury. PMID:29482641
Novel Dual-Action Targeted Nanomedicine in Mice With Metastatic Thyroid Cancer and Pancreatic Neuroendocrine Tumors. PMID:29481652
A novel joint analysis framework improves identification of differentially expressed genes in cross disease transcriptomic analysis. PMID:29467826
Distinguishing Human Peripheral Blood NK Cells from CD56dimCD16dimCD69+CD103+ Resident Nasal Mucosal Lavage Fluid Cells. PMID:29467466
Epigenome comparisons reveal linkage between gene expression and postnatal remodeling of chromatin domain topology. PMID:29466355
Boolean analysis identifies CD38 as a biomarker of aggressive localized prostate cancer. PMID:29464091
Longitudinal analysis strategies for modelling epigenetic trajectories. PMID:29462323
A hybrid gene selection approach to create the S1500+ targeted gene sets for use in high-throughput transcriptomics. PMID:29462216
Selection of GalNAc-conjugated siRNAs with limited off-target-driven rat hepatotoxicity. PMID:29459660
CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses. PMID:29458351
Mixed-species RNAseq analysis of human lymphoma cells adhering to mouse stromal cells identifies a core gene set that is also differentially expressed in the lymph node microenvironment of mantle cell lymphoma and chronic lymphocytic leukemia patients. PMID:29449436
Development of a primary human Small Intestine-on-a-Chip using biopsy-derived organoids. PMID:29440725
Small RNAs of Haloferax mediterranei: Identification and Potential Involvement in Nitrogen Metabolism. PMID:29439418
hMENA is a key regulator in endothelin-1/β-arrestin1-induced invadopodial function and metastatic process. PMID:29439204
IKKα is required in the intestinal epithelial cells for tumour stemness. PMID:29438366
Mutational Pleiotropy and the Strength of Stabilizing Selection Within and Between Functional Modules of Gene Expression. PMID:29437825
Combining laser-assisted microdissection (LAM) and RNA-seq allows to perform a comprehensive transcriptomic analysis of epidermal cells of Arabidopsis embryo. PMID:29434651
Up-regulation of hexokinase II contributes to rituximab-chemotherapy resistance and is a clinically relevant target for therapeutic development. PMID:29423101
Signatures of Altered Gene Expression in Dorsal Root Ganglia of a Fabry Disease Mouse Model. PMID:29422837
MELK expression correlates with tumor mitotic activity but is not required for cancer growth. PMID:29417930
Radiation-induced alternative transcripts as detected in total and polysome-bound mRNA. PMID:29416646
Transcriptome-wide survey of gene expression changes and alternative splicing in Trichophyton rubrum in response to undecanoic acid. PMID:29410524
PD-1 axis expression in musculoskeletal tumors and antitumor effect of nivolumab in osteosarcoma model of humanized mouse. PMID:29409495
Single-cell profiling of peanut-responsive T cells in patients with peanut allergy reveals heterogeneous effector TH2 subsets. PMID:29408715
Mitochondrial CoQ deficiency is a common driver of mitochondrial oxidants and insulin resistance. PMID:29402381
A practical solution for preserving single cells for RNA sequencing. PMID:29391536
Modified Cross-Linking, Ligation, and Sequencing of Hybrids (qCLASH) Identifies Kaposi's Sarcoma-Associated Herpesvirus MicroRNA Targets in Endothelial Cells. PMID:29386283
Germline contamination and leakage in whole genome somatic single nucleotide variant detection. PMID:29385983
Vital ex vivo tissue labeling and pathology-guided micropunching to characterize cellular heterogeneity in the tissue microenvironment. PMID:29384072
Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-β signaling and malignant features in vitro and in vivo. PMID:29383126
Transcriptional profiling of NCI/ADR-RES cells unveils a complex network of signaling pathways and molecular mechanisms of drug resistance. PMID:29379303
A Two-Stage Whole-Genome Gene Expression Association Study of Young-Onset Hypertension in Han Chinese Population of Taiwan. PMID:29379041
Additive Effects of Quorum Sensing Anti-Activators on Pseudomonas aeruginosa Virulence Traits and Transcriptome. PMID:29375519
Biofilm formation and transcriptome analysis of Streptococcus gallolyticus subsp. gallolyticus in response to lysozyme. PMID:29373594
Cell-surface marker discovery for lung cancer. PMID:29371917
The Biotrophic Development of Ustilago maydis Studied by RNA-Seq Analysis. PMID:29371439
Comparative analysis of mouse and human placentae across gestation reveals species-specific regulators of placental development. PMID:29361559
The Bioinformatic Analysis of the Dysregulated Genes and MicroRNAs in Entorhinal Cortex, Hippocampus, and Blood for Alzheimer's Disease. PMID:29359159
Gene annotation bias impedes biomedical research. PMID:29358745
The RNA-Binding Protein NONO Coordinates Hepatic Adaptation to Feeding. PMID:29358041
DataMed - an open source discovery index for finding biomedical datasets. PMID:29346583
The GPR120 agonist TUG-891 promotes metabolic health by stimulating mitochondrial respiration in brown fat. PMID:29343498
Identification of bladder cancer prognostic biomarkers using an ageing gene-related competitive endogenous RNA network. PMID:29340088
A novel messenger RNA signature as a prognostic biomarker for predicting relapse in pancreatic ductal adenocarcinoma. PMID:29340021
Application of Weighted Gene Co-expression Network Analysis for Data from Paired Design. PMID:29330528
Base-Resolution Analysis of DNA Methylation Patterns Downstream of Dnmt3a in Mouse Naïve B Cells. PMID:29326230
Omics Assisted N-terminal Proteoform and Protein Expression Profiling On Methionine Aminopeptidase 1 (MetAP1) Deletion. PMID:29317475
Toxoplasma gondii Infection Is Associated with Mitochondrial Dysfunction in-Vitro. PMID:29312892
Integrated Analysis of Gene Expression Differences in Twins Discordant for Disease and Binary Phenotypes. PMID:29311748
Transcriptomic Analysis Reveals Novel Mechanisms Mediating Islet Dysfunction in the Intrauterine Growth-Restricted Rat. PMID:29309562
Boolean network modeling in systems pharmacology. PMID:29307099
POU6f1 Mediates Neuropeptide-Dependent Plasticity in the Adult Brain. PMID:29305536
A novel prospective isolation of murine fetal liver progenitors to study in utero hematopoietic defects. PMID:29300724
ASXL1 and BIM germ line variants predict response and identify CML patients with the greatest risk of imatinib failure. PMID:29296778
Clonal evolution underlying leukemia progression and Richter transformation in patients with ibrutinib-relapsed CLL. PMID:29296715
Identification and validation long non-coding RNAs of oral squamous cell carcinoma by bioinformatics method. PMID:29296179
Impact of Consuming Extra-Virgin Olive Oil or Nuts within a Mediterranean Diet on DNA Methylation in Peripheral White Blood Cells within the PREDIMED-Navarra Randomized Controlled Trial: A Role for Dietary Lipids. PMID:29295516
Mutations in the DNA methylation pathway and number of driver mutations predict response to azacitidine in myelodysplastic syndromes. PMID:29291002
Identification and Functional Validation of a Biomarker for the Diagnosis of Miltefosine Relapse during Visceral Leishmaniasis. PMID:29280431
Cancer transcriptome profiling at the juncture of clinical translation. PMID:29279605
Indian Hedgehog Suppresses a Stromal Cell-Driven Intestinal Immune Response. PMID:29276753
PITX1 promotes chondrogenesis and myogenesis in mouse hindlimbs through conserved regulatory targets. PMID:29273440
Transcriptional Response to Lactic Acid Stress in the Hybrid Yeast Zygosaccharomyces parabailii. PMID:29269498
Super-delta: a new differential gene expression analysis procedure with robust data normalization. PMID:29268715
Circular RNA expression is abundant and correlated to aggressiveness in early-stage bladder cancer. PMID:29263845
Mining the transcriptome for rare disease therapies: a comparison of the efficiencies of two data mining approaches and a targeted cell-based drug screen. PMID:29263829
Characterization of epithelial-mesenchymal transition intermediate/hybrid phenotypes associated to resistance to EGFR inhibitors in non-small cell lung cancer cell lines. PMID:29262566
Clearance of a persistent picornavirus infection is associated with enhanced pro-apoptotic and cellular immune responses. PMID:29259271
Bioinformatics analysis of differentially expressed gene profiles associated with systemic lupus erythematosus. PMID:29257335
High expression of FLT3 is a risk factor in leukemia. PMID:29257272
Loss of Intercalated Cells (ITCs) in the Mouse Amygdala of Tshz1 Mutants Correlates with Fear, Depression, and Social Interaction Phenotypes. PMID:29255003
FZD4 Marks Lateral Plate Mesoderm and Signals with NORRIN to Increase Cardiomyocyte Induction from Pluripotent Stem Cell-Derived Cardiac Progenitors. PMID:29249665
Potential Diagnostic Power of Blood Circular RNA Expression in Active Pulmonary Tuberculosis. PMID:29248507
Peritoneal tissue-resident macrophages are metabolically poised to engage microbes using tissue-niche fuels. PMID:29234000
Ensemble Modeling Approach Targeting Heterogeneous RNA-Seq data: Application to Melanoma Pseudogenes. PMID:29229974
Noncanonical thyroid hormone signaling mediates cardiometabolic effects in vivo. PMID:29229863
SUV420H2 is an epigenetic regulator of epithelial/mesenchymal states in pancreatic cancer. PMID:29229751
Global gene expression in two potato cultivars in response to 'Candidatus Liberibacter solanacearum' infection. PMID:29228896
In-Cardiome: integrated knowledgebase for coronary artery disease enabling translational research. PMID:29220465
SFMetaDB: a comprehensive annotation of mouse RNA splicing factor RNA-Seq datasets. PMID:29220461
Annotating gene sets by mining large literature collections with protein networks. PMID:29218918
Advances in Text Mining and Visualization for Precision Medicine. PMID:29218914
Treatment with a DNA methyltransferase inhibitor feminizes zebrafish and induces long-term expression changes in the gonads. PMID:29216900
Systematic integrative analysis of gene expression identifies HNF4A as the central gene in pathogenesis of non-alcoholic steatohepatitis. PMID:29216278
Profiling invasive Plasmodium falciparum merozoites using an integrated omics approach. PMID:29215067
Platelet-rich plasma inhibits RANKL-induced osteoclast differentiation through activation of Wnt pathway during bone remodeling. PMID:29207140
Slam protein dictates subcellular localization and translation of its own mRNA. PMID:29206227
Cross-Laboratory Analysis of Brain Cell Type Transcriptomes with Applications to Interpretation of Bulk Tissue Data. PMID:29204516
Mediator Complex Subunits MED2, MED5, MED16, and MED23 Genetically Interact in the Regulation of Phenylpropanoid Biosynthesis. PMID:29203634
Lymph Node Metastases in Colon Cancer Are Polyclonal. PMID:29203589
Mitochondrial fission is associated with UCP1 activity in human brite/beige adipocytes. PMID:29198749
Protection of macrophages from intracellular pathogens by miR-182-5p mimic-a gene expression meta-analysis approach. PMID:29197182
A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles. PMID:29195078
Transcription Factor-Mediated Control of Anthocyanin Biosynthesis in Vegetative Tissues. PMID:29192027
Genetic variation at the microRNA binding site of CAV1 gene is associated with lung cancer susceptibility. PMID:29190968
The IDO inhibitor 1-methyl tryptophan activates the aryl hydrocarbon receptor response in mesenchymal stromal cells. PMID:29190885
Conditional Loss of Hoxa5 Function Early after Birth Impacts on Expression of Genes with Synaptic Function. PMID:29187810
Integrative Bioinformatic Analysis of Transcriptomic Data Identifies Conserved Molecular Pathways Underlying Ionizing Radiation-Induced Bystander Effects (RIBE). PMID:29186820
Translational bioinformatics in mental health: open access data sources and computational biomarker discovery. PMID:29186302
RNA sequencing reveals candidate genes and polymorphisms related to sperm DNA integrity in testis tissue from boars. PMID:29183316
Selection of internal references for qRT-PCR assays of human hepatocellular carcinoma cell lines. PMID:29180379
Nutrient-Colimited Trichodesmium as a Nitrogen Source or Sink in a Future Ocean. PMID:29180365
ENCoRE: an efficient software for CRISPR screens identifies new players in extrinsic apoptosis. PMID:29178829
A COUP-TFII Human Embryonic Stem Cell Reporter Line to Identify and Select Atrial Cardiomyocytes. PMID:29173897
The histone code reader Spin1 controls skeletal muscle development. PMID:29168801
Novel structural features drive DNA binding properties of Cmr, a CRP family protein in TB complex mycobacteria. PMID:29165665
Inhibition of HOX/PBX dimer formation leads to necroptosis in acute myeloid leukemia cells. PMID:29163771
NRF2 regulates endothelial glycolysis and proliferation with miR-93 and mediates the effects of oxidized phospholipids on endothelial activation. PMID:29161413
Regulation of Sucrose Transporters and Phloem Loading in Response to Environmental Cues. PMID:29158330
Multiplex Proximity Ligation Assay to Identify Potential Prognostic Biomarkers for Improved Survival in Locally Advanced Pancreatic Cancer Patients Treated With Stereotactic Body Radiation Therapy. PMID:29157747
Identification of potential tissue-specific cancer biomarkers and development of cancer versus normal genomic classifiers. PMID:29156751
Comprehensive functional enrichment analysis of male infertility. PMID:29150651
Changes in chromatin state reveal ARNT2 at a node of a tumorigenic transcription factor signature driving glioblastoma cell aggressiveness. PMID:29149419
A transcriptomic insight into the impacts of mast cells in lung, breast, and colon cancers. PMID:29147625
Hypomethylation of HOXA4 promoter is common in Silver-Russell syndrome and growth restriction and associates with stature in healthy children. PMID:29146936
Global analysis of gene expression mediated by OX1 orexin receptor signaling in a hypothalamic cell line. PMID:29145494
Innate Cell-Mediated Cytotoxic Activity of European Sea Bass Leucocytes Against Nodavirus-Infected Cells: A Functional and RNA-seq Study. PMID:29133947
A Novel Mechanism of Inactivating Antibacterial Nitro Compounds in the Human Pathogen Staphylococcus aureus by Overexpression of a NADH-Dependent Flavin Nitroreductase. PMID:29133557
Spatial Control of Gene Expression by miR319-Regulated TCP Transcription Factors in Leaf Development. PMID:29133375
Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data. PMID:29130882
Isl1 mediates mesenchymal expansion in the developing external genitalia via regulation of Bmp4, Fgf10 and Wnt5a. PMID:29126155
Missing data and technical variability in single-cell RNA-sequencing experiments. PMID:29121214
ADAM9 promotes lung cancer progression through vascular remodeling by VEGFA, ANGPT2, and PLAT. PMID:29118335
Stress hormones promote EGFR inhibitor resistance in NSCLC: Implications for combinations with β-blockers. PMID:29118262
General response of Salmonella enterica serovar Typhimurium to desiccation: A new role for the virulence factors sopD and sseD in survival. PMID:29117268
Crosstalk between Receptor and Non-receptor Mediated Chemical Modes of Action in Rat Livers Converges through a Dysregulated Gene Expression Network at Tumor Suppressor Tp53. PMID:29114260
Restricted Presence of POU6F2 in Human Corneal Endothelial Cells Uncovered by Extension of the Promoter-level Expression Atlas. PMID:29113774
In vivo functional analysis of L-rhamnose metabolic pathway in Aspergillus niger: a tool to identify the potential inducer of RhaR. PMID:29110642
Deep Learning Accurately Predicts Estrogen Receptor Status in Breast Cancer Metabolomics Data. PMID:29110491
Transcriptional responses of wheat and the cereal cyst nematode Heterodera avenae during their early contact stage. PMID:29101332
Cellular, ultrastructural and molecular analyses of epidermal cell development in the planarian Schmidtea mediterranea. PMID:29100657
Gene expression information improves reliability of receptor status in breast cancer patients. PMID:29100391
Autoimmunity and autoinflammation: A systems view on signaling pathway dysregulation profiles. PMID:29099860
A molecular roadmap of the AGM region reveals BMPER as a novel regulator of HSC maturation. PMID:29093060
GPR68, a proton-sensing GPCR, mediates interaction of cancer-associated fibroblasts and cancer cells. PMID:29092903
Post-weaning epiphysiolysis causes distal femur dysplasia and foreshortened hindlimbs in fetuin-A-deficient mice. PMID:29088242
The conserved RNA helicase YTHDC2 regulates the transition from proliferation to differentiation in the germline. PMID:29087293
APC downregulated 1 inhibits breast cancer cell invasion by inhibiting the canonical WNT signaling pathway. PMID:29085490
Immune Repertoire after Immunization As Seen by Next-Generation Sequencing and Proteomics. PMID:29085363
Glycosylation-related gene expression in HT29-MTX-E12 cells upon infection by Helicobacter pylori. PMID:29085225
In-silico gene essentiality analysis of polyamine biosynthesis reveals APRT as a potential target in cancer. PMID:29084986
Integrated Proteomic and Transcriptomic Analysis Reveals Long Noncoding RNA HOX Transcript Antisense Intergenic RNA (HOTAIR) Promotes Hepatocellular Carcinoma Cell Proliferation by Regulating Opioid Growth Factor Receptor (OGFr). PMID:29079719
Comparative genomics of geographically distant Fusarium fujikuroi isolates revealed two distinct pathotypes correlating with secondary metabolite profiles. PMID:29073267
Cross-tissue integration of genetic and epigenetic data offers insight into autism spectrum disorder. PMID:29066808
Gene isoforms as expression-based biomarkers predictive of drug response in vitro. PMID:29066719
Ubiquitin-Specific Protease USP6 Regulates the Stability of the c-Jun Protein. PMID:29061731
The SIN3A histone deacetylase complex is required for a complete transcriptional response to hypoxia. PMID:29059365
PpNAC1, a main regulator of phenylalanine biosynthesis and utilization in maritime pine. PMID:29055073
Genome-wide prediction of DNase I hypersensitivity using gene expression. PMID:29051481
A molecular atlas of the developing ectoderm defines neural, neural crest, placode, and nonneural progenitor identity in vertebrates. PMID:29049289
miR-3656 expression enhances the chemosensitivity of pancreatic cancer to gemcitabine through modulation of the RHOF/EMT axis. PMID:29048402
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
Roles of Female and Male Genotype in Post-Mating Responses in Drosophila melanogaster. PMID:29036644
ScanGEO: parallel mining of high-throughput gene expression data. PMID:29036513
Smooth quantile normalization. PMID:29036413
Hedgehog-mesenchyme gene signature identifies bi-modal prognosis in luminal and basal breast cancer sub-types. PMID:29034935
Designing Dietary Recommendations Using System Level Interactomics Analysis and Network-Based Inference. PMID:29033850
Single-cell RNA sequencing reveals developmental heterogeneity among early lymphoid progenitors. PMID:29030486
RBPJ/CBF1 interacts with L3MBTL3/MBT1 to promote repression of Notch signaling via histone demethylase KDM1A/LSD1. PMID:29030483
Human CD8+ EMRA T cells display a senescence-associated secretory phenotype regulated by p38 MAPK. PMID:29024417
Differential gene expression in disease: a comparison between high-throughput studies and the literature. PMID:29020950
Genomic Programming of Human Neonatal Dendritic Cells in Congenital Systemic and In Vitro Cytomegalovirus Infection Reveal Plastic and Robust Immune Pathway Biology Responses. PMID:28993767
Effect of diabetes status and hyperglycemia on global DNA methylation and hydroxymethylation. PMID:28993426
SCENIC: single-cell regulatory network inference and clustering. PMID:28991892
Architectural alterations of the fission yeast genome during the cell cycle. PMID:28991264
Investigating the microRNA-mRNA regulatory network in acute myeloid leukemia. PMID:28989535
Identifying HIPK1 as Target of miR-22-3p Enhancing Recombinant Protein Production From HEK 293 Cell by Using Microarray and HTP siRNA Screen. PMID:28987030
Impact of sequencing depth and read length on single cell RNA sequencing data of T cells. PMID:28986563
RNA sequencing identifies novel non-coding RNA and exon-specific effects associated with cigarette smoking. PMID:28985737
A link prediction approach to cancer drug sensitivity prediction. PMID:28984192
Usefulness of Transcriptional Blood Biomarkers as a Non-invasive Surrogate Marker of Mucosal Healing and Endoscopic Response in Ulcerative Colitis. PMID:28981629
IMOTA: an interactive multi-omics tissue atlas for the analysis of human miRNA-target interactions. PMID:28977416
Targeting the alternative sigma factor RpoN to combat virulence in Pseudomonas aeruginosa. PMID:28974743
Meta-analysis of transcriptomic datasets identifies genes enriched in the mammalian circadian pacemaker. PMID:28973476
Epigenetic regulation of gene expression in cancer: techniques, resources and analysis. PMID:28968850
A framework for estimating and testing qualitative interactions with applications to predictive biomarkers. PMID:28968765
Identification of candidate genes associated with triple negative breast cancer. PMID:28966727
Transcriptomic responses of the endangered freshwater mussel Margaritifera margaritifera to trace metal contamination in the Dronne River, France. PMID:28963680
Statistically controlled identification of differentially expressed genes in one-to-one cell line comparisons of the CMAP database for drug repositioning. PMID:28962576
Inference and interrogation of a coregulatory network in the context of lipid accumulation in Yarrowia lipolytica. PMID:28955503
Stable Gene Regulatory Network Modeling From Steady-State Data. PMID:28952574
Filamentation Involves Two Overlapping, but Distinct, Programs of Filamentation in the Pathogenic Fungus Candida albicans. PMID:28951491
Pathway and network-based analysis of genome-wide association studies and RT-PCR validation in polycystic ovary syndrome. PMID:28949383
Peroxisome proliferator-activated receptor gamma (PPARγ) regulates lactase expression and activity in the gut. PMID:28947679
Priming and Activation of Inflammasome by Canarypox Virus Vector ALVAC via the cGAS/IFI16-STING-Type I IFN Pathway and AIM2 Sensor. PMID:28947539
Integrated metabolic models for xenobiotic induced mitochondrial toxicity in skeletal muscle. PMID:28942197
Computational Approaches to Identify Genetic Interactions for Cancer Therapeutics. PMID:28941356
Differential expression and co-expression gene networks reveal candidate biomarkers of boar taint in non-castrated pigs. PMID:28939879
The Transcriptome of Estrogen-Independent Mammary Growth in Female Mice Reveals That Not All Mammary Glands Are Created Equally. PMID:28938404
Systematic integration of biomedical knowledge prioritizes drugs for repurposing. PMID:28936969
Light and Plastid Signals Regulate Different Sets of Genes in the Albino Mutant Pap7-1. PMID:28935841
A comprehensive, cell specific microRNA catalogue of human peripheral blood. PMID:28934507
Intercalated disc in failing hearts from patients with dilated cardiomyopathy: Its role in the depressed left ventricular function. PMID:28934278
Comparative transcriptomics of female and male gametocytes in Plasmodium berghei and the evolution of sex in alveolates. PMID:28923023
Complete Circular Genome Sequence and Temperature Independent Adaptation to Anaerobiosis of Listeria weihenstephanensis DSM 24698. PMID:28919887
An HDAC3-PROX1 corepressor module acts on HNF4α to control hepatic triglycerides. PMID:28916805
Data exploration, quality control and statistical analysis of ChIP-exo/nexus experiments. PMID:28911122
Screening and identification of key biomarkers in hepatocellular carcinoma: Evidence from bioinformatic analysis. PMID:28901457
Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation. PMID:28899353
Determining the optimal number of independent components for reproducible transcriptomic data analysis. PMID:28893186
Mining the Volatilomes of Plant-Associated Microbiota for New Biocontrol Solutions. PMID:28890716
MicroRNA Profiling Reveals Distinct Profiles for Tissue-Derived and Cultured Endothelial Cells. PMID:28887500
Integrated expression profiles analysis reveals novel predictive biomarker in pancreatic ductal adenocarcinoma. PMID:28881752
An in-silico approach to predict and exploit synthetic lethality in cancer metabolism. PMID:28878380
FunctionAnnotator, a versatile and efficient web tool for non-model organism annotation. PMID:28874813
HT-SuperSAGE of the gut tissue of a Vip3Aa-resistant Heliothis virescens (Lepidoptera: Noctuidae) strain provides insights into the basis of resistance. PMID:28872766
A Protocol for Using Gene Set Enrichment Analysis to Identify the Appropriate Animal Model for Translational Research. PMID:28872130
Molecular Analyses Reveal Inflammatory Mediators in the Solid Component and Cyst Fluid of Human Adamantinomatous Craniopharyngioma. PMID:28859336
Retinol saturase coordinates liver metabolism by regulating ChREBP activity. PMID:28855500
Ribosome signatures aid bacterial translation initiation site identification. PMID:28854918
Study on molecular mechanism of ANOS1 promoting development of colorectal cancer. PMID:28854193
Novel evidence for complement system activation in chick myopia and hyperopia models: a meta-analysis of transcriptome datasets. PMID:28852117
Genome-wide expression and response to exposure-based psychological therapy for anxiety disorders. PMID:28850109
Mycobacterium bovis Bacillus Calmette-Guérin Alters Melanoma Microenvironment Favoring Antitumor T Cell Responses and Improving M2 Macrophage Function. PMID:28848560
Expression and Regulatory Network Analysis of miR-140-3p, a New Potential Serum Biomarker for Autism Spectrum Disorder. PMID:28848387
An improved analysis methodology for translational profiling by microarray. PMID:28842509
Heterogeneous Tumor-Immune Microenvironments among Differentially Growing Metastases in an Ovarian Cancer Patient. PMID:28841418
Microbial regulation of microRNA expression in the amygdala and prefrontal cortex. PMID:28838324
Treating the placenta to prevent adverse effects of gestational hypoxia on fetal brain development. PMID:28831049
Measuring mRNA Levels Over Time During the Yeast S. cerevisiae Hypoxic Response. PMID:28829420
DELLA genes restrict inflorescence meristem function independently of plant height. PMID:28827519
A novel SH2 recognition mechanism recruits Spt6 to the doubly phosphorylated RNA polymerase II linker at sites of transcription. PMID:28826505
Ribonucleotide Reductases from Bifidobacteria Contain Multiple Conserved Indels Distinguishing Them from All Other Organisms: In Silico Analysis of the Possible Role of a 43 aa Bifidobacteria-Specific Insert in the Class III RNR Homolog. PMID:28824557
Molecular bases for differential aging programs between flag and second leaves during grain-filling in rice. PMID:28821707
Sources to variability in circulating human miRNA signatures. PMID:28820329
Whole-transcriptome microarray analysis reveals regulation of Rab4 by RBM5 in neurons. PMID:28818525
Analysis of the small non-protein-coding RNA profile of mouse spermatozoa reveals specific enrichment of piRNAs within mature spermatozoa. PMID:28816603
Therapeutic Antibodies to Ganglioside GD2 Evolved from Highly Selective Germline Antibodies. PMID:28813678
Totipotency segregates between the sister blastomeres of two-cell stage mouse embryos. PMID:28811525
Pro- and anti-inflammatory responses of peripheral blood mononuclear cells induced by Staphylococcus aureus and Pseudomonas aeruginosa phages. PMID:28808331
Critical role for arginase 2 in obesity-associated pancreatic cancer. PMID:28808255
DNA Microarray Analysis of Estrogen Responsive Genes in Ishikawa Cells by Glabridin. PMID:28804245
Identification and characterization of a long non-coding RNA up-regulated during HIV-1 infection. PMID:28803142
Transcriptional Analysis of an Ammonium-Excreting Strain of Azotobacter vinelandii Deregulated for Nitrogen Fixation. PMID:28802272
Comprehensive miRNA expression profiling in human T-cell acute lymphoblastic leukemia by small RNA-sequencing. PMID:28801656
EGFR Mutations Compromise Hypoxia-Associated Radiation Resistance through Impaired Replication Fork-Associated DNA Damage Repair. PMID:28801308
The nucleoid protein Dps binds genomic DNA of Escherichia coli in a non-random manner. PMID:28800583
Analytical Strategy to Prioritize Alzheimer's Disease Candidate Genes in Gene Regulatory Networks Using Public Expression Data. PMID:28800327
MicroRNA-132 promotes fibroblast migration via regulating RAS p21 protein activator 1 in skin wound healing. PMID:28798331
Identification and characterization of a new source of adult human neural progenitors. PMID:28796246
Host plant driven transcriptome plasticity in the salivary glands of the cabbage looper (Trichoplusia ni). PMID:28792546
Ventromorphins: A New Class of Small Molecule Activators of the Canonical BMP Signaling Pathway. PMID:28787124
Bioinformatics resources for deciphering the biogenesis and action pathways of plant small RNAs. PMID:28786034
Early involvement of cellular stress and inflammatory signals in the pathogenesis of tubulointerstitial kidney disease due to UMOD mutations. PMID:28785050
Cutting Edge: IL-2-Induced Expression of the Amino Acid Transporters SLC1A5 and CD98 Is a Prerequisite for NKG2D-Mediated Activation of Human NK Cells. PMID:28784848
Developmental disruption of amygdala transcriptome and socioemotional behavior in rats exposed to valproic acid prenatally. PMID:28775827
Transcriptome and Metabolite Changes during Hydrogen Cyanamide-Induced Floral Bud Break in Sweet Cherry. PMID:28769948
Identification of key genes and pathways in Parkinson's disease through integrated analysis. PMID:28765971
Heme and nitric oxide binding by the transcriptional regulator DnrF from the marine bacterium Dinoroseobacter shibae increases napD promoter affinity. PMID:28765283
The metabolic regulator mTORC1 controls terminal myeloid differentiation. PMID:28763796
Integrated diagnostic network construction reveals a 4-gene panel and 5 cancer hallmarks driving breast cancer heterogeneity. PMID:28754978
The Drosophila Duox maturation factor is a key component of a positive feedback loop that sustains regeneration signaling. PMID:28753614
Quantifying Gene Regulatory Relationships with Association Measures: A Comparative Study. PMID:28751908
miR-130b directly targets ARHGAP1 to drive activation of a metastatic CDC42-PAK1-AP1 positive feedback loop in Ewing sarcoma. PMID:28748534
Dissecting the contributions of time and microbe density to variation in immune gene expression. PMID:28747473
Arginase1 Deficiency in Monocytes/Macrophages Upregulates Inducible Nitric Oxide Synthase To Promote Cutaneous Contact Hypersensitivity. PMID:28747341
Whole blood microRNA expression may not be useful for screening non-small cell lung cancer. PMID:28742859
The STAT4/MLL1 Epigenetic Axis Regulates the Antimicrobial Functions of Murine Macrophages. PMID:28733487
ERK/MAPK Signaling Is Required for Pathway-Specific Striatal Motor Functions. PMID:28733355
Chloroplast Redox Status Modulates Genome-Wide Plant Responses during the Non-host Interaction of Tobacco with the Hemibiotrophic Bacterium Xanthomonas campestris pv. vesicatoria. PMID:28725231
Gene expression reversal toward pre-adult levels in the aging human brain and age-related loss of cellular identity. PMID:28724976
Predicting susceptibility to tuberculosis based on gene expression profiling in dendritic cells. PMID:28720766
CLIC, a tool for expanding biological pathways based on co-expression across thousands of datasets. PMID:28719601
Loss of DIP2C in RKO cells stimulates changes in DNA methylation and epithelial-mesenchymal transition. PMID:28716088
Microarray analysis reveals key genes and pathways in Tetralogy of Fallot. PMID:28713939
Identification of Conserved and Novel MicroRNAs in Blueberry. PMID:28713413
Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks. PMID:28711280
The CINSARC signature as a prognostic marker for clinical outcome in multiple neoplasms. PMID:28710396
Biological analysis of cancer specific microRNAs on function modeling in osteosarcoma. PMID:28710380
Profiling Ssb-Nascent Chain Interactions Reveals Principles of Hsp70-Assisted Folding. PMID:28708998
Rv3723/LucA coordinates fatty acid and cholesterol uptake in Mycobacterium tuberculosis. PMID:28708968
Lower Expression of SLC27A1 Enhances Intramuscular Fat Deposition in Chicken via Down-Regulated Fatty Acid Oxidation Mediated by CPT1A. PMID:28706492
Sexual dimorphisms of mRNA and miRNA in human/murine heart disease. PMID:28704447
GT-rich promoters can drive RNA pol II transcription and deposition of H2A.Z in African trypanosomes. PMID:28701485
Deletion of Gas2l3 in mice leads to specific defects in cardiomyocyte cytokinesis during development. PMID:28698371
6S RNA in Rhodobacter sphaeroides: 6S RNA and pRNA transcript levels peak in late exponential phase and gene deletion causes a high salt stress phenotype. PMID:28692405
Reorganization of gene network for degradation of polycyclic aromatic hydrocarbons (PAHs) in Pseudomonas aeruginosa PAO1 under several conditions. PMID:28685384
Genome-wide mapping and analysis of aryl hydrocarbon receptor (AHR)- and aryl hydrocarbon receptor repressor (AHRR)-binding sites in human breast cancer cells. PMID:28681081
A Novel Unsupervised Algorithm for Biological Process-based Analysis on Cancer. PMID:28680165
Connected Gene Communities Underlie Transcriptional Changes in Cornelia de Lange Syndrome. PMID:28679547
The methyltransferase SETDB1 regulates a large neuron-specific topological chromatin domain. PMID:28671686
CausalR: extracting mechanistic sense from genome scale data. PMID:28666369
dRNA-seq transcriptional profiling of the FK506 biosynthetic gene cluster in Streptomyces tsukubaensis NRRL18488 and general analysis of the transcriptome. PMID:28665778
KDM2B, an H3K36-specific demethylase, regulates apoptotic response of GBM cells to TRAIL. PMID:28661478
Functional Dissection of the Pol V Largest Subunit CTD in RNA-Directed DNA Methylation. PMID:28658626
Identification of Jak-STAT signaling involvement in sarcoidosis severity via a novel microRNA-regulated peripheral blood mononuclear cell gene signature. PMID:28652588
Deciphering the role of the signal- and Sty1 kinase-dependent phosphorylation of the stress-responsive transcription factor Atf1 on gene activation. PMID:28652406
Protein homeostasis of a metastable subproteome associated with Alzheimer's disease. PMID:28652376
Identifying global expression patterns and key regulators in epithelial to mesenchymal transition through multi-study integration. PMID:28651527
Multivalent binding of PWWP2A to H2A.Z regulates mitosis and neural crest differentiation. PMID:28645917
A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency. PMID:28625162
Safe and Efficient Silencing with a Pol II, but Not a Pol lII, Promoter Expressing an Artificial miRNA Targeting Human Huntingtin. PMID:28624208
TGF-beta/atRA-induced Tregs express a selected set of microRNAs involved in the repression of transcripts related to Th17 differentiation. PMID:28620241
Insights from Global Analyses of Long Noncoding RNAs in Breast Cancer. PMID:28616363
Tricellulin is regulated via interleukin-13-receptor α2, affects macromolecule uptake, and is decreased in ulcerative colitis. PMID:28612843
Involvement of Chromatin Remodeling Genes and the Rho GTPases RhoB and CDC42 in Ovarian Clear Cell Carcinoma. PMID:28611940
Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes. PMID:28609292
PHF6 regulates phenotypic plasticity through chromatin organization within lineage-specific genes. PMID:28607179
Neighbours of cancer-related proteins have key influence on pathogenesis and could increase the drug target space for anticancer therapies. PMID:28603644
Hepatic expression profiles in retroviral infection: relevance to drug hypersensitivity risk. PMID:28603631
Uniform neural tissue models produced on synthetic hydrogels using standard culture techniques. PMID:28599598
High-dose maternal folic acid supplementation before conception impairs reversal learning in offspring mice. PMID:28596566
Genetic Dissection of Nutrition-Induced Plasticity in Insulin/Insulin-Like Growth Factor Signaling and Median Life Span in a Drosophila Multiparent Population. PMID:28592498
High-resolution promoter map of human limbal epithelial cells cultured with keratinocyte growth factor and rho kinase inhibitor. PMID:28588247
NaviSE: superenhancer navigator integrating epigenomics signal algebra. PMID:28587674
Identification of the miRNA-target gene regulatory network in intracranial aneurysm based on microarray expression data. PMID:28587396
PA3225 Is a Transcriptional Repressor of Antibiotic Resistance Mechanisms in Pseudomonas aeruginosa. PMID:28584154
Newborn sex-specific transcriptome signatures and gestational exposure to fine particles: findings from the ENVIRONAGE birth cohort. PMID:28583124
Major hnRNP proteins act as general TDP-43 functional modifiers both in Drosophila and human neuronal cells. PMID:28575377
Gene Expression (mRNA) Markers for Differentiating between Malignant and Benign Follicular Thyroid Tumours. PMID:28574441
MicroRNA profiling in the dentate gyrus in epileptic rats: The role of miR-187-3p. PMID:28562528
Cooperation between a hierarchical set of recruitment sites targets the X chromosome for dosage compensation. PMID:28562241
Systems-based approach to examine the cytokine responses in primary mouse lung macrophages infected with low pathogenic avian Influenza virus circulating in South East Asia. PMID:28558796
Crops In Silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform. PMID:28555150
Non-coding RNAs in the Ovarian Follicle. PMID:28553318
p16 Loss and E2F/cell cycle deregulation in infant posterior fossa ependymoma. PMID:28548702
Transcriptomics technologies. PMID:28545146
eIF1 modulates the recognition of suboptimal translation initiation sites and steers gene expression via uORFs. PMID:28541577
Identifying CpG sites with different differential methylation frequencies in colorectal cancer tissues based on individualized differential methylation analysis. PMID:28537885
RNA-dependent chromatin association of transcription elongation factors and Pol II CTD kinases. PMID:28537551
Induction of resident memory T cells enhances the efficacy of cancer vaccine. PMID:28537262
Genetic variants in the transcription regulatory region of MEGF10 are associated with autism in Chinese Han population. PMID:28536440
Deregulated expression of miR-29a-3p, miR-494-3p and miR-660-5p affects sensitivity to tyrosine kinase inhibitors in CML leukemic stem cells. PMID:28533480
Abnormal expression of ATP1A1 and ATP1A2 in breast cancer. PMID:28529692
Drosophila melanogaster positive transcriptional elongation factors regulate metabolic and sex-biased expression in adults. PMID:28521739
Candidate miRNAs and pathogenesis investigation for hepatocellular carcinoma based on bioinformatics analysis. PMID:28521446
Essential Function of the Serine Hydroxymethyl Transferase (SHMT) Gene During Rapid Syncytial Cell Cycles in Drosophila. PMID:28515048
An RpoHI-Dependent Response Promotes Outgrowth after Extended Stationary Phase in the Alphaproteobacterium Rhodobacter sphaeroides. PMID:28507242
Toxic Electrophiles Induce Expression of the Multidrug Efflux Pump MexEF-OprN in Pseudomonas aeruginosa through a Novel Transcriptional Regulator, CmrA. PMID:28507116
Ranking metrics in gene set enrichment analysis: do they matter? PMID:28499413
Differences in Flower Transcriptome between Grapevine Clones Are Related to Their Cluster Compactness, Fruitfulness, and Berry Size. PMID:28496449
RNA Polymerase III Subunit POLR3G Regulates Specific Subsets of PolyA+ and SmallRNA Transcriptomes and Splicing in Human Pluripotent Stem Cells. PMID:28494942
Relationship between regulatory pattern of gene expression level and gene function. PMID:28494005
In vivo and in vitro ageing results in accumulation of de novo copy number variations in bulls. PMID:28487564
Study of Meta-analysis strategies for network inference using information-theoretic approaches. PMID:28484519
Integration of Immune Cell Populations, mRNA-Seq, and CpG Methylation to Better Predict Humoral Immunity to Influenza Vaccination: Dependence of mRNA-Seq/CpG Methylation on Immune Cell Populations. PMID:28484452
Intermittent glucocorticoid steroid dosing enhances muscle repair without eliciting muscle atrophy. PMID:28481224
Anti-complement component 5 antibody targeting MG4 domain inhibits choroidal neovascularization. PMID:28477014
FnrL and Three Dnr Regulators Are Used for the Metabolic Adaptation to Low Oxygen Tension in Dinoroseobacter shibae. PMID:28473807
High-Throughput Screening Data Interpretation in the Context of In Vivo Transcriptomic Responses to Oral Cr(VI) Exposure. PMID:28472532
Annotating function to differentially expressed LincRNAs in myelodysplastic syndrome using a network-based method. PMID:28472271
EnHERV: Enrichment analysis of specific human endogenous retrovirus patterns and their neighboring genes. PMID:28472109
CTCF and cohesin regulate chromatin loop stability with distinct dynamics. PMID:28467304
Heat shock and prolonged heat stress attenuate neurotoxin and sporulation gene expression in group I Clostridium botulinum strain ATCC 3502. PMID:28464023
Analysis of the in planta transcriptome expressed by the corn pathogen Pantoea stewartii subsp. stewartii via RNA-Seq. PMID:28462040
Expression profile of mitochondrial voltage-dependent anion channel-1 (VDAC1) influenced genes is associated with pulmonary hypertension. PMID:28461778
Gene expression patterns in the progression of canine copper-associated chronic hepatitis. PMID:28459846
DUX-family transcription factors regulate zygotic genome activation in placental mammals. PMID:28459456
Conservation and innovation in the DUX4-family gene network. PMID:28459454
Responses to Hypoxia and Endoplasmic Reticulum Stress Discriminate the Development of Vitreous and Floury Endosperms of Conventional Maize (Zea mays) Inbred Lines. PMID:28450877
Progressive changes in non-coding RNA profile in leucocytes with age. PMID:28448962
Transcriptional response of Escherichia coli to ammonia and glucose fluctuations. PMID:28447391
Differential host gene responses from infection with neurovirulent and partially-neurovirulent strains of Venezuelan equine encephalitis virus. PMID:28446152
Toxicogenomic module associations with pathogenesis: a network-based approach to understanding drug toxicity. PMID:28440344
Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans. PMID:28438122
Mutant uromodulin expression leads to altered homeostasis of the endoplasmic reticulum and activates the unfolded protein response. PMID:28437467
Identification of NTRK3 Fusions in Childhood Melanocytic Neoplasms. PMID:28433076
Cross-disorder comparative analysis of comorbid conditions reveals novel autism candidate genes. PMID:28427329
Expression of the Maize Dof1 Transcription Factor in Wheat and Sorghum. PMID:28424717
Responses of the Housefly, Musca domestica, to the Hytrosavirus Replication: Impacts on Host's Vitellogenesis and Immunity. PMID:28424677
Deciphering the Regulatory Network between the SREBP Pathway and Protein Secretion in Neurospora crassa. PMID:28420736
Genetic sequence-based prediction of long-range chromatin interactions suggests a potential role of short tandem repeat sequences in genome organization. PMID:28420341
The pathway intermediate 2-keto-3-deoxy-L-galactonate mediates the induction of genes involved in D-galacturonic acid utilization in Aspergillus niger. PMID:28417461
High expression of miR-125b-2 and SNORD116 noncoding RNA clusters characterize ERG-related B cell precursor acute lymphoblastic leukemia. PMID:28415578
Transcriptional networks are associated with resistance to Mycobacterium tuberculosis infection. PMID:28414762
goSTAG: gene ontology subtrees to tag and annotate genes within a set. PMID:28413437
Differential gene expression and transport functionality in the bundle sheath versus mesophyll - a potential role in leaf mineral homeostasis. PMID:28407076
Longitudinal peripheral blood transcriptional analysis of a patient with severe Ebola virus disease. PMID:28404864
MiRNA profiling of gastrointestinal stromal tumors by next-generation sequencing. PMID:28402935
Nonsense-mediated mRNA decay in Tetrahymena is EJC independent and requires a protozoa-specific nuclease. PMID:28402567
Identification of RUNX1 as a Mediator of Aberrant Retinal Angiogenesis. PMID:28400392
Landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity. PMID:28395144
The integrative omics of white-rot fungus Pycnoporus coccineus reveals co-regulated CAZymes for orchestrated lignocellulose breakdown. PMID:28394946
Profiling transcriptomes of human SH-SY5Y neuroblastoma cells exposed to maleic acid. PMID:28392987
Exploring the differences in metabolic behavior of astrocyte and glioblastoma: a flux balance analysis approach. PMID:28392849
Melanoma-Derived iPCCs Show Differential Tumorigenicity and Therapy Response. PMID:28392221
Coordination of Meristem Doming and the Floral Transition by Late Termination, a Kelch Repeat Protein. PMID:28389586
Recognition memory-induced gene expression in the perirhinal cortex: A transcriptomic analysis. PMID:28389337
Global analysis of gene expression reveals mRNA superinduction is required for the inducible immune response to a bacterial pathogen. PMID:28383283
Co-expression of AFAP1-AS1 and PD-1 predicts poor prognosis in nasopharyngeal carcinoma. PMID:28380458
Elucidation of the calcineurin-Crz1 stress response transcriptional network in the human fungal pathogen Cryptococcus neoformans. PMID:28376087
Comparison of tissue/disease specific integrated networks using directed graphlet signatures. PMID:28361704
Novel therapeutic effects of sesamin on diabetes-induced cardiac dysfunction. PMID:28358428
Computational Analysis of Specific MicroRNA Biomarkers for Noninvasive Early Cancer Detection. PMID:28357401
Time resolved DNA occupancy dynamics during the respiratory oscillation uncover a global reset point in the yeast growth program. PMID:28357254
Transcription factor Etv5 is essential for the maintenance of alveolar type II cells. PMID:28351980
Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism. PMID:28351387
Modification of the Streptococcus mutans transcriptome by LrgAB and environmental stressors. PMID:28348880
Estimating genome-wide regulatory activity from multi-omics data sets using mathematical optimization. PMID:28347313
WT1 expression in breast cancer disrupts the epithelial/mesenchymal balance of tumour cells and correlates with the metabolic response to docetaxel. PMID:28345629
A Genome-wide Analysis of Human Pluripotent Stem Cell-Derived Endothelial Cells in 2D or 3D Culture. PMID:28343999
Small chromosomal regions position themselves autonomously according to their chromatin class. PMID:28341771
Cross disease analysis of co-functional microRNA pairs on a reconstructed network of disease-gene-microRNA tripartite. PMID:28340554
In silico search for modifier genes associated with pancreatic and liver disease in Cystic Fibrosis. PMID:28339466
Analysis of hepatic transcript profile and plasma lipid profile in early lactating dairy cows fed grape seed and grape marc meal extract. PMID:28335726
The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq. PMID:28334889
The Wilms tumor protein Wt1 contributes to female fertility by regulating oviductal proteostasis. PMID:28334862
H3.Y discriminates between HIRA and DAXX chaperone complexes and reveals unexpected insights into human DAXX-H3.3-H4 binding and deposition requirements. PMID:28334823
FUNNEL-GSEA: FUNctioNal ELastic-net regression in time-course gene set enrichment analysis. PMID:28334094
Simultaneous analysis of miRNA-mRNA in human meningiomas by integrating transcriptome: A relationship between PTX3 and miR-29c. PMID:28327132
Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana. PMID:28320402
Perturbation of microbiota in one-day old broiler chickens with antibiotic for 24 hours negatively affects intestinal immune development. PMID:28320307
Identification of dysregulated genes in rheumatoid arthritis based on bioinformatics analysis. PMID:28316886
Identification and characterization of a missense mutation in the O-linked β-N-acetylglucosamine (O-GlcNAc) transferase gene that segregates with X-linked intellectual disability. PMID:28302723
Sex differences in the molecular signature of the developing mouse hippocampus. PMID:28302071
sRNA154 a newly identified regulator of nitrogen fixation in Methanosarcina mazei strain Gö1. PMID:28296572
An Exploration of Charge Compensating Ion Channels across the Phagocytic Vacuole of Neutrophils. PMID:28293191
A comparative analytical assay of gene regulatory networks inferred using microarray and RNA-seq datasets. PMID:28293077
Light Modulates Metabolic Pathways and Other Novel Physiological Traits in the Human Pathogen Acinetobacter baumannii. PMID:28289081
Hepatic Transcriptome Profiles of Mice with Diet-Induced Nonalcoholic Steatohepatitis Treated with Astaxanthin and Vitamin E. PMID:28282876
Specific and Novel microRNAs Are Regulated as Response to Fungal Infection in Human Dendritic Cells. PMID:28280489
The within-host dynamics of infection in trans-generationally primed flour beetles. PMID:28277618
miR-193a-3p interaction with HMGB1 downregulates human endothelial cell proliferation and migration. PMID:28276476
De novo computational identification of stress-related sequence motifs and microRNA target sites in untranslated regions of a plant translatome. PMID:28276452
SVMRFE based approach for prediction of most discriminatory gene target for type II diabetes. PMID:28275550
Identifying Novel Transcriptional and Epigenetic Features of Nuclear Lamina-associated Genes. PMID:28273906
Coordination of auxin-triggered leaf initiation by tomato LEAFLESS. PMID:28270611
DCYTB is a predictor of outcome in breast cancer that functions via iron-independent mechanisms. PMID:28270217
Rapid Sampling of Escherichia coli After Changing Oxygen Conditions Reveals Transcriptional Dynamics. PMID:28264512
Transcriptional Reprogramming at Genome-Scale of Lactobacillus plantarum WCFS1 in Response to Olive Oil Challenge. PMID:28261192
Gene expression profiling in bladder cancer identifies potential therapeutic targets. PMID:28259975
Prostate apoptosis response 4 (PAR4) expression modulates WNT signaling pathways in MCF7 breast cancer cells: A possible mechanism underlying PAR4-mediated docetaxel chemosensitivity. PMID:28259909
Two-way learning with one-way supervision for gene expression data. PMID:28257645
Integrated systems biology analysis of KSHV latent infection reveals viral induction and reliance on peroxisome mediated lipid metabolism. PMID:28257516
Neuroblastoma cells depend on HDAC11 for mitotic cell cycle progression and survival. PMID:28252645
Altered regulation and expression of genes by BET family of proteins in COPD patients. PMID:28248992
ZEB1 regulates glioma stemness through LIF repression. PMID:28246407
Cellulose-Derived Oligomers Act as Damage-Associated Molecular Patterns and Trigger Defense-Like Responses. PMID:28242654
Characterization of bovine embryos cultured under conditions appropriate for sustaining human naïve pluripotency. PMID:28241084
Essentiality of mmpL3 and impact of its silencing on Mycobacterium tuberculosis gene expression. PMID:28240248
Asymmetric interactions between doublesex and tissue- and sex-specific target genes mediate sexual dimorphism in beetles. PMID:28239147
Proteome and Secretome Analysis Reveals Differential Post-transcriptional Regulation of Toll-like Receptor Responses. PMID:28235783
MicroRNA-independent functions of DGCR8 are essential for neocortical development and TBR1 expression. PMID:28232627
Autocrine Loop Involving IL-6 Family Member LIF, LIF Receptor, and STAT4 Drives Sustained Fibroblast Production of Inflammatory Mediators. PMID:28228280
Cross-talk between the glucocorticoid receptor and MyoD family inhibitor domain-containing protein provides a new mechanism for generating tissue-specific responses to glucocorticoids. PMID:28223352
Astrocytic Calcium Waves Signal Brain Injury to Neural Stem and Progenitor Cells. PMID:28216142
Elf5 is a principal cell lineage specific transcription factor in the kidney that contributes to Aqp2 and Avpr2 gene expression. PMID:28215940
Two-stage genome-wide association study identifies a novel susceptibility locus associated with melanoma. PMID:28212542
The Legionella pneumophila genome evolved to accommodate multiple regulatory mechanisms controlled by the CsrA-system. PMID:28212376
Short-Chain Chitin Oligomers: Promoters of Plant Growth. PMID:28212295
High-resolution profiling of NMD targets in yeast reveals translational fidelity as a basis for substrate selection. PMID:28209632
Making life difficult for Clostridium difficile: augmenting the pathogen's metabolic model with transcriptomic and codon usage data for better therapeutic target characterization. PMID:28209199
Aurora A regulates expression of AR-V7 in models of castrate resistant prostate cancer. PMID:28205582
Pistil Transcriptome Analysis to Disclose Genes and Gene Products Related to Aposporous Apomixis in Hypericum perforatum L. PMID:28203244
Using global gene expression to discriminate thin melanomas with poor outcomes. PMID:28197532
Biocomplexity and Fractality in the Search of Biomarkers of Aging and Pathology: Focus on Mitochondrial DNA and Alzheimer's Disease. PMID:28197358
Transcription Profiling of Bacillus subtilis Cells Infected with AR9, a Giant Phage Encoding Two Multisubunit RNA Polymerases. PMID:28196958
Analysis of miRNA, mRNA, and TF interactions through network-based methods. PMID:28194173
Simultaneous identification of robust synergistic subnetwork markers for effective cancer prognosis. PMID:28194169
Transcriptional Mechanisms of Resistance to Anti-PD-1 Therapy. PMID:28193624
A novel point mutation in RpoB improves osmotolerance and succinic acid production in Escherichia coli. PMID:28193207
A novel RNA sequencing data analysis method for cell line authentication. PMID:28192450
Upregulation of FAM84B during prostate cancer progression. PMID:28186973
An empirically driven data reduction method on the human 450K methylation array to remove tissue specific non-variable CpGs. PMID:28184257
Transcriptomic Profiling of Egg Quality in Sea Bass (Dicentrarchus labrax) Sheds Light on Genes Involved in Ubiquitination and Translation. PMID:28181038
Individualized analysis reveals CpG sites with methylation aberrations in almost all lung adenocarcinoma tissues. PMID:28178989
Mouse Dux is myotoxic and shares partial functional homology with its human paralog DUX4. PMID:28173143
Unique genetic responses revealed in RNA-seq of the spleen of chickens stimulated with lipopolysaccharide and short-term heat. PMID:28166270
TGF-β1 along with other platelet contents augments Treg cells to suppress anti-FVIII immune responses in hemophilia A mice. PMID:28164173
Loss of CD44dim Expression from Early Progenitor Cells Marks T-Cell Lineage Commitment in the Human Thymus. PMID:28163708
Physiological Responses and Gene Co-Expression Network of Mycorrhizal Roots under K+ Deprivation. PMID:28159827
Genome-Wide Transcriptional Start Site Mapping and sRNA Identification in the Pathogen Leptospira interrogans. PMID:28154810
A scalable algorithm for structure identification of complex gene regulatory network from temporal expression data. PMID:28143596
Unsupervised detection of regulatory gene expression information in different genomic regions enables gene expression ranking. PMID:28143396
Transcriptional Profiling in Experimental Visceral Leishmaniasis Reveals a Broad Splenic Inflammatory Environment that Conditions Macrophages toward a Disease-Promoting Phenotype. PMID:28141856
Impact of Neutron Exposure on Global Gene Expression in a Human Peripheral Blood Model. PMID:28140791
Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization. PMID:28133571
Vitiligo blood transcriptomics provides new insights into disease mechanisms and identifies potential novel therapeutic targets. PMID:28129744
A Systematic Framework for Drug Repositioning from Integrated Omics and Drug Phenotype Profiles Using Pathway-Drug Network. PMID:28127549
Regulation of myeloid cells by activated T cells determines the efficacy of PD-1 blockade. PMID:28123870
A systematic comparative evaluation of biclustering techniques. PMID:28114903
Transcriptome profiling of gene expression during immunisation trial against Fasciola hepatica: identification of genes and pathways involved in conferring immunoprotection in a murine model. PMID:28114888
RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets. PMID:28108657
A Common Variant of IL-6R is Associated with Elevated IL-6 Pathway Activity in Alzheimer's Disease Brains. PMID:28106546
Characterization and in vivo regulon determination of an ECF sigma factor and its cognate anti-sigma factor in Nostoc punctiforme. PMID:28105698
Splenic CD4+ T Cells in Progressive Visceral Leishmaniasis Show a Mixed Effector-Regulatory Phenotype and Impair Macrophage Effector Function through Inhibitory Receptor Expression. PMID:28103263
Role of miR-34a-5p in Hematopoietic Progenitor Cells Proliferation and Fate Decision: Novel Insights into the Pathogenesis of Primary Myelofibrosis. PMID:28098757
MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration. PMID:28095799
iGC-an integrated analysis package of gene expression and copy number alteration. PMID:28088185
MicroRNA based Pan-Cancer Diagnosis and Treatment Recommendation. PMID:28086747
RYK promotes the stemness of glioblastoma cells via the WNT/ β-catenin pathway. PMID:28086236
Testicular Dysgenesis Syndrome and Long-Lasting Epigenetic Silencing of Mouse Sperm Genes Involved in the Reproductive System after Prenatal Exposure to DEHP. PMID:28085963
Sequential Targeting of CD52 and TNF Allows Early Minimization Therapy in Kidney Transplantation: From a Biomarker to Targeting in a Proof-Of-Concept Trial. PMID:28085915
Vps33b is crucial for structural and functional hepatocyte polarity. PMID:28082148
Establishment of a integrative multi-omics expression database CKDdb in the context of chronic kidney disease (CKD). PMID:28079125
From the Cover: Embryonic Exposure to TCDD Impacts Osteogenesis of the Axial Skeleton in Japanese medaka, Oryzias latipes. PMID:28077779
Muscle developmental defects in heterogeneous nuclear Ribonucleoprotein A1 knockout mice. PMID:28077597
Computational Prediction of the Global Functional Genomic Landscape: Applications, Methods, and Challenges. PMID:28076869
Pax-5 is a potent regulator of E-cadherin and breast cancer malignant processes. PMID:28076843
Targeting BET proteins improves the therapeutic efficacy of BCL-2 inhibition in T-cell acute lymphoblastic leukemia. PMID:28074072
Expression of CD14, IL10, and Tolerogenic Signature in Dendritic Cells Inversely Correlate with Clinical and Immunologic Response to TARP Vaccination in Prostate Cancer Patients. PMID:28073842
Breast Cancer Malignant Processes are Regulated by Pax-5 Through the Disruption of FAK Signaling Pathways. PMID:28070224
Mutant U2AF1-expressing cells are sensitive to pharmacological modulation of the spliceosome. PMID:28067246
DNA methylation assessment from human slow- and fast-twitch skeletal muscle fibers. PMID:28057818
Identification of Biomarkers for Breast Cancer Using Databases. PMID:28053957
Myoblast replication is reduced in the IUGR fetus despite maintained proliferative capacity in vitro. PMID:28053000
Linking Hematopoietic Differentiation to Co-Expressed Sets of Pluripotency-Associated and Imprinted Genes and to Regulatory microRNA-Transcription Factor Motifs. PMID:28052084
Batch effects and the effective design of single-cell gene expression studies. PMID:28045081
Novel Biomarker MicroRNAs for Subtyping of Acute Coronary Syndrome: A Bioinformatics Approach. PMID:28044128
Comparative "Omics" of the Fusarium fujikuroi Species Complex Highlights Differences in Genetic Potential and Metabolite Synthesis. PMID:28040774
Quantitative assessment of the diagnostic role of FHIT promoter methylation in non-small cell lung cancer. PMID:28036263
Neuroblastoma, a Paradigm for Big Data Science in Pediatric Oncology. PMID:28035989
Activating transcription factor 3 is crucial for antitumor activity and to strengthen the antiviral properties of Onconase. PMID:28035074
PML-RARA-associated cooperating mutations belong to a transcriptional network that is deregulated in myeloid leukemias. PMID:28025581
Alternative splicing in tomato pollen in response to heat stress. PMID:28025318
Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping. PMID:28024297
Function of AP2/ERF Transcription Factors Involved in the Regulation of Specialized Metabolism in Ophiorrhiza pumila Revealed by Transcriptomics and Metabolomics. PMID:28018397
Changing POU dimerization preferences converts Oct6 into a pluripotency inducer. PMID:28007765
Knowledge-Guided Bioinformatics Model for Identifying Autism Spectrum Disorder Diagnostic MicroRNA Biomarkers. PMID:28000768
Identification of Polycystic Ovary Syndrome (PCOS) Specific Genes in Cumulus and Mural Granulosa Cells. PMID:27997581
Aberrant methylation of CDH13 can be a diagnostic biomarker for lung adenocarcinoma. PMID:27994665
Inducible super-enhancers are organized based on canonical signal-specific transcription factor binding elements. PMID:27994038
Circulating cell-free DNA-based epigenetic assay can detect early breast cancer. PMID:27993161
Exposure of Bacterial Biofilms to Electrical Current Leads to Cell Death Mediated in Part by Reactive Oxygen Species. PMID:27992529
PAX2 function, regulation and targeting in fallopian tube-derived high-grade serous ovarian cancer. PMID:27991925
Gene Expression Correlated with Severe Asthma Characteristics Reveals Heterogeneous Mechanisms of Severe Disease. PMID:27984699
Sepsis Diagnostics: From Discovery to Application. PMID:27984279
Evaluating side effects of nanoparticle-mediated siRNA delivery to mesenchymal stem cells using next generation sequencing and enrichment analysis. PMID:27981244
"Gap hunting" to characterize clustered probe signals in Illumina methylation array data. PMID:27980682
Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes. PMID:27965291
Prior knowledge guided eQTL mapping for identifying candidate genes. PMID:27964730
Synergistic drug combinations from electronic health records and gene expression. PMID:27940607
Stromal hedgehog signaling maintains smooth muscle and hampers micro-invasive prostate cancer. PMID:27935821
Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation. PMID:27933038
Expression of Cav1.3 calcium channel in the human and mouse colon: posttranscriptional inhibition by IFNγ. PMID:27932504
miR-17∼92 family clusters control iNKT cell ontogenesis via modulation of TGF-β signaling. PMID:27930306
Cellular and molecular characterization of a stem rust resistance locus on wheat chromosome 7AL. PMID:27927228
Transcriptional Network Architecture of Breast Cancer Molecular Subtypes. PMID:27920729
Advax, a Delta Inulin Microparticle, Potentiates In-built Adjuvant Property of Co-administered Vaccines. PMID:27919753
TRPM2 SNP genotype previously associated with susceptibility to Rhodococcus equi pneumonia in Quarter Horse foals displays differential gene expression identified using RNA-Seq. PMID:27919223
Human Intervention Study to Assess the Effects of Supplementation with Olive Leaf Extract on Peripheral Blood Mononuclear Cell Gene Expression. PMID:27918443
Cyanobacteria as Chassis for Industrial Biotechnology: Progress and Prospects. PMID:27916886
Complex genetics architecture contributes to Salmonella resistance in AcB60 mice. PMID:27913859
Chromatin landscapes and genetic risk in systemic lupus. PMID:27906046
Identification of biomarker microRNAs for predicting the response of colorectal cancer to neoadjuvant chemoradiotherapy based on microRNA regulatory network. PMID:27903980
Transcriptomics of Environmental Enrichment Reveals a Role for Retinoic Acid Signaling in Addiction. PMID:27899881
MEF2 transcription factors are key regulators of sprouting angiogenesis. PMID:27898394
EMPOWERING MULTI-COHORT GENE EXPRESSION ANALYSIS TO INCREASE REPRODUCIBILITY. PMID:27896970
Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes. PMID:27895109
Identification of genes and signaling pathways associated with diabetic neuropathy using a weighted correlation network analysis: A consort study. PMID:27893688
Whole-Cell Cancer Vaccines Induce Large Antibody Responses to Carbohydrates and Glycoproteins. PMID:27889407
Time-Course Analysis of Gene Expression During the Saccharomyces cerevisiae Hypoxic Response. PMID:27883312
The microRNA toolkit of insects. PMID:27883064
Three distinct cell populations express extracellular matrix proteins and increase in number during skeletal muscle fibrosis. PMID:27881411
Forward Genetic Screens in Zebrafish Identify Pre-mRNA-Processing Pathways Regulating Early T Cell Development. PMID:27880902
High-specificity bioinformatics framework for epigenomic profiling of discordant twins reveals specific and shared markers for ACPA and ACPA-positive rheumatoid arthritis. PMID:27876072
Myeloid-Specific Gene Deletion of Protein Phosphatase 2A Magnifies MyD88- and TRIF-Dependent Inflammation following Endotoxin Challenge. PMID:27872207
Conservation of immune gene signatures in solid tumors and prognostic implications. PMID:27871313
Dietary Intake Influences Adult Fertility and Offspring Fitness in Zebrafish. PMID:27870856
The histone demethylase KDM4B regulates peritoneal seeding of ovarian cancer. PMID:27869162
Reprogramming mouse fibroblasts into engraftable myeloerythroid and lymphoid progenitors. PMID:27869129
Global transcriptome responses including small RNAs during mixed-species interactions with methicillin-resistant Staphylococcus aureus and Pseudomonas aeruginosa. PMID:27868360
Genome-wide DNA methylation analysis identifies MEGF10 as a novel epigenetically repressed candidate tumor suppressor gene in neuroblastoma. PMID:27862318
Transcriptomic responses in the oral cavity of F344 rats and B6C3F1 mice following exposure to Cr(VI): Implications for risk assessment. PMID:27859739
Identification of an Efficient Gene Expression Panel for Glioblastoma Classification. PMID:27855170
In silico Pathway Activation Network Decomposition Analysis (iPANDA) as a method for biomarker development. PMID:27848968
A meta-analysis of public microarray data identifies gene regulatory pathways deregulated in peripheral blood mononuclear cells from individuals with Systemic Lupus Erythematosus compared to those without. PMID:27846842
GEN3VA: aggregation and analysis of gene expression signatures from related studies. PMID:27846806
Proliferation rates and gene expression profiles in human lymphoblastoid cell lines from patients with depression characterized in response to antidepressant drug therapy. PMID:27845776
Discriminating cancer-related and cancer-unrelated chemoradiation-response genes for locally advanced rectal cancers. PMID:27845363
Integrative analysis of genetic data sets reveals a shared innate immune component in autism spectrum disorder and its co-morbidities. PMID:27842596
VRS2 regulates hormone-mediated inflorescence patterning in barley. PMID:27841879
Transcriptome profiling of NIH3T3 cell lines expressing opsin and the P23H opsin mutant identifies candidate drugs for the treatment of retinitis pigmentosa. PMID:27838510
OTX015 (MK-8628), a novel BET inhibitor, exhibits antitumor activity in non-small cell and small cell lung cancer models harboring different oncogenic mutations. PMID:27835869
NUAK1 (ARK5) Is Associated with Poor Prognosis in Ovarian Cancer. PMID:27833898
Arnica montana Stimulates Extracellular Matrix Gene Expression in a Macrophage Cell Line Differentiated to Wound-Healing Phenotype. PMID:27832158
Potential molecular characteristics in situ in response to repetitive UVB irradiation. PMID:27829444
Different tissue phagocytes sample apoptotic cells to direct distinct homeostasis programs. PMID:27828940
Pubertal and adult windows of susceptibility to a high animal fat diet in Trp53-null mammary tumorigenesis. PMID:27825136
Ankyrin-3 as a molecular marker of early-life stress and vulnerability to psychiatric disorders. PMID:27824361
Discovery and replication of a peripheral tissue DNA methylation biosignature to augment a suicide prediction model. PMID:27822318
Group B Streptococcus circumvents neutrophils and neutrophil extracellular traps during amniotic cavity invasion and preterm labor. PMID:27819066
Gene expression profiles and protein-protein interaction networks in amyotrophic lateral sclerosis patients with C9orf72 mutation. PMID:27814735
Integrative analysis for identification of shared markers from various functional cells/tissues for rheumatoid arthritis. PMID:27812736
Comparative Gene Expression Profiling of Primary and Metastatic Renal Cell Carcinoma Stem Cell-Like Cancer Cells. PMID:27812180
Changes in mammary histology and transcriptome profiles by low-dose exposure to environmental phenols at critical windows of development. PMID:27810681
A map of mobile DNA insertions in the NCI-60 human cancer cell panel. PMID:27807467
Transcriptional Analysis of serk1 and serk3 Coreceptor Mutants. PMID:27803191
The Conserved Dcw Gene Cluster of R. sphaeroides Is Preceded by an Uncommonly Extended 5' Leader Featuring the sRNA UpsM. PMID:27802301
Identifying reproducible cancer-associated highly expressed genes with important functional significances using multiple datasets. PMID:27796338
Hepatic transcriptome implications for palm fruit juice deterrence of type 2 diabetes mellitus in young male Nile rats. PMID:27795741
CPI-17 drives oncogenic Ras signaling in human melanomas via Ezrin-Radixin-Moesin family proteins. PMID:27793041
Single cell lineage tracing reveals a role for TgfβR2 in intestinal stem cell dynamics and differentiation. PMID:27791005
Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse. PMID:27789702
Exploring the intrinsic differences among breast tumor subtypes defined using immunohistochemistry markers based on the decision tree. PMID:27786176
A statistical approach for identifying differential distributions in single-cell RNA-seq experiments. PMID:27782827
CLIP-GENE: a web service of the condition specific context-laid integrative analysis for gene prioritization in mouse TF knockout experiments. PMID:27776539
Computational Analysis of G-Quadruplex Forming Sequences across Chromosomes Reveals High Density Patterns Near the Terminal Ends. PMID:27776185
Gene expression analysis reveals important pathways for drought response in leaves and roots of a wheat cultivar adapted to rainfed cropping in the Cerrado biome. PMID:27768155
Upregulation of HLA Expression in Primary Uveal Melanoma by Infiltrating Leukocytes. PMID:27764126
The Transcriptome of Rhabdomyosarcoma Cells Infected with Cytolytic and Non-Cytolytic Variants of Coxsackievirus B2 Ohio-1. PMID:27760161
Deficiency of base excision repair enzyme NEIL3 drives increased predisposition to autoimmunity. PMID:27760045
Characterization of Transient Receptor Potential Vanilloid-1 (TRPV1) Variant Activation by Coal Fly Ash Particles and Associations with Altered Transient Receptor Potential Ankyrin-1 (TRPA1) Expression and Asthma. PMID:27758864
Methylome analysis for spina bifida shows SOX18 hypomethylation as a risk factor with evidence for a complex (epi)genetic interplay to affect neural tube development. PMID:27757173
RhoA controls retinoid signaling by ROCK dependent regulation of retinol metabolism. PMID:27754752
Diabetes-linked transcription factor HNF4α regulates metabolism of endogenous methylarginines and β-aminoisobutyric acid by controlling expression of alanine-glyoxylate aminotransferase 2. PMID:27752141
Coordinated Activities of Multiple Myc-dependent and Myc-independent Biosynthetic Pathways in Hepatoblastoma. PMID:27738108
CNARA: reliability assessment for genomic copy number profiles. PMID:27733115
Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer Supports No More Than Three Subtypes. PMID:27729437
Genome-Wide Interaction Analyses between Genetic Variants and Alcohol Consumption and Smoking for Risk of Colorectal Cancer. PMID:27723779
Convergent transcriptomics and proteomics of environmental enrichment and cocaine identifies novel therapeutic strategies for addiction. PMID:27717806
Exploring timing activation of functional pathway based on differential co-expression analysis in preimplantation embryogenesis. PMID:27705919
Self-Antigen-Driven Thymic B Cell Class Switching Promotes T Cell Central Tolerance. PMID:27705788
Neuronal Splicing Regulator RBFOX3 (NeuN) Regulates Adult Hippocampal Neurogenesis and Synaptogenesis. PMID:27701470
A cytotoxic anti-IL-3Rα antibody targets key cells and cytokines implicated in systemic lupus erythematosus. PMID:27699260
Safety and efficacy of the JAK inhibitor tofacitinib citrate in patients with alopecia areata. PMID:27699252
Upregulation of IFN-Inducible and Damage-Response Pathways in Chronic Graft-versus-Host Disease. PMID:27694491
Characterisation of equine satellite cell transcriptomic profile response to β-hydroxy-β-methylbutyrate (HMB). PMID:27691998
A penicillin-binding protein inhibits selection of colistin-resistant, lipooligosaccharide-deficient Acinetobacter baumannii. PMID:27681618
Characterization and phosphoproteomic analysis of a human immortalized podocyte model of Fabry disease generated using CRISPR/Cas9 technology. PMID:27681560
In search for geroprotectors: in silico screening and in vitro validation of signalome-level mimetics of young healthy state. PMID:27677171
Data-Driven Metabolic Pathway Compositions Enhance Cancer Survival Prediction. PMID:27673682
Novel ABCG2 Antagonists Reverse Topotecan-Mediated Chemotherapeutic Resistance in Ovarian Carcinoma Xenografts. PMID:27671528
Characteristics of Pos19 - A Small Coding RNA in the Oxidative Stress Response of Rhodobacter sphaeroides. PMID:27669425
The Challenge of Stability in High-Throughput Gene Expression Analysis: Comprehensive Selection and Evaluation of Reference Genes for BALB/c Mice Spleen Samples in the Leishmania infantum Infection Model. PMID:27668434
Modelling TFE renal cell carcinoma in mice reveals a critical role of WNT signaling. PMID:27668431
Data set for transcriptome analysis of Escherichia coli exposed to nickel. PMID:27668277
Control of Oriented Tissue Growth through Repression of Organ Boundary Genes Promotes Stem Morphogenesis. PMID:27666746
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
Systematically characterizing dysfunctional long intergenic non-coding RNAs in multiple brain regions of major psychosis. PMID:27661005
Detecting cognizable trends of gene expression in a time series RNA-sequencing experiment: a bootstrap approach. PMID:27659329
Trinitrobenzene sulfonic acid-induced intestinal injury in neonatal mice activates transcriptional networks similar to those seen in human necrotizing enterocolitis. PMID:27656771
Expression and methylation data from SLE patient and healthy control blood samples subdivided with respect to ARID3a levels. PMID:27656675
miR-125b affects mitochondrial biogenesis and impairs brite adipocyte formation and function. PMID:27656399
Uncovering synthetic lethal interactions for therapeutic targets and predictive markers in lung adenocarcinoma. PMID:27655641
DNA Microarray Platform for Detection and Surveillance of Viruses Transmitted by Small Mammals and Arthropods. PMID:27654806
Global transcriptome dysregulation in second trimester fetuses with FMR1 expansions. PMID:27646161
Diverse fates of uracilated HIV-1 DNA during infection of myeloid lineage cells. PMID:27644592
Global analysis of transcription in castration-resistant prostate cancer cells uncovers active enhancers and direct androgen receptor targets. PMID:27641228
Functional roles of MMP14 and MMP15 in early postnatal mammary gland development. PMID:27633994
Subpathway-CorSP: Identification of metabolic subpathways via integrating expression correlations and topological features between metabolites and genes of interest within pathways. PMID:27625019
Large-scale microarray profiling reveals four stages of immune escape in non-Hodgkin lymphomas. PMID:27622044
Investigating the Control of Chlorophyll Degradation by Genomic Correlation Mining. PMID:27618630
Portraying breast cancers with long noncoding RNAs. PMID:27617288
Regulatory Cross-Talks and Cascades in Rice Hormone Biosynthesis Pathways Contribute to Stress Signaling. PMID:27617021
Pramipexole induced place preference after L-dopa therapy and nigral dopaminergic loss: linking behavior to transcriptional modifications. PMID:27614895
A robust data scaling algorithm to improve classification accuracies in biomedical data. PMID:27612635
Ultrasonic Surgical Aspirate is a Reliable Source For Culturing Glioblastoma Stem Cells. PMID:27605047
Unbiased identification of signal-activated transcription factors by barcoded synthetic tandem repeat promoter screening (BC-STAR-PROM). PMID:27601530
Cancer Biomarkers from Genome-Scale DNA Methylation: Comparison of Evolutionary and Semantic Analysis Methods. PMID:27600245
Enhancing Interpretability of Gene Signatures with Prior Biological Knowledge. PMID:27600081
Global Profiling of the Cellular Alternative RNA Splicing Landscape during Virus-Host Interactions. PMID:27598998
A Mycobacterium avium subsp. paratuberculosis Predicted Serine Protease Is Associated with Acid Stress and Intraphagosomal Survival. PMID:27597934
Genotypes of cancer stem cells characterized by epithelial-to-mesenchymal transition and proliferation related functions. PMID:27597445
Identification and Characterization of the Dermal Panniculus Carnosus Muscle Stem Cells. PMID:27594590
Identification of BCL11B as a regulator of adipogenesis. PMID:27586877
Promoter Architecture and Sex-Specific Gene Expression in Daphnia pulex. PMID:27585846
A Small Protein Associated with Fungal Energy Metabolism Affects the Virulence of Cryptococcus neoformans in Mammals. PMID:27583447
A novel method for the identification of conserved structural patterns in RNA: From small scale to high-throughput applications. PMID:27580722
Epigenetic Loss of MLH1 Expression in Normal Human Hematopoietic Stem Cell Clones is Defined by the Promoter CpG Methylation Pattern Observed by High-Throughput Methylation Specific Sequencing. PMID:27570841
The transcriptional and splicing landscape of intestinal organoids undergoing nutrient starvation or endoplasmic reticulum stress. PMID:27561422
Characterization of Gene Expression Patterns among Artificially Developed Cancer Stem Cells Using Spherical Self-Organizing Map. PMID:27559294
EpiTracer - an algorithm for identifying epicenters in condition-specific biological networks. PMID:27556637
Systematic selection of small molecules to promote differentiation of embryonic stem cells and experimental validation for generating cardiomyocytes. PMID:27551501
fluff: exploratory analysis and visualization of high-throughput sequencing data. PMID:27547532
Exocytosis of polyubiquitinated proteins in bortezomib-resistant leukemia cells: a role for MARCKS in acquired resistance to proteasome inhibitors. PMID:27542283
Genome-wide association study identifies 14 novel risk alleles associated with basal cell carcinoma. PMID:27539887
MiR-4653-3p and its target gene FRS2 are prognostic biomarkers for hormone receptor positive breast cancer patients receiving tamoxifen as adjuvant endocrine therapy. PMID:27533459
A single nucleotide polymorphism genotyping platform for the authentication of patient derived xenografts. PMID:27528024
Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq). PMID:27519343
Transcriptome analysis of copper homeostasis genes reveals coordinated upregulation of SLC31A1,SCO1, and COX11 in colorectal cancer. PMID:27516958
The human olfactory transcriptome. PMID:27515280
Time-course gene expression data on the transcriptional effects of Aminaphtone on ECV304 endothelial cells. PMID:27508230
Differential expression of skeletal muscle genes following administration of clenbuterol to exercised horses. PMID:27506674
Regulation of proinflammatory genes by the circulating microRNA hsa-miR-939. PMID:27498764
RNA expression profile of calcified bicuspid, tricuspid, and normal human aortic valves by RNA sequencing. PMID:27495158
A long noncoding RNA signature for ulcerative colitis identifies IFNG-AS1 as an enhancer of inflammation. PMID:27492330
Backmasking in the yeast genome: encoding overlapping information for protein-coding and RNA degradation. PMID:27492286
White Adipose Tissue Browning in the R6/2 Mouse Model of Huntington's Disease. PMID:27486903
Transcriptomic profile adaptations following exposure of equine satellite cells to nutriactive phytochemical gamma-oryzanol. PMID:27482297
Using ILP to Identify Pathway Activation Patterns in Systems Biology. PMID:27478883
New Cell Adhesion Molecules in Human Ischemic Cardiomyopathy. PCDHGA3 Implications in Decreased Stroke Volume and Ventricular Dysfunction. PMID:27472518
The Landscape of A-to-I RNA Editome Is Shaped by Both Positive and Purifying Selection. PMID:27467689
Inverse association between carbohydrate consumption and plasma adropin concentrations in humans. PMID:27460714
Machine Learning of Protein Interactions in Fungal Secretory Pathways. PMID:27441920
Targeted genomic analysis reveals widespread autoimmune disease association with regulatory variants in the TNF superfamily cytokine signalling network. PMID:27435189
Coordinate Regulation of Metabolite Glycosylation and Stress Hormone Biosynthesis by TT8 in Arabidopsis. PMID:27432888
Comparison of In Vivo Gene Expression Profiling of RPE/Choroid following Intravitreal Injection of Dexamethasone and Triamcinolone Acetonide. PMID:27429799
Gremlin-1 Overexpression in Mouse Lung Reduces Silica-Induced Lymphocyte Recruitment - A Link to Idiopathic Pulmonary Fibrosis through Negative Correlation with CXCL10 Chemokine. PMID:27428020
Molecular signatures of neural connectivity in the olfactory cortex. PMID:27426965
Efficient generation of patient-matched malignant and normal primary cell cultures from clear cell renal cell carcinoma patients: clinically relevant models for research and personalized medicine. PMID:27422173
Regulation of a polyamine transporter by the conserved 3' UTR-derived sRNA SorX confers resistance to singlet oxygen and organic hydroperoxides in Rhodobacter sphaeroides. PMID:27420112
Calreticulin mediates an invasive breast cancer phenotype through the transcriptional dysregulation of p53 and MAPK pathways. PMID:27418879
miRNA Profile in Three Different Normal Human Ocular Tissues by miRNA-Seq. PMID:27415791
Polycomb-Mediated Repression and Sonic Hedgehog Signaling Interact to Regulate Merkel Cell Specification during Skin Development. PMID:27414999
Type IV collagen drives alveolar epithelial-endothelial association and the morphogenetic movements of septation. PMID:27412481
Obtaining Human Ischemic Stroke Gene Expression Biomarkers from Animal Models: A Cross-species Validation Study. PMID:27407070
The biofilm inhibitor Carolacton inhibits planktonic growth of virulent pneumococci via a conserved target. PMID:27404808
Non-canonical NF-κB pathway activation predicts outcome in borderline oestrogen receptor positive breast carcinoma. PMID:27404455
A consolidated analysis of the physiologic and molecular responses induced under acid stress in the legume-symbiont model-soil bacterium Sinorhizobium meliloti. PMID:27404346
Overcoming the matched-sample bottleneck: an orthogonal approach to integrate omic data. PMID:27403564
Developmental regulation of myeloerythroid progenitor function by the Lin28b-let-7-Hmga2 axis. PMID:27401346
Integrated Omic Analysis of a Guinea Pig Model of Heart Failure and Sudden Cardiac Death. PMID:27399916
NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease. PMID:27392431
Algorithms for differential splicing detection using exon arrays: a comparative assessment. PMID:27391904
Non-myogenic tumors display altered expression of dystrophin (DMD) and a high frequency of genetic alterations. PMID:27391342
Transition of an Anaerobic Escherichia coli Culture to Aerobiosis: Balancing mRNA and Protein Levels in a Demand-Directed Dynamic Flux Balance Analysis. PMID:27384956
Embryonic lethal abnormal vision proteins and adenine and uridine-rich element mRNAs after global cerebral ischemia and reperfusion in the rat. PMID:27381823
Systematic Identification of Anti-Fungal Drug Targets by a Metabolic Network Approach. PMID:27379244
High-throughput sequencing and de novo transcriptome assembly of Swertia japonica to identify genes involved in the biosynthesis of therapeutic metabolites. PMID:27378356
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
Type IV pili promote early biofilm formation by Clostridium difficile. PMID:27369898
Proteomic Screening and Lasso Regression Reveal Differential Signaling in Insulin and Insulin-like Growth Factor I (IGF1) Pathways. PMID:27364358
Prior knowledge transfer across transcriptional data sets and technologies using compositional statistics yields new mislabelled ovarian cell line. PMID:27353327
Identification of miRNA/mRNA-Negative Regulation Pairs in Nasopharyngeal Carcinoma. PMID:27350400
Knock-down of the methyltransferase Kmt6 relieves H3K27me3 and results in induction of cryptic and otherwise silent secondary metabolite gene clusters in Fusarium fujikuroi. PMID:27348741
FOXR2 Interacts with MYC to Promote Its Transcriptional Activities and Tumorigenesis. PMID:27346356
Filtered selection coupled with support vector machines generate a functionally relevant prediction model for colorectal cancer. PMID:27330311
Biomarkers of Tolerance in Kidney Transplantation: Are We Predicting Tolerance or Response to Immunosuppressive Treatment? PMID:27328267
A Mechanistic Beta-Binomial Probability Model for mRNA Sequencing Data. PMID:27326762
Transcriptional Profiling of Mycobacterium tuberculosis Exposed to In Vitro Lysosomal Stress. PMID:27324481
Gene expression prediction using low-rank matrix completion. PMID:27317252
AKT isoforms modulate Th1-like Treg generation and function in human autoimmune disease. PMID:27312110
Analysis of aggregated cell-cell statistical distances within pathways unveils therapeutic-resistance mechanisms in circulating tumor cells. PMID:27307648
What time is it? Deep learning approaches for circadian rhythms. PMID:27307647
The Regulation of rRNA Gene Transcription during Directed Differentiation of Human Embryonic Stem Cells. PMID:27299313
A Novel Mechanism of Host-Pathogen Interaction through sRNA in Bacterial Outer Membrane Vesicles. PMID:27295279
Folic acid induces cell type-specific changes in the transcriptome of breast cancer cell lines: a proof-of-concept study. PMID:27293554
Human Argonaute 2 Is Tethered to Ribosomal RNA through MicroRNA Interactions. PMID:27288410
Phorbol ester-mediated re-expression of endogenous LAT adapter in J.CaM2 cells: a model for dissecting drivers and blockers of LAT transcription. PMID:27278128
SSX2 regulates focal adhesion but does not drive the epithelial to mesenchymal transition in prostate cancer. PMID:27276714
Analysis of the Microprocessor in Dictyostelium: The Role of RbdB, a dsRNA Binding Protein. PMID:27272207
Bioinformatics resources for pollen. PMID:27271281
Long-lived antigen-induced IgM plasma cells demonstrate somatic mutations and contribute to long-term protection. PMID:27270306
Transcriptomic comparison of Drosophila snRNP biogenesis mutants reveals mutant-specific changes in pre-mRNA processing: implications for spinal muscular atrophy. PMID:27268418
Defining the identity of mouse embryonic dermal fibroblasts. PMID:27265328
Defining the Minimal Factors Required for Erythropoiesis through Direct Lineage Conversion. PMID:27264182
Transcriptome Profiling Identifies Multiplexin as a Target of SAGA Deubiquitinase Activity in Glia Required for Precise Axon Guidance During Drosophila Visual Development. PMID:27261002
Selection for reduced translation costs at the intronic 5' end in fungi. PMID:27260512
Breast cancer subtype predictors revisited: from consensus to concordance? PMID:27259591
Chemotherapy-related cachexia is associated with mitochondrial depletion and the activation of ERK1/2 and p38 MAPKs. PMID:27259276
Diagnostic value of microRNAs in asbestos exposure and malignant mesothelioma: systematic review and qualitative meta-analysis. PMID:27259231
Integrated omics approaches provide strategies for rapid erythromycin yield increase in Saccharopolyspora erythraea. PMID:27255285
Minor intron splicing is regulated by FUS and affected by ALS-associated FUS mutants. PMID:27252488
Differences in DNA Repair Capacity, Cell Death and Transcriptional Response after Irradiation between a Radiosensitive and a Radioresistant Cell Line. PMID:27245205
Coronary artery disease susceptibility gene ADTRP regulates cell cycle progression, proliferation, and apoptosis by global gene expression regulation. PMID:27235449
Deleterious assembly of the lamin A/C mutant p.S143P causes ER stress in familial dilated cardiomyopathy. PMID:27235420
The CsrA-FliW network controls polar localization of the dual-function flagellin mRNA in Campylobacter jejuni. PMID:27229370
Glucocorticoid receptor isoforms direct distinct mitochondrial programs to regulate ATP production. PMID:27226058
The Regulation of Cytokine Networks in Hippocampal CA1 Differentiates Extinction from Those Required for the Maintenance of Contextual Fear Memory after Recall. PMID:27224427
klf2a couples mechanotransduction and zebrafish valve morphogenesis through fibronectin synthesis. PMID:27221222
Abundance and Temperature Dependency of Protein-Protein Interaction Revealed by Interface Structure Analysis and Stability Evolution. PMID:27220911
Identification of FRA-1 as a novel player in pancreatic cancer in cooperation with a MUC1: ERK signaling axis. PMID:27220889
A robust (re-)annotation approach to generate unbiased mapping references for RNA-seq-based analyses of differential expression across closely related species. PMID:27220689
Transcriptomic and proteomic analyses of core metabolism in Clostridium termitidis CT1112 during growth on α-cellulose, xylan, cellobiose and xylose. PMID:27215540
The lncRNA SLNCR1 Mediates Melanoma Invasion through a Conserved SRA1-like Region. PMID:27210747
Altered gene expression in the lower respiratory tract of Car6 (-/-) mice. PMID:27209317
DNetDB: The human disease network database based on dysfunctional regulation mechanism. PMID:27209279
Cartography of Pathway Signal Perturbations Identifies Distinct Molecular Pathomechanisms in Malignant and Chronic Lung Diseases. PMID:27200087
Prevention of antipsychotic-induced hyperglycaemia by vitamin D: a data mining prediction followed by experimental exploration of the molecular mechanism. PMID:27199286
Identification of the long, edited dsRNAome of LPS-stimulated immune cells. PMID:27197207
Immunogenic Subtypes of Breast Cancer Delineated by Gene Classifiers of Immune Responsiveness. PMID:27197066
Identification of polycystic ovary syndrome potential drug targets based on pathobiological similarity in the protein-protein interaction network. PMID:27191267
Pervasive Effects of Aging on Gene Expression in Wild Wolves. PMID:27189566
Whole-transcriptome analysis of UUO mouse model of renal fibrosis reveals new molecular players in kidney diseases. PMID:27189340
A critical role for the Drosophila dopamine D1-like receptor Dop1R2 at the onset of metamorphosis. PMID:27184815
U2AF35(S34F) Promotes Transformation by Directing Aberrant ATG7 Pre-mRNA 3' End Formation. PMID:27184077
Associations between whole peripheral blood fatty acids and DNA methylation in humans. PMID:27181711
High Persister Mutants in Mycobacterium tuberculosis. PMID:27176494
The transcriptional activator GaaR of Aspergillus niger is required for release and utilization of d-galacturonic acid from pectin. PMID:27174630
Microarray Gene Expression Analysis to Evaluate Cell Type Specific Expression of Targets Relevant for Immunotherapy of Hematological Malignancies. PMID:27171398
The arabidopsis cyclic nucleotide interactome. PMID:27170143
Negative control of CSL gene transcription by stress/DNA damage response and p53. PMID:27163456
Uptake of dietary milk miRNAs by adult humans: a validation study. PMID:27158459
MiR-16 mediates trastuzumab and lapatinib response in ErbB-2-positive breast and gastric cancer via its novel targets CCNJ and FUBP1. PMID:27157613
Transcriptional signatures of brain aging and Alzheimer's disease: What are our rodent models telling us? PMID:27155503
Cerebellar neurodegeneration in a new rat model of episodic hepatic encephalopathy. PMID:27154504
Molecular characterization of Gleason patterns 3 and 4 prostate cancer using reverse Warburg effect-associated genes. PMID:27152194
In vivo gene expression in a Staphylococcus aureus prosthetic joint infection characterized by RNA sequencing and metabolomics: a pilot study. PMID:27150914
RNA-seq Transcriptome Analysis of Panax japonicus, and Its Comparison with Other Panax Species to Identify Potential Genes Involved in the Saponins Biosynthesis. PMID:27148308
Integrating DNA Methylation and Gene Expression Data in the Development of the Soybean-Bradyrhizobium N2-Fixing Symbiosis. PMID:27148207
Reconstructed Metabolic Network Models Predict Flux-Level Metabolic Reprogramming in Glioblastoma. PMID:27147948
Assessment of FBA Based Gene Essentiality Analysis in Cancer with a Fast Context-Specific Network Reconstruction Method. PMID:27145226
Ontology-based annotations and semantic relations in large-scale (epi)genomics data. PMID:27142216
Identification of the BRD1 interaction network and its impact on mental disorder risk. PMID:27142060
Deletion of inositol hexakisphosphate kinase 1 (IP6K1) reduces cell migration and invasion, conferring protection from aerodigestive tract carcinoma in mice. PMID:27140681
Cassava (Manihot esculenta) transcriptome analysis in response to infection by the fungus Colletotrichum gloeosporioides using an oligonucleotide-DNA microarray. PMID:27138000
Interferon Regulatory Factor 8 (IRF8) Impairs Induction of Interferon Induced with Tetratricopeptide Repeat Motif (IFIT) Gene Family Members. PMID:27137933
Identification of key regulators of pancreatic cancer progression through multidimensional systems-level analysis. PMID:27137215
2,3,7,8 Tetrachlorodibenzo-p-dioxin-induced RNA abundance changes identify Ackr3, Col18a1, Cyb5a and Glud1 as candidate mediators of toxicity. PMID:27136898
Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats. PMID:27135913
Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing. PMID:27135536
Keeping Control: The Role of Senescence and Development in Plant Pathogenesis and Defense. PMID:27135337
Mitochondrial Stress Induces Chromatin Reorganization to Promote Longevity and UPR(mt). PMID:27133166
Age-Dependent Pancreatic Gene Regulation Reveals Mechanisms Governing Human β Cell Function. PMID:27133132
Establishing an analytic pipeline for genome-wide DNA methylation. PMID:27127542
Characterization of key triacylglycerol biosynthesis processes in rhodococci. PMID:27126051
Genetics of PCOS: A systematic bioinformatics approach to unveil the proteins responsible for PCOS. PMID:27114910
Immune activation of the host cell induces drug tolerance in Mycobacterium tuberculosis both in vitro and in vivo. PMID:27114608
Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis - a rich resource to identify new transcripts, proteins and to study gene regulation. PMID:27107716
Cisplatin selects for stem-like cells in osteosarcoma by activating Notch signaling. PMID:27102300
Survival in acute myeloid leukemia is associated with NKp44 splice variants. PMID:27102296
CIP2A Promotes T-Cell Activation and Immune Response to Listeria monocytogenes Infection. PMID:27100879
A new molecular signature method for prediction of driver cancer pathways from transcriptional data. PMID:27098033
The Influence of the Global Gene Expression Shift on Downstream Analyses. PMID:27092944
Learning from Co-expression Networks: Possibilities and Challenges. PMID:27092161
Arachidonic and oleic acid exert distinct effects on the DNA methylome. PMID:27088456
Identification and Evolutionary Analysis of Potential Candidate Genes in a Human Eating Disorder. PMID:27088090
Two sets of RNAi components are required for heterochromatin formation in trans triggered by truncated transgenes. PMID:27085807
Pathway activation strength is a novel independent prognostic biomarker for cetuximab sensitivity in colorectal cancer patients. PMID:27081524
s-SHIP expression identifies a subset of murine basal prostate cells as neonatal stem cells. PMID:27081082
In silico methods for drug repurposing and pharmacology. PMID:27080087
Fatty Acid Oxidation is Impaired in An Orthologous Mouse Model of Autosomal Dominant Polycystic Kidney Disease. PMID:27077126
Data set for transcriptional response to depletion of the Shoc2 scaffolding protein. PMID:27077079
Transcriptomic and metabolomic profiling of ionic liquid stimuli unveils enhanced secondary metabolism in Aspergillus nidulans. PMID:27072538
Contrasting invertebrate immune defense behaviors caused by a single gene, the Caenorhabditis elegans neuropeptide receptor gene npr-1. PMID:27066825
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
Mga2 Transcription Factor Regulates an Oxygen-responsive Lipid Homeostasis Pathway in Fission Yeast. PMID:27053105
Development of a prediction model for radiosensitivity using the expression values of genes and long non-coding RNAs. PMID:27050376
Genome-Wide Expression Profiling Reveals S100B as Biomarker for Invasive Aspergillosis. PMID:27047454
Reconstruction of the Regulatory Network for Bacillus subtilis and Reconciliation with Gene Expression Data. PMID:27047450
A Thermodynamic-Based Interpretation of Protein Expression Heterogeneity in Different Glioblastoma Multiforme Tumors Identifies Tumor-Specific Unbalanced Processes. PMID:27035264
Assessing Concordance of Drug-Induced Transcriptional Response in Rodent Liver and Cultured Hepatocytes. PMID:27028627
Overexpression of Ran GTPase Components Regulating Nuclear Export, but not Mitotic Spindle Assembly, Marks Chromosome Instability and Poor Prognosis in Breast Cancer. PMID:27023921
UV-B Perception and Acclimation in Chlamydomonas reinhardtii. PMID:27020958
Integrative network modeling approaches to personalized cancer medicine. PMID:27019658
Linker histone variant H1T targets rDNA repeats. PMID:27018843
Can data repositories help find effective treatments for complex diseases? PMID:27018167
Androgen deprivation therapy sensitizes triple negative breast cancer cells to immune-mediated lysis through androgen receptor independent modulation of osteoprotegerin. PMID:27015557
The retinoblastoma protein regulates hypoxia-inducible genetic programs, tumor cell invasiveness and neuroendocrine differentiation in prostate cancer cells. PMID:27015368
HNdb: an integrated database of gene and protein information on head and neck squamous cell carcinoma. PMID:27013077
Condensin I and II behaviour in interphase nuclei and cells undergoing premature chromosome condensation. PMID:27008552
The Gene Expression Omnibus Database. PMID:27008011
An individualized prognostic signature and multi‑omics distinction for early stage hepatocellular carcinoma patients with surgical resection. PMID:27006471
Polysome Profiling Links Translational Control to the Radioresponse of Glioblastoma Stem-like Cells. PMID:27005284
UniBic: Sequential row-based biclustering algorithm for analysis of gene expression data. PMID:27001340
Spatiotemporal transcriptome provides insights into early fruit development of tomato (Solanum lycopersicum). PMID:26988970
Bifidobacterium thermophilum RBL67 impacts on growth and virulence gene expression of Salmonella enterica subsp. enterica serovar Typhimurium. PMID:26988691
Human adaptation and population differentiation in the light of ancient genomes. PMID:26988143
GeneAnalytics: An Integrative Gene Set Analysis Tool for Next Generation Sequencing, RNAseq and Microarray Data. PMID:26983021
Transcriptional analysis of antiviral small molecule therapeutics as agonists of the RLR pathway. PMID:26981429
Computational gene expression profiling under salt stress reveals patterns of co-expression. PMID:26981411
Transcriptional profile of immediate response to ionizing radiation exposure. PMID:26981369
Identification and Characterization of msf, a Novel Virulence Factor in Haemophilus influenzae. PMID:26977929
Patterns of Transcriptional Response to 1,25-Dihydroxyvitamin D3 and Bacterial Lipopolysaccharide in Primary Human Monocytes. PMID:26976439
Cellular Tracking and Gene Profiling of Fusarium graminearum during Maize Stalk Rot Disease Development Elucidates Its Strategies in Confronting Phosphorus Limitation in the Host Apoplast. PMID:26974960
RNA-binding protein IGF2BP3 targeting of oncogenic transcripts promotes hematopoietic progenitor proliferation. PMID:26974154
Transcriptomic Analysis Using Olive Varieties and Breeding Progenies Identifies Candidate Genes Involved in Plant Architecture. PMID:26973682
Gene expression changes in damaged osteoarthritic cartilage identify a signature of non-chondrogenic and mechanical responses. PMID:26973327
Comorbidities of Psoriasis - Exploring the Links by Network Approach. PMID:26966903
Programming of Plant Leaf Senescence with Temporal and Inter-Organellar Coordination of Transcriptome in Arabidopsis. PMID:26966169
12-HETER1/GPR31, a high-affinity 12(S)-hydroxyeicosatetraenoic acid receptor, is significantly up-regulated in prostate cancer and plays a critical role in prostate cancer progression. PMID:26965684
Activation of Myenteric Glia during Acute Inflammation In Vitro and In Vivo. PMID:26964064
Toward improved phosphorus efficiency in monogastrics-interplay of serum, minerals, bone, and immune system after divergent dietary phosphorus supply in swine. PMID:26962023
Integrated mRNA and miRNA expression profiling in blood reveals candidate biomarkers associated with endurance exercise in the horse. PMID:26960911
Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes. PMID:26960548
Translational Meta-analytical Methods to Localize the Regulatory Patterns of Neurological Disorders in the Human Brain. PMID:26958307
Combining Human Disease Genetics and Mouse Model Phenotypes towards Drug Repositioning for Parkinson's disease. PMID:26958284
The TGF-β pathway is activated by 5-fluorouracil treatment in drug resistant colorectal carcinoma cells. PMID:26956045
Serological and Genetic Evidence for Altered Complement System Functionality in Systemic Lupus Erythematosus: Findings of the GAPAID Consortium. PMID:26950932
Comparative evaluation of isoform-level gene expression estimation algorithms for RNA-seq and exon-array platforms. PMID:26944083
Weighted gene co-expression network analysis identifies specific modules and hub genes related to coronary artery disease. PMID:26944061
The Brewed Rice Vinegar Kurozu Increases HSPA1A Expression and Ameliorates Cognitive Dysfunction in Aged P8 Mice. PMID:26943920
High-throughput discovery of post-transcriptional cis-regulatory elements. PMID:26941072
The transcriptome of NaCl-treated Limonium bicolor leaves reveals the genes controlling salt secretion of salt gland. PMID:26936070
Quantitative assessment of ribosome drop-off in E. coli. PMID:26935582
Integrated analysis of DNA methylation profiles and gene expression profiles to identify genes associated with pilocytic astrocytomas. PMID:26934913
Alternatively Activated Macrophages Boost Induced Regulatory T and Th17 Cell Responses during Immunotherapy for Colitis. PMID:26927797
An interactive environment for agile analysis and visualization of ChIP-sequencing data. PMID:26926434
The Human Toxome Collaboratorium: A Shared Environment for Multi-Omic Computational Collaboration within a Consortium. PMID:26924983
An integrated genomics analysis of epigenetic subtypes in human breast tumors links DNA methylation patterns to chromatin states in normal mammary cells. PMID:26923702
GATA3-dependent cellular reprogramming requires activation-domain dependent recruitment of a chromatin remodeler. PMID:26922637
Distribution of miRNA expression across human tissues. PMID:26921406
Thymic stromal lymphopoietin (TSLP) inhibits human colon tumor growth by promoting apoptosis of tumor cells. PMID:26919238
A nuclear-directed human pancreatic ribonuclease (PE5) targets the metabolic phenotype of cancer cells. PMID:26918450
Reduced-representation Phosphosignatures Measured by Quantitative Targeted MS Capture Cellular States and Enable Large-scale Comparison of Drug-induced Phenotypes. PMID:26912667
Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes. PMID:26912365
Quantitative analysis by next generation sequencing of hematopoietic stem and progenitor cells (LSK) and of splenic B cells transcriptomes from wild-type and Usp3-knockout mice. PMID:26909367
Using Multi-objective Optimization to Identify Dynamical Network Biomarkers as Early-warning Signals of Complex Diseases. PMID:26906975
αCP binding to a cytosine-rich subset of polypyrimidine tracts drives a novel pathway of cassette exon splicing in the mammalian transcriptome. PMID:26896798
Interleukin-6 is a potential therapeutic target in interleukin-6 dependent, estrogen receptor-α-positive breast cancer. PMID:26893580
Positional proteomics reveals differences in N-terminal proteoform stability. PMID:26893308
Discovering gene re-ranking efficiency and conserved gene-gene relationships derived from gene co-expression network analysis on breast cancer data. PMID:26892392
Role of miR-222-3p in c-Src-Mediated Regulation of Osteoclastogenesis. PMID:26891296
MiR-449a Affects Epithelial Proliferation during the Pseudoglandular and Canalicular Phases of Avian and Mammal Lung Development. PMID:26891231
DNA methylation variation of human-specific Alu repeats. PMID:26890526
Oestrogen receptor β regulates epigenetic patterns at specific genomic loci through interaction with thymine DNA glycosylase. PMID:26889208
Profiling placental and fetal DNA methylation in human neural tube defects. PMID:26889207
Microarray Analysis of Gene Expression in Saccharomyces cerevisiae kap108Δ Mutants upon Addition of Oxidative Stress. PMID:26888869
miR-182 Modulates Myocardial Hypertrophic Response Induced by Angiogenesis in Heart. PMID:26888314
New tools for studying microglia in the mouse and human CNS. PMID:26884166
Physiological evidence for diversification of IFNα- and IFNβ-mediated response programs in different autoimmune diseases. PMID:26882897
ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis. PMID:26882475
Therapeutic potential of targeting microRNA-10b in established intracranial glioblastoma: first steps toward the clinic. PMID:26881967
Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice. PMID:26881867
Genomic and transcriptomic hallmarks of poorly differentiated and anaplastic thyroid cancers. PMID:26878173
Translational bioinformatics in the era of real-time biomedical, health care and wellness data streams. PMID:26876889
Single-cell Transcriptome Study as Big Data. PMID:26876720
RONIN Is an Essential Transcriptional Regulator of Genes Required for Mitochondrial Function in the Developing Retina. PMID:26876175
Gene expression inference with deep learning. PMID:26873929
Reciprocal Effects on Neurocognitive and Metabolic Phenotypes in Mouse Models of 16p11.2 Deletion and Duplication Syndromes. PMID:26872257
Social threat exposure in juvenile mice promotes cocaine-seeking by altering blood clotting and brain vasculature. PMID:26870906
Regulation of the tumour suppressor PDCD4 by miR-499 and miR-21 in oropharyngeal cancers. PMID:26867589
Identification of Targets of CUG-BP, Elav-Like Family Member 1 (CELF1) Regulation in Embryonic Heart Muscle. PMID:26866591
A genome-wide search for epigenetically [corrected] regulated genes in zebra finch using MethylCap-seq and RNA-seq. PMID:26864856
Differential Expression of Genes and DNA Methylation associated with Prenatal Protein Undernutrition by Albumen Removal in an avian model. PMID:26861190
New insights into the Plasmodium vivax transcriptome using RNA-Seq. PMID:26858037
Loss of the transcription factor Meis1 prevents sympathetic neurons target-field innervation and increases susceptibility to sudden cardiac death. PMID:26857994
Integrative Genomic Analyses Yield Cell-Cycle Regulatory Programs with Prognostic Value. PMID:26856934
Dictyocaulus viviparus genome, variome and transcriptome elucidate lungworm biology and support future intervention. PMID:26856411
JAK-STAT and G-protein-coupled receptor signaling pathways are frequently altered in epitheliotropic intestinal T-cell lymphoma. PMID:26854024
Gene set analysis using sufficient dimension reduction. PMID:26852017
Identification of CdnL, a Putative Transcriptional Regulator Involved in Repair and Outgrowth of Heat-Damaged Bacillus cereus Spores. PMID:26849219
Characterization of chromatin accessibility with a transposome hypersensitive sites sequencing (THS-seq) assay. PMID:26846207
The Role of DNA Methylation in Cardiovascular Risk and Disease: Methodological Aspects, Study Design, and Data Analysis for Epidemiological Studies. PMID:26837743
Benchmarking Procedures for High-Throughput Context Specific Reconstruction Algorithms. PMID:26834640
Chemical Inhibition of Wild-Type p53-Induced Phosphatase 1 (WIP1/PPM1D) by GSK2830371 Potentiates the Sensitivity to MDM2 Inhibitors in a p53-Dependent Manner. PMID:26832796
IgG Glycome in Colorectal Cancer. PMID:26831718
A multiplex immunoassay for the non-invasive detection of bladder cancer. PMID:26830497
Reduced CYFIP1 in Human Neural Progenitors Results in Dysregulation of Schizophrenia and Epilepsy Gene Networks. PMID:26824476
Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans. PMID:26821746
Missing value imputation for microRNA expression data by using a GO-based similarity measure. PMID:26818962
MatP regulates the coordinated action of topoisomerase IV and MukBEF in chromosome segregation. PMID:26818444
Prediction of drugs having opposite effects on disease genes in a directed network. PMID:26818006
PMD: A Resource for Archiving and Analyzing Protein Microarray data. PMID:26813635
Gene signature of the post-Chernobyl papillary thyroid cancer. PMID:26810418
Identification of factors involved in target RNA-directed microRNA degradation. PMID:26809675
Accelerating Adverse Outcome Pathway Development Using Publicly Available Data Sources. PMID:26809562
Estrogen Receptor Alpha (ESR1)-Dependent Regulation of the Mouse Oviductal Transcriptome. PMID:26808832
RUNX1B Expression Is Highly Heterogeneous and Distinguishes Megakaryocytic and Erythroid Lineage Fate in Adult Mouse Hematopoiesis. PMID:26808730
A Novel Biomarker Panel Examining Response to Gemcitabine with or without Erlotinib for Pancreatic Cancer Therapy in NCIC Clinical Trials Group PA.3. PMID:26808546
A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2 alpha. PMID:26798136
Identification of Crowding Stress Tolerance Co-Expression Networks Involved in Sweet Corn Yield. PMID:26796516
Transcriptome Changes in Hirschfeldia incana in Response to Lead Exposure. PMID:26793211
Global Regulation of Gene Expression by the MafR Protein of Enterococcus faecalis. PMID:26793169
CD28 Deficiency Enhances Type I IFN Production by Murine Plasmacytoid Dendritic Cells. PMID:26773151
New players in heterochromatin silencing: histone variant H3.3 and the ATRX/DAXX chaperone. PMID:26773061
Postponing the Hypoglycemic Response to Partial Hepatectomy Delays Mouse Liver Regeneration. PMID:26772417
Transcriptome responses in alfalfa associated with tolerance to intensive animal grazing. PMID:26763747
Novel insights into human respiratory syncytial virus-host factor interactions through integrated proteomics and transcriptomics analysis. PMID:26760927
The Pseudomonas aeruginosa PAO1 Two-Component Regulator CarSR Regulates Calcium Homeostasis and Calcium-Induced Virulence Factor Production through Its Regulatory Targets CarO and CarP. PMID:26755627
Testing the kinship theory of intragenomic conflict in honey bees (Apis mellifera). PMID:26755583
Whole Blood Transcriptomics Is Relevant to Identify Molecular Changes in Response to Genetic Selection for Feed Efficiency and Nutritional Status in the Pig. PMID:26752050
Type III Methyltransferase M.NgoAX from Neisseria gonorrhoeae FA1090 Regulates Biofilm Formation and Interactions with Human Cells. PMID:26733970
Transcriptional profiling and muscle cross-section analysis reveal signs of ischemia reperfusion injury following total knee arthroplasty with tourniquet. PMID:26733251
ChainRank, a chain prioritisation method for contextualisation of biological networks. PMID:26729273
Multiple Transcriptome Data Analysis Reveals Biologically Relevant Atopic Dermatitis Signature Genes and Pathways. PMID:26717000
Improving Cancer Gene Expression Data Quality through a TCGA Data-Driven Evaluation of Identifier Filtering. PMID:26715829
EntropyExplorer: an R package for computing and comparing differential Shannon entropy, differential coefficient of variation and differential expression. PMID:26714840
Patients with Dilated Cardiomyopathy and Sustained Monomorphic Ventricular Tachycardia Show Up-Regulation of KCNN3 and KCNJ2 Genes and CACNG8-Linked Left Ventricular Dysfunction. PMID:26710323
The Macrophage Inhibitor CNI-1493 Blocks Metastasis in a Mouse Model of Ewing Sarcoma through Inhibition of Extravasation. PMID:26709919
WheatExp: an RNA-seq expression database for polyploid wheat. PMID:26705106
Comparative analysis of blood and saliva expression profiles in chronic and refractory periodontitis patients. PMID:26705104
The human milk oligosaccharide 2'-fucosyllactose augments the adaptive response to extensive intestinal. PMID:26702137
Transcriptional changes in sensory ganglia associated with primary afferent axon collateral sprouting in spared dermatome model. PMID:26697387
Assessment of microRNA expression in mouse epididymal epithelial cells and spermatozoa by next generation sequencing. PMID:26697376
Prediction of Druggable Proteins Using Machine Learning and Systems Biology: A Mini-Review. PMID:26696900
Conserved and highly expressed tRNA derived fragments in zebrafish. PMID:26694924
iCLIP identifies novel roles for SAFB1 in regulating RNA processing and neuronal function. PMID:26694817
Neurospora crassa transcriptomics reveals oxidative stress and plasma membrane homeostasis biology genes as key targets in response to chitosan. PMID:26694141
Prediction of tissue-specific effects of gene knockout on apoptosis in different anatomical structures of human brain. PMID:26693857
Interleukin-1 antagonism moderates the inflammatory state associated with Type 1 diabetes during clinical trials conducted at disease onset. PMID:26692253
MiR-338-5p sensitizes glioblastoma cells to radiation through regulation of genes involved in DNA damage response. PMID:26692101
Understanding gene expression in coronary artery disease through global profiling, network analysis and independent validation of key candidate genes. PMID:26690514
Predicting target proteins for drug candidate compounds based on drug-induced gene expression data in a chemical structure-independent manner. PMID:26684652
Expression Profiling after Prolonged Experimental Febrile Seizures in Mice Suggests Structural Remodeling in the Hippocampus. PMID:26684451
Molecular analysis of pediatric brain tumors identifies microRNAs in pilocytic astrocytomas that target the MAPK and NF-κB pathways. PMID:26682910
Infection by Herpes Simplex Virus 1 Causes Near-Complete Loss of RNA Polymerase II Occupancy on the Host Cell Genome. PMID:26676778
Targeting Innate Immunity for Antiviral Therapy through Small Molecule Agonists of the RLR Pathway. PMID:26676770
A human haploid gene trap collection to study lncRNAs with unusual RNA biology. PMID:26670263
Actin remodeling confers BRAF inhibitor resistance to melanoma cells through YAP/TAZ activation. PMID:26668268
Immune modulators in disease: integrating knowledge from the biomedical literature and gene expression. PMID:26661719
Intermittent Hypoxia Alters Gene Expression in Peripheral Blood Mononuclear Cells of Healthy Volunteers. PMID:26657991
A genome-scale screen reveals context-dependent ovarian cancer sensitivity to miRNA overexpression. PMID:26655797
Diguanylate Cyclases AdrA and STM1987 Regulate Salmonella enterica Exopolysaccharide Production during Plant Colonization in an Environment-Dependent Manner. PMID:26655751
iRDA: a new filter towards predictive, stable, and enriched candidate genes. PMID:26647162
Rapid Increase in frequency of gene copy-number variants during experimental evolution in Caenorhabditis elegans. PMID:26645535
Identifying Novel Transcriptional Regulators with Circadian Expression. PMID:26644408
AKT Inhibition Promotes Nonautonomous Cancer Cell Survival. PMID:26637368
Intra-Gene DNA Methylation Variability Is a Clinically Independent Prognostic Marker in Women's Cancers. PMID:26629914
Genetic architecture of early pre-inflammatory stage transcription signatures of autoimmune diabetes in the pancreatic lymph nodes of the NOD mouse reveals significant gene enrichment on chromosomes 6 and 7. PMID:26629415
BRAFV600E-Associated Gene Expression Profile: Early Changes in the Transcriptome, Based on a Transgenic Mouse Model of Papillary Thyroid Carcinoma. PMID:26625260
Loss of Ezh2 promotes a midbrain-to-forebrain identity switch by direct gene derepression and Wnt-dependent regulation. PMID:26621269
σ Factor and Anti-σ Factor That Control Swarming Motility and Biofilm Formation in Pseudomonas aeruginosa. PMID:26620262
Mapping DNA methylation across development, genotype and schizophrenia in the human frontal cortex. PMID:26619358
C-terminal domains of a histone demethylase interact with a pair of transcription factors and mediate specific chromatin association. PMID:26617990
Increased collagen cross-linking is a signature of dystrophin-deficient muscle. PMID:26616495
Data standards can boost metabolomics research, and if there is a will, there is a way. PMID:26612985
Gatekeeper role of brain antigen-presenting CD11c+ cells in neuroinflammation. PMID:26612827
A novel xenograft model to study the role of TSLP-induced CRLF2 signals in normal and malignant human B lymphopoiesis. PMID:26611474
Identification of sample annotation errors in gene expression datasets. PMID:26608184
The sialyl-glycolipid stage-specific embryonic antigen 4 marks a subpopulation of chemotherapy-resistant breast cancer cells with mesenchymal features. PMID:26607327
Impact of SNPs on methylation readouts by Illumina Infinium HumanMethylation450 BeadChip Array: implications for comparative population studies. PMID:26607064
Transcriptome analysis of GVHD reveals aurora kinase A as a targetable pathway for disease prevention. PMID:26606970
Gene expression profiles and protein-protein interaction network analysis in AIDS patients with HIV-associated encephalitis and dementia. PMID:26604827
Telomere binding protein TRB1 is associated with promoters of translation machinery genes in vivo. PMID:26597966
Isolation and characterization of circulating lymphatic endothelial colony forming cells. PMID:26597759
Gene-expression signature functional annotation of breast cancer tumours in function of age. PMID:26597277
Nuclear factor, erythroid 2-like 2-associated molecular signature predicts lung cancer survival. PMID:26596768
Precision Subtypes of T Cell-Mediated Rejection Identified by Molecular Profiles. PMID:26594210
SBR-Blood: systems biology repository for hematopoietic cells. PMID:26590403
Mycobacterial infection induces a specific human innate immune response. PMID:26586179
Transcriptome analysis reveals regulatory networks underlying differential susceptibility to Botrytis cinerea in response to nitrogen availability in Solanum lycopersicum. PMID:26583019
Ectodysplasin/NF-κB Promotes Mammary Cell Fate via Wnt/β-catenin Pathway. PMID:26581094
De novo transcriptome profiling of cold-stressed siliques during pod filling stages in Indian mustard (Brassica juncea L.). PMID:26579175
Combined Genome-Wide CSF Aβ-42's Associations and Simple Network Properties Highlight New Risk Factors for Alzheimer's Disease. PMID:26576771
Mining for novel candidate clock genes in the circadian regulatory network. PMID:26576534
An Effective Method to Identify Shared Pathways and Common Factors among Neurodegenerative Diseases. PMID:26575483
Five omic technologies are concordant in differentiating the biochemical characteristics of the berries of five grapevine (Vitis vinifera L.) cultivars. PMID:26573226
NRP1 is targeted by miR-130a and miR-130b, and is associated with multidrug resistance in epithelial ovarian cancer based on integrated gene network analysis. PMID:26573160
Gene expression and immunochemical localization of major cytochrome P450 drug-metabolizing enzymes in bovine nasal olfactory and respiratory mucosa. PMID:26572092
The effects of long-term daily folic acid and vitamin B12 supplementation on genome-wide DNA methylation in elderly subjects. PMID:26568774
Intra-tumor genetic heterogeneity in rectal cancer. PMID:26568296
A comprehensive multiomics approach toward understanding the relationship between aging and dementia. PMID:26564964
Dysregulation of bile acid homeostasis in parenteral nutrition mouse model. PMID:26564717
From System-Wide Differential Gene Expression to Perturbed Regulatory Factors: A Combinatorial Approach. PMID:26562430
Survival analysis and microarray profiling identify Cd40 as a candidate for the Salmonella susceptibility locus, Ity5. PMID:26562079
Primary Amine Oxidase of Escherichia coli Is a Metabolic Enzyme that Can Use a Human Leukocyte Molecule as a Substrate. PMID:26556595
Transcriptome-wide analysis supports environmental adaptations of two Pinus pinaster populations from contrasting habitats. PMID:26545587
CXCL1 is elevated in the urine of bladder cancer patients. PMID:26543745
Identification and functional studies of regulatory variants responsible for the association of NRG3 with a delusion phenotype in schizophrenia. PMID:26528484
IRAK1 is a novel DEK transcriptional target and is essential for head and neck cancer cell survival. PMID:26527316
Puberty-specific promotion of mammary tumorigenesis by a high animal fat diet. PMID:26526858
NeuroD1 reprograms chromatin and transcription factor landscapes to induce the neuronal program. PMID:26516211
Novel gene sets improve set-level classification of prokaryotic gene expression data. PMID:26511329
Comparing the normalization methods for the differential analysis of Illumina high-throughput RNA-Seq data. PMID:26511205
Prior infection with Type A Francisella tularensis antagonizes the pulmonary transcriptional response to an aerosolized Toll-like receptor 4 agonist. PMID:26510639
Transcriptomic Changes Due to Cytoplasmic TDP-43 Expression Reveal Dysregulation of Histone Transcripts and Nuclear Chromatin. PMID:26510133
Specific inhibition by synthetic analogs of pyruvate reveals that the pyruvate dehydrogenase reaction is essential for metabolism and viability of glioblastoma cells. PMID:26503465
Quercetin suppresses immune cell accumulation and improves mitochondrial gene expression in adipose tissue of diet-induced obese mice. PMID:26499876
Transcriptional profiles of pilocytic astrocytoma are related to their three different locations, but not to radiological tumor features. PMID:26497896
Oct4-induced oligodendrocyte progenitor cells enhance functional recovery in spinal cord injury model. PMID:26497893
Inhibition of the miR-155 target NIAM phenocopies the growth promoting effect of miR-155 in B-cell lymphoma. PMID:26497687
Tumor-host signaling interaction reveals a systemic, age-dependent splenic immune influence on tumor development. PMID:26497558
MtiBase: a database for decoding microRNA target sites located within CDS and 5'UTR regions from CLIP-Seq and expression profile datasets. PMID:26490638
A functional module-based exploration between inflammation and cancer in esophagus. PMID:26489668
New global analysis of the microRNA transcriptome of primary tumors and lymph node metastases of papillary thyroid cancer. PMID:26487287
A mutation in the nucleoporin-107 gene causes XX gonadal dysgenesis. PMID:26485283
Time-series analysis of the transcriptome of the re-establishment of desiccation tolerance by ABA in germinated Arabidopsis thaliana seeds. PMID:26484244
A ChIP-on-chip tiling array approach detects functional histone-free regions associated with boundaries at vertebrate HOX genes. PMID:26484075
Integrated analysis of the local and systemic changes preceding the development of post-partum cytological endometritis. PMID:26482908
NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases. PMID:26475471
Identification of two mutations increasing the methanol tolerance of Corynebacterium glutamicum. PMID:26474849
Potential involvement of miR-375 in the premalignant progression of oral squamous cell carcinoma mediated via transcription factor KLF5. PMID:26474386
Different exercise modalities have distinct effects on the integrin-linked kinase (ILK) and Ca2+ signaling pathways in the male rat bone. PMID:26471755
Genome-wide identification and functional analysis of lincRNAs acting as miRNA targets or decoys in maize. PMID:26470872
Gene-expression profiling of buccal epithelium among non-smoking women exposed to household air pollution from smoky coal. PMID:26468118
Whole transcriptome profiling reveals the RNA content of motor axons. PMID:26464439
Sample size reassessment for a two-stage design controlling the false discovery rate. PMID:26461844
Broad-spectrum antibodies against self-antigens and cytokines in RAG deficiency. PMID:26457731
Molecular adaptation of Lactobacillus plantarum WCFS1 to gallic acid revealed by genome-scale transcriptomic signature and physiological analysis. PMID:26453568
A cross-cancer differential co-expression network reveals microRNA-regulated oncogenic functional modules. PMID:26448606
Whole Genome Expression Microarray Analysis of Highly Versus Poorly Tumorigenic Murine Melanoma Cell Lines Provides Insights into Factors That Regulate Tumor Growth, Metastasis, and Immunogenicity. PMID:26441959
Mammary Stem Cell Self-Renewal Is Regulated by Slit2/Robo1 Signaling through SNAI1 and mINSC. PMID:26440891
Synergistic Gene Expression Signature Observed in TK6 Cells upon Co-Exposure to UVC-Irradiation and Protein Kinase C-Activating Tumor Promoters. PMID:26431317
A Comparison of transgenic and wild type soybean seeds: analysis of transcriptome profiles using RNA-Seq. PMID:26427366
The idiopathic preterm delivery methylation profile in umbilical cord blood DNA. PMID:26419829
Vigilant keratinocytes trigger pathogen-associated molecular pattern signaling in response to streptococcal M1 protein. PMID:26416902
The decrease in histone methyltransferase EZH2 in response to fluid shear stress alters endothelial gene expression and promotes quiescence. PMID:26416763
MicroRNAs and Their Targets Are Differentially Regulated in Adult and Neonatal Mouse CD8+ T Cells. PMID:26416483
Molecular portraits revealing the heterogeneity of breast tumor subtypes defined using immunohistochemistry markers. PMID:26404658
Transcriptomics Profiling of Alzheimer's Disease Reveal Neurovascular Defects, Altered Amyloid-β Homeostasis, and Deregulated Expression of Long Noncoding RNAs. PMID:26402107
Whose Gene Is It Anyway? The Effect of Preparation Purity on Neutrophil Transcriptome Studies. PMID:26401909
Modulation of MicroRNA Cluster miR-183-96-182 Expression by Epstein-Barr Virus Latent Membrane Protein 1. PMID:26401047
ATM deficiency promotes development of murine B-cell lymphomas that resemble diffuse large B-cell lymphoma in humans. PMID:26400962
Translational compensation of genomic instability in neuroblastoma. PMID:26399178
Enhanced virome sequencing using targeted sequence capture. PMID:26395152
Autism-like syndrome is induced by pharmacological suppression of BET proteins in young mice. PMID:26392221
Merkel cell polyomavirus T antigens promote cell proliferation and inflammatory cytokine gene expression. PMID:26385761
Extracting tumor tissue immune status from expression profiles: correlating renal cancer prognosis with tumor-associated immunome. PMID:26384298
1918 pandemic influenza virus and Streptococcus pneumoniae co-infection results in activation of coagulation and widespread pulmonary thrombosis in mice and humans. PMID:26383585
MetaRNA-Seq: An Interactive Tool to Browse and Annotate Metadata from RNA-Seq Studies. PMID:26380270
DNA Damage Response Checkpoint Activation Drives KP1019 Dependent Pre-Anaphase Cell Cycle Delay in S. cerevisiae. PMID:26375390
Cross-Talk in the Female Rat Mammary Gland: Influence of Aryl Hydrocarbon Receptor on Estrogen Receptor Signaling. PMID:26372666
Identification of transcripts regulated by CUG-BP, Elav-like family member 1 (CELF1) in primary embryonic cardiomyocytes by RNA-seq. PMID:26366374
Epigenetic synergy between decitabine and platinum derivatives. PMID:26366234
Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases. PMID:26362267
High-fructose diet during periadolescent development increases depressive-like behavior and remodels the hypothalamic transcriptome in male rats. PMID:26356038
WDR5 Expression Is Prognostic of Breast Cancer Outcome. PMID:26355959
Cross Platform Standardisation of an Experimental Pipeline for Use in the Identification of Dysregulated Human Circulating MiRNAs. PMID:26355751
DKK1 is a potential novel mediator of cisplatin-refractoriness in non-small cell lung cancer cell lines. PMID:26353782
Biochemical isolation of Argonaute protein complexes by Ago-APP. PMID:26351695
Growth-Phase-Specific Modulation of Cell Morphology and Gene Expression by an Archaeal Histone Protein. PMID:26350964
New Technologies for Studying Biofilms. PMID:26350329
Turning publicly available gene expression data into discoveries using gene set context analysis. PMID:26350211
RNA sequencing provides exquisite insight into the manipulation of the alveolar macrophage by tubercle bacilli. PMID:26346536
Geroprotectors.org: a new, structured and curated database of current therapeutic interventions in aging and age-related disease. PMID:26342919
A distinct gene expression signature characterizes human neuroblastoma cancer stem cells. PMID:26342562
ABO blood type correlates with survival on prostate cancer vaccine therapy. PMID:26338967
Seq-ing improved gene expression estimates from microarrays using machine learning. PMID:26338512
Global analysis of asymmetric RNA enrichment in oocytes reveals low conservation between closely related Xenopus species. PMID:26337391
Na+/K+-ATPase α1 subunit, a novel therapeutic target for hepatocellular carcinoma. PMID:26334094
Comparative Analysis of Label-Free and 8-Plex iTRAQ Approach for Quantitative Tissue Proteomic Analysis. PMID:26331617
Deciphering Cis-Regulatory Element Mediated Combinatorial Regulation in Rice under Blast Infected Condition. PMID:26327607
Microarray Analysis of Copy Number Variants on the Human Y Chromosome Reveals Novel and Frequent Duplications Overrepresented in Specific Haplogroups. PMID:26322892
Lhx5 controls mamillary differentiation in the developing hypothalamus of the mouse. PMID:26321924
The histone variant H2A.Z is an important regulator of enhancer activity. PMID:26319018
Citing a Data Repository: A Case Study of the Protein Data Bank. PMID:26317409
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. PMID:26313928
The RNA-binding protein Sam68 regulates expression and transcription function of the androgen receptor splice variant AR-V7. PMID:26310125
Mitochondrial uncoupling links lipid catabolism to Akt inhibition and resistance to tumorigenesis. PMID:26310111
Immune cell subsets and their gene expression profiles from human PBMC isolated by Vacutainer Cell Preparation Tube (CPT™) and standard density gradient. PMID:26307036
Integrating Gene Regulatory Networks to identify cancer-specific genes. PMID:26306224
The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity. PMID:26306205
Oligoribonuclease is a central feature of cyclic diguanylate signaling in Pseudomonas aeruginosa. PMID:26305928
Cis-acting signals modulate the efficiency of programmed DNA elimination in Paramecium tetraurelia. PMID:26304543
Perivascular Mesenchymal Stem Cells From the Adult Human Brain Harbor No Instrinsic Neuroectodermal but High Mesodermal Differentiation Potential. PMID:26304036
Finding mouse models of human lymphomas and leukemia's using the Jackson laboratory mouse tumor biology database. PMID:26302176
Transcriptomic changes in the plant pathogenic fungus Rhizoctonia solani AG-3 in response to the antagonistic bacteria Serratia proteamaculans and Serratia plymuthica. PMID:26296338
DIS3 shapes the RNA polymerase II transcriptome in humans by degrading a variety of unwanted transcripts. PMID:26294688
Evaluation of Left Ventricle Function by Regional Fractional Area Change (RFAC) in a Mouse Model of Myocardial Infarction Secondary to Valsartan Treatment. PMID:26291973
Dipeptide species regulate p38MAPK-Smad3 signalling to maintain chronic myelogenous leukaemia stem cells. PMID:26289811
Macrophage cell death and transcriptional response are actively triggered by the fungal virulence factor Cbp1 during H. capsulatum infection. PMID:26288377
Exercise-mimetic AICAR transiently benefits brain function. PMID:26286955
Topologically inferring pathway activity toward precise cancer classification via integrating genomic and metabolomic data: prostate cancer as a case. PMID:26286638
Uterine overdistention induces preterm labor mediated by inflammation: observations in pregnant women and nonhuman primates. PMID:26284599
aRrayLasso: a network-based approach to microarray interconversion. PMID:26283699
EphA2 Expression Is a Key Driver of Migration and Invasion and a Poor Prognostic Marker in Colorectal Cancer. PMID:26283684
Simultaneous Host-Pathogen Transcriptome Analysis during Granulibacter bethesdensis Infection of Neutrophils from Healthy Subjects and Patients with Chronic Granulomatous Disease. PMID:26283340
Functional Analysis and Characterization of Differential Coexpression Networks. PMID:26282208
Analysis of Polygenic Mutants Suggests a Role for Mediator in Regulating Transcriptional Activation Distance in Saccharomyces cerevisiae. PMID:26281848
ApiAP2 Factors as Candidate Regulators of Stochastic Commitment to Merozoite Production in Theileria annulata. PMID:26273826
Gene Coexpression and Evolutionary Conservation Analysis of the Human Preimplantation Embryos. PMID:26273607
Derivation of a fifteen gene prognostic panel for six cancers. PMID:26272668
Next Generation Sequencing Analysis Reveals Segmental Patterns of microRNA Expression in Mouse Epididymal Epithelial Cells. PMID:26270822
Modulator of apoptosis 1 (MOAP-1) is a tumor suppressor protein linked to the RASSF1A protein. PMID:26269600
Integrative systems analysis of diet-induced obesity identified a critical transition in the transcriptomes of the murine liver and epididymal white adipose tissue. PMID:26268884
Transcription Factor Repertoire of Homeostatic Eosinophilopoiesis. PMID:26268651
Systems biology approach to studying proliferation-dependent prognostic subnetworks in breast cancer. PMID:26257336
Proton irradiation impacts age-driven modulations of cancer progression influenced by immune system transcriptome modifications from splenic tissue. PMID:26253138
Potential roles of microRNA-29a in the molecular pathophysiology of T-cell acute lymphoblastic leukemia. PMID:26251039
Gene Expression Profile in the Liver of BALB/c Mice Infected with Fasciola hepatica. PMID:26247779
Self-renewing diploid Axin2(+) cells fuel homeostatic renewal of the liver. PMID:26245375
Prenatal Exposure to DEHP Affects Spermatogenesis and Sperm DNA Methylation in a Strain-Dependent Manner. PMID:26244509
Understanding the aristolochic acid toxicities in rat kidneys with regulatory networks. PMID:26243830
A transcriptomal analysis of bovine oviductal epithelial cells collected during the follicular phase versus the luteal phase of the estrous cycle. PMID:26242217
Tissue Remodelling following Resection of Porcine Liver. PMID:26240819
Proteomics analysis reveals differentially activated pathways that operate in peanut gynophores at different developmental stages. PMID:26239120
IscR of Rhodobacter sphaeroides functions as repressor of genes for iron-sulfur metabolism and represents a new type of iron-sulfur-binding protein. PMID:26235649
mRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA-sequencing data. PMID:26234653
Identification of Oxygen-Responsive Transcripts in the Silage Inoculant Lactobacillus buchneri CD034 by RNA Sequencing. PMID:26230316
Differential miRNA expression in inherently high- and low-active inbred mice. PMID:26229004
Integrated genomic analyses identify KDM1A's role in cell proliferation via modulating E2F signaling activity and associate with poor clinical outcome in oral cancer. PMID:26225839
Transcriptome Profiling of Developing Murine Lens Through RNA Sequencing. PMID:26225632
Differential gene methylation in paired glioblastomas suggests a role of immune response pathways in tumor progression. PMID:26224161
Small molecule and RNAi induced phenotype transition of expanded and primary colonic epithelial cells. PMID:26223582
Biological processes and pathway changes in isoflurane-induced anesthesia revealed by bioinformatics analysis of gene expression profiles. PMID:26223573
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
Integrated systems approach identifies risk regulatory pathways and key regulators in coronary artery disease. PMID:26208504
Gene Expression in Experimental Aortic Coarctation and Repair: Candidate Genes for Therapeutic Intervention? PMID:26207811
Copy-number variations in hepatoblastoma associate with unique clinical features. PMID:26201635
Empirical comparison of structure-based pathway methods. PMID:26197809
MDA-MB-231 breast cancer cells overexpressing single VEGF isoforms display distinct colonisation characteristics. PMID:26196186
A tuberculosis ontology for host systems biology. PMID:26190839
Functional Analysis of Chicken IRF7 in Response to dsRNA Analog Poly(I:C) by Integrating Overexpression and Knockdown. PMID:26186542
Pharyngeal Satellite Cells Undergo Myogenesis Under Basal Conditions and Are Required for Pharyngeal Muscle Maintenance. PMID:26178867
Genome-Wide Reprogramming of Transcript Architecture by Temperature Specifies the Developmental States of the Human Pathogen Histoplasma. PMID:26177267
Systemic and Ocular Long Pentraxin 3 in Patients with Age-Related Macular Degeneration. PMID:26176960
Identification of reproducible drug-resistance-related dysregulated genes in small-scale cancer cell line experiments. PMID:26173481
LXRs link metabolism to inflammation through Abca1-dependent regulation of membrane composition and TLR signaling. PMID:26173179
Characteristic expression of MSX1, MSX2, TBX2 and ENTPD1 in dental pulp cells. PMID:26171167
Methylating micronutrient supplementation during pregnancy influences foetal hepatic gene expression and IGF signalling and increases foetal weight. PMID:26169873
Transcriptional fingerprinting of "browning" white fat identifies NRG4 as a novel adipokine. PMID:26167402
Olfactomedin 4 Serves as a Marker for Disease Severity in Pediatric Respiratory Syncytial Virus (RSV) Infection. PMID:26162090
Simulated Microgravity Exerts an Age-Dependent Effect on the Differentiation of Cardiovascular Progenitors Isolated from the Human Heart. PMID:26161778
Using gene expression signatures to identify novel treatment strategies in gulf war illness. PMID:26156520
Survival Rate and Transcriptional Response upon Infection with the Generalist Parasite Beauveria bassiana in a World-Wide Sample of Drosophila melanogaster. PMID:26154519
NKX2-5 mutations causative for congenital heart disease retain functionality and are directed to hundreds of targets. PMID:26146939
Immunobiotic Lactobacillus administered post-exposure averts the lethal sequelae of respiratory virus infection. PMID:26145728
Bioinformatics analysis to identify the differentially expressed genes of glaucoma. PMID:26135629
Identification of Chemical Inhibitors of β-Catenin-Driven Liver Tumorigenesis in Zebrafish. PMID:26134322
An Integrated Prognostic Classifier for Stage I Lung Adenocarcinoma Based on mRNA, microRNA, and DNA Methylation Biomarkers. PMID:26134223
Genetic Analysis of T Cell Lymphomas in Carbon Ion-Irradiated Mice Reveals Frequent Interstitial Chromosome Deletions: Implications for Second Cancer Induction in Normal Tissues during Carbon Ion Radiotherapy. PMID:26125582
A second trigeminal CGRP receptor: function and expression of the AMY1 receptor. PMID:26125036
MicroRNA-132 enhances transition from inflammation to proliferation during wound healing. PMID:26121747
Identification of Cyclobutane Pyrimidine Dimer-Responsive Genes Using UVB-Irradiated Human Keratinocytes Transfected with In Vitro-Synthesized Photolyase mRNA. PMID:26121660
Kidney Regeneration: Lessons from Development. PMID:26120499
IL-10 Production in Macrophages Is Regulated by a TLR-Driven CREB-Mediated Mechanism That Is Linked to Genes Involved in Cell Metabolism. PMID:26116503
Expression quantitative trait locus analysis for translational medicine. PMID:26110023
In Pursuit of New Imprinting Syndromes by Epimutation Screening in Idiopathic Neurodevelopmental Disorder Patients. PMID:26106604
Synaptic microRNAs Coordinately Regulate Synaptic mRNAs: Perturbation by Chronic Alcohol Consumption. PMID:26105134
A salt-regulated peptide derived from the CAP superfamily protein negatively regulates salt-stress tolerance in Arabidopsis. PMID:26093145
A predicted protein interactome identifies conserved global networks and disease resistance subnetworks in maize. PMID:26089837
Extensive rewiring of epithelial-stromal co-expression networks in breast cancer. PMID:26087699
Evidence for Immune Response, Axonal Dysfunction and Reduced Endocytosis in the Substantia Nigra in Early Stage Parkinson's Disease. PMID:26087293
Selection for Improved Energy Use Efficiency and Drought Tolerance in Canola Results in Distinct Transcriptome and Epigenome Changes. PMID:26082400
Targeting PBK/TOPK decreases growth and survival of glioma initiating cells in vitro and attenuates tumor growth in vivo. PMID:26081429
Autoantigen microarrays reveal autoantibodies associated with proliferative nephritis and active disease in pediatric systemic lupus erythematosus. PMID:26081107
Genome-wide transcriptomic analysis of a superior biomass-degrading strain of A. fumigatus revealed active lignocellulose-degrading genes. PMID:26076650
Silencing of Essential Genes within a Highly Coordinated Operon in Escherichia coli. PMID:26070674
Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA. PMID:26070627
Identification of Gene and MicroRNA Signatures for Oral Cancer Developed from Oral Leukoplakia. PMID:26064958
The TF-miRNA Coregulation Network in Oral Lichen Planus. PMID:26064947
Lysosome and Cytoskeleton Pathways Are Robustly Enriched in the Blood of Septic Patients: A Meta-Analysis of Transcriptomic Data. PMID:26063982
A Pitx2-MicroRNA Pathway Modulates Cell Proliferation in Myoblasts and Skeletal-Muscle Satellite Cells and Promotes Their Commitment to a Myogenic Cell Fate. PMID:26055324
Differential MicroRNA Expression in Human Macrophages with Mycobacterium tuberculosis Infection of Beijing/W and Non-Beijing/W Strain Types. PMID:26053546
E2F8 promotes hepatic steatosis through FABP3 expression in diet-induced obesity in zebrafish. PMID:26052340
An integrated genomic analysis of papillary renal cell carcinoma type 1 uncovers the role of focal adhesion and extracellular matrix pathways. PMID:26051997
The pervasiveness and plasticity of circadian oscillations: the coupled circadian-oscillators framework. PMID:26049162
Impact of microfluidic processing on bacterial ribonucleic acid expression. PMID:26045727
High mobility group protein-mediated transcription requires DNA damage marker γ-H2AX. PMID:26045162
Combined analysis of gene regulatory network and SNV information enhances identification of potential gene markers in mouse knockout studies with small number of samples. PMID:26044212
Integrative analyses of cancer data: a review from a statistical perspective. PMID:26041968
quantro: a data-driven approach to guide the choice of an appropriate normalization method. PMID:26040460
Identification of novel gene targets and putative regulators of arsenic-associated DNA methylation in human urothelial cells and bladder cancer. PMID:26039340
FGFR2 is overexpressed in myxoid liposarcoma and inhibition of FGFR signaling impairs tumor growth in vitro. PMID:26036639
Deletion of the App-Runx1 region in mice models human partial monosomy 21. PMID:26035870
Transcription factor p63 bookmarks and regulates dynamic enhancers during epidermal differentiation. PMID:26034101
Dietary MicroRNA Database (DMD): An Archive Database and Analytic Tool for Food-Borne microRNAs. PMID:26030752
Dnmt1 is essential to maintain progenitors in the perinatal intestinal epithelium. PMID:26023099
Whole Genome Sequence of Multiple Myeloma-Prone C57BL/KaLwRij Mouse Strain Suggests the Origin of Disease Involves Multiple Cell Types. PMID:26020268
GECluster: a novel protein complex prediction method. PMID:26019559
The combination of HDAC and aminopeptidase inhibitors is highly synergistic in myeloma and leads to disruption of the NFκB signalling pathway. PMID:26015393
Low folate and selenium in the mouse maternal diet alters liver gene expression patterns in the offspring after weaning. PMID:26007332
RasGRP1 opposes proliferative EGFR-SOS1-Ras signals and restricts intestinal epithelial cell growth. PMID:26005835
In Vivo imaging reveals extracellular vesicle-mediated phenocopying of metastatic behavior. PMID:26000481
The kinase DYRK1A reciprocally regulates the differentiation of Th17 and regulatory T cells. PMID:25998054
Gene set enrichment analysis of pathways and transcription factors associated with diabetic retinopathy using a microarray dataset. PMID:25997411
A Combined Omics Approach to Generate the Surface Atlas of Human Naive CD4+ T Cells during Early T-Cell Receptor Activation. PMID:25991687
Significant expansion of the REST/NRSF cistrome in human versus mouse embryonic stem cells: potential implications for neural development. PMID:25990720
Identification of targets for rational pharmacological therapy in childhood craniopharyngioma. PMID:25990246
The fission yeast MTREC complex targets CUTs and unspliced pre-mRNAs to the nuclear exosome. PMID:25989903
Reverse enGENEering of Regulatory Networks from Big Data: A Roadmap for Biologists. PMID:25983554
Repression by H-NS of genes required for the biosynthesis of the Vibrio cholerae biofilm matrix is modulated by the second messenger cyclic diguanylic acid. PMID:25982817
Latent Pathways Identification by Microarray Expression Profiles in Thyroid-Associated Ophthalmopathy Patients. PMID:25982257
A ranking-based meta-analysis reveals let-7 family as a meta-signature for grade classification in breast cancer. PMID:25978727
Cell Cycle Control by the Master Regulator CtrA in Sinorhizobium meliloti. PMID:25978424
GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions. PMID:25971742
Genome-wide gene expression analysis for target genes to differentiate patients with intestinal tuberculosis and Crohn's disease and discriminative value of FOXP3 mRNA expression. PMID:25969456
Interleukin-6/STAT3 Pathway Signaling Drives an Inflammatory Phenotype in Group A Ependymoma. PMID:25968456
Probe Region Expression Estimation for RNA-Seq Data for Improved Microarray Comparability. PMID:25966034
Mutant U2AF1 Expression Alters Hematopoiesis and Pre-mRNA Splicing In Vivo. PMID:25965570
Revisiting the transcriptional analysis of primary tumours and associated nodal metastases with enhanced biological and statistical controls: application to thyroid cancer. PMID:25965298
Revealing the Molecular Portrait of Triple Negative Breast Tumors in an Understudied Population through Omics Analysis of Formalin-Fixed and Paraffin-Embedded Tissues. PMID:25961742
Investigation into the annotation of protocol sequencing steps in the sequence read archive. PMID:25960871
Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing xylem. PMID:25957781
Gene expression profiling of porcine mammary epithelial cells after challenge with Escherichia coli and Staphylococcus aureus in vitro. PMID:25948480
Activation of defence pathways in Scots pine bark after feeding by pine weevil (Hylobius abietis). PMID:25943104
Bias in ligation-based small RNA sequencing library construction is determined by adaptor and RNA structure. PMID:25942392
Genome-wide co-occupancy of AML1-ETO and N-CoR defines the t(8;21) AML signature in leukemic cells. PMID:25928846
Identification of sample-specific regulations using integrative network level analysis. PMID:25928379
New Noncoding Lytic Transcripts Derived from the Epstein-Barr Virus Latency Origin of Replication, oriP, Are Hyperedited, Bind the Paraspeckle Protein, NONO/p54nrb, and Support Viral Lytic Transcription. PMID:25926645
Argonaute 2 Binds Directly to tRNA Genes and Promotes Gene Repression in cis. PMID:25918241
Tracking the Elusive Function of Bacillus subtilis Hfq. PMID:25915524
Protein microarrays: a new tool for the study of autoantibodies in immunodeficiency. PMID:25904912
A technology platform to assess multiple cancer agents simultaneously within a patient's tumor. PMID:25904742
Re-replication of a centromere induces chromosomal instability and aneuploidy. PMID:25901968
Functional and mechanistic studies of XPC DNA-repair complex as transcriptional coactivator in embryonic stem cells. PMID:25901318
Modulation of dendritic cell alternative activation and function by the vitamin A metabolite retinoic acid. PMID:25899567
ChiNet uncovers rewired transcription subnetworks in tolerant yeast for advanced biofuels conversion. PMID:25897127
Histone modifications induced by MDV infection at early cytolytic and latency phases. PMID:25896894
Anti-repulsive Guidance Molecule C (RGMc) Antibodies Increases Serum Iron in Rats and Cynomolgus Monkeys by Hepcidin Downregulation. PMID:25896304
Gene Expression Analyses during Spontaneous Reversal of Cardiomyopathy in Mice with Repressed Nuclear CUG-BP, Elav-Like Family (CELF) Activity in Heart Muscle. PMID:25894229
Integrated compensatory network is activated in the absence of NCC phosphorylation. PMID:25893600
Systems medicine: evolution of systems biology from bench to bedside. PMID:25891169
Kinetics of gene expression and bone remodelling in the clinical phase of collagen-induced arthritis. PMID:25889670
miR-10b-5p expression in Huntington's disease brain relates to age of onset and the extent of striatal involvement. PMID:25889241
Combinatorial Conflicting Homozygosity (CCH) analysis enables the rapid identification of shared genomic regions in the presence of multiple phenocopies. PMID:25888400
A mRNA landscape of bovine embryos after standard and MAPK-inhibited culture conditions: a comparative analysis. PMID:25888366
Identifying module biomarker in type 2 diabetes mellitus by discriminative area of functional activity. PMID:25888350
Copy number variations in high and low fertility breeding boars. PMID:25888238
Identification of active miRNA and transcription factor regulatory pathways in human obesity-related inflammation. PMID:25887648
Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila. PMID:25887553
Copy number variation in Y chromosome multicopy genes is linked to a paternal parent-of-origin effect on CNS autoimmune disease in female offspring. PMID:25886764
Denoising perturbation signatures reveal an actionable AKT-signaling gene module underlying a poor clinical outcome in endocrine-treated ER+ breast cancer. PMID:25886003
The role of HGF/MET and FGF/FGFR in fibroblast-derived growth stimulation and lapatinib-resistance of esophageal squamous cell carcinoma. PMID:25884729
The ependymal region of the adult human spinal cord differs from other species and shows ependymoma-like features. PMID:25882650
Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions. PMID:25881257
Nourishment level affects caste-related gene expression in Polistes wasps. PMID:25880983
Advanced age is associated with worsened outcomes and a unique genomic response in severely injured patients with hemorrhagic shock. PMID:25880307
Global gene expression in granulosa cells of growing, plateau and atretic dominant follicles in cattle. PMID:25879740
Transcriptional programming of human macrophages: on the way to systems immunology. PMID:25877862
Understanding developmental and adaptive cues in pine through metabolite profiling and co-expression network analysis. PMID:25873654
Molecular mechanism of flocculation self-recognition in yeast and its role in mating and survival. PMID:25873380
Metabolic reprogramming in triple-negative breast cancer through Myc suppression of TXNIP. PMID:25870263
GWAS for executive function and processing speed suggests involvement of the CADM2 gene. PMID:25869804
Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state. PMID:25865119
Retinoic acid-independent expression of Meis2 during autopod patterning in the developing bat and mouse limb. PMID:25861444
Modeling discrete survival time using genomic feature data. PMID:25861216
MYB controls erythroid versus megakaryocyte lineage fate decision through the miR-486-3p-mediated downregulation of MAF. PMID:25857263
Histone methyltransferase Setd8 represses Gata2 expression and regulates erythroid maturation. PMID:25848090
Regulatory network inferred using expression data of small sample size: application and validation in erythroid system. PMID:25840044
Clinical decision support systems for improving diagnostic accuracy and achieving precision medicine. PMID:25834725
Disease-Associated Single-Nucleotide Polymorphisms From Noncoding Regions in Juvenile Idiopathic Arthritis Are Located Within or Adjacent to Functional Genomic Elements of Human Neutrophils and CD4+ T Cells. PMID:25833190
A comparative study of improvements Pre-filter methods bring on feature selection using microarray data. PMID:25825671
Expression profiles of 151 pediatric low-grade gliomas reveal molecular differences associated with location and histological subtype. PMID:25825052
Conditioned medium from human amniotic mesenchymal stromal cells limits infarct size and enhances angiogenesis. PMID:25824141
Transcriptomics of maternal and fetal membranes can discriminate between gestational-age matched preterm neonates with and without cognitive impairment diagnosed at 18-24 months. PMID:25822971
Transcriptome analysis of post-hatch breast muscle in legacy and modern broiler chickens reveals enrichment of several regulators of myogenic growth. PMID:25821972
RNA polymerase II pausing can be retained or acquired during activation of genes involved in the epithelial to mesenchymal transition. PMID:25820424
Isoflavones in soy flour diet have different effects on whole-genome expression patterns than purified isoflavone mix in human MCF-7 breast tumors in ovariectomized athymic nude mice. PMID:25820259
Biomarker-based classification of bacterial and fungal whole-blood infections in a genome-wide expression study. PMID:25814982
Parallel epigenomic and transcriptomic responses to viral infection in honey bees (Apis mellifera). PMID:25811620
Dual RNA sequencing reveals the expression of unique transcriptomic signatures in lipopolysaccharide-induced BV-2 microglial cells. PMID:25811458
Herb-Partitioned Moxibustion and the miRNAs Related to Crohn's Disease: A Study Based on Rat Models. PMID:25810742
A gene co-expression network predicts functional genes controlling the re-establishment of desiccation tolerance in germinated Arabidopsis thaliana seeds. PMID:25809152
Discovery of molecular markers to discriminate corneal endothelial cells in the human body. PMID:25807145
SRD: a Staphylococcus regulatory RNA database. PMID:25805861
Gene expression profiling to investigate tyrosol-induced lifespan extension in Caenorhabditis elegans. PMID:25804201
Identification of a microRNA signature for the diagnosis of fibromyalgia. PMID:25803872
T-cell activation and early gene response in dogs. PMID:25803042
Loss of Lrig1 leads to expansion of Brunner glands followed by duodenal adenomas with gastric metaplasia. PMID:25794708
IP3 3-kinase B controls hematopoietic stem cell homeostasis and prevents lethal hematopoietic failure in mice. PMID:25788703
HSET overexpression fuels tumor progression via centrosome clustering-independent mechanisms in breast cancer patients. PMID:25788277
Optimal drug prediction from personal genomics profiles. PMID:25781964
Functional analysis of sirtuin genes in multiple Plasmodium falciparum strains. PMID:25780929
The carbon starvation response of the ectomycorrhizal fungus Paxillus involutus. PMID:25778509
A cluster of four homologous small RNAs modulates C1 metabolism and the pyruvate dehydrogenase complex in Rhodobacter sphaeroides under various stress conditions. PMID:25777678
The Sinorhizobium meliloti SyrM regulon: effects on global gene expression are mediated by syrA and nodD3. PMID:25777671
Microbial forensics: predicting phenotypic characteristics and environmental conditions from large-scale gene expression profiles. PMID:25774498
A New Augmentation Based Algorithm for Extracting Maximal Chordal Subgraphs. PMID:25767331
Haploinsufficiency of Hedgehog interacting protein causes increased emphysema induced by cigarette smoke through network rewiring. PMID:25763110
A novel miRNA-based predictive model for biochemical failure following post-prostatectomy salvage radiation therapy. PMID:25760964
Expression of three topologically distinct membrane proteins elicits unique stress response pathways in the yeast Saccharomyces cerevisiae. PMID:25759377
Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli. PMID:25757888
Tracking the best reference genes for RT-qPCR data normalization in filamentous fungi. PMID:25757610
Language workbench user interfaces for data analysis. PMID:25755929
Histone Deacetylase Inhibitors (HDACi) Cause the Selective Depletion of Bromodomain Containing Proteins (BCPs). PMID:25755299
Arabidopsis flower specific defense gene expression patterns affect resistance to pathogens. PMID:25750645
A continuous molecular roadmap to iPSC reprogramming through progression analysis of single-cell mass cytometry. PMID:25748935
A melanoma subtype with intrinsic resistance to BRAF inhibition identified by receptor tyrosine kinases gene-driven classification. PMID:25742786
Systems biology approaches for advancing the discovery of effective drug combinations. PMID:25741385
Toxicogenomics profiling of bone marrow from rats treated with topotecan in combination with oxaliplatin: a mechanistic strategy to inform combination toxicity. PMID:25729387
Potent degradation of neuronal miRNAs induced by highly complementary targets. PMID:25724380
Early telomerase inactivation accelerates aging independently of telomere length. PMID:25723167
Gateways to the FANTOM5 promoter level mammalian expression atlas. PMID:25723102
Lysosomal calcium signalling regulates autophagy through calcineurin and TFEB. PMID:25720963
A MEIG1/PACRG complex in the manchette is essential for building the sperm flagella. PMID:25715396
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
Gene expression in obliterative bronchiolitis-like lesions in 2,3-pentanedione-exposed rats. PMID:25710175
CD14 and complement crosstalk and largely mediate the transcriptional response to Escherichia coli in human whole blood as revealed by DNA microarray. PMID:25706641
Oncogenic properties of apoptotic tumor cells in aggressive B cell lymphoma. PMID:25702581
The PDZ-domain protein Whirlin facilitates mechanosensory signaling in mammalian proprioceptors. PMID:25698744
Functions of BET proteins in erythroid gene expression. PMID:25696920
Transcriptional attenuation controls macrolide inducible efflux and resistance in Streptococcus pneumoniae and in other Gram-positive bacteria containing mef/mel(msr(D)) elements. PMID:25695510
The arabidopsis DNA polymerase δ has a role in the deposition of transcriptionally active epigenetic marks, development and flowering. PMID:25693187
Comparison of drought stress response and gene expression between a GM maize variety and a near-isogenic non-GM variety. PMID:25692547
Evidence-based translation for the genomic responses of murine models for the study of human immunity. PMID:25680113
Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling. PMID:25679813
Transcriptome and metabolome analysis of plant sulfate starvation and resupply provides novel information on transcriptional regulation of metabolism associated with sulfur, nitrogen and phosphorus nutritional responses in Arabidopsis. PMID:25674096
A statistically inferred microRNA network identifies breast cancer target miR-940 as an actin cytoskeleton regulator. PMID:25673565
Ribosomal and immune transcripts associate with relapse in acquired ADAMTS13-deficient thrombotic thrombocytopenic purpura. PMID:25671313
FlowerNet: a gene expression correlation network for anther and pollen development. PMID:25667314
Identification and validation of the methylation biomarkers of non-small cell lung cancer (NSCLC). PMID:25657825
microRNA profiling in the zoonotic parasite Echinococcus canadensis using a high-throughput approach. PMID:25656283
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
Antigen expression determines adenoviral vaccine potency independent of IFN and STING signaling. PMID:25642773
Human promoters are intrinsically directional. PMID:25639469
Messenger RNA processing is altered in autosomal dominant leukodystrophy. PMID:25637521
Prioritizing causal disease genes using unbiased genomic features. PMID:25633252
Using the canary genome to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds. PMID:25631560
PhenomeExpress: a refined network analysis of expression datasets by inclusion of known disease phenotypes. PMID:25631385
Evolutionary adaptation of an AraC-like regulatory protein in Citrobacter rodentium and Escherichia species. PMID:25624355
A systems-level approach to parental genomic imprinting: the imprinted gene network includes extracellular matrix genes and regulates cell cycle exit and differentiation. PMID:25614607
Memory T cells specific for murine cytomegalovirus re-emerge after multiple challenges and recapitulate immunity in various adoptive transfer scenarios. PMID:25595792
Peax: interactive visual analysis and exploration of complex clinical phenotype and gene expression association. PMID:25592601
Contribution of non-reference alleles in mtDNA of Alzheimer's disease patients. PMID:25590040
Defining the transcriptomic landscape of Candida glabrata by RNA-Seq. PMID:25586221
Sublethal concentrations of carbapenems alter cell morphology and genomic expression of Klebsiella pneumoniae biofilms. PMID:25583711
Targeted exploration and analysis of large cross-platform human transcriptomic compendia. PMID:25581801
A subcutaneous adipose tissue-liver signalling axis controls hepatic gluconeogenesis. PMID:25581158
A survey of computational intelligence techniques in protein function prediction. PMID:25574395
The dam replacing gene product enhances Neisseria gonorrhoeae FA1090 viability and biofilm formation. PMID:25566225
Gene regulatory network analysis reveals differences in site-specific cell fate determination in mammalian brain. PMID:25565969
The naked endosperm genes encode duplicate INDETERMINATE domain transcription factors required for maize endosperm cell patterning and differentiation. PMID:25552497
SUMO ligase PIAS1 functions as a target gene selective androgen receptor coregulator on prostate cancer cell chromatin. PMID:25552417
Expression of tumor necrosis factor-alpha-mediated genes predicts recurrence-free survival in lung cancer. PMID:25548907
Transcriptional analysis of micro-dissected articular cartilage in post-traumatic murine osteoarthritis. PMID:25545425
Transcriptome analysis of Enterococcus faecalis during mammalian infection shows cells undergo adaptation and exist in a stringent response state. PMID:25545155
Analysis of the basal chordate Botryllus schlosseri reveals a set of genes associated with fertility. PMID:25542255
Bioinformatic identification of connective tissue growth factor as an osteogenic protein within skeletal muscle. PMID:25539834
Reproducibility enhancement and differential expression of non predefined functional gene sets in human genome. PMID:25539829
TSLP expression: analysis with a ZsGreen TSLP reporter mouse. PMID:25539812
Changes in activity of metabolic and regulatory pathways during germination of S. coelicolor. PMID:25539760
The relative importance of DNA methylation and Dnmt2-mediated epigenetic regulation on Wolbachia densities and cytoplasmic incompatibility. PMID:25538866
Global analysis of methylation profiles from high resolution CpG data. PMID:25537884
MicroRNA-7 inhibits multiple oncogenic pathways to suppress HER2Δ16 mediated breast tumorigenesis and reverse trastuzumab resistance. PMID:25532106
RNA-seq analysis reveals significant transcriptome changes in turbot (Scophthalmus maximus) suffering severe enteromyxosis. PMID:25526753
Assessment of cancer cell line representativeness using microarrays for Merkel cell carcinoma. PMID:25521454
Protein acetylation affects acetate metabolism, motility and acid stress response in Escherichia coli. PMID:25518064
Genes associated with thermosensitive genic male sterility in rice identified by comparative expression profiling. PMID:25512054
MicroRNA Profiling of Laser-Microdissected Hepatocellular Carcinoma Reveals an Oncogenic Phenotype of the Tumor Capsule. PMID:25500075
MiR-score: a novel 6-microRNA signature that predicts survival outcomes in patients with malignant pleural mesothelioma. PMID:25497279
RNA-seq analysis of broiler liver transcriptome reveals novel responses to high ambient temperature. PMID:25494716
Natural Variation in Fish Transcriptomes: Comparative Analysis of the Fathead Minnow (Pimephales promelas) and Zebrafish (Danio rerio). PMID:25493933
Meta-analysis of human methylomes reveals stably methylated sequences surrounding CpG islands associated with high gene expression. PMID:25493099
Pathomx: an interactive workflow-based tool for the analysis of metabolomic data. PMID:25490956
Establishment of the neurogenic boundary of the mouse retina requires cooperation of SOX2 and WNT signaling. PMID:25488119
Gene Expression Characterization of HPV Positive Head and Neck Cancer to Predict Response to Chemoradiation. PMID:25481760
Human Hematopoietic Signal peptide-containing Secreted 1 (hHSS1) modulates genes and pathways in glioma: implications for the regulation of tumorigenicity and angiogenesis. PMID:25481245
Genetic variants modify the effect of age on APOE methylation in the Genetics of Lipid Lowering Drugs and Diet Network study. PMID:25476875
The COPD Knowledge Base: enabling data analysis and computational simulation in translational COPD research. PMID:25471253
TRIM37 is a new histone H2A ubiquitin ligase and breast cancer oncoprotein. PMID:25470042
Comparative gene expression of Wigglesworthia inhabiting non-infected and Trypanosoma brucei gambiense-infected Glossina palpalis gambiensis flies. PMID:25452752
The novel small leucine-rich protein chondroadherin-like (CHADL) is expressed in cartilage and modulates chondrocyte differentiation. PMID:25451920
Diversity, expression and mRNA targeting abilities of Argonaute-targeting miRNAs among selected vascular plants. PMID:25443390
Functional characterization of a Nudix hydrolase AtNUDX8 upon pathogen attack indicates a positive role in plant immune responses. PMID:25436909
Impact of analytic provenance in genome analysis. PMID:25435180
Gene expression microarray analysis of the sciatic nerve of mice with diabetic neuropathy. PMID:25435094
Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms. PMID:25431329
Transcriptional evidence for the role of chronic venlafaxine treatment in neurotrophic signaling and neuroplasticity including also Glutamatergic [corrected] - and insulin-mediated neuronal processes. PMID:25423262
The phenotypic manifestations of rare genic CNVs in autism spectrum disorder. PMID:25421404
SHMT1 knockdown induces apoptosis in lung cancer cells by causing uracil misincorporation. PMID:25412303
Shift in GATA3 functions, and GATA3 mutations, control progression and clinical presentation in breast cancer. PMID:25410484
Uromodulin retention in thick ascending limb of Henle's loop affects SCD1 in neighboring proximal tubule: renal transcriptome studies in mouse models of uromodulin-associated kidney disease. PMID:25409434
Transcriptional profiling of human epithelial cells infected with plasmid-bearing and plasmid-deficient Chlamydia trachomatis. PMID:25404022
Glucose tolerance is associated with differential expression of microRNAs in skeletal muscle: results from studies of twins with and without type 2 diabetes. PMID:25403480
Genomic landscape of metastatic colorectal cancer. PMID:25394515
The Aspergillus nidulans metZ gene encodes a transcription factor involved in regulation of sulfur metabolism in this fungus and other Eurotiales. PMID:25391366
Genomic characterization of variable surface antigens reveals a telomere position effect as a prerequisite for RNA interference-mediated silencing in Paramecium tetraurelia. PMID:25389173
CpG preconditioning regulates miRNA expression that modulates genomic reprogramming associated with neuroprotection against ischemic injury. PMID:25388675
Prolonged growth of a clinical Staphylococcus aureus strain selects for a stable small-colony-variant cell type. PMID:25385795
Sustained β-catenin activity in dermal fibroblasts promotes fibrosis by up-regulating expression of extracellular matrix protein-coding genes. PMID:25385294
Broad integration of expression maps and co-expression networks compassing novel gene functions in the brain. PMID:25382412
Landscape of DNA methylation on the X chromosome reflects CpG density, functional chromatin state and X-chromosome inactivation. PMID:25381334
Proteomics for systems toxicology. PMID:25379146
Current advances in systems and integrative biology. PMID:25379142
Identification of under-detected periodicity in time-series microarray data by using empirical mode decomposition. PMID:25372711
Exonic variants associated with development of aspirin exacerbated respiratory diseases. PMID:25372592
How difficult is inference of mammalian causal gene regulatory networks? PMID:25369032
Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress. PMID:25362847
Systems analysis reveals down-regulation of a network of pro-survival miRNAs drives the apoptotic response in dilated cardiomyopathy. PMID:25361207
STAT3 inhibition suppresses proliferation of retinoblastoma through down-regulation of positive feedback loop of STAT3/miR-17-92 clusters. PMID:25359779
Genome-wide distribution of RNA-DNA hybrids identifies RNase H targets in tRNA genes, retrotransposons and mitochondria. PMID:25357144
Argonaute proteins affect siRNA levels and accumulation of a novel extrachromosomal DNA from the Dictyostelium retrotransposon DIRS-1. PMID:25352599
Topic modeling for cluster analysis of large biological and medical datasets. PMID:25350106
A novel peptide interferes with Mycobacterium tuberculosis virulence and survival. PMID:25349777
Transcriptome profiling of developing photoreceptor subtypes reveals candidate genes involved in avian photoreceptor diversification. PMID:25349106
Human placental transcriptome shows sexually dimorphic gene expression and responsiveness to maternal dietary n-3 long-chain polyunsaturated fatty acid intervention during pregnancy. PMID:25348288
Mineralocorticoid effects in the late gestation ovine fetal lung. PMID:25347852
A composite model for subgroup identification and prediction via bicluster analysis. PMID:25347824
MitProNet: A knowledgebase and analysis platform of proteome, interactome and diseases for mammalian mitochondria. PMID:25347823
Expression profile of Caenorhabditis elegans mutant for the Werner syndrome gene ortholog reveals the impact of vitamin C on development to increase life span. PMID:25346348
Transcriptomic profiling facilitates classification of response to influenza challenge. PMID:25345603
The Notch driven long non-coding RNA repertoire in T-cell acute lymphoblastic leukemia. PMID:25344525
Topographical transcriptome mapping of the mouse medial ganglionic eminence by spatially resolved RNA-seq. PMID:25344199
Transcriptomics of desiccation tolerance in the streptophyte green alga Klebsormidium reveal a land plant-like defense reaction. PMID:25340847
The nuclear immune receptor RPS4 is required for RRS1SLH1-dependent constitutive defense activation in Arabidopsis thaliana. PMID:25340333
Integrative investigation on breast cancer in ER, PR and HER2-defined subgroups using mRNA and miRNA expression profiling. PMID:25338681
Analysis of gene expression in induced pluripotent stem cell-derived human neurons exposed to botulinum neurotoxin A subtype 1 and a type A atoxic derivative. PMID:25337697
Divergent gene activation in peripheral blood and tissues of patients with rheumatoid arthritis, psoriatic arthritis and psoriasis following infliximab therapy. PMID:25333715
Identification of antigenic proteins of the nosocomial pathogen Klebsiella pneumoniae. PMID:25333280
Removing batch effects for prediction problems with frozen surrogate variable analysis. PMID:25332844
Profound impact of Hfq on nutrient acquisition, metabolism and motility in the plant pathogen Agrobacterium tumefaciens. PMID:25330313
GroupRank: rank candidate genes in PPI network by differentially expressed gene groups. PMID:25330105
An integrated cell purification and genomics strategy reveals multiple regulators of pancreas development. PMID:25330008
Transcriptome analysis indicates considerable divergence in alternative splicing between duplicated genes in Arabidopsis thaliana. PMID:25326238
Hidden treasures in "ancient" microarrays: gene-expression portrays biology and potential resistance pathways of major lung cancer subtypes and normal tissue. PMID:25325012
A novel class of somatic small RNAs similar to germ cell pachytene PIWI-interacting small RNAs. PMID:25320077
Inhalation of rod-like carbon nanotubes causes unconventional allergic airway inflammation. PMID:25318534
Increased CYFIP1 dosage alters cellular and dendritic morphology and dysregulates mTOR. PMID:25311365
Generation of mice lacking DUF1220 protein domains: effects on fecundity and hyperactivity. PMID:25308000
Comprehensive characterization of cancer subtype associated long non-coding RNAs and their clinical implications. PMID:25307233
Identification and characterization of Wilt and salt stress-responsive microRNAs in chickpea through high-throughput sequencing. PMID:25295754
Whole-genome expression profile in zebrafish embryos after chronic exposure to morphine: identification of new genes associated with neuronal function and mu opioid receptor expression. PMID:25294025
Development and validation of an Haemophilus influenzae supragenome hybridization (SGH) array for transcriptomic analyses. PMID:25290153
Comparing bacterial community composition of healthy and dark spot-affected Siderastrea siderea in Florida and the Caribbean. PMID:25289937
Comparative study of computational methods for reconstructing genetic networks of cancer-related pathways. PMID:25288880
Comparative network analysis via differential graphlet communities. PMID:25283527
Detecting temporal protein complexes from dynamic protein-protein interaction networks. PMID:25282536
RING finger protein RNF207, a novel regulator of cardiac excitation. PMID:25281747
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
Coronavirus non-structural protein 16: evasion, attenuation, and possible treatments. PMID:25278144
Retrotransposon-based profiling of mammalian epigenomes: DNA methylation of IAP LTRs in embryonic stem, somatic and cancer cells. PMID:25277721
Transcriptome-wide characterization of the eIF4A signature highlights plasticity in translation regulation. PMID:25273840
Treatment of potato tubers with the synthetic cytokinin 1-(α-ethylbenzyl)-3-nitroguanidine results in rapid termination of endodormancy and induction of transcripts associated with cell proliferation and growth. PMID:25270889
Identification of co-expression gene networks, regulatory genes and pathways for obesity based on adipose tissue RNA Sequencing in a porcine model. PMID:25270054
DupChecker: a bioconductor package for checking high-throughput genomic data redundancy in meta-analysis. PMID:25267467
Characterization of p-hydroxycinnamate catabolism in a soil Actinobacterium. PMID:25266382
Hybrid Bayesian-rank integration approach improves the predictive power of genomic dataset aggregation. PMID:25266226
Translational control of the oogenic program by components of OMA ribonucleoprotein particles in Caenorhabditis elegans. PMID:25261697
Subcellular transcriptome alterations in a cell culture model of spinal muscular atrophy point to widespread defects in axonal growth and presynaptic differentiation. PMID:25246652
Population- and sex-biased gene expression in the excretion organs of Drosophila melanogaster. PMID:25246242
G9a/GLP-dependent H3K9me2 patterning alters chromatin structure at CpG islands in hematopoietic progenitors. PMID:25237399
SNP-guided identification of monoallelic DNA-methylation events from enrichment-based sequencing data. PMID:25237057
DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. PMID:25236618
IL-5 triggers a cooperative cytokine network that promotes eosinophil precursor maturation. PMID:25230753
Molecular subtyping of serous ovarian tumors reveals multiple connections to intrinsic breast cancer subtypes. PMID:25226589
Growth-promoting and tumourigenic activity of c-Myc is suppressed by Hhex. PMID:25220416
Role of oxygen and the OxyR protein in the response to iron limitation in Rhodobacter sphaeroides. PMID:25220182
Glial enriched gene expression profiling identifies novel factors regulating the proliferation of specific glial subtypes in the Drosophila brain. PMID:25217886
Discovery and validation of new potential biomarkers for early detection of colon cancer. PMID:25215506
Plasmodium falciparum infection induces expression of a mosquito salivary protein (Agaphelin) that targets neutrophil function and inhibits thrombosis without impairing hemostasis. PMID:25211214
Uterine epithelial cell estrogen receptor alpha-dependent and -independent genomic profiles that underlie estrogen responses in mice. PMID:25210133
Cloning and characterization of an apolipoprotein C2 promoter in the mouse central nervous system. PMID:25206486
Identification of microRNAs and their targets in tomato infected with Cucumber mosaic virus based on deep sequencing. PMID:25204630
PDE7B is a novel, prognostically significant mediator of glioblastoma growth whose expression is regulated by endothelial cells. PMID:25203500
Modulation of intestinal microbiota by the probiotic VSL#3 resets brain gene expression and ameliorates the age-related deficit in LTP. PMID:25202975
Performance evaluation of DNA copy number segmentation methods. PMID:25202135
The concentrations of EGFR, LRG1, ITIH4, and F5 in serum correlate with the number of colonic adenomas in ApcPirc/+ rats. PMID:25200834
Biological network exploration with Cytoscape 3. PMID:25199793
Genome-wide binding and transcriptome analysis of human farnesoid X receptor in primary human hepatocytes. PMID:25198545
Blood-gene expression reveals reduced circadian rhythmicity in individuals resistant to sleep deprivation. PMID:25197809
Identification of gene expression biomarkers for predicting radiation exposure. PMID:25189756
Interaction of age and mechanical stability on bone defect healing: an early transcriptional analysis of fracture hematoma in rat. PMID:25187955
KIT is a frequent target for epigenetic silencing in cutaneous melanoma. PMID:25178104
Dietary fatty acids alter left ventricular myocardial gene expression in Wistar rats. PMID:25172377
Mucosal transcriptomics implicates under expression of BRINP3 in the pathogenesis of ulcerative colitis. PMID:25171508
Systems-based analyses of brain regions functionally impacted in Parkinson's disease reveals underlying causal mechanisms. PMID:25170892
Synovial phenotypes in rheumatoid arthritis correlate with response to biologic therapeutics. PMID:25167216
Microarray R-based analysis of complex lysate experiments with MIRACLE. PMID:25161257
Dynamic gene expression patterns in animal models of early and late heart failure reveal biphasic-bidirectional transcriptional activation of signaling pathways. PMID:25159852
HrrF is the Fur-regulated small RNA in nontypeable Haemophilus influenzae. PMID:25157846
A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites. PMID:25156699
RNA-sequencing analysis of HepG2 cells treated with atorvastatin. PMID:25153832
IL-17/Th17 pathway is activated in acne lesions. PMID:25153527
Characterization of wastewater treatment plant microbial communities and the effects of carbon sources on diversity in laboratory models. PMID:25148472
Expression of nicotinamide phosphoribosyltransferase-influenced genes predicts recurrence-free survival in lung and breast cancers. PMID:25146220
Effects of GWAS-associated genetic variants on lncRNAs within IBD and T1D candidate loci. PMID:25144376
Germ cell nuclear factor regulates gametogenesis in developing gonads. PMID:25140725
Functional networks of nucleocytoplasmic transport-related genes differentiate ischemic and dilated cardiomyopathies. A new therapeutic opportunity. PMID:25137373
Genetic and pharmacological reactivation of the mammalian inactive X chromosome. PMID:25136103
A Plasmodium falciparum histone deacetylase regulates antigenic variation and gametocyte conversion. PMID:25121747
RNAseq analysis of cassava reveals similar plant responses upon infection with pathogenic and non-pathogenic strains of Xanthomonas axonopodis pv. manihotis. PMID:25120000
Modeling dynamic functional relationship networks and application to ex vivo human erythroid differentiation. PMID:25115705
Tight regulation of ubiquitin-mediated DNA damage response by USP3 preserves the functional integrity of hematopoietic stem cells. PMID:25113974
Characterization of BPSS1521 (bprD), a regulator of Burkholderia pseudomallei virulence gene expression in the mouse model. PMID:25111708
Comparison of molecular signatures from multiple skin diseases identifies mechanisms of immunopathogenesis. PMID:25111617
Stress response of Salmonella enterica serovar typhimurium to acidified nitrite. PMID:25107963
Preliminary characterization of IL32 in basal-like/triple negative compared to other types of breast cell lines and tissues. PMID:25100201
Semantic Web repositories for genomics data using the eXframe platform. PMID:25093072
BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological data. PMID:25089180
Whole-genome analysis of muscle founder cells implicates the chromatin regulator Sin3A in muscle identity. PMID:25088419
A thyroid hormone challenge in hypothyroid rats identifies T3 regulated genes in the hypothalamus and in models with altered energy balance and glucose homeostasis. PMID:25087834
Gene set enrichment analysis for multiple continuous phenotypes. PMID:25086605
Glucocorticoid receptor binds half sites as a monomer and regulates specific target genes. PMID:25085117
The RNA editing enzyme APOBEC1 induces somatic mutations and a compatible mutational signature is present in esophageal adenocarcinomas. PMID:25085003
DEAD-box helicase DP103 defines metastatic potential of human breast cancers. PMID:25083991
Genetical and comparative genomics of Brassica under altered Ca supply identifies Arabidopsis Ca-transporter orthologs. PMID:25082855
Transcriptional correlates of disease outcome in anticoagulant-treated non-human primates infected with ebolavirus. PMID:25079789
Antifungal drug resistance evoked via RNAi-dependent epimutations. PMID:25079329
Functional and genetic analysis of the colon cancer network. PMID:25079297
Profiling dose-dependent activation of p53-mediated signaling pathways by chemicals with distinct mechanisms of DNA damage. PMID:25078064
Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation. PMID:25074712
Inactivation of thyA in Staphylococcus aureus attenuates virulence and has a strong impact on metabolism and virulence gene expression. PMID:25073642
Functionally diverse dendritic mRNAs rapidly associate with ribosomes following a novel experience. PMID:25072471
Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria. PMID:25071821
CRTC1/MAML2 gain-of-function interactions with MYC create a gene signature predictive of cancers with CREB-MYC involvement. PMID:25071166
Activin A balance regulates epithelial invasiveness and tumorigenesis. PMID:25068654
Gene expression profiling reveals similarities between the spatial architectures of postnatal articular and growth plate cartilage. PMID:25068449
Reduced pachytene piRNAs and translation underlie spermiogenic arrest in Maelstrom mutant mice. PMID:25063675
Proteasome function is required for platelet production. PMID:25061876
Cannabidiol exerts sebostatic and antiinflammatory effects on human sebocytes. PMID:25061872
Genomic profiling of rice roots with short- and long-term chromium stress. PMID:25056418
Interrogation of allelic chromatin states in human cells by high-density ChIP-genotyping. PMID:25055051
Genes involved in the osteoarthritis process identified through genome wide expression analysis in articular cartilage; the RAAK study. PMID:25054223
Hypoxia represses microRNA biogenesis proteins in breast cancer cells. PMID:25052766
Gene expression profiling of peri-implant healing of PLGA-Li+ implants suggests an activated Wnt signaling pathway in vivo. PMID:25047349
Transcription factor Sp4 regulates expression of nervous wreck 2 to control NMDAR1 levels and dendrite patterning. PMID:25045015
Elucidating how the saprophytic fungus Aspergillus nidulans uses the plant polyester suberin as carbon source. PMID:25043916
Identifying mouse models for skin cancer using the Mouse Tumor Biology Database. PMID:25040013
Exome sequencing identifies highly recurrent MED12 somatic mutations in breast fibroadenoma. PMID:25038752
LANA binds to multiple active viral and cellular promoters and associates with the H3K4methyltransferase hSET1 complex. PMID:25033463
Data integration in the era of omics: current and future challenges. PMID:25032990
Genome-wide analysis reveals divergent patterns of gene expression during zygotic and somatic embryo maturation of Theobroma cacao L., the chocolate tree. PMID:25030026
KIFCI, a novel putative prognostic biomarker for ovarian adenocarcinomas: delineating protein interaction networks and signaling circuitries. PMID:25028599
Intercellular network structure and regulatory motifs in the human hematopoietic system. PMID:25028490
Genetic targets of hydrogen sulfide in ventilator-induced lung injury--a microarray study. PMID:25025333
Reproducible combinatorial regulatory networks elucidate novel oncogenic microRNAs in non-small cell lung cancer. PMID:25024357
An improved method for computing q-values when the distribution of effect sizes is asymmetric. PMID:25024290
Comprehensive identification of essential pathways and transcription factors related to epilepsy by gene set enrichment analysis on microarray datasets. PMID:25016997
A large-scale RNAi-based mouse tumorigenesis screen identifies new lung cancer tumor suppressors that repress FGFR signaling. PMID:25015643
Transcriptional network control of normal and leukaemic haematopoiesis. PMID:25014893
Degree-adjusted algorithm for prioritisation of candidate disease genes from gene expression and protein interactome. PMID:25014224
Life on the edge: functional genomic response of Ignicoccus hospitalis to the presence of Nanoarchaeum equitans. PMID:25012904
Stability of the CpG island methylator phenotype during glioma progression and identification of methylated loci in secondary glioblastomas. PMID:25012071
Genome-wide profiling of 8-oxoguanine reveals its association with spatial positioning in nucleus. PMID:25008760
Alterations in circulating miRNA levels following early-stage estrogen receptor-positive breast cancer resection in post-menopausal women. PMID:25004125
Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature. PMID:25003194
An integrative analysis of meningioma tumors reveals the determinant genes and pathways of malignant transformation. PMID:25003081
RNA sequencing analysis of the broad-host-range strain Sinorhizobium fredii NGR234 identifies a large set of genes linked to quorum sensing-dependent regulation in the background of a traI and ngrI deletion mutant. PMID:25002423
Developmental cell fate and virulence are linked to trehalose homeostasis in Cryptococcus neoformans. PMID:25001408
Comparing reference-based RNA-Seq mapping methods for non-human primate data. PMID:25001289
piRNAQuest: searching the piRNAome for silencers. PMID:24997126
Transcriptome analysis reveals signature of adaptation to landscape fragmentation. PMID:24988207
Clinic-genomic association mining for colorectal cancer using publicly available datasets. PMID:24987669
Gene response in rice plants treated with continuous fog influenced by pH, was similar to that treated with biotic stress. PMID:24987489
Transforming growth factor beta receptor type III is a tumor promoter in mesenchymal-stem like triple negative breast cancer. PMID:24985072
SUMOylation modulates the transcriptional activity of androgen receptor in a target gene and pathway selective manner. PMID:24981513
Comprehensive transcriptome analysis unravels the existence of crucial genes regulating primary metabolism during adventitious root formation in Petunia hybrida. PMID:24978694
The inferred cardiogenic gene regulatory network in the mammalian heart. PMID:24971943
Batch effect confounding leads to strong bias in performance estimates obtained by cross-validation. PMID:24967636
Novel insights into the regulatory architecture of CD4+ T cells in rheumatoid arthritis. PMID:24959711
Human enteroendocrine cell responses to infection with Chlamydia trachomatis: a microarray study. PMID:24959205
Detection of expressional changes induced by intrauterine growth restriction in the developing rat mammary gland via exploratory pathways analysis. PMID:24955840
Supplemental carnitine affects the microRNA expression profile in skeletal muscle of obese Zucker rats. PMID:24952657
Breast cancer prognosis risk estimation using integrated gene expression and clinical data. PMID:24949450
CSNK1E/CTNNB1 are synthetic lethal to TP53 in colorectal cancer and are markers for prognosis. PMID:24947187
Glycogen Synthase Kinase 3β in Pancreatic Cancer and its Implications in Chemotherapy and Radiation Therapy. PMID:24944842
A method for detecting long non-coding RNAs with tiled RNA expression microarrays. PMID:24937006
Bone marrow endosteal mesenchymal progenitors depend on HIF factors for maintenance and regulation of hematopoiesis. PMID:24936467
Phenotype prediction based on genome-wide DNA methylation data. PMID:24934728
Interruption of KLF5 acetylation converts its function from tumor suppressor to tumor promoter in prostate cancer cells. PMID:24931571
RNase J is required for processing of a small number of RNAs in Rhodobacter sphaeroides. PMID:24922065
External validation of a multiplex urinary protein panel for the detection of bladder cancer in a multicenter cohort. PMID:24920641
Expression profiling of the wheat pathogen Zymoseptoria tritici reveals genomic patterns of transcription and host-specific regulatory programs. PMID:24920004
Mesenchymal precursor cells maintain the differentiation and proliferation potentials of breast epithelial cells. PMID:24916766
MOPED 2.5--an integrated multi-omics resource: multi-omics profiling expression database now includes transcriptomics data. PMID:24910945
Quality control on the frontier. PMID:24904650
Identification of potential therapeutic targets in a model of neuropathic pain. PMID:24904634
Allen Brain Atlas-Driven Visualizations: a web-based gene expression energy visualization tool. PMID:24904397
Gene expression profiling of brains from bovine spongiform encephalopathy (BSE)-infected cynomolgus macaques. PMID:24898206
Peroxidasin is essential for eye development in the mouse. PMID:24895407
Identification of genomic loci associated with Rhodococcus equi susceptibility in foals. PMID:24892408
Maternal experience with predation risk influences genome-wide embryonic gene expression in threespined sticklebacks (Gasterosteus aculeatus). PMID:24887438
Intergenerational genomic DNA methylation patterns in mouse hybrid strains. PMID:24887417
Amerindian-specific regions under positive selection harbour new lipid variants in Latinos. PMID:24886709
EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics. PMID:24884414
CD80 and PD-L2 define functionally distinct memory B cell subsets that are independent of antibody isotype. PMID:24880458
The Emerging Role of Reactive Oxygen Species Signaling during Lateral Root Development. PMID:24879433
Impact of gene dosage on gene expression, biological processes and survival in cervical cancer: a genome-wide follow-up study. PMID:24879114
Differential Shannon entropy and differential coefficient of variation: alternatives and augmentations to differential expression in the search for disease-related genes. PMID:24878729
Hypoxia-mediated retinal neovascularization and vascular leakage in diabetic retina is suppressed by HIF-1α destabilization by SH-1242 and SH-1280, novel hsp90 inhibitors. PMID:24875598
The PhoP-dependent ncRNA Mcr7 modulates the TAT secretion system in Mycobacterium tuberculosis. PMID:24874799
Mechanisms for the adverse effects of late gestational increases in maternal cortisol on the heart revealed by transcriptomic analyses of the fetal septum. PMID:24867915
β-Cryptoxanthin alleviates diet-induced nonalcoholic steatohepatitis by suppressing inflammatory gene expression in mice. PMID:24858832
RNA-Seq and expression microarray highlight different aspects of the fetal amniotic fluid transcriptome. PMID:24852236
Genus beta human papillomavirus E6 proteins vary in their effects on the transactivation of p53 target genes. PMID:24850740
Rapid proliferation and differentiation impairs the development of memory CD8+ T cells in early life. PMID:24850719
MiRNome and transcriptome aided pathway analysis in human regulatory T cells. PMID:24848933
Distinct gene expression profiles in ovarian cancer linked to Lynch syndrome. PMID:24848881
Niacin in pharmacological doses alters microRNA expression in skeletal muscle of obese Zucker rats. PMID:24847987
Global adaptation to a lipid environment triggers the dormancy-related phenotype of Mycobacterium tuberculosis. PMID:24846381
The epigenetic bivalency of core pancreatic β-cell transcription factor genes within mouse pluripotent embryonic stem cells is not affected by knockdown of the polycomb repressive complex 2, SUZ12. PMID:24845830
MiRNAting control of DNA methylation. PMID:24845501
Targeted tandem duplication of a large chromosomal segment in Aspergillus oryzae. PMID:24837372
DNA replication is an integral part of the mouse oocyte's reprogramming machinery. PMID:24836291
Exploiting a Reference Genome in Terms of Duplications: The Network of Paralogs and Single Copy Genes in Arabidopsis thaliana. PMID:24833233
Importance of the RNA secondary structure for the relative accumulation of clustered viral microRNAs. PMID:24831544
Striking differences between knockout and wild-type mice in global gene expression variability. PMID:24830645
Cross-platform toxicogenomics for the prediction of non-genotoxic hepatocarcinogenesis in rat. PMID:24830643
Identification of heparin-binding EGF-like growth factor (HB-EGF) as a biomarker for lysophosphatidic acid receptor type 1 (LPA1) activation in human breast and prostate cancers. PMID:24828490
Cell competition is a tumour suppressor mechanism in the thymus. PMID:24828041
A naturally occurring, noncanonical GTP aptamer made of simple tandem repeats. PMID:24824832
Genome-wide characterization reveals complex interplay between TP53 and TP63 in response to genotoxic stress. PMID:24823795
Chronic unpredictable stress regulates visceral adipocyte-mediated glucose metabolism and inflammatory circuits in male rats. PMID:24819750
Lipid profiling and transcriptomic analysis reveals a functional interplay between estradiol and growth hormone in liver. PMID:24816529
Genetic dissection of the Drosophila melanogaster female head transcriptome reveals widespread allelic heterogeneity. PMID:24810915
Palmdelphin, a novel target of p53 with Ser46 phosphorylation, controls cell death in response to DNA damage. PMID:24810057
Identification of miRNA-mediated core gene module for glioma patient prediction by integrating high-throughput miRNA, mRNA expression and pathway structure. PMID:24809850
Genome-defence small RNAs exapted for epigenetic mating-type inheritance. PMID:24805235
Involvement of endocytosis and alternative splicing in the formation of the pathological process in the early stages of Parkinson's disease. PMID:24804238
Integrating omics technologies to study pulmonary physiology and pathology at the systems level. PMID:24802001
Effect of chronic valproic Acid treatment on hepatic gene expression profile in wfs1 knockout mouse. PMID:24799886
Genetic analysis of the assimilation of C5-dicarboxylic acids in Pseudomonas aeruginosa PAO1. PMID:24794562
Pleiotropic mutations are subject to strong stabilizing selection. PMID:24793289
Evolutionary approach for relative gene expression algorithms. PMID:24790574
Single nucleotide variants in transcription factors associate more tightly with phenotype than with gene expression. PMID:24784239
Protein-specific prediction of mRNA binding using RNA sequences, binding motifs and predicted secondary structures. PMID:24780077
TGF-beta signalling in the adult neurogenic niche promotes stem cell quiescence as well as generation of new neurons. PMID:24779367
Dissection of estrogen receptor alpha signaling pathways in osteoblasts using RNA-sequencing. PMID:24776842
Air toxics and epigenetic effects: ozone altered microRNAs in the sputum of human subjects. PMID:24771714
The bromodomain protein BRD4 regulates the KEAP1/NRF2-dependent oxidative stress response. PMID:24763052
Molecular signatures differentiate immune states in type 1 diabetic families. PMID:24760139
Wolbachia infection modifies the profile, shuttling and structure of microRNAs in a mosquito cell line. PMID:24759922
Breast tumor specific mutation in GATA3 affects physiological mechanisms regulating transcription factor turnover. PMID:24758297
Gene expression pattern of cells from inflamed and normal areas of osteoarthritis synovial membrane. PMID:24757147
Expression microarray identifies the unliganded glucocorticoid receptor as a regulator of gene expression in mammary epithelial cells. PMID:24755251
Oncogene-like induction of cellular invasion from centrosome amplification. PMID:24739973
Transcriptional dissection of pancreatic tumors engrafted in mice. PMID:24739241
Expression of a truncated ATHB17 protein in maize increases ear weight at silking. PMID:24736658
MLL fusion-driven activation of CDK6 potentiates proliferation in MLL-rearranged infant ALL. PMID:24736461
Identification of mRNAs and lincRNAs associated with lung cancer progression using next-generation RNA sequencing from laser micro-dissected archival FFPE tissue specimens. PMID:24735754
The very low density lipoprotein receptor attenuates house dust mite-induced airway inflammation by suppressing dendritic cell-mediated adaptive immune responses. PMID:24733846
A family of nonclassical class I MHC genes contributes to ultrasensitive chemodetection by mouse vomeronasal sensory neurons. PMID:24719092
Fatty acid elongation in non-alcoholic steatohepatitis and hepatocellular carcinoma. PMID:24714086
Urinary protein biomarker panel for the detection of recurrent bladder cancer. PMID:24714076
Pulsatile exposure to simulated reflux leads to changes in gene expression in a 3D model of oesophageal mucosa. PMID:24713057
SFGD: a comprehensive platform for mining functional information from soybean transcriptome data and its use in identifying acyl-lipid metabolism pathways. PMID:24712981
Patient-derived xenografts of triple-negative breast cancer reproduce molecular features of patient tumors and respond to mTOR inhibition. PMID:24708766
Predicting gene ontology annotations of orphan GWAS genes using protein-protein interactions. PMID:24708602
A functional screen for copper homeostasis genes identifies a pharmacologically tractable cellular system. PMID:24708151
Critical role of extracellular vesicles in modulating the cellular effects of cytokines. PMID:24705984
Parallel clustering algorithm for large-scale biological data sets. PMID:24705246
Extensively self-renewing erythroblasts derived from transgenic β-yac mice is a novel model system for studying globin switching and erythroid maturation. PMID:24704162
Genome-wide meta-analysis of maize heterosis reveals the potential role of additive gene expression at pericentromeric loci. PMID:24693880
Relationship of gene expression in the injured human meniscus to body mass index: a biologic connection between obesity and osteoarthritis. PMID:24692131
DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns. PMID:24690455
CD36 deletion improves recovery from spinal cord injury. PMID:24690303
Biomarker signature identification in "omics" data with multi-class outcome. PMID:24688712
Simultaneous multi-analyte urinary protein assay for bladder cancer detection. PMID:24684904
Identification of novel reference genes based on MeSH categories. PMID:24682035
SLC25A1, or CIC, is a novel transcriptional target of mutant p53 and a negative tumor prognostic marker. PMID:24681808
Signaling by IL-6 promotes alternative activation of macrophages to limit endotoxemia and obesity-associated resistance to insulin. PMID:24681566
Plant systems biology: insights, advances and challenges. PMID:24671625
Global gene expression in endometrium of high and low fertility heifers during the mid-luteal phase of the estrous cycle. PMID:24669966
Acetylation of histone H3 at lysine 64 regulates nucleosome dynamics and facilitates transcription. PMID:24668167
Hmga2 is required for canonical WNT signaling during lung development. PMID:24661562
TLR4 ligands lipopolysaccharide and monophosphoryl lipid a differentially regulate effector and memory CD8+ T Cell differentiation. PMID:24659688
TDP2 protects transcription from abortive topoisomerase activity and is required for normal neural function. PMID:24658003
Remodeling of the sarcomeric cytoskeleton in cardiac ventricular myocytes during heart failure and after cardiac resynchronization therapy. PMID:24657727
INsPeCT: INtegrative Platform for Cancer Transcriptomics. PMID:24653643
Long non-coding RNA and alternative splicing modulations in Parkinson's leukocytes identified by RNA sequencing. PMID:24651478
Tissue specific DNA methylation in normal human breast epithelium and in breast cancer. PMID:24651077
Gene regulatory and metabolic adaptation processes of Dinoroseobacter shibae DFL12T during oxygen depletion. PMID:24648520
Systematic assessment of prognostic gene signatures for breast cancer shows distinct influence of time and ER status. PMID:24645668
Evolutionary conservation of the eumetazoan gene regulatory landscape. PMID:24642862
Extreme sensitivity of gene expression in human SH-SY5Y neurocytes to ultra-low doses of Gelsemium sempervirens. PMID:24642002
Genome-wide copy number variant discovery in dogs using the CanineHD genotyping array. PMID:24640994
Negative elongation factor is required for the maintenance of proviral latency but does not induce promoter-proximal pausing of RNA polymerase II on the HIV long terminal repeat. PMID:24636995
Navigating and mining modENCODE data. PMID:24636835
Gene expression differences predict treatment outcome of merkel cell carcinoma patients. PMID:24634783
A BRCA1 deficient-like signature is enriched in breast cancer brain metastases and predicts DNA damage-induced poly (ADP-ribose) polymerase inhibitor sensitivity. PMID:24625110
Arabidopsis thaliana RALF1 opposes brassinosteroid effects on root cell elongation and lateral root formation. PMID:24620000
A personalized committee classification approach to improving prediction of breast cancer metastasis. PMID:24618465
Combinatorial cytokine code generates anti-viral state in dendritic cells. PMID:24616721
Extracellular vesicles in luminal fluid of the ovine uterus. PMID:24614226
Exploring the molecular causes of hepatitis B virus vaccination response: an approach with epigenomic and transcriptomic data. PMID:24612962
The functional consequences of variation in transcription factor binding. PMID:24603674
A network pharmacology approach to understanding the mechanisms of action of traditional medicine: Bushenhuoxue formula for treatment of chronic kidney disease. PMID:24598793
Modeling the Drosophila gene cluster regulation network for muscle development. PMID:24594656
A systems biological approach reveals multiple crosstalk mechanism between gram-positive and negative bacterial infections: an insight into core mechanism and unique molecular signatures. PMID:24587173
Automated detection of off-label drug use. PMID:24586689
Altered miRNA expression in canine retinas during normal development and in models of retinal degeneration. PMID:24581223
Abandon the mouse research ship? Not just yet! PMID:24569509
Statistical insights into major human muscular diseases. PMID:24569163
Identification of a BET family bromodomain/casein kinase II/TAF-containing complex as a regulator of mitotic condensin function. PMID:24565511
Weighted set enrichment of gene expression data. PMID:24565001
A novel approach to minimize false discovery rate in genome-wide data analysis. PMID:24564975
Systematically profiling and annotating long intergenic non-coding RNAs in human embryonic stem cell. PMID:24564552
Application of microRNA and mRNA expression profiling on prognostic biomarker discovery for hepatocellular carcinoma. PMID:24564407
MaTSE: the gene expression time-series explorer. PMID:24564291
Improving reliability and absolute quantification of human brain microarray data by filtering and scaling probes using RNA-Seq. PMID:24564186
A splicing-dependent transcriptional checkpoint associated with prespliceosome formation. PMID:24560925
Breast cancer subtype specific classifiers of response to neoadjuvant chemotherapy do not outperform classifiers trained on all subtypes. PMID:24558399
BiNA: a visual analytics tool for biological network data. PMID:24551056
The gene regulatory network for breast cancer: integrated regulatory landscape of cancer hallmarks. PMID:24550935
Immunological Outcome in Haploidentical-HSC Transplanted Patients Treated with IL-10-Anergized Donor T Cells. PMID:24550909
Brown and white adipose tissues: intrinsic differences in gene expression and response to cold exposure in mice. PMID:24549398
Fenofibrate induces apoptosis of triple-negative breast cancer cells via activation of NF-κB pathway. PMID:24529079
Derivation and maintenance of murine trophoblast stem cells under defined conditions. PMID:24527396
Translational Bioinformatics Approaches to Drug Development. PMID:24527359
High-Throughput Single-Cell Analysis for Wound Healing Applications. PMID:24527358
CXCL10 is critical for the progression and maintenance of depigmentation in a mouse model of vitiligo. PMID:24523323
Gene expression profiling reveals GC and CEACAM1 as new tools in the diagnosis of lung carcinoids. PMID:24518592
Global miRNA expression analysis of serous and clear cell ovarian carcinomas identifies differentially expressed miRNAs including miR-200c-3p as a prognostic marker. PMID:24512620
Cytokinin as a mediator for regulating root system architecture in response to environmental cues. PMID:24509549
Pristane-induced arthritis loci interact with the Slc11a1 gene to determine susceptibility in mice selected for high inflammation. PMID:24505471
Loss of FTO antagonises Wnt signaling and leads to developmental defects associated with ciliopathies. PMID:24503721
All-trans retinoic acid-triggered antimicrobial activity against Mycobacterium tuberculosis is dependent on NPC2. PMID:24501203
De novo prediction of PTBP1 binding and splicing targets reveals unexpected features of its RNA recognition and function. PMID:24499931
A GNAS mutation found in pancreatic intraductal papillary mucinous neoplasms induces drastic alterations of gene expression profiles with upregulation of mucin genes. PMID:24498386
De novo synthesis of milk triglycerides in humans. PMID:24496312
KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation. PMID:24495580
Accounting for cellular heterogeneity is critical in epigenome-wide association studies. PMID:24495553
Statistical analysis of differential gene expression relative to a fold change threshold on NanoString data of mouse odorant receptor genes. PMID:24495268
Mutant p53-associated myosin-X upregulation promotes breast cancer invasion and metastasis. PMID:24487586
Hunting complex differential gene interaction patterns across molecular contexts. PMID:24482443
The interplay of light and oxygen in the reactive oxygen stress response of Chlamydomonas reinhardtii dissected by quantitative mass spectrometry. PMID:24482124
Transcriptome analysis of Vibrio parahaemolyticus in type III secretion system 1 inducing conditions. PMID:24478989
Attenuation and restoration of severe acute respiratory syndrome coronavirus mutant lacking 2'-o-methyltransferase activity. PMID:24478444
Minimum information about a biofilm experiment (MIABiE): standards for reporting experiments and data on sessile microbial communities living at interfaces. PMID:24478124
Transcriptomic meta-analysis of multiple sclerosis and its experimental models. PMID:24475162
Comprehensive analysis of β-catenin target genes in colorectal carcinoma cell lines with deregulated Wnt/β-catenin signaling. PMID:24467841
Microarray analysis of rat pancreas reveals altered expression of Alox15 and regenerating islet-derived genes in response to iron deficiency and overload. PMID:24465846
The development of a high density linkage map for black tiger shrimp (Penaeus monodon) based on cSNPs. PMID:24465553
Pathway analysis for drug repositioning based on public database mining. PMID:24460210
Nutrient limitation governs Staphylococcus aureus metabolism and niche adaptation in the human nose. PMID:24453967
A generic tool for transcription factor target gene discovery in Arabidopsis cell suspension cultures based on tandem chromatin affinity purification. PMID:24453163
IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics. PMID:24451627
Differential gene expression in small and large rainbow trout derived from two seasonal spawning groups. PMID:24450799
Fast-evolving microRNAs are highly expressed in the early embryo of Drosophila virilis. PMID:24448446
GATA2 as a potential metastasis-driving gene in prostate cancer. PMID:24448395
AMPK agonist AICAR improves cognition and motor coordination in young and aged mice. PMID:24443745
Types of DNA methylation status of the interspersed repetitive sequences for LINE-1, Alu, HERV-E and HERV-K in the neutrophils from systemic lupus erythematosus patients and healthy controls. PMID:24430577
Genes showing altered expression in the medial preoptic area in the highly social maternal phenotype are related to autism and other disorders with social deficits. PMID:24423034
Salicylic acid is an indispensable component of the Ny-1 resistance-gene-mediated response against Potato virus Y infection in potato. PMID:24420577
CD44 is a negative cell surface marker for pluripotent stem cell identification during human fibroblast reprogramming. PMID:24416407
Mutation screening and array comparative genomic hybridization using a 180K oligonucleotide array in VACTERL association. PMID:24416387
RSK2 is a modulator of craniofacial development. PMID:24416220
DevMouse, the mouse developmental methylome database and analysis tools. PMID:24408217
A long-term demasculinization of X-linked intergenic noncoding RNAs in Drosophila melanogaster. PMID:24407956
The nature and extent of mutational pleiotropy in gene expression of male Drosophila serrata. PMID:24402375
Global regulation of mRNA translation and stability in the early Drosophila embryo by the Smaug RNA-binding protein. PMID:24393533
Spatial control of adult stem cell fate using nanotopographic cues. PMID:24388388
Characterization of the yehUT two-component regulatory system of Salmonella enterica Serovar Typhi and Typhimurium. PMID:24386394
Protein complex identification by integrating protein-protein interaction evidence from multiple sources. PMID:24386289
MicroRNA-132 is enriched in developing axons, locally regulates Rasa1 mRNA, and promotes axon extension. PMID:24381269
Gene expression analysis indicates CB1 receptor upregulation in the hippocampus and neurotoxic effects in the frontal cortex 3 weeks after single-dose MDMA administration in Dark Agouti rats. PMID:24378229
IpsA, a novel LacI-type regulator, is required for inositol-derived lipid formation in Corynebacteria and Mycobacteria. PMID:24377418
Partitioning the human transcriptome using HKera, a novel classifier of housekeeping and tissue-specific genes. PMID:24376628
An emerging picture of the seed desiccome: confirmed regulators and newcomers identified using transcriptome comparison. PMID:24376450
Homology modeling and molecular docking for the science curriculum. PMID:24376157
Structural polymorphism in the promoter of pfmrp2 confers Plasmodium falciparum tolerance to quinoline drugs. PMID:24372851
Leukocyte transcriptome from chickens infected with avian pathogenic Escherichia coli identifies pathways associated with resistance. PMID:24371566
Identification of reproducible gene expression signatures in lung adenocarcinoma. PMID:24369726
Mantle cell lymphoma in cyclin D1 transgenic mice with Bim-deficient B cells. PMID:24352880
Transcriptional profiling of hilar nodes from pigs after experimental infection with Actinobacillus pleuropneumoniae. PMID:24351863
Biased gene expression in early honeybee larval development. PMID:24350621
Microarray analysis of transcriptome of medulla identifies potential biomarkers for Parkinson's disease. PMID:24350239
Curcumin intake affects miRNA signature in murine melanoma with mmu-miR-205-5p most significantly altered. PMID:24349037
Power and stability properties of resampling-based multiple testing procedures with applications to gene oncology studies. PMID:24348741
Integrative DNA methylation and gene expression analysis in high-grade soft tissue sarcomas. PMID:24345474
Identification of expressed and conserved human noncoding RNAs. PMID:24344320
Transcriptome analysis of leaf and root of rice seedling to acute dehydration. PMID:24341907
Bcl-xL silencing induces alterations in hsa-miR-608 expression and subsequent cell death in A549 and SK-LU1 human lung adenocarcinoma cells. PMID:24339958
Efficient keratinocyte differentiation strictly depends on JNK-induced soluble factors in fibroblasts. PMID:24335928
Can transcriptomics provide insight into the chemopreventive mechanisms of complex mixtures of phytochemicals in humans? PMID:24328558
Prenatal arsenic exposure and the epigenome: altered microRNAs associated with innate and adaptive immune signaling in newborn cord blood. PMID:24327377
Whole transcriptome characterization of the effects of dehydration and rehydration on Cladonia rangiferina, the grey reindeer lichen. PMID:24325588
Microarray and morphological analysis of early postnatal CRB2 mutant retinas on a pure C57BL/6J genetic background. PMID:24324803
Simultaneous transcriptional profiling of bacteria and their host cells. PMID:24324615
SIOMICS: a novel approach for systematic identification of motifs in ChIP-seq data. PMID:24322294
The oncogenic properties of EWS/WT1 of desmoplastic small round cell tumors are unmasked by loss of p53 in murine embryonic fibroblasts. PMID:24321497
Evolutionary history of mitogen-activated protein kinase (MAPK) genes in Lotus, Medicago, and Phaseolus. PMID:24317362
Protein microarray analysis of antibody responses to Plasmodium falciparum in western Kenyan highland sites with differing transmission levels. PMID:24312649
A machine learned classifier that uses gene expression data to accurately predict estrogen receptor status. PMID:24312637
Assessing differential expression in two-color microarrays: a resampling-based empirical Bayes approach. PMID:24312198
A multi-level multi-scale approach to study essential genes in Mycobacterium tuberculosis. PMID:24308365
HEFT: eQTL analysis of many thousands of expressed genes while simultaneously controlling for hidden factors. PMID:24307700
Lipopolysaccharide activates Toll-like receptor 4 (TLR4)-mediated NF-κB signaling pathway and proinflammatory response in human pericytes. PMID:24307174
Formaldehyde-associated changes in microRNAs: tissue and temporal specificity in the rat nose, white blood cells, and bone marrow. PMID:24304932
CellFinder: a cell data repository. PMID:24304896
Non-growing Rhodopseudomonas palustris increases the hydrogen gas yield from acetate by shifting from the glyoxylate shunt to the tricarboxylic acid cycle. PMID:24302724
Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster. PMID:24302569
Comparative transcript profiling by SuperSAGE identifies novel candidate genes for controlling potato quantitative resistance to late blight not compromised by late maturity. PMID:24294214
Array data extractor (ADE): a LabVIEW program to extract and merge gene array data. PMID:24289243
Identification of breast cancer patients based on human signaling network motifs. PMID:24284521
FOXD1 promotes nephron progenitor differentiation by repressing decorin in the embryonic kidney. PMID:24284212
BORIS/CTCFL is an RNA-binding protein that associates with polysomes. PMID:24279897
The microRNAome of pregnancy: deciphering miRNA networks at the maternal-fetal interface. PMID:24278102
Enhancement of oxidative and drought tolerance in Arabidopsis by overaccumulation of antioxidant flavonoids. PMID:24274116
Slit2-Robo4 pathway modulates lipopolysaccharide-induced endothelial inflammation and its expression is dysregulated during endotoxemia. PMID:24272999
Abnormalities in glycogen metabolism in a patient with alpers' syndrome presenting with hypoglycemia. PMID:24272679
The Gene Expression Barcode 3.0: improved data processing and mining tools. PMID:24271388
MultiFacTV: module detection from higher-order time series biological data. PMID:24268038
Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture. PMID:24267747
Global bidirectional transcription of the Epstein-Barr virus genome during reactivation. PMID:24257595
Identification of RNase L-dependent, 3'-end-modified, viral small RNAs in Sindbis virus-infected mammalian cells. PMID:24255120
Downregulation of Max dimerization protein 3 is involved in decreased visceral adipose tissue by inhibiting adipocyte differentiation in zebrafish and mice. PMID:24254064
Iron-binding haemerythrin RING ubiquitin ligases regulate plant iron responses and accumulation. PMID:24253678
Deep sequencing identification of novel glucocorticoid-responsive miRNAs in apoptotic primary lymphocytes. PMID:24250753
Combinatory microarray and SuperSAGE analyses identify pairing-dependently transcribed genes in Schistosoma mansoni males, including follistatin. PMID:24244773
Prediction of drug-target interactions for drug repositioning only based on genomic expression similarity. PMID:24244130
Molecular sub-group-specific immunophenotypic changes are associated with outcome in recurrent posterior fossa ependymoma. PMID:24240813
The transcription factor ATOH8 is regulated by erythropoietic activity and regulates HAMP transcription and cellular pSMAD1,5,8 levels. PMID:24236640
MicroRNA-20a constrains p300-driven myocardial angiogenic transcription by direct targeting of p300. PMID:24236097
Quantitative network measures as biomarkers for classifying prostate cancer disease states: a systems approach to diagnostic biomarkers. PMID:24236006
Integrating in silico resources to map a signaling network. PMID:24233784
Protein expression profiles of intestinal epithelial co-cultures: effect of functionalised carbon nanotube exposure. PMID:24228069
In search of epigenetic marks in testes and sperm cells of differentially fed boars. PMID:24223838
Phosphorylation-dependent derepression by the response regulator HnoC in the Shewanella oneidensis nitric oxide signaling network. PMID:24218564
Wnt signaling in triple negative breast cancer is associated with metastasis. PMID:24209998
Transcriptome-wide mapping of pea seed ageing reveals a pivotal role for genes related to oxidative stress and programmed cell death. PMID:24205239
Microarray analysis of tomato's early and late wound response reveals new regulatory targets for Leucine aminopeptidase A. PMID:24205013
Human neonatal cardiovascular progenitors: unlocking the secret to regenerative ability. PMID:24204836
Ten simple rules for reproducible computational research. PMID:24204232
A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development. PMID:24195446
High-throughput 3D screening reveals differences in drug sensitivities between culture models of JIMT1 breast cancer cells. PMID:24194875
Functional analysis of sporophytic transcripts repressed by the female gametophyte in the ovule of Arabidopsis thaliana. PMID:24194852
Bivalve omics: state of the art and potential applications for the biomonitoring of harmful marine compounds. PMID:24189277
Molecular mechanisms of system responses to novel stimuli are predictable from public data. PMID:24185701
The BET family of proteins targets moloney murine leukemia virus integration near transcription start sites. PMID:24183673
HypoxiaDB: a database of hypoxia-regulated proteins. PMID:24178989
Analysis of expressed SNPs identifies variable extents of expression from the human inactive X chromosome. PMID:24176135
Promoters maintain their relative activity levels under different growth conditions. PMID:24169404
Divergent compensatory responses to high-fat diet between C57BL6/J and C57BLKS/J inbred mouse strains. PMID:24169046
Inference of sigma factor controlled networks by using numerical modeling applied to microarray time series data of the germinating prokaryote. PMID:24157841
The ESX-3 secretion system is necessary for iron and zinc homeostasis in Mycobacterium tuberculosis. PMID:24155985
Conserved molecular signatures of neurogenesis in the hippocampal subgranular zone of rodents and primates. PMID:24154525
Relationship between gene responses and symptoms induced by Rice grassy stunt virus. PMID:24151491
Positively correlated miRNA-mRNA regulatory networks in mouse frontal cortex during early stages of alcohol dependence. PMID:24148570
PhysioSpace: relating gene expression experiments from heterogeneous sources using shared physiological processes. PMID:24147039
F11R is a novel monocyte prognostic biomarker for malignant glioma. PMID:24147027
Identifying genes relevant to specific biological conditions in time course microarray experiments. PMID:24146889
Hsp70-Hsp40 chaperone complex functions in controlling polarized growth by repressing Hsf1-driven heat stress-associated transcription. PMID:24146635
Analysis of cell surface markers specific for transplantable rod photoreceptors. PMID:24146539
The Ets transcription factor EHF as a regulator of cornea epithelial cell identity. PMID:24142692
Construction of the influenza A virus infection-induced cell-specific inflammatory regulatory network based on mutual information and optimization. PMID:24138989
The housekeeping gene hypoxanthine guanine phosphoribosyltransferase (HPRT) regulates multiple developmental and metabolic pathways of murine embryonic stem cell neuronal differentiation. PMID:24130677
Manipulation of the HIF-Vegf pathway rescues methyl tert-butyl ether (MTBE)-induced vascular lesions. PMID:24128854
Decreased bone formation and increased osteoclastogenesis cause bone loss in mucolipidosis II. PMID:24127423
Genetically engineered transvestites reveal novel mating genes in budding yeast. PMID:24121774
Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots. PMID:24119003
Inferring tumour purity and stromal and immune cell admixture from expression data. PMID:24113773
Spt6 regulates intragenic and antisense transcription, nucleosome positioning, and histone modifications genome-wide in fission yeast. PMID:24100010
Silver nanowire exposure results in internalization and toxicity to Daphnia magna. PMID:24099093
Canonical Nlrp3 inflammasome links systemic low-grade inflammation to functional decline in aging. PMID:24093676
Downregulation of 14q32 microRNAs in Primary Human Desmoplastic Medulloblastoma. PMID:24093088
SLIT3-ROBO4 activation promotes vascular network formation in human engineered tissue and angiogenesis in vivo. PMID:24090675
From genes to milk: genomic organization and epigenetic regulation of the mammary transcriptome. PMID:24086428
Root transcript profiling of two Rorippa species reveals gene clusters associated with extreme submergence tolerance. PMID:24077074
Mass fingerprinting of complex mixtures: protein inference from high-resolution peptide masses and predicted retention times. PMID:24074221
Network-based inference framework for identifying cancer genes from gene expression data. PMID:24073403
Differential host response, rather than early viral replication efficiency, correlates with pathogenicity caused by influenza viruses. PMID:24073225
Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas. PMID:24071850
RNA-Seq reveals spliceosome and proteasome genes as most consistent transcripts in human cancer cells. PMID:24069164
A genome-wide systematic analysis reveals different and predictive proliferation expression signatures of cancerous vs. non-cancerous cells. PMID:24068970
Expression signature as a biomarker for prenatal diagnosis of trisomy 21. PMID:24066117
Small RNA profiling of Xenopus embryos reveals novel miRNAs and a new class of small RNAs derived from intronic transposable elements. PMID:24065776
Genome-wide transcriptional response of Trichoderma reesei to lignocellulose using RNA sequencing and comparison with Aspergillus niger. PMID:24060058
BD-Func: a streamlined algorithm for predicting activation and inhibition of pathways. PMID:24058887
Plasticity of blood- and lymphatic endothelial cells and marker identification. PMID:24058540
Knockdown of human TCF4 affects multiple signaling pathways involved in cell survival, epithelial to mesenchymal transition and neuronal differentiation. PMID:24058414
Snf1 is a regulator of lipid accumulation in Yarrowia lipolytica. PMID:24056466
Role of type II pneumocyte senescence in radiation-induced lung fibrosis. PMID:24052614
Human cell toxicogenomic analysis linking reactive oxygen species to the toxicity of monohaloacetic acid drinking water disinfection byproducts. PMID:24050308
A kinetic analysis of the auxin transcriptome reveals cell wall remodeling proteins that modulate lateral root development in Arabidopsis. PMID:24045021
The membrane-bound NAC transcription factor ANAC013 functions in mitochondrial retrograde regulation of the oxidative stress response in Arabidopsis. PMID:24045019
An immunological fingerprint differentiates muscular lymphatics from arteries and veins. PMID:24044756
LEA polypeptide profiling of recalcitrant and orthodox legume seeds reveals ABI3-regulated LEA protein abundance linked to desiccation tolerance. PMID:24043848
Stem cells isolated from adipose tissue of obese patients show changes in their transcriptomic profile that indicate loss in stemcellness and increased commitment to an adipocyte-like phenotype. PMID:24040759
Genome-wide study of the adaptation of Saccharomyces cerevisiae to the early stages of wine fermentation. PMID:24040173
Role and regulation of the Flp/Tad pilus in the virulence of Pectobacterium atrosepticum SCRI1043 and Pectobacterium wasabiae SCC3193. PMID:24040039
Global features of gene expression on the proteome and transcriptome levels in S. coelicolor during germination. PMID:24039809
Altered expression of cyclin A 1 in muscle of patients with facioscapulohumeral muscle dystrophy (FSHD-1). PMID:24019929
Analysis of the RelA:CBP/p300 interaction reveals its involvement in NF-κB-driven transcription. PMID:24019758
DNA damage leads to progressive replicative decline but extends the life span of long-lived mutant animals. PMID:24013725
The Oct1 homolog Nubbin is a repressor of NF-κB-dependent immune gene expression that increases the tolerance to gut microbiota. PMID:24010524
Standardization of sample collection, isolation and analysis methods in extracellular vesicle research. PMID:24009894
A nuclear calcium-sensing pathway is critical for gene regulation and salt stress tolerance in Arabidopsis. PMID:24009530
Small RNAs derived from lncRNA RNase MRP have gene-silencing activity relevant to human cartilage-hair hypoplasia. PMID:24009312
Inferring Boolean network states from partial information. PMID:24006954
Developmental arrest of Drosophila survival motor neuron (Smn) mutants accounts for differences in expression of minor intron-containing genes. PMID:24006466
Essential role for Dnmt1 in the prevention and maintenance of MYC-induced T-cell lymphomas. PMID:24001767
Arabidopsis Polycomb Repressive Complex 2 binding sites contain putative GAGA factor binding motifs within coding regions of genes. PMID:24001316
Microarray-assisted fine mapping of quantitative trait loci on chromosome 15 for susceptibility to seizure-induced cell death in mice. PMID:24001120
Regulated expression of polysaccharide utilization and capsular biosynthesis loci in biofilm and planktonic Bacteroides thetaiotaomicron during growth in chemostats. PMID:23996813
Extensive cooperation of immune master regulators IRF3 and NFκB in RNA Pol II recruitment and pause release in human innate antiviral transcription. PMID:23994473
Pleiotropic effects of the trichloroethylene-associated P81S VHL mutation on metabolism, apoptosis, and ATM-mediated DNA damage response. PMID:23990666
PhenDisco: phenotype discovery system for the database of genotypes and phenotypes. PMID:23989082
RNA-Seq effectively monitors gene expression in Eutrema salsugineum plants growing in an extreme natural habitat and in controlled growth cabinet conditions. PMID:23984645
Screening biomarkers of prostate cancer by integrating microRNA and mRNA microarrays. PMID:23984644
Review of processing and analysis methods for DNA methylation array data. PMID:23982603
Retinoic acid-dependent regulation of miR-19 expression elicits vertebrate axis defects. PMID:23975936
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. PMID:23975260
Transposon mutagenesis identified chromosomal and plasmid genes essential for adaptation of the marine bacterium Dinoroseobacter shibae to anaerobic conditions. PMID:23974024
ARX regulates cortical intermediate progenitor cell expansion and upper layer neuron formation through repression of Cdkn1c. PMID:23968833
Expansion of multipotent stem cells from the adult human brain. PMID:23967194
Elucidation of how cancer cells avoid acidosis through comparative transcriptomic data analysis. PMID:23967163
Global expression profiling reveals genetic programs underlying the developmental divergence between mouse and human embryogenesis. PMID:23961710
Microenvironment-Dependent Phenotypic Changes in a SCID Mouse Model for Malignant Mesothelioma. PMID:23951555
Combining evidence of preferential gene-tissue relationships from multiple sources. PMID:23950964
Defining cell-type specificity at the transcriptional level in human disease. PMID:23950145
Gentrepid V2.0: a web server for candidate disease gene prediction. PMID:23947436
Genome-wide analysis of Staufen-associated mRNAs identifies secondary structures that confer target specificity. PMID:23945942
New network topology approaches reveal differential correlation patterns in breast cancer. PMID:23945349
Genome-wide survey by ChIP-seq reveals YY1 regulation of lincRNAs in skeletal myogenesis. PMID:23942234
A network integration approach to predict conserved regulators related to pathogenicity of influenza and SARS-CoV respiratory viruses. PMID:23935999
A strong anti-inflammatory signature revealed by liver transcription profiling of Tmprss6-/- mice. PMID:23922777
The tumour suppressor miR-34c targets MET in prostate cancer cells. PMID:23922103
Integrated genetic and epigenetic analysis of childhood acute lymphoblastic leukemia. PMID:23921123
Identification and systematic annotation of tissue-specific differentially methylated regions using the Illumina 450k array. PMID:23919675
Uterine NK cells regulate endometrial bleeding in women and are suppressed by the progesterone receptor modulator asoprisnil. PMID:23913972
Methodological approaches for using synchrotron X-ray fluorescence (SXRF) imaging as a tool in ionomics: examples from Arabidopsis thaliana. PMID:23912758
Serum from humans on long-term calorie restriction enhances stress resistance in cell culture. PMID:23912304
The molecular components of the extracellular protein-degradation pathways of the ectomycorrhizal fungus Paxillus involutus. PMID:23902518
Immune response of the Caribbean sea fan, Gorgonia ventalina, exposed to an Aplanochytrium parasite as revealed by transcriptome sequencing. PMID:23898300
Submergence confers immunity mediated by the WRKY22 transcription factor in Arabidopsis. PMID:23897923
Cold-induced changes in gene expression in brown adipose tissue, white adipose tissue and liver. PMID:23894377
Influenza A/Hong Kong/156/1997(H5N1) virus NS1 gene mutations F103L and M106I both increase IFN antagonism, virulence and cytoplasmic localization but differ in binding to RIG-I and CPSF30. PMID:23886034
Discovery of structural alterations in solid tumor oligodendroglioma by single molecule analysis. PMID:23885787
Microarray characterization of gene expression changes in blood during acute ethanol exposure. PMID:23883607
Identification of genes critical for resistance to infection by West Nile virus using RNA-Seq analysis. PMID:23881275
Regulation of lipid synthesis genes and milk fat production in human mammary epithelial cells during secretory activation. PMID:23880316
High-throughput identification of reference genes for research and clinical RT-qPCR analysis of breast cancer samples. PMID:23876162
Corruption of the intra-gene DNA methylation architecture is a hallmark of cancer. PMID:23874574
High-throughput miRNA and mRNA sequencing of paired colorectal normal, tumor and metastasis tissues and bioinformatic modeling of miRNA-1 therapeutic applications. PMID:23874421
LifeMap Discovery™: the embryonic development, stem cells, and regenerative medicine research portal. PMID:23874394
Effects of the plant growth-promoting bacterium Burkholderia phytofirmans PsJN throughout the life cycle of Arabidopsis thaliana. PMID:23869243
Insights into TREM2 biology by network analysis of human brain gene expression data. PMID:23855984
Conditional deletion of PTEN in peripheral T cells augments TCR-mediated activation but does not abrogate CD28 dependency or prevent anergy induction. PMID:23851688
Dynamic expression of 3' UTRs revealed by Poisson hidden Markov modeling of RNA-Seq: implications in gene expression profiling. PMID:23845781
Differences in the degree of cerulein-induced chronic pancreatitis in C57BL/6 mouse substrains lead to new insights in identification of potential risk factors in the development of chronic pancreatitis. PMID:23845568
Connectivity Mapping for Candidate Therapeutics Identification Using Next Generation Sequencing RNA-Seq Data. PMID:23840550
Impact of heat shock transcription factor 1 on global gene expression profiles in cells which induce either cytoprotective or pro-apoptotic response following hyperthermia. PMID:23834426
DNA methylation in nasal epithelial cells from smokers: identification of ULBP3-related effects. PMID:23831618
Utilization of never-medicated bipolar disorder patients towards development and validation of a peripheral biomarker profile. PMID:23826396
Assessing Global Transcriptome Changes in Response to South African Cassava Mosaic Virus [ZA-99] Infection in Susceptible Arabidopsis thaliana. PMID:23826319
Inferring epitopes of a polymorphic antigen amidst broadly cross-reactive antibodies using protein microarrays: a study of OspC proteins of Borrelia burgdorferi. PMID:23826301
Modeling exon expression using histone modifications. PMID:23825663
Genomic Stability of Aggregatibacter actinomycetemcomitans during Persistent Oral Infection in Human. PMID:23824402
microRNAs Involved in Regulating Spontaneous Recovery in Embolic Stroke Model. PMID:23823624
Integrative "omics"-approach discovers dynamic and regulatory features of bacterial stress responses. PMID:23818867
Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding. PMID:23818864
Linear combination test for gene set analysis of a continuous phenotype. PMID:23815123
Elevation of Eosinophil-Derived Neurotoxin in Plasma of the Subjects with Aspirin-Exacerbated Respiratory Disease: A Possible Peripheral Blood Protein Biomarker. PMID:23805255
The Y chromosome as a regulatory element shaping immune cell transcriptomes and susceptibility to autoimmune disease. PMID:23800453
Mining breast cancer genes with a network based noise-tolerant approach. PMID:23799982
A comparative analysis of transcription factor expression during metazoan embryonic development. PMID:23799133
eFG: an electronic resource for Fusarium graminearum. PMID:23798489
GeneMANIA prediction server 2013 update. PMID:23794635
Combined small RNA and degradome sequencing reveals novel miRNAs and their targets in response to low nitrate availability in maize. PMID:23788746
Carbon availability triggers the decomposition of plant litter and assimilation of nitrogen by an ectomycorrhizal fungus. PMID:23788332
ATG4B/autophagin-1 regulates intestinal homeostasis and protects mice from experimental colitis. PMID:23782979
Inhibition of TGF-β and EGF pathway gene expression and migration of oral carcinoma cells by mucosa-associated lymphoid tissue 1. PMID:23778523
Analyzing the soybean transcriptome during autoregulation of mycorrhization identifies the transcription factors GmNF-YA1a/b as positive regulators of arbuscular mycorrhization. PMID:23777981
Role of the aryl hydrocarbon receptor in carcinogenesis and potential as a drug target. PMID:23771949
Integrated analysis of microRNA and mRNA expression: adding biological significance to microRNA target predictions. PMID:23771142
A Prader-Willi locus lncRNA cloud modulates diurnal genes and energy expenditure. PMID:23771028
Multiplex protein signature for the detection of bladder cancer in voided urine samples. PMID:23764080
Novel Integrative Genomics Approach for Associating GWAS Information with Intrinsic Subtypes of Breast Cancer. PMID:23761956
Molecular mechanisms of toxicity of silver nanoparticles in zebrafish embryos. PMID:23758687
The responses of Vitreoscilla hemoglobin-expressing hybrid aspen (Populus tremula × tremuloides) exposed to 24-h herbivory: expression of hemoglobin and stress-related genes in exposed and nonorthostichous leaves. PMID:23744275
A rapid transcriptome response is associated with desiccation resistance in aerially-exposed killifish embryos. PMID:23741328
Temporal induction of immunoregulatory processes coincides with age-dependent resistance to viral-induced type 1 diabetes. PMID:23739610
Selective tropism of Seneca Valley virus for variant subtype small cell lung cancer. PMID:23739064
Distinct roles of KAP1, HP1 and G9a/GLP in silencing of the two-cell-specific retrotransposon MERVL in mouse ES cells. PMID:23735015
A task-based approach for Gene Ontology evaluation. PMID:23734599
Rapid identification of novel immunodominant proteins and characterization of a specific linear epitope of Campylobacter jejuni. PMID:23734261
Drosophila host model reveals new enterococcus faecalis quorum-sensing associated virulence factors. PMID:23734216
Lytic infection of Lactococcus lactis by bacteriophages Tuc2009 and c2 triggers alternative transcriptional host responses. PMID:23728817
PMTED: a plant microRNA target expression database. PMID:23725466
Phenotypic characterization of retinoic acid differentiated SH-SY5Y cells by transcriptional profiling. PMID:23724009
Large scale expression changes of genes related to neuronal signaling and developmental processes found in lateral septum of postpartum outbred mice. PMID:23717492
Small RNA sequencing-microarray analyses in Parkinson leukocytes reveal deep brain stimulation-induced splicing changes that classify brain region transcriptomes. PMID:23717260
Recapitulating maladaptive, multiscale remodeling of failing myocardium on a chip. PMID:23716679
FeoB-mediated uptake of iron by Francisella tularensis. PMID:23716605
Metal dyshomeostasis and inflammation in Alzheimer's and Parkinson's diseases: possible impact of environmental exposures. PMID:23710288
Genes and pathways underlying regional and cell type changes in Alzheimer's disease. PMID:23705665
Autotoxicity mechanism of Oryza sativa: transcriptome response in rice roots exposed to ferulic acid. PMID:23705659
Ptc6 is required for proper rapamycin-induced down-regulation of the genes coding for ribosomal and rRNA processing proteins in S. cerevisiae. PMID:23704987
The genomic landscape of cohesin-associated chromatin interactions. PMID:23704192
Gene expression changes in the colon epithelium are similar to those of intact colon during late inflammation in interleukin-10 gene deficient mice. PMID:23700416
Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription. PMID:23699410
Cells surviving fractional killing by TRAIL exhibit transient but sustainable resistance and inflammatory phenotypes. PMID:23699397
Transcriptional profiling of swine lung tissue after experimental infection with Actinobacillus pleuropneumoniae. PMID:23698783
High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates. PMID:23696746
Probiotics VSL#3 protect against development of visceral pain in murine model of irritable bowel syndrome. PMID:23691109
Francisella tularensis subsp. tularensis induces a unique pulmonary inflammatory response: role of bacterial gene expression in temporal regulation of host defense responses. PMID:23690939
The neurotrophic compound J147 reverses cognitive impairment in aged Alzheimer's disease mice. PMID:23673233
Cross-platform microarray meta-analysis for the mouse jejunum selects novel reference genes with highly uniform levels of expression. PMID:23671661
Differences in gastric carcinoma microenvironment stratify according to EBV infection intensity: implications for possible immune adjuvant therapy. PMID:23671415
Effect of avian influenza A H5N1 infection on the expression of microRNA-141 in human respiratory epithelial cells. PMID:23663545
p63 attenuates epithelial to mesenchymal potential in an experimental prostate cell model. PMID:23658742
Female bias in Rhox6 and 9 regulation by the histone demethylase KDM6A. PMID:23658530
Targeting the treponemal microbiome of digital dermatitis infections by high-resolution phylogenetic analyses and comparison with fluorescent in situ hybridization. PMID:23658264
Iterative rank-order normalization of gene expression microarray data. PMID:23647742
Adaptation of the hydrocarbonoclastic bacterium Alcanivorax borkumensis SK2 to alkanes and toxic organic compounds: a physiological and transcriptomic approach. PMID:23645199
Genome-wide analysis of the GH3 family in apple (Malus × domestica). PMID:23638690
Age-mediated transcriptomic changes in adult mouse substantia nigra. PMID:23638090
The hourglass and the early conservation models--co-existing patterns of developmental constraints in vertebrates. PMID:23637639
Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types. PMID:23637631
Candidate cancer-targeting agents identified by expression-profiling arrays. PMID:23637543
Chapter 15: disease gene prioritization. PMID:23633938
Cluster analysis reveals differential transcript profiles associated with resistance training-induced human skeletal muscle hypertrophy. PMID:23632419
Chronic carvedilol treatment partially reverses the right ventricular failure transcriptional profile in experimental pulmonary hypertension. PMID:23632417
miR-222 contributes to sex-dimorphic cardiac eNOS expression via ets-1. PMID:23632416
A comprehensive analysis of adiponectin QTLs using SNP association, SNP cis-effects on peripheral blood gene expression and gene expression correlation identified novel metabolic syndrome (MetS) genes with potential role in carcinogenesis and systemic inflammation. PMID:23628382
Parity induces differentiation and reduces Wnt/Notch signaling ratio and proliferation potential of basal stem/progenitor cells isolated from mouse mammary epithelium. PMID:23621987
Interactions between immunity, proliferation and molecular subtype in breast cancer prognosis. PMID:23618380
Serum biomarkers for neurofibromatosis type 1 and early detection of malignant peripheral nerve-sheath tumors. PMID:23618374
Genome-wide analysis of alternative splicing during dendritic cell response to a bacterial challenge. PMID:23613991
Proteomic profiling of halloysite clay nanotube exposure in intestinal cell co-culture. PMID:23606564
MePR: a novel human mesenchymal progenitor model with characteristics of pluripotency. PMID:23597129
Drug target prediction and repositioning using an integrated network-based approach. PMID:23593264
The transcriptional response to nonself in the fungus Podospora anserina. PMID:23589521
Visualizing time-related data in biology, a review. PMID:23585583
An integrated approach to uncover driver genes in breast cancer methylation genomes. PMID:23579546
A local regulatory network around three NAC transcription factors in stress responses and senescence in Arabidopsis leaves. PMID:23578292
Correction of spatial bias in oligonucleotide array data. PMID:23573083
miR-205 negatively regulates the androgen receptor and is associated with adverse outcome of prostate cancer patients. PMID:23571738
Key role for the alternative sigma factor, SigH, in the intracellular life of Mycobacterium avium subsp. paratuberculosis during macrophage stress. PMID:23569115
High natural gene expression variation in the reef-building coral Acropora millepora: potential for acclimative and adaptive plasticity. PMID:23565725
Next-generation sequencing and microarray-based interrogation of microRNAs from formalin-fixed, paraffin-embedded tissue: preliminary assessment of cross-platform concordance. PMID:23562991
Functional requirements for bacteriophage growth: gene essentiality and expression in mycobacteriophage Giles. PMID:23560716
Zebularine regulates early stages of mESC differentiation: effect on cardiac commitment. PMID:23559004
DNA copy number profiling reveals extensive genomic loss in hereditary BRCA1 and BRCA2 ovarian carcinomas. PMID:23558894
Global gene expression analysis reveals pathway differences between teratogenic and non-teratogenic exposure concentrations of bisphenol A and 17β-estradiol in embryonic zebrafish. PMID:23557687
Differential network analysis reveals genetic effects on catalepsy modules. PMID:23555609
Strong EGFR signaling in cell line models of ERBB2-amplified breast cancer attenuates response towards ERBB2-targeting drugs. PMID:23552733
curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome. PMID:23550061
Following the 'tracks': Tramtrack69 regulates epithelial tube expansion in the Drosophila ovary through Paxillin, Dynamin, and the homeobox protein Mirror. PMID:23545328
Effect of acute stressor and serotonin transporter genotype on amygdala first wave transcriptome in mice. PMID:23536833
Stem cell-like gene expression in ovarian cancer predicts type II subtype and prognosis. PMID:23536770
Temozolomide-mediated DNA methylation in human myeloid precursor cells: differential involvement of intrinsic and extrinsic apoptotic pathways. PMID:23536437
Identification of Robust Pathway Markers for Cancer through Rank-Based Pathway Activity Inference. PMID:23533400
The computational analysis of human testis transcriptome reveals closer ties to pluripotency. PMID:23531778
Molars and incisors: show your microarray IDs. PMID:23531410
Genes associated with the cis-regulatory functions of intragenic LINE-1 elements. PMID:23530910
Key role for a glutathione transferase in multiple-herbicide resistance in grass weeds. PMID:23530204
Normalizing gene expression by quantitative PCR during somatic embryogenesis in two representative conifer species: Pinus pinaster and Picea abies. PMID:23529547
The neuron-specific chromatin regulatory subunit BAF53b is necessary for synaptic plasticity and memory. PMID:23525042
Differential expression analysis for pathways. PMID:23516350
PQBP1, a factor linked to intellectual disability, affects alternative splicing associated with neurite outgrowth. PMID:23512658
Post-weaning selenium and folate supplementation affects gene and protein expression and global DNA methylation in mice fed high-fat diets. PMID:23497688
Global mapping of transcription start sites and promoter motifs in the symbiotic α-proteobacterium Sinorhizobium meliloti 1021. PMID:23497287
AUREA: an open-source software system for accurate and user-friendly identification of relative expression molecular signatures. PMID:23496976
An inferential framework for biological network hypothesis tests. PMID:23496778
Arabidopsis copper transport protein COPT2 participates in the cross talk between iron deficiency responses and low-phosphate signaling. PMID:23487432
Altered subcellular localization of heat shock protein 90 is associated with impaired expression of the aryl hydrocarbon receptor pathway in dogs. PMID:23472125
MicroRNA-762 is upregulated in human corneal epithelial cells in response to tear fluid and Pseudomonas aeruginosa antigens and negatively regulates the expression of host defense genes encoding RNase7 and ST2. PMID:23469087
Delineating the cytogenomic and epigenomic landscapes of glioma stem cell lines. PMID:23468990
Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates. PMID:23467541
A sympathetic neuron autonomous role for Egr3-mediated gene regulation in dendrite morphogenesis and target tissue innervation. PMID:23467373
FBH1 protects melanocytes from transformation and is deregulated in melanomas. PMID:23466708
virtualArray: a R/bioconductor package to merge raw data from different microarray platforms. PMID:23452776
Aberrant gene expression in dogs with portosystemic shunts. PMID:23451256
Estrogen signalling and the metabolic syndrome: targeting the hepatic estrogen receptor alpha action. PMID:23451233
Genetic and genomic analysis of Rhizoctonia solani interactions with Arabidopsis; evidence of resistance mediated through NADPH oxidases. PMID:23451091
Cytosolic streaming in vegetative mycelium and aerial structures of Aspergillus niger. PMID:23450745
The effect of natamycin on the transcriptome of conidia of Aspergillus niger. PMID:23449730
Germination of conidia of Aspergillus niger is accompanied by major changes in RNA profiles. PMID:23449598
Two-way AIC: detection of differentially expressed genes from large scale microarray meta-dataset. PMID:23445621
Molecular characterisation of colour formation in the prawn Fenneropenaeus merguiensis. PMID:23441225
Loss of T cell progenitor checkpoint control underlies leukemia initiation in Rag1-deficient nonobese diabetic mice. PMID:23440410
Gene expression analyses implicate an alternative splicing program in regulating contractile gene expression and serum response factor activity in mice. PMID:23437181
Oil palm phenolics confer neuroprotective effects involving cognitive and motor functions in mice. PMID:23433062
Active subnetwork recovery with a mechanism-dependent scoring function; with application to angiogenesis and organogenesis studies. PMID:23432934
Effect of the leptin receptor Q223R polymorphism on the host transcriptome following infection with Entamoeba histolytica. PMID:23429533
MetaSeq: privacy preserving meta-analysis of sequencing-based association studies. PMID:23424140
Interpreting personal transcriptomes: personalized mechanism-scale profiling of RNA-seq data. PMID:23424121
Comparison of the transcriptomes of long-term label retaining-cells and control cells microdissected from mammary epithelium: an initial study to characterize potential stem/progenitor cells. PMID:23423481
Epigenetic epistatic interactions constrain the evolution of gene expression. PMID:23423319
An Integrative Genomics Approach for Associating GWAS Information with Triple-Negative Breast Cancer. PMID:23423317
Cross-species transcriptional network analysis reveals conservation and variation in response to metal stress in cyanobacteria. PMID:23421563
canEvolve: a web portal for integrative oncogenomics. PMID:23418540
Stallion sperm transcriptome comprises functionally coherent coding and regulatory RNAs as revealed by microarray analysis and RNA-seq. PMID:23409192
Low-density lipoprotein receptor-related protein 1 variant interacts with saturated fatty acids in Puerto Ricans. PMID:23404896
The investigational Aurora kinase A inhibitor MLN8237 induces defects in cell viability and cell-cycle progression in malignant bladder cancer cells in vitro and in vivo. PMID:23403633
Frequencies and prognostic impact of RAS mutations in MLL-rearranged acute lymphoblastic leukemia in infants. PMID:23403319
Common bean (Phaseolus vulgaris L.) PvTIFY orchestrates global changes in transcript profile response to jasmonate and phosphorus deficiency. PMID:23402340
The mouse cytosine-5 RNA methyltransferase NSun2 is a component of the chromatoid body and required for testis differentiation. PMID:23401851
A local genetic algorithm for the identification of condition-specific microRNA-gene modules. PMID:23401666
Genomic responses in mouse models poorly mimic human inflammatory diseases. PMID:23401516
Genome-wide meta-analyses of multiancestry cohorts identify multiple new susceptibility loci for refractive error and myopia. PMID:23396134
Developmental and environmental regulation of Aquaporin gene expression across Populus species: divergence or redundancy? PMID:23393587
Constitutive activation of NOTCH1 signaling in Sertoli cells causes gonocyte exit from quiescence. PMID:23391689
Characterization of transcriptional changes in ERG rearrangement-positive prostate cancer identifies the regulation of metabolic sensors such as neuropeptide Y. PMID:23390522
Novel genes underlying beta cell survival in metabolic stress. PMID:23390342
Borrelia host adaptation Regulator (BadR) regulates rpoS to modulate host adaptation and virulence factors in Borrelia burgdorferi. PMID:23387366
Feeder-free generation and long-term culture of human induced pluripotent stem cells using pericellular matrix of decidua derived mesenchymal cells. PMID:23383118
The 3D organization of the yeast genome correlates with co-expression and reflects functional relations between genes. PMID:23382942
Whole genome gene expression analysis reveals casiopeína-induced apoptosis pathways. PMID:23382936
Molecular profiling of cutaneous squamous cell carcinomas and actinic keratoses from organ transplant recipients. PMID:23379751
A DEAD box RNA helicase is critical for pre-mRNA splicing, cold-responsive gene regulation, and cold tolerance in Arabidopsis. PMID:23371945
A novel method for the normalization of microRNA RT-PCR data. PMID:23369279
Discovery and analysis of consistent active sub-networks in cancers. PMID:23368093
An antiviral role for antimicrobial peptides during the arthropod response to alphavirus replication. PMID:23365449
Release of severe acute respiratory syndrome coronavirus nuclear import block enhances host transcription in human lung cells. PMID:23365422
Serum antibodies to blood group A predict survival on PROSTVAC-VF. PMID:23362327
Gene expression profiling of early intervertebral disc degeneration reveals a down-regulation of canonical Wnt signaling and caveolin-1 expression: implications for development of regenerative strategies. PMID:23360510
Data submission and quality in microarray-based microRNA profiling. PMID:23358751
Centromere-like regions in the budding yeast genome. PMID:23349633
Expression analysis in multiple muscle groups and serum reveals complexity in the microRNA transcriptome of the mdx mouse with implications for therapy. PMID:23344181
Gene expression deregulation in postnatal skeletal muscle of TK2 deficient mice reveals a lower pool of proliferating myogenic progenitor cells. PMID:23341978
Alterations in cardiac DNA methylation in human dilated cardiomyopathy. PMID:23341106
MicroRNA paraffin-based studies in osteosarcoma reveal reproducible independent prognostic profiles at 14q32. PMID:23339462
Exact statistical tests for the intersection of independent lists of genes. PMID:23335952
Transcriptional profiling of the Arabidopsis abscission mutant hae hsl2 by RNA-Seq. PMID:23327667
Transcriptome profile analysis of young floral buds of fertile and sterile plants from the self-pollinated offspring of the hybrid between novel restorer line NR1 and Nsa CMS line in Brassica napus. PMID:23324545
Comparative gene expression between two yeast species. PMID:23324262
Formaldehyde and epigenetic alterations: microRNA changes in the nasal epithelium of nonhuman primates. PMID:23322811
MicroRNA expression profiling of peripheral blood samples predicts resistance to first-line sunitinib in advanced renal cell carcinoma patients. PMID:23308047
Knowledge Driven Variable Selection (KDVS) - a new approach to enrichment analysis of gene signatures obtained from high-throughput data. PMID:23302187
Chapter 2: Data-driven view of disease biology. PMID:23300408
Chapter 3: Small molecules and disease. PMID:23300405
Deregulation of lipid metabolism pathway genes in nasopharyngeal carcinoma cells. PMID:23292678
StRAP: an integrated resource for profiling high-throughput cancer genomic data from stress response studies. PMID:23284744
A synthetic interaction screen identifies factors selectively required for proliferation and TERT transcription in p53-deficient human cancer cells. PMID:23284306
Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function. PMID:23284291
Meta-analytical biomarker search of EST expression data reveals three differentially expressed candidates. PMID:23282184
Elevated levels of circulating microRNA-200 family members correlate with serous epithelial ovarian cancer. PMID:23272653
Reuse of public genome-wide gene expression data. PMID:23269463
Pressure-overload hypertrophy of the developing heart reveals activation of divergent gene and protein pathways in the left and right ventricular myocardium. PMID:23262132
Unlocking the potential of publicly available microarray data using inSilicoDb and inSilicoMerging R/Bioconductor packages. PMID:23259851
A microRNA network regulates proliferative timing and extracellular matrix synthesis during cellular quiescence in fibroblasts. PMID:23259597
Cutoff Finder: a comprehensive and straightforward Web application enabling rapid biomarker cutoff optimization. PMID:23251644
Transcriptome profiling of rabbit parthenogenetic blastocysts developed under in vivo conditions. PMID:23251477
Chromosome 19 annotations with disease speciation: a first report from the Global Research Consortium. PMID:23249167
Toward a molecular pathogenic pathway for Yersinia pestis YopM. PMID:23248776
Microarray analysis of gene expression profiles in ripening pineapple fruits. PMID:23245313
ChIP-on-chip analysis identifies IL-22 as direct target gene of ectopically expressed FOXP3 transcription factor in human T cells. PMID:23244505
Whole-genome reconstruction and mutational signatures in gastric cancer. PMID:23237666
Validation of MIMGO: a method to identify differentially expressed GO terms in a microarray dataset. PMID:23232071
Clarifying off-target effects for torcetrapib using network pharmacology and reverse docking approach. PMID:23228038
Coral thermal tolerance: tuning gene expression to resist thermal stress. PMID:23226355
Temporal colonic gene expression profiling in the recurrent colitis model identifies early and chronic inflammatory processes. PMID:23226271
Exploiting parallel R in the cloud with SPRINT. PMID:23223611
High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis. PMID:23222129
Identification of avian RIG-I responsive genes during influenza infection. PMID:23220072
Systems approaches to influenza-virus host interactions and the pathogenesis of highly virulent and pandemic viruses. PMID:23218769
Piwi-interacting RNAs protect DNA against loss during Oxytricha genome rearrangement. PMID:23217708
miRNA profiles of monocyte-lineage cells are consistent with complicated roles in HIV-1 restriction. PMID:23202444
Whole miRNome-wide differential co-expression of microRNAs. PMID:23200138
Using genome-wide expression profiling to define gene networks relevant to the study of complex traits: from RNA integrity to network topology. PMID:23195313
Comparative genomic hybridization and transcriptome analysis with a pan-genome microarray reveal distinctions between JP2 and non-JP2 genotypes of Aggregatibacter actinomycetemcomitans. PMID:23194436
NCBI GEO: archive for functional genomics data sets--update. PMID:23193258
Zic3 is required in the extra-cardiac perinodal region of the lateral plate mesoderm for left-right patterning and heart development. PMID:23184148
Identification of maternally-loaded RNA transcripts in unfertilized eggs of Tribolium castaneum. PMID:23181844
Correlation networks visualization. PMID:23181065
RiceFREND: a platform for retrieving coexpressed gene networks in rice. PMID:23180784
RiceXPro version 3.0: expanding the informatics resource for rice transcriptome. PMID:23180765
Vitamin D receptor signaling mechanisms: integrated actions of a well-defined transcription factor. PMID:23178257
Salinomycin induces cell death and differentiation in head and neck squamous cell carcinoma stem cells despite activation of epithelial-mesenchymal transition and Akt. PMID:23176396
Impact of Lactobacillus plantarum sortase on target protein sorting, gastrointestinal persistence, and host immune response modulation. PMID:23175652
Identification of novel genes involved in DNA damage response by screening a genome-wide Schizosaccharomyces pombe deletion library. PMID:23173672
Impact of 4 Lactobacillus plantarum capsular polysaccharide clusters on surface glycan composition and host cell signaling. PMID:23170998
Association of genes with physiological functions by comparative analysis of pooled expression microarray data. PMID:23170034
Building a statistical model for predicting cancer genes. PMID:23166609
The genetic regulation of the terminating phase of liver regeneration. PMID:23164283
Visual analysis of transcriptome data in the context of anatomical structures and biological networks. PMID:23162564
Identifying reference genes with stable expression from high throughput sequence data. PMID:23162540
Genomic profiling of rectal adenoma and carcinoma by array-based comparative genomic hybridization. PMID:23158542
Evidence for conserved post-transcriptional roles of unitary pseudogenes and for frequent bifunctionality of mRNAs. PMID:23153069
Non-canonical TAF complexes regulate active promoters in human embryonic stem cells. PMID:23150797
Quality controls in cellular immunotherapies: rapid assessment of clinical grade dendritic cells by gene expression profiling. PMID:23147403
Maternal diets trigger sex-specific divergent trajectories of gene expression and epigenetic systems in mouse placenta. PMID:23144842
A characterization of the oral microbiome in allogeneic stem cell transplant patients. PMID:23144704
Computer-assisted annotation of murine Sertoli cell small RNA transcriptome. PMID:23136297
A Steiner tree-based method for biomarker discovery and classification in breast cancer metastasis. PMID:23134806
Pregnancy induces transcriptional activation of the peripheral innate immune system and increases oxidative DNA damage among healthy third trimester pregnant women. PMID:23133592
Theory on the coupled stochastic dynamics of transcription and splice-site recognition. PMID:23133354
miR-10b*, a master inhibitor of the cell cycle, is down-regulated in human breast tumours. PMID:23125021
DNA methylation profile of Aire-deficient mouse medullary thymic epithelial cells. PMID:23116172
Selective gene-expression profiling of migratory tumor cells in vivo predicts clinical outcome in breast cancer patients. PMID:23113900
Transcriptomic markers meet the real world: finding diagnostic signatures of corticosteroid treatment in commercial beef samples. PMID:23110699
An integrative computational systems biology approach identifies differentially regulated dynamic transcriptome signatures which drive the initiation of human T helper cell differentiation. PMID:23110343
Ultrastructural observation and gene expression profiling of Schistosoma japonicum derived from two natural reservoir hosts, water buffalo and yellow cattle. PMID:23110087
Carabin deficiency in B cells increases BCR-TLR9 costimulation-induced autoimmunity. PMID:23109291
Arabidopsis bZIP16 transcription factor integrates light and hormone signaling pathways to regulate early seedling development. PMID:23104829
Large-scale functional organization of long-range chromatin interaction networks. PMID:23103170
Revisiting global gene expression analysis. PMID:23101621
A candidate molecular biomarker panel for the detection of bladder cancer. PMID:23097579
Transcription factor ATF5 is required for terminal differentiation and survival of olfactory sensory neurons. PMID:23090999
The effect of curcumin on human bronchial epithelial cells exposed to fine particulate matter: a predictive analysis. PMID:23090021
Embedding siRNA sequences targeting apolipoprotein B100 in shRNA and miRNA scaffolds results in differential processing and in vivo efficacy. PMID:23089734
Gene expression anti-profiles as a basis for accurate universal cancer signatures. PMID:23088656
Comparative transcriptome analysis of tobacco (Nicotiana tabacum) leaves to identify aroma compound-related genes expressed in different cultivated regions. PMID:23079704
Molecular deregulation induced by silencing of the high mobility group protein A2 gene in retinoblastoma cells. PMID:23077401
Inflammatory mediators alter the astrocyte transcriptome and calcium signaling elicited by multiple G-protein-coupled receptors. PMID:23077035
Conserved DNA methylation patterns in healthy blood cells and extensive changes in leukemia measured by a new quantitative technique. PMID:23075513
Inference of temporally varying Bayesian networks. PMID:23074260
Gene expression profiling unravels cancer-related hepatic molecular signatures in steatohepatitis but not in steatosis. PMID:23071592
Proteomic analysis of mouse models of Niemann-Pick C disease reveals alterations in the steady-state levels of lysosomal proteins within the brain. PMID:23070805
Identification of novel growth phase- and media-dependent small non-coding RNAs in Streptococcus pyogenes M49 using intergenic tiling arrays. PMID:23062031
DAMTC regulates cytoskeletal reorganization and cell motility in human lung adenocarcinoma cell line: an integrated proteomics and transcriptomics approach. PMID:23059821
Integrating constitutive gene expression and chemoactivity: mining the NCI60 anticancer screen. PMID:23056181
Gene expression responses to FUS, EWS, and TAF15 reduction and stress granule sequestration analyses identifies FET-protein non-redundant functions. PMID:23049996
miR-BAG: bagging based identification of microRNA precursors. PMID:23049860
PAGED: a pathway and gene-set enrichment database to enable molecular phenotype discoveries. PMID:23046413
Precise probes of type II interferon activity define the origin of interferon signatures in target tissues in rheumatic diseases. PMID:23045702
The zinc-responsive regulon of Neisseria meningitidis comprises 17 genes under control of a Zur element. PMID:23043002
ZNF385B and VEGFA are strongly differentially expressed in serous ovarian carcinomas and correlate with survival. PMID:23029477
MicroRNA expression profiles of whole blood in lung adenocarcinoma. PMID:23029380
Analyzing gene expression from whole tissue vs. different cell types reveals the central role of neurons in predicting severity of Alzheimer's disease. PMID:23029292
Cooperativity of stress-responsive transcription factors in core hypoxia-inducible factor binding regions. PMID:23029193
Melanoma-associated cancer-testis antigen 16 (CT16) regulates the expression of apoptotic and antiapoptotic genes and promotes cell survival. PMID:23028975
Transcriptome tomography for brain analysis in the web-accessible anatomical space. PMID:23028969
Microarray analysis of microRNA expression during axolotl limb regeneration. PMID:23028429
Convergence of the transcriptional responses to heat shock and singlet oxygen stresses. PMID:23028346
Tissue-specific functional networks for prioritizing phenotype and disease genes. PMID:23028291
Transcriptomic and metabolomic analysis of Yukon Thellungiella plants grown in cabinets and their natural habitat show phenotypic plasticity. PMID:23025749
Rhesus monkey cumulus cells revert to a mural granulosa cell state after an ovulatory stimulus. PMID:23008515
Exposure to solute stress affects genome-wide expression but not the polycyclic aromatic hydrocarbon-degrading activity of Sphingomonas sp. strain LH128 in biofilms. PMID:23001650
Transcriptome-wide analysis of exosome targets. PMID:23000172
Evolutionary insights into scleractinian corals using comparative genomic hybridizations. PMID:22994626
Poplar wood rays are involved in seasonal remodeling of tree physiology. PMID:22992511
Cis-regulatory signatures of orthologous stress-associated bZIP transcription factors from rice, sorghum and Arabidopsis based on phylogenetic footprints. PMID:22992304
Transcriptional profiling in facioscapulohumeral muscular dystrophy to identify candidate biomarkers. PMID:22988124
Transcriptomic changes and signalling pathways induced by arsenic stress in rice roots. PMID:22987115
Bioinformatics for cancer immunology and immunotherapy. PMID:22986455
Myelin-derived lipids modulate macrophage activity by liver X receptor activation. PMID:22984598
Immune complex signatures of patients with active and inactive SLE revealed by multiplex protein binding analysis on antigen microarrays. PMID:22984570
MMP7 is a target of the tumour-associated antigen EpCAM. PMID:22974215
oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets. PMID:22973536
Transcriptional signatures as a disease-specific and predictive inflammatory biomarker for type 1 diabetes. PMID:22972474
Microarray and proteomic analysis of the cardioprotective effects of cold blood cardioplegia in the mature and aged male and female. PMID:22968637
Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells. PMID:22968442
AbsIDconvert: an absolute approach for converting genetic identifiers at different granularities. PMID:22967011
Integrative systems biology approaches in asthma pharmacogenomics. PMID:22966888
Transcriptional regulation of the GPX1 gene by TFAP2C and aberrant CpG methylation in human breast cancer. PMID:22964634
Transcriptome analysis of rice root responses to potassium deficiency. PMID:22963580
Proteomic profiling identifies dysregulated pathways in small cell lung cancer and novel therapeutic targets including PARP1. PMID:22961666
Short-term erythropoietin treatment does not substantially modulate monocyte transcriptomes of patients with combined heart and renal failure. PMID:22957013
ATXN2-CAG42 sequesters PABPC1 into insolubility and induces FBXW8 in cerebellum of old ataxic knock-in mice. PMID:22956915
Sperm mRNA transcripts are indicators of sub-chronic low dose testicular injury in the Fischer 344 rat. PMID:22952946
Expression profile of telomere-associated genes in multiple myeloma. PMID:22947336
Glucosylated hydroxymethyluracil, DNA base J, prevents transcriptional readthrough in Leishmania. PMID:22939620
Identification of the Streptococcus mutans LytST two-component regulon reveals its contribution to oxidative stress tolerance. PMID:22937869
Gene isoform specificity through enhancer-associated antisense transcription. PMID:22937057
Urinary BTA: indicator of bladder cancer or of hematuria. PMID:22932760
Gelsolin induces colorectal tumor cell invasion via modulation of the urokinase-type plasminogen activator cascade. PMID:22927998
Arabinose is metabolized via a phosphoketolase pathway in Clostridium acetobutylicum ATCC 824. PMID:22922942
Prediction of gene network models in limb muscle precursors. PMID:22917675
Systematic prediction of cis-regulatory elements in the Chlamydomonas reinhardtii genome using comparative genomics. PMID:22915576
Global changes in gene expression during compatible and incompatible interactions of cowpea (Vigna unguiculata L.) with the root parasitic angiosperm Striga gesnerioides. PMID:22900582
Emerging putative biomarkers: the role of alpha 2 and 6 integrins in susceptibility, treatment, and prognosis. PMID:22900191
A distinct influenza infection signature in the blood transcriptome of patients with severe community-acquired pneumonia. PMID:22898401
H2.0-like homeobox regulates early hematopoiesis and promotes acute myeloid leukemia. PMID:22897850
Assessing numerical dependence in gene expression summaries with the jackknife expression difference. PMID:22876276
Snf1-related kinase inhibits colon cancer cell proliferation through calcyclin-binding protein-dependent reduction of β-catenin. PMID:22874833
miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets. PMID:22870325
Regulation and gene expression profiling of NKG2D positive human cytomegalovirus-primed CD4+ T-cells. PMID:22870231
Detection of biomarkers for hepatocellular carcinoma using a hybrid univariate gene selection methods. PMID:22867264
CD8 lineage-specific regulation of interleukin-7 receptor expression by the transcriptional repressor Gfi1. PMID:22865857
Genome-wide responses of the model archaeon Halobacterium sp. strain NRC-1 to oxygen limitation. PMID:22865851
Comparative transcriptional analysis of clinically relevant heat stress response in Clostridium difficile strain 630. PMID:22860125
Discovery and validation of gene classifiers for endocrine-disrupting chemicals in zebrafish (danio rerio). PMID:22849515
Genome-wide transcriptional response of the archaeon Thermococcus gammatolerans to cadmium. PMID:22848664
One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data. PMID:22844089
Coex-Rank: An approach incorporating co-expression information for combined analysis of microarray data. PMID:22842118
Subnetwork-based analysis of chronic lymphocytic leukemia identifies pathways that associate with disease progression. PMID:22837534
GRHL3/GET1 and trithorax group members collaborate to activate the epidermal progenitor differentiation program. PMID:22829784
A microRNA activity map of human mesenchymal tumors: connections to oncogenic pathways; an integrative transcriptomic study. PMID:22823907
The emerging paradigm of network medicine in the study of human disease. PMID:22821909
C3KO mouse expression analysis: downregulation of the muscular dystrophy Ky protein and alterations in muscle aging. PMID:22820870
Global analysis of the small RNA transcriptome in different ploidies and genomic combinations of a vertebrate complex--the Squalius alburnoides. PMID:22815952
Role of heat-stable enterotoxins in the induction of early immune responses in piglets after infection with enterotoxigenic Escherichia coli. PMID:22815904
Twist1 transcriptional targets in the developing atrio-ventricular canal of the mouse. PMID:22815831
Gene Expression Commons: an open platform for absolute gene expression profiling. PMID:22815738
Microarray analysis of Xenopus endoderm expressing Ptf1a. PMID:22815262
Testing the limits of 454 pyrotag sequencing: reproducibility, quantitative assessment and comparison to T-RFLP fingerprinting of aquifer microbes. PMID:22808168
Transcriptomes reveal genetic signatures underlying physiological variations imposed by different fermentation conditions in Lactobacillus plantarum. PMID:22802930
Increased immune gene expression and immune cell infiltration in high-grade astrocytoma distinguish long-term from short-term survivors. PMID:22802421
Network-enabled gene expression analysis. PMID:22799258
Identification of common and distinctive mechanisms of resistance to different anti-IGF-IR agents in Ewing's sarcoma. PMID:22798295
Differences in gene expression between strabismic and normal human extraocular muscles. PMID:22786898
An automated bayesian framework for integrative gene expression analysis and predictive medicine. PMID:22779059
Dual RpoH sigma factors and transcriptional plasticity in a symbiotic bacterium. PMID:22773790
Cytotoxic mechanisms employed by mouse T cells to destroy pancreatic β-cells. PMID:22773667
A comparative analysis of biclustering algorithms for gene expression data. PMID:22772837
SFTA2--a novel secretory peptide highly expressed in the lung--is modulated by lipopolysaccharide but not hyperoxia. PMID:22768197
A retinoblastoma orthologue is a major regulator of S-phase, mitotic, and developmental gene expression in Dictyostelium. PMID:22768168
A single promoter inversion switches Photorhabdus between pathogenic and mutualistic states. PMID:22767929
HP1a targets the Drosophila KDM4A demethylase to a subset of heterochromatic genes to regulate H3K36me3 levels. PMID:22761891
The maximum clique enumeration problem: algorithms, applications, and implementations. PMID:22759429
The Choice between MapMan and Gene Ontology for Automated Gene Function Prediction in Plant Science. PMID:22754563
The chemoattractant chemerin suppresses melanoma by recruiting natural killer cell antitumor defenses. PMID:22753924
Computational tools for prioritizing candidate genes: boosting disease gene discovery. PMID:22751426
Insertion-deletions in a FADS2 intron 1 conserved regulatory locus control expression of fatty acid desaturases 1 and 2 and modulate response to simvastatin. PMID:22748975
Conserved rules govern genetic interaction degree across species. PMID:22747640
Disease-linked microRNA-21 exhibits drastically reduced mRNA binding and silencing activity in healthy mouse liver. PMID:22740638
Toxicogenomic profiles in relation to maternal immunotoxic exposure and immune functionality in newborns. PMID:22738990
Linking the transcriptional profiles and the physiological states of Mycobacterium tuberculosis during an extended intracellular infection. PMID:22737072
Potassium starvation in yeast: mechanisms of homeostasis revealed by mathematical modeling. PMID:22737060
Identification of androgen-regulated genes in human prostate. PMID:22735730
WhiB5, a transcriptional regulator that contributes to Mycobacterium tuberculosis virulence and reactivation. PMID:22733573
Identification of yeast genes that confer resistance to chitosan oligosaccharide (COS) using chemogenomics. PMID:22727066
The heterotrimeric laminin coiled-coil domain exerts anti-adhesive effects and induces a pro-invasive phenotype. PMID:22723936
Detection of simultaneous group effects in microRNA expression and related target gene sets. PMID:22723856
Generation of Calhm1 knockout mouse and characterization of calhm1 gene expression. PMID:22723178
Prenatal arsenic exposure alters gene expression in the adult liver to a proinflammatory state contributing to accelerated atherosclerosis. PMID:22719926
Down-weighting overlapping genes improves gene set analysis. PMID:22713124
Cancer/testis antigens and urological malignancies. PMID:22710665
ERK5 protein promotes, whereas MEK1 protein differentially regulates, the Toll-like receptor 2 protein-dependent activation of human endothelial cells and monocytes. PMID:22707717
Long noncoding RNAs in C. elegans. PMID:22707570
Labellum transcriptome reveals alkene biosynthetic genes involved in orchid sexual deception and pollination-induced senescence. PMID:22706647
Genetic variation in T-box binding element functionally affects SCN5A/SCN10A enhancer. PMID:22706305
The application of nonsense-mediated mRNA decay inhibition to the identification of breast cancer susceptibility genes. PMID:22703186
Gene expression changes in the septum: possible implications for microRNAs in sculpting the maternal brain. PMID:22701680
Extensive gene-specific translational reprogramming in a model of B cell differentiation and Abl-dependent transformation. PMID:22693568
MiR-146a as marker of senescence-associated pro-inflammatory status in cells involved in vascular remodelling. PMID:22692818
Global gene profiling of VCP-associated inclusion body myopathy. PMID:22686199
Insecticide resistance mechanisms in the green peach aphid Myzus persicae (Hemiptera: Aphididae) I: A transcriptomic survey. PMID:22685538
Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE. PMID:22685160
Neonatal diethylstilbestrol exposure alters the metabolic profile of uterine epithelial cells. PMID:22679223
Identifying dysregulated pathways in cancers from pathway interaction networks. PMID:22676414
A new mouse model for mania shares genetic correlates with human bipolar disorder. PMID:22675514
Genomic islands as a marker to differentiate between clinical and environmental Burkholderia pseudomallei. PMID:22675491
Phthalate exposure changes the metabolic profile of cardiac muscle cells. PMID:22672789
Coculture with hematopoietic stem cells protects cardiomyocytes against apoptosis via paracrine activation of AKT. PMID:22672705
Gene regulation of UDP-galactose synthesis and transport: potential rate-limiting processes in initiation of milk production in humans. PMID:22649065
A systems biology approach reveals common metastatic pathways in osteosarcoma. PMID:22640921
Gene regulation by cytokinin in Arabidopsis. PMID:22639635
SLocX: Predicting Subcellular Localization of Arabidopsis Proteins Leveraging Gene Expression Data. PMID:22639594
Differential gene expression in the EphA4 knockout spinal cord and analysis of the inflammatory response following spinal cord injury. PMID:22629434
Systems biology approach to identify gene network signatures for colorectal cancer. PMID:22629282
The practical effect of batch on genomic prediction. PMID:22611599
Relax with CouchDB--into the non-relational DBMS era of bioinformatics. PMID:22609849
Comparative transcriptomic analysis of streptococcus pseudopneumoniae with viridans group streptococci. PMID:22607240
Genome-wide recruitment to Polycomb-modified chromatin and activity regulation of the synovial sarcoma oncogene SYT-SSX2. PMID:22594313
Observation of dually decoded regions of the human genome using ribosome profiling data. PMID:22593554
Hypocotyl transcriptome reveals auxin regulation of growth-promoting genes through GA-dependent and -independent pathways. PMID:22590525
Learning transcriptional regulatory relationships using sparse graphical models. PMID:22586449
miRFANs: an integrated database for Arabidopsis thaliana microRNA function annotations. PMID:22583976
Genome-wide analysis of p63 binding sites identifies AP-2 factors as co-regulators of epidermal differentiation. PMID:22573176
Growth factor TGF-β induces intestinal epithelial cell (IEC-6) differentiation: miR-146b as a regulatory component in the negative feedback loop. PMID:22570175
Identity by descent mapping of founder mutations in cancer using high-resolution tumor SNP data. PMID:22567117
Defining the limits of physiological plasticity: how gene expression can assess and predict the consequences of ocean change. PMID:22566679
Identification of genes with a correlation between copy number and expression in gastric cancer. PMID:22559327
Regulation of motility of myogenic cells in filling limb muscle anlagen by Pitx2. PMID:22558231
Utilizing RNA-Seq data for de novo coexpression network inference. PMID:22556371
Genomic analysis of reactive astrogliosis. PMID:22553043
Paternal Benzo[a]pyrene Exposure Modulates MicroRNA Expression Patterns in the Developing Mouse Embryo. PMID:22548065
A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response. PMID:22546241
mRNA-Seq analysis of the Pseudoperonospora cubensis transcriptome during cucumber (Cucumis sativus L.) infection. PMID:22545137
Expression profiling of Cucumis sativus in response to infection by Pseudoperonospora cubensis. PMID:22545095
Erythroid-specific transcriptional changes in PBMCs from pulmonary hypertension patients. PMID:22545094
NLRP10 is a NOD-like receptor essential to initiate adaptive immunity by dendritic cells. PMID:22538615
Zebrafish globin switching occurs in two developmental stages and is controlled by the LCR. PMID:22537494
Characterization of the transcriptome profiles related to globin gene switching during in vitro erythroid maturation. PMID:22537182
Chemocentric informatics approach to drug discovery: identification and experimental validation of selective estrogen receptor modulators as ligands of 5-hydroxytryptamine-6 receptors and as potential cognition enhancers. PMID:22537153
Modulation of activation-associated host cell gene expression by the apicomplexan parasite Theileria annulata. PMID:22533473
Transcriptional portrait of Actinobacillus pleuropneumoniae during acute disease--potential strategies for survival and persistence in the host. PMID:22530048
Oil palm phenolics attenuate changes caused by an atherogenic diet in mice. PMID:22527284
Dynamic antagonism between phytochromes and PIF family basic helix-loop-helix factors induces selective reciprocal responses to light and shade in a rapidly responsive transcriptional network in Arabidopsis. PMID:22517317
Microarray analysis of gene expression in West Nile virus-infected human retinal pigment epithelium. PMID:22509103
How can microarrays unlock asthma? PMID:22500180
Continuous infusion of 20-hydroxyecdysone increased mass of triceps brachii in C57BL/6 mice. PMID:22495969
Neuronal and epithelial cell rescue resolves chronic systemic inflammation in the lipid storage disorder Niemann-Pick C. PMID:22493001
Comparative analysis of Lactobacillus plantarum WCFS1 transcriptomes by using DNA microarray and next-generation sequencing technologies. PMID:22492454
A novel class of cysteine protease receptors that mediate lysosomal transport. PMID:22486861
Integrated inference and analysis of regulatory networks from multi-level measurements. PMID:22482944
Population differences in transcript-regulator expression quantitative trait loci. PMID:22479588
Critical evaluation of imprinted gene expression by RNA-Seq: a new perspective. PMID:22479196
Virulence regulator EspR of Mycobacterium tuberculosis is a nucleoid-associated protein. PMID:22479184
The ectomycorrhizal fungus Paxillus involutus converts organic matter in plant litter using a trimmed brown-rot mechanism involving Fenton chemistry. PMID:22469289
Epigenetic variability in cells of normal cytology is associated with the risk of future morphological transformation. PMID:22453031
A previously unknown oxalyl-CoA synthetase is important for oxalate catabolism in Arabidopsis. PMID:22447686
Transcriptional architecture of the primate neocortex. PMID:22445337
T-2 toxin induced Salmonella Typhimurium intoxication results in decreased Salmonella numbers in the cecum contents of pigs, despite marked effects on Salmonella-host cell interactions. PMID:22440148
Isoniazid resistance without a loss of fitness in Mycobacterium tuberculosis. PMID:22434196
The Saccharomyces cerevisiae Nrd1-Nab3 transcription termination pathway acts in opposition to Ras signaling and mediates response to nutrient depletion. PMID:22431520
Old and new stories: revelations from functional analysis of the bovine mammary transcriptome during the lactation cycle. PMID:22428004
Sleeping Beauty mutagenesis reveals cooperating mutations and pathways in pancreatic adenocarcinoma. PMID:22421440
Role of the gut endoderm in relaying left-right patterning in mice. PMID:22412348
A microRNA superfamily regulates nucleotide binding site-leucine-rich repeats and other mRNAs. PMID:22408077
Translation initiation factor eIF4E is a target for tumor cell radiosensitization. PMID:22397984
Function-based discovery of significant transcriptional temporal patterns in insulin stimulated muscle cells. PMID:22396763
Genetic basis of hidden phenotypic variation revealed by increased translational readthrough in yeast. PMID:22396662
Deciphering the molecular basis of wine yeast fermentation traits using a combined genetic and genomic approach. PMID:22384338
Identification of new genes involved in human adipogenesis and fat storage. PMID:22384002
Ten years of pathway analysis: current approaches and outstanding challenges. PMID:22383865
Plastids are major regulators of light signaling in Arabidopsis. PMID:22383539
Nrf2 links epidermal barrier function with antioxidant defense. PMID:22383093
Antimicrobial effect and mode of action of terpeneless cold-pressed Valencia orange essential oil on methicillin-resistant Staphylococcus aureus. PMID:22372962
Low red/far-red ratios reduce Arabidopsis resistance to Botrytis cinerea and jasmonate responses via a COI1-JAZ10-dependent, salicylic acid-independent mechanism. PMID:22371506
Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics. PMID:22369646
Genetic copy number variants in myocardial infarction patients with hyperlipidemia. PMID:22369086
Expression of the Arabidopsis thaliana BBX32 gene in soybean increases grain yield. PMID:22363475
Investigations on transgenerational epigenetic response down the male line in F2 pigs. PMID:22359544
Identifying neighborhoods of coordinated gene expression and metabolite profiles. PMID:22355360
Genome-Wide Scale-Free Network Inference for Candida albicans. PMID:22355294
DNA replication stress differentially regulates G1/S genes via Rad53-dependent inactivation of Nrm1. PMID:22333915
Gene expression profiling of primary male breast cancers reveals two unique subgroups and identifies N-acetyltransferase-1 (NAT1) as a novel prognostic biomarker. PMID:22333393
Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function. PMID:22328084
Strain-related differences in antibody-mediated changes in gene expression are associated with differences in capsule and location of binding. PMID:22327012
Regulation of microRNA expression in the heart by the ATF6 branch of the ER stress response. PMID:22326432
The latent membrane protein 1 (LMP1) oncogene of Epstein-Barr virus can simultaneously induce and inhibit apoptosis in B cells. PMID:22318153
Genome-wide definition of the SigF regulon in Mycobacterium tuberculosis. PMID:22307756
MYC-driven tumorigenesis is inhibited by WRN syndrome gene deficiency. PMID:22301954
Expressed sequences and polymorphisms in rohu carp (Labeo rohita, Hamilton) revealed by mRNA-seq. PMID:22298294
A comparative study of gene-expression data of basal cell carcinoma and melanoma reveals new insights about the two cancers. PMID:22295108
Genome-wide repression of NF-κB target genes by transcription factor MIBP1 and its modulation by O-linked β-N-acetylglucosamine (O-GlcNAc) transferase. PMID:22294689
Widespread RNA 3'-end oligouridylation in mammals. PMID:22291204
Colorectal adenoma to carcinoma progression is accompanied by changes in gene expression associated with ageing, chromosomal instability, and fatty acid metabolism. PMID:22278361
Functional genomics resources for the North Atlantic copepod, Calanus finmarchicus: EST database and physiological microarray. PMID:22277925
Interleukin-1 receptor-associated kinase-3 is a key inhibitor of inflammation in obesity and metabolic syndrome. PMID:22272346
Toxicogenomic biomarkers for liver toxicity. PMID:22271975
The primary transcriptome of barley chloroplasts: numerous noncoding RNAs and the dominating role of the plastid-encoded RNA polymerase. PMID:22267485
Integrating heterogeneous high-throughput data for meta-dimensional pharmacogenomics and disease-related studies. PMID:22256870
Nearest hyperplane distance neighbor clustering algorithm applied to gene co-expression analysis in Alzheimer's disease. PMID:22255598
Measures of association for identifying microRNA-mRNA pairs of biological interest. PMID:22253745
MicroRNAs control neurobehavioral development and function in zebrafish. PMID:22253472
Widespread translational control contributes to the regulation of Arabidopsis photomorphogenesis. PMID:22252389
Hyperthermophilic Thermotoga species differ with respect to specific carbohydrate transporters and glycoside hydrolases. PMID:22247137
Ars2 promotes proper replication-dependent histone mRNA 3' end formation. PMID:22244333
The absence of P2X7 receptors (P2rx7) on non-haematopoietic cells leads to selective alteration in mood-related behaviour with dysregulated gene expression and stress reactivity in mice. PMID:22243662
Global gene expression analysis of the interaction between cancer cells and osteoblasts to predict bone metastasis in breast cancer. PMID:22235336
Systems-based approaches to cardiovascular disease. PMID:22231714
Combination of a novel gene expression signature with a clinical nomogram improves the prediction of survival in high-risk bladder cancer. PMID:22228636
GATA4 expression is primarily regulated via a miR-26b-dependent post-transcriptional mechanism during cardiac hypertrophy. PMID:22219180
Differential gene expression from microarray analysis distinguishes woven and lamellar bone formation in the rat ulna following mechanical loading. PMID:22216249
Preservation of ranking order in the expression of human Housekeeping genes. PMID:22216246
Affymetrix GeneChip microarray preprocessing for multivariate analyses. PMID:22210854
Deletion of KDM6A, a histone demethylase interacting with MLL2, in three patients with Kabuki syndrome. PMID:22197486
The re-establishment of desiccation tolerance in germinated Arabidopsis thaliana seeds and its associated transcriptome. PMID:22195004
Insights into hypoxic systemic responses based on analyses of transcriptional regulation in Arabidopsis. PMID:22194941
Influence of 17β-estradiol on gene expression of Paracoccidioides during mycelia-to-yeast transition. PMID:22194832
Activation of endothelial TLR2 by bacterial lipoprotein upregulates proteins specific for the neutrophil response. PMID:22186927
Identification of proprotein convertase substrates using genome-wide expression correlation analysis. PMID:22185580
Complex human glucocorticoid receptor dim mutations define glucocorticoid induced apoptotic resistance in bone cells. PMID:22174376
Small interfering RNA against transcription factor STAT6 leads to increased cholesterol synthesis in lung cancer cell lines. PMID:22162773
Histone deacetylase inhibition decreases proliferation and potentiates the effect of ionizing radiation in atypical teratoid/rhabdoid tumor cells. PMID:22156471
Changes in transcriptional orientation are associated with increases in evolutionary rates of enterobacterial genes. PMID:22152004
Stress induced Salmonella Typhimurium recrudescence in pigs coincides with cortisol induced increased intracellular proliferation in macrophages. PMID:22151081
Segmental chromosomal alterations lead to a higher risk of relapse in infants with MYCN-non-amplified localised unresectable/disseminated neuroblastoma (a SIOPEN collaborative study). PMID:22146831
Comparative microbial modules resource: generation and visualization of multi-species biclusters. PMID:22144874
Loss of Dnmt3b function upregulates the tumor modifier Ment and accelerates mouse lymphomagenesis. PMID:22133874
Relative impact of key sources of systematic noise in Affymetrix and Illumina gene-expression microarray experiments. PMID:22133085
Genome-wide identification of microRNAs in response to low nitrate availability in maize leaves and roots. PMID:22132192
Transcriptomic analyses during the transition from biomass production to lipid accumulation in the oleaginous yeast Yarrowia lipolytica. PMID:22132183
Strategies to explore functional genomics data sets in NCBI's GEO database. PMID:22130872
Isolation of novel multipotent neural crest-derived stem cells from adult human inferior turbinate. PMID:22128806
Gene expression and network-based analysis reveals a novel role for hsa-miR-9 and drug control over the p38 network in glioblastoma multiforme progression. PMID:22122801
MetaQC: objective quality control and inclusion/exclusion criteria for genomic meta-analysis. PMID:22116060
FBXO11 targets BCL6 for degradation and is inactivated in diffuse large B-cell lymphomas. PMID:22113614
Antisense suppression of the small chloroplast protein CP12 in tobacco: a transcriptional viewpoint. PMID:22112458
RNA-Seq reveals infection-related global gene changes in Phytophthora phaseoli, the causal agent of lima bean downy mildew. PMID:22112294
Optimal deconvolution of transcriptional profiling data using quadratic programming with application to complex clinical blood samples. PMID:22110609
eXframe: reusable framework for storage, analysis and visualization of genomics experiments. PMID:22103807
Average rank-based score to measure deregulation of molecular pathway gene sets. PMID:22096597
Evaluation of the NOD/SCID xenograft model for glucocorticoid-regulated gene expression in childhood B-cell precursor acute lymphoblastic leukemia. PMID:22093874
Perturbation of FliL interferes with Proteus mirabilis swarmer cell gene expression and differentiation. PMID:22081397
Tbx20 regulates a genetic program essential to adult mouse cardiomyocyte function. PMID:22080862
Integrated transcriptome and binding sites analysis implicates E2F in the regulation of self-renewal in human pluripotent stem cells. PMID:22076139
Evolutionary history and functional characterization of the amphibian xenosensor CAR. PMID:22074953
Genome-wide binding map of the HIV-1 Tat protein to the human genome. PMID:22073215
Identification and characterization of Hoxa9 binding sites in hematopoietic cells. PMID:22072553
Modeling the transcriptional consequences of epidermal growth factor receptor ablation in Ras-initiated squamous cancer. PMID:22068661
Identification of transcriptome profiles and signaling pathways for the allelochemical juglone in rice roots. PMID:22065257
Thousands of cis-regulatory sequence combinations are shared by Arabidopsis and poplar. PMID:22058225
PlantNATsDB: a comprehensive database of plant natural antisense transcripts. PMID:22058132
Effect of rickettsial toxin VapC on its eukaryotic host. PMID:22046301
An integrated transcriptomic and meta-analysis of hepatoma cells reveals factors that influence susceptibility to HCV infection. PMID:22046242
Network based consensus gene signatures for biomarker discovery in breast cancer. PMID:22046239
Effect of L-carnitine on the hepatic transcript profile in piglets as animal model. PMID:22040461
Anthrax lethal toxin-induced gene expression changes in mouse lung. PMID:22039574
Targeted gene-silencing reveals the functional significance of myocardin signaling in the failing heart. PMID:22028870
Transcriptome-wide binding sites for components of the Saccharomyces cerevisiae non-poly(A) termination pathway: Nrd1, Nab3, and Sen1. PMID:22028667
Graph constrained discriminant analysis: a new method for the integration of a graph into a classification process. PMID:22022543
The molecular signature underlying the thymic migration and maturation of TCRαβ+ CD4+ CD8 thymocytes. PMID:22022412
A non-canonical DNA structure is a binding motif for the transcription factor SP1 in vitro. PMID:22021377
Transcriptional regulation of co-expressed microRNA target genes. PMID:22002038
Expression of FACT in mammalian tissues suggests its role in maintaining of undifferentiated state of cells. PMID:21998152
Reprogramming of mesenchymal stem cells by the synovial sarcoma-associated oncogene SYT-SSX2. PMID:21996728
Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium. PMID:21992415
Microarray analysis of genes associated with cell surface NIS protein levels in breast cancer. PMID:21989294
A gene signature in histologically normal surgical margins is predictive of oral carcinoma recurrence. PMID:21989116
Skin healing and scale regeneration in fed and unfed sea bream, Sparus auratus. PMID:21981800
Gene expression biomarkers provide sensitive indicators of in planta nitrogen status in maize. PMID:21980173
Sildenafil improves epicenter vascular perfusion but not hindlimb functional recovery after contusive spinal cord injury in mice. PMID:21970599
Molecular profiling of stomatal meristemoids reveals new component of asymmetric cell division and commonalities among stem cell populations in Arabidopsis. PMID:21963668
Classification of unknown primary tumors with a data-driven method based on a large microarray reference database. PMID:21955394
Regulation of IL-2 gene expression by Siva and FOXP3 in human T cells. PMID:21955384
Yeast Nrd1, Nab3, and Sen1 transcriptome-wide binding maps suggest multiple roles in post-transcriptional RNA processing. PMID:21954178
The transcriptome of a human polar body accurately reflects its sibling oocyte. PMID:21953461
Spleen transcriptome response to infection with avian pathogenic Escherichia coli in broiler chickens. PMID:21951686
Discovering biological connections between experimental conditions based on common patterns of differential gene expression. PMID:21951600
Integrated analyses of copy number variations and gene expression in lung adenocarcinoma. PMID:21935476
Transcriptional profiling of chondrodysplasia growth plate cartilage reveals adaptive ER-stress networks that allow survival but disrupt hypertrophy. PMID:21935428
Ligand-independent phosphorylation of the glucocorticoid receptor integrates cellular stress pathways with nuclear receptor signaling. PMID:21930780
High IGFBP2 expression correlates with tumor severity in pediatric rhabdomyosarcoma. PMID:21924226
Insights into eyestalk ablation mechanism to induce ovarian maturation in the black tiger shrimp. PMID:21915325
Ehrlichia chaffeensis transcriptome in mammalian and arthropod hosts reveals differential gene expression and post transcriptional regulation. PMID:21915290
Ranking candidate disease genes from gene expression and protein interaction: a Katz-centrality based approach. PMID:21912686
A promoter DNA demethylation landscape of human hematopoietic differentiation. PMID:21911366
miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. PMID:21911355
Deep brain stimulation induces rapidly reversible transcript changes in Parkinson's leucocytes. PMID:21910823
The mycotoxin deoxynivalenol potentiates intestinal inflammation by Salmonella typhimurium in porcine ileal loops. PMID:21909370
Integrative cancer genomics (IntOGen) in Biomart. PMID:21903633
Toward the blood-borne miRNome of human diseases. PMID:21892151
Soybean homologs of MPK4 negatively regulate defense responses and positively regulate growth and development. PMID:21878550
An integrative genomics approach to biomarker discovery in breast cancer. PMID:21869864
Host regulatory network response to infection with highly pathogenic H5N1 avian influenza virus. PMID:21865398
Differential transcriptomic profiles effected by oil palm phenolics indicate novel health outcomes. PMID:21864415
Genome-based analysis of the nonhuman primate Macaca fascicularis as a model for drug safety assessment. PMID:21862625
mir-11 limits the proapoptotic function of its host gene, dE2f1. PMID:21856777
High-throughput identification of potential minor histocompatibility antigens by MHC tetramer-based screening: feasibility and limitations. PMID:21850230
Discovery and preclinical validation of drug indications using compendia of public gene expression data. PMID:21849665
The need for the pathology community to sponsor a whole slide imaging repository with technical guidance from the pathology informatics community. PMID:21845229
Antibacterial mechanism of action of arylamide foldamers. PMID:21844313
Resistance to Plasmopara viticola in a grapevine segregating population is associated with stilbenoid accumulation and with specific host transcriptional responses. PMID:21838877
Fibrogenic and redox-related but not proinflammatory genes are upregulated in Lewis rat model of chronic silicosis. PMID:21830856
Genome-wide integration on transcription factors, histone acetylation and gene expression reveals genes co-regulated by histone modification patterns. PMID:21829453
Reciprocal transcriptional regulation of metabolic and signaling pathways correlates with disease severity in heart failure. PMID:21828333
Eliminating SF-1 (NR5A1) sumoylation in vivo results in ectopic hedgehog signaling and disruption of endocrine development. PMID:21820362
Single cell transcriptomics of neighboring hyphae of Aspergillus niger. PMID:21816052
DAF-12 regulates a connected network of genes to ensure robust developmental decisions. PMID:21814518
Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription. PMID:21810278
Characterization of early host responses in adults with dengue disease. PMID:21810247
3'UTR elements inhibit Ras-induced C/EBPβ post-translational activation and senescence in tumour cells. PMID:21804532
STIM1 as a key regulator for Ca2+ homeostasis in skeletal-muscle development and function. PMID:21798093
Crx broadly modulates the pineal transcriptome. PMID:21797868
In vivo neuronal subtype-specific targets of Atoh1 (Math1) in dorsal spinal cord. PMID:21795538
Biphasic gene expression changes elicited by Phakopsora pachyrhizi in soybean correlate with fungal penetration and haustoria formation. PMID:21791600
Predictive and prognostic molecular markers for cancer medicine. PMID:21789130
Large-scale methylation domains mark a functional subset of neuronally expressed genes. PMID:21784875
DMRT1 prevents female reprogramming in the postnatal mammalian testis. PMID:21775990
Similarity of mouse perivascular and brown adipose tissues and their resistance to diet-induced inflammation. PMID:21765057
Post-transcription initiation function of the ubiquitous SAGA complex in tissue-specific gene activation. PMID:21764853
An evaluation protocol for subtype-specific breast cancer event prediction. PMID:21760900
Remodeling lipid metabolism and improving insulin responsiveness in human primary myotubes. PMID:21760887
A toxicogenomic comparison of primary and photochemically altered air pollutant mixtures. PMID:21757418
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. PMID:21750106
A screening assay based on host-pathogen interaction models identifies a set of novel antifungal benzimidazole derivatives. PMID:21746957
Genome-wide gene expression profiling of fertilization competent mycelium in opposite mating types in the heterothallic fungus Podospora anserina. PMID:21738678
Positive outcomes of oil palm phenolics on degenerative diseases in animal models. PMID:21736778
Meta-analysis of multiple microarray datasets reveals a common gene signature of metastasis in solid tumors. PMID:21736749
miRNA studies in in vitro and in vivo activated hepatic stellate cells. PMID:21734783
Bile salts induce resistance to polymyxin in enterohemorrhagic Escherichia coli O157:H7. PMID:21725004
Transcriptional profiling of Medicago truncatula under salt stress identified a novel CBF transcription factor MtCBF4 that plays an important role in abiotic stress responses. PMID:21718548
Copy number variants in candidate genes are genetic modifiers of Hirschsprung disease. PMID:21712996
Comparative kinetic analyses of gene profiles of naïve CD4+ and CD8+ T cells from young and old animals reveal novel age-related alterations. PMID:21711441
Chromatin structure characteristics of pre-miRNA genomic sequences. PMID:21702984
BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results. PMID:21702939
A genome-wide DNA methylation study in colorectal carcinoma. PMID:21699707
Integrative computational biology for cancer research. PMID:21691773
The role of bioinformatics in studying rheumatic and autoimmune disorders. PMID:21691330
Nab2 functions in the metabolism of RNA driven by polymerases II and III. PMID:21680710
Genome-wide association study of schizophrenia in Japanese population. PMID:21674006
The characterisation of piRNA-related 19mers in the mouse. PMID:21672259
Transcriptomic analysis of Clostridium thermocellum ATCC 27405 cellulose fermentation. PMID:21672225
Inflammatory gene regulatory networks in amnion cells following cytokine stimulation: translational systems approach to modeling human parturition. PMID:21655103
An atlas of tissue-specific conserved coexpression for functional annotation and disease gene prediction. PMID:21654723
PREDICT: a method for inferring novel drug indications with application to personalized medicine. PMID:21654673
Genome-scale analysis of replication timing: from bench to bioinformatics. PMID:21637205
Absence of repellents in Ustilago maydis induces genes encoding small secreted proteins. PMID:21626092
The plant cuticle is required for osmotic stress regulation of abscisic acid biosynthesis and osmotic stress tolerance in Arabidopsis. PMID:21610183
The transcriptome of human epicardial, mediastinal and subcutaneous adipose tissues in men with coronary artery disease. PMID:21603615
Integrative mRNA profiling comparing cultured primary cells with clinical samples reveals PLK1 and C20orf20 as therapeutic targets in cutaneous squamous cell carcinoma. PMID:21602893
Prospecting for genes involved in transcriptional regulation of plant defenses, a bioinformatics approach. PMID:21595873
Transcriptome analysis by GeneTrail revealed regulation of functional categories in response to alterations of iron homeostasis in Arabidopsis thaliana. PMID:21592396
Identification and replication of loci involved in camptothecin-induced cytotoxicity using CEPH pedigrees. PMID:21573211
Tat RNA silencing suppressor activity contributes to perturbation of lymphocyte miRNA by HIV-1. PMID:21569500
Transcriptome response of high- and low-light-adapted Prochlorococcus strains to changing iron availability. PMID:21562599
The role of indirect connections in gene networks in predicting function. PMID:21551147
Assessing affymetrix GeneChip microarray quality. PMID:21548974
EXORDIUM-LIKE1 promotes growth during low carbon availability in Arabidopsis. PMID:21543728
Human cytomegalovirus IE1 protein elicits a type II interferon-like host cell response that depends on activated STAT1 but not interferon-γ. PMID:21533215
Aberrant epigenetic and genetic marks are seen in myelodysplastic leukocytes and reveal Dock4 as a candidate pathogenic gene on chromosome 7q. PMID:21532034
Tracheal occlusion modulates the gene expression profile of the medial thalamus in anesthetized rats. PMID:21527662
Gene expression profiles from discordant monozygotic twins suggest that molecular pathways are shared among multiple systemic autoimmune diseases. PMID:21521520
Epigenomic and RNA structural correlates of polyadenylation. PMID:21508683
Methylation and loss of Secreted Frizzled-Related Protein 3 enhances melanoma cell migration and invasion. PMID:21494614
Extensive effects of in vitro oocyte maturation on rhesus monkey cumulus cell transcriptome. PMID:21487073
H3 lysine 4 is acetylated at active gene promoters and is regulated by H3 lysine 4 methylation. PMID:21483810
Integration of transcriptomics, proteomics, and microRNA analyses reveals novel microRNA regulation of targets in the mammalian inner ear. PMID:21483685
Immediate reduction of Salmonella enterica serotype typhimurium viability via membrane destabilization following exposure to multiple-hurdle treatments with heated, acidified organic acid salt solutions. PMID:21478311
Identification of SERPINA1 as single marker for papillary thyroid carcinoma through microarray meta analysis and quantification of its discriminatory power in independent validation. PMID:21470421
Crosstalk between c-Jun and TAp73alpha/beta contributes to the apoptosis-survival balance. PMID:21459846
Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data. PMID:21453538
High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation. PMID:21447789
A 44K microarray dataset of the changing transcriptome in developing Atlantic salmon (Salmo salar L.). PMID:21447175
Relationship between symptoms and gene expression induced by the infection of three strains of Rice dwarf virus. PMID:21445363
PlaNet: combined sequence and expression comparisons across plant networks derived from seven species. PMID:21441431
Meta-analysis of gene expression microarrays with missing replicates. PMID:21435268
COP1-mediated degradation of BBX22/LZF1 optimizes seedling development in Arabidopsis. PMID:21427283
Apolipoproteins in the brain: implications for neurological and psychiatric disorders. PMID:21423873
Hypomethylation of intragenic LINE-1 represses transcription in cancer cells through AGO2. PMID:21423624
The human TTAGGG repeat factors 1 and 2 bind to a subset of interstitial telomeric sequences and satellite repeats. PMID:21423270
Effect of Xpcl1 activation and p27(Kip1) loss on gene expression in murine lymphoma. PMID:21412408
Use of transcriptional signatures induced in lymphoid and myeloid cell lines as an inflammatory biomarker in Type 1 diabetes. PMID:21406607
Making sense of cancer genomic data. PMID:21406553
Shmt1 heterozygosity impairs folate-dependent thymidylate synthesis capacity and modifies risk of Apc(min)-mediated intestinal cancer risk. PMID:21406397
Identification of genes involved in cell wall biogenesis in grasses by differential gene expression profiling of elongating and non-elongating maize internodes. PMID:21402660
The impact of quantitative optimization of hybridization conditions on gene expression analysis. PMID:21401920
Phosphoproteomic analysis reveals an intrinsic pathway for the regulation of histone deacetylase 7 that controls the function of cytotoxic T lymphocytes. PMID:21399638
Population-genetic properties of differentiated human copy-number polymorphisms. PMID:21397061
Role of p53 serine 46 in p53 target gene regulation. PMID:21394211
Interorgan coordination of the murine adaptive response to fasting. PMID:21393243
Rat diaphragm mitochondria have lower intrinsic respiratory rates than mitochondria in limb muscles. PMID:21389333
Removing batch effects in analysis of expression microarray data: an evaluation of six batch adjustment methods. PMID:21386892
The expanded human disease network combining protein-protein interaction information. PMID:21386875
Identification of microRNA-mRNA modules using microarray data. PMID:21375780
Reconstruction of the regulatory network of Lactobacillus plantarum WCFS1 on basis of correlated gene expression and conserved regulatory motifs. PMID:21375715
Microarray analysis of differential gene expression profile in peripheral blood cells of patients with human essential hypertension. PMID:21369372
Peripheral blood gene expression profiles in metabolic syndrome, coronary artery disease and type 2 diabetes. PMID:21368773
MicroRNA-183 family expression in hair cell development and requirement of microRNAs for hair cell maintenance and survival. PMID:21360794
Distinct early molecular responses to mutations causing vLINCL and JNCL presage ATP synthase subunit C accumulation in cerebellar cells. PMID:21359198
Association of FABP5 expression with poor survival in triple-negative breast cancer: implication for retinoic acid therapy. PMID:21356353
Gene expression throughout a vertebrate's embryogenesis. PMID:21356103
In depth analysis of genes and pathways of the mammary gland involved in the pathogenesis of bovine Escherichia coli-mastitis. PMID:21352611
Kaposi's sarcoma-associated herpesvirus viral interferon regulatory factor 3 inhibits gamma interferon and major histocompatibility complex class II expression. PMID:21345951
IL-17-induced NF-kappaB activation via CIKS/Act1: physiologic significance and signaling mechanisms. PMID:21335551
Meta-analysis of muscle transcriptome data using the MADMuscle database reveals biologically relevant gene patterns. PMID:21324190
Translocation of the cytoplasmic domain of ADAM13 to the nucleus is essential for Calpain8-a expression and cranial neural crest cell migration. PMID:21316592
Brain perihematoma genomic profile following spontaneous human intracerebral hemorrhage. PMID:21311749
Histone deacetylase inhibitors in the treatment of muscular dystrophies: epigenetic drugs for genetic diseases. PMID:21308150
Identification of candidate small-molecule therapeutics to cancer by gene-signature perturbation in connectivity mapping. PMID:21305029
Gene expression meta-analysis identifies VDAC1 as a predictor of poor outcome in early stage non-small cell lung cancer. PMID:21297950
PERP regulates enamel formation via effects on cell-cell adhesion and gene expression. PMID:21285247
Detecting cancer gene networks characterized by recurrent genomic alterations in a population. PMID:21283511
Identification of Tat-SF1 cellular targets by exon array analysis reveals dual roles in transcription and splicing. PMID:21282347
Isolation and characterization of progenitor-like cells from human renal proximal tubules. PMID:21281815
Loss of subcellular lipid transport due to ARV1 deficiency disrupts organelle homeostasis and activates the unfolded protein response. PMID:21266578
Characterisation and expression of microRNAs in developing wings of the neotropical butterfly Heliconius melpomene. PMID:21266089
MicroRNA controlled adenovirus mediates anti-cancer efficacy without affecting endogenous microRNA activity. PMID:21264344
Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples. PMID:21261984
Indole and 7-hydroxyindole diminish Pseudomonas aeruginosa virulence. PMID:21261883
Lyngbyoic acid, a "tagged" fatty acid from a marine cyanobacterium, disrupts quorum sensing in Pseudomonas aeruginosa. PMID:21258753
Biological assessment of robust noise models in microarray data analysis. PMID:21252077
Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network. PMID:21247874
Transcriptome profiling of the rice blast fungus during invasive plant infection and in vitro stresses. PMID:21247492
MMP1 bimodal expression and differential response to inflammatory mediators is linked to promoter polymorphisms. PMID:21244711
A Bayesian framework for inference of the genotype-phenotype map for segregating populations. PMID:21242536
Field transcriptome revealed critical developmental and physiological transitions involved in the expression of growth potential in japonica rice. PMID:21226959
Selenium toxicity but not deficient or super-nutritional selenium status vastly alters the transcriptome in rodents. PMID:21226930
A ß-D: -xylosidase and a PR-4B precursor identified as genes accounting for differences in peach cold storage tolerance. PMID:21221699
Microarray analysis of XOPS-mCFP zebrafish retina identifies genes associated with rod photoreceptor degeneration and regeneration. PMID:21217106
Functional specialization of Piwi proteins in Paramecium tetraurelia from post-transcriptional gene silencing to genome remodelling. PMID:21216825
Functional analysis of Rfx6 and mutant variants associated with neonatal diabetes. PMID:21215266
Mammalian stem cells reprogramming in response to terahertz radiation. PMID:21209821
Short-term administration of rhGH increases markers of cellular proliferation but not milk protein gene expression in normal lactating women. PMID:21205870
Matrix metalloproteinase-8 deficiency increases joint inflammation and bone erosion in the K/BxN serum-transfer arthritis model. PMID:21190566
Comprehensive gene-expression survey identifies wif1 as a modulator of cardiomyocyte differentiation. PMID:21179454
The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes. PMID:21177656
Silicon enhances suberization and lignification in roots of rice (Oryza sativa). PMID:21172812
Association of tissue lineage and gene expression: conservatively and differentially expressed genes define common and special functions of tissues. PMID:21172044
Expression profiling of formalin-fixed paraffin-embedded primary breast tumors using cancer-specific and whole genome gene panels on the DASL® platform. PMID:21172013
A scalable approach for discovering conserved active subnetworks across species. PMID:21170309
CD47 knockout mice exhibit improved recovery from spinal cord injury. PMID:21168495
Mthfd1 is a modifier of chemically induced intestinal carcinogenesis. PMID:21156972
Systematic identification of placental epigenetic signatures for the noninvasive prenatal detection of Edwards syndrome. PMID:21152411
A transcription factor map as revealed by a genome-wide gene expression analysis of whole-blood mRNA transcriptome in multiple sclerosis. PMID:21152067
Analysis of kinase gene expression patterns across 5681 human tissue samples reveals functional genomic taxonomy of the kinome. PMID:21151926
Global gene expression profiling of a population exposed to a range of benzene levels. PMID:21147609
Epigenetic changes induced by air toxics: formaldehyde exposure alters miRNA expression profiles in human lung cells. PMID:21147603
Fine-scale genetic mapping of a hybrid sterility factor between Drosophila simulans and D. mauritiana: the varied and elusive functions of "speciation genes". PMID:21144061
Comparative profiling of the transcriptional response to iron restriction in six serotypes of Actinobacillus pleuropneumoniae with different virulence potential. PMID:21143895
Structure and expression of the maize (Zea mays L.) SUN-domain protein gene family: evidence for the existence of two divergent classes of SUN proteins in plants. PMID:21143845
FBG1 is a promiscuous ubiquitin ligase that sequesters APC2 and causes S-phase arrest. PMID:21135578
Chronic intermittent hypoxia induces lung growth in adult mice. PMID:21131398
Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. PMID:21130701
Mining Affymetrix microarray data for long non-coding RNAs: altered expression in the nucleus accumbens of heroin abusers. PMID:21128942
GAMMA-BASED CLUSTERING VIA ORDERED MEANS WITH APPLICATION TO GENE-EXPRESSION ANALYSIS. PMID:21113321
NCBI GEO: archive for functional genomics data sets--10 years on. PMID:21097893
Primosomal proteins DnaD and DnaB are recruited to chromosomal regions bound by DnaA in Bacillus subtilis. PMID:21097613
Deducing corticotropin-releasing hormone receptor type 1 signaling networks from gene expression data by usage of genetic algorithms and graphical Gaussian models. PMID:21092110
The transcriptional regulator Rok binds A+T-rich DNA and is involved in repression of a mobile genetic element in Bacillus subtilis. PMID:21085634
Escherichia coli global gene expression in urine from women with urinary tract infection. PMID:21085611
Physiology of Pseudomonas aeruginosa in biofilms as revealed by transcriptome analysis. PMID:21083928
Proteomics and transcriptomics characterization of bile stress response in probiotic Lactobacillus rhamnosus GG. PMID:21078892
Feasibility of using gene expression analysis to study canine soft tissue sarcomas. PMID:21076837
Algorithm-driven artifacts in median polish summarization of microarray data. PMID:21070630
A comparative analysis of gene-expression data of multiple cancer types. PMID:21060876
Identification and optimization of classifier genes from multi-class earthworm microarray dataset. PMID:21060837
RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media. PMID:21057108
IGRhCellID: integrated genomic resources of human cell lines for identification. PMID:21051335
Specified species in gingival crevicular fluid predict bacterial diversity. PMID:21049043
Ancestral centriole and flagella proteins identified by analysis of Naegleria differentiation. PMID:21045110
Integrative systems biology for data-driven knowledge discovery. PMID:21044756
Stromal microenvironment processes unveiled by biological component analysis of gene expression in xenograft tumor models. PMID:21044358
Prioritizing genes associated with prostate cancer development. PMID:21044312
Myogenin regulates exercise capacity and skeletal muscle metabolism in the adult mouse. PMID:21042574
Ubiquitin accumulation in autophagy-deficient mice is dependent on the Nrf2-mediated stress response pathway: a potential role for protein aggregation in autophagic substrate selection. PMID:21041446
eXtraembryonic ENdoderm (XEN) stem cells produce factors that activate heart formation. PMID:20975998
CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data. PMID:20972221
The role of epidermal growth factor in the healing tympanic membrane following perforation in rats. PMID:20967565
Seasonal changes in bacterial and archaeal gene expression patterns across salinity gradients in the Columbia River coastal margin. PMID:20967204
Comparative survival analysis of breast cancer microarray studies identifies important prognostic genetic pathways. PMID:20964848
MediPlEx - a tool to combine in silico & experimental gene expression profiles of the model legume Medicago truncatula. PMID:20958970
Practical application of toxicogenomics for profiling toxicant-induced biological perturbations. PMID:20957103
Temporal gene expression profiling during rat femoral marrow ablation-induced intramembranous bone regeneration. PMID:20957030
Hal4 and Hal5 protein kinases are required for general control of carbon and nitrogen uptake and metabolism. PMID:20952580
CancerResource: a comprehensive database of cancer-relevant proteins and compound interactions supported by experimental knowledge. PMID:20952398
Epigenetic antagonism between polycomb and SWI/SNF complexes during oncogenic transformation. PMID:20951942
RB-pathway disruption in breast cancer: differential association with disease subtypes, disease-specific prognosis and therapeutic response. PMID:20948315
Alkaline-stress response in Glycine soja leaf identifies specific transcription factors and ABA-mediated signaling factors. PMID:20938706
Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia. PMID:20932287
Ontology-based meta-analysis of global collections of high-throughput public data. PMID:20927376
Robust assignment of cancer subtypes from expression data using a uni-variate gene expression average as classifier. PMID:20925936
Multi-species integrative biclustering. PMID:20920250
Features of cryptic promoters and their varied reliance on bromodomain-containing factors. PMID:20886085
Gene expression study of monocytes/macrophages during early foreign body reaction and identification of potential precursors of myofibroblasts. PMID:20886081
Dysregulation of the mitogen granulin in human cancer through the miR-15/107 microRNA gene group. PMID:20884628
Nutrient-regulated transcriptional responses in the brown tide-forming alga Aureococcus anophagefferens. PMID:20880332
Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis. PMID:20876091
Asymmetric microarray data produces gene lists highly predictive of research literature on multiple cancer types. PMID:20875095
A Brassica exon array for whole-transcript gene expression profiling. PMID:20862292
BAFF receptor signaling aids the differentiation of immature B cells into transitional B cells following tonic BCR signaling. PMID:20861359
Girafe--an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads. PMID:20861030
Characterization of a novel Lactobacillus species closely related to Lactobacillus johnsonii using a combination of molecular and comparative genomics methods. PMID:20849602
The forkhead transcription factor Hcm1 promotes mitochondrial biogenesis and stress resistance in yeast. PMID:20847055
Gene and noncoding RNA regulation underlying photoreceptor protection: microarray study of dietary antioxidant saffron and photobiomodulation in rat retina. PMID:20844572
A systems biology approach to identify effective cocktail drugs. PMID:20840734
Systemic gut microbial modulation of bile acid metabolism in host tissue compartments. PMID:20837534
In silico models of cancer. PMID:20836040
MitoGenesisDB: an expression data mining tool to explore spatio-temporal dynamics of mitochondrial biogenesis. PMID:20833631
Genomic distance entrained clustering and regression modelling highlights interacting genomic regions contributing to proliferation in breast cancer. PMID:20825665
Finding the right questions: exploratory pathway analysis to enhance biological discovery in large datasets. PMID:20824171
Using expression genetics to study the neurobiology of ethanol and alcoholism. PMID:20813241
Gene expression following induction of regeneration in Drosophila wing imaginal discs. Expression profile of regenerating wing discs. PMID:20813047
Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus. PMID:20808887
A maternal low protein diet has pronounced effects on mitochondrial gene expression in offspring liver and skeletal muscle; protective effect of taurine. PMID:20804614
Analyzing schizophrenia by DNA microarrays. PMID:20801428
The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. PMID:20797886
Current concepts of follicle-stimulating hormone receptor gene regulation. PMID:20739665
Molecular analysis of ex-vivo CD133+ GBM cells revealed a common invasive and angiogenic profile but different proliferative signatures among high grade gliomas. PMID:20735813
Transcriptional regulation by CHIP/LDB complexes. PMID:20730086
Gene Expression Browser: large-scale and cross-experiment microarray data integration, management, search & visualization. PMID:20727159
Molecular and functional characterization of allogantigen-specific anergic T cells suitable for cell therapy. PMID:20713457
Alpha-synuclein deficiency leads to increased glyoxalase I expression and glycation stress. PMID:20711648
A comparative analysis of extra-embryonic endoderm cell lines. PMID:20711519
Integration of metabolism and virulence by Clostridium difficile CodY. PMID:20709897
Deletion of genes encoding cytochrome oxidases and quinol monooxygenase blocks the aerobic-anaerobic shift in Escherichia coli K-12 MG1655. PMID:20709841
Transcription profiling of fertilization and early seed development events in a solanaceous species using a 7.7 K cDNA microarray from Solanum chacoense ovules. PMID:20704744
Microarray meta-analysis database (M(2)DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database. PMID:20698961
Transcriptional profiling of intrinsic PNS factors in the postnatal mouse. PMID:20696251
Identification of testis-relevant genes using in silico analysis from testis ESTs and cDNA microarray in the black tiger shrimp (Penaeus monodon). PMID:20696033
Detecting novel genes with sparse arrays. PMID:20691772
Integrative analysis of large scale expression profiles reveals core transcriptional response and coordination between multiple cellular processes in a cyanobacterium. PMID:20678200
Transcriptome analysis of alkali shock and alkali adaptation in Listeria monocytogenes 10403S. PMID:20677981
Reconstruction of the core and extended regulons of global transcription factors. PMID:20661434
Characterization of a Clp protease gene regulator and the reaeration response in Mycobacterium tuberculosis. PMID:20661284
Rank-rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures. PMID:20660011
Global transcriptome profiling of wild soybean (Glycine soja) roots under NaHCO3 treatment. PMID:20653984
Genome-wide expression profiling deciphers host responses altered during dengue shock syndrome and reveals the role of innate immunity in severe dengue. PMID:20652028
Effective knowledge management in translational medicine. PMID:20642836
Power training and postmenopausal hormone therapy affect transcriptional control of specific co-regulated gene clusters in skeletal muscle. PMID:20640546
Identification of primary gene targets of TFAP2C in hormone responsive breast carcinoma cells. PMID:20629094
Functional genetic diversity among Mycobacterium tuberculosis complex clinical isolates: delineation of conserved core and lineage-specific transcriptomes during intracellular survival. PMID:20628579
Neighborhood rough set reduction-based gene selection and prioritization for gene expression profile analysis and molecular cancer classification. PMID:20625410
Independent component analysis: mining microarray data for fundamental human gene expression modules. PMID:20619355
Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways. PMID:20616000
High-throughput profiling of amino acids in strains of the Saccharomyces cerevisiae deletion collection. PMID:20610602
Small RNAs, DNA methylation and transposable elements in wheat. PMID:20584339
Increased mutation frequency in redox-impaired Escherichia coli due to RelA- and RpoS-mediated repression of DNA repair. PMID:20581184
Innate immune processes are sufficient for driving silicosis in mice. PMID:20576854
Immature cell populations and an erythropoiesis gene-expression signature in systemic juvenile idiopathic arthritis: implications for pathogenesis. PMID:20576155
Transcriptional profile analysis of RPGRORF15 frameshift mutation identifies novel genes associated with retinal degeneration. PMID:20574030
Elevated cyclic AMP levels in T lymphocytes transformed by human T-cell lymphotropic virus type 1. PMID:20573814
Alternative splicing is frequent during early embryonic development in mouse. PMID:20573213
Global transcriptional response to carbonic anhydrase IX deficiency in the mouse stomach. PMID:20573196
Molecular subtypes of breast cancer are associated with characteristic DNA methylation patterns. PMID:20565864
A general framework for optimization of probes for gene expression microarray and its application to the fungus Podospora anserina. PMID:20565839
Accessibility of the Drosophila genome discriminates PcG repression, H4K16 acetylation and replication timing. PMID:20562853
Metatranscriptomic analysis of the response of river biofilms to pharmaceutical products, using anonymous DNA microarrays. PMID:20562274
Identification of novel epithelial ovarian cancer biomarkers by cross-laboratory microarray analysis. PMID:20556581
A gene network switch enhances the oxidative capacity of ovine skeletal muscle during late fetal development. PMID:20546621
Lactobacillus acidophilus induces virus immune defence genes in murine dendritic cells by a Toll-like receptor-2-dependent mechanism. PMID:20545783
The lytic transcriptome of Kaposi's sarcoma-associated herpesvirus reveals extensive transcription of noncoding regions, including regions antisense to important genes. PMID:20534856
UFFizi: a generic platform for ranking informative features. PMID:20525252
Response of the mouse lung transcriptome to welding fume: effects of stainless and mild steel fumes on lung gene expression in A/J and C57BL/6J mice. PMID:20525249
Deletion of von Hippel-Lindau in glomerular podocytes results in glomerular basement membrane thickening, ectopic subepithelial deposition of collagen {alpha}1{alpha}2{alpha}1(IV), expression of neuroglobin, and proteinuria. PMID:20522651
Germline-dependent gene expression in distant non-gonadal somatic tissues of Drosophila. PMID:20515475
The correlation pattern of acquired copy number changes in 164 ETV6/RUNX1-positive childhood acute lymphoblastic leukemias. PMID:20513752
Changes in DnaA-dependent gene expression contribute to the transcriptional and developmental response of Bacillus subtilis to manganese limitation in Luria-Bertani medium. PMID:20511500
Induction of neuro-protective/regenerative genes in stem cells infiltrating post-ischemic brain tissue. PMID:20509949
Fast integration of heterogeneous data sources for predicting gene function with limited annotation. PMID:20507895
Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset. PMID:20507584
Gene expression profile in circulating mononuclear cells after exposure to ultrafine carbon particles. PMID:20507211
An eScience-Bayes strategy for analyzing omics data. PMID:20504364
Benzo(a)pyrene induces similar gene expression changes in testis of DNA repair proficient and deficient mice. PMID:20504355
Functional and gene network analyses of transcriptional signatures characterizing pre-weaned bovine mammary parenchyma or fat pad uncovered novel inter-tissue signaling networks during development. PMID:20504330
Development of a cross-platform biomarker signature to detect renal transplant tolerance in humans. PMID:20501943
Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context. PMID:20500821
Re-annotation is an essential step in systems biology modeling of functional genomics data. PMID:20498845
Drawing networks of rejection - a systems biological approach to the identification of candidate genes in heart transplantation. PMID:20497491
Expression of miR-196b is not exclusively MLL-driven but is especially linked to activation of HOXA genes in pediatric acute lymphoblastic leukemia. PMID:20494936
Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PMID:20485568
The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution. PMID:20485561
The RNA binding protein Tudor-SN is essential for stress tolerance and stabilizes levels of stress-responsive mRNAs encoding secreted proteins in Arabidopsis. PMID:20484005
Detecting microRNA activity from gene expression data. PMID:20482775
Identification of components associated with thermal acclimation of photosystem II in Synechocystis sp. PCC6803. PMID:20463904
Genome-wide changes accompanying the knockdown of Ep-CAM in retinoblastoma. PMID:20461151
Hedgehog pathway-regulated gene networks in cerebellum development and tumorigenesis. PMID:20460306
Thiamine biosynthesis in Saccharomyces cerevisiae is regulated by the NAD+-dependent histone deacetylase Hst1. PMID:20439498
Detection of gene orthology from gene co-expression and protein interaction networks. PMID:20438654
Gene expression atlas for human embryogenesis. PMID:20430792
Alternate protein kinase A activity identifies a unique population of stromal cells in adult bone. PMID:20421483
Gene enrichment profiles reveal T-cell development, differentiation, and lineage-specific transcription factors including ZBTB25 as a novel NF-AT repressor. PMID:20410506
MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. PMID:20407027
Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis. PMID:20406493
Proliferation and pluripotency of human embryonic stem cells maintained on type I collagen. PMID:20367282
Using pre-existing microarray datasets to increase experimental power: application to insulin resistance. PMID:20361040
Bayesian approach to transforming public gene expression repositories into disease diagnosis databases. PMID:20360561
Onecut-2 knockout mice fail to thrive during early postnatal period and have altered patterns of gene expression in small intestine. PMID:20354101
Dissecting interferon-induced transcriptional programs in human peripheral blood cells. PMID:20339534
Reciprocal regulation of metabolic and signaling pathways. PMID:20334672
Widespread transcriptional autosomal dosage compensation in Drosophila correlates with gene expression level. PMID:20333221
Significance of light, sugar, and amino acid supply for diurnal gene regulation in developing barley caryopses. PMID:20304969
Global and unbiased detection of splice junctions from RNA-seq data. PMID:20236510
High-resolution genomic profiling of human papillomavirus-associated vulval neoplasia. PMID:20234371
Analysis of the genome content of Lactococcus garvieae by genomic interspecies microarray hybridization. PMID:20233401
RNA isolation method for single embryo transcriptome analysis in zebrafish. PMID:20233395
MiDReG: a method of mining developmentally regulated genes using Boolean implications. PMID:20231483
Systematic planning of genome-scale experiments in poorly studied species. PMID:20221257
Array-based transcript profiling and limiting-dilution reverse transcription-PCR analysis identify additional latent genes in Kaposi's sarcoma-associated herpesvirus. PMID:20219929
Homozygous deletion mapping in myeloma samples identifies genes and an expression signature relevant to pathogenesis and outcome. PMID:20215539
Conserved regulatory motifs at phenylethanolamine N-methyltransferase (PNMT) are disrupted by common functional genetic variation: an integrated computational/experimental approach. PMID:20204374
MicroRNAs of Bombyx mori identified by Solexa sequencing. PMID:20199675
Neonatal maternal deprivation response and developmental changes in gene expression revealed by hypothalamic gene expression profiling in mice. PMID:20195375
Role of the Sinorhizobium meliloti global regulator Hfq in gene regulation and symbiosis. PMID:20192823
Multiple common variants for celiac disease influencing immune gene expression. PMID:20190752
Genome-wide analysis reveals distinct substrate specificities of Rrp6, Dis3, and core exosome subunits. PMID:20185544
Differential gene expression in adipose stem cells cultured in allogeneic human serum versus fetal bovine serum. PMID:20184435
Gene expression prediction by soft integration and the elastic net-best performance of the DREAM3 gene expression challenge. PMID:20169069
Increased incidence of rare codon clusters at 5' and 3' gene termini: implications for function. PMID:20167116
High-throughput assessment of CpG site methylation for distinguishing between HCV-cirrhosis and HCV-associated hepatocellular carcinoma. PMID:20165882
Broad spectrum microarray for fingerprint-based bacterial species identification. PMID:20163710
Transcription of proteinase 3 and related myelopoiesis genes in peripheral blood mononuclear cells of patients with active Wegener's granulomatosis. PMID:20155833
Increased sinusoidal flow is not the primary stimulus to liver regeneration. PMID:20148099
Classification of genes and putative biomarker identification using distribution metrics on expression profiles. PMID:20140228
Regulation of gene expression in hepatic cells by the mammalian Target of Rapamycin (mTOR). PMID:20140209
Coexpression analysis of tomato genes and experimental verification of coordinated expression of genes found in a functionally enriched coexpression module. PMID:20130013
Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging. PMID:20128910
Candidate genes for alcohol preference identified by expression profiling in alcohol-preferring and -nonpreferring reciprocal congenic rats. PMID:20128895
MicroRNAs show diverse and dynamic expression patterns in multiple tissues of Bombyx mori. PMID:20122259
Functional genomic study of exogenous n-butanol stress in Escherichia coli. PMID:20118358
Alternative route for glyoxylate consumption during growth on two-carbon compounds by Methylobacterium extorquens AM1. PMID:20118267
Changes in gene expression in regions of the extended amygdala of alcohol-preferring rats after binge-like alcohol drinking. PMID:20116196
The submergence tolerance regulator Sub1A mediates stress-responsive expression of AP2/ERF transcription factors. PMID:20107022
Modeling complex genetic and environmental influences on comorbid bipolar disorder with tobacco use disorder. PMID:20102619
Copy number variation in the genomes of twelve natural isolates of Caenorhabditis elegans. PMID:20100350
ChIP-chip designs to interrogate the genome of Xenopus embryos for transcription factor binding and epigenetic regulation. PMID:20098671
Frozen robust multiarray analysis (fRMA). PMID:20097884
Expanded multilocus sequence typing and comparative genomic hybridization of Campylobacter coli isolates from multiple hosts. PMID:20097815
Spatial and temporal regulation of gene expression in the mammalian growth plate. PMID:20096814
Expression profiling of S. pombe acetyltransferase mutants identifies redundant pathways of gene regulation. PMID:20096118
Gene expression profiling of peripheral blood cells for early detection of breast cancer. PMID:20078854
PepD participates in the mycobacterial stress response mediated through MprAB and SigE. PMID:20061478
Genome-wide identification of hypoxia-inducible factor binding sites and target genes by a probabilistic model integrating transcription-profiling data and in silico binding site prediction. PMID:20061373
DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia. PMID:20060365
Antibodies specifically target AML antigen NuSAP1 after allogeneic bone marrow transplantation. PMID:20053754
Effects of moderate drinking during pregnancy on placental gene expression. PMID:20053520
IGF-I induced genes in stromal fibroblasts predict the clinical outcome of breast and lung cancer patients. PMID:20051100
Cardiovascular networks: systems-based approaches to cardiovascular disease. PMID:20048233
Novel early response genes in osteoblasts exposed to dynamic fluid flow. PMID:20047941
Correlating measurements across samples improves accuracy of large-scale expression profile experiments. PMID:20042104
A gene expression signature of invasive potential in metastatic melanoma cells. PMID:20041153
Effects of temperature on gene expression in embryos of the coral Montastraea faveolata. PMID:20030803
Androgen regulated genes in human prostate xenografts in mice: relation to BPH and prostate cancer. PMID:20027305
Chimeric mouse tumor models reveal differences in pathway activation between ERBB family- and KRAS-dependent lung adenocarcinomas. PMID:20023657
Discovering collectively informative descriptors from high-throughput experiments. PMID:20021653
Mixture-model based estimation of gene expression variance from public database improves identification of differentially expressed genes in small sized microarray data. PMID:20015947
Molecular evolution of sex-biased genes in the Drosophila ananassae subgroup. PMID:20015359
Developmental profiling of postnatal dentate gyrus progenitors provides evidence for dynamic cell-autonomous regulation. PMID:20014381
Estradiol stimulates vasodilatory and metabolic pathways in cultured human endothelial cells. PMID:20011585
Sialic acid utilisation and synthesis in the neonatal rat revisited. PMID:20011510
ConceptGen: a gene set enrichment and gene set relation mapping tool. PMID:20007254
Systems biology of embryogenesis. PMID:20003850
Dissecting the dynamics of dysregulation of cellular processes in mouse mammary gland tumor. PMID:20003387
The pitfalls of platform comparison: DNA copy number array technologies assessed. PMID:19995423
Biomarker detection in the integration of multiple multi-class genomic studies. PMID:19965884
Two-transcript gene expression classifiers in the diagnosis and prognosis of human diseases. PMID:19961616
A model selection approach to discover age-dependent gene expression patterns using quantile regression models. PMID:19958479
Consensus miRNA expression profiles derived from interplatform normalization of microarray data. PMID:19948767
Novel rank-based statistical methods reveal microRNAs with differential expression in multiple cancer types. PMID:19946373
Detection call algorithms for high-throughput gene expression microarray data. PMID:19939941
Data reporting standards: making the things we use better. PMID:19939294
p38gamma mitogen-activated protein kinase is a key regulator in skeletal muscle metabolic adaptation in mice. PMID:19936205
A genome-wide characterization of microRNA genes in maize. PMID:19936050
Exon array analysis of head and neck cancers identifies a hypoxia related splice variant of LAMA3 associated with a poor prognosis. PMID:19936049
Members of the LBD family of transcription factors repress anthocyanin synthesis and affect additional nitrogen responses in Arabidopsis. PMID:19933203
Differentially expressed genes for aggressive pecking behaviour in laying hens. PMID:19925670
The Drosophila PGC-1 homologue Spargel coordinates mitochondrial activity to insulin signalling. PMID:19910925
FoxJ1-dependent gene expression is required for differentiation of radial glia into ependymal cells and a subset of astrocytes in the postnatal brain. PMID:19906869
An expression database for roots of the model legume Medicago truncatula under salt stress. PMID:19906315
CITED2 and NCOR2 in anti-oestrogen resistance and progression of breast cancer. PMID:19904269
Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling. PMID:19901961
Analysis of chromosomal aberration (1, 3, and 8) and association of microRNAs in uveal melanoma. PMID:19898689
Matrix factorization for recovery of biological processes from microarray data. PMID:19897089
Use of microarray hybridization to identify Brugia genes involved in mosquito infectivity. PMID:19894065
Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors. PMID:19893621
Analysis of gene expression and physiological responses in three Mexican maize landraces under drought stress and recovery irrigation. PMID:19888455
Relationship between CAD risk genotype in the chromosome 9p21 locus and gene expression. Identification of eight new ANRIL splice variants. PMID:19888323
Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression. PMID:19887574
ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization. PMID:19863798
A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays. PMID:19860899
Patterns of DNA-sequence divergence between Drosophila miranda and D. pseudoobscura. PMID:19859648
Transcriptional regulation of membrane lipid homeostasis in Escherichia coli. PMID:19854834
Comprehensive gene and microRNA expression profiling reveals a role for microRNAs in human liver development. PMID:19841744
Probe-level analysis of expression microarrays characterizes isoform-specific degradation during mouse oocyte maturation. PMID:19834616
Survival Online: a web-based service for the analysis of correlations between gene expression and clinical and follow-up data. PMID:19828070
STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data. PMID:19828039
Rapamycin response in tumorigenic and non-tumorigenic hepatic cell lines. PMID:19816606
Genoproteomic mining of urothelial cancer suggests {gamma}-glutamyl hydrolase and diazepam-binding inhibitor as putative urinary markers of outcome after chemotherapy. PMID:19815704
Facilitating functional annotation of chicken microarray data. PMID:19811685
MicroRNAs show mutually exclusive expression patterns in the brain of adult male rats. PMID:19806225
Early over expression of messenger RNA for multiple genes, including insulin, in the Pancreatic Lymph Nodes of NOD mice is associated with Islet Autoimmunity. PMID:19799787
AP-2gamma promotes proliferation in breast tumour cells by direct repression of the CDKN1A gene. PMID:19798054
Global transcriptional response to Hfe deficiency and dietary iron overload in mouse liver and duodenum. PMID:19787063
MicroRNA expression profiling during the life cycle of the silkworm (Bombyx mori). PMID:19785751
A secretory phospholipase A2-mediated neuroprotection and anti-apoptosis. PMID:19775433
Global identification of targets of the Arabidopsis MADS domain protein AGAMOUS-Like15. PMID:19767455
A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos. PMID:19758566
New insights into molecular pathways associated with flatfish ovarian development and atresia revealed by transcriptional analysis. PMID:19754951
Glucocorticoids with different chemical structures but similar glucocorticoid receptor potency regulate subsets of common and unique genes in human trabecular meshwork cells. PMID:19744340
Nutrition controls mitochondrial biogenesis in the Drosophila adipose tissue through Delg and cyclin D/Cdk4. PMID:19742324
Meta-coexpression conservation analysis of microarray data: a "subset" approach provides insight into brain-derived neurotrophic factor regulation. PMID:19737418
A high throughput experimental approach to identify miRNA targets in human cells. PMID:19734348
Human TCR-alpha beta+ CD4- CD8- T cells can derive from CD8+ T cells and display an inflammatory effector phenotype. PMID:19734235
The Drosophila HP1 homolog Rhino is required for transposon silencing and piRNA production by dual-strand clusters. PMID:19732946
Plasmodium falciparum heterochromatin protein 1 marks genomic loci linked to phenotypic variation of exported virulence factors. PMID:19730695
GEM-TREND: a web tool for gene expression data mining toward relevant network discovery. PMID:19728865
Systems-level modeling of cancer-fibroblast interaction. PMID:19727395
Evolution of sex-dependent gene expression in three recently diverged species of Drosophila. PMID:19720861
NF-E2-related factor 2 regulates the stress response to UVA-1-oxidized phospholipids in skin cells. PMID:19720622
Penetration of the stigma and style elicits a novel transcriptome in pollen tubes, pointing to genes critical for growth in a pistil. PMID:19714218
A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis. PMID:19713416
A reliable measure of similarity based on dependency for short time series: an application to gene expression networks. PMID:19712487
BMP signaling induces cell-type-specific changes in gene expression programs of human keratinocytes and fibroblasts. PMID:19710687
Peripheral blood T cells in acute myeloid leukemia (AML) patients at diagnosis have abnormal phenotype and genotype and form defective immune synapses with AML blasts. PMID:19710498
GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction. PMID:19703314
Gene regulation in parthenocarpic tomato fruit. PMID:19700496
Identification of brain transcriptional variation reproduced in peripheral blood: an approach for mapping brain expression traits. PMID:19692348
Microarray and real-time PCR analyses of the responses of high-arctic soil bacteria to hydrocarbon pollution and bioremediation treatments. PMID:19684169
Targeted deletion of Dicer disrupts lens morphogenesis, corneal epithelium stratification, and whole eye development. PMID:19681134
Impact of the TCR signal on regulatory T cell homeostasis, function, and trafficking. PMID:19668367
Gene expression changes in the nucleus accumbens of alcohol-preferring rats following chronic ethanol consumption. PMID:19666046
Rapid and spontaneous loss of phthiocerol dimycocerosate (PDIM) from Mycobacterium tuberculosis grown in vitro: implications for virulence studies. PMID:19661177
Limb immobilization induces a coordinate down-regulation of mitochondrial and other metabolic pathways in men and women. PMID:19654872
Moderate strength (0.23-0.28 T) static magnetic fields (SMF) modulate signaling and differentiation in human embryonic cells. PMID:19653909
Increased local expression of coagulation factor X contributes to the fibrotic response in human and murine lung injury. PMID:19652365
MDS and secondary AML display unique patterns and abundance of aberrant DNA methylation. PMID:19652201
Differential response of C57BL/6J mouse and DBA/2J mouse to optic nerve crush. PMID:19643015
Chromosome aberrations resulting from double-strand DNA breaks at a naturally occurring yeast fragile site composed of inverted ty elements are independent of Mre11p and Sae2p. PMID:19635935
NeuroD6 genomic signature bridging neuronal differentiation to survival via the molecular chaperone network. PMID:19610105
Low-risk susceptibility alleles in 40 human breast cancer cell lines. PMID:19607694
Leukemia inhibitory factor regulates the timing of oligodendrocyte development and myelination in the postnatal optic nerve. PMID:19598242
Microarray analysis of lymphatic tissue reveals stage-specific, gene expression signatures in HIV-1 infection. PMID:19596987
Array-based DNA methylation profiling in follicular lymphoma. PMID:19587707
NCBI Peptidome: a new public repository for mass spectrometry peptide identifications. PMID:19587658
The RNA-binding motif protein 15B (RBM15B/OTT3) acts as cofactor of the nuclear export receptor NXF1. PMID:19586903
Subtype-specific peripheral blood gene expression profiles in recent-onset juvenile idiopathic arthritis. PMID:19565513
FOXP3 inhibits activation-induced NFAT2 expression in T cells thereby limiting effector cytokine expression. PMID:19564342
A gene signature for post-infectious chronic fatigue syndrome. PMID:19555476
Impact of animal strain on gene expression in a rat model of acute cardiac rejection. PMID:19552812
Physiological and toxicological transcriptome changes in HepG2 cells exposed to copper. PMID:19549813
Unsupervised assessment of microarray data quality using a Gaussian mixture model. PMID:19545436
HOXA3 modulates injury-induced mobilization and recruitment of bone marrow-derived cells. PMID:19544454
HORMONOMETER: a tool for discerning transcript signatures of hormone action in the Arabidopsis transcriptome. PMID:19535475
Lasp1 gene disruption is linked to enhanced cell migration and tumor formation. PMID:19531578
Placenta-derived fetal specific mRNA is more readily detectable in maternal plasma than in whole blood. PMID:19516908
Role of cholesterol pathways in norovirus replication. PMID:19515767
An exploratory pathways analysis of temporal changes induced by spinal cord injury in the rat bladder wall: insights on remodeling and inflammation. PMID:19513121
Gene expression profiling of intestinal regeneration in the sea cucumber. PMID:19505337
Pilin regulation in the pilT mutant of Neisseria gonorrhoeae strain MS11. PMID:19486161
Profile of estrogen-responsive genes in an estrogen-specific mammary gland outgrowth model. PMID:19484750
Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array. PMID:19480707
Identification of gene co-regulatory modules and associated cis-elements involved in degenerative heart disease. PMID:19476647
PathExpress update: the enzyme neighbourhood method of associating gene-expression data with metabolic pathways. PMID:19474337
An rtt109-independent role for vps75 in transcription-associated nucleosome dynamics. PMID:19470761
Ripening-regulated susceptibility of tomato fruit to Botrytis cinerea requires NOR but not RIN or ethylene. PMID:19465579
Gene expression profiles of sporadic canine hemangiosarcoma are uniquely associated with breed. PMID:19461996
A novel information retrieval model for high-throughput molecular medicine modalities. PMID:19458790
Epigenomic profiling indicates a role for DNA methylation in early postnatal liver development. PMID:19457928
Transcriptomic and proteomic analysis of global ischemia and cardioprotection in the rabbit heart. PMID:19454556
Transcriptional signatures of Itk-deficient CD3+, CD4+ and CD8+ T-cells. PMID:19450280
Assessing reliability of protein-protein interactions by integrative analysis of data in model organisms. PMID:19426453
Integration of tomato reproductive developmental landmarks and expression profiles, and the effect of SUN on fruit shape. PMID:19422692
High-resolution analysis of copy number alterations and associated expression changes in ovarian tumors. PMID:19419571
Gene expression profiling for the investigation of soft tissue sarcoma pathogenesis and the identification of diagnostic, prognostic, and predictive biomarkers. PMID:19412622
Convergence of biomarkers, bioinformatics and nanotechnology for individualized cancer treatment. PMID:19409634
Genomic DNA microarray comparison of gene expression patterns in Paracoccidioides brasiliensis mycelia and yeasts in vitro. PMID:19406900
The tetraspanin Tm4sf3 is localized to the ventral pancreas and regulates fusion of the dorsal and ventral pancreatic buds. PMID:19403659
Web-queryable large-scale data sets for hypothesis generation in plant biology. PMID:19401381
Absence of SPARC leads to impaired lens circulation. PMID:19401199
GeneRegionScan: a Bioconductor package for probe-level analysis of specific, small regions of the genome. PMID:19398447
Repertoire of microRNAs in epithelial ovarian cancer as determined by next generation sequencing of small RNA cDNA libraries. PMID:19390579
Grape seed extract acting on astrocytes reveals neuronal protection against oxidative stress via interleukin-6-mediated mechanisms. PMID:19381798
Increased antibiotic resistance of Escherichia coli in mature biofilms. PMID:19376922
A specialized outer layer of the primary cell wall joins elongating cotton fibers into tissue-like bundles. PMID:19369592
Biologic and immunologic effects of knockout of human cytomegalovirus pp65 nuclear localization signal. PMID:19369477
Thymic OX40 expression discriminates cells undergoing strong responses to selection ligands. PMID:19342632
Histone deacetylase inhibition elicits an evolutionarily conserved self-renewal program in embryonic stem cells. PMID:19341625
Hexosamine template. A platform for modulating gene expression and for sugar-based drug discovery. PMID:19326913
Estrogen receptor beta is required for optimal cAMP production in mouse granulosa cells. PMID:19324971
Detection of genomic deletions in rice using oligonucleotide microarrays. PMID:19320995
A cross-study transcriptional analysis of Parkinson's disease. PMID:19305504
Transcriptome analysis of synaptoneurosomes identifies neuroplasticity genes overexpressed in incipient Alzheimer's disease. PMID:19295912
T7-based linear amplification of low concentration mRNA samples using beads and microfluidics for global gene expression measurements. PMID:19294302
ebTrack: an environmental bioinformatics system built upon ArrayTrack. PMID:19278561
Chromatin state marks cell-type- and gender-specific replication of the Drosophila genome. PMID:19270159
Depletion of the cullin Cdc53p induces morphogenetic changes in Candida albicans. PMID:19270112
SiPaGene: A new repository for instant online retrieval, sharing and meta-analyses of GeneChip expression data. PMID:19265543
Cellular expression of midkine-a and midkine-b during retinal development and photoreceptor regeneration in zebrafish. PMID:19263476
BRB-ArrayTools Data Archive for human cancer gene expression: a unique and efficient data sharing resource. PMID:19259398
Prediction and verification of mouse tRNA gene families. PMID:19246989
Effects of differential glycosylation of glycodelins on lymphocyte survival. PMID:19240032
Salicylic acid confers resistance to a biotrophic rust pathogen, Puccinia substriata, in pearl millet (Pennisetum glaucum). PMID:19236576
PVY(NTN) elicits a diverse gene expression response in different potato genotypes in the first 12 h after inoculation. PMID:19236574
Analysis of variance components reveals the contribution of sample processing to transcript variation. PMID:19233957
Using differential gene expression to study Entamoeba histolytica pathogenesis. PMID:19217826
Gene expression profiling of the tumor microenvironment during breast cancer progression. PMID:19187537
Expression diversity and evolutionary dynamics of rice duplicate genes. PMID:19184107
Repeatability of published microarray gene expression analyses. PMID:19174838
Infection and genotype remodel the entire soybean transcriptome. PMID:19171053
Genome-wide epigenetic analysis delineates a biologically distinct immature acute leukemia with myeloid/T-lymphoid features. PMID:19168792
Reconfiguring the quorum-sensing regulator SdiA of Escherichia coli to control biofilm formation via indole and N-acylhomoserine lactones. PMID:19168658
Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. PMID:19159457
Gene expression patterns induced by HPV-16 L1 virus-like particles in leukocytes from vaccine recipients. PMID:19155521
A subtype of childhood acute lymphoblastic leukaemia with poor treatment outcome: a genome-wide classification study. PMID:19138562
Differentially expressed genes during malting and correlation with malting quality phenotypes in barley (Hordeum vulgare L.). PMID:19132335
Acute mixed lineage leukemia in children: the experience of St Jude Children's Research Hospital. PMID:19131545
Using pathway signatures as means of identifying similarities among microarray experiments. PMID:19125200
Origins of the Xylella fastidiosa prophage-like regions and their impact in genome differentiation. PMID:19116666
Night/day changes in pineal expression of >600 genes: central role of adrenergic/cAMP signaling. PMID:19103603
Pleiotropic effects in Eya3 knockout mice. PMID:19102749
GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments. PMID:19099609
TATA-binding protein variants that bypass the requirement for Mot1 in vivo. PMID:19098311
Complex fate of paralogs. PMID:19094234
A protein interaction based model for schizophrenia study. PMID:19091023
Identification of G1-regulated genes in normally cycling human cells. PMID:19079774
Co-inhibition of Plasmodium falciparum S-adenosylmethionine decarboxylase/ornithine decarboxylase reveals perturbation-specific compensatory mechanisms by transcriptome, proteome, and metabolome analyses. PMID:19073607
Gene expression profile in pelvic organ prolapse. PMID:19056808
Analyzing ChIP-chip data using bioconductor. PMID:19043553
Changes in gene expression pattern of human primary macrophages induced by carbosilane dendrimer 2G-NN16. PMID:19034630
EMAAS: an extensible grid-based rich internet application for microarray data analysis and management. PMID:19032776
A comparison of four clustering methods for brain expression microarray data. PMID:19032745
Synaptogenesis in purified cortical subplate neurons. PMID:19029062
Gene expression in the human mammary epithelium during lactation: the milk fat globule transcriptome. PMID:19018045
Expression profiles of switch-like genes accurately classify tissue and infectious disease phenotypes in model-based classification. PMID:19014681
Gene set analyses for interpreting microarray experiments on prokaryotic organisms. PMID:18986519
Boolean implication networks derived from large scale, whole genome microarray datasets. PMID:18973690
A chemical genomics study identifies Snf1 as a repressor of GCN4 translation. PMID:18955495
NCBI GEO: archive for high-throughput functional genomic data. PMID:18940857
Experimental analysis of oligonucleotide microarray design criteria to detect deletions by comparative genomic hybridization. PMID:18940006
Norvaline is accumulated after a down-shift of oxygen in Escherichia coli W3110. PMID:18940002
SVD-based anatomy of gene expressions for correlation analysis in Arabidopsis thaliana. PMID:18931094
Loss of RNase R induces competence development in Legionella pneumophila. PMID:18849432
Targets of the Entamoeba histolytica transcription factor URE3-BP. PMID:18846235
GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus. PMID:18842599
Glycogen synthase kinase 3beta-mediated serine phosphorylation of the human glucocorticoid receptor redirects gene expression profiles. PMID:18838540
Organogenic nodule development in hop (Humulus lupulus L.): transcript and metabolic responses. PMID:18823540
Bioinformatic and statistical analysis of the optic nerve head in a primate model of ocular hypertension. PMID:18822132
Single-species microarrays and comparative transcriptomics. PMID:18815615
Global transcription and metabolic flux analysis of Escherichia coli in glucose-limited fed-batch cultivations. PMID:18806003
Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues. PMID:18803840
Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis. PMID:18775970
Key issues in conducting a meta-analysis of gene expression microarray datasets. PMID:18767902
Cdc7-Dbf4 kinase overexpression in multiple cancers and tumor cell lines is correlated with p53 inactivation. PMID:18714392
Genome-wide search for yeast RNase P substrates reveals role in maturation of intron-encoded box C/D small nucleolar RNAs. PMID:18713869
Differential regulation of Listeria monocytogenes internalin and internalin-like genes by sigmaB and PrfA as revealed by subgenomic microarray analyses. PMID:18713061
A decade of genome-wide gene expression profiling in acute myeloid leukemia: flashback and prospects. PMID:18703705
Microarray analysis of human monocytes infected with Francisella tularensis identifies new targets of host response subversion. PMID:18698339
Superposition of transcriptional behaviors determines gene state. PMID:18682855
The Arabidopsis NFYA5 transcription factor is regulated transcriptionally and posttranscriptionally to promote drought resistance. PMID:18682547
Two new clock proteins, LWD1 and LWD2, regulate Arabidopsis photoperiodic flowering. PMID:18676661
Molecular credentialing of rodent bladder carcinogenesis models. PMID:18670642
Accessing and integrating data and knowledge for biomedical research. PMID:18660883
Gene expression patterns of sulfur starvation in Synechocystis sp. PCC 6803. PMID:18644144
Global gene expression profiles suggest an important role for nutrient acquisition in early pathogenesis in a plant model of Pseudomonas aeruginosa infection. PMID:18641163
MN1 affects expression of genes involved in hematopoiesis and can enhance as well as inhibit RAR/RXR-induced gene expression. PMID:18632758
Standardization Initiatives in the (eco)toxicogenomics domain: a review. PMID:18629184
Navigating public microarray databases. PMID:18629145
A bistable gene switch for antibiotic biosynthesis: the butyrolactone regulon in Streptomyces coelicolor. PMID:18628968
MAIDS resistance-associated gene expression patterns in secondary lymphoid organs. PMID:18612634
Differential variability analysis of gene expression and its application to human diseases. PMID:18586739
Genome-wide analysis of ruminant Staphylococcus aureus reveals diversification of the core genome. PMID:18567666
Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data. PMID:18560577
Id1 is a common downstream target of oncogenic tyrosine kinases in leukemic cells. PMID:18559972
Whole genome assessment of the retinal response to diabetes reveals a progressive neurovascular inflammatory response. PMID:18554398
Transcriptional repression of c-Myb and GATA-2 is involved in the biologic effects of C/EBPalpha in p210BCR/ABL-expressing cells. PMID:18550858
Protein translation and cell death: the role of rare tRNAs in biofilm formation and in activating dormant phage killer genes. PMID:18545668
Combined analysis of murine and human microarrays and ChIP analysis reveals genes associated with the ability of MYC to maintain tumorigenesis. PMID:18535662
Calprotectin is released from human skeletal muscle tissue during exercise. PMID:18511485
Fine expression profiling of full-length transcripts using a size-unbiased cDNA library prepared with the vector-capping method. PMID:18487259
HCLS 2.0/3.0: health care and life sciences data mashup using Web 2.0/3.0. PMID:18487092
Individual mRNA expression profiles reveal the effects of specific microRNAs. PMID:18485210
Microarray retriever: a web-based tool for searching and large scale retrieval of public microarray data. PMID:18463138
Global transcription in pluripotent embryonic stem cells. PMID:18462694
Identification of woolliness response genes in peach fruit after post-harvest treatments. PMID:18453640
Phylogenetic and comparative gene expression analysis of barley (Hordeum vulgare) WRKY transcription factor family reveals putatively retained functions between monocots and dicots. PMID:18442363
Conserved co-expression for candidate disease gene prioritization. PMID:18433471
Uncovering signal transduction networks from high-throughput data by integer linear programming. PMID:18411207
Differential gene expression in the nucleus accumbens with ethanol self-administration in inbred alcohol-preferring rats. PMID:18405950
Genome wide transcriptional profiling in breast cancer cells reveals distinct changes in hormone receptor target genes and chromatin modifying enzymes after proteasome inhibition. PMID:18381591
A software framework for microarray and gene expression object model (MAGE-OM) array design annotation. PMID:18366695
The R1 conjugative plasmid increases Escherichia coli biofilm formation through an envelope stress response. PMID:18344336
A visual data mining tool that facilitates reconstruction of transcription regulatory networks. PMID:18320038
Temporal transcriptomic microarray analysis of "Dehalococcoides ethenogenes" strain 195 during the transition into stationary phase. PMID:18310438
Gene expression by the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough grown on an iron electrode under cathodic protection conditions. PMID:18310429
Discovery of agents that eradicate leukemia stem cells using an in silico screen of public gene expression data. PMID:18305216
A new perspective on transcriptional system regulation (TSR): towards TSR profiling. PMID:18297136
Activation of counter-regulatory mechanisms in a rat renal acute rejection model. PMID:18261221
Up regulation in gene expression of chromatin remodelling factors in cervical intraepithelial neoplasia. PMID:18248679
Pathways change in expression during replicative aging in Saccharomyces cerevisiae. PMID:18245757
Transcriptomic identification of candidate genes involved in sunflower responses to chilling and salt stresses based on cDNA microarray analysis. PMID:18221554
EzArray: a web-based highly automated Affymetrix expression array data management and analysis system. PMID:18218103
The role of particulate matter-associated zinc in cardiac injury in rats. PMID:18197293
Switch-like genes populate cell communication pathways and are enriched for extracellular proteins. PMID:18177501
Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines. PMID:18154662
Computational prediction of protein-protein interactions. PMID:18095187
AffyTrees: facilitating comparative analysis of Affymetrix plant microarray chips. PMID:18065560
Discovery of novel alternatively spliced C. elegans transcripts by computational analysis of SAGE data. PMID:18053145
BioCAD: an information fusion platform for bio-network inference and analysis. PMID:18047703
Characterization of zfs1 as an mRNA-binding and -destabilizing protein in Schizosaccharomyces pombe. PMID:18042546
Comparative analysis of the sigma B-dependent stress responses in Listeria monocytogenes and Listeria innocua strains exposed to selected stress conditions. PMID:18024685
Demasculinization of X chromosomes in the Drosophila genus. PMID:17994090
Host pathogen protein interactions predicted by comparative modeling. PMID:17965183
Prediction potential of candidate biomarker sets identified and validated on gene expression data from multiple datasets. PMID:17963508
CEBS--Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data. PMID:17962311
miRGator: an integrated system for functional annotation of microRNAs. PMID:17942429
Weighted analysis of general microarray experiments. PMID:17937807
Phenotypic and transcriptomic analyses demonstrate interactions between the transcriptional regulators CtsR and Sigma B in Listeria monocytogenes. PMID:17933929
Gene profile analysis of osteoblast genes differentially regulated by histone deacetylase inhibitors. PMID:17925016
Gene expression trees in lymphoid development. PMID:17925013
High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer. PMID:17925008
Sharing and reusing gene expression profiling data in neuroscience. PMID:17917127
Cadmium triggers an integrated reprogramming of the metabolism of Synechocystis PCC6803, under the control of the Slr1738 regulator. PMID:17910763
Linking microarray reporters with protein functions. PMID:17897448
Reversible and permanent effects of tobacco smoke exposure on airway epithelial gene expression. PMID:17894889
SAGETTARIUS: a program to reduce the number of tags mapped to multiple transcripts and to plan SAGE sequencing stages. PMID:17884916
Evidence based selection of housekeeping genes. PMID:17878933
EDISA: extracting biclusters from multiple time-series of gene expression profiles. PMID:17850657
The embryonic muscle transcriptome of Caenorhabditis elegans. PMID:17848203
Structure and function of the Escherichia coli protein YmgB: a protein critical for biofilm formation and acid-resistance. PMID:17765265
PARE: a tool for comparing protein abundance and mRNA expression data. PMID:17718915
Genetic and molecular epidemiology. PMID:17699527
An "Electronic Fluorescent Pictograph" browser for exploring and analyzing large-scale biological data sets. PMID:17684564
Statistical analysis and significance testing of serial analysis of gene expression data using a Poisson mixture model. PMID:17683533
Selective regulation of bone cell apoptosis by translational isoforms of the glucocorticoid receptor. PMID:17682054
Meta-analysis of microarray results: challenges, opportunities, and recommendations for standardization. PMID:17651921
Arabidopsis Gene Family Profiler (aGFP)--user-oriented transcriptomic database with easy-to-use graphic interface. PMID:17645793
Identification of novel genes expressed during mouse tooth development by microarray gene expression analysis. PMID:17626284
Cell-specific microarray profiling experiments reveal a comprehensive picture of gene expression in the C. elegans nervous system. PMID:17612406
Strategy for encoding and comparison of gene expression signatures. PMID:17612401
Function of periplasmic hydrogenases in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. PMID:17601789
The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci. PMID:17567993
Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data. PMID:17559689
An efficient pseudomedian filter for tiling microrrays. PMID:17555595
PrestOMIC, an open source application for dissemination of proteomic datasets by individual laboratories. PMID:17553161
Molecular evidence for a link between the N363S glucocorticoid receptor polymorphism and altered gene expression. PMID:17535992
Functional gene expression differences between inbred alcohol-preferring and -non-preferring rats in five brain regions. PMID:17517326
Indole is an inter-species biofilm signal mediated by SdiA. PMID:17511876
Enterohemorrhagic Escherichia coli biofilms are inhibited by 7-hydroxyindole and stimulated by isatin. PMID:17483266
Decline of nucleotide excision repair capacity in aging Caenorhabditis elegans. PMID:17472752
Functional dissection of the ash2 and ash1 transcriptomes provides insights into the transcriptional basis of wing phenotypes and reveals conserved protein interactions. PMID:17466076
Molecular characterisation of the early response in pigs to experimental infection with Actinobacillus pleuropneumoniae using cDNA microarrays. PMID:17466061
Identification of candidate genes for alcohol preference by expression profiling of congenic rat strains. PMID:17451403
Identification of genes implicated in methapyrilene-induced hepatotoxicity by comparing differential gene expression in target and nontarget tissue. PMID:17450226
Up-regulation of tissue factor in human pulmonary artery endothelial cells after ultrafine particle exposure. PMID:17450221
The genopolis microarray database. PMID:17430566
DNA microarray data integration by ortholog gene analysis reveals potential molecular mechanisms of estrogen-dependent growth of human uterine fibroids. PMID:17407572
Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting. PMID:17400893
Graph-based identification of cancer signaling pathways from published gene expression signatures using PubLiME. PMID:17389643
Sharing detailed research data is associated with increased citation rate. PMID:17375194
Temperature-dependent expression of Listeria monocytogenes internalin and internalin-like genes suggests functional diversity of these proteins among the listeriae. PMID:17337561
From bytes to bedside: data integration and computational biology for translational cancer research. PMID:17319736
High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PMID:17299599
Genome-wide profiling and analysis of Arabidopsis siRNAs. PMID:17298187
YcfR (BhsA) influences Escherichia coli biofilm formation through stress response and surface hydrophobicity. PMID:17293424
A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. PMID:17270048
Global reconstruction of the human metabolic network based on genomic and bibliomic data. PMID:17267599
Human glucocorticoid receptor beta binds RU-486 and is transcriptionally active. PMID:17242213
DiscoverySpace: an interactive data analysis application. PMID:17210078
RINGdb: an integrated database for G protein-coupled receptors and regulators of G protein signaling. PMID:17173697
Model-driven user interfaces for bioinformatics data resources: regenerating the wheel as an alternative to reinventing it. PMID:17169146
Databases of free expression. PMID:17143588
Localization of a long-range cis-regulatory element of IL13 by allelic transcript ratio mapping. PMID:17135570
ArrayExpress--a public database of microarray experiments and gene expression profiles. PMID:17132828
Absolute enrichment: gene set enrichment analysis for homeostatic systems. PMID:17130162
NCBI GEO: mining tens of millions of expression profiles--database and tools update. PMID:17099226
Mining expressed sequence tags identifies cancer markers of clinical interest. PMID:17078886
Signatures from tissue-specific MPSS libraries identify transcripts preferentially expressed in the mouse inner ear. PMID:17049805
Novel mRNA targets for tristetraprolin (TTP) identified by global analysis of stabilized transcripts in TTP-deficient fibroblasts. PMID:17030620
A new locus for autosomal dominant amelogenesis imperfecta on chromosome 8q24.3. PMID:17024372
Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. PMID:17010196
The reactive oxygen species network pathways:an essential prerequisite for perception of pathogen attack and the acquired disease resistance in plants. PMID:17006022
Global comparative transcriptome analysis identifies gene network regulating secondary xylem development in Arabidopsis thaliana. PMID:16969662
Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. PMID:16939800
Mining microarray data at NCBI's Gene Expression Omnibus (GEO)*. PMID:16888359
An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes. PMID:16855282
An alpha-galactosidase with an essential function during leaf development. PMID:16845526
Identical probes on different high-density oligonucleotide microarrays can produce different measurements of gene expression. PMID:16776839
Expression profiling of the mouse early embryo: reflections and perspectives. PMID:16739220
Early days: genomics and human responses to infection. PMID:16679048
Assessment of the relationship between pre-chip and post-chip quality measures for Affymetrix GeneChip expression data. PMID:16623940
YliH (BssR) and YceP (BssS) regulate Escherichia coli K-12 biofilm formation by influencing cell signaling. PMID:16597943
Modulation of the transcription regulatory program in yeast cells committed to sporulation. PMID:16542486
NABP1, a novel RORgamma-regulated gene encoding a single-stranded nucleic-acid-binding protein. PMID:16533169
Meeting report: Validation of toxicogenomics-based test systems: ECVAM-ICCVAM/NICEATM considerations for regulatory use. PMID:16507466
Global analysis of X-chromosome dosage compensation. PMID:16507155
The PowerAtlas: a power and sample size atlas for microarray experimental design and research. PMID:16504070
Expression profiling identifies novel candidate genes for ethanol sensitivity QTLs. PMID:16465594
The Arabidopsis zinc finger-homeodomain genes encode proteins with unique biochemical properties that are coordinately expressed during floral development. PMID:16428600
A molecular signature of epithelial host defense: comparative gene expression analysis of cultured bronchial epithelial cells and keratinocytes. PMID:16420688
Recent applications of DNA microarray technology to toxicology and ecotoxicology. PMID:16393650
Biased alternative polyadenylation in human tissues. PMID:16356263
Mining published lists of cancer related microarray experiments: identification of a gene expression signature having a critical role in cell-cycle control. PMID:16351740
A quantization method based on threshold optimization for microarray short time series. PMID:16351737
Reverse-engineering gene-regulatory networks using evolutionary algorithms and grid computing. PMID:16328947
MiMiR: a comprehensive solution for storage, annotation and exchange of microarray data. PMID:16280078
MyoD induces myogenic differentiation through cooperation of its NH2- and COOH-terminal regions. PMID:16275751
Transformation of expression intensities across generations of Affymetrix microarrays using sequence matching and regression modeling. PMID:16224098
Unexpectedly high bacterial diversity in arctic tundra relative to boreal forest soils, revealed by serial analysis of ribosomal sequence tags. PMID:16204479
L2L: a simple tool for discovering the hidden significance in microarray expression data. PMID:16168088
XenDB: full length cDNA prediction and cross species mapping in Xenopus laevis. PMID:16162280
Storing, linking, and mining microarray databases using SRS. PMID:16048644
Reproducible clusters from microarray research: whither? PMID:16026595
Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray. PMID:15998450
Regulation of mouse hepatic genes in response to diet induced obesity, insulin resistance and fasting induced weight reduction. PMID:15985155
Evaluation of the similarity of gene expression data estimated with SAGE and Affymetrix GeneChips. PMID:15955238
Local coexpression domains of two to four genes in the genome of Arabidopsis. PMID:15923337
Loss-of-function mutations in chitin responsive genes show increased susceptibility to the powdery mildew pathogen Erysiphe cichoracearum. PMID:15923325
Novel response to microtubule perturbation in meiosis. PMID:15899877
The Arabidopsis AtRaptor genes are essential for post-embryonic plant growth. PMID:15845148
MARS: microarray analysis, retrieval, and storage system. PMID:15836795
Profile of changes in gene expression in cultured hippocampal neurones evoked by the GABAB receptor agonist baclofen. PMID:15784695
Quantitative inference of dynamic regulatory pathways via microarray data. PMID:15748298
Can Zipf's law be adapted to normalize microarrays? PMID:15727680
Evolutionary significance of gene expression divergence. PMID:15716085
Presenilin-1-dependent transcriptome changes. PMID:15703411
Microarray analysis confirms the specificity of a Chlamydomonas reinhardtii chloroplast RNA stability mutant. PMID:15665248
BarleyBase--an expression profiling database for plant genomics. PMID:15608273
The Stanford Microarray Database accommodates additional microarray platforms and data formats. PMID:15608265
NCBI GEO: mining millions of expression profiles--database and tools. PMID:15608262
ArrayExpress--a public repository for microarray gene expression data at the EBI. PMID:15608260
FlyBase: genes and gene models. PMID:15608223
CLOE: identification of putative functional relationships among genes by comparison of expression profiles between two species. PMID:15550177
Comparative profiling of lipid-soluble antioxidants and transcripts reveals two phases of photo-oxidative stress in a xanthophyll-deficient mutant of Chlamydomonas reinhardtii. PMID:15517390
Combining gene expression data from different generations of oligonucleotide arrays. PMID:15504239
In control: systematic assessment of microarray performance. PMID:15459748
PEDRo: a database for storing, searching and disseminating experimental proteomics data. PMID:15377392
GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. PMID:15375207
Handling multiple testing while interpreting microarrays with the Gene Ontology Database. PMID:15350198
Standards for microarray data: an open letter. PMID:15345376
Improving identification of differentially expressed genes in microarray studies using information from public databases. PMID:15345054
Performance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations. PMID:15345031
Submission of microarray data to public repositories. PMID:15340489
Selective and mutational patterns associated with gene expression in humans: influences on synonymous composition and intron presence. PMID:15280243
GOAL: automated Gene Ontology analysis of expression profiles. PMID:15215435
KARMA: a web server application for comparing and annotating heterogeneous microarray platforms. PMID:15215426
CARRIE web service: automated transcriptional regulatory network inference and interactive analysis. PMID:15215383
A survey of ovary-, testis-, and soma-biased gene expression in Drosophila melanogaster adults. PMID:15186491
Coexpression analysis of human genes across many microarray data sets. PMID:15173114
A bioinformatics analysis of memory consolidation reveals involvement of the transcription factor c-rel. PMID:15102909
Charting gene regulatory networks: strategies, challenges and perspectives. PMID:15080794
A gene atlas of the mouse and human protein-encoding transcriptomes. PMID:15075390
MiCoViTo: a tool for gene-centric comparison and visualization of yeast transcriptome states. PMID:15053844
Database development in toxicogenomics: issues and efforts. PMID:15033600
FlyGEM, a full transcriptome array platform for the Drosophila community. PMID:15003122
Anomalies in the expression profile of interspecific hybrids of Drosophila melanogaster and Drosophila simulans. PMID:14962989
Expression array annotation using the BioMediator biological data integration system and the BioConductor analytic platform. PMID:14728212
Scratching the (T cell) surface. PMID:14709166
The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface. PMID:14681485
NASCArrays: a repository for microarray data generated by NASC's transcriptomics service. PMID:14681484
CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature. PMID:14681477
The Mouse SAGE Site: database of public mouse SAGE libraries. PMID:14681462
yMGV: a cross-species expression data mining tool. PMID:14681424
Database resources of the National Center for Biotechnology Information: update. PMID:14681353
ArrayTrack--supporting toxicogenomic research at the U.S. Food and Drug Administration National Center for Toxicological Research. PMID:14630514
Evaluation of gene expression measurements from commercial microarray platforms. PMID:14500831
Rapid evolution of male-biased gene expression in Drosophila. PMID:12907700
SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. PMID:12519986
ArrayExpress--a public repository for microarray gene expression data at the EBI. PMID:12519949
Database resources of the National Center for Biotechnology. PMID:12519941
Paucity of genes on the Drosophila X chromosome showing male-biased expression. PMID:12511656
Gene expression profiling with DNA microarrays: advancing our understanding of psychiatric disorders. PMID:12462404
BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data. PMID:12186655
Database resources of the National Center for Biotechnology Information: 2002 update. PMID:11752242 -
NCBI GEO: archive for functional genomics data sets--update
PubMed citations: 3337.
3337 articles citing: NCBI GEO: archive for functional genomics data sets--update
Network-Based Pharmacology and Bioinformatics Study on the Mechanism of Action of Gujiansan in the Treatment of Steroid-Induced Avascular Necrosis of the Femoral Head. PMID:35915795
Effects of Sleep Disorders and Circadian Rhythm Changes on Male Reproductive Health: A Systematic Review and Meta-analysis. PMID:35910569
Role of ferroptosis-related genes in coronary atherosclerosis and identification of key genes: integration of bioinformatics analysis and experimental validation. PMID:35906548
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
Aberrant androgen action in prostatic progenitor cells induces oncogenesis and tumor development through IGF1 and Wnt axes. PMID:35902588
The Potential Anti-remodeling Effect of Paroxetine After Myocardial Infarction May Be Blunted by Beta-Blockers. PMID:35898267
Systematic Analysis of Long Non-Coding RNA Genes in Nonalcoholic Fatty Liver Disease. PMID:35893239
Stemness Correlates Inversely with MHC Class I Expression in Pediatric Small Round Blue Cell Tumors. PMID:35892842
Proteotranscriptomics - A facilitator in omics research. PMID:35891789
Biological interacting units identified in human protein networks reveal tissue-functional diversification and its impact on disease. PMID:35891788
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
Statistical Bioinformatics to Uncover the Underlying Biological Mechanisms That Linked Smoking with Type 2 Diabetes Patients Using Transcritpomic and GWAS Analysis. PMID:35889263
Meta-Analysis of RNA Sequencing Data of Arabidopsis and Rice under Hypoxia. PMID:35888167
Evaluating the Link between BAFF System Gene Expression and Acute Rejection Development in Kidney Transplantation. PMID:35887720
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
MicroRNA-138-5p Targets Pro-Apoptotic Factors and Favors Neural Cell Survival: Analysis in the Injured Spinal Cord. PMID:35884864
OMiCC: An expanded and enhanced platform for meta-analysis of public gene expression data. PMID:35880119
Arecoline Is Associated With Inhibition of Cuproptosis and Proliferation of Cancer-Associated Fibroblasts in Oral Squamous Cell Carcinoma: A Potential Mechanism for Tumor Metastasis. PMID:35875097
Longevity-Promoting Pathways and Transcription Factors Respond to and Control Extracellular Matrix Dynamics During Aging and Disease. PMID:35874275
Chromatin Separation Regulators Predict the Prognosis and Immune Microenvironment Estimation in Lung Adenocarcinoma. PMID:35873497
Identification of circRNA-miRNA-mRNA Regulatory Network and Crucial Signaling Pathway Axis Involved in Tetralogy of Fallot. PMID:35873466
A Cluster of Metabolic-Related Genes Serve as Potential Prognostic Biomarkers for Renal Cell Carcinoma. PMID:35873461
EpiVisR: exploratory data analysis and visualization in epigenome-wide association analyses. PMID:35870905
Genome-wide association study in minority children with asthma implicates DNAH5 in bronchodilator responsiveness. PMID:35869121
Identification of Immune-Associated Genes in Diagnosing Aortic Valve Calcification With Metabolic Syndrome by Integrated Bioinformatics Analysis and Machine Learning. PMID:35865542
Targeting Streptomyces-Derived Streptenol Derivatives against Gynecological Cancer Target PIK3CA: An In Silico Approach. PMID:35860806
Advances and Trends in Omics Technology Development. PMID:35860739
Circulating miRNAs as Epigenetic Mediators of Periodontitis and Preeclampsia Association. PMID:35860693
Identification of osteoporosis based on gene biomarkers using support vector machine. PMID:35859791
gene2gauss: A multi-view gaussian gene embedding learner for analyzing transcriptomic networks. PMID:35854722
Un-biased housekeeping gene panel selection for high-validity gene expression analysis. PMID:35853974
JAK2-CHK2 signaling safeguards the integrity of the mitotic spindle assembly checkpoint and genome stability. PMID:35851582
Exploration of dilated cardiomyopathy for biomarkers and immune microenvironment: evidence from RNA-seq. PMID:35850644
A Single-Center Follow-Up Study of Low-Grade Gastric Intraepithelial Neoplasia and the Screening of Key Genes of Precancerous Lesions. PMID:35847930
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
An Immunity-Related Gene Model Predicts Prognosis in Cholangiocarcinoma. PMID:35847907
Integrative Proteo-Genomic Analysis for Recurrent Survival Prognosis in Colon Adenocarcinoma. PMID:35847888
RAC3 Inhibition Induces Autophagy to Impair Metastasis in Bladder Cancer Cells via the PI3K/AKT/mTOR Pathway. PMID:35847878
Assessing author willingness to enter study information into structured data templates as part of the manuscript submission process: A pilot study. PMID:35846467
Differential Expression Profiles of mRNA and Noncoding RNA and Analysis of Competitive Endogenous RNA Regulatory Networks in Nonalcoholic Steatohepatitis. PMID:35844837
Integrated Analysis of Gene Co-Expression Network and Prediction Model Indicates Immune-Related Roles of the Identified Biomarkers in Sepsis and Sepsis-Induced Acute Respiratory Distress Syndrome. PMID:35844622
Single-Cell RNA Sequencing Unravels Upregulation of Immune Cell Crosstalk in Relapsed Pediatric Ependymoma. PMID:35844565
Key Signature Genes of Early Terminal Granulocytic Differentiation Distinguish Sepsis From Systemic Inflammatory Response Syndrome on Intensive Care Unit Admission. PMID:35844509
Integrated computational approaches to screen gene expression data to determine key genes and therapeutic targets for type-2 diabetes mellitus. PMID:35844380
Pan-sarcoma characterization of lncRNAs in the crosstalk of EMT and tumour immunity identifies distinct clinical outcomes and potential implications for immunotherapy. PMID:35842562
Identification and validation of necroptosis-related prognostic gene signature and tumor immune microenvironment infiltration characterization in esophageal carcinoma. PMID:35840882
Uncovering a Genetic Polymorphism Located in Huntingtin Associated Protein 1 in Modulation of Central Pain Sensitization Signaling Pathways. PMID:35837121
Exploration of Shared Gene Signatures and Molecular Mechanisms Between Periodontitis and Nonalcoholic Fatty Liver Disease. PMID:35836570
Identification of Key Genes and Potential Pathways Associated with Mastitis Induced by E. coli. PMID:35834114
Identifying Potential Effective Diagnostic and Prognostic Biomarkers in Sepsis by Bioinformatics Analysis and Validation. PMID:35832399
The Big Picture of Neurodegeneration: A Meta Study to Extract the Essential Evidence on Neurodegenerative Diseases in a Network-Based Approach. PMID:35832065
Domination based classification algorithms for the controllability analysis of biological interaction networks. PMID:35831440
Histone demethylase JMJD3 downregulation protects against aberrant force-induced osteoarthritis through epigenetic control of NR4A1. PMID:35831280
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
Qin Huang formula enhances the effect of Adriamycin in B-cell lymphoma via increasing tumor infiltrating lymphocytes by targeting toll-like receptor signaling pathway. PMID:35818037
Network Pharmacology and Bioinformatics Methods Reveal the Mechanism of Berberine in the Treatment of Ischaemic Stroke. PMID:35815278
REPS1 as a Potential Biomarker in Alzheimer's Disease and Vascular Dementia. PMID:35813961
Identification of Hub Genes and Immune-Related Pathways for Membranous Nephropathy by Bioinformatics Analysis. PMID:35812314
Identification and Validation of Candidate Gene Module Along With Immune Cells Infiltration Patterns in Atherosclerosis Progression to Plaque Rupture via Transcriptome Analysis. PMID:35811739
Gene Co-Expression Network Tools and Databases for Crop Improvement. PMID:35807577
miR-218-5p/RUNX2 Axis Positively Regulates Proliferation and Is Associated with Poor Prognosis in Cervical Cancer. PMID:35805994
Novel Drug Candidate Prediction for Intrahepatic Cholangiocarcinoma via Hub Gene Network Analysis and Connectivity Mapping. PMID:35805055
A novel signature derived from metabolism-related genes GPT and SMS to predict prognosis of laryngeal squamous cell carcinoma. PMID:35804447
Identification of Potential miRNA-mRNA Regulatory Network in Denervated Muscular Atrophy by Bioinformatic Analysis. PMID:35800215
Integrated Single-Cell RNA-Sequencing Analysis of Gastric Cancer Identifies FABP1 as a Novel Prognostic Biomarker. PMID:35799608
DNA methylation fingerprint of hepatocellular carcinoma from tissue and liquid biopsies. PMID:35798798
Vitexin Mitigates Staphylococcus aureus-Induced Mastitis via Regulation of ROS/ER Stress/NF-κB/MAPK Pathway. PMID:35795861
Integration of Genetic and Immune Infiltration Insights into Data Mining of Multiple Sclerosis Pathogenesis. PMID:35795733
Recent Advances in Cancer Drug Discovery Through the Use of Phenotypic Reporter Systems, Connectivity Mapping, and Pooled CRISPR Screening. PMID:35795568
Downregulation of LRRC19 Is Associated with Poor Prognosis in Colorectal Cancer. PMID:35794979
Identification of genes and key pathways underlying the pathophysiological association between nonalcoholic fatty liver disease and atrial fibrillation. PMID:35790963
Highly perturbed genes and hub genes associated with type 2 diabetes in different tissues of adult humans: a bioinformatics analytic workflow. PMID:35788821
Altered mitochondrial microenvironment at the spotlight of musculoskeletal aging and Alzheimer's disease. PMID:35788655
GoPeaks: histone modification peak calling for CUT&Tag. PMID:35788238
The Potential Role of CDH1 as an Oncogene Combined With Related miRNAs and Their Diagnostic Value in Breast Cancer. PMID:35784532
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
Identification of miRNA-mRNA Pairs in the Alzheimer's Disease Expression Profile and Explore the Effect of miR-26a-5p/PTGS2 on Amyloid-β Induced Neurotoxicity in Alzheimer's Disease Cell Model. PMID:35783137
Characterization of the Immune Infiltration Landscape and Identification of Prognostic Biomarkers for Esophageal Cancer. PMID:35780460
CDK6 is upregulated and may be a potential therapeutic target in enzalutamide-resistant castration-resistant prostate cancer. PMID:35780240
Exploring Ganweikang Tablet as a Candidate Drug for NAFLD Through Network Pharmacology Analysis and Experimental Validation. PMID:35774609
RhythmicDB: A Database of Predicted Multi-Frequency Rhythmic Transcripts. PMID:35774515
Identification of Hub Genes for Early Diagnosis and Predicting Prognosis in Colon Adenocarcinoma. PMID:35774271
Differentiation of T Helper 17 Cells May Mediate the Abnormal Humoral Immunity in IgA Nephropathy and Inflammatory Bowel Disease Based on Shared Genetic Effects. PMID:35769467
Identification of hub genes predicting the development of prostate cancer from benign prostate hyperplasia and analyzing their clinical value in prostate cancer by bioinformatic analysis. PMID:35768705
Liver glycogen phosphorylase is upregulated in glioblastoma and provides a metabolic vulnerability to high dose radiation. PMID:35764612
A transcriptome atlas and interactive analysis platform for autoimmune disease. PMID:35758882
Clinical Values of the Identified Hub Genes in Systemic Lupus Erythematosus. PMID:35757684
TMED2/9/10 Serve as Biomarkers for Poor Prognosis in Head and Neck Squamous Carcinoma. PMID:35754792
Exploring the possible molecular targeting mechanism of Saussurea involucrata in the treatment of COVID-19 based on bioinformatics and network pharmacology. PMID:35751193
Model scenarios for cell cycle re-entry in Alzheimer's disease. PMID:35747391
Long Non-Coding RNA MIR31HG Promotes the Transforming Growth Factor β-Induced Epithelial-Mesenchymal Transition in Pancreatic Ductal Adenocarcinoma Cells. PMID:35743003
Predicting High Blood Pressure Using DNA Methylome-Based Machine Learning Models. PMID:35740428
Mechanisms Underlying Antipsychotic-Induced NAFLD and Iron Dysregulation: A Multi-Omic Approach. PMID:35740245
Lipid metabolism-related lncRNA SLC25A21-AS1 promotes the progression of oesophageal squamous cell carcinoma by regulating the NPM1/c-Myc axis and SLC25A21 expression. PMID:35735113
MLBioIGE: integration and interplay of machine learning and bioinformatics approach to identify the genetic effect of SARS-COV-2 on idiopathic pulmonary fibrosis patients. PMID:35734766
Peptidylarginine Deiminase 2 Autoantibodies Are Linked to Less Severe Disease in Multiple Sclerosis and Post-treatment Lyme Disease. PMID:35734473
Prognostic Value of Cancer-Associated Fibroblast-Related Gene Signatures in Hepatocellular Carcinoma. PMID:35733776
Circular RNA hsa_circ_0000437 may be used as a new indicator for the diagnosis and prognosis of hepatocellular carcinoma. PMID:35730467
Transcriptomic and proteomic profiling of peptidase expression in Fasciola hepatica eggs developing at host's body temperature. PMID:35725898
Network pharmacological analysis of active components of Tongqiao Huoxue Decoction in the treatment of intracerebral hemorrhage. PMID:35722393
A Robust Immuno-Prognostic Model of Non-Muscle-Invasive Bladder Cancer Indicates Dynamic Interaction in Tumor Immune Microenvironment Contributes to Cancer Progression. PMID:35719408
In silico drug repurposing against SARS-CoV-2 using an integrative transcriptomic profiling approach: Hydrocortisone and Benzhydrocodone as potential drug candidates against COVID-19. PMID:35718334
scCAN: single-cell clustering using autoencoder and network fusion. PMID:35715568
Identification of Prognosis-Related Molecular Subgroups and Construction of a Prognostic Prediction Model Using Immune-Related Genes in Pancreatic Cancer. PMID:35712127
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
The Underlying Molecular Basis and Mechanisms of Venous Thrombosis in Patients with Osteomyelitis: A Data-Driven Analysis. PMID:35711689
Integrated analysis reveals the pivotal interactions between immune cells in the melanoma tumor microenvironment. PMID:35710862
Just Add Data: automated predictive modeling for knowledge discovery and feature selection. PMID:35710826
T-cell trans-synaptic vesicles are distinct and carry greater effector content than constitutive extracellular vesicles. PMID:35710644
Trophinin-associated protein expression correlates with shorter survival of patients with glioma: a study based on multiple data fusion analysis. PMID:35708862
Premature Infants Have Normal Maturation of the T Cell Receptor Repertoire at Term. PMID:35707545
Revealing Potential Spinal Cord Injury Biomarkers and Immune Cell Infiltration Characteristics in Mice. PMID:35706450
Network approaches for modeling the effect of drugs and diseases. PMID:35704883
Gene expression profiling and protein-protein interaction analysis reveals the dynamic role of MCM7 in Alzheimer's disorder and breast cancer. PMID:35698583
Systematic lncRNA mapping to genome-wide co-essential modules uncovers cancer dependency on uncharacterized lncRNAs. PMID:35695878
Decoding the Mechanism behind the Pathogenesis of the Focal Segmental Glomerulosclerosis. PMID:35693262
Identification of Biomarkers for Predicting Ovarian Reserve of Primordial Follicle via Transcriptomic Analysis. PMID:35692832
TACSTD2 upregulation is an early reaction to lung infection. PMID:35688908
Role of Nucleolin in Endometrial Precancerous Hyperplasia and Carcinogenesis: Ex Vivo and In Silico Study. PMID:35682908
A Genomic Information Management System for Maintaining Healthy Genomic States and Application of Genomic Big Data in Clinical Research. PMID:35682641
LncRNA ZNF582-AS1 Expression and Methylation in Breast Cancer and Its Biological and Clinical Implications. PMID:35681777
Expression of Trace Amine-Associated Receptors in the Murine and Human Hippocampus Based on Public Transcriptomic Data. PMID:35681508
Identification of biomarkers for immunotherapy response in prostate cancer and potential drugs to alleviate immunosuppression. PMID:35680563
Discovering gene regulatory networks of multiple phenotypic groups using dynamic Bayesian networks. PMID:35679575
Circ_0006174 promotes the malignancy of colorectal cancer cell via the miR‑1205/CCBE1/Wnt pathway. PMID:35674190
Comprehensive analysis of the expression and prognosis of YPEL family members in clear cell renal cell cancer. PMID:35674183
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
Effects of Inhibitors of SLC9A-Type Sodium-Proton Exchangers on Survival Motor Neuron 2 (SMN2) mRNA Splicing and Expression. PMID:35667685
miR-548d-3p inhibits the invasion and migration of gastric cancer cells by targeting GKN1. PMID:35666636
Solute carrier family 2 members 1 and 2 as prognostic biomarkers in hepatocellular carcinoma associated with immune infiltration. PMID:35665115
The DNA glycosylase NEIL2 plays a vital role in combating SARS-CoV-2 infection. PMID:35665009
Identification of hub genes and molecular pathways in human T-lymphotropic virus type 1 associated diseases using protein-protein interactions networks. PMID:35664724
INSC Is Down-Regulated in Colon Cancer and Correlated to Immune Infiltration. PMID:35664320
NFE2L3 as a Novel Biomarker Associated With IL-2/STAT5/NLRP3 Signaling Pathway in Malignant Pleural Mesothelioma and Other Cancers. PMID:35664314
Transcriptional profiling of transport mechanisms and regulatory pathways in rat choroid plexus. PMID:35659263
UBE2S promotes the development of ovarian cancer by promoting PI3K/AKT/mTOR signaling pathway to regulate cell cycle and apoptosis. PMID:35658829
GeMI: interactive interface for transformer-based Genomic Metadata Integration. PMID:35657113
m6A Regulator-Mediated Methylation Modification Patterns and Characteristics in COVID-19 Patients. PMID:35655464
A stromal Integrated Stress Response activates perivascular cancer-associated fibroblasts to drive angiogenesis and tumour progression. PMID:35654839
Evaluation of Biomarkers and Immune Microenvironment of Osteoarthritis: Evidence From Omics Data and Machine Learning. PMID:35651940
COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning. PMID:35649389
In Silico Integration of Transcriptome and Interactome Predicts an ETP-ALL-Specific Transcriptional Footprint that Decodes its Developmental Propensity. PMID:35646901
The LINC01929/miR-6875-5p/ADAMTS12 Axis in the ceRNA Network Regulates the Development of Advanced Bladder Cancer. PMID:35646642
Transcriptomic datasets of cancer patients treated with immune-checkpoint inhibitors: a systematic review. PMID:35641998
ExpressVis: a biologist-oriented interactive web server for exploring multi-omics data. PMID:35639516
Identification of Ferroptosis-Related Hub Genes and Their Association with Immune Infiltration in Chronic Obstructive Pulmonary Disease by Bioinformatics Analysis. PMID:35637927
Single-cell transcriptomics of adult macaque hippocampus reveals neural precursor cell populations. PMID:35637371
Disclosing Potential Key Genes, Therapeutic Targets and Agents for Non-Small Cell Lung Cancer: Evidence from Integrative Bioinformatics Analysis. PMID:35632527
Consensus Gene Co-Expression Network Analysis Identifies Novel Genes Associated with Severity of Fibrotic Lung Disease. PMID:35628257
Correlation of NTRK1 Downregulation with Low Levels of Tumor-Infiltrating Immune Cells and Poor Prognosis of Prostate Cancer Revealed by Gene Network Analysis. PMID:35627227
Gene Expression Meta-Analysis of Potential Shared and Unique Pathways between Autoimmune Diseases under Anti-TNFα Therapy. PMID:35627163
Validation of Novel Molecular Imaging Targets Identified by Functional Genomic mRNA Profiling to Detect Dysplasia in Barrett's Esophagus. PMID:35626066
Trifluoperazine and Its Analog Suppressed the Tumorigenicity of Non-Small Cell Lung Cancer Cell; Applicability of Antipsychotic Drugs to Lung Cancer Treatment. PMID:35625784
Asthma and Post-Asthmatic Fibrosis: A Search for New Promising Molecular Markers of Transition from Acute Inflammation to Pulmonary Fibrosis. PMID:35625754
Signaling Pathways Involved in Myocardial Ischemia-Reperfusion Injury and Cardioprotection: A Systematic Review of Transcriptomic Studies in Sus scrofa. PMID:35621843
CGRP and the Calcitonin Receptor are Co-Expressed in Mouse, Rat and Human Trigeminal Ganglia Neurons. PMID:35620595
CDC25C is a prognostic biomarker and correlated with mitochondrial homeostasis in pancreatic adenocarcinoma. PMID:35615982
Gene co-expression network based on part mutual information for gene-to-gene relationship and gene-cancer correlation analysis. PMID:35610556
TP53-inducible putative long noncoding RNAs encode functional polypeptides that suppress cell proliferation. PMID:35609991
GEOexplorer: a webserver for gene expression analysis and visualisation. PMID:35609980
Identification of hub biomarkers and immune cell infiltration in polymyositis and dermatomyositis. PMID:35609018
Construction of three-gene-based prognostic signature and analysis of immune cells infiltration in children and young adults with B-acute lymphoblastic leukemia. PMID:35603962
Exercise Modifies the Transcriptional Regulatory Features of Monocytes in Alzheimer's Patients: A Multi-Omics Integration Analysis Based on Single Cell Technology. PMID:35592698
Identification of Alzheimer's Disease Molecular Subtypes Based on Parallel Large-Scale Sequencing. PMID:35592696
Exploration of the System-Level Mechanisms of the Herbal Drug FDY003 for Pancreatic Cancer Treatment: A Network Pharmacological Investigation. PMID:35591866
Inhibition of mitochondrial complex I reverses NOTCH1-driven metabolic reprogramming in T-cell acute lymphoblastic leukemia. PMID:35589701
An Artificial Intelligence-guided signature reveals the shared host immune response in MIS-C and Kawasaki disease. PMID:35577777
System-Wide Analysis of the GATC-Binding Nucleoid-Associated Protein Gbn and Its Impact on Streptomyces Development. PMID:35575488
Multiscale Time-resolved Analysis Reveals Remaining Behavioral Rhythms in Mice Without Canonical Circadian Clocks. PMID:35575430
Integrated Analysis of Transcriptome Data Revealed AURKA and KIF20A as Critical Genes in Medulloblastoma Progression. PMID:35574421
A Prognostic Gene Signature for Hepatocellular Carcinoma. PMID:35574316
Integrated gene expression profiling analysis reveals SERPINA3, FCN3, FREM1, MNS1 as candidate biomarkers in heart failure and their correlation with immune infiltration. PMID:35572891
Pyroptosis-Related Gene Signature and Expression Patterns in the Deterioration of Atherosclerosis. PMID:35571620
Identification of Important Modules and Hub Gene in Chronic Kidney Disease Based on WGCNA. PMID:35571562
Heterogeneous microenvironment analysis to explore the potential regulatory role of endothelial-mesenchymal transition in idiopathic pulmonary fibrosis. PMID:35571445
Genome-Scale Metabolic Model Analysis of Metabolic Differences between Lauren Diffuse and Intestinal Subtypes in Gastric Cancer. PMID:35565469
Multiomic Profiling Identified EGF Receptor Signaling as a Potential Inhibitor of Type I Interferon Response in Models of Oncolytic Therapy by Vesicular Stomatitis Virus. PMID:35563635
Artificial Intelligence Predictor for Alzheimer's Disease Trained on Blood Transcriptome: The Role of Oxidative Stress. PMID:35563628
Cloning and Functional Characterization of Dog OCT1 and OCT2: Another Step in Exploring Species Differences in Organic Cation Transporters. PMID:35563491
Plasma Aldo-Keto Reductase Family 1 Member B10 as a Biomarker Performs Well in the Diagnosis of Nonalcoholic Steatohepatitis and Fibrosis. PMID:35563425
Upregulation of the Long Non-coding RNA LINC01480 Is Associated With Immune Infiltration in Coronary Artery Disease Based on an Immune-Related lncRNA-mRNA Co-expression Network. PMID:35557532
COVID-19 mortality is associated with pre-existing impaired innate immunity in health conditions. PMID:35547187
Identification of miRNA-mRNA-TF regulatory networks in peripheral blood mononuclear cells of type 1 diabetes. PMID:35534828
LAMP2 as a Biomarker Related to Prognosis and Immune Infiltration in Esophageal Cancer and Other Cancers: A Comprehensive Pan-Cancer Analysis. PMID:35530327
SigCom LINCS: data and metadata search engine for a million gene expression signatures. PMID:35524556
Predicting Novel Drug Candidates for Pancreatic Neuroendocrine Tumors via Gene Signature Comparison and Connectivity Mapping. PMID:35508682
MrgprF acts as a tumor suppressor in cutaneous melanoma by restraining PI3K/Akt signaling. PMID:35504869
MTG16 regulates colonic epithelial differentiation, colitis, and tumorigenesis by repressing E protein transcription factors. PMID:35503250
Bringing machine learning to research on intellectual and developmental disabilities: taking inspiration from neurological diseases. PMID:35501679
The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data. PMID:35501320
Prognostic comparative genes predict targets for sorafenib combination therapies in hepatocellular carcinoma. PMID:35495118
Development and Validation of TACE Refractoriness-Related Diagnostic and Prognostic Scores and Characterization of Tumor Microenvironment Infiltration in Hepatocellular Carcinoma. PMID:35493518
Computational methods directed towards drug repurposing for COVID-19: advantages and limitations. PMID:35492747
Temporal and sex-dependent gene expression patterns in a renal ischemia-reperfusion injury and recovery pig model. PMID:35484379
Identification and validation of prognosis-associated DNA repair gene signatures in colorectal cancer. PMID:35484177
Computational and experimental methods for classifying variants of unknown clinical significance. PMID:35483875
Silencing ATF3 Might Delay TBHP-Induced Intervertebral Disc Degeneration by Repressing NPC Ferroptosis, Apoptosis, and ECM Degradation. PMID:35480873
CD19 and POU2AF1 are Potential Immune-Related Biomarkers Involved in the Emphysema of COPD: On Multiple Microarray Analysis. PMID:35479834
AFF3 is a novel prognostic biomarker and a potential target for immunotherapy in gastric cancer. PMID:35478418
Screening of Medications for Idiopathic Membranous Nephropathy Using Glomerular Whole-Genome Sequencing. PMID:35465008
Bioinformatics and System Biology Approach to Identify the Influences of COVID-19 on Rheumatoid Arthritis. PMID:35464423
Identification of the potential biological target molecules related to primary open-angle glaucoma. PMID:35461232
Adipose tissue-specific ablation of Ces1d causes metabolic dysregulation in mice. PMID:35459739
Recognition of a Novel Gene Signature for Human Glioblastoma. PMID:35456975
ASTool: An Easy-to-Use Tool to Accurately Identify Alternative Splicing Events from Plant RNA-Seq Data. PMID:35456896
Identification of Potential Key Genes in Prostate Cancer with Gene Expression, Pivotal Pathways and Regulatory Networks Analysis Using Integrated Bioinformatics Methods. PMID:35456461
Transcriptional Profiling and Deriving a Seven-Gene Signature That Discriminates Active and Latent Tuberculosis: An Integrative Bioinformatics Approach. PMID:35456421
Sphingolipid Metabolism as a New Predictive Target Correlated with Aging and AD: A Transcriptomic Analysis. PMID:35454332
Tubulin Alpha 1b Is Associated with the Immune Cell Infiltration and the Response of HCC Patients to Immunotherapy. PMID:35453905
Mitochondrial Genetics Reinforces Multiple Layers of Interaction in Alzheimer's Disease. PMID:35453630
Alternative Splicing of Neuropeptide Prohormone and Receptor Genes Associated with Pain Sensitivity Was Detected with Zero-Inflated Models. PMID:35453627
An Analysis Regarding the Association Between Connexins and Colorectal Cancer (CRC) Tumor Microenvironment. PMID:35449599
ER Stress in COVID-19 and Parkinson's Disease: In Vitro and In Silico Evidences. PMID:35448038
UBE2D1 and COX7C as Potential Biomarkers of Diabetes-Related Sepsis. PMID:35445133
Glycoprotein nonmetastatic melanoma protein B regulates lysosomal integrity and lifespan of senescent cells. PMID:35444208
Comprehensive network medicine-based drug repositioning via integration of therapeutic efficacy and side effects. PMID:35443763
3JC48-3 (methyl 4'-methyl-5-(7-nitrobenzo[c][1,2,5]oxadiazol-4-yl)-[1,1'-biphenyl]-3-carboxylate): a novel MYC/MAX dimerization inhibitor reduces prostate cancer growth. PMID:35440696
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
Loss of E-cadherin leads to Id2-dependent inhibition of cell cycle progression in metastatic lobular breast cancer. PMID:35437308
PELO facilitates PLK1-induced the ubiquitination and degradation of Smad4 and promotes the progression of prostate cancer. PMID:35437307
Integrated Bioinformatics Algorithms and Experimental Validation to Explore Robust Biomarkers and Landscape of Immune Cell Infiltration in Dilated Cardiomyopathy. PMID:35433865
Molecular Signatures of Mitochondrial Complexes Involved in Alzheimer's Disease via Oxidative Phosphorylation and Retrograde Endocannabinoid Signaling Pathways. PMID:35432724
Integrative Analysis of Biomarkers and Mechanisms in Adamantinomatous Craniopharyngioma. PMID:35432485
The human ion channel TRPM2 modulates cell survival in neuroblastoma through E2F1 and FOXM1. PMID:35428820
Systematic Characterization of the Clinical Relevance of KPNA4 in Pancreatic Ductal Adenocarcinoma. PMID:35425701
Integrative Analysis for Identification of Therapeutic Targets and Prognostic Signatures in Non-Small Cell Lung Cancer. PMID:35422618
A systematic review and functional bioinformatics analysis of genes associated with Crohn's disease identify more than 120 related genes. PMID:35418025
Human pluripotent stem cell-derived kidney organoids for personalized congenital and idiopathic nephrotic syndrome modeling. PMID:35417019
PTH2R is related to cell proliferation and migration in ovarian cancer: a multi-omics analysis of bioinformatics and experiments. PMID:35410353
Neural network modeling of differential binding between wild-type and mutant CTCF reveals putative binding preferences for zinc fingers 1-2. PMID:35410161
Are transient protein-protein interactions more dispensable? PMID:35404956
Association Between Asthma and Reduced Androgen Receptor Expression in Airways. PMID:35402761
Construction of MicroRNA-mRNA Regulatory Network in the Molecular Mechanisms of Bleomycin-Induced Pulmonary Fibrosis. PMID:35402615
Comprehensive Analysis of YTHDF1 Immune Infiltrates and ceRNA in Human Esophageal Carcinoma. PMID:35401696
Defining Molecular Treatment Targets for Bladder Pain Syndrome/Interstitial Cystitis: Uncovering Adhesion Molecules. PMID:35401223
CircSEC24A (hsa_circ_0003528) interference suppresses epithelial-mesenchymal transition of hepatocellular carcinoma cells via miR-421/MMP3 axis. PMID:35400271
The downregulation of fibrinogen-like protein 1 inhibits the proliferation of lung adenocarcinoma via regulating MYC-target genes. PMID:35399566
SLC2A1 is a Diagnostic Biomarker Involved in Immune Infiltration of Colorectal Cancer and Associated With m6A Modification and ceRNA. PMID:35399515
RGMQL: scalable and interoperable computing of heterogeneous omics big data and metadata in R/Bioconductor. PMID:35392801
Using a Machine Learning Approach to Identify Key Biomarkers for Renal Clear Cell Carcinoma. PMID:35392028
Identification of Novel Biomarkers With Diagnostic Value and Immune Infiltration in Burn Injury. PMID:35391790
Identification of host transcriptome-guided repurposable drugs for SARS-CoV-1 infections and their validation with SARS-CoV-2 infections by using the integrated bioinformatics approaches. PMID:35390032
Predicted mouse interactome and network-based interpretation of differentially expressed genes. PMID:35390003
Kinetochore-associated protein 1 promotes the invasion and tumorigenicity of cervical cancer cells via matrix metalloproteinase-2 and matrix metalloproteinase-9. PMID:35389773
Elevated BTG2 improves the radiosensitivity of non-small cell lung cancer (NSCLC) through apoptosis. PMID:35388633
Identification of Key Drug Targets and Molecular Mechanisms of Curcumae Rhizoma Acting on HBV-Related HCC: Weighted Correlation Network and Network Pharmacological Analyses. PMID:35388301
Identification of lncRNA/circRNA-miRNA-mRNA ceRNA Network as Biomarkers for Hepatocellular Carcinoma. PMID:35386284
Identification of lncRNAs and Their Regulatory Relationships with mRNAs in Response to Cryptococcus neoformans Infection of THP-1 Cells. PMID:35378790
Characterization of the Secretome, Transcriptome, and Proteome of Human β Cell Line EndoC-βH1. PMID:35378291
Exploration of the Potential Mechanism of Qi Yin San Liang San Decoction in the Treatment of EGFRI-Related Adverse Skin Reactions Using Network Pharmacology and In Vitro Experiments. PMID:35372072
Osteoarticular Involvement-Associated Biomarkers and Pathways in Psoriasis: The Shared Pathway With Ankylosing Spondylitis. PMID:35371093
Integrated Bioinformatics and Validation Reveal IL1B and Its Related Molecules as Potential Biomarkers in Chronic Spontaneous Urticaria. PMID:35371000
Insight Into the Long Noncoding RNA and mRNA Coexpression Profile in the Human Blood Transcriptome Upon Leishmania infantum Infection. PMID:35370994
Identification of Potential Diagnostic and Prognostic Biomarkers for Gastric Cancer Based on Bioinformatic Analysis. PMID:35368700
Identification of GGT5 as a Novel Prognostic Biomarker for Gastric Cancer and its Correlation With Immune Cell Infiltration. PMID:35368661
A Novel Deep Learning Method to Predict Lung Cancer Long-Term Survival With Biological Knowledge Incorporated Gene Expression Images and Clinical Data. PMID:35368657
Identification of novel genes in Behcet's disease using integrated bioinformatic analysis. PMID:35364782
ImmuMethy, a database of DNA methylation plasticity at a single cytosine resolution in human blood and immune cells. PMID:35363305
ALGAEFUN with MARACAS, microALGAE FUNctional enrichment tool for MicroAlgae RnA-seq and Chip-seq AnalysiS. PMID:35361110
A Pilot Study of Blood-Based Methylation Markers Associated With Pancreatic Cancer. PMID:35360846
Eight Differential miRNAs in DN Identified by Microarray Analysis as Novel Biomarkers. PMID:35359345
Construction and Validation of Two Hepatocellular Carcinoma-Progression Prognostic Scores Based on Gene Set Variation Analysis. PMID:35356272
The Shared Mechanism and Candidate Drugs of Multiple Sclerosis and Sjögren's Syndrome Analyzed by Bioinformatics Based on GWAS and Transcriptome Data. PMID:35356004
An integrated analysis of prognostic and immune infiltrates for hub genes as potential survival indicators in patients with lung adenocarcinoma. PMID:35354488
Comprehensive Genetic Analysis of Tuberculosis and Identification of Candidate Biomarkers. PMID:35345666
PharmOmics: A species- and tissue-specific drug signature database and gene-network-based drug repositioning tool. PMID:35345455
Relationship between circadian genes and memory impairment caused by sleep deprivation. PMID:35341046
Machine Learning-Based Identification of Colon Cancer Candidate Diagnostics Genes. PMID:35336739
Identification of hub genes for adult patients with sepsis via RNA sequencing. PMID:35332254
Overexpressing PLOD Family Genes Predict Poor Prognosis in Pancreatic Cancer. PMID:35330878
Collagen Family and Other Matrix Remodeling Proteins Identified by Bioinformatics Analysis as Hub Genes Involved in Gastric Cancer Progression and Prognosis. PMID:35328635
Bioinformatics Analysis and Identification of Potential Genes Associated with Pathogenesis and Prognosis of Gastric Cancer. PMID:35325407
Allelic imbalance of HLA-B expression in human lung cells infected with coronavirus and other respiratory viruses. PMID:35322240
Identification of potentially functional circular RNAs hsa_circ_0070934 and hsa_circ_0004315 as prognostic factors of hepatocellular carcinoma by integrated bioinformatics analysis. PMID:35322101
Identifying large-scale interaction atlases using probabilistic graphs and external knowledge. PMID:35321220
Oral Neutrophil Free Fatty Acid Receptors Expression May Link Oral Host and Microbiome Lipid Metabolism. PMID:35320973
Using bioinformatics and systems biology to discover common pathogenetic processes between sarcoidosis and COVID-19. PMID:35317263
Comprehensive bioinformatic analysis reveals oncogenic role of H2A.Z isoforms in cervical cancer progression. PMID:35317119
StemSC: a cross-dataset human stemness index for single-cell samples. PMID:35313979
Therapy-resistant and -sensitive lncRNAs, SNHG1 and UBL7-AS1 promote glioblastoma cell proliferation. PMID:35313638
Overexpression of CISD1 Predicts Worse Survival in Hepatocarcinoma Patients. PMID:35313629
Target-Dependent Coordinated Biogenesis of Secondary MicroRNAs by miR-146a Balances Macrophage Activation Processes. PMID:35311564
Promoter Hypomethylation of TGFBR3 as a Risk Factor of Alzheimer's Disease: An Integrated Epigenomic-Transcriptomic Analysis. PMID:35310542
Analysis of potential genetic biomarkers using machine learning methods and immune infiltration regulatory mechanisms underlying atrial fibrillation. PMID:35305619
Genome-wide DNA methylation profiling in differentiating Crohn's disease from intestinal tuberculosis. PMID:35305241
Cardiac protection by pirfenidone after myocardial infarction: a bioinformatic analysis. PMID:35304529
Assessment of the targeted effect of Sijunzi decoction on the colorectal cancer microenvironment via the ESTIMATE algorithm. PMID:35303006
ARAF suppresses ERBB3 expression and metastasis in a subset of lung cancers. PMID:35302851
Screening and Analysis of Potential Critical Gene in Acute Myocardial Infarction Based on a miRNA-mRNA Regulatory Network. PMID:35300139
Discovering Novel Biomarkers Associated with the Pathogenesis of Psoriasis: Evidence from Bioinformatic Analysis. PMID:35300136
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
Bioinformatics and Machine Learning Methods to Identify FN1 as a Novel Biomarker of Aortic Valve Calcification. PMID:35295271
Methylation pattern of polymorphically imprinted nc886 is not conserved across mammalia. PMID:35294436
Artificial intelligence-rationalized balanced PPARα/γ dual agonism resets dysregulated macrophage processes in inflammatory bowel disease. PMID:35288651
Untargeted metabolomics analysis of esophageal squamous cell cancer progression. PMID:35287685
Identification of ITGAX and CCR1 as potential biomarkers of atherosclerosis via Gene Set Enrichment Analysis. PMID:35287505
A COMPASS for VESPUCCI: A FAIR Way to Explore the Grapevine Transcriptomic Landscape. PMID:35283898
The Key Genes Underlying Pathophysiology Correlation Between the Acute Myocardial Infarction and COVID-19. PMID:35282650
Exploring the Communal Pathogenesis, Ferroptosis Mechanism, and Potential Therapeutic Targets of Dilated Cardiomyopathy and Hypertrophic Cardiomyopathy via a Microarray Data Analysis. PMID:35282347
Identification of a seven-gene prognostic signature using the gene expression profile of osteosarcoma. PMID:35282067
Revealing Calcium Signaling Pathway as Novel Mechanism of Danhong Injection for Treating Acute Myocardial Infarction by Systems Pharmacology and Experiment Validation. PMID:35281886
Identification of Type 2 Diabetes Based on a Ten-Gene Biomarker Prediction Model Constructed Using a Support Vector Machine Algorithm. PMID:35281591
Secondary structure prediction for RNA sequences including N6-methyladenosine. PMID:35277476
Dysregulation of Human Somatic piRNA Expression in Parkinson's Disease Subtypes and Stages. PMID:35269612
Pseudotime Analysis Reveals Exponential Trends in DNA Methylation Aging with Mortality Associated Timescales. PMID:35269389
Diurnal and circadian rhythmicity of the human blood transcriptome overlaps with organ- and tissue-specific expression of a non-human primate. PMID:35264172
A nonredundant role for T cell-derived interleukin 22 in antibacterial defense of colonic crypts. PMID:35263568
The schizophrenia-associated variant in SLC39A8 alters protein glycosylation in the mouse brain. PMID:35260802
CASCADE: high-throughput characterization of regulatory complex binding altered by non-coding variants. PMID:35252945
Deciphering Cell-Type-Specific Gene Expression Signatures of Cardiac Diseases Through Reconstruction of Bulk Transcriptomes. PMID:35252172
Expression and Prognostic Value of Glucose Transporter 3 in Diffuse Large B Cell Lymphoma. PMID:35250277
Decoding Human Genome Regulatory Features That Influence HIV-1 Proviral Expression and Fate Through an Integrated Genomics Approach. PMID:35250265
Region-based analysis of rare genomic variants in whole-genome sequencing datasets reveal two novel Alzheimer's disease-associated genes: DTNB and DLG2. PMID:35246634
Gene coexpression analysis in Arabidopsis thaliana based on public microarray data. PMID:35243384
Identification of potential microRNA groups for the diagnosis of hepatocellular carcinoma (HCC) using microarray datasets and bioinformatics tools. PMID:35243101
LPAR2 correlated with different prognosis and immune cell infiltration in head and neck squamous cell carcinoma and kidney renal clear cell carcinoma. PMID:35241179
Downregulation of Three Immune-Specific Core Genes and the Regulatory Pathways in Children and Adult Friedreich's Ataxia: A Comprehensive Analysis Based on Microarray. PMID:35237223
JAK-STAT core cancer pathway: An integrative cancer interactome analysis. PMID:35229974
Identification of key genes associated with polycystic ovary syndrome (PCOS) and ovarian cancer using an integrated bioinformatics analysis. PMID:35227296
Screening the components of Saussurea involucrata for novel targets for the treatment of NSCLC using network pharmacology. PMID:35227278
Potential biomarkers in the fibrosis progression of nonalcoholic steatohepatitis (NASH). PMID:35226336
Predicting Diagnostic Gene Biomarkers Associated With Immune Checkpoints, N6-Methyladenosine, and Ferroptosis in Patients With Acute Myocardial Infarction. PMID:35224064
Plasma Concentration of Tumor Necrosis Factor-Stimulated Gene-6 as a Novel Diagnostic and 3-Month Prognostic Indicator in Non-Cardioembolic Acute Ischemic Stroke. PMID:35222359
Characterization of Metronidazole-Resistant Giardia intestinalis Lines by Comparative Transcriptomics and Proteomics. PMID:35222342
Identification of Molecular Signatures and Candidate Drugs in Vascular Dementia by Bioinformatics Analyses. PMID:35221911
Functional Roles and Targets of COVID-19 in Blood Cells Determined Using Bioinformatics Analyses. PMID:35221679
Bruceine D Identified as a Drug Candidate against Breast Cancer by a Novel Drug Selection Pipeline and Cell Viability Assay. PMID:35215292
Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery. PMID:35213534
Metabolic profiling of prostate cancer in skeletal microenvironments identifies G6PD as a key mediator of growth and survival. PMID:35213227
Comparative Genomics of Clostridium baratii Reveals Strain-Level Diversity in Toxin Abundance. PMID:35208668
Molecular Profiling Reveals Characteristic and Decisive Signatures in Patients after Allogeneic Stem Cell Transplantation Suffering from Invasive Pulmonary Aspergillosis. PMID:35205926
DRPPM-EASY: A Web-Based Framework for Integrative Analysis of Multi-Omics Cancer Datasets. PMID:35205126
Identification of Potential Targets Linked to the Cardiovascular/Alzheimer's Axis through Bioinformatics Approaches. PMID:35203598
Impact of Maternal Obesity on Liver Disease in the Offspring: A Comprehensive Transcriptomic Analysis and Confirmation of Results in a Murine Model. PMID:35203502
Identification of Dysregulated Expression of G Protein Coupled Receptors in Endocrine Tumors by Bioinformatics Analysis: Potential Drug Targets? PMID:35203352
FibroDB: Expression Analysis of Protein-Coding and Long Non-Coding RNA Genes in Fibrosis. PMID:35202087
Network based systems biology approach to identify diseasome and comorbidity associations of Systemic Sclerosis with cancers. PMID:35198765
TMAO-Activated Hepatocyte-Derived Exosomes Are Widely Distributed in Mice with Different Patterns and Promote Vascular Inflammation. PMID:35198242
Identification of Potential Cytokinin Responsive Key Genes in Rice Treated With Trans-Zeatin Through Systems Biology Approach. PMID:35198001
PI3K-regulated Glycine N-methyltransferase is required for the development of prostate cancer. PMID:35197445
Targets and Potential Mechanism of Scutellaria baicalensis in Treatment of Primary Hepatocellular Carcinoma Based on Bioinformatics Analysis. PMID:35190740
Circular RNA hsa_circ_0083756 promotes intervertebral disc degeneration by sponging miR-558 and regulating TREM1 expression. PMID:35187741
Transcription factor protein interactomes reveal genetic determinants in heart disease. PMID:35182466
Olfactory receptors contribute to progression of kidney fibrosis. PMID:35181660
Aldehyde Dehydrogenase 2 Family Member (ALDH2) Is a Therapeutic Index for Oxaliplatin Response on Colorectal Cancer Therapy with Dysfunction p53. PMID:35178443
Metabolic Variation Dictates Cardiac Pathogenesis in Patients With Tetralogy of Fallot. PMID:35174118
Using publicly available transcriptomic data to identify mechanistic and diagnostic biomarkers in azoospermia and overall male infertility. PMID:35173218
A data-driven biocomputing pipeline with meta-analysis on high throughput transcriptomics to identify genome-wide miRNA markers associated with type 2 diabetes. PMID:35169647
Selenium binding protein 1 inhibits tumor angiogenesis in colorectal cancers by blocking the Delta-like ligand 4/Notch1 signaling pathway. PMID:35158204
Syntenin Regulated by miR-216b Promotes Cancer Progression in Pancreatic Cancer. PMID:35155233
Effect of PAIP1 on the metastatic potential and prognostic significance in oral squamous cell carcinoma. PMID:35153296
Multi-omics data identified TP53 and LRP1B as key regulatory gene related to immune phenotypes via EPCAM in HCC. PMID:35150083
Osmotic stress induces long-term biofilm survival in Liberibacter crescens. PMID:35148684
A mechanistic modeling framework reveals the key principles underlying tumor metabolism. PMID:35148308
Plasma lipidomics analysis reveals altered lipids signature in patients with osteonecrosis of the femoral head. PMID:35147763
Immune Infiltration of CD8+ T Cells in Patients With Diabetic Pancreatic Cancer Reduces the Malignancy of Cancer Tissues: An In Silico Study. PMID:35145483
Identification of Shared Genes and Pathways in Periodontitis and Type 2 Diabetes by Bioinformatics Analysis. PMID:35145474
Genes and Signaling Pathways Involved in the Regulation of Selenium-Enriched Yeast on Liver Metabolism and Health of Broiler (Gallus gallus). PMID:35143018
Network Pharmacology- and Molecular Docking-Based Identification of Potential Phytocompounds from Argyreia capitiformis in the Treatment of Inflammation. PMID:35140801
Comprehensive Landscape of Immune Infiltration and Aberrant Pathway Activation in Ischemic Stroke. PMID:35140708
The Multi-Omics Analysis of Key Genes Regulating EGFR-TKI Resistance, Immune Infiltration, SCLC Transformation in EGFR-Mutant NSCLC. PMID:35140497
Fused feature signatures to probe tumour radiogenomics relationships. PMID:35140267
Plotgardener: Cultivating precise multi-panel figures in R. PMID:35134826
PlantGF: an analysis and annotation platform for plant gene families. PMID:35134149
CTCFL regulates the PI3K-Akt pathway and it is a target for personalized ovarian cancer therapy. PMID:35132075
Screening and Identification of Survival-Associated Splicing Factors in Lung Squamous Cell Carcinoma. PMID:35126467
Transcriptomic Landscape of Herbivore Oviposition in Arabidopsis: A Systematic Review. PMID:35126411
PBK/TOPK Inhibitor Suppresses the Progression of Prolactinomas. PMID:35126305
Mouse genomic and cellular annotations. PMID:35124726
Estrogen modulation of the pronociceptive effects of serotonin on female rat trigeminal sensory neurons is timing dependent and dosage dependent and requires estrogen receptor alpha. PMID:35121697
Anota2seq Analysis for Transcriptome-Wide Studies of mRNA Translation. PMID:35119670
Screening of differential expressed genes from gene chip and sequencing data and evaluate its prognostic values in males with digestive system neoplasms. PMID:35116986
Identification of high expression profiles of miR-31-5p and its vital role in lung squamous cell carcinoma: a survey based on qRT-PCR and bioinformatics analysis. PMID:35116817
A role of TTI1 in the colorectal cancer by promoting proliferation. PMID:35116463
Screening key prognostic factors and constructing survival prognostic risk prediction model based on ceRNA network in early lung adenocarcinoma. PMID:35116321
Selected by bioinformatics and molecular docking analysis, Dhea and 2-14,15-Eg are effective against cholangiocarcinoma. PMID:35113866
Construction and Validation of a Novel Ferroptosis-Related Prognostic Model for Acute Myeloid Leukemia. PMID:35111195
Screening of Important Markers in Peripheral Blood Mononuclear Cells to Predict Female Osteoporosis Risk Using LASSO Regression Algorithm and SVM Method. PMID:35110962
Exploring the synergistic effects of cabozantinib and a programmed cell death protein 1 inhibitor in metastatic renal cell carcinoma with machine learning. PMID:35106125
Liver-specific LINC01146, a promising prognostic indicator, inhibits the malignant phenotype of hepatocellular carcinoma cells both in vitro and in vivo. PMID:35101062
Downregulation of PIK3CB Involved in Alzheimer's Disease via Apoptosis, Axon Guidance, and FoxO Signaling Pathway. PMID:35096262
Identification of Novel Subtypes in Lung Adenocarcinoma: Evidence from Gene Set Variation Analysis in Tumor and Adjacent Nontumor Samples. PMID:35096200
Construction of the Classification Model Using Key Genes Identified Between Benign and Malignant Thyroid Nodules From Comprehensive Transcriptomic Data. PMID:35096008
An Immune Feature-Based, Three-Gene Scoring System for Prognostic Prediction of Head-and-Neck Squamous Cell Carcinoma. PMID:35087741
FOXO4 May Be a Biomarker of Postmenopausal Osteoporosis. PMID:35082523
Role of Hub Genes in the Occurrence and Development of Testicular Cancer Based on Bioinformatics. PMID:35082515
Presence of periodontal pathogenic bacteria in blood of patients with coronary artery disease. PMID:35075206
Identification of key regulators in Sarcoidosis through multidimensional systems biological approach. PMID:35075176
Ontology-based identification and prioritization of candidate drugs for epilepsy from literature. PMID:35073996
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
GMQN: A Reference-Based Method for Correcting Batch Effects and Probe Bias in HumanMethylation BeadChip. PMID:35069703
A Practical Strategy for Exploring the Pharmacological Mechanism of Luteolin Against COVID-19/Asthma Comorbidity: Findings of System Pharmacology and Bioinformatics Analysis. PMID:35069542
Identification of Core Genes and Pathways in Melanoma Metastasis via Bioinformatics Analysis. PMID:35054979
Deregulation of Trace Amine-Associated Receptors (TAAR) Expression and Signaling Mode in Melanoma. PMID:35053262
Smell Detection Agent Optimisation Framework and Systems Biology Approach to Detect Dys-Regulated Subnetwork in Cancer Data. PMID:35053185
TimesVector-Web: A Web Service for Analysing Time Course Transcriptome Data with Multiple Conditions. PMID:35052413
Ubiquitous Aberration in Cholesterol Metabolism across Pancreatic Ductal Adenocarcinoma. PMID:35050168
Identification of Hub Genes of Keloid Fibroblasts by Coexpression Network Analysis and Degree Algorithm. PMID:35047146
Identification of m6A-Associated Gene DST as a Prognostic and Immune-Associated Biomarker in Breast Cancer Patients. PMID:35046711
Identification of hub genes associated with COVID-19 and idiopathic pulmonary fibrosis by integrated bioinformatics analysis. PMID:35045126
Circ_0004354 might compete with circ_0040039 to induce NPCs death and inflammatory response by targeting miR-345-3p-FAF1/TP73 axis in intervertebral disc degeneration. PMID:35039758
Harnessing big data to characterize immune-related adverse events. PMID:35039679
Identification of potential immunotherapy biomarkers for breast cancer by bioinformatics analysis. PMID:35037689
Gene regulatory network inference in long-lived C. elegans reveals modular properties that are predictive of novel aging genes. PMID:35036864
Salivary miRNAs as non-invasive biomarkers of hepatocellular carcinoma: a pilot study. PMID:35036096
The Role and Mechanism of SIRT6 in Regulating Phenotype Transformation of Vascular Smooth Muscle Cells in Abdominal Aortic Aneurysm. PMID:35035519
Lower RNA expression of ALDH1A1 distinguishes the favorable risk group in acute myeloid leukemia. PMID:35028852
Characterization of an Autophagy-Immune Related Genes Score Signature and Prognostic Model and its Correlation with Immune Response for Bladder Cancer. PMID:35023971
Identification of Differentially Expressed Genes and Pathways in Human Atrial Fibrillation by Bioinformatics Analysis. PMID:35023949
Mammalian brain glycoproteins exhibit diminished glycan complexity compared to other tissues. PMID:35022400
Identification of cardiomyopathy-related core genes through human metabolic networks and expression data. PMID:35016605
Integrative omics analysis identifies biomarkers of idiopathic pulmonary fibrosis. PMID:35015148
[Identification of potential hub genes of Alzheimer's disease by weighted gene co-expression network analysis]. PMID:35012905
Anticancer Activities of 9-chloro-6-(piperazin-1-yl)-11H-indeno[1,2-c] quinolin-11-one (SJ10) in Glioblastoma Multiforme (GBM) Chemoradioresistant Cell Cycle-Related Oncogenic Signatures. PMID:35008426
The Molecular Landscape of Medulloblastoma in Teenagers and Young Adults. PMID:35008416
Overlapping Genetic Architecture Between Schizophrenia and Neurodegenerative Disorders. PMID:35004692
COVID-19 Transcriptomic Atlas: A Comprehensive Analysis of COVID-19 Related Transcriptomics Datasets. PMID:35003208
CircCCNB1 silencing acting as a miR-106b-5p sponge inhibited GPM6A expression to promote HCC progression by enhancing DYNC1I1 expression and activating the AKT/ERK signaling pathway. PMID:35002514
Prognostic Significance of CCNB2 Expression in Triple-Negative Breast Cancer. PMID:35002325
ADAMTS8 Expression is a Potential Prognostic Biomarker for Postoperative Metastasis in Lymph Node-Negative Early-Stage Invasive Breast Carcinoma Patients. PMID:35002288
Network analysis of host-pathogen protein interactions in microbe induced cardiovascular diseases. PMID:35001887
Identification of a five-miRNA signature as a novel potential prognostic biomarker in patients with nasopharyngeal carcinoma. PMID:34998434
Meta-analysis of whole-genome gene expression datasets assessing the effects of IDH1 and IDH2 mutations in isogenic disease models. PMID:34997121
Evaluation of animal model congruence to human depression based on large-scale gene expression patterns of the CNS. PMID:34997033
miR-590-3 and SP1 Promote Neuronal Apoptosis in Patients with Alzheimer's Disease via AMPK Signaling Pathway. PMID:34992508
Potential Molecular Mechanisms and Remdesivir Treatment for Acute Respiratory Syndrome Corona Virus 2 Infection/COVID 19 Through RNA Sequencing and Bioinformatics Analysis. PMID:34992355
Netrin-1 promotes retinoblastoma-associated angiogenesis. PMID:34988192
High Expression of Ubiquitin-Specific Protease 39 and Its Roles in Prognosis in Patients with Hepatocellular Carcinoma. PMID:34987596
Role of BCAR4 in prostate cancer cell autophagy. PMID:34984190
Widespread choroid plexus contamination in sampling and profiling of brain tissue. PMID:34983929
Fluctuating methylation clocks for cell lineage tracing at high temporal resolution in human tissues. PMID:34980912
Computational challenges in detection of cancer using cell-free DNA methylation. PMID:34976309
Understanding Gene Expression and Transcriptome Profiling of COVID-19: An Initiative Towards the Mapping of Protective Immunity Genes Against SARS-CoV-2 Infection. PMID:34975833
Identification of Hub Genes and Immune Cell Infiltration Characteristics in Alzheimer's Disease. PMID:34966527
Significance of CD47 and Its Association With Tumor Immune Microenvironment Heterogeneity in Ovarian Cancer. PMID:34966389
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
CircRNA RERE Promotes the Oxidative Stress-Induced Apoptosis and Autophagy of Nucleus Pulposus Cells through the miR-299-5p/Galectin-3 Axis. PMID:34956563
Integrative genomic analysis of PPP3R1 in Alzheimer's disease: a potential biomarker for predictive, preventive, and personalized medical approach. PMID:34956428
Bacillus subtilis natto Derivatives Inhibit Enterococcal Biofilm Formation via Restructuring of the Cell Envelope. PMID:34956152
Construction and Analysis of a Diagnostic Model Based on Differential Expression Genes in Patients With Major Depressive Disorder. PMID:34955918
A β-Catenin-TCF-Sensitive Locus Control Region Mediates GUCY2C Ligand Loss in Colorectal Cancer. PMID:34954189
ITGB3BP is a potential biomarker associated with poor prognosis of glioma. PMID:34953037
Identification and Clinical Validation of Key Extracellular Proteins as the Potential Biomarkers in Relapsing-Remitting Multiple Sclerosis. PMID:34950135
SARS-CoV-2 Exacerbates Beta-Amyloid Neurotoxicity, Inflammation and Oxidative Stress in Alzheimer's Disease Patients. PMID:34948400
A Detailed Gene Expression Map of Giardia Encystation. PMID:34946882
Differential Expression of Polyamine Pathways in Human Pancreatic Tumor Progression and Effects of Polyamine Blockade on Tumor Microenvironment. PMID:34945011
8-Hydroxydaidzein Downregulates JAK/STAT, MMP, Oxidative Phosphorylation, and PI3K/AKT Pathways in K562 Cells. PMID:34944720
Comparison of Oxidative and Hypoxic Stress Responsive Genes from Meta-Analysis of Public Transcriptomes. PMID:34944646
Expression, Regulation, and Functions of the Galectin-16 Gene in Human Cells and Tissues. PMID:34944551
Prognostic and Genomic Analysis of Proteasome 20S Subunit Alpha (PSMA) Family Members in Breast Cancer. PMID:34943457
Integrative computational approach identifies immune-relevant biomarkers in ulcerative colitis. PMID:34939750
Prognostic Value of mRNAsi/Corrected mRNAsi Calculated by the One-Class Logistic Regression Machine-Learning Algorithm in Glioblastoma Within Multiple Datasets. PMID:34938774
Development and Validation of a Six-Gene Prognostic Signature for Bladder Cancer. PMID:34938313
Perspective of the GEMSTONE Consortium on Current and Future Approaches to Functional Validation for Skeletal Genetic Disease Using Cellular, Molecular and Animal-Modeling Techniques. PMID:34938269
Identification of potential key genes and functional role of CENPF in osteosarcoma using bioinformatics and experimental analysis. PMID:34934449
Metabolic syndrome related gene signature predicts the prognosis of patients with pancreatic ductal carcinoma. A novel link between metabolic dysregulation and pancreatic ductal carcinoma. PMID:34930261
Four Autophagy-Related Long Noncoding RNAs Provide Coexpression and ceRNA Mechanisms in Retinoblastoma through Bioinformatics and Experimental Evidence. PMID:34926945
NFAT as a Biomarker and Therapeutic Target in Non-Small Cell Lung Cancer-Related Brain Metastasis. PMID:34917508
Identification of Key Deregulated RNA-Binding Proteins in Pancreatic Cancer by Meta-Analysis and Prediction of Their Role as Modulators of Oncogenesis. PMID:34912796
The Vista of Application of Specific Anaphylaxis Accurate Diagnosis Based on DNA Single-Nucleotide Methylation Sites. PMID:34908915
Identification and Development of Subtypes with Poor Prognosis in Gastric Cancer Based on Both Hypoxia and Immune Cell Infiltration. PMID:34908867
Identification of potential core genes in colorectal carcinoma and key genes in colorectal cancer liver metastasis using bioinformatics analysis. PMID:34907282
Relation Extraction of Protein Complexes from Dynamic Protein-Protein Interaction Network. PMID:34904064
The prognostic and clinical significance of IFI44L aberrant downregulation in patients with oral squamous cell carcinoma. PMID:34903206
Using MMRFBiolinks R-Package for Discovering Prognostic Markers in Multiple Myeloma. PMID:34902136
Improving Analysis and Annotation of Microarray Data with Protein Interactions. PMID:34902122
Metabolic Reprogramming and Reconstruction: Integration of Experimental and Computational Studies to Set the Path Forward in ADPKD. PMID:34901057
In Silico Analysis of Sperm From Ejaculates with Different Semen Characteristics. PMID:34900641
Activation of Intracellular Complement in Lungs of Patients With Severe COVID-19 Disease Decreases T-Cell Activity in the Lungs. PMID:34899680
CoRE-ATAC: A deep learning model for the functional classification of regulatory elements from single cell and bulk ATAC-seq data. PMID:34898596
Metformin alleviates the calcification of aortic valve interstitial cells through activating the PI3K/AKT pathway in an AMPK dependent way. PMID:34895136
Comparative analysis of aneurysm subtypes associated genes based on protein-protein interaction network. PMID:34895131
Deep Conservation of Histone Variants in Thermococcales Archaea. PMID:34894218
Integrative analysis of immune-related multi-omics profiles identifies distinct prognosis and tumor microenvironment patterns in osteosarcoma. PMID:34894177
Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects. PMID:34890448
Functional Screenings Identify Regulatory Variants Associated with Breast Cancer Susceptibility. PMID:34889888
A Review of Prostate Organogenesis and a Role for iPSC-Derived Prostate Organoids to Study Prostate Development and Disease. PMID:34884905
The MAPK Signaling Pathway Presents Novel Molecular Targets for Therapeutic Intervention after Traumatic Spinal Cord Injury: A Comparative Cross-Species Transcriptional Analysis. PMID:34884738
Sparsely Connected Autoencoders: A Multi-Purpose Tool for Single Cell omics Analysis. PMID:34884559
Optimal dimensionality selection for independent component analysis of transcriptomic data. PMID:34879815
Identification of ferroptosis-related genes as potential biomarkers of tongue squamous cell carcinoma using an integrated bioinformatics approach. PMID:34878732
piRBase: integrating piRNA annotation in all aspects. PMID:34871445
LIMD2 is a Prognostic and Predictive Marker in Patients With Esophageal Cancer Based on a ceRNA Network Analysis. PMID:34868263
Large Multicohort Study Reveals a Prostate Cancer Susceptibility Allele at 5p15 Regulating TERT via Androgen Signaling-Orchestrated Chromatin Binding of E2F1 and MYC. PMID:34858826
GFI1 tethers the NuRD complex to open and transcriptionally active chromatin in myeloid progenitors. PMID:34857890
LncRNA PKMYT1AR promotes cancer stem cell maintenance in non-small cell lung cancer via activating Wnt signaling pathway. PMID:34856993
miRTarBase update 2022: an informative resource for experimentally validated miRNA-target interactions. PMID:34850920
JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. PMID:34850907
Addressing noise in co-expression network construction. PMID:34850822
CircNet 2.0: an updated database for exploring circular RNA regulatory networks in cancers. PMID:34850139
Expression Atlas update: gene and protein expression in multiple species. PMID:34850121
Role of the trace amine associated receptor 5 (TAAR5) in the sensorimotor functions. PMID:34845253
recount3: summaries and queries for large-scale RNA-seq expression and splicing. PMID:34844637
Non-coding RNAs and related molecules associated with form-deprivation myopia in mice. PMID:34841657
Prognostic and immune infiltration signatures of proteasome 26S subunit, non-ATPase (PSMD) family genes in breast cancer patients. PMID:34839279
Identification of Differentially Expressed Genes in Different Glioblastoma Regions and Their Association with Cancer Stem Cell Development and Temozolomide Response. PMID:34834399
The Transcription Factor FEZF1, a Direct Target of EWSR1-FLI1 in Ewing Sarcoma Cells, Regulates the Expression of Neural-Specific Genes. PMID:34830820
Deep Learning for Human Disease Detection, Subtype Classification, and Treatment Response Prediction Using Epigenomic Data. PMID:34829962
Computer-Aided Design for Identifying Anticancer Targets in Genome-Scale Metabolic Models of Colon Cancer. PMID:34827109
In silico Methods for Identification of Potential Therapeutic Targets. PMID:34826045
Identification and Integrate Analysis of Key Biomarkers for Diagnosis and Prognosis of Non-Small Cell Lung Cancer Based on Bioinformatics Analysis. PMID:34825846
Identification of Genes Potentially Associated with Melanoma Tumorigenesis Through Co-Expression Network Analysis. PMID:34824546
Genes and regulatory mechanisms associated with experimentally-induced bovine respiratory disease identified using supervised machine learning methodology. PMID:34824337
High endogenous CCL2 expression promotes the aggressive phenotype of human inflammatory breast cancer. PMID:34824220
Effects of photodeoxygenation on cell biology using dibenzothiophene S-oxide derivatives as O(3P)-precursors. PMID:34822125
Identification of miRNAs and genes for predicting Barrett's esophagus progressing to esophageal adenocarcinoma using miRNA-mRNA integrated analysis. PMID:34818353
Long non-coding RNA H19 mediates N-acetyltransferase 1 gene methylation in the development of tamoxifen resistance in breast cancer. PMID:34815764
Screening of Parkinson's Differential MicroRNA Based on GEO Database and Its Clinical Verification. PMID:34812409
Core genes involved in the regulation of acute lung injury and their association with COVID-19 and tumor progression: A bioinformatics and experimental study. PMID:34807957
Identification and Validation of Afatinib Potential Drug Resistance Gene BIRC5 in Non-Small Cell Lung Cancer. PMID:34804966
Methods to Develop an in silico Clinical Trial: Computational Head-to-Head Comparison of Lisdexamfetamine and Methylphenidate. PMID:34803764
Bioinformatics analyses of the pathogenesis and new biomarkers of chronic obstructive pulmonary disease. PMID:34797299
CircleBase: an integrated resource and analysis platform for human eccDNAs. PMID:34792166
R-loopBase: a knowledgebase for genome-wide R-loop formation and regulation. PMID:34792163
DiseaseMeth version 3.0: a major expansion and update of the human disease methylation database. PMID:34792145
Circular RNA-associated ceRNA network involved in HIF-1 signalling in triple-negative breast cancer: circ_0047303 as a potential key regulator. PMID:34791795
proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms. PMID:34791440
DISCO: a database of Deeply Integrated human Single-Cell Omics data. PMID:34791375
MicroRNA-146a Serves as a Biomarker for Adverse Prognosis of ST-Segment Elevation Myocardial Infarction. PMID:34786024
Multidimensional Analysis of the Role of Charged Multivesicular Body Protein 7 in Pan-Cancer. PMID:34785938
Identification and Validation of Autophagy-Related Genes as Potential Biomarkers and Therapeutic Targets in Atrial Fibrillation. PMID:34785936
Hub microRNAs and genes in the development of atrial fibrillation identified by weighted gene co-expression network analysis. PMID:34781940
Toxoplasma gondii GRA28 Is Required for Placenta-Specific Induction of the Regulatory Chemokine CCL22 in Human and Mouse. PMID:34781732
Linking Diabetes Mellitus with Alzheimer's Disease: Bioinformatics Analysis for the Potential Pathways and Characteristic Genes. PMID:34779951
Machine learning and network medicine approaches for drug repositioning for COVID-19. PMID:34778851
NOT-Gated CD93 CAR T Cells Effectively Target AML with Minimized Endothelial Cross-Reactivity. PMID:34778803
Trends in biological data integration for the selection of enzymes and transcription factors related to cellulose and hemicellulose degradation in fungi. PMID:34777932
Analysis of transcriptomic data sets supports the role of IL-6 in NETosis and immunothrombosis in severe COVID-19. PMID:34775962
Bioinformatics approach to identify common gene signatures of patients with coronavirus 2019 and lung adenocarcinoma. PMID:34775559
Drug metabolism-related eight-gene signature can predict the prognosis of gastric adenocarcinoma. PMID:34773716
Expression Levels of RAD51 Inversely Correlate with Survival of Glioblastoma Patients. PMID:34771522
SARS-CoV-2 Exposed Mesenchymal Stromal Cell from Congenital Pulmonary Airway Malformations: Transcriptomic Analysis and the Expression of Immunomodulatory Genes. PMID:34769246
Breast Cancer CAFs: Spectrum of Phenotypes and Promising Targeting Avenues. PMID:34769066
An RNA-Seq-Based Framework for Characterizing Canine Prostate Cancer and Prioritizing Clinically Relevant Biomarker Candidate Genes. PMID:34768937
PDK1 Inhibitor BX795 Improves Cisplatin and Radio-Efficacy in Oral Squamous Cell Carcinoma by Downregulating the PDK1/CD47/Akt-Mediated Glycolysis Signaling Pathway. PMID:34768921
Cigarette smoking-associated isoform switching and 3' UTR lengthening via alternative polyadenylation. PMID:34763026
scEnhancer: a single-cell enhancer resource with annotation across hundreds of tissue/cell types in three species. PMID:34761274
A Multi-Center Validated Subtyping Model of Esophageal Cancer Based on Three Metabolism-Related Genes. PMID:34760709
IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis. PMID:34755877
Identification of hub genes and transcription factor-miRNA-mRNA pathways in mice and human renal ischemia-reperfusion injury. PMID:34754625
Comparing the epigenetic landscape in myonuclei purified with a PCM1 antibody from a fast/glycolytic and a slow/oxidative muscle. PMID:34752468
ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments. PMID:34751401
Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service. PMID:34749633
BioSamples database: FAIRer samples metadata to accelerate research data management. PMID:34747489
Pol3Base: a resource for decoding the interactome, expression, evolution, epitranscriptome and disease variations of Pol III-transcribed ncRNAs. PMID:34747466
Computational workflow for functional characterization of COVID-19 through secondary data analysis. PMID:34746856
Crosstalk between Circulatory Microenvironment and Vascular Endothelial Cells in Acute Myocardial Infarction. PMID:34744446
The Rat Genome Database (RGD) facilitates genomic and phenotypic data integration across multiple species for biomedical research. PMID:34741192
BDdb: a comprehensive platform for exploration and utilization of birth defect multi-omics data. PMID:34736471
MiR-29c inhibits the metastasis of oral squamous cell carcinoma and promotes its cell cycle arrest by targeting SERPINH1. PMID:34733975
Comparison of critical biomarkers in 2 erectile dysfunction models based on GEO and NOS-cGMP-PDE5 pathway. PMID:34731136
The landscape of prognostic and immunological role of myosin light chain 9 (MYL9) in human tumors. PMID:34729929
Comprehensive understanding of Tn5 insertion preference improves transcription regulatory element identification. PMID:34729473
Monitoring CAR T cell generation with a CD8-targeted lentiviral vector by single-cell transcriptomics. PMID:34729382
Bioinformatic analysis of key pathways and genes shared between endometriosis and ovarian cancer. PMID:34727222
Prognostic evaluation and immune infiltration analysis of five bioinformatic selected genes in hepatocellular carcinoma. PMID:34726341
Relationships between type 2 diabetes, cell dysfunction, and redox signaling: A meta-analysis of single-cell gene expression of human pancreatic α- and β-cells. PMID:34725923
Potential Role and Clinical Value of PPP2CA in Hepatocellular Carcinoma. PMID:34722181
Effect of SARS-CoV-2 infection on host competing endogenous RNA and miRNA network. PMID:34722003
Peripheral Blood-Based Gene Expression Studies in Schizophrenia: A Systematic Review. PMID:34721526
Identification of Potential Prognostic and Predictive Biomarkers for Immune-Checkpoint Inhibitor Response in Small Cell Lung Cancer. PMID:34719665
EWAS Open Platform: integrated data, knowledge and toolkit for epigenome-wide association study. PMID:34718752
RPS: a comprehensive database of RNAs involved in liquid-liquid phase separation. PMID:34718734
MetazExp: a database for gene expression and alternative splicing profiles and their analyses based on 53 615 public RNA-seq samples in 72 metazoan species. PMID:34718719
CCR5 is a prognostic biomarker and an immune regulator for triple negative breast cancer. PMID:34717291
The long non-coding RNA HOXA11-AS activates ITGB3 expression to promote the migration and invasion of gastric cancer by sponging miR-124-3p. PMID:34715856
Screening of key biomarkers of tendinopathy based on bioinformatics and machine learning algorithms. PMID:34714891
Machine learning applications in RNA modification sites prediction. PMID:34712397
Gene Co-Expression Analysis Identified Preserved and Survival-Related Modules in Severe Blunt Trauma, Burns, Sepsis, and Systemic Inflammatory Response Syndrome. PMID:34707398
Identification and drug-induced reversion of molecular signatures of Alzheimer's disease onset and progression in AppNL-G-F, AppNL-F, and 3xTg-AD mouse models. PMID:34702310
Sensitive, reliable and robust circRNA detection from RNA-seq with CirComPara2. PMID:34698333
PIM1 phosphorylation of the androgen receptor and 14-3-3 ζ regulates gene transcription in prostate cancer. PMID:34697370
Bioinformatics screening of biomarkers related to liver cancer. PMID:34696748
GJA1 promotes hepatocellular carcinoma progression by mediating TGF-β-induced activation and the epithelial-mesenchymal transition of hepatic stellate cells. PMID:34693020
Prioritization of Diagnostic and Prognostic Biomarkers for Lupus Nephritis Based on Integrated Bioinformatics Analyses. PMID:34692653
ADAR1 restricts ZBP1-mediated immune response and PANoptosis to promote tumorigenesis. PMID:34686350
Transcriptomic Biomarkers for Tuberculosis: Validation of NPC2 as a Single mRNA Biomarker to Diagnose TB, Predict Disease Progression, and Monitor Treatment Response. PMID:34685683
Gene Network Analysis of Alzheimer's Disease Based on Network and Statistical Methods. PMID:34682089
Novel NFκB Inhibitor SC75741 Mitigates Chondrocyte Degradation and Prevents Activated Fibroblast Transformation by Modulating miR-21/GDF-5/SOX5 Signaling. PMID:34681754
ARGEOS: A New Bioinformatic Tool for Detailed Systematics Search in GEO and ArrayExpress. PMID:34681124
Expression Profiles and Prognostic Value of FABPs in Colorectal Adenocarcinomas. PMID:34680577
Reverse Engineering of the Pediatric Sepsis Regulatory Network and Identification of Master Regulators. PMID:34680414
CXCR4 is a Novel Biomarker Correlated With Malignant Transformation and Immune Infiltrates in Gastric Precancerous Lesions. PMID:34676245
Trends in oligomannosylation and α1,2-mannosidase expression in human cancers. PMID:34676051
Analysis of Communal Molecular Mechanism and Potential Therapeutic Targets in Heart Failure and Type 2 Diabetes Mellitus. PMID:34675622
Screening and predicted value of potential biomarkers for breast cancer using bioinformatics analysis. PMID:34675265
Meta-analysis of COVID-19 single-cell studies confirms eight key immune responses. PMID:34675242
Global Histone H3 Lysine 4 Trimethylation (H3K4me3) Landscape Changes in Response to TGFβ. PMID:34671716
Deciphering the link between Diabetes mellitus and SARS-CoV-2 infection through differential targeting of microRNAs in the human pancreas. PMID:34669152
Revelation of Pivotal Genes Pertinent to Alzheimer's Pathogenesis: A Methodical Evaluation of 32 GEO Datasets. PMID:34668150
Bioinformatics Prediction and Analysis of MicroRNAs and Their Targets as Biomarkers for Prostate Cancer: A Preliminary Study. PMID:34665432
ASMdb: a comprehensive database for allele-specific DNA methylation in diverse organisms. PMID:34664666
SysInflam HuDB, a Web Resource for Mining Human Blood Cells Transcriptomic Data Associated with Systemic Inflammatory Responses to Sepsis. PMID:34663591
Identification of key genes for HNSCC from public databases using bioinformatics analysis. PMID:34663338
Identification of a prognostic chemoresistance-related gene signature associated with immune microenvironment in breast cancer. PMID:34661511
Expression Levels of Three Key Genes CCNB1, CDC20, and CENPF in HCC Are Associated With Antitumor Immunity. PMID:34660300
Bioinformatic and experimental analyses of key biomarkers in pancreatic cancer. PMID:34659505
Tree-Based Co-Clustering Identifies Chromatin Accessibility Patterns Associated With Hematopoietic Lineage Structure. PMID:34659332
PlGF Reduction Compromises Angiogenesis in Diabetic Foot Disease Through Macrophages. PMID:34659227
Text mining-based word representations for biomedical data analysis and protein-protein interaction networks in machine learning tasks. PMID:34653224
Gene Expression Characteristics of Liver Tissue Reveal the Underlying Pathogenesis of Hepatocellular Carcinoma. PMID:34651050
CDC45 modulates MCM7 expression and inhibits cell proliferation by suppressing the PI3K/AKT pathway in acute myeloid leukemia. PMID:34650692
Transcriptome-Wide Association Study Provides Insights Into the Genetic Component of Gene Expression in Anxiety. PMID:34650599
GNG7 and ADCY1 as diagnostic and prognostic biomarkers for pancreatic adenocarcinoma through bioinformatic-based analyses. PMID:34650124
A brain-specific pgc1α fusion transcript affects gene expression and behavioural outcomes in mice. PMID:34649938
Meta-Analysis illustrates possible role of lipopolysaccharide (LPS)-induced tissue injury in nasopharyngeal carcinoma (NPC) pathogenesis. PMID:34648530
Expression and clinical significance of TIMELESS in glioma. PMID:34646412
Identification of the Molecular Subgroups in Idiopathic Pulmonary Fibrosis by Gene Expression Profiles. PMID:34646338
Exploring the Molecular Mechanism of Astragali Radix-Curcumae Rhizoma against Gastric Intraepithelial Neoplasia by Network Pharmacology and Molecular Docking. PMID:34646329
The network interplay of interferon and Toll-like receptor signaling pathways in the anti-Candida immune response. PMID:34645905
CancerSCEM: a database of single-cell expression map across various human cancers. PMID:34643725
A Survey of Autoencoder Algorithms to Pave the Diagnosis of Rare Diseases. PMID:34639231
Integrating Statistical and Machine-Learning Approach for Meta-Analysis of Bisphenol A-Exposure Datasets Reveals Effects on Mouse Gene Expression within Pathways of Apoptosis and Cell Survival. PMID:34639124
Differentiation of the High Night Temperature Response in Leaf Segments of Rice Cultivars with Contrasting Tolerance. PMID:34638787
Potential Therapeutic and Prognostic Values of LSM Family Genes in Breast Cancer. PMID:34638387
Predictive regulatory and metabolic network models for systems analysis of Clostridioides difficile. PMID:34637780
VThunter: a database for single-cell screening of virus target cells in the animal kingdom. PMID:34634807
CKAP2L, as an Independent Risk Factor, Closely Related to the Prognosis of Glioma. PMID:34631884
Scouting for common genes in the heterogenous hypoxic tumor microenvironment and their validation in glioblastoma. PMID:34631352
SPT6 loss permits the transdifferentiation of keratinocytes into an intestinal fate that resembles Barrett's metaplasia. PMID:34622168
ERK1/2-EGR1-SRSF10 Axis Mediated Alternative Splicing Plays a Critical Role in Head and Neck Cancer. PMID:34616729
Integrative bioinformatics and experimental analysis revealed down-regulated CDC42EP3 as a novel prognostic target for ovarian cancer and its roles in immune infiltration. PMID:34616622
Editorial: Big Data and Machine Learning in Cancer Genomics. PMID:34616439
Microglia Mediate the Occurrence and Development of Alzheimer's Disease Through Ligand-Receptor Axis Communication. PMID:34616287
Use of relevancy and complementary information for discriminatory gene selection from high-dimensional gene expression data. PMID:34613963
huARdb: human Antigen Receptor database for interactive clonotype-transcriptome analysis at the single-cell level. PMID:34606616
Comprehensive Analysis of the Prognostic Significance of Hsa-miR-100-5p and Its Related Gene Signature in Stomach Adenocarcinoma. PMID:34604236
M6A Classification Combined With Tumor Microenvironment Immune Characteristics Analysis of Bladder Cancer. PMID:34604051
Bioinformatics and system biology approaches to identify pathophysiological impact of COVID-19 to the progression and severity of neurological diseases. PMID:34601390
A framework for validating AI in precision medicine: considerations from the European ITFoC consortium. PMID:34600518
Productive visualization of high-throughput sequencing data using the SeqCode open portable platform. PMID:34599234
Randomized trial drug controlled compendious transcriptome analysis supporting broad and phase specific therapeutic potential of multiple candidates in COVID-19. PMID:34597919
The profile analysis of circular RNAs in cervical cancer. PMID:34596168
Identification of key genes in osteosarcoma - before and after CDK7 treatment. PMID:34596127
Identification of hub genes and candidate drugs in hepatocellular carcinoma by integrated bioinformatics analysis. PMID:34596112
Identification of the Effects of Chondroitin Sulfate on Inhibiting CDKs in Colorectal Cancer Based on Bioinformatic Analysis and Experimental Validation. PMID:34595111
Systematic investigation of cytokine signaling activity at the tissue and single-cell levels. PMID:34594031
Transcriptomic analyses and experimental verification reveal potential biomarkers and biological pathways of urinary tract infection. PMID:34592898
Evidence for the butyrate metabolism as key pathway improving ulcerative colitis in both pediatric and adult patients. PMID:34592880
Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels. PMID:34591957
Identifying key genes and screening therapeutic agents associated with diabetes mellitus and HCV-related hepatocellular carcinoma by bioinformatics analysis. PMID:34588861
Large-scale identification of extracellular plant miRNAs in mammals implicates their dietary intake. PMID:34587184
HNRNPC Promotes Proliferation, Metastasis and Predicts Prognosis in Prostate Cancer. PMID:34584453
Network Pharmacology Reveals That Resveratrol Can Alleviate COVID-19-Related Hyperinflammation. PMID:34580601
Integration and gene co-expression network analysis of scRNA-seq transcriptomes reveal heterogeneity and key functional genes in human spermatogenesis. PMID:34580317
Discovering the DNA-Binding Consensus of the Thermus thermophilus HB8 Transcriptional Regulator TTHA1359. PMID:34576207
Microcystin-LR (MC-LR) Triggers Inflammatory Responses in Macrophages. PMID:34576099
Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning. PMID:34575658
Novel Approach Combining Transcriptional and Evolutionary Signatures to Identify New Multiciliation Genes. PMID:34573434
Validation and Selection of New Reference Genes for RT-qPCR Analysis in Pediatric Glioma of Different Grades. PMID:34573317
Transcriptomic profiling in canines and humans reveals cancer specific gene modules and biological mechanisms common to both species. PMID:34570764
CTR-DB, an omnibus for patient-derived gene expression signatures correlated with cancer drug response. PMID:34570230
Biodata Mining of Differentially Expressed Genes between Acute Myocardial Infarction and Unstable Angina Based on Integrated Bioinformatics. PMID:34568491
Immune Mechanism, Gene Module, and Molecular Subtype Identification of Astragalus Membranaceus in the Treatment of Dilated Cardiomyopathy: An Integrated Bioinformatics Study. PMID:34567206
Robust metabolic transcriptional components in 34,494 patient-derived cancer-related samples and cell lines. PMID:34565468
Glycolysis related gene expression signature in predicting prognosis of laryngeal squamous cell carcinoma. PMID:34565301
Anomaly detection in genomic catalogues using unsupervised multi-view autoencoders. PMID:34563116
Malignant Tumor Purity Reveals the Driven and Prognostic Role of CD3E in Low-Grade Glioma Microenvironment. PMID:34557404
Association between chronic periodontitis and the risk of Alzheimer's disease: combination of text mining and GEO dataset. PMID:34556089
PmiREN2.0: from data annotation to functional exploration of plant microRNAs. PMID:34554254
Classifiers for Predicting Coronary Artery Disease Based on Gene Expression Profiles in Peripheral Blood Mononuclear Cells. PMID:34552349
RNALocate v2.0: an updated resource for RNA subcellular localization with increased coverage and annotation. PMID:34551440
A prion accelerates proliferation at the expense of lifespan. PMID:34545808
An insertion variant of MGMT disrupts a STAT1 binding site and confers susceptibility to glioma. PMID:34544433
The gene expression patterns of neuronal cells reveal the pathogenesis of autism. PMID:34540009
SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling. PMID:34536568
TISMO: syngeneic mouse tumor database to model tumor immunity and immunotherapy response. PMID:34534350
Identification of hub genes and functional modules in colon adenocarcinoma based on public databases by bioinformatics analysis. PMID:34532115
Identification of Novel Gene Signatures using Next-Generation Sequencing Data from COVID-19 Infection Models: Focus on Neuro-COVID and Potential Therapeutics. PMID:34531741
circMine: a comprehensive database to integrate, analyze and visualize human disease-related circRNA transcriptome. PMID:34530446
Prognostic impact of a lymphocyte activation-associated gene signature in GBM based on transcriptome analysis. PMID:34527446
KCa channel blockers increase effectiveness of the EGF receptor TK inhibitor erlotinib in non-small cell lung cancer cells (A549). PMID:34526525
DNA methylation and gene expression profiles to identify childhood atopic asthma associated genes. PMID:34525985
IGFBP-2 as a biomarker in NAFLD improves hepatic steatosis: an integrated bioinformatics and experimental study. PMID:34524971
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
Shortening of 3' UTRs in most cell types composing tumor tissues implicates alternative polyadenylation in protein metabolism. PMID:34521731
Targeting non-canonical pathways as a strategy to modulate the sodium iodide symporter. PMID:34520744
Comparative analysis of RNA enrichment methods for preparation of Cryptococcus neoformans RNA sequencing libraries. PMID:34518880
Integrated weighted gene co-expression network analysis uncovers STAT1(signal transducer and activator of transcription 1) and IFI44L (interferon-induced protein 44-like) as key genes in pulmonary arterial hypertension. PMID:34516357
Long non-coding RNA LINC01296 acts as a migration and invasion promoter in head and neck squamous cell carcinoma and predicts poor prognosis. PMID:34515611
Clustering Alzheimer's Disease Gene Expression Dataset Reveals Underlying Sexually Dimorphic and Disease Status Profiles. PMID:34514337
Potential Role of NEU1 in Hepatocellular Carcinoma: A Study Based on Comprehensive Bioinformatical Analysis. PMID:34513919
ESPL1 Is a Novel Prognostic Biomarker Associated With the Malignant Features of Glioma. PMID:34512713
In Silico Methods for the Identification of Diagnostic and Favorable Prognostic Markers in Acute Myeloid Leukemia. PMID:34502522
Identification and Validation of Esophageal Squamous Cell Carcinoma Targets for Fluorescence Molecular Endoscopy. PMID:34502178
miRNAs as Regulators of the Early Local Response to Burn Injuries. PMID:34502118
ViMIC: a database of human disease-related virus mutations, integration sites and cis-effects. PMID:34500462
CancerMIRNome: an interactive analysis and visualization database for miRNome profiles of human cancer. PMID:34500460
Glucotoxicity Activation of IL6 and IL11 and Subsequent Induction of Fibrosis May Be Involved in the Pathogenesis of Islet Dysfunction. PMID:34497830
lncRNA BORG:TRIM28 Complexes Drive Metastatic Progression by Inducing α6 Integrin/CD49f Expression in Breast Cancer Stem Cells. PMID:34497119
Identification of Key lncRNA-mRNA Pairs and Functional lncRNAs in Breast Cancer by Integrative Analysis of TCGA Data. PMID:34490040
Tear Lipocalin and Lipocalin-Interacting Membrane Receptor. PMID:34489718
Carcinogenic effect of adenylosuccinate lyase (ADSL) in prostate cancer development and progression through the cell cycle pathway. PMID:34488772
Synthetic Evaluation of MicroRNA-1-3p Expression in Head and Neck Squamous Cell Carcinoma Based on Microarray Chips and MicroRNA Sequencing. PMID:34485523
Screening and Identification of Key Biomarkers of Gastric Cancer: Three Genes Jointly Predict Gastric Cancer. PMID:34485109
A Meta-Analysis of Bioelectric Data in Cancer, Embryogenesis, and Regeneration. PMID:34476377
INHBA is a novel mediator regulating cellular senescence and immune evasion in colorectal cancer. PMID:34476008
Novel diagnostic and prognostic biomarkers of colorectal cancer: Capable to overcome the heterogeneity-specific barrier and valid for global applications. PMID:34473751
ARMT: An automatic RNA-seq data mining tool based on comprehensive and integrative analysis in cancer research. PMID:34471489
A computational approach for identification of core modules from a co-expression network and GWAS data. PMID:34467232
Comparative Bioinformatics Characteristic of Bladder Cancer Stage 2 from Stage 4 Expression Profile: A Network-Based Study. PMID:34466446
Construction of miRNA-mRNA network for the identification of key biological markers and their associated pathways in IgA nephropathy by employing the integrated bioinformatics analysis. PMID:34466069
Alpha-smooth Muscle Actin Expression in the Stroma Predicts Resistance to Trastuzumab in Patients with Early-stage HER2-positive Breast Cancer. PMID:34465600
Adult stem cell-derived complete lung organoid models emulate lung disease in COVID-19. PMID:34463615
Statistical guidelines for quality control of next-generation sequencing techniques. PMID:34462322
The Fibrosis-Targeted Collagen/Integrins Gene Profile Predicts Risk of Metastasis in Pulmonary Neuroendocrine Neoplasms. PMID:34458147
ImmuCellDB: An Indicative Database of Immune Cell Composition From Different Tissues and Disease Conditions in Mouse and Human. PMID:34456903
New Insights Into Mitochondrial Dysfunction at Disease Susceptibility Loci in the Development of Type 2 Diabetes. PMID:34456865
Condition-Specific Molecular Network Analysis Revealed That Flagellar Proteins Are Involved in Electron Transfer Processes of Shewanella piezotolerans WP3. PMID:34456634
Identification and Functional Validation of Differentially Expressed microRNAs in Ascites-Derived Ovarian Cancer Cells Compared with Primary Tumour Tissue. PMID:34456588
Multi-Tissue Transcriptomic-Informed In Silico Investigation of Drugs for the Treatment of Dengue Fever Disease. PMID:34452405
RNA Sequencing Analyses for Deciphering Potato Molecular Responses. PMID:34448155
Pattern of TAAR5 Expression in the Human Brain Based on Transcriptome Datasets Analysis. PMID:34445502
A Convergent Functional Genomics Analysis to Identify Biological Regulators Mediating Effects of Creatine Supplementation. PMID:34444681
Statistical Approach of Gene Set Analysis with Quantitative Trait Loci for Crop Gene Expression Studies. PMID:34441085
PlantMirP2: An Accurate, Fast and Easy-To-Use Program for Plant Pre-miRNA and miRNA Prediction. PMID:34440454
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
Non-Tumor CCAAT/Enhancer-Binding Protein Delta Potentiates Tumor Cell Extravasation and Pancreatic Cancer Metastasis Formation. PMID:34439745
Identification of a circRNA-miRNA-mRNA regulatory network for exploring novel therapeutic options for glioma. PMID:34434651
Editorial: Integration of Multi-Omics Techniques in Cancer. PMID:34434225
Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility. PMID:34431696
Potential Arabidopsis thaliana glucosinolate genes identified from the co-expression modules using graph clustering approach. PMID:34430080
Perturbed transcriptional profiles after chronic low dose rate radiation in mice. PMID:34428250
C-X-C motif chemokine ligand 12: a potential therapeutic target in Duchenne muscular dystrophy. PMID:34424816
A network-based systems biology approach for identification of shared Gene signatures between male and female in COVID-19 datasets. PMID:34423108
CD86 Molecule Might Be a Novel Immune-Related Prognostic Biomarker for Patients With Bladder Cancer by Bioinformatics and Experimental Assays. PMID:34422632
Bioinformatics analysis of constructing a HCV-related hepatocellular carcinoma miRNA-mRNA regulation network. PMID:34414965
Integrated Bioinformatics Analysis to Identify Alternative Therapeutic Targets for Alzheimer's Disease: Insights from a Synaptic Machinery Perspective. PMID:34414562
Searchlight: automated bulk RNA-seq exploration and visualisation using dynamically generated R scripts. PMID:34412594
A systematic review of datasets that can help elucidate relationships among gene expression, race, and immunohistochemistry-defined subtypes in breast cancer. PMID:34412551
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
Inhibition of STAT3 enhances sensitivity to tamoxifen in tamoxifen-resistant breast cancer cells. PMID:34407787
Human iPS-derived pre-epicardial cells direct cardiomyocyte aggregation expansion and organization in vitro. PMID:34404774
POSTAR3: an updated platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins. PMID:34403477
Evaluating of Gene Expression Alteration after Garlic Consumption, Analyzing through Bioinformatics Approach. PMID:34400942
MiR-508-3p promotes proliferation and inhibits apoptosis of middle ear cholesteatoma cells by targeting PTEN/PI3K/AKT pathway. PMID:34400892
Construction of a Potentially Functional circRNA-miRNA-mRNA Network in Intervertebral Disc Degeneration by Bioinformatics Analysis. PMID:34395625
Prognostic Prediction, Immune Microenvironment, and Drug Resistance Value of Collagen Type I Alpha 1 Chain: From Gastrointestinal Cancers to Pan-Cancer Analysis. PMID:34395525
Bioinformatics Analysis and Functional Verification of ADAMTS9-AS1/AS2 in Lung Adenocarcinoma. PMID:34395250
Bioinformatic Analysis of Prognostic and Immune-Related Genes in Pancreatic Cancer. PMID:34394706
Filtering of Data-Driven Gene Regulatory Networks Using Drosophila melanogaster as a Case Study. PMID:34394179
Identification of COVID-19 prognostic markers and therapeutic targets through meta-analysis and validation of Omics data from nasopharyngeal samples. PMID:34392148
Precision treatment exploration of breast cancer based on heterogeneity analysis of lncRNAs at the single-cell level. PMID:34388989
Arabidopsis Coexpression Tool: a tool for gene coexpression analysis in Arabidopsis thaliana. PMID:34381973
KAT2A-mediated AR translocation into nucleus promotes abiraterone-resistance in castration-resistant prostate cancer. PMID:34381019
Comparative transcriptome analyses reveal genes associated with SARS-CoV-2 infection of human lung epithelial cells. PMID:34376762
Blood Circulating miRNA Pairs as a Robust Signature for Early Detection of Esophageal Cancer. PMID:34368003
Gene Expression Meta-Analysis Reveals Interferon-Induced Genes Associated With SARS Infection in Lungs. PMID:34367154
Molecular Characterization and Elucidation of Pathways to Identify Novel Therapeutic Targets in Pulmonary Arterial Hypertension. PMID:34366885
Male Infertility Knowledgebase: decoding the genetic and disease landscape. PMID:34363073
Endogenous and Therapeutic Estrogens: Maestro Conductors of the Microenvironment of ER+ Breast Cancers. PMID:34359625
In silico drug repurposing in COVID-19: A network-based analysis. PMID:34358753
Extracellular Matrix-Related Hubs Genes Have Adverse Effects on Gastric Adenocarcinoma Prognosis Based on Bioinformatics Analysis. PMID:34356118
An Immune-Related Gene-Based Signature as Prognostic Tool in Ovarian Serous Cystadenocarcinoma. PMID:34354370
Transcriptional landscape of cellular networks reveal interactions driving the dormancy mechanisms in cancer. PMID:34349126
TRAIP modulates the IGFBP3/AKT pathway to enhance the invasion and proliferation of osteosarcoma by promoting KANK1 degradation. PMID:34349117
Ubiquitination-Related miRNA-mRNA Interaction Is a Potential Mechanism in the Progression of Retinoblastoma. PMID:34347012
CanImmunother: a manually curated database for identification of cancer immunotherapies associating with biomarkers, targets, and clinical effects. PMID:34345532
Identification of Multiple Hub Genes and Pathways in Hepatocellular Carcinoma: A Bioinformatics Analysis. PMID:34337056
A Potential circRNA-miRNA-mRNA Regulatory Network in Asthmatic Airway Epithelial Cells Identified by Integrated Analysis of Microarray Datasets. PMID:34336929
Integrative Functional Genomic Analysis of Molecular Signatures and Mechanistic Pathways in the Cell Cycle Underlying Alzheimer's Disease. PMID:34336099
NPM1 Is a Prognostic Biomarker Involved in Immune Infiltration of Lung Adenocarcinoma and Associated With m6A Modification and Glycolysis. PMID:34335635
Follistatin-Like 3 Correlates With Lymph Node Metastasis and Serves as a Biomarker of Extracellular Matrix Remodeling in Colorectal Cancer. PMID:34335633
Aurora kinase A (AURKA) promotes the progression and imatinib resistance of advanced gastrointestinal stromal tumors. PMID:34332577
Identification of serum prognostic marker miRNAs and construction of microRNA-mRNA networks of esophageal cancer. PMID:34329340
Prognoses and genomic analyses of proteasome 26S subunit, ATPase (PSMC) family genes in clinical breast cancer. PMID:34329194
AnnoMiner is a new web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators. PMID:34326396
RNA sequencing identifies global transcriptional changes in peripheral CD4+ cells during active oesophagitis and following epicutaneous immunotherapy in eosinophilic oesophagitis. PMID:34322233
Genome wide analysis implicates upregulation of proteasome pathway in major depressive disorder. PMID:34321460
Reboot: a straightforward approach to identify genes and splicing isoforms associated with cancer patient prognosis. PMID:34316711
Extracellular NLRP3 inflammasome particles are internalized by human coronary artery smooth muscle cells and induce pro-atherogenic effects. PMID:34312415
Small Proteins; Big Questions. PMID:34309401
DNA methylation analysis improves the prognostication of acute myeloid leukemia. PMID:34308417
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
Examining the Effector Mechanisms of the Feishu Acupoint (BL13) in the Treatment of Pneumonia Based on Systematic Acupuncture and Moxibustion Research. PMID:34306143
MegaLMM: Mega-scale linear mixed models for genomic predictions with thousands of traits. PMID:34301310
Insights into the molecular mechanisms of Huangqi decoction on liver fibrosis via computational systems pharmacology approaches. PMID:34301291
Identification of Novel RNA Binding Proteins Influencing Circular RNA Expression in Hepatocellular Carcinoma. PMID:34299096
Web tools to perform long non-coding RNAs analysis in oncology research. PMID:34296748
Screening of hub genes and evaluation of the growth regulatory role of CD44 in metastatic prostate cancer. PMID:34296309
Circular RNA TADA2A promotes proliferation and migration via modulating of miR‑638/KIAA0101 signal in non‑small cell lung cancer. PMID:34296306
Characterizing the Metabolic and Immune Landscape of Non-small Cell Lung Cancer Reveals Prognostic Biomarkers Through Omics Data Integration. PMID:34295900
Integrative bioinformatics approaches to map key biological markers and therapeutic drugs in Extramammary Paget's disease of the scrotum. PMID:34292991
Identification of autosomal recessive nonsyndromic hearing impairment genes through the study of consanguineous and non-consanguineous families: past, present, and future. PMID:34291353
An integrative study of genetic variants with brain tissue expression identifies viral etiology and potential drug targets of multiple sclerosis. PMID:34284104
Meta-Analysis of Microdissected Breast Tumors Reveals Genes Regulated in the Stroma but Hidden in Bulk Analysis. PMID:34282769
Deleterious Effects of SARS-CoV-2 Infection on Human Pancreatic Cells. PMID:34282405
A hypoxia risk signature for the tumor immune microenvironment evaluation and prognosis prediction in acute myeloid leukemia. PMID:34282207
RAB5C, SYNJ1, and RNF19B promote male ankylosing spondylitis by regulating immune cell infiltration. PMID:34277811
Differential Packaging Into Outer Membrane Vesicles Upon Oxidative Stress Reveals a General Mechanism for Cargo Selectivity. PMID:34276573
The chromatin, topological and regulatory properties of pluripotency-associated poised enhancers are conserved in vivo. PMID:34272393
Expression levels of chemokine (C-X-C motif) ligands CXCL1 and CXCL3 as prognostic biomarkers in rectal adenocarcinoma: evidence from Gene Expression Omnibus (GEO) analyses. PMID:34269159
Identification of Potential Key Genes and Regulatory Markers in Essential Thrombocythemia Through Integrated Bioinformatics Analysis and Clinical Validation. PMID:34267539
A network-biology approach for identification of key genes and pathways involved in malignant peritoneal mesothelioma. PMID:34261301
CD40L modulates transcriptional signatures of neutrophils in the bone marrow associated with development and trafficking. PMID:34255742
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
Neuropilin-2 Is Associated With Increased Hepatoblastoma Cell Viability and Motility. PMID:34239847
The Research on the Treatment of Metastatic Skin Cutaneous Melanoma by Huanglian Jiedu Decoction Based on the Analysis of Immune Infiltration Analysis. PMID:34239596
Integrative analysis of key candidate genes and signaling pathways in acute coronary syndrome related to obstructive sleep apnea by bioinformatics. PMID:34239024
Predicting synchronized gene coexpression patterns from fibration symmetries in gene regulatory networks in bacteria. PMID:34238210
Cell Proliferation and Apoptosis-Related Genes Affect the Development of Human Nasopharyngeal Carcinoma Through PI3K/AKT Signaling Pathway. PMID:34236626
Circulating microRNAs as Potential Diagnostic Biomarkers for Poor Sleep Quality. PMID:34234603
Screening of key biomarkers and immune infiltration in Pulmonary Arterial Hypertension via integrated bioinformatics analysis. PMID:34233597
Identification of potential core genes in esophageal carcinoma using bioinformatics analysis. PMID:34232175
Altered Gene Expression in the Testis of Infertile Patients with Nonobstructive Azoospermia. PMID:34221106
Aberrantly methylated-differentially genes and pathways among Iranian patients with colorectal cancer. PMID:34217303
Rank-in: enabling integrative analysis across microarray and RNA-seq for cancer. PMID:34214174
IRF1 as a potential biomarker in Mycobacterium tuberculosis infection. PMID:34213077
IGFBP2 Is a Potential Master Regulator Driving the Dysregulated Gene Network Responsible for Short Survival in Glioblastoma Multiforme. PMID:34211498
Systems Toxicology Approach for Assessing Developmental Neurotoxicity in Larval Zebrafish. PMID:34211495
High expression of DNA damage-inducible transcript 4 (DDIT4) is associated with advanced pathological features in the patients with colorectal cancer. PMID:34211002
Site-Specific and Common Prostate Cancer Metastasis Genes as Suggested by Meta-Analysis of Gene Expression Data. PMID:34209195
Cleaning the Medicago Microarray Database to Improve Gene Function Analysis. PMID:34207216
Differential Regulation of Gonadotropins as Revealed by Transcriptomes of Distinct LH and FSH Cells of Fish Pituitary. PMID:34204216
Transcription factor RFX7 governs a tumor suppressor network in response to p53 and stress. PMID:34197623
MicroRNAs expression analysis shows key affirmation of Synaptopodin-2 as a novel prognostic and therapeutic biomarker for colorectal and cervical cancers. PMID:34195444
Bioinformatic Analysis Reveals Central Role for Tumor-Infiltrating Immune Cells in Uveal Melanoma Progression. PMID:34195299
miR-320a in serum exosomes promotes myocardial fibroblast proliferation via regulating the PIK3CA/Akt/mTOR signaling pathway in HEH2 cells. PMID:34194551
Comprehensive analysis of DNA methylation and gene expression profiles in gestational diabetes mellitus. PMID:34190178
CircRNA_100290 promotes GC cell proliferation and invasion via the miR-29b-3p/ITGA11 axis and is regulated by EIF4A3. PMID:34182990
Identification ACTA2 and KDR as key proteins for prognosis of PD-1/PD-L1 blockade therapy in melanoma. PMID:34179721
ADHFE1 is a correlative factor of patient survival in cancer. PMID:34179501
The transcriptome of circulating cells indicates potential biomarkers and therapeutic targets in the course of hypertension-related myocardial infarction. PMID:34179317
Reconstruction of Intercellular Signaling Network by Cytokine-Receptor Interactions. PMID:34179188
Cross-Tissue Transcriptomic Analysis Leveraging Machine Learning Approaches Identifies New Biomarkers for Rheumatoid Arthritis. PMID:34177888
Bioinformatics analysis of differentially expressed genes and pathways in the development of cervical cancer. PMID:34174849
Altered expression of SARS-CoV-2 entry and processing genes by Porphyromonas gingivalis-derived lipopolysaccharide, inflammatory cytokines and prostaglandin E2 in human gingival fibroblasts. PMID:34174588
The single-cell epigenomic and transcriptional landscape of immunity to influenza vaccination. PMID:34174187
Reference Module-Based Analysis of Ovarian Cancer Transcriptome Identifies Important Modules and Potential Drugs. PMID:34173117
gEAR: Gene Expression Analysis Resource portal for community-driven, multi-omic data exploration. PMID:34172972
Bioactivity descriptors for uncharacterized chemical compounds. PMID:34168145
Identification of hub genes in thyroid carcinoma to predict prognosis by integrated bioinformatics analysis. PMID:34167437
PHENSIM: Phenotype Simulator. PMID:34166365
Bioinformatics Analysis Identifies Potential Ferroptosis Key Genes in the Pathogenesis of Intracerebral Hemorrhage. PMID:34163322
Identification of Independent and Communal Differentially Expressed Genes as Well as Potential Therapeutic Targets in Ischemic Heart Failure and Non-Ischemic Heart Failure. PMID:34163213
Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research. PMID:34159360
Modulation of the effects of class Ib antiarrhythmics on cardiac NaV1.5-encoded channels by accessory NaVβ subunits. PMID:34156986
A small RNA regulates pprM, a modulator of pleiotropic proteins promoting DNA repair, in Deinococcus radiodurans under ionizing radiation. PMID:34155239
MicroRNA profiles in five pairs of early gastric cancer tissues and adjacent non-cancerous tissues. PMID:34149906
Upregulated LINC00319 aggravates neuronal injury induced by oxygen-glucose deprivation via modulating miR-200a-3p. PMID:34149890
Differential analysis revealing APOC1 to be a diagnostic and prognostic marker for liver metastases of colorectal cancer. PMID:34141744
Effects of arsenic and heavy metals on metabolic pathways in cells of human origin: Similarities and differences. PMID:34141598
Assessing the Contribution of Relative Macrophage Frequencies to Subcutaneous Adipose Tissue. PMID:34136521
Proteomics and Epidemiological Models of Human Aging. PMID:34135771
Specific Interaction of DDX6 with an RNA Hairpin in the 3' UTR of the Dengue Virus Genome Mediates G1 Phase Arrest. PMID:34132569
A bioinformatics approach for identifying potential molecular mechanisms and key genes involved in COVID-19 associated cardiac remodeling. PMID:34131597
Capitalizing on transcriptome profiling to optimize and identify targets for promoting early murine folliculogenesis in vitro. PMID:34131220
ISL1 promoted tumorigenesis and EMT via Aurora kinase A-induced activation of PI3K/AKT signaling pathway in neuroblastoma. PMID:34131100
Network-based transcriptomic analysis identifies the genetic effect of COVID-19 to chronic kidney disease patients: A bioinformatics approach. PMID:34127904
AI-guided discovery of the invariant host response to viral pandemics. PMID:34127431
Altered Genes and Biological Functions in Response to Severe Burns. PMID:34124262
Antibody-recruiting protein-catalyzed capture agents to combat antibiotic-resistant bacteria. PMID:34122810
Transcriptional Start Site Coverage Analysis in Plasma Cell-Free DNA Reveals Disease Severity and Tissue Specificity of COVID-19 Patients. PMID:34122515
Exploring the Pathogenesis of Psoriasis Complicated With Atherosclerosis via Microarray Data Analysis. PMID:34122426
Elevated metallothionein expression in long-lived species mediates the influence of cadmium accumulation on aging. PMID:34117600
Identification of Disease-Specific Hub Biomarkers and Immune Infiltration in Osteoarthritis and Rheumatoid Arthritis Synovial Tissues by Bioinformatics Analysis. PMID:34113405
miR-340 Promotes Retinoblastoma Cell Proliferation, Migration and Invasion Through Targeting WIF1. PMID:34113129
Identification of Ten Mitosis Genes Associated with Tamoxifen Resistance in Breast Cancer. PMID:34113127
Single-cell RNA sequencing of human femoral head in vivo. PMID:34111027
Identification of TYR, TYRP1, DCT and LARP7 as related biomarkers and immune infiltration characteristics of vitiligo via comprehensive strategies. PMID:34107850
Decoding empagliflozin's molecular mechanism of action in heart failure with preserved ejection fraction using artificial intelligence. PMID:34103605
Gene expression changes and DNA damage after ex vivo exposure of peripheral blood cells to various CT photon spectra. PMID:34103547
HOXA13 in etiology and oncogenic potential of Barrett's esophagus. PMID:34099670
Therapeutic Targeting of Repurposed Anticancer Drugs in Alzheimer's Disease: Using the Multiomics Approach. PMID:34095679
Development of a Machine Learning-Based Autophagy-Related lncRNA Signature to Improve Prognosis Prediction in Osteosarcoma Patients. PMID:34095215
Expression Analysis of Long Non-Coding RNAs Related With FOXM1, GATA3, FOXA1 and ESR1 in Breast Tissues. PMID:34094972
Sequence of the supernumerary B chromosome of maize provides insight into its drive mechanism and evolution. PMID:34088847
Integrin α5 promotes migration and invasion through the FAK/STAT3/AKT signaling pathway in icotinib-resistant non-small cell lung cancer cells. PMID:34084223
Identification of potential therapeutic targets for atherosclerosis by analysing the gene signature related to different immune cells and immune regulators in atheromatous plaques. PMID:34082770
Cell Type-Specific Differentiation Between Indica and Japonica Rice Root Tip Responses to Different Environments Based on Single-Cell RNA Sequencing. PMID:34079581
Identification of biomarkers, pathways and potential therapeutic target for docetaxel resistant prostate cancer. PMID:34077304
CovidExpress: an interactive portal for intuitive investigation on SARS-CoV-2 related transcriptomes. PMID:34075382
In-Silico Evaluation of Genetic Alterations in Ovarian Carcinoma and Therapeutic Efficacy of NSC777201, as a Novel Multi-Target Agent for TTK, NEK2, and CDK1. PMID:34072728
Transcription Factor β-Catenin Plays a Key Role in Fluid Flow Shear Stress-Mediated Glomerular Injury in Solitary Kidney. PMID:34069476
Multi-Omic Meta-Analysis of Transcriptomes and the Bibliome Uncovers Novel Hypoxia-Inducible Genes. PMID:34065451
TSCCA: A tensor sparse CCA method for detecting microRNA-gene patterns from multiple cancers. PMID:34061840
MicroRNA-182 improves spinal cord injury in mice by modulating apoptosis and the inflammatory response via IKKβ/NF-κB. PMID:34059758
GLEANER: a web server for GermLine cycle Expression ANalysis and Epigenetic Roadmap visualization. PMID:34058973
Immune characterization and profiles of SARS-CoV-2 infected patients reveals potential host therapeutic targets and SARS-CoV-2 oncogenesis mechanism. PMID:34058265
Modeling the 3D genome of plants. PMID:34057011
Optimal sample size for calibrating DNA methylation age estimators. PMID:34053192
Identification of circRNA-miRNA-mRNA networks contributes to explore underlying pathogenesis and therapy strategy of gastric cancer. PMID:34049561
Gene-Based Tests of a Genome-Wide Association Study Dataset Highlight Novel Multiple Sclerosis Risk Genes. PMID:34045940
High expression of USP18 is associated with the growth of colorectal carcinoma. PMID:34042164
Genome-wide identification of potential biomarkers in multiple myeloma using meta-analysis of mRNA and miRNA expression data. PMID:34040057
CPA: a web-based platform for consensus pathway analysis and interactive visualization. PMID:34037798
Evaluation of RNA quality and functional transcriptome of beef longissimus thoracis over time post-mortem. PMID:34033656
Application of multi-omics data integration and machine learning approaches to identify epigenetic and transcriptomic differences between in vitro and in vivo produced bovine embryos. PMID:34029343
Analysis of multi-omics differences in left-side and right-side colon cancer. PMID:34026368
Network-based analysis of key regulatory genes implicated in Type 2 Diabetes Mellitus and Recurrent Miscarriages in Turner Syndrome. PMID:34021221
Hub biomarkers for the diagnosis and treatment of glioblastoma based on microarray technology. PMID:34018447
Integrated bioinformatic analysis reveals the underlying molecular mechanism of and potential drugs for pulmonary arterial hypertension. PMID:34016786
Bioinformatics analysis and identification of genes and molecular pathways in steroid-induced osteonecrosis of the femoral head. PMID:34016144
CAP2 contributes to tumorigenesis in gastric cancer by targeting transcription factor SOX9. PMID:34012625
Housekeeping genes involved in non-malignant breast phenotypes are widely expressed in multiple cancers and provide novel biomarkers of tumor classification. PMID:34008752
Activated mast cells in skeletal muscle can be a potential mediator for cancer-associated cachexia. PMID:34008339
S100 calcium binding protein A6 and associated long noncoding ribonucleic acids as biomarkers in the diagnosis and staging of primary biliary cholangitis. PMID:34007134
OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions. PMID:33999180
Polycomb Factor PHF19 Controls Cell Growth and Differentiation Toward Erythroid Pathway in Chronic Myeloid Leukemia Cells. PMID:33996816
Identification of Key Functional Gene Signatures Indicative of Dedifferentiation in Papillary Thyroid Cancer. PMID:33996555
Identification of the key target profiles underlying the drugs of narrow therapeutic index for treating cancer and cardiovascular disease. PMID:33995923
Genome-wide analysis of primary microRNA expression using H3K36me3 ChIP-seq data. PMID:33995896
Five-gene signature associating with Gleason score serve as novel biomarkers for identifying early recurring events and contributing to early diagnosis for Prostate Adenocarcinoma. PMID:33995639
Novel Insight Into the Role of Immune Dysregulation in Amyotrophic Lateral Sclerosis Based on Bioinformatic Analysis. PMID:33994932
Identifying the Potential Therapeutic Targets for Atopic Dermatitis Through the Immune Infiltration Analysis and Construction of a ceRNA Network. PMID:33994801
Bioinformatics and system biology approaches to identify the diseasome and comorbidities complexities of SARS-CoV-2 infection with the digestive tract disorders. PMID:33993223
Wavelet Screening identifies regions highly enriched for differentially methylated loci for orofacial clefts. PMID:33987535
Centromere protein N may be a novel malignant prognostic biomarker for hepatocellular carcinoma. PMID:33987018
The endosomal RIN2/Rab5C machinery prevents VEGFR2 degradation to control gene expression and tip cell identity during angiogenesis. PMID:33983539
Application of multiple omics and network projection analyses to drug repositioning for pathogenic mosquito-borne viruses. PMID:33980888
Expression Pattern and Prognostic Value of EPHA/EFNA in Breast Cancer by Bioinformatics Analysis: Revealing Its Importance in Chemotherapy. PMID:33977106
Prediction and analysis of novel key genes ITGAX, LAPTM5, SERPINE1 in clear cell renal cell carcinoma through bioinformatics analysis. PMID:33976979
The Relationship Between Menopause and Metabolic Syndrome: Experimental and Bioinformatics Analysis. PMID:33973091
Identification of potential autophagy-associated lncRNA in prostate cancer. PMID:33971627
A novel genomic model for predicting the likelihood of delayed graft function in DCD kidney transplantation. PMID:33968652
Prognostic value of members of NFAT family for pan-cancer and a prediction model based on NFAT2 in bladder cancer. PMID:33962392
Fructose-1,6-bisphosphatase aggravates oxidative stress-induced apoptosis in asthma by suppressing the Nrf2 pathway. PMID:33960626
The peripheral and core regions of virus-host network of COVID-19. PMID:33956950
Bioinformatics analysis of laryngeal squamous cell carcinoma: seeking key candidate genes and pathways. PMID:33954053
iPSC-endothelial cell phenotypic drug screening and in silico analyses identify tyrphostin-AG1296 for pulmonary arterial hypertension. PMID:33952674
ZFP90 drives the initiation of colitis-associated colorectal cancer via a microbiota-dependent strategy. PMID:33947304
Bioinformatic analysis and validation of microRNA-508-3p as a protective predictor by targeting NR4A3/MEK axis in pulmonary arterial hypertension. PMID:33942991
Identification of CDC20 as an immune infiltration-correlated prognostic biomarker in hepatocellular carcinoma. PMID:33942202
Genetic network and gene set enrichment analyses identify MND1 as potential diagnostic and therapeutic target gene for lung adenocarcinoma. PMID:33941804
Protein structure-based gene expression signatures. PMID:33941686
Strategies for detecting and identifying biological signals amidst the variation commonly found in RNA sequencing data. PMID:33941086
Human methylome variation across Infinium 450K data on the Gene Expression Omnibus. PMID:33937763
A Bioinformatic Analysis of Correlations between Polymeric Immunoglobulin Receptor (PIGR) and Liver Fibrosis Progression. PMID:33937393
Identifying and Validating Potential Biomarkers of Early Stage Lung Adenocarcinoma Diagnosis and Prognosis. PMID:33937050
Opportunities and Challenges in Democratizing Immunology Datasets. PMID:33936065
Integrated analysis and identification of nine-gene signature associated to oral squamous cell carcinoma pathogenesis. PMID:33928003
A Panel of Five-lncRNA Signature as a Potential Biomarker for Predicting Survival in Gastric and Thoracic Cancers. PMID:33927753
Comprehensive Analysis of Prognostic and Genetic Signatures for General Transcription Factor III (GTF3) in Clinical Colorectal Cancer Patients Using Bioinformatics Approaches. PMID:33925358
Hypoxia Transcriptomic Modifications Induced by Proton Irradiation in U87 Glioblastoma Multiforme Cell Line. PMID:33923454
Analysis of LAGEs Family Gene Signature and Prognostic Relevance in Breast Cancer. PMID:33921749
Fish-Ing for Enhancers in the Heart. PMID:33920121
The prognostic value of an autophagy-related lncRNA signature in hepatocellular carcinoma. PMID:33910497
Analysis workflow of publicly available RNA-sequencing datasets. PMID:33907739
Integrative analysis of the gastric cancer long non-coding RNA-associated competing endogenous RNA network. PMID:33907566
Targeting the tumor stroma: integrative analysis reveal GATA2 and TORYAIP1 as novel prognostic targets in breast and ovarian cancer. PMID:33907495
Ulcerative colitis immune cell landscapes and differentially expressed gene signatures determine novel regulators and predict clinical response to biologic therapy. PMID:33907256
M6ADD: a comprehensive database of m6A modifications in diseases. PMID:33906563
Identification of hub genes associated with obesity-induced hepatocellular carcinoma risk based on integrated bioinformatics analysis. PMID:33900477
Investigating Molecular Determinants of Cancer Cell Resistance to Ionizing Radiation Through an Integrative Bioinformatics Approach. PMID:33898418
Identification of Metastasis-Associated MicroRNAs in Metastatic Melanoma by miRNA Expression Profile and Experimental Validation. PMID:33897771
Application of systems biology-based in silico tools to optimize treatment strategy identification in Still's disease. PMID:33892792
Finding associations in a heterogeneous setting: statistical test for aberration enrichment. PMID:33892787
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
Inferring molecular mechanisms of dexamethasone therapy in severe COVID-19 from existing transcriptomic data. PMID:33887367
T cell self-reactivity during thymic development dictates the timing of positive selection. PMID:33884954
SCD leads to the development and progression of acute myocardial infarction through the AMPK signaling pathway. PMID:33879068
Gene fusion of IL7 involved in the regulation of idiopathic pulmonary fibrosis. PMID:33878985
Modeling transcriptional regulation using gene regulatory networks based on multi-omics data sources. PMID:33874910
Bioinformatic analysis identifies potential biomarkers and therapeutic targets of septic-shock-associated acute kidney injury. PMID:33863396
Biomarkers mining for spinal cord injury based on integrated multi-transcriptome expression profile data. PMID:33863336
Malignant pleural mesothelioma co-opts BCL-XL and autophagy to escape apoptosis. PMID:33859162
Bioinformatics analysis of lncRNA‑associated ceRNA network in melanoma. PMID:33854593
Integrated transcription factor profiling with transcriptome analysis identifies L1PA2 transposons as global regulatory modulators in a breast cancer model. PMID:33850167
Identification and analysis of key genes associated with acute myocardial infarction by integrated bioinformatics methods. PMID:33847684
Bioinformatics and system biology approach to identify the influences of SARS-CoV-2 infections to idiopathic pulmonary fibrosis and chronic obstructive pulmonary disease patients. PMID:33847347
Phgdh serves a protective role in Il‑1β induced chondrocyte inflammation and oxidative‑stress damage. PMID:33846783
Discovering key transcriptomic regulators in pancreatic ductal adenocarcinoma using Dirichlet process Gaussian mixture model. PMID:33846515
Nutrigenomics reveals potential genetic underpinning of diverse taste preference of Chinese men. PMID:33843022
Potential targets identified in adenoid cystic carcinoma point out new directions for further research. PMID:33841642
Functional annotation of lung cancer‒associated genetic variants by cell type‒specific epigenome and long-range chromatin interactome. PMID:33840167
Bioinformatics and machine learning approach identifies potential drug targets and pathways in COVID-19. PMID:33839760
Blind normalization of public high-throughput databases. PMID:33816884
Screening of Hub Genes Associated with Pulmonary Arterial Hypertension by Integrated Bioinformatic Analysis. PMID:33816621
Differences in Tumor Immune Microenvironment in Metastatic Sites of Breast Cancer. PMID:33816302
An Integrated Data Analysis of mRNA, miRNA and Signaling Pathways in Pancreatic Cancer. PMID:33813720
Signaling Pathways Regulated by Silica Nanoparticles. PMID:33807638
Silencing of Sphingosine kinase 1 Affects Maturation Pathways in Mouse Neonatal Cardiomyocytes. PMID:33807180
Acyl-Acyl Carrier Protein Desaturases and Plant Biotic Interactions. PMID:33803674
Analysis of MCM Proteins' Role as a Potential Target of Statins in Patients with Acute Type A Aortic Dissection through Bioinformatics. PMID:33803192
Does Saccharomyces cerevisiae Require Specific Post-Translational Silencing against Leaky Translation of Hac1up? PMID:33802931
MicroRNAs: Potential Targets for Developing Stress-Tolerant Crops. PMID:33800690
On the Consistency between Gene Expression and the Gene Regulatory Network of Corynebacterium glutamicum. PMID:33796877
Immune Interaction Map of Human SARS-CoV-2 Target Genes: Implications for Therapeutic Avenues. PMID:33796097
UHRF1 Induces Methylation of the TXNIP Promoter and Down-Regulates Gene Expression in Cervical Cancer. PMID:33795533
Effector and regulator: Diverse functions of C. elegans C-type lectin-like domain proteins. PMID:33793670
The SARS-CoV-2 receptor angiotensin-converting enzyme 2 (ACE2) in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: analysis of high-throughput epigenetic and gene expression studies. PMID:33791744
Transcriptional networks in at-risk individuals identify signatures of type 1 diabetes progression. PMID:33790023
Consensus Transcriptional Landscape of Human End-Stage Heart Failure. PMID:33787284
HIV-1 integration sites in CD4+ T cells during primary, chronic, and late presentation of HIV-1 infection. PMID:33784259
Screening of osteoarthritis diagnostic markers based on immune-related genes and immune infiltration. PMID:33782454
CTD Anatomy: analyzing chemical-induced phenotypes and exposures from an anatomical perspective, with implications for environmental health studies. PMID:33768211
A lineage-specific requirement for YY1 Polycomb Group protein function in early T cell development. PMID:33766932
Hepatic steatosis and steatohepatitis: a functional meta-analysis of sex-based differences in transcriptomic studies. PMID:33766130
Re-routing of Sugar Catabolism Provides a Better Insight Into Fungal Flexibility in Using Plant Biomass-Derived Monomers as Substrates. PMID:33763411
Leveraging Single-Cell RNA-seq Data to Uncover the Association Between Cell Type and Chronic Liver Diseases. PMID:33763117
Transcriptome-based approaches for clarification of nutritional responses and improvement of crop production. PMID:33762878
Colon epithelial cell TGFβ signaling modulates the expression of tight junction proteins and barrier function in mice. PMID:33759564
GAUGE-Annotated Microbial Transcriptomic Data Facilitate Parallel Mining and High-Throughput Reanalysis To Form Data-Driven Hypotheses. PMID:33758032
Transcriptomic analysis of the trade-off between endurance and burst-performance in the frog Xenopus allofraseri. PMID:33757428
GPRC5A: An emerging prognostic biomarker for predicting malignancy of Pancreatic Cancer based on bioinformatics analysis. PMID:33753999
Blockade of IL-22 signaling reverses erythroid dysfunction in stress-induced anemias. PMID:33753942
Construction of Decision Trees Based on Gene Expression Omnibus Data to Classify Bladder Cancer and Its Subtypes. PMID:33753712
Applications of genetic-epigenetic tissue mapping for plasma DNA in prenatal testing, transplantation and oncology. PMID:33752803
Non-coding RNA Identification in Osteonecrosis of the Femoral Head Using Competitive Endogenous RNA Network Analysis. PMID:33749138
High Expression of CLEC11A Predicts Favorable Prognosis in Acute Myeloid Leukemia. PMID:33747924
Identification of potential oncogenes in triple-negative breast cancer based on bioinformatics analyses. PMID:33747220
Identification of MEG8/miR-378d/SOBP axis as a novel regulatory network and associated with immune infiltrates in ovarian carcinoma by integrated bioinformatics analysis. PMID:33742531
Identification of molecular biomarkers and pathways of NSCLC: insights from a systems biomedicine perspective. PMID:33742334
Epidemiological transcriptomic data supports BCG protection in viral diseases including COVID-19. PMID:33737124
Screening and verification of hub genes involved in osteoarthritis using bioinformatics. PMID:33732303
Identification of m6A-Associated RNA Binding Proteins Using an Integrative Computational Framework. PMID:33732286
Identification of key genes in hepatitis B associated hepatocellular carcinoma based on WGCNA. PMID:33726794
Multi-omics approaches for revealing the complexity of cardiovascular disease. PMID:33725119
A unified framework for inferring the multi-scale organization of chromatin domains from Hi-C. PMID:33724986
Correcting signal biases and detecting regulatory elements in STARR-seq data. PMID:33722938
Multi-omics approach reveals the contribution of KLU to leaf longevity and drought tolerance. PMID:33721894
Integrated Protein-Protein Interaction and Weighted Gene Co-expression Network Analysis Uncover Three Key Genes in Hepatoblastoma. PMID:33718368
Single-Cell RNA Sequencing and Quantitative Proteomics Analysis Elucidate Marker Genes and Molecular Mechanisms in Hypoplastic Left Heart Patients With Heart Failure. PMID:33718359
Hypocrisy Around Medical Patient Data: Issues of Access for Biomedical Research, Data Quality, Usefulness for the Purpose and Omics Data as Game Changer. PMID:33717311
Loss-of-function mutations in the histone methyltransferase EZH2 promote chemotherapy resistance in AML. PMID:33712646
Global discovery of lupus genetic risk variant allelic enhancer activity. PMID:33712590
Identification of four key prognostic genes and three potential drugs in human papillomavirus negative head and neck squamous cell carcinoma. PMID:33712015
Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the Future. PMID:33711481
Genetic controls of Tas1r3-independent sucrose consumption in mice. PMID:33710367
Establishment of Novel DNA Methylation-Based Prostate Cancer Subtypes and a Risk-Predicting Eight-Gene Signature. PMID:33708770
Explaining decisions of graph convolutional neural networks: patient-specific molecular subnetworks responsible for metastasis prediction in breast cancer. PMID:33706810
Comprehensive analysis of autophagy-related genes and patterns of immune cell infiltration in valvular atrial fibrillation. PMID:33706714
Identification and Validation of Key Genes in Hepatocellular Carcinoma by Bioinformatics Analysis. PMID:33688500
Using Gene Expression Music Algorithms (GEMusicA) for the Characterization of Human Stem Cells. PMID:33687681
A Molecular Interaction Map of Klebsiella pneumoniae and Its Human Host Reveals Potential Mechanisms of Host Cell Subversion. PMID:33679637
HIR V2: a human interactome resource for the biological interpretation of differentially expressed genes via gene set linkage analysis. PMID:33677507
Improving gene function predictions using independent transcriptional components. PMID:33674610
Calcium-Regulated Protein CarP Responds to Multiple Host Signals and Mediates Regulation of Pseudomonas aeruginosa Virulence by Calcium. PMID:33674436
seqQscorer: automated quality control of next-generation sequencing data using machine learning. PMID:33673854
Insulin-Like Growth Factor 2 As a Possible Neuroprotective Agent and Memory Enhancer-Its Comparative Expression, Processing and Signaling in Mammalian CNS. PMID:33673334
Gene Regulatory Network of ETS Domain Transcription Factors in Different Stages of Glioma. PMID:33671331
Meta-Analysis of Oxidative Transcriptomes in Insects. PMID:33669076
Identification of theranostic factors for patients developing metastasis after surgery for early-stage lung adenocarcinoma. PMID:33664854
Inhibiting β-catenin disables nucleolar functions in triple-negative breast cancer. PMID:33664239
DeltaNeTS+: elucidating the mechanism of drugs and diseases using gene expression and transcriptional regulatory networks. PMID:33663384
Cancer-Associated Fibroblasts Positively Correlate with Dedifferentiation and Aggressiveness of Thyroid Cancer. PMID:33654411
Structural variant detection in cancer genomes: computational challenges and perspectives for precision oncology. PMID:33654267
Computational screening of potential glioma-related genes and drugs based on analysis of GEO dataset and text mining. PMID:33635875
Knockdown of RIPK2 Inhibits Proliferation and Migration, and Induces Apoptosis via the NF-κB Signaling Pathway in Gastric Cancer. PMID:33633788
Immune Profiling of Parkinson's Disease Revealed Its Association With a Subset of Infiltrating Cells and Signature Genes. PMID:33633562
Identification BCL6 and miR-30 family associating with Ibrutinib resistance in activated B-cell-like diffuse large B-cell lymphoma. PMID:33629212
Determining novel candidate anti-hepatocellular carcinoma drugs using interaction networks and molecular docking between drug targets and natural compounds of SiNiSan. PMID:33628636
Integrative analysis of liver-specific non-coding regulatory SNPs associated with the risk of coronary artery disease. PMID:33626337
Identification and Characterisation of Putative Enhancer Elements in Mouse Embryonic Stem Cells. PMID:33623376
Immune characterization and profiles of SARS-CoV-2 infected patients reveals potential host therapeutic targets and SARS-CoV-2 oncogenesis mechanism. PMID:33619493
High-throughput screening and validation of antibodies against synaptic proteins to explore opioid signaling dynamics. PMID:33619305
Concomitant gain and loss of function pathomechanisms in C9ORF72 amyotrophic lateral sclerosis. PMID:33619157
Inferring perturbation profiles of cancer samples. PMID:33617647
High expression of tumor susceptibility gene 101 (TSG101) is associated with more aggressive behavior in colorectal carcinoma. PMID:33616717
Comprehensive Analysis of the Immune Infiltrates and Aberrant Pathways Activation in Atherosclerotic Plaque. PMID:33614738
Prognostic implications of cell division cycle protein 45 expression in hepatocellular carcinoma. PMID:33614286
A risk score model with five long non-coding RNAs for predicting prognosis in gastric cancer: an integrated analysis combining TCGA and GEO datasets. PMID:33614260
Identification of Hub Genes and Immune Infiltration in Psoriasis by Bioinformatics Method. PMID:33613635
Roux-en-Y Gastric Bypass Downregulates Angiotensin-Converting Enzyme 2 (ACE2) Gene Expression in Subcutaneous White Adipose Tissue: A Putative Protective Mechanism Against Severe COVID-19. PMID:33611766
Accurate feature selection improves single-cell RNA-seq cell clustering. PMID:33611426
Ageing transcriptome meta-analysis reveals similarities and differences between key mammalian tissues. PMID:33611312
Processing and Analysis of RNA-seq Data from Public Resources. PMID:33606253
Curation of over 10 000 transcriptomic studies to enable data reuse. PMID:33599246
PATZ1 (MAZR) Co-occupies Genomic Sites With p53 and Inhibits Liver Cancer Cell Proliferation via Regulating p27. PMID:33598459
CDK6 Is a Potential Prognostic Biomarker in Acute Myeloid Leukemia. PMID:33597968
Cross-species examination of X-chromosome inactivation highlights domains of escape from silencing. PMID:33597016
Study on cocoonase, sericin, and degumming of silk cocoon: computational and experimental. PMID:33594479
Role of opiorphin genes in prostate cancer growth and progression. PMID:33593085
Dimensionality reduction using singular vectors. PMID:33589703
Creation of a gene expression portrait of depression and its application for identifying potential treatments. PMID:33589676
SARS-CoV-2 Proteins Exploit Host's Genetic and Epigenetic Mediators for the Annexation of Key Host Signaling Pathways. PMID:33585554
Microbial Metabolic Genes Crucial for S. aureus Biofilms: An Insight From Re-analysis of Publicly Available Microarray Datasets. PMID:33584569
Tissue-specific transcriptome profiling of the Arabidopsis inflorescence stem reveals local cellular signatures. PMID:33582756
Identification of key biomarkers and functional pathways in osteosarcomas with lung metastasis: Evidence from bioinformatics analysis. PMID:33578541
Hopeful monsters: unintended sequencing of famously malformed mite mitochondrial tRNAs reveals widespread expression and processing of sense-antisense pairs. PMID:33575653
Computational deconvolution to estimate cell type-specific gene expression from bulk data. PMID:33575652
Covering all your bases: incorporating intron signal from RNA-seq data. PMID:33575621
Systematic Construction and Validation of an RNA-Binding Protein-Associated Model for Prognosis Prediction in Hepatocellular Carcinoma. PMID:33575212
Key genes in youth colorectal cancer based on data mining and verification by reverse transcription-quantitative PCR. PMID:33574933
Hsa_circ_0043278 Inhibits Tumorigenesis and is Downregulated in Colorectal Cancer. PMID:33568942
Detecting differentially methylated regions using a fast wavelet-based approach to functional association analysis. PMID:33568045
Transcriptomic Analyses Reveal Gene Expression Profiles and Networks in Nasopharyngeal Carcinoma. PMID:33564686
Combined identification of ARID1A, CSMD1, and SENP3 as effective prognostic biomarkers for hepatocellular carcinoma. PMID:33558447
Gastric Bypass Increases Circulating Bile Acids and Activates Hepatic Farnesoid X Receptor (FXR) but Requires Intact Peroxisome Proliferator Activator Receptor Alpha (PPARα) Signaling to Significantly Reduce Liver Fat Content. PMID:33555523
P4HA1 regulates human colorectal cancer cells through HIF1α-mediated Wnt signaling. PMID:33552264
A Meta-Analysis of the Effects of High-LET Ionizing Radiations in Human Gene Expression. PMID:33546472
A Novel mRNA-miRNA Regulatory Sub-Network Associated With Prognosis of Metastatic Clear Cell Renal Cell Carcinoma. PMID:33542901
Inducing Apoptosis and Suppressing Inflammatory Reactions in Synovial Fibroblasts are Two Important Ways for Guizhi-Shaoyao-Zhimu Decoction Against Rheumatoid Arthritis. PMID:33542641
Clinical and Biological Subtypes of B-cell Lymphoma Revealed by Microenvironmental Signatures. PMID:33541860
PhasiRNAnalyzer: an integrated analyser for plant phased siRNAs. PMID:33541212
Metabolic Versatility of Mycobacterium tuberculosis during Infection and Dormancy. PMID:33540752
GEOlimma: differential expression analysis and feature selection using pre-existing microarray data. PMID:33535967
ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways. PMID:33534793
Myeloid-derived suppressor cell (MDSC) key genes analysis in rat anti-CD28-induced immune tolerance kidney transplantation. PMID:33532310
P2X7 Receptor Induces Pyroptotic Inflammation and Cartilage Degradation in Osteoarthritis via NF-κB/NLRP3 Crosstalk. PMID:33532039
Independent component analysis recovers consistent regulatory signals from disparate datasets. PMID:33529205
Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 infection induces dysregulation of immunity: in silico gene expression analysis. PMID:33526974
Human pathways in animal models: possibilities and limitations. PMID:33524155
High expression of MAPK-14 promoting the death of chondrocytes is an important signal of osteoarthritis process. PMID:33520453
A Qualitative Transcriptional Signature for the Risk Assessment of Precancerous Colorectal Lesions. PMID:33519891
High Throughput Sequencing of MicroRNA in Rainbow Trout Plasma, Mucus, and Surrounding Water Following Acute Stress. PMID:33519501
Polycythemia Vera and Essential Thrombocythemia Patients Exhibit Unique Serum Metabolic Profiles Compared to Healthy Individuals and Secondary Thrombocytosis Patients. PMID:33513807
Unveiling the dimer/monomer propensities of Smad MH1-DNA complexes. PMID:33510867
Construction of a TF-miRNA-gene feed-forward loop network predicts biomarkers and potential drugs for myasthenia gravis. PMID:33510225
MethCORR infers gene expression from DNA methylation and allows molecular analysis of ten common cancer types using fresh-frozen and formalin-fixed paraffin-embedded tumor samples. PMID:33509261
Identification of drug combinations on the basis of machine learning to maximize anti-aging effects. PMID:33507975
Cryptotanshinone Is a Intervention for ER-Positive Breast Cancer: An Integrated Approach to the Study of Natural Product Intervention Mechanisms. PMID:33505309
Endophilin A2 deficiency protects rodents from autoimmune arthritis by modulating T cell activation. PMID:33504785
Transcriptomic markers in pediatric septic shock prognosis: an integrative analysis of gene expression profiles. PMID:33503200
MYBPC2 and MYL1 as Significant Gene Markers for Rhabdomyosarcoma. PMID:33499774
Pathway Tools Visualization of Organism-Scale Metabolic Networks. PMID:33499002
Genomic Adaption and Mutational Patterns in a HaCaT Subline Resistant to Alkylating Agents and Ionizing Radiation. PMID:33498964
IPPC: an interactive platform for prostate cancer multi-omics data integration and analysis. PMID:33493265
Molecular Diversity of Clinically Stable Human Kidney Allografts. PMID:33492376
The Identification and Verification of Key Long Noncoding RNAs in Ischemic Stroke. PMID:33490236
RUNX1/RUNX1T1 mediates alternative splicing and reorganises the transcriptional landscape in leukemia. PMID:33483506
Integrative computational approach identifies drug targets in CD4+ T-cell-mediated immune disorders. PMID:33483502
Identification of Potential Risk Genes and the Immune Landscape of Idiopathic Pulmonary Arterial Hypertension via Microarray Gene Expression Dataset Reanalysis. PMID:33478117
Identification of potential biomarkers of peripheral blood mononuclear cell in hepatocellular carcinoma using bioinformatic analysis: A protocol for systematic review and meta-analysis. PMID:33466191
Bioinformatics and system biology approach to identify the influences of COVID-19 on cardiovascular and hypertensive comorbidities. PMID:33458761
C3, C3AR1, HLA-DRA, and HLA-E as potential prognostic biomarkers for renal clear cell carcinoma. PMID:33457236
HEMGN and SLC2A1 might be potential diagnostic biomarkers of steroid-induced osteonecrosis of femoral head: study based on WGCNA and DEGs screening. PMID:33451334
AlzGPS: a genome-wide positioning systems platform to catalyze multi-omics for Alzheimer's drug discovery. PMID:33441136
Identification of the tubulointerstitial infiltrating immune cell landscape and immune marker related molecular patterns in lupus nephritis using bioinformatics analysis. PMID:33437795
Identification of circ-FAM169A sponges miR-583 involved in the regulation of intervertebral disc degeneration. PMID:33437631
MiR-26a-5p as a Reference to Normalize MicroRNA qRT-PCR Levels in Plasma Exosomes of Pediatric Hematological Malignancies. PMID:33429910
TMEM158 May Serve as a Diagnostic Biomarker for Anaplastic Thyroid Carcinoma: An Integrated Bioinformatic Analysis. PMID:33428142
Biofilm-specific uptake of a 4-pyridone-based iron chelator by Pseudomonas aeruginosa. PMID:33428087
Gender Differences in Rheumatoid Arthritis: Interleukin-4 Plays an Important Role. PMID:33426089
Upregulation of RAC3 in bladder cancer predicts adverse clinical outcome and increased tumor immune response. PMID:33425095
Comparative Expression Analysis of Stress-Inducible Candidate Genes in Response to Cold and Drought in Tea Plant [Camellia sinensis (L.) Kuntze]. PMID:33424935
Identify Molecular Mechanisms of Jiangzhi Decoction on Nonalcoholic Fatty Liver Disease by Network Pharmacology Analysis and Experimental Validation. PMID:33415161
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
Shotgun proteomics of peach fruit reveals major metabolic pathways associated to ripening. PMID:33413072
METTL3/YTHDF2 m6A axis accelerates colorectal carcinogenesis through epigenetically suppressing YPEL5. PMID:33411363
Identification and Validation of Two Lung Adenocarcinoma-Development Characteristic Gene Sets for Diagnosing Lung Adenocarcinoma and Predicting Prognosis. PMID:33408736
Diagnostic and prognostic value of FOXD1 expression in head and neck squamous cell carcinoma. PMID:33403027
Disome-seq reveals widespread ribosome collisions that promote cotranslational protein folding. PMID:33402206
Comprehensive upstream and downstream regulatory analyses identify miR-675-3p as a potential prognostic biomarker in melanoma. PMID:33400243
Identification of KIF4A and its effect on the progression of lung adenocarcinoma based on the bioinformatics analysis. PMID:33398330
Identification of differentially expressed genes, signaling pathways and immune infiltration in rheumatoid arthritis by integrated bioinformatics analysis. PMID:33397492
Pan-Cancer Molecular Patterns and Biological Implications Associated with a Tumor-Specific Molecular Signature. PMID:33396205
Identification of key genes involved in post-traumatic stress disorder: Evidence from bioinformatics analysis. PMID:33392005
Upregulation of peroxisome proliferator-activated receptor-α and the lipid metabolism pathway promotes carcinogenesis of ampullary cancer. PMID:33390794
HeartBioPortal2.0: new developments and updates for genetic ancestry and cardiometabolic quantitative traits in diverse human populations. PMID:33382884
Second-hand smoke and NFE2L2 genotype interaction increases paediatric asthma risk and severity. PMID:33382170
Identification of Core Prognosis-Related Candidate Genes in Chinese Gastric Cancer Population Based on Integrated Bioinformatics. PMID:33381592
Understanding the unimodal distributions of cancer occurrence rates: it takes two factors for a cancer to occur. PMID:33377150
Novel therapeutic compounds for prostate adenocarcinoma treatment: An analysis using bioinformatic approaches and the CMap database. PMID:33371142
Neuron type-specific increase in lamin B1 contributes to nuclear dysfunction in Huntington's disease. PMID:33369245
Interaction network of immune-associated genes affecting the prognosis of patients with glioblastoma. PMID:33365061
An Educational Bioinformatics Project to Improve Genome Annotation. PMID:33365016
Analysis of Pan-omics Data in Human Interactome Network (APODHIN). PMID:33363571
State of the Field in Multi-Omics Research: From Computational Needs to Data Mining and Sharing. PMID:33362867
Acyl-CoA Thioesterase 8 and 11 as Novel Biomarkers for Clear Cell Renal Cell Carcinoma. PMID:33362855
Identification and Complete Validation of Prognostic Gene Signatures for Human Papillomavirus-Associated Cancers: Integrated Approach Covering Different Anatomical Locations. PMID:33361419
Impact of Sequencing Depth and Library Preparation on Toxicological Interpretation of RNA-Seq Data in a "Three-Sample" Scenario. PMID:33354967
Evidence of TCM Theory in Treating the Same Disease with Different Methods: Treatment of Pneumonia with Ephedra sinica and Scutellariae Radix as an Example. PMID:33354223
MS4A1 expression and function in T cells in the colorectal cancer tumor microenvironment. PMID:33352466
The epigenetic regulator Mll1 is required for Wnt-driven intestinal tumorigenesis and cancer stemness. PMID:33349639
FAM83A as a Potential Biological Marker Is Regulated by miR-206 to Promote Cervical Cancer Progression Through PI3K/AKT/mTOR Pathway. PMID:33344485
Identify and Validate the Transcriptomic, Functional Network, and Predictive Validity of FBXL19-AS1 in Hepatocellular Carcinoma. PMID:33344260
Identification of significant genes signatures and prognostic biomarkers in cervical squamous carcinoma via bioinformatic data. PMID:33344075
The lncRNA Toolkit: Databases and In Silico Tools for lncRNA Analysis. PMID:33339309
Neural Networks Recapitulation by Cancer Cells Promotes Disease Progression: A Novel Role of p73 Isoforms in Cancer-Neuronal Crosstalk. PMID:33339112
MuscleAtlasExplorer: a web service for studying gene expression in human skeletal muscle. PMID:33338203
Coupling of autism genes to tissue-wide expression and dysfunction of synapse, calcium signalling and transcriptional regulation. PMID:33338084
GABRD promotes progression and predicts poor prognosis in colorectal cancer. PMID:33336074
A Neutrophil-Driven Inflammatory Signature Characterizes the Blood Transcriptome Fingerprint of Psoriasis. PMID:33329570
Cyano Enone-Bearing Triterpenoid Soloxolone Methyl Inhibits Epithelial-Mesenchymal Transition of Human Lung Adenocarcinoma Cells In Vitro and Metastasis of Murine Melanoma In Vivo. PMID:33327637
AnnoLnc: A One-Stop Portal to Systematically Annotate Novel Human Long Noncoding RNAs. PMID:33326073
Integrated Multichip Analysis Identifies Potential Key Genes in the Pathogenesis of Nonalcoholic Steatohepatitis. PMID:33324350
Characteristics of immune cell infiltration and associated diagnostic biomarkers in ulcerative colitis: results from bioinformatics analysis. PMID:33323040
CDKN2A-Inactivated Pancreatic Ductal Adenocarcinoma Exhibits Therapeutic Sensitivity to Paclitaxel: A Bioinformatics Study. PMID:33322698
The Association between the Usage of Non-Steroidal Anti-Inflammatory Drugs and Cognitive Status: Analysis of Longitudinal and Cross-Sectional Studies from the Global Alzheimer's Association Interactive Network and Transcriptomic Data. PMID:33321871
Identification of the hub genes RUNX2 and FN1 in gastric cancer. PMID:33313404
Identification and prognostic value of DLGAP5 in endometrial cancer. PMID:33312770
Common Factors in Neurodegeneration: A Meta-Study Revealing Shared Patterns on a Multi-Omics Scale. PMID:33302607
The transcriptomic profiling of SARS-CoV-2 compared to SARS, MERS, EBOV, and H1N1. PMID:33301474
Identification of Functional Genes in Pterygium Based on Bioinformatics Analysis. PMID:33299863
Next-generation sequencing analysis of circulating micro-RNA expression in response to parabolic flight as a spaceflight analogue. PMID:33298968
carP, encoding a Ca2+-regulated putative phytase, is evolutionarily conserved in Pseudomonas aeruginosa and has potential as a biomarker. PMID:33295862
SNRPB-mediated RNA splicing drives tumor cell proliferation and stemness in hepatocellular carcinoma. PMID:33289700
Statistical Approach for Biologically Relevant Gene Selection from High-Throughput Gene Expression Data. PMID:33286973
Differentially Expressed mRNAs and Their Long Noncoding RNA Regulatory Network with Helicobacter pylori-Associated Diseases including Atrophic Gastritis and Gastric Cancer. PMID:33282942
Role of COL3A1 and POSTN on Pathologic Stages of Esophageal Cancer. PMID:33280513
Age-related DNA methylation changes are sex-specific: a comprehensive assessment. PMID:33276343
Computational identification of biomarker genes for lung cancer considering treatment and non-treatment studies. PMID:33272232
BPI and KIR6.1 as significant hub genes for vein graft restenosis. PMID:33259239
The vascular landscape of human cancer. PMID:33258803
Scaffold association factor B (SAFB) is required for expression of prenyltransferases and RAS membrane association. PMID:33257571
An informatics research platform to make public gene expression time-course datasets reusable for more scientific discoveries. PMID:33247935
Inhibition of the CCL2 receptor, CCR2, enhances tumor response to immune checkpoint therapy. PMID:33247183
SPOCK2 Serves as a Potential Prognostic Marker and Correlates With Immune Infiltration in Lung Adenocarcinoma. PMID:33244319
Tetrachloroethene respiration in Sulfurospirillum species is regulated by a two-component system as unraveled by comparative genomics, transcriptomics, and regulator binding studies. PMID:33242236
scREAD: A Single-Cell RNA-Seq Database for Alzheimer's Disease. PMID:33241205
Molecular Basis of Cardiac and Vascular Injuries Associated With COVID-19. PMID:33240937
Accessing NCBI data using the NCBI Sequence Viewer and Genome Data Viewer (GDV). PMID:33239395
Inhibiting the P2X4 Receptor Suppresses Prostate Cancer Growth In Vitro and In Vivo, Suggesting a Potential Clinical Target. PMID:33233569
HGF-Induced PD-L1 Expression in Head and Neck Cancer: Preclinical and Clinical Findings. PMID:33233528
GTRD: an integrated view of transcription regulation. PMID:33231677
The Inhibitory Role of miR-486-5p on CSC Phenotype Has Diagnostic and Prognostic Potential in Colorectal Cancer. PMID:33227890
Global Gene Expression Profiling Reveals Isorhamnetin Induces Hepatic-Lineage Specific Differentiation in Human Amniotic Epithelial Cells. PMID:33224947
Gene Expression Signatures Identify Biologically Homogenous Subgroups of Grade 2 Meningiomas. PMID:33224871
Perversely expressed long noncoding RNAs can alter host response and viral proliferation in SARS-CoV-2 infection. PMID:33224264
Investigating the Effects of Ibuprofen on the Gene Expression Profile in Hippocampus of Mice Model of Alzheimer's Disease through Bioinformatics Analysis. PMID:33224242
ZFHX3 Promotes the Proliferation and Tumor Growth of ER-Positive Breast Cancer Cells Likely by Enhancing Stem-Like Features and MYC and TBX3 Transcription. PMID:33217982
Polygenic Risk Score of Longevity Predicts Longer Survival Across an Age Continuum. PMID:33216869
Biophysical and X-ray structural studies of the (GGGTT)3GGG G-quadruplex in complex with N-methyl mesoporphyrin IX. PMID:33206666
Tracing the footsteps of autophagy in computational biology. PMID:33201177
Differentiation potential and mRNA profiles of human dedifferentiated adipose cells and adipose‑derived stem cells from young donors. PMID:33200799
Development of cancer prognostic signature based on pan-cancer proteomics. PMID:33200655
Comprehensive Identification of Key Genes Involved in Development of Diabetes Mellitus-Related Atherogenesis Using Weighted Gene Correlation Network Analysis. PMID:33195466
Identification of Key Genes in Lung Adenocarcinoma and Establishment of Prognostic Mode. PMID:33195408
Prognostic model of invasive ductal carcinoma of the breast based on differentially expressed glycolysis-related genes. PMID:33194424
DPPN-SVM: Computational Identification of Mis-Localized Proteins in Cancers by Integrating Differential Gene Expressions With Dynamic Protein-Protein Interaction Networks. PMID:33193746
A Five-Gene-Pair-Based Prognostic Signature for Predicting the Relapse Risk of Early Stage ER+ Breast Cancer. PMID:33193655
Guidelines for reporting single-cell RNA-seq experiments. PMID:33188371
Fra-2/AP-1 regulates melanoma cell metastasis by downregulating Fam212b. PMID:33188281
Evolution of Embryo Implantation Was Enabled by the Origin of Decidual Stromal Cells in Eutherian Mammals. PMID:33185661
TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment. PMID:33179754
OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes. PMID:33179748
Posttranscriptional Gene Regulatory Networks in Chronic Airway Inflammatory Diseases: In silico Mapping of RNA-Binding Protein Expression in Airway Epithelium. PMID:33178205
CCL5-dependent mast cell infiltration into the tumor microenvironment in clear cell renal cell carcinoma patients. PMID:33177244
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021. PMID:33175170
GlycoPOST realizes FAIR principles for glycomics mass spectrometry data. PMID:33174597
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
The Zebrafish Information Network: major gene page and home page updates. PMID:33170210
Data mining of immune-related prognostic genes in metastatic melanoma microenvironment. PMID:33169786
CRELD1 modulates homeostasis of the immune system in mice and humans. PMID:33169013
Pan-transcriptome-based candidate therapeutic discovery for idiopathic pulmonary fibrosis. PMID:33167785
Single-cell analyses identify dysfunctional CD16+ CD8 T cells in smokers. PMID:33163982
Inhibition of AURKB, regulated by pseudogene MTND4P12, confers synthetic lethality to PARP inhibition in skin cutaneous melanoma. PMID:33163283
Maximizing the reusability of gene expression data by predicting missing metadata. PMID:33156882
A network medicine approach to investigation and population-based validation of disease manifestations and drug repurposing for COVID-19. PMID:33156843
Identification of NLRP3 Inflammation-Related Gene Promoter Hypomethylation in Diabetic Retinopathy. PMID:33156339
Artificial Intelligence (AI)-Based Systems Biology Approaches in Multi-Omics Data Analysis of Cancer. PMID:33154949
Widespread Traces of Lytic Kaposi Sarcoma-Associated Herpesvirus in Primary Effusion Lymphoma at Single-Cell Resolution. PMID:33154001
Gene Expression Profiling of Type 2 Diabetes Mellitus by Bioinformatics Analysis. PMID:33149760
Widespread transcriptional disruption of the microRNA biogenesis machinery in brain and peripheral tissues of individuals with schizophrenia. PMID:33149139
High Expression of UBB, RAC1, and ITGB1 Predicts Worse Prognosis among Nonsmoking Patients with Lung Adenocarcinoma through Bioinformatics Analysis. PMID:33134373
Identification of differentially expressed genes in ulcerative colitis and verification in a colitis mouse model by bioinformatics analyses. PMID:33132649
Integrated TCGA and GEO analysis showed that SMAD7 is an independent prognostic factor for lung adenocarcinoma. PMID:33126329
SMARCD3 is a potential prognostic marker and therapeutic target in CAFs. PMID:33125346
lncRNA KTN1‑AS1 promotes glioma cell proliferation and invasion by negatively regulating miR‑505‑3p. PMID:33125151
IFN-γ Mediates the Development of Systemic Lupus Erythematosus. PMID:33123584
Screening and identification of key genes and pathways in metastatic uveal melanoma based on gene expression using bioinformatic analysis. PMID:33120861
Integration of gene profile to explore the hub genes of lung adenocarcinoma: A quasi-experimental study. PMID:33120770
[Spindle assembly checkpoint complex-related genes TTK and MAD2L1 are over-expressed in lung adenocarcinoma: a big data and bioinformatics analysis]. PMID:33118511
Identification and Validation of Novel Genes in Anaplastic Thyroid Carcinoma via Bioinformatics Analysis. PMID:33116838
Determination and Dissection of DNA-Binding Specificity for the Thermus thermophilus HB8 Transcriptional Regulator TTHB099. PMID:33114549
Blood-based epigenetic estimators of chronological age in human adults using DNA methylation data from the Illumina MethylationEPIC array. PMID:33109080
MN1 overexpression with varying tumor grade is a promising predictor of survival of glioma patients. PMID:33105486
Integrated Microarray to Identify the Hub miRNAs and Constructed miRNA-mRNA Network in Neuroblastoma Via Bioinformatics Analysis. PMID:33104965
Genome-wide analysis of therapeutic response uncovers molecular pathways governing tamoxifen resistance in ER+ breast cancer. PMID:33099086
VARAdb: a comprehensive variation annotation database for human. PMID:33095866
Meta-gene markers predict meningioma recurrence with high accuracy. PMID:33093491
The FAM171A2 gene is a key regulator of progranulin expression and modifies the risk of multiple neurodegenerative diseases. PMID:33087363
crisprSQL: a novel database platform for CRISPR/Cas off-target cleavage assays. PMID:33084893
Common gene signatures and key pathways in hypopharyngeal and esophageal squamous cell carcinoma: Evidence from bioinformatic analysis. PMID:33080677
iRHOM2: A Regulator of Palmoplantar Biology, Inflammation, and Viral Susceptibility. PMID:33080304
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
A flexible, interpretable, and accurate approach for imputing the expression of unmeasured genes. PMID:33074331
In-depth characterization of the biomarkers based on tumor-infiltrated immune cells reveals implications for diagnosis and prognosis in hepatocellular carcinoma. PMID:33073226
Assessing the consequences of environmental exposures on the expression of the human receptor and proteases involved in SARS-CoV-2 cell-entry. PMID:33069705
Connectivity Mapping Identifies BI-2536 as a Potential Drug to Treat Diabetic Kidney Disease. PMID:33067313
Transcriptome analysis of Brucella abortus S19∆per immunized mouse spleen revealed activation of MHC-I and MHC-II pathways. PMID:33062939
Expression of collagen type 1 alpha 1 indicates lymph node metastasis and poor outcomes in squamous cell carcinomas of the lung. PMID:33062455
Whole transcriptomic network analysis using Co-expression Differential Network Analysis (CoDiNA). PMID:33057419
Bioinformatic gene analysis for potential therapeutic targets of Huntington's disease in pre-symptomatic and symptomatic stage. PMID:33054835
A Mechanism Underlying Sex-Associated Differences in Ankylosing Spondylitis: Troponin C2, Fast Skeletal Type (TNNC2) and Calcium Signaling Pathway. PMID:33052895
Identification of potential key genes and miRNAs involved in Hepatoblastoma pathogenesis and prognosis. PMID:33051830
Manually curated and harmonised transcriptomics datasets of psoriasis and atopic dermatitis patients. PMID:33051456
EXO70A2 Is Critical for Exocyst Complex Function in Pollen Development. PMID:33051268
Time-Resolved Profiling Reveals ATF3 as a Novel Mediator of Endocrine Resistance in Breast Cancer. PMID:33050633
Machine learning approach to integrated endometrial transcriptomic datasets reveals biomarkers predicting uterine receptivity in cattle at seven days after estrous. PMID:33046742
INTEDE: interactome of drug-metabolizing enzymes. PMID:33045737
iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning. PMID:33045728
Identification and validation of a ten-gene set variation score as a diagnostic and prognostic stratification tool in hepatocellular carcinoma. PMID:33042448
In Silico Prediction of Molecular Targets of Astragaloside IV for Alleviation of COVID-19 Hyperinflammation by Systems Network Pharmacology and Bioinformatic Gene Expression Analysis. PMID:33041797
The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals. PMID:33037820
Diagnostic and prognostic value of thymidylate synthase expression in breast cancer. PMID:33030246
Bioinformatics Analysis of Genes and Mechanisms in Postherpetic Neuralgia. PMID:33029266
Ten simple rules for annotating sequencing experiments. PMID:33017400
Investigating genetic drivers of dermatomyositis pathogenesis using meta-analysis. PMID:33015383
A Novel Gene Signature to Predict Survival Time and Incident Ventricular Arrhythmias in Patients with Dilated Cardiomyopathy. PMID:33014188
Neural Network Deconvolution Method for Resolving Pathway-Level Progression of Tumor Clonal Expression Programs With Application to Breast Cancer Brain Metastases. PMID:33013452
Reanalysis of Gene Expression Profiles of CD4+ T Cells Treated with HIV-1 Latency Reversal Agents. PMID:33007800
Identification of NUF2 and FAM83D as potential biomarkers in triple-negative breast cancer. PMID:33005492
Identification of a nine-gene prognostic signature for gastric carcinoma using integrated bioinformatics analyses. PMID:33005292
Salt tolerance involved candidate genes in rice: an integrative meta-analysis approach. PMID:33004003
Knockdown of SERPINE1 reverses resistance of triple‑negative breast cancer to paclitaxel via suppression of VEGFA. PMID:33000256
Protein Arginine Methyltransferase 5 Promotes pICln-Dependent Androgen Receptor Transcription in Castration-Resistant Prostate Cancer. PMID:32999000
Role of SARS-CoV-2 in Altering the RNA-Binding Protein and miRNA-Directed Post-Transcriptional Regulatory Networks in Humans. PMID:32993015
A Prognostic Prediction Model Developed Based on Four CpG Sites and Weighted Correlation Network Analysis Identified DNAJB1 as a Novel Biomarker for Pancreatic Cancer. PMID:32984053
Potential role of cellular miRNAs in coronavirus-host interplay. PMID:32983652
STAB: a spatio-temporal cell atlas of the human brain. PMID:32976581
Identifying Hub Genes, Key Pathways and Immune Cell Infiltration Characteristics in Pediatric and Adult Ulcerative Colitis by Integrated Bioinformatic Analysis. PMID:32974809
Matrix Metallopeptidase 14: A Candidate Prognostic Biomarker for Diffuse Large B-Cell Lymphoma. PMID:32974187
HLA-DPA1 gene is a potential predictor with prognostic values in multiple myeloma. PMID:32972413
An immune-related gene signature for determining Ewing sarcoma prognosis based on machine learning. PMID:32968877
Unveiling Sex-Based Differences in the Effects of Alcohol Abuse: A Comprehensive Functional Meta-Analysis of Transcriptomic Studies. PMID:32967293
Accurate Blood-Based Diagnostic Biosignatures for Alzheimer's Disease via Automated Machine Learning. PMID:32962113
Signal Transduction Pathway Activity in High-Grade, Serous Ovarian Carcinoma Reveals a More Favorable Prognosis in Tumors with Low PI3K and High NF-κB Pathway Activity: A Novel Approach to a Long-Standing Enigma. PMID:32961868
Systematic Analysis of Cold Stress Response and Diurnal Rhythm Using Transcriptome Data in Rice Reveals the Molecular Networks Related to Various Biological Processes. PMID:32961678
Development and validation of a cancer stem cell-related signature for prognostic prediction in pancreatic ductal adenocarcinoma. PMID:32958051
Transcription factor expression as a predictor of colon cancer prognosis: a machine learning practice. PMID:32957968
A panel of 8 miRNAs as a novel diagnostic biomarker in pancreatic cancer. PMID:32957376
Analysis, identification and visualization of subgroups in genomics. PMID:32954413
Occurrence of differing metabolic dysregulations, a glucose driven and another fatty acid centric in gastric cancer subtypes. PMID:32949316
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
Integration of microarray data and literature mining identifies a sex bias in DPP4+CD4+ T cells in HIV-1 infection. PMID:32946499
Single-cell RNA-seq reveals the immune escape and drug resistance mechanisms of mantle cell lymphoma. PMID:32944402
A novel microRNA-based signature predicts prognosis among nasopharyngeal cancer patients. PMID:32941074
Quantitative mapping of transcriptome and proteome dynamics during polarization of human iPSC-derived neurons. PMID:32940601
LAMP3 induces apoptosis and autoantigen release in Sjögren's syndrome patients. PMID:32939030
Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation. PMID:32933554
Investigating potential molecular mechanisms of serum exosomal miRNAs in colorectal cancer based on bioinformatics analysis. PMID:32925795
Potential mechanism of RRM2 for promoting Cervical Cancer based on weighted gene co-expression network analysis. PMID:32922202
The Expression and Potential Role of Tubulin Alpha 1b in Wilms' Tumor. PMID:32908931
DNA Primase Subunit 1 Expression in Hepatocellular Carcinoma and Its Clinical Implication. PMID:32908930
Discovery of Prognostic Signature Genes for Overall Survival Prediction in Gastric Cancer. PMID:32908579
1-Methyl-D-tryptophan activates aryl hydrocarbon receptor, a pathway associated with bladder cancer progression. PMID:32907554
Drug Repositioning for P-Glycoprotein Mediated Co-Expression Networks in Colorectal Cancer. PMID:32903699
The Utility of Resolving Asthma Molecular Signatures Using Tissue-Specific Transcriptome Data. PMID:32900903
Non-Coding RNAs in the Brain-Heart Axis: The Case of Parkinson's Disease. PMID:32899928
Bioinformatic analysis reveals hub genes and pathways that promote melanoma metastasis. PMID:32894090
Non-Coding RNA Databases in Cardiovascular Research. PMID:32887511
Identification of novel biomarkers involved in pulmonary arterial hypertension based on multiple-microarray analysis. PMID:32886110
Functional Modular Network Identifies the Key Genes of Preoperative Inhalation Anesthesia and Intravenous Anesthesia in Off-Pump Coronary Artery Bypass Grafting. PMID:32879635
Lymphocyte infiltration and key differentially expressed genes in the ulcerative colitis. PMID:32871953
Does single gene expression omnibus data mining analysis apply for only tumors and not mental illness? A preliminary study on bipolar disorder based on bioinformatics methodology. PMID:32871949
Identification of key pathways and genes shared between Crohn's disease and breast cancer using bioinformatics analysis. PMID:32863932
Overexpression of close homolog of L1 enhances the chemosensitivity of lung cancer cells via inhibition of the Akt pathway. PMID:32863924
Prediction and Analysis of SARS-CoV-2-Targeting MicroRNA in Human Lung Epithelium. PMID:32858958
Explorative Combined Lipid and Transcriptomic Profiling of Substantia Nigra and Putamen in Parkinson's Disease. PMID:32858884
Salmonella enterica serovar Typhimurium inhibits the innate immune response and promotes apoptosis in a ribosomal/TRP53-dependent manner in swine neutrophils. PMID:32854785
Development of Multiscale Transcriptional Regulatory Network in Esophageal Cancer Based on Integrated Analysis. PMID:32851080
A Bioinformatics Research on Novel Mechanism of Compound Kushen Injection for Treating Breast Cancer by Network Pharmacology and Molecular Docking Verification. PMID:32849897
Identification of Gene Signatures for Diagnosis and Prognosis of Hepatocellular Carcinomas Patients at Early Stage. PMID:32849835
Screening and Identification of Therapeutic Targets for Pulmonary Arterial Hypertension Through Microarray Technology. PMID:32849793
MicroRNAs Modulate the Pathogenesis of Alzheimer's Disease: An In Silico Analysis in the Human Brain. PMID:32846925
Identification of differentially expressed genes between mucinous adenocarcinoma and other adenocarcinoma of colorectal cancer using bioinformatics analysis. PMID:32840168
Clustering analysis of tumor metabolic networks. PMID:32838750
Study of Osteoarthritis-Related Hub Genes Based on Bioinformatics Analysis. PMID:32832544
The Polycomb-associated factor PHF19 controls hematopoietic stem cell state and differentiation. PMID:32821835
Cancer-Derived Transforming Growth Factor-β Modulates Tumor-Associated Macrophages in Ampullary Cancer. PMID:32821120
miR-30d Induced Apoptosis by Targeting Sox4 to Inhibit the Proliferation, Invasion and Migration of Nephroblastoma. PMID:32821117
Development of a prognostic gene signature based on an immunogenomic infiltration analysis of osteosarcoma. PMID:32820615
Isolation of novel citrus and plum fruit promoters and their functional characterization for fruit biotechnology. PMID:32819338
Targeting Hypoxia Sensitizes TNBC to Cisplatin and Promotes Inhibition of Both Bulk and Cancer Stem Cells. PMID:32806648
The Application of Single-Cell RNA Sequencing in Vaccinology. PMID:32802896
Potential Molecular Mechanism of the NPPB Gene in Postischemic Heart Failure with and without T2DM. PMID:32802835
Construction and Investigation of MicroRNA-mRNA Regulatory Network of Gastric Cancer with Helicobacter pylori Infection. PMID:32802507
Integrated Framework of the Immune-Defense Transcriptional Signatures in the Arabidopsis Shoot Apical Meristem. PMID:32796535
Transcriptome profiles acquired during cell expansion and licensing validate mesenchymal stromal cell lineage genes. PMID:32795342
Discovery of Selenocysteine as a Potential Nanomedicine Promotes Cartilage Regeneration With Enhanced Immune Response by Text Mining and Biomedical Databases. PMID:32792959
Detecting ulcerative colitis from colon samples using efficient feature selection and machine learning. PMID:32792678
Construct a circRNA/miRNA/mRNA regulatory network to explore potential pathogenesis and therapy options of clear cell renal cell carcinoma. PMID:32788609
Sex-Specific Transcriptome Differences in Human Adipose Mesenchymal Stem Cells. PMID:32784482
Identification of transcriptomic markers for developing idiopathic pulmonary fibrosis: an integrative analysis of gene expression profiles. PMID:32782692
Lipophilic signals lead to organ-specific gene expression changes in Arabidopsis seedlings. PMID:32775951
Integrated Bioinformatic Analysis Identifies Networks and Promising Biomarkers for Hepatitis B Virus-Related Hepatocellular Carcinoma. PMID:32775402
Identification of novel biomarkers and small-molecule compounds for nasopharyngeal carcinoma with metastasis. PMID:32769887
Molecular Signatures and Networks of Cardiomyocyte Differentiation in Humans and Mice. PMID:32769060
WNT2-Mediated FZD2 Stabilization Regulates Esophageal Cancer Metastasis via STAT3 Signaling. PMID:32766155
Bioinformatics analysis shows that TOP2A functions as a key candidate gene in the progression of cervical cancer. PMID:32765860
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
ABC-GWAS: Functional Annotation of Estrogen Receptor-Positive Breast Cancer Genetic Variants. PMID:32765587
Genomic data imputation with variational auto-encoders. PMID:32761097
Analysis of Differentially Expressed Genes and Molecular Pathways in Familial Hypercholesterolemia Involved in Atherosclerosis: A Systematic and Bioinformatics Approach. PMID:32760426
Systems Biology Will Direct Vascular-Targeted Therapy for Obesity. PMID:32760294
Gene Expression Clustering and Selected Head and Neck Cancer Gene Signatures Highlight Risk Probability Differences in Oral Premalignant Lesions. PMID:32756466
Identification of key genes and pathways involved in vitiligo development based on integrated analysis. PMID:32756109
Eight immune-related genes predict survival outcomes and immune characteristics in breast cancer. PMID:32756008
Chromatin accessibility landscape of pediatric T-lymphoblastic leukemia and human T-cell precursors. PMID:32755029
Machine learning-based classification and diagnosis of clinical cardiomyopathies. PMID:32744882
A module of multifactor-mediated dysfunction guides the molecular typing of coronary heart disease. PMID:32743916
Identification of key genes of human bone marrow stromal cells adipogenesis at an early stage. PMID:32742785
Aberrant methylation and microRNA-target regulation are associated with downregulated NEURL1B: a diagnostic and prognostic target in colon cancer. PMID:32742189
The hepatocyte clock and feeding control chronophysiology of multiple liver cell types. PMID:32732282
Detecting sample swaps in diverse NGS data types using linkage disequilibrium. PMID:32728101
The Roles of Imprinted SLC22A18 and SLC22A18AS Gene Overexpression Caused by Promoter CpG Island Hypomethylation as Diagnostic and Prognostic Biomarkers for Non-Small Cell Lung Cancer Patients. PMID:32726996
Functional Genomics of Epileptogenesis in Animal Models and Humans. PMID:32725455
Long non-coding RNA EWSAT1 contributes to the proliferation and invasion of glioma by sponging miR-152-3p. PMID:32724428
Contributions of de novo variants to systemic lupus erythematosus. PMID:32724065
Regulator combinations identify systemic sclerosis patients with more severe disease. PMID:32721949
Histone deacetylase inhibitors induce medulloblastoma cell death independent of HDACs recruited in REST repression complexes. PMID:32720471
Genetic Etiology Shared by Multiple Sclerosis and Ischemic Stroke. PMID:32719717
MicroRNA signatures of perioperative myocardial injury after elective noncardiac surgery: a prospective observational mechanistic cohort study. PMID:32718726
Construction of a novel prognostic-predicting model correlated to ovarian cancer. PMID:32716025
Downregulation of miR‑193a‑3p via targeting cyclin D1 in thyroid cancer. PMID:32705210
Potentially repurposable drugs for COVID-19 identified from SARS-CoV-2 Host Protein Interactome. PMID:32702734
Comprehensive Study of Different Expressed Genes and Their Functional Modules in Anesthesia for Off-Pump Coronary Artery Bypass Grafting. PMID:32695821
Liver macrophages regulate systemic metabolism through non-inflammatory factors. PMID:32694874
Responsible, practical genomic data sharing that accelerates research. PMID:32694666
Unique molecular signatures of microRNAs in ocular fluids and plasma in diabetic retinopathy. PMID:32692745
Identification and validation of novel DNA methylation markers for early diagnosis of lung adenocarcinoma. PMID:32688456
Gene expression profiling identifies the role of Zac1 in cervical cancer metastasis. PMID:32678267
Role of SARS-CoV-2 in altering the RNA binding protein and miRNA directed post-transcriptional regulatory networks in humans. PMID:32676599
Estimation of Hub Genes and Infiltrating Immune Cells in Non-Smoking Females with Lung Adenocarcinoma by Integrated Bioinformatic Analysis. PMID:32669531
Progesterone receptor membrane component 1 regulates lipid homeostasis and drives oncogenic signaling resulting in breast cancer progression. PMID:32660617
Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. PMID:32652120
Searching large-scale scRNA-seq databases via unbiased cell embedding with Cell BLAST. PMID:32651388
Weighted correlation gene network analysis reveals a new stemness index-related survival model for prognostic prediction in hepatocellular carcinoma. PMID:32644941
SARS-CoV-2 infection risk assessment in the endometrium: viral infection-related gene expression across the menstrual cycle. PMID:32641214
Systematic profiling of ACE2 expression in diverse physiological and pathological conditions for COVID-19/SARS-CoV-2. PMID:32639084
Identification of genes in hepatocellular carcinoma induced by non-alcoholic fatty liver disease. PMID:32623384
Histoepigenetic analysis of the mesothelin network within pancreatic ductal adenocarcinoma cells reveals regulation of retinoic acid receptor gamma and AKT by mesothelin. PMID:32616712
Microglial Remodeling of the Extracellular Matrix Promotes Synapse Plasticity. PMID:32615087
IGAP-integrative genome analysis pipeline reveals new gene regulatory model associated with nonspecific TF-DNA binding affinity. PMID:32612751
An Analysis Regarding the Association Between the ISLR Gene and Gastric Carcinogenesis. PMID:32612640
Interferon-Induced Protein 44 and Interferon-Induced Protein 44-Like Restrict Replication of Respiratory Syncytial Virus. PMID:32611756
Selective Neuronal Vulnerability in Alzheimer's Disease: A Network-Based Analysis. PMID:32603655
Trans-generational epigenetic regulation associated with the amelioration of Duchenne Muscular Dystrophy. PMID:32596946
Identification of hydatidosis-related modules and key regulatory genes. PMID:32596042
Interferon-Induced Transmembrane Protein (IFITM3) Is Upregulated Explicitly in SARS-CoV-2 Infected Lung Epithelial Cells. PMID:32595654
Integration of transcriptomic profile of SARS-CoV-2 infected normal human bronchial epithelial cells with metabolic and protein-protein interaction networks. PMID:32595353
Comprehensive Analysis of Key Genes and Regulatory Elements in Osteosarcoma Affected by Bone Matrix Mineral With Prognostic Values. PMID:32582282
Identification of Target Genes and Transcription Factors in Mice with LMNA-Related Dilated Cardiomyopathy by Integrated Bioinformatic Analyses. PMID:32581210
Construction, analysis and validation of co-expression network to understand stress adaptation in Deinococcus radiodurans R1. PMID:32579573
Comprehensive Analysis of Candidate Diagnostic and Prognostic Biomarkers Associated with Lung Adenocarcinoma. PMID:32578582
A circular RNA map for human induced pluripotent stem cells of foetal origin. PMID:32574961
Mitochondrial CLPP2 Assists Coordination and Homeostasis of Respiratory Complexes. PMID:32571844
CUL1-Mediated Organelle Fission Pathway Inhibits the Development of Chronic Obstructive Pulmonary Disease. PMID:32565880
COnTORT: COmprehensive Transcriptomic ORganizational Tool for Simultaneously Retrieving and Organizing Numerous Gene Expression Data Sets from the NCBI Gene Expression Omnibus Database. PMID:32554783
Identification of DEGs and transcription factors involved in H. pylori-associated inflammation and their relevance with gastric cancer. PMID:32547867
Intragenic recruitment of NF-κB drives splicing modifications upon activation by the oncogene Tax of HTLV-1. PMID:32546717
Integrated analysis of a compendium of RNA-Seq datasets for splicing factors. PMID:32546682
Integrative computational epigenomics to build data-driven gene regulation hypotheses. PMID:32543653
Unveiling prognostics biomarkers of tyrosine metabolism reprogramming in liver cancer by cross-platform gene expression analyses. PMID:32542016
RWRMTN: a tool for predicting disease-associated microRNAs based on a microRNA-target gene network. PMID:32539680
Identification of genes associated with gastric cancer survival and construction of a nomogram to improve risk stratification for patients with gastric cancer. PMID:32537023
The circRNA-miRNA-mRNA regulatory network in systemic lupus erythematosus. PMID:32533339
CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis. PMID:32533075
The Landscape of Iron Metabolism-Related and Methylated Genes in the Prognosis Prediction of Clear Cell Renal Cell Carcinoma. PMID:32528886
Bioinformatics analysis of the circRNA-miRNA-mRNA network for non-small cell lung cancer. PMID:32527185
Novel Comprehensive Bioinformatics Approaches to Determine the Molecular Genetic Susceptibility Profile of Moderate and Severe Asthma. PMID:32512817
Identifying multiple collagen gene family members as potential gastric cancer biomarkers using integrated bioinformatics analysis. PMID:32509452
Spatial Patterns of Gene Expression in Bacterial Genomes. PMID:32506154
Could the Heat Shock Proteins 70 Family Members Exacerbate the Immune Response in Multiple Sclerosis? An in Silico Study. PMID:32503176
Circular RNA HIPK3: A Key Circular RNA in a Variety of Human Cancers. PMID:32500032
Landscape of immune cell gene expression is unique in predominantly WHO grade 1 skull base meningiomas when compared to convexity. PMID:32493984
Scoring functions for drug-effect similarity. PMID:32484516
Available Software for Meta-analyses of Genome-wide Expression Studies. PMID:32476989
Whole blood transcriptomic investigation identifies long non-coding RNAs as regulators in sepsis. PMID:32471511
Increased effect of two-fraction radiotherapy in conjunction with IDO1 inhibition in experimental glioblastoma. PMID:32469935
Computational analysis and verification of molecular genetic targets for glioblastoma. PMID:32469390
Pan-transcriptomic analysis identified common differentially expressed genes of Acinetobacter baumannii in response to polymyxin treatments. PMID:32469363
Bioinformatics Analysis and Identification of Underlying Biomarkers Potentially Linking Allergic Rhinitis and Asthma. PMID:32460303
Immune-Related Prognostic Model in Colon Cancer: A Gene Expression-Based Study. PMID:32457797
Transcriptome profiling of porcine testis tissue reveals genes related to sperm hyperactive motility. PMID:32456687
Trioxolone Methyl, a Novel Cyano Enone-Bearing 18βH-Glycyrrhetinic Acid Derivative, Ameliorates Dextran Sulphate Sodium-Induced Colitis in Mice. PMID:32455822
A disintegrin and metalloproteinase domain 17-epidermal growth factor receptor signaling contributes to oral cancer pain. PMID:32453136
Integrative In Silico Analysis of Genome-Wide DNA Methylation Profiles in Schizophrenia. PMID:32451840
Homeobox transcription factor OsZHD2 promotes root meristem activity in rice by inducing ethylene biosynthesis. PMID:32449922
Identification of EMT-related high-risk stage II colorectal cancer and characterisation of metastasis-related genes. PMID:32435058
A meta-analysis of gene expression data highlights synaptic dysfunction in the hippocampus of brains with Alzheimer's disease. PMID:32433480
Identification of population-level differentially expressed genes in one-phenotype data. PMID:32428201
Dysregulation of Signaling Pathways Due to Differentially Expressed Genes From the B-Cell Transcriptomes of Systemic Lupus Erythematosus Patients - A Bioinformatics Approach. PMID:32426333
Identification of Immune Cell Landscape and Construction of a Novel Diagnostic Nomogram for Crohn's Disease. PMID:32425988
Detecting qualitative changes in biological systems. PMID:32424123
Identification of Upstream Transcriptional Regulators of Ischemic Cardiomyopathy Using Cardiac RNA-Seq Meta-Analysis. PMID:32423033
Overexpression of MYEOV predicting poor prognosis in patients with pancreatic ductal adenocarcinoma. PMID:32420813
MCM2 and NUSAP1 Are Potential Biomarkers for the Diagnosis and Prognosis of Pancreatic Cancer. PMID:32420375
Integrated miRNAome and Transcriptome Analysis Reveals Argonaute 2-Mediated Defense Responses Against the Devastating Phytopathogen Sclerotinia sclerotiorum. PMID:32411168
Alternative splicing of LSD1+8a in neuroendocrine prostate cancer is mediated by SRRM4. PMID:32403054
Integrating biological knowledge and gene expression data using pathway-guided random forests: a benchmarking study. PMID:32399562
Could CTSK and COL4A2 be specific biomarkers of poor prognosis for patients with gastric cancer in Asia?-a microarray analysis based on regional population. PMID:32399279
Slit2/Robo1 Mitigates DSS-induced Ulcerative Colitis by Activating Autophagy in Intestinal Stem Cell. PMID:32398956
Chromenopyrimidinone Controls Stemness and Malignancy by suppressing CD133 Expression in Hepatocellular Carcinoma. PMID:32397206
MyoMiner: explore gene co-expression in normal and pathological muscle. PMID:32393257
Integrating Genome-Wide Association Studies and Gene Expression Profiles With Chemical-Genes Interaction Networks to Identify Chemicals Associated With Colorectal Cancer. PMID:32391058
A risk score system based on DNA methylation levels and a nomogram survival model for lung squamous cell carcinoma. PMID:32377703
Knockdown of CDCA8 inhibits the proliferation and enhances the apoptosis of bladder cancer cells. PMID:32377458
Loss of SRSF2 triggers hepatic progenitor cell activation and tumor development in mice. PMID:32372053
Identification of potential microRNA panels for pancreatic cancer diagnosis using microarray datasets and bioinformatics methods. PMID:32371926
Identification of key genes, pathways and potential therapeutic agents for IgA nephropathy using an integrated bioinformatics analysis. PMID:32370650
Molecular Signatures of JMJD10/MINA53 in Gastric Cancer. PMID:32370161
Towards the routine use of in silico screenings for drug discovery using metabolic modelling. PMID:32369553
Histone deacetylase 1 and 2 drive differentiation and fusion of progenitor cells in human placental trophoblasts. PMID:32366868
The circular RNA FAM169A functions as a competitive endogenous RNA and regulates intervertebral disc degeneration by targeting miR-583 and BTRC. PMID:32366862
NAD(P)-dependent steroid dehydrogenase-like is involved in breast cancer cell growth and metastasis. PMID:32366230
No evidence for an increased liver uptake of SARS-CoV-2 in metabolic-associated fatty liver disease. PMID:32360995
Integrated analysis of immunocyte infiltration and differential gene expression in tricuspid aortic valve-associated thoracic aortic aneurysms. PMID:32355729
Comprehensive analysis of the SLC16A gene family in pancreatic cancer via integrated bioinformatics. PMID:32355273
Combining signal and sequence to detect RNA polymerase initiation in ATAC-seq data. PMID:32353042
Polymorphisms in miRNA binding sites involved in metabolic diseases in mice and humans. PMID:32350386
Integrating SWATH-MS Proteomics and Transcriptome Analysis Identifies CHI3L1 as a Plasma Biomarker for Early Gastric Cancer. PMID:32346614
Identification of Key Genes Related to Lung Squamous Cell Carcinoma Using Bioinformatics Analysis. PMID:32340320
Association of respiratory allergy, asthma, and expression of the SARS-CoV-2 receptor ACE2. PMID:32333915
MethCORR modelling of methylomes from formalin-fixed paraffin-embedded tissue enables characterization and prognostication of colorectal cancer. PMID:32332866
Immunoproteasome Genes Are Modulated in CD34+ JAK2V617F Mutated Cells from Primary Myelofibrosis Patients. PMID:32331228
Transcriptomics in Toxicogenomics, Part I: Experimental Design, Technologies, Publicly Available Data, and Regulatory Aspects. PMID:32326418
Sequential Interferon β-Cisplatin Treatment Enhances the Surface Exposure of Calreticulin in Cancer Cells via an Interferon Regulatory Factor 1-Dependent Manner. PMID:32326356
Drought Stress Responses in Context-Specific Genome-Scale Metabolic Models of Arabidopsis thaliana. PMID:32325728
Identification of lung adenocarcinoma biomarkers based on bioinformatic analysis and human samples. PMID:32323809
Circular RNA Circ100084 functions as sponge of miR‑23a‑5p to regulate IGF2 expression in hepatocellular carcinoma. PMID:32323783
A novel microRNA signature for pathological grading in lung adenocarcinoma based on TCGA and GEO data. PMID:32323746
Computational Approach to Identifying Universal Macrophage Biomarkers. PMID:32322218
Genome‑wide DNA methylation regulation analysis of long non‑coding RNAs in glioblastoma. PMID:32319552
SPEED2: inferring upstream pathway activity from differential gene expression. PMID:32313938
The Predicted Key Molecules, Functions, and Pathways That Bridge Mild Cognitive Impairment (MCI) and Alzheimer's Disease (AD). PMID:32308643
The Molecular Processes in the Trabecular Meshwork After Exposure to Corticosteroids and in Corticosteroid-Induced Ocular Hypertension. PMID:32305042
INHBA is a prognostic predictor for patients with colon adenocarcinoma. PMID:32293338
Blood Gene Expression Profile Study Revealed the Activation of Apoptosis and p53 Signaling Pathway May Be the Potential Molecular Mechanisms of Ionizing Radiation Damage and Radiation-Induced Bystander Effects. PMID:32284698
Bioinformatic identification of hub genes and key pathways in neutrophils of patients with acute respiratory distress syndrome. PMID:32282748
Bioinformatics Analysis for Multiple Gene Expression Profiles in Sepsis. PMID:32280132
eXplainable Artificial Intelligence (XAI) for the identification of biologically relevant gene expression patterns in longitudinal human studies, insights from obesity research. PMID:32275707
Protein Kinase A Is Involved in Neuropathic Pain by Activating the p38MAPK Pathway to Mediate Spinal Cord Cell Apoptosis. PMID:32273830
Molecular mechanisms and prognostic markers in head and neck squamous cell carcinoma: a bioinformatic analysis. PMID:32269674
Test of Arabidopsis Space Transcriptome: A Discovery Environment to Explore Multiple Plant Biology Spaceflight Experiments. PMID:32265943
Comprehensive gene and pathway analysis of cervical cancer progression. PMID:32256826
Expression profile analysis identifies key genes as prognostic markers for metastasis of osteosarcoma. PMID:32256213
The Mitochondrial Iron-Regulated (MIR) gene is Oryza genus specific and evolved before speciation within the Oryza sativa complex. PMID:32253515
A Continuum of Evolving De Novo Genes Drives Protein-Coding Novelty in Drosophila. PMID:32253450
Leveraging biological and statistical covariates improves the detection power in epigenome-wide association testing. PMID:32252795
Highly robust model of transcription regulator activity predicts breast cancer overall survival. PMID:32241272
Meta-Analysis Based on Nonconvex Regularization. PMID:32238826
GRB10 and E2F3 as Diagnostic Markers of Osteoarthritis and Their Correlation with Immune Infiltration. PMID:32235747
LAG3 (LAG-3, CD223) DNA methylation correlates with LAG3 expression by tumor and immune cells, immune cell infiltration, and overall survival in clear cell renal cell carcinoma. PMID:32234847
Fibration symmetries uncover the building blocks of biological networks. PMID:32234788
Transcriptomic and Functional Screens Reveal MicroRNAs That Modulate Prostate Cancer Metastasis. PMID:32231998
A Systematic Bioinformatics Workflow With Meta-Analytics Identified Potential Pathogenic Factors of Alzheimer's Disease. PMID:32231518
Extracellular Protease ADAMTS1 Is Required at Early Stages of Human Uveal Melanoma Development by Inducing Stemness and Endothelial-Like Features on Tumor Cells. PMID:32230715
The Landscape of Somatic Copy Number Alterations in Head and Neck Squamous Cell Carcinoma. PMID:32226775
Decreased Expression of NUSAP1 Predicts Poor Overall Survival in Cervical Cancer. PMID:32226503
The conserved regulatory basis of mRNA contributions to the early Drosophila embryo differs between the maternal and zygotic genomes. PMID:32226006
Potential mechanisms and serum biomarkers involved in sex differences in pulmonary arterial hypertension. PMID:32221085
Whole-transcriptome analysis reveals a potential hsa_circ_0001955/hsa_circ_0000977-mediated miRNA-mRNA regulatory sub-network in colorectal cancer. PMID:32221048
Regulatory Mechanism of ITGBL1 in the Metastasis of Colorectal Cancer. PMID:32211321
SBMLSimulator: A Java Tool for Model Simulation and Parameter Estimation in Systems Biology. PMID:32211200
An mRNA-mRNA Interaction Couples Expression of a Virulence Factor and Its Chaperone in Listeria monocytogenes. PMID:32209466
Standard machine learning approaches outperform deep representation learning on phenotype prediction from transcriptomics data. PMID:32197580
Network-based computational approach to identify genetic links between cardiomyopathy and its risk factors. PMID:32196466
Overexpression of miR-206 in osteosarcoma and its associated molecular mechanisms as assessed through TCGA and GEO databases. PMID:32194668
Altered secretory and neuroprotective function of the choroid plexus in progressive multiple sclerosis. PMID:32192527
Repair mechanism of astrocytes and non-astrocytes in spinal cord injury. PMID:32190622
RASflow: an RNA-Seq analysis workflow with Snakemake. PMID:32183729
Identification of key genes and pathways of diagnosis and prognosis in cervical cancer by bioinformatics analysis. PMID:32181600
Integrative Analysis of MicroRNA and Gene Interactions for Revealing Candidate Signatures in Prostate Cancer. PMID:32180804
Hepamine - A Liver Disease Microarray Database, Visualization Platform and Data-Mining Resource. PMID:32179762
Effects of High-Dose Ionizing Radiation in Human Gene Expression: A Meta-Analysis. PMID:32178397
Identification of the differential expression of genes and upstream microRNAs in small cell lung cancer compared with normal lung based on bioinformatics analysis. PMID:32176034
Systematical Analysis of the Cancer Genome Atlas Database Reveals EMCN/MUC15 Combination as a Prognostic Signature for Gastric Cancer. PMID:32175327
MoAIMS: efficient software for detection of enriched regions of MeRIP-Seq. PMID:32171255
Genes associated with inflammation may serve as biomarkers for the diagnosis of coronary artery disease and ischaemic stroke. PMID:32164735
Screening and identification of critical biomarkers in erectile dysfunction: evidence from bioinformatic analysis. PMID:32161689
Fibroblast-specific genome-scale modelling predicts an imbalance in amino acid metabolism in Refsum disease. PMID:32160399
Effects of fasting on the expression pattern of FGFs in different skeletal muscle fibre types and sexes in mice. PMID:32156311
miR-1323 Promotes Cell Migration in Lung Adenocarcinoma by Targeting Cbl-b and Is an Early Prognostic Biomarker. PMID:32154175
A paracrine activin A-mDia2 axis promotes squamous carcinogenesis via fibroblast reprogramming. PMID:32150356
Downregulation of orosomucoid 2 acts as a prognostic factor associated with cancer-promoting pathways in liver cancer. PMID:32148378
CancerLivER: a database of liver cancer gene expression resources and biomarkers. PMID:32147717
NBIA: a network-based integrative analysis framework - applied to pathway analysis. PMID:32144346
GXD's RNA-Seq and Microarray Experiment Search: using curated metadata to reliably find mouse expression studies of interest. PMID:32140729
The Prognostic Significance of Metabolic Syndrome and a Related Six-lncRNA Signature in Esophageal Squamous Cell Carcinoma. PMID:32133283
Leptin and fractalkine: novel subcutaneous cytokines in burn injury. PMID:32127397
CDK1 and CDC20 overexpression in patients with colorectal cancer are associated with poor prognosis: evidence from integrated bioinformatics analysis. PMID:32127012
Comprehensive analysis of differential immunocyte infiltration and the potential ceRNA networks during epicardial adipose tissue development in congenital heart disease. PMID:32122382
Probe Signal Values in mRNA Arrays Imply an Excessive Involvement of Neutrophil FCGR1 in Tuberculosis. PMID:32118006
Comprehensive Review of Web Servers and Bioinformatics Tools for Cancer Prognosis Analysis. PMID:32117725
Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age. PMID:32114984
Transcriptome differences in adipose stromal cells derived from pre- and postmenopausal women. PMID:32111240
Restraining Lysosomal Activity Preserves Hematopoietic Stem Cell Quiescence and Potency. PMID:32109377
A Novel Three-miRNA Signature Identified Using Bioinformatics Predicts Survival in Esophageal Carcinoma. PMID:32104700
Data libraries - the missing element for modeling biological systems. PMID:32100391
Equivalent change enrichment analysis: assessing equivalent and inverse change in biological pathways between diverse experiments. PMID:32093613
Vitamin D Receptor Overexpression in β-Cells Ameliorates Diabetes in Mice. PMID:32086292
Hierarchical chromatin organization detected by TADpole. PMID:32083658
A Guide to Conquer the Biological Network Era Using Graph Theory. PMID:32083072
Microglia control vascular architecture via a TGFβ1 dependent paracrine mechanism linked to tissue mechanics. PMID:32080187
Misregulation of ELK1, AP1, and E12 Transcription Factor Networks Is Associated with Melanoma Progression. PMID:32079144
Disrupted Gene Networks in Subfertile Hybrid House Mice. PMID:32076722
Prognostic values of a novel multi-mRNA signature for predicting relapse of cholangiocarcinoma. PMID:32071556
IPF pathogenesis is dependent upon TGFβ induction of IGF-1. PMID:32067272
The IL1β-HER2-CLDN18/CLDN4 axis mediates lung barrier damage in ARDS. PMID:32065780
Gene signatures and potential therapeutic targets of amino acid metabolism in estrogen receptor-positive breast cancer. PMID:32064155
A systems approach to infectious disease. PMID:32060427
Identification and validation of key genes with prognostic value in non-small-cell lung cancer via integrated bioinformatics analysis. PMID:32059076
Enhancing reproducibility of gene expression analysis with known protein functional relationships: The concept of well-associated protein. PMID:32058996
Identification of Hub Genes and Pathways in Gastric Adenocarcinoma Based on Bioinformatics Analysis. PMID:32058995
A systematic integrative approach reveals novel microRNAs in diabetic nephropathy. PMID:32055241
GsmPlot: a web server to visualize epigenome data in NCBI. PMID:32050905
Transcriptional Signatures of Tau and Amyloid Neuropathology. PMID:32049030
Screening and Identification of Key Biomarkers for Bladder Cancer: A Study Based on TCGA and GEO Data. PMID:32047816
A Functional Landscape of CKD Entities From Public Transcriptomic Data. PMID:32043035
A Network-Based Bioinformatics Approach to Identify Molecular Biomarkers for Type 2 Diabetes that Are Linked to the Progression of Neurological Diseases. PMID:32041280
Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data. PMID:32039697
Identification of a Two-Gene (PML-EPB41) Signature With Independent Prognostic Value in Osteosarcoma. PMID:32039036
APC-β-catenin-TCF signaling silences the intestinal guanylin-GUCY2C tumor suppressor axis. PMID:32037952
PlaPPISite: a comprehensive resource for plant protein-protein interaction sites. PMID:32028878
Comprehensive analysis of tumor necrosis factor receptor TNFRSF9 (4-1BB) DNA methylation with regard to molecular and clinicopathological features, immune infiltrates, and response prediction to immunotherapy in melanoma. PMID:32028068
Toward a gold standard for benchmarking gene set enrichment analysis. PMID:32026945
Synthetic analogues of 2-oxo acids discriminate metabolic contribution of the 2-oxoglutarate and 2-oxoadipate dehydrogenases in mammalian cells and tissues. PMID:32024885
Transcriptional effects of copy number alterations in a large set of human cancers. PMID:32024838
Cytosolic GLUTAMINE SYNTHETASE1;1 Modulates Metabolism and Chloroplast Development in Roots. PMID:32024696
Bioinformatics for Renal and Urinary Proteomics: Call for Aggrandization. PMID:32024005
Construction of a prognosis‑associated long noncoding RNA‑mRNA network for multiple myeloma based on microarray and bioinformatics analysis. PMID:32016443
Identification of a potentially functional circRNA-miRNA-mRNA regulatory network for investigating pathogenesis and providing possible biomarkers of bladder cancer. PMID:32015691
Dual disruption of aldehyde dehydrogenases 1 and 3 promotes functional changes in the glutathione redox system and enhances chemosensitivity in nonsmall cell lung cancer. PMID:32015486
Gene expression profile and bioinformatics analysis revealed key molecular characteristics of chordoma-before and after TNF- a treatment. PMID:32011476
Screening of potential biomarkers and their predictive value in early stage non-small cell lung cancer: a bioinformatics analysis. PMID:32010558
RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs for discerning baseline expression exclusivity of candidate biomarkers. PMID:32009518
Analysis of circular RNA-associated competing endogenous RNA network in breast cancer. PMID:32002039
Identification of Platform-Independent Diagnostic Biomarker Panel for Hepatocellular Carcinoma Using Large-Scale Transcriptomics Data. PMID:31998366
Transcriptome Analysis of Pineal Glands in the Mouse Model of Alzheimer's Disease. PMID:31998073
Narrowing the Gap Between In Vitro and In Vivo Genetic Profiles by Deconvoluting Toxicogenomic Data In Silico. PMID:31992983
Key genes with prognostic values in suppression of osteosarcoma metastasis using comprehensive analysis. PMID:31992246
A comparison of curated gene sets versus transcriptomics-derived gene signatures for detecting pathway activation in immune cells. PMID:31992182
Integrated bioinformatics analysis for the screening of hub genes and therapeutic drugs in ovarian cancer. PMID:31987036
All of gene expression (AOE): An integrated index for public gene expression databases. PMID:31978081
Harnessing symbiotic plant-fungus interactions to unleash hidden forces from extreme plant ecosystems. PMID:31976537
Identification of aberrantly methylated‑differentially expressed genes and gene ontology in prostate cancer. PMID:31974616
CRL4-Cereblon complex in Thalidomide Embryopathy: a translational investigation. PMID:31964914
Exceptional Response of Metastatic Chromophobe Renal Cell Carcinoma to Vascular Endothelial Growth Factor (VEGF) Inhibitors: Should Increased VEGF-C Expression Be Used to Guide Treatment? PMID:31956465
Open Data for Differential Network Analysis in Glioma. PMID:31952211
Prevalence and architecture of posttranscriptionally impaired synonymous mutations in 8,320 genomes across 22 cancer types. PMID:31950163
Integrated Bioinformatics Analysis Identifies Hub Genes Associated with the Pathogenesis and Prognosis of Esophageal Squamous Cell Carcinoma. PMID:31950035
Discovery of microarray-identified genes associated with the progression of cervical intraepithelial neoplasia. PMID:31949653
FOXM1 functions collaboratively with PLAU to promote gastric cancer progression. PMID:31949481
PulmonDB: a curated lung disease gene expression database. PMID:31949184
Meta-Analysis of Dilated Cardiomyopathy Using Cardiac RNA-Seq Transcriptomic Datasets. PMID:31948008
Site-Specific Expression Pattern of PIWI-Interacting RNA in Skin and Oral Mucosal Wound Healing. PMID:31947648
The Influence of Met Receptor Level on HGF-Induced Glycolytic Reprogramming in Head and Neck Squamous Cell Carcinoma. PMID:31940827
In Vitro, In Vivo, and In Silico Methods for Assessment of Muscle Size and Muscle Growth Regulation. PMID:31939770
Sorafenib Inhibits Ribonucleotide Reductase Regulatory Subunit M2 (RRM2) in Hepatocellular Carcinoma Cells. PMID:31936661
Meta-Analysis of Hypoxic Transcriptomes from Public Databases. PMID:31936636
General and Genomic DNA-Binding Specificity for the Thermus thermophilus HB8 Transcription Factor TTHB023. PMID:31935968
Comparing DNA methylation profiles across different tissues associated with the diagnosis of pediatric asthma. PMID:31932625
Integrative Bioinformatics Approaches to Map Potential Novel Genes and Pathways Involved in Ovarian Cancer. PMID:31921802
Comparative analysis on the expression of L1 loci using various RNA-Seq preparations. PMID:31921361
Meta-Analysis of in vitro-Differentiated Macrophages Identifies Transcriptomic Signatures That Classify Disease Macrophages in vivo. PMID:31921150
DNA hypermethylation associated with upregulated gene expression in prostate cancer demonstrates the diversity of epigenetic regulation. PMID:31914996
Transcriptome analyses identify hub genes and potential mechanisms in adenoid cystic carcinoma. PMID:31914060
Tissue of origin dictates GOT1 dependence and confers synthetic lethality to radiotherapy. PMID:31908776
Identification and characterization of genes frequently responsive to Xanthomonas oryzae pv. oryzae and Magnaporthe oryzae infections in rice. PMID:31906847
RNAInter in 2020: RNA interactome repository with increased coverage and annotation. PMID:31906603
Machine and deep learning approaches for cancer drug repurposing. PMID:31904426
Molecular modelling and docking analysis of pleurocidin (an antimicrobial peptide) like peptides with enterotoxin H from Klebsilla pneumonia. PMID:31902985
Bile and urine peptide marker profiles: access keys to molecular pathways and biological processes in cholangiocarcinoma. PMID:31900160
Identification of key candidate tumor biomarkers in non-small-cell lung cancer by in silico analysis. PMID:31897214
Gene expression-based analysis identified NTNG1 and HGF as biomarkers for diabetic kidney disease. PMID:31895808
Comprehensive identification and characterization of somatic copy number alterations in triple‑negative breast cancer. PMID:31894314
Integrative Gene Expression Profiling Analysis to Investigate Potential Prognostic Biomarkers for Colorectal Cancer. PMID:31893510
Integrated analysis of gene modulation profile identifies pathogenic factors and pathways in the liver of diabetic mice. PMID:31890673
Integrative Analysis of Axolotl Gene Expression Data from Regenerative and Wound Healing Limb Tissues. PMID:31889169
High-level integration of murine intestinal transcriptomics data highlights the importance of the complement system in mucosal homeostasis. PMID:31888466
Bioinformatic Analysis of Circular RNA-Associated ceRNA Network Associated with Hepatocellular Carcinoma. PMID:31886256
Identification of Key Genes and Prognostic Value Analysis in Hepatocellular Carcinoma by Integrated Bioinformatics Analysis. PMID:31886163
STAT3 speeds up progression of osteoarthritis through NF-κB signaling pathway. PMID:31885710
Analysis of gene expression profiles and protein-protein interaction networks in multiple tissues of systemic sclerosis. PMID:31881890
Genome-Scale Metabolic Modeling with Protein Expressions of Normal and Cancerous Colorectal Tissues for Oncogene Inference. PMID:31881674
Mutations in PDLIM5 are rare in dilated cardiomyopathy but are emerging as potential disease modifiers. PMID:31880413
Genetic links between endometriosis and cancers in women. PMID:31879572
The circadian clock protein REVERBα inhibits pulmonary fibrosis development. PMID:31879343
Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation. PMID:31876091
Gene Expression Meta-Analysis Reveals Concordance in Gene Activation, Pathway, and Cell-Type Enrichment in Dermatomyositis Target Tissues. PMID:31872188
Systematic analysis of gene expression profiles reveals prognostic stratification and underlying mechanisms for muscle-invasive bladder cancer. PMID:31866765
VIO: ontology classification and study of vaccine responses given various experimental and analytical conditions. PMID:31865910
Transcriptome analysis-identified long noncoding RNA CRNDE in maintaining endothelial cell proliferation, migration, and tube formation. PMID:31863035
Hdac3, Setdb1, and Kap1 mark H3K9me3/H3K14ac bivalent regions in young and aged liver. PMID:31858687
Identification of lung cancer gene markers through kernel maximum mean discrepancy and information entropy. PMID:31856830
The InsP7 phosphatase Siw14 regulates inositol pyrophosphate levels to control localization of the general stress response transcription factor Msn2. PMID:31848224
MeinteR: A framework to prioritize DNA methylation aberrations based on conformational and cis-regulatory element enrichment. PMID:31844073
BCL2 and hsa-miR-181a-5p are potential biomarkers associated with papillary thyroid cancer based on bioinformatics analysis. PMID:31842912
Vascular PPARβ/δ Promotes Tumor Angiogenesis and Progression. PMID:31842402
cDC2 and plasmacytoid dendritic cells diminish from tissues of patients with non-Hodgkin orbital lymphoma and idiopathic orbital inflammation. PMID:31841217
Systematic Analysis of Transcriptomic Profile of the Effects of Low Dose Atropine Treatment on Scleral Fibroblasts using Next-Generation Sequencing and Bioinformatics. PMID:31839753
Engaging a community to enable disease-centric data sharing with the NF Data Portal. PMID:31836719
Use of gene expression studies to investigate the human immunological response to malaria infection. PMID:31835999
TRANSNAP: a web database providing comprehensive information on Japanese pear transcriptome. PMID:31831861
Differences in the intrinsic spatial dynamics of the chromatin contribute to cell differentiation. PMID:31828312
Modeling Progressive Fibrosis with Pluripotent Stem Cells Identifies an Anti-fibrotic Small Molecule. PMID:31825831
Screening Hub Genes as Prognostic Biomarkers of Hepatocellular Carcinoma by Bioinformatics Analysis. PMID:31822116
Integrated analysis identifies DUSP5 as a novel prognostic indicator for thyroid follicular carcinoma. PMID:31821724
Identification of Hub Genes in Pediatric Medulloblastoma by Multiple-Microarray Analysis. PMID:31820345
NicheNet: modeling intercellular communication by linking ligands to target genes. PMID:31819264
A comprehensive resource for retrieving, visualizing, and integrating functional genomics data. PMID:31818883
Identification of molecular correlations of RBM8A with autophagy in Alzheimer's disease. PMID:31816601
A Bioinformatic Approach for the Identification of Molecular Determinants of Resistance/Sensitivity to Cancer Thermotherapy. PMID:31814876
MELK is Upregulated in Advanced Clear Cell Renal Cell Carcinoma and Promotes Disease Progression by Phosphorylating PRAS40. PMID:31813279
GliomaDB: A Web Server for Integrating Glioma Omics Data and Interactive Analysis. PMID:31811943
A twenty gene-based gene set variation score reflects the pathological progression from cirrhosis to hepatocellular carcinoma. PMID:31811111
Human gene expression variability and its dependence on methylation and aging. PMID:31810449
A novel genetic circuitry governing hypoxic metabolic flexibility, commensalism and virulence in the fungal pathogen Candida albicans. PMID:31809527
Slow skeletal muscle troponin T, titin and myosin light chain 3 are candidate prognostic biomarkers for Ewing's sarcoma. PMID:31807166
Emerging Roles Of hsa-circ-0046600 Targeting The miR-640/HIF-1α Signalling Pathway In The Progression Of HCC. PMID:31807009
Identification and Integrated Analysis of Key Biomarkers for Diagnosis and Prognosis of Non-Small Cell Lung Cancer. PMID:31805030
New Approaches for Quantitative Reconstruction of Radiation Dose in Human Blood Cells. PMID:31804590
Stress-induced changes in the expression of antioxidant system genes for rice (Oryza sativa L.) and bread wheat (Triticum aestivum L.). PMID:31803533
TIMP1 Is A Potential Key Gene Associated With The Pathogenesis And Prognosis Of Ulcerative Colitis-Associated Colorectal Cancer. PMID:31802901
Cardioinformatics: the nexus of bioinformatics and precision cardiology. PMID:31802103
c-Jun overexpression in CAR T cells induces exhaustion resistance. PMID:31802004
mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations. PMID:31799603
A novel circRNA-miRNA-mRNA network identifies circ-YOD1 as a biomarker for coronary artery disease. PMID:31797949
The Escherichia coli transcriptome mostly consists of independently regulated modules. PMID:31797920
The notch target gene HEYL modulates metastasis forming capacity of colorectal cancer patient-derived spheroid cells in vivo. PMID:31796022
Identification of Susceptibility Genes to Allergic Rhinitis by Gene Expression Data Sets. PMID:31794148
Identification of key candidate genes for colorectal cancer by bioinformatics analysis. PMID:31788116
The core genes involved in the promotion of depression in patients with ovarian cancer. PMID:31788074
Identification of key genes and evaluation of clinical outcomes in lung squamous cell carcinoma using integrated bioinformatics analysis. PMID:31788059
HTRgene: a computational method to perform the integrated analysis of multiple heterogeneous time-series data: case analysis of cold and heat stress response signaling genes in Arabidopsis. PMID:31787073
Integrating the Ribonucleic Acid Sequencing Data From Various Studies for Exploring the Multiple Sclerosis-Related Long Noncoding Ribonucleic Acids and Their Functions. PMID:31781177
Genetic Predisposition to Glioma Mediated by a MAPKAP1 Enhancer Variant. PMID:31773361
Bioinformatics analysis of hepatic gene expression profiles in type 2 diabetes mellitus. PMID:31772629
Mega-Analysis of Gene Expression in Mouse Models of Alzheimer's Disease. PMID:31767574
TACITuS: transcriptomic data collector, integrator, and selector on big data platform. PMID:31757212
Identifying gene function and module connections by the integration of multispecies expression compendia. PMID:31754022
The ENCODE Portal as an Epigenomics Resource. PMID:31751002
Prospective validation in epithelial tumors of a gene expression predictor of liver metastasis derived from uveal melanoma. PMID:31748560
ADAPTS: Automated deconvolution augmentation of profiles for tissue specific cells. PMID:31743345
EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species. PMID:31740966
Non-del(5q) myelodysplastic syndromes-associated loci detected by SNP-array genome-wide association meta-analysis. PMID:31738830
Gene Expression and Fatty Acid Profiling in Longissimus thoracis Muscle, Subcutaneous Fat, and Liver of Light Lambs in Response to Concentrate or Alfalfa Grazing. PMID:31737049
Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a model organism database. PMID:31733057
DIANA-LncBase v3: indexing experimentally supported miRNA targets on non-coding transcripts. PMID:31732741
Deciphering signalling network in broad spectrum Near Isogenic Lines of rice resistant to Magnaporthe oryzae. PMID:31729398
Characterisation of the developing heart in a pressure overloaded model utilising RNA sequencing to direct functional analysis. PMID:31724174
Sex Differences in the Blood Transcriptome Identify Robust Changes in Immune Cell Proportions with Aging and Influenza Infection. PMID:31722210
Virtual screening of a MDR-TB WhiB6 target identified by gene expression profiling. PMID:31719765
Functional association between NUCKS1 gene and Parkinson disease: A potential susceptibility biomarker. PMID:31719764
Recurrent functional misinterpretation of RNA-seq data caused by sample-specific gene length bias. PMID:31714939
RPGeNet v2.0: expanding the universe of retinal disease gene interactions network. PMID:31712826
FreeHi-C simulates high-fidelity Hi-C data for benchmarking and data augmentation. PMID:31712779
Decreased plasma phospholipid concentrations and increased acid sphingomyelinase activity are accurate biomarkers for community-acquired pneumonia. PMID:31711507
Cell-Free DNA Methylation Profiling Analysis-Technologies and Bioinformatics. PMID:31698791
Measurement of Conditional Relatedness Between Genes Using Fully Convolutional Neural Network. PMID:31695723
AppleMDO: A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States. PMID:31695717
Genetic Interactions Affect Lung Function in Patients with Systemic Sclerosis. PMID:31694854
Co-regulation map of the human proteome enables identification of protein functions. PMID:31690884
Analysis of the structural variability of topologically associated domains as revealed by Hi-C. PMID:31687663
Regulation of Pyridine Nucleotide Metabolism During Tomato Fruit Development Through Transcript and Protein Profiling. PMID:31681351
MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect. PMID:31679514
Conserved Eukaryotic Kinase CK2 Chaperone Intrinsically Disordered Protein Interactions. PMID:31676471
NPInter v4.0: an integrated database of ncRNA interactions. PMID:31670377
A data driven approach reveals disease similarity on a molecular level. PMID:31666984
ERO1α promotes hypoxic tumor progression and is associated with poor prognosis in pancreatic cancer. PMID:31666928
Expression Atlas update: from tissues to single cells. PMID:31665515
BBCancer: an expression atlas of blood-based biomarkers in the early diagnosis of cancers. PMID:31665503
ReMap 2020: a database of regulatory regions from an integrative analysis of Human and Arabidopsis DNA-binding sequencing experiments. PMID:31665499
miR‑760 regulates skeletal muscle proliferation in rheumatoid arthritis by targeting Myo18b. PMID:31661144
Identification of a five-miRNA signature predicting survival in cutaneous melanoma cancer patients. PMID:31660262
The TargetMine Data Warehouse: Enhancement and Updates. PMID:31649722
Integrated Analysis of Brain Transcriptome Reveals Convergent Molecular Pathways in Autism Spectrum Disorder. PMID:31649562
PhyloMagnet: fast and accurate screening of short-read meta-omics data using gene-centric phylogenetics. PMID:31647547
miRTarBase 2020: updates to the experimentally validated microRNA-target interaction database. PMID:31647101
Potential molecular mechanism of ACE gene at different time points in STEMI patients based on genome-wide microarray dataset. PMID:31647035
Network-Based Functional Prediction Augments Genetic Association To Predict Candidate Genes for Histamine Hypersensitivity in Mice. PMID:31645420
A semi-supervised machine learning framework for microRNA classification. PMID:31639051
Upregulation of miR‑132‑3p in cholangiocarcinoma tissues: A study based on RT‑qPCR, The Cancer Genome Atlas miRNA sequencing, Gene Expression Omnibus microarray data and bioinformatics analyses. PMID:31638221
Integrated Bioinformatics Data Analysis Reveals Prognostic Significance Of SIDT1 In Triple-Negative Breast Cancer. PMID:31632087
C3orf70 Is Involved in Neural and Neurobehavioral Development. PMID:31623237
Identification of potential key genes in esophageal adenocarcinoma using bioinformatics. PMID:31616504
Variance-Preserving Estimation of Intensity Values Obtained From Omics Experiments. PMID:31616468
Translational Application of Circulating DNA in Oncology: Review of the Last Decades Achievements. PMID:31615102
Biological Network Approaches and Applications in Rare Disease Studies. PMID:31614842
Transcriptome visualization and data availability at the Saccharomyces Genome Database. PMID:31612944
Electron transport chain biogenesis activated by a JNK-insulin-Myc relay primes mitochondrial inheritance in Drosophila. PMID:31612862
Identification of hub genes and construction of transcriptional regulatory network for the progression of colon adenocarcinoma hub genes and TF regulatory network of colon adenocarcinoma. PMID:31612481
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
Identification of key biomarkers and potential molecular mechanisms in lung cancer by bioinformatics analysis. PMID:31611952
Deep learning for stage prediction in neuroblastoma using gene expression data. PMID:31610626
PmiREN: a comprehensive encyclopedia of plant miRNAs. PMID:31602478
Identification of key candidate genes and pathways in glioblastoma by integrated bioinformatical analysis. PMID:31602219
A feature selection strategy for gene expression time series experiments with hidden Markov models. PMID:31600242
SEAweb: the small RNA Expression Atlas web application. PMID:31598718
KnockTF: a comprehensive human gene expression profile database with knockdown/knockout of transcription factors. PMID:31598675
A qualitative transcriptional signature for determining the grade of colorectal adenocarcinoma. PMID:31595030
Bringing radiomics into a multi-omics framework for a comprehensive genotype-phenotype characterization of oncological diseases. PMID:31590671
DNA Methylation Markers for Pan-Cancer Prediction by Deep Learning. PMID:31590287
EWAS Data Hub: a resource of DNA methylation array data and metadata. PMID:31584095
High-efficiency CRISPR induction of t(9;11) chromosomal translocations and acute leukemias in human blood stem cells. PMID:31582391
An Integrated Bioinformatics Analysis Repurposes an Antihelminthic Drug Niclosamide for Treating HMGA2-Overexpressing Human Colorectal Cancer. PMID:31581665
Experimental and Computational Approaches to Direct Cell Reprogramming: Recent Advancement and Future Challenges. PMID:31581647
Molecular evolution of the meiotic recombination pathway in mammals. PMID:31579931
MicroRNA-424 regulates cisplatin resistance of gastric cancer by targeting SMURF1 based on GEO database and primary validation in human gastric cancer tissues. PMID:31571913
The CLN3 gene and protein: What we know. PMID:31568712
Identification of gene and microRNA changes in response to smoking in human airway epithelium by bioinformatics analyses. PMID:31568004
ELTD1 facilitates glioma proliferation, migration and invasion by activating JAK/STAT3/HIF-1α signaling axis. PMID:31554859
Proton Therapy and Src Family Kinase Inhibitor Combined Treatments on U87 Human Glioblastoma Multiforme Cell Line. PMID:31554327
Signatures of cell death and proliferation in perturbation transcriptomics data-from confounding factor to effective prediction. PMID:31552418
Integrated Analysis of Multiple Microarray Studies to Identify Novel Gene Signatures in Non-alcoholic Fatty Liver Disease. PMID:31551930
Drug repurposing for breast cancer therapy: Old weapon for new battle. PMID:31550502
Targeted transcriptional modulation with type I CRISPR-Cas systems in human cells. PMID:31548729
Screening and identification of biomarkers for systemic sclerosis via microarray technology. PMID:31545397
Multi-view based integrative analysis of gene expression data for identifying biomarkers. PMID:31534156
Identification of Key Pathways and Genes of Acute Respiratory Distress Syndrome Specific Neutrophil Phenotype. PMID:31531373
Integrative analysis of the contribution of mRNAs and long non‑coding RNAs to the pathogenesis of asthma. PMID:31524265
Identification of hub genes and molecular mechanisms in infant acute lymphoblastic leukemia with MLL gene rearrangement. PMID:31523525
Deep insights into the response of human cervical carcinoma cells to a new cyano enone-bearing triterpenoid soloxolone methyl: a transcriptome analysis. PMID:31523389
Suitability of ultrasound-guided fine-needle aspiration biopsy for transcriptome sequencing of the canine prostate. PMID:31519932
Murine Perinatal β-Cell Proliferation and the Differentiation of Human Stem Cell-Derived Insulin-Expressing Cells Require NEUROD1. PMID:31519700
Identification of β-catenin target genes in colorectal cancer by interrogating gene fitness screening data. PMID:31516589
Identification of differentially expressed genes between primary lung cancer and lymph node metastasis via bioinformatic analysis. PMID:31516588
Dysregulation of N6-methyladenosine regulators predicts poor patient survival in mantle cell lymphoma. PMID:31516580
Bioinformatics analysis identifies hub genes and pathways in nasopharyngeal carcinoma. PMID:31516577
Cross-disease analysis identified novel common genes for both lung adenocarcinoma and lung squamous cell carcinoma. PMID:31516564
The Cancer-Associated Genetic Variant Rs3903072 Modulates Immune Cells in the Tumor Microenvironment. PMID:31507631
Considerations for Strategic Use of High-Throughput Transcriptomics Chemical Screening Data in Regulatory Decisions. PMID:31501805
Gestational Diabetes Mellitus Regulatory Network Identifies hsa-miR-145-5p and hsa-miR-875-5p as Potential Biomarkers. PMID:31497041
VARIDT 1.0: variability of drug transporter database. PMID:31495872
A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases. PMID:31494632
Computer aided analysis of disease linked protein networks. PMID:31485137
Transcriptome based Identification of silver stress responsive sRNAs from Bacillus cereus ATCC14579. PMID:31485133
CiiiDER: A tool for predicting and analysing transcription factor binding sites. PMID:31483836
Interrogation of a live-attenuated enterotoxigenic Escherichia coli vaccine highlights features unique to wild-type infection. PMID:31482013
Identification of Hub Genes and Key Pathways Associated With Bipolar Disorder Based on Weighted Gene Co-expression Network Analysis. PMID:31481902
Potentially repurposable drugs for schizophrenia identified from its interactome. PMID:31481665
Serotonin and Dopamine Receptor Expression in Solid Tumours Including Rare Cancers. PMID:31478179
Peripheral blood DNA methylation differences in twin pairs discordant for Alzheimer's disease. PMID:31477183
Novel computational model of gastrula morphogenesis to identify spatial discriminator genes by self-organizing map (SOM) clustering. PMID:31467377
Multi-study reanalysis of 2,213 acute myeloid leukemia patients reveals age- and sex-dependent gene expression signatures. PMID:31455838
Reporters of TCR signaling identify arthritogenic T cells in murine and human autoimmune arthritis. PMID:31455730
Screening and identification of potential target genes in head and neck cancer using bioinformatics analysis. PMID:31452775
Identification of aberrantly methylated differentially expressed genes in glioblastoma multiforme and their association with patient survival. PMID:31452706
JNK1 Induces Notch1 Expression to Regulate Genes Governing Photoreceptor Production. PMID:31450635
Target Genes of Autism Risk Loci in Brain Frontal Cortex. PMID:31447881
Calvarial osteoblast gene expression in patients with craniosynostosis leads to novel polygenic mouse model. PMID:31442251
The Inducible Response of the Nematode Caenorhabditis elegans to Members of Its Natural Microbiota Across Development and Adult Life. PMID:31440221
Statistical genomics in rare cancer. PMID:31437624
A de novo evolved gene in the house mouse regulates female pregnancy cycles. PMID:31436535
Leveraging cell-specific differentially methylated regions to identify leukocyte infiltration in adipose tissue. PMID:31433079
Identification of key miRNA‑mRNA pairs in septic mice by bioinformatics analysis. PMID:31432183
MAP‑1B, PACS‑2 and AHCYL1 are regulated by miR‑34A/B/C and miR‑449 in neuroplasticity following traumatic spinal cord injury in rats: Preliminary explorative results from microarray data. PMID:31432119
Identification of candidate genes and miRNAs associated with neuropathic pain induced by spared nerve injury. PMID:31432094
HSP90/AXL/eIF4E-regulated unfolded protein response as an acquired vulnerability in drug-resistant KRAS-mutant lung cancer. PMID:31431614
CFEA: a cell-free epigenome atlas in human diseases. PMID:31428785
Differential Expression Profiles of the Transcriptome and miRNA Interactome in Synovial Fibroblasts of Rheumatoid Arthritis Revealed by Next Generation Sequencing. PMID:31426562
Integrated bioinformatics analysis to identify 15 hub genes in breast cancer. PMID:31423162
Analysis of transcription factor- and ncRNA-mediated potential pathogenic gene modules in Alzheimer's disease. PMID:31422384
Exploring the new horizons of drug repurposing: A vital tool for turning hard work into smart work. PMID:31421629
Systematic analysis of the frequently amplified 2p15-p16.1 locus reveals PAPOLG as a potential proto-oncogene in follicular and transformed follicular lymphoma. PMID:31410080
A role for Regulator of G protein Signaling-12 (RGS12) in the balance between myoblast proliferation and differentiation. PMID:31408461
The epigenetic factor BORIS (CTCFL) controls the androgen receptor regulatory network in ovarian cancer. PMID:31406110
Progress in data interoperability to support computational toxicology and chemical safety evaluation. PMID:31404555
Heterocellular gene signatures reveal luminal-A breast cancer heterogeneity and differential therapeutic responses. PMID:31396557
Can Biofilm Be Reversed Through Quorum Sensing in Pseudomonas aeruginosa? PMID:31396166
An influenza virus-triggered SUMO switch orchestrates co-opted endogenous retroviruses to stimulate host antiviral immunity. PMID:31391303
Connecting signaling and metabolic pathways in EGF receptor-mediated oncogenesis of glioblastoma. PMID:31386654
Identifying miltefosine-resistant key genes in protein-protein interactions network and experimental verification in Iranian Leishmania major. PMID:31385238
Integration of Gene Expression Profile Data to Verify Hub Genes of Patients with Stanford A Aortic Dissection. PMID:31380418
Analysis of methylation datasets identified significantly changed genes and functional pathways in osteoarthritis. PMID:31376087
Identification of key candidate targets and pathways for the targeted treatment of leukemia stem cells of chronic myelogenous leukemia using bioinformatics analysis. PMID:31373443
An integrative bioinformatics analysis identified miR-375 as a candidate key regulator of malignant breast cancer. PMID:31372832
Disparity in Tumor Immune Microenvironment of Breast Cancer and Prognostic Impact: Asian Versus Western Populations. PMID:31371522
Dissection of acute stimulus-inducible nucleosome remodeling in mammalian cells. PMID:31371436
Radiosensitizing effect of curcumin-loaded lipid nanoparticles in breast cancer cells. PMID:31366901
Daphnia stressor database: Taking advantage of a decade of Daphnia '-omics' data for gene annotation. PMID:31366898
Multi-view Co-training for microRNA Prediction. PMID:31358877
Tumor intrinsic immunity related proteins may be novel tumor suppressors in some types of cancer. PMID:31358815
RNA sequencing profiling of the retina in C57BL/6J and DBA/2J mice: Enhancing the retinal microarray data sets from GeneNetwork. PMID:31354228
A novel pan-cancer biomarker plasma heat shock protein 90alpha and its diagnosis determinants in clinic. PMID:31343810
Identification and Interaction Analysis of Significant Genes and MicroRNAs in Pterygium. PMID:31341891
A plea for taking all available clinical information into account when assessing the predictive value of omics data. PMID:31340753
Identification of Gene Changes Induced by Dexamethasone in the Anterior Segment of the Human Eye Using Bioinformatics Analysis. PMID:31339875
Identification of differentially expressed genes in small and non-small cell lung cancer based on meta-analysis of mRNA. PMID:31338439
Genetic mapping in Diversity Outbred mice identifies a Trpa1 variant influencing late-phase formalin response. PMID:31335644
Upregulation of nucleoprotein AHNAK is associated with poor outcome of pancreatic ductal adenocarcinoma prognosis via mediating epithelial-mesenchymal transition. PMID:31333803
Microenvironment of ruptured cerebral aneurysms discovered using data driven analysis of gene expression. PMID:31329646
Important regulatory function of transient receptor potential ankyrin 1 receptors in age-related learning and memory alterations of mice. PMID:31327098
SMAC, a computational system to link literature, biomedical and expression data. PMID:31324861
Bioinformatics-based discovery of PYGM and TNNC2 as potential biomarkers of head and neck squamous cell carcinoma. PMID:31324732
Identification of differentially expressed genes in hip cartilage with femoral head necrosis, based on genome‑wide expression profiles. PMID:31322206
mTORC1/AMPK responses define a core gene set for developmental cell fate switching. PMID:31319820
Membrane protein-regulated networks across human cancers. PMID:31311925
Centromere Satellite Repeats Have Undergone Rapid Changes in Polyploid Wheat Subgenomes. PMID:31311836
Identification of novel genes associated with a poor prognosis in pancreatic ductal adenocarcinoma via a bioinformatics analysis. PMID:31311829
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
A Comprehensive Survey on the Terpene Synthase Gene Family Provides New Insight into Its Evolutionary Patterns. PMID:31304957
Loss of Bcl-G, a Bcl-2 family member, augments the development of inflammation-associated colorectal cancer. PMID:31296963
Regulation of tumor angiogenesis and mesenchymal-endothelial transition by p38α through TGF-β and JNK signaling. PMID:31296856
Systematic evaluation of RNA-Seq preparation protocol performance. PMID:31296163
Screening of immunosuppressive factors for biomarkers of breast cancer malignancy phenotypes and subtype-specific targeted therapy. PMID:31293831
Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates. PMID:31292258
Bioinformatics prediction and analysis of hub genes and pathways of three types of gynecological cancer. PMID:31289534
Identification of potential diagnostic and therapeutic target genes for lung squamous cell carcinoma. PMID:31289486
MTHFD2 links RNA methylation to metabolic reprogramming in renal cell carcinoma. PMID:31289360
Pathological changes are associated with shifts in the employment of synonymous codons at the transcriptome level. PMID:31288782
Stromal integrin α11 regulates PDGFR-β signaling and promotes breast cancer progression. PMID:31287804
Identification and Characterization of Preferred DNA-Binding Sites for the Thermus thermophilus HB8 Transcriptional Regulator TTHA0973. PMID:31284644
Genome-wide functional association networks: background, data & state-of-the-art resources. PMID:31281921
Identification of age- and gender-associated long noncoding RNAs in the human brain with Alzheimer's disease. PMID:31280115
Identification of crucial miRNAs and genes in esophageal squamous cell carcinoma by miRNA-mRNA integrated analysis. PMID:31277149
Cross-species functional modules link proteostasis to human normal aging. PMID:31269015
Meta-Analysis of Microarray Expression Studies on Metformin in Cancer Cell Lines. PMID:31261735
L1000 Viewer: A Search Engine and Web Interface for the LINCS Data Repository. PMID:31258549
PropaNet: Time-Varying Condition-Specific Transcriptional Network Construction by Network Propagation. PMID:31258543
Inferring Interaction Networks From Multi-Omics Data. PMID:31249591
Gene expression signature of atypical breast hyperplasia and regulation by SFRP1. PMID:31248446
Leveraging the Role of the Metastatic Associated Protein Anterior Gradient Homologue 2 in Unfolded Protein Degradation: A Novel Therapeutic Biomarker for Cancer. PMID:31247903
Identification of gene expression logical invariants in Arabidopsis. PMID:31245766
Cross-species complementation reveals conserved functions for EARLY FLOWERING 3 between monocots and dicots. PMID:31245666
Co-expression Network Analysis Elucidated a Core Module in Association With Prognosis of Non-functioning Non-invasive Human Pituitary Adenoma. PMID:31244774
In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR. PMID:31244651
Gene Expression Profiles Induced by High-dose Ionizing Radiation in MDA-MB-231 Triple-negative Breast Cancer Cell Line. PMID:31243106
Essential guidelines for computational method benchmarking. PMID:31221194
BCScreen: A gene panel to test for breast carcinogenesis in chemical safety screening. PMID:31218268
Noncoding deletions reveal a gene that is critical for intestinal function. PMID:31217582
Characterizing building blocks of resource constrained biological networks. PMID:31216986
Analysis of Genes Involved in Ulcerative Colitis Activity and Tumorigenesis Through Systematic Mining of Gene Co-expression Networks. PMID:31214045
Identification of key genes and pathways in Ewing's sarcoma patients associated with metastasis and poor prognosis. PMID:31213834
Locally advanced rectal cancer transcriptomic-based secretome analysis reveals novel biomarkers useful to identify patients according to neoadjuvant chemoradiotherapy response. PMID:31213644
Identify the Key Active Ingredients and Pharmacological Mechanisms of Compound XiongShao Capsule in Treating Diabetic Peripheral Neuropathy by Network Pharmacology Approach. PMID:31210774
Chickspress: a resource for chicken gene expression. PMID:31210271
Mitochondrial Transcriptome Control and Intercompartment Cross-Talk During Plant Development. PMID:31200566
Comprehensive bioinformatics analysis of trabecular meshwork gene expression data to unravel the molecular pathogenesis of primary open-angle glaucoma. PMID:31197946
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
A novel member of Prame family, Gm12794c, counteracts retinoic acid differentiation through the methyltransferase activity of PRC2. PMID:31186534
Using literature-based discovery to identify candidate genes for the interaction between myocardial infarction and depression. PMID:31185929
A novel lncRNA-miRNA-mRNA triple network identifies lncRNA TWF1 as an important regulator of miRNA and gene expression in coronary artery disease. PMID:31182968
Bioinformatics analysis of the regulatory lncRNA‑miRNA‑mRNA network and drug prediction in patients with hypertrophic cardiomyopathy. PMID:31180540
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 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
IL-27 promotes the expansion of self-renewing CD8+ T cells in persistent viral infection. PMID:31164392
Prenatal Particulate Air Pollution and DNA Methylation in Newborns: An Epigenome-Wide Meta-Analysis. PMID:31148503
RNAmod: an integrated system for the annotation of mRNA modifications. PMID:31147718
Identification of hub genes and therapeutic drugs in esophageal squamous cell carcinoma based on integrated bioinformatics strategy. PMID:31139019
Identification of leukemia stem cell expression signatures through Monte Carlo feature selection strategy and support vector machine. PMID:31138902
Comprehensive analysis of key genes and microRNAs in radioresistant nasopharyngeal carcinoma. PMID:31138194
Gene Expression Studies to Identify Significant Genes in AR, MTOR, MAPK Pathways and their Overlapping Regulatory Role in Prostate Cancer. PMID:31136301
Systems Pharmacogenomic Landscape of Drug Similarities from LINCS data: Drug Association Networks. PMID:31127155
KEGG-expressed genes and pathways in intervertebral disc degeneration: Protocol for a systematic review and data mining. PMID:31124977
Discovering Biomarkers and Pathways Shared by Alzheimer's Disease and Ischemic Stroke to Identify Novel Therapeutic Targets. PMID:31121943
MultiPLIER: A Transfer Learning Framework for Transcriptomics Reveals Systemic Features of Rare Disease. PMID:31121115
Assessment of Novel Genome-Wide Significant Gene Loci and Lesion Growth in Geographic Atrophy Secondary to Age-Related Macular Degeneration. PMID:31120506
Acid-Sensitive Ion Channels Are Expressed in Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes. PMID:31119982
Killer-like receptors and GPR56 progressive expression defines cytokine production of human CD4+ memory T cells. PMID:31118448
ALS blood expression profiling identifies new biomarkers, patient subgroups, and evidence for neutrophilia and hypoxia. PMID:31118040
Geneshot: search engine for ranking genes from arbitrary text queries. PMID:31114885
pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. PMID:31114675
The Placental Atlas Tool (PAT): A collaborative research and discovery platform for the placental research community. PMID:31103066
Multiple genetic loci affect place learning and memory performance in Drosophila melanogaster. PMID:31095869
Genome-wide analysis revealed sex-specific gene expression in asthmatics. PMID:31095684
An Investigation about Gene Modules Associated with hDPSC Differentiation for Adolescents. PMID:31089336
A universal transcriptomic signature of age reveals the temporal scaling of Caenorhabditis elegans aging trajectories. PMID:31089188
AKIRIN1: A Potential New Reference Gene in Human Natural Killer Cells and Granulocytes in Sepsis. PMID:31075840
Extracting predictors for lung adenocarcinoma based on Granger causality test and stepwise character selection. PMID:31074380
GScluster: network-weighted gene-set clustering analysis. PMID:31072324
PAX7 target gene repression is a superior FSHD biomarker than DUX4 target gene activation, associating with pathological severity and identifying FSHD at the single-cell level. PMID:31067297
Molecular footprint of Medawar's mutation accumulation process in mammalian aging. PMID:31062469
Human transposons are an abundant supply of transcription factor binding sites and promoter activities in breast cancer cell lines. PMID:31061680
Prospective molecular mechanism of COL5A1 in breast cancer based on a microarray, RNA sequencing and immunohistochemistry. PMID:31059074
Benchmarker: An Unbiased, Association-Data-Driven Strategy to Evaluate Gene Prioritization Algorithms. PMID:31056107
Muscle Gene Sets: a versatile methodological aid to functional genomics in the neuromuscular field. PMID:31053169
Profiling of chromatin accessibility and identification of general cis-regulatory mechanisms that control two ocular lens differentiation pathways. PMID:31053165
Identification of Novel MicroRNAs and Their Diagnostic and Prognostic Significance in Oral Cancer. PMID:31052345
Distinct amino acid and lipid perturbations characterize acute versus chronic malaria. PMID:31045574
Mate choice and gene expression signatures associated with nutritional adaptation in the medfly (Ceratitis capitata). PMID:31040302
Associations between Maternal Tobacco Smoke Exposure and the Cord Blood [Formula: see text] DNA Methylome. PMID:31039056
Navigating in vitro bioactivity data by investigating available resources using model compounds. PMID:31036807
Cyclin C Regulated Oxidative Stress Responsive Transcriptome in Mus musculus Embryonic Fibroblasts. PMID:31036676
Molecular insights into an ancient form of Paget's disease of bone. PMID:31036632
Integrative Approach to Reveal Cell Type Specificity and Gene Candidates for Psoriatic Arthritis Outside the MHC. PMID:31031798
Atlas of RNA sequencing profiles for normal human tissues. PMID:31015567
Modeling Protein Destiny in Developing Fruit. PMID:31015299
The widespread increase in inter-individual variability of gene expression in the human brain with age. PMID:31003228
Transcriptome Analysis Revealed a Highly Connected Gene Module Associated With Cirrhosis to Hepatocellular Carcinoma Development. PMID:31001331
Simultaneous Interrogation of Cancer Omics to Identify Subtypes With Significant Clinical Differences. PMID:30984238
Identification of Shared Genes Between Ischemic Stroke and Parkinson's Disease Using Genome-Wide Association Studies. PMID:30984102
Integrative Analysis Reveals Subtype-Specific Regulatory Determinants in Triple Negative Breast Cancer. PMID:30974831
Identification of Target Genes at Juvenile Idiopathic Arthritis GWAS Loci in Human Neutrophils. PMID:30972099
Identification of ChIP-seq and RIME grade antibodies for Estrogen Receptor alpha. PMID:30970003
Axitinib exposure triggers endothelial cells senescence through ROS accumulation and ATM activation. PMID:30967634
Novel insights into gene expression regulation during meiosis revealed by translation elongation dynamics. PMID:30962948
Integrated analysis of gene expression changes associated with coronary artery disease. PMID:30961613
Reusable building blocks in biological systems. PMID:30958230
Elucidating the transcriptional program of feline injection-site sarcoma using a cross-species mRNA-sequencing approach. PMID:30947707
Atypical Chemokine Receptor 1 (DARC/ACKR1) in Breast Tumors Is Associated with Survival, Circulating Chemokines, Tumor-Infiltrating Immune Cells, and African Ancestry. PMID:30944146
Digital expression explorer 2: a repository of uniformly processed RNA sequencing data. PMID:30942868
Screening of disorders associated with osteosarcoma by integrated network analysis. PMID:30936265
Generally applicable transcriptome-wide analysis of translation using anota2seq. PMID:30926999
Ethylene Response Factor ERF11 Activates BT4 Transcription to Regulate Immunity to Pseudomonas syringae. PMID:30926656
Investigation of molecular biomarker candidates for diagnosis and prognosis of chronic periodontitis by bioinformatics analysis of pooled microarray gene expression datasets in Gene Expression Omnibus (GEO). PMID:30922293
Predicting enhancers in mammalian genomes using supervised hidden Markov models. PMID:30917778
The Kinome of Human Alveolar Type II and Basal Cells, and Its Reprogramming in Lung Cancer. PMID:30917006
Effects of early social deprivation on epigenetic statuses and adaptive behavior of young children: A study based on a cohort of institutionalized infants and toddlers. PMID:30913238
Advancing Computational Toxicology in the Big Data Era by Artificial Intelligence: Data-Driven and Mechanism-Driven Modeling for Chemical Toxicity. PMID:30907586
Cell lines and immune classification of glioblastoma define patient's prognosis. PMID:30899088
Retinal and circulating miRNA expression patterns in diabetic retinopathy: An in silico and in vivo approach. PMID:30883703
Predicting MicroRNA Target Genes and Identifying Hub Genes in IIA Stage Colon Cancer Patients Using Bioinformatics Analysis. PMID:30881993
Identification of Important Effector Proteins in the FOXJ1 Transcriptional Network Associated With Ciliogenesis and Ciliary Function. PMID:30881373
Network meta-analysis correlates with analysis of merged independent transcriptome expression data. PMID:30876387
Comprehensive analysis of the GATA transcription factor gene family in breast carcinoma using gene microarrays, online databases and integrated bioinformatics. PMID:30872657
Analysis of differential gene expression and alternative splicing is significantly influenced by choice of reference genome. PMID:30872414
Extracellular Vesicles as Diagnostics and Therapeutics for Structural Epilepsies. PMID:30871144
Herb Target Prediction Based on Representation Learning of Symptom related Heterogeneous Network. PMID:30867892
Meta-analysis suggests evidence of novel stress-related pathway components in Orsay virus - Caenorhabditis elegans viral model. PMID:30867481
Bioinformatic exploration of OLFML2B overexpression in gastric cancer base on multiple analyzing tools. PMID:30866865
Construction and dissection of the ceRNA‑ceRNA network reveals critical modules in depression. PMID:30864711
Using Machine Learning to Measure Relatedness Between Genes: A Multi-Features Model. PMID:30862804
Regulatory network reconstruction of five essential microRNAs for survival analysis in breast cancer by integrating miRNA and mRNA expression datasets. PMID:30859354
Holistic optimization of an RNA-seq workflow for multi-threaded environments. PMID:30859176
Tripartite motif-containing 15 overexpression in non-small cell lung cancer is associated with poor patient prognoses. PMID:30854090
Integrated DNA methylation and gene expression analysis in the pathogenesis of coronary artery disease. PMID:30844764
New molecular insights on the response of the green alga Tetraselmis suecica to nitrogen starvation. PMID:30833632
YESdb: integrative analysis of environmental stress in yeast. PMID:30821814
Don't brush off buccal data heterogeneity. PMID:30821575
Reconstruction and analysis of circRNA‑miRNA‑mRNA network in the pathology of cervical cancer. PMID:30816541
Genome‑wide DNA methylation profile of thymomas and potential epigenetic regulation of thymoma subtypes. PMID:30816514
Clinical and research applications of a brain tumor tissue bank in the age of precision medicine. PMID:30816054
Integrated machine learning pipeline for aberrant biomarker enrichment (i-mAB): characterizing clusters of differentiation within a compendium of systemic lupus erythematosus patients. PMID:30815180
The analysis of a time-course transcriptome profile by systems biology approaches reveals key molecular processes in acute kidney injury. PMID:30815016
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
Bioinformatics analyses of differentially expressed genes associated with spinal cord injury: A microarray-based analysis in a mouse model. PMID:30804258
Predicted secreted protein analysis reveals synaptogenic function of Clstn3 during WAT browning and BAT activation in mice. PMID:30796355
Oxylipins mediate cell-to-cell communication in Pseudomonas aeruginosa. PMID:30793044
LINC01127 promotes the development of ovarian tumors by regulating the cell cycle. PMID:30787997
Genetic programming of macrophages generates an in vitro model for the human erythroid island niche. PMID:30787325
Cell Identity Codes: Understanding Cell Identity from Gene Expression Profiles using Deep Neural Networks. PMID:30787315
Transforming growth factor β-induced epithelial-to-mesenchymal signature predicts metastasis-free survival in non-small cell lung cancer. PMID:30783512
New guidelines for DNA methylome studies regarding 5-hydroxymethylcytosine for understanding transcriptional regulation. PMID:30782641
Hepatic differentiation of human pluripotent stem cells by developmental stage-related metabolomics products. PMID:30776728
A multifaceted small RNA modulates gene expression upon glucose limitation in Staphylococcus aureus. PMID:30760492
Bioinformatic gene analysis for potential biomarkers and therapeutic targets of atrial fibrillation-related stroke. PMID:30760287
A Genome-Scale Co-Functional Network of Xanthomonas Genes Can Accurately Reconstruct Regulatory Circuits Controlled by Two-Component Signaling Systems. PMID:30759970
CDRgator: An Integrative Navigator of Cancer Drug Resistance Gene Signatures. PMID:30759968
The Downregulation of MicroRNA hsa-miR-340-5p in IAV-Infected A549 Cells Suppresses Viral Replication by Targeting RIG-I and OAS2. PMID:30753994
eUTOPIA: solUTion for Omics data PreprocessIng and Analysis. PMID:30728855
T Cells Play a Causal Role in Diastolic Dysfunction during Uremic Cardiomyopathy. PMID:30728178
Aberrantly DNA Methylated-Differentially Expressed Genes and Pathways in Hepatocellular Carcinoma. PMID:30719129
Loss of Forkhead Box O3 Facilitates Inflammatory Colon Cancer: Transcriptome Profiling of the Immune Landscape and Novel Targets. PMID:30718226
Functional homogeneity and specificity of topological modules in human proteome. PMID:30717667
Cancer cell-expressed SLAMF7 is not required for CD47-mediated phagocytosis. PMID:30710089
ZEB1 Is a Transcription Factor That Is Prognostic and Predictive in Diffuse Gliomas. PMID:30705664
Conserved regulation of RNA processing in somatic cell reprogramming. PMID:30704403
Generative modeling of multi-mapping reads with mHi-C advances analysis of Hi-C studies. PMID:30702424
The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function. PMID:30698741
Loss of CRWN Nuclear Proteins Induces Cell Death and Salicylic Acid Defense Signaling. PMID:30696746
First step toward gene expression data integration: transcriptomic data acquisition with COMMAND>_. PMID:30691411
Assessment of weighted topological overlap (wTO) to improve fidelity of gene co-expression networks. PMID:30691386
A Computational Framework for Genome-wide Characterization of the Human Disease Landscape. PMID:30685436
Stems cells, big data and compendium-based analyses for identifying cell types, signalling pathways and gene regulatory networks. PMID:30684132
Drug repositioning for dengue haemorrhagic fever by integrating multiple omics analyses. PMID:30679503
Prediction of functional microRNA targets by integrative modeling of microRNA binding and target expression data. PMID:30670076
Bioinformatics analysis of sex differences in arrhythmogenic right ventricular cardiomyopathy. PMID:30664203
Deduction of Novel Genes Potentially Involved in Upper Tract Urothelial Carcinoma Using Next-Generation Sequencing and Bioinformatics Approaches. PMID:30662333
Inflammation in Traumatic Brain Injury: Roles for Toxic A1 Astrocytes and Microglial-Astrocytic Crosstalk. PMID:30661228
Proteo-Transcriptomic Dynamics of Cellular Response to HIV-1 Infection. PMID:30659199
Identification of Prognostic Biomarker Signatures and Candidate Drugs in Colorectal Cancer: Insights from Systems Biology Analysis. PMID:30658502
Long non-coding RNA transcriptome of uncharacterized samples can be accurately imputed using protein-coding genes. PMID:30657858
Identification of core genes and prediction of miRNAs associated with osteoporosis using a bioinformatics approach. PMID:30655789
LIPG-promoted lipid storage mediates adaptation to oxidative stress in breast cancer. PMID:30653260
Restructured GEO: restructuring Gene Expression Omnibus metadata for genome dynamics analysis. PMID:30649296
Secretory High-Mobility Group Box 1 Protein Affects Regulatory T Cell Differentiation in Neuroblastoma Microenvironment In Vitro. PMID:30643519
Identification of hub genes and outcome in colon cancer based on bioinformatics analysis. PMID:30643458
Identifying primary site of lung-limited Cancer of unknown primary based on relative gene expression orderings. PMID:30642283
HSP90 inhibitor geldanamycin reverts IL-13- and IL-17-induced airway goblet cell metaplasia. PMID:30640172
Identification of key regulators of pancreatic ductal adenocarcinoma using bioinformatics analysis of microarray data. PMID:30633213
Proteome Analysis of Human Neutrophil Granulocytes From Patients With Monogenic Disease Using Data-independent Acquisition. PMID:30630937
MicroRNA Expression Profiles Identify Biomarker for Differentiating the Embolic Stroke from Thrombotic Stroke. PMID:30627556
Biological Pathways Leading From ANGPTL8 to Diabetes Mellitus-A Co-expression Network Based Analysis. PMID:30627105
The long non-coding RNA LINC00941 and SPRR5 are novel regulators of human epidermal homeostasis. PMID:30622217
Transcriptomic profiles of tissues from rats treated with anticancer drug combinations. PMID:30620345
Predicting peptide presentation by major histocompatibility complex class I: an improved machine learning approach to the immunopeptidome. PMID:30611210
plyranges: a grammar of genomic data transformation. PMID:30609939
Biomarker Discovery for Immunotherapy of Pituitary Adenomas: Enhanced Robustness and Prediction Ability by Modern Computational Tools. PMID:30609812
Phosphatidylglycerols are induced by gut dysbiosis and inflammation, and favorably modulate adipose tissue remodeling in obesity. PMID:30608881
Identification of potential miRNA-mRNA regulatory network contributing to pathogenesis of HBV-related HCC. PMID:30602391
Mining data and metadata from the gene expression omnibus. PMID:30594974
Key genes and co-expression network analysis in the livers of type 2 diabetes patients. PMID:30592156
Modeling human prostate cancer progression in vitro. PMID:30590461
Activation of IL-8 and its participation in cancer in schizophrenia patients: new evidence for the autoimmune hypothesis of schizophrenia. PMID:30587991
Plant stress RNA-seq Nexus: a stress-specific transcriptome database in plant cells. PMID:30587128
Predicting growth rate from gene expression. PMID:30578321
Capturing context-specific regulation in molecular interaction networks. PMID:30577761
BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language. PMID:30576488
Causal Inference Network of Genes Related with Bone Metastasis of Breast Cancer and Osteoblasts Using Causal Bayesian Networks. PMID:30574470
Construction and analysis of the lncRNA‑miRNA‑mRNA network based on competitive endogenous RNA reveals functional genes in heart failure. PMID:30569169
Plasma miR-21, miR-155, miR-10b, and Let-7a as the potential biomarkers for the monitoring of breast cancer patients. PMID:30568292
Systematic polypharmacology and drug repurposing via an integrated L1000-based Connectivity Map database mining. PMID:30564416
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
Identification of new molecular targets for PET imaging of the microglial anti-inflammatory activation state. PMID:30555554
Personalized Medicine and Molecular Interaction Networks in Amyotrophic Lateral Sclerosis (ALS): Current Knowledge. PMID:30551677
Potential clinical value and putative biological function of miR-122-5p in hepatocellular carcinoma: A comprehensive study using microarray and RNA sequencing data. PMID:30546424
Regulators of Salmonella-host interaction identified by peripheral blood transcriptome profiling: roles of TGFB1 and TRP53 in intracellular Salmonella replication in pigs. PMID:30541630
Identification of deleterious and regulatory genomic variations in known asthma loci. PMID:30541564
Integrated analysis reveals key genes with prognostic value in lung adenocarcinoma. PMID:30538558
PDX Finder: A portal for patient-derived tumor xenograft model discovery. PMID:30535239
A Simple Guideline to Assess the Characteristics of RNA-Seq Data. PMID:30519573
Overexpression of RALY promotes migration and predicts poor prognosis in hepatocellular carcinoma. PMID:30519104
Tissue-Specific Down-Regulation of the Long Non-Coding RNAs PCAT18 and LINC01133 in Gastric Cancer Development. PMID:30518158
SWIM tool application to expression data of glioblastoma stem-like cell lines, corresponding primary tumors and conventional glioma cell lines. PMID:30497369
Updating genome annotation for the microbial cell factory Aspergillus niger using gene co-expression networks. PMID:30496528
Genetic, Transcriptome, Proteomic, and Epidemiological Evidence for Blood-Brain Barrier Disruption and Polymicrobial Brain Invasion as Determinant Factors in Alzheimer's Disease. PMID:30480234
STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. PMID:30476243
Effect of intra-ovarian injection of mesenchymal stem cells in aged mares. PMID:30470961
Identification of a transcriptome profile associated with improvement of organ function in septic shock patients after early supportive therapy. PMID:30463588
Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis. PMID:30462313
Using single nucleotide variations in single-cell RNA-seq to identify subpopulations and genotype-phenotype linkage. PMID:30459309
RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs database. PMID:30453895
Genome-Wide Transcriptional and Functional Analysis of Human T Lymphocytes Treated with Benzo[α]pyrene. PMID:30453624
GTRD: a database on gene transcription regulation-2019 update. PMID:30445619
Long non-coding RNA H19 promotes TDRG1 expression and cisplatin resistance by sequestering miRNA-106b-5p in seminoma. PMID:30430771
Determining the Balance Between Drug Efficacy and Safety by the Network and Biological System Profile of Its Therapeutic Target. PMID:30429792
funcExplorer: a tool for fast data-driven functional characterisation of high-throughput expression data. PMID:30428831
Gene expression analyses identify a relationship between stanniocalcin 2 and the malignant behavior of colorectal cancer. PMID:30425508
A Comparison of the TempO-Seq S1500+ Platform to RNA-Seq and Microarray Using Rat Liver Mode of Action Samples. PMID:30420870
HumanNet v2: human gene networks for disease research. PMID:30418591
The Pathogenesis of Atherosclerosis Based on Human Signaling Networks and Stem Cell Expression Data. PMID:30416382
Comparative mRNA and miRNA transcriptome analysis of a mouse model of IGFIR-driven lung cancer. PMID:30412601
Identification of Differentially Expressed Genes under the Regulation of Transcription Factors in Osteosarcoma. PMID:30411296
Lentivirus-mediated overexpression of HSDL2 suppresses cell proliferation and induces apoptosis in cholangiocarcinoma. PMID:30410369
IID 2018 update: context-specific physical protein-protein interactions in human, model organisms and domesticated species. PMID:30407591
Systems-Mapping of Herbal Effects on Complex Diseases Using the Network-Perturbation Signatures. PMID:30405409
Elucidating the role of Agl in bladder carcinogenesis by generation and characterization of genetically engineered mice. PMID:30403777
Mammalian pigmentation is regulated by a distinct cAMP-dependent mechanism that controls melanosome pH. PMID:30401788
Circular RNAs in Muscle Function and Disease. PMID:30400273
Enabling precision medicine in neonatology, an integrated repository for preterm birth research. PMID:30398470
Effects of simulated microgravity on the expression profiles of RNA during osteogenic differentiation of human bone marrow mesenchymal stem cells. PMID:30397970
RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12. PMID:30395280
Transcriptome analysis of Xenopus orofacial tissues deficient in retinoic acid receptor function. PMID:30390632
Predicting bacterial growth conditions from mRNA and protein abundances. PMID:30388153
SAGD: a comprehensive sex-associated gene database from transcriptomes. PMID:30380119
Biologically relevant laminin as chemically defined and fully human platform for human epidermal keratinocyte culture. PMID:30377295
YHMI: a web tool to identify histone modifications and histone/chromatin regulators from a gene list in yeast. PMID:30371756
Identification of Potential miRNAs Biomarkers for High-Grade Prostate Cancer by Integrated Bioinformatics Analysis. PMID:30367364
EWAS Atlas: a curated knowledgebase of epigenome-wide association studies. PMID:30364969
A Systems Analysis With "Simplified Source-Sink Model" Reveals Metabolic Reprogramming in a Pair of Source-to-Sink Organs During Early Fruit Development in Tomato by LED Light Treatments. PMID:30364178
Non-canonical Drosophila X chromosome dosage compensation and repressive topologically associated domains. PMID:30355339
Regulation of human glioma cell migration, tumor growth, and stemness gene expression using a Lck targeted inhibitor. PMID:30353164
3D Network exploration and visualisation for lifespan data. PMID:30352578
A multi-tissue full lifespan epigenetic clock for mice. PMID:30348905
An integrative tissue-network approach to identify and test human disease genes. PMID:30346941
Genetic expression profile-based screening of genes and pathways associated with papillary thyroid carcinoma. PMID:30344727
SeqOthello: querying RNA-seq experiments at scale. PMID:30340508
Single-Cell RNA Sequencing Reveals Novel Markers of Male Pituitary Stem Cells and Hormone-Producing Cell Types. PMID:30335147
sEst: Accurate Sex-Estimation and Abnormality Detection in Methylation Microarray Data. PMID:30326623
EWASdb: epigenome-wide association study database. PMID:30321400
Genome-Wide Association and Mechanistic Studies Indicate That Immune Response Contributes to Alzheimer's Disease Development. PMID:30319691
Identification of key gene pathways and coexpression networks of islets in human type 2 diabetes. PMID:30319280
Transcriptional repressor GATA binding 1-mediated repression of SRY-box 2 expression suppresses cancer stem cell functions and tumor initiation. PMID:30315105
A miRNA Combination as Promising Biomarker for Hepatocellular Carcinoma Diagnosis: A Study Based on Bioinformatics Analysis. PMID:30310500
CaSTLe - Classification of single cells by transfer learning: Harnessing the power of publicly available single cell RNA sequencing experiments to annotate new experiments. PMID:30304022
A Class 1 Histone Deacetylase as Major Regulator of Secondary Metabolite Production in Aspergillus nidulans. PMID:30283426
SUMO-Targeted Ubiquitin Ligases (STUbLs) Reduce the Toxicity and Abnormal Transcriptional Activity Associated With a Mutant, Aggregation-Prone Fragment of Huntingtin. PMID:30279700
New insights into the cellular temporal response to proteostatic stress. PMID:30272558
Identification of invasion-metastasis-associated microRNAs in hepatocellular carcinoma based on bioinformatic analysis and experimental validation. PMID:30268144
PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System. PMID:30266409
Leukemia inhibitory factor inhibits erythropoietin-induced myelin gene expression in oligodendrocytes. PMID:30261841
Topological alternate centrality measure capturing drug targets in the network of MAPK pathways. PMID:30259868
Fold change based approach for identification of significant network markers in breast, lung and prostate cancer. PMID:30259866
Key elements involved in Epstein-Barr virus-associated gastric cancer and their network regulation. PMID:30258285
Tunable structure priors for Bayesian rule learning for knowledge integrated biomarker discovery. PMID:30254965
Continuity of transcriptomes among colorectal cancer subtypes based on meta-analysis. PMID:30253799
Expression of LRIG1, a Negative Regulator of EGFR, Is Dynamically Altered during Different Stages of Gastric Carcinogenesis. PMID:30248341
Identifying and validating blood mRNA biomarkers for acute and chronic insufficient sleep in humans: a machine learning approach. PMID:30247731
POSTAR2: deciphering the post-transcriptional regulatory logics. PMID:30239819
Concomitant PPARα and FXR Activation as a Putative Mechanism of NASH Improvement after Gastric Bypass Surgery: a GEO Datasets Analysis. PMID:30206765
Modified LDL Particles Activate Inflammatory Pathways in Monocyte-derived Macrophages: Transcriptome Analysis. PMID:30205792
Identification of candidate genes and proteins in aging skeletal muscle (sarcopenia) using gene expression and structural analysis. PMID:30202641
Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms. PMID:30202060
HeteroMeth: A Database of Cell-to-cell Heterogeneity in DNA Methylation. PMID:30196115
microCLIP super learning framework uncovers functional transcriptome-wide miRNA interactions. PMID:30190538
Integration of Gene Expression Profile Data to Screen and Verify Hub Genes Involved in Osteoarthritis. PMID:30186872
Peptidyl arginine deiminase 2 (Padi2) is expressed in Sertoli cells in a specific manner and regulated by SOX9 during testicular development. PMID:30185873
Integration of gene interaction information into a reweighted random survival forest approach for accurate survival prediction and survival biomarker discovery. PMID:30181543
Identification of hub genes and analysis of prognostic values in pancreatic ductal adenocarcinoma by integrated bioinformatics methods. PMID:30173393
Prediction of Novel Drugs and Diseases for Hepatocellular Carcinoma Based on Multi-Source Simulated Annealing Based Random Walk. PMID:30173379
Understanding and predicting disease relationships through similarity fusion. PMID:30169824
Loss of LDAH associated with prostate cancer and hearing loss. PMID:30169630
Identification and Interaction Analysis of Molecular Markers in Colorectal Cancer by Integrated Bioinformatics Analysis. PMID:30168505
Large-scale in silico identification of drugs exerting sex-specific effects in the heart. PMID:30157868
Harnessing the biological complexity of Big Data from LINCS gene expression signatures. PMID:30157183
An interaction network driven approach for identifying biomarkers for progressing cervical intraepithelial neoplasia. PMID:30150654
Exploring the Role of Fallopian Ciliated Cells in the Pathogenesis of High-Grade Serous Ovarian Cancer. PMID:30149579
Turning omics data into therapeutic insights. PMID:30149217
Transcriptional Profiling Suggests Extensive Metabolic Rewiring of Human and Mouse Macrophages during Early Interferon Alpha Responses. PMID:30147442
Association of tamoxifen resistance and lipid reprogramming in breast cancer. PMID:30143015
The Defense Response of Nicotiana benthamiana to Peanut Stunt Virus Infection in the Presence of Symptom Exacerbating Satellite RNA. PMID:30142955
Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655. PMID:30137486
COL1A1: A potential therapeutic target for colorectal cancer expressing wild-type or mutant KRAS. PMID:30132520
DNA topoisomerase 1 and 2A function as oncogenes in liver cancer and may be direct targets of nitidine chloride. PMID:30132517
TRIQ: a new method to evaluate triclusters. PMID:30127855
Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response. PMID:30127393
Tau protein aggregation is associated with cellular senescence in the brain. PMID:30126037
Review of Drug Repositioning Approaches and Resources. PMID:30123072
Systematic Analysis of Differential Expression Profile in Rheumatoid Arthritis Chondrocytes Using Next-Generation Sequencing and Bioinformatics Approaches. PMID:30123050
Prediagnostic circulating markers of inflammation and risk of oesophageal adenocarcinoma: a study within the National Cancer Institute Cohort Consortium. PMID:30121626
A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0. PMID:30115066
Comprehensive integrated analysis of gene expression datasets identifies key anti-cancer targets in different stages of breast cancer. PMID:30112036
QsRNA-seq: a method for high-throughput profiling and quantifying small RNAs. PMID:30107842
Revealing a human p53 universe. PMID:30107566
Apparent bias toward long gene misregulation in MeCP2 syndromes disappears after controlling for baseline variations. PMID:30104565
Identification of prognostic risk factors for esophageal adenocarcinoma using bioinformatics analysis. PMID:30100738
Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding. PMID:30097539
Rat BodyMap transcriptomes reveal unique circular RNA features across tissue types and developmental stages. PMID:30093490
A circRNA-miRNA-mRNA network identification for exploring underlying pathogenesis and therapy strategy of hepatocellular carcinoma. PMID:30092792
BART: bioinformatics array research tool. PMID:30089462
Douglas-Fir ( Pseudotsuga menziesii (Mirb.) Franco) Transcriptome Profile Changes Induced by Diesel Emissions Generated with CeO2 Nanoparticle Fuel Borne Catalyst. PMID:30075627
PAK2-c-Myc-PKM2 axis plays an essential role in head and neck oncogenesis via regulating Warburg effect. PMID:30068946
exoRBase: a database of circRNA, lncRNA and mRNA in human blood exosomes. PMID:30053265
HDncRNA: a comprehensive database of non-coding RNAs associated with heart diseases. PMID:30053237
The epiGenomic Efficient Correlator (epiGeEC) tool allows fast comparison of user datasets with thousands of public epigenomic datasets. PMID:30052804
Co-inhibition of mTORC1, HDAC and ESR1α retards the growth of triple-negative breast cancer and suppresses cancer stem cells. PMID:30050079
Epigenetic activation of HORMAD1 in basal-like breast cancer: role in Rucaparib sensitivity. PMID:30046392
Network Rewiring in Cancer: Applications to Melanoma Cell Lines and the Cancer Genome Atlas Patients. PMID:30042785
Epigenetic Variability Confounds Transcriptome but Not Proteome Profiling for Coexpression-based Gene Function Prediction. PMID:30042154
A merged lung cancer transcriptome dataset for clinical predictive modeling. PMID:30040079
Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity. PMID:30039798
Investigation of epigenetic regulatory networks associated with autism spectrum disorder (ASD) by integrated global LINE-1 methylation and gene expression profiling analyses. PMID:30036398
Abnormal RNA stability in amyotrophic lateral sclerosis. PMID:30030424
Potential biomarkers and therapeutic targets in cervical cancer: Insights from the meta-analysis of transcriptomics data within network biomedicine perspective. PMID:30020984
Network-based genetic investigation of virulence-associated phenotypes in methicillin-resistant Staphylococcus aureus. PMID:30018396
Downregulation of miR‑486‑5p in papillary thyroid carcinoma tissue: A study based on microarray and miRNA sequencing. PMID:30015845
Identification of potential target genes in pancreatic ductal adenocarcinoma by bioinformatics analysis. PMID:30013637
A meta-analysis of transcriptome datasets characterizes malignant transformation from melanocytes and nevi to melanoma. PMID:30008882
Bioinformatic identification of key genes and analysis of prognostic values in clear cell renal cell carcinoma. PMID:30008862
PAREsnip2: a tool for high-throughput prediction of small RNA targets from degradome sequencing data using configurable targeting rules. PMID:30007348
Review and Meta-Analyses of TAAR1 Expression in the Immune System and Cancers. PMID:29997511
Cyclin G and the Polycomb Repressive complexes PRC1 and PR-DUB cooperate for developmental stability. PMID:29995890
Integrated multifactor analysis explores core dysfunctional modules in autism spectrum disorder. PMID:29989084
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
Expression of Adhesive Pili and the Collagen-Binding Adhesin Ace Is Activated by ArgR Family Transcription Factors in Enterococcus faecalis. PMID:29986940
BrainEXP: a database featuring with spatiotemporal expression variations and co-expression organizations in human brains. PMID:29985970
Trends in the development of miRNA bioinformatics tools. PMID:29982332
An Artificial Neural Network Integrated Pipeline for Biomarker Discovery Using Alzheimer's Disease as a Case Study. PMID:29977480
PASI: A novel pathway method to identify delicate group effects. PMID:29975740
Identification of Antifungal Targets Based on Computer Modeling. PMID:29973534
HEAT INDUCIBLE LIPASE1 Remodels Chloroplastic Monogalactosyldiacylglycerol by Liberating α-Linolenic Acid in Arabidopsis Leaves under Heat Stress. PMID:29967047
Gene expression-based drug repurposing to target aging. PMID:29959820
Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species. PMID:29958539
Therapy-induced stress response is associated with downregulation of pre-mRNA splicing in cancer cells. PMID:29950180
Evidence for plant-derived xenomiRs based on a large-scale analysis of public small RNA sequencing data from human samples. PMID:29949574
RBPMetaDB: a comprehensive annotation of mouse RNA-Seq datasets with perturbations of RNA-binding proteins. PMID:29931156
Integrated multi-omics data analysis identifying novel drug sensitivity-associated molecular targets of hepatocellular carcinoma cells. PMID:29930714
Overexpression of CXXC5 is a strong poor prognostic factor in ER+ breast cancer. PMID:29928427
Computational Methods for Predicting Protein-Protein Interactions Using Various Protein Features. PMID:29927082
DeCoST: A New Approach in Drug Repurposing From Control System Theory. PMID:29922160
Differential Expression and Pathway Analysis in Drug-Resistant Triple-Negative Breast Cancer Cell Lines Using RNASeq Analysis. PMID:29921827
Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center. PMID:29917015
GlpR Is a Direct Transcriptional Repressor of Fructose Metabolic Genes in Haloferax volcanii. PMID:29914986
LHX2 Mediates the FGF-to-SHH Regulatory Loop during Limb Development. PMID:29914077
Germline mutations and somatic inactivation of TRIM28 in Wilms tumour. PMID:29912901
Comprehensive evaluation of differential lncRNA and gene expression in patients with intervertebral disc degeneration. PMID:29901136
Identification and functional analysis of differentially expressed genes associated with cerebral ischemia/reperfusion injury through bioinformatics methods. PMID:29901134
Prediction of protein-DNA interactions of transcription factors linking proteomics and transcriptomics data. PMID:29900118
Multi-omics "upstream analysis" of regulatory genomic regions helps identifying targets against methotrexate resistance of colon cancer. PMID:29900117
A quantitative mass spectrometry-based approach to monitor the dynamics of endogenous chromatin-associated protein complexes. PMID:29899353
MLH1 Promoter Methylation and Prediction/Prognosis of Gastric Cancer: A Systematic Review and Meta and Bioinformatic Analysis. PMID:29896277
Genome-wide identification and characterization of the RIO atypical kinase family in plants. PMID:29892951
A Nasal Brush-based Classifier of Asthma Identified by Machine Learning Analysis of Nasal RNA Sequence Data. PMID:29891868
Lipid phosphate phosphatase 3 regulates adipocyte sphingolipid synthesis, but not developmental adipogenesis or diet-induced obesity in mice. PMID:29889835
Gene expression profiling of breast cancer cell lines treated with proton and electron radiations. PMID:29888960
Analysis of differentially expressed genes, clinical value and biological pathways in prostate cancer. PMID:29887958
Differentially Expressed Genes in Osteomyelitis Induced by Staphylococcus aureus Infection. PMID:29887852
The coupling of transcriptome and proteome adaptation during development and heat stress response of tomato pollen. PMID:29884134
Identification of key genes in human airway epithelial cells in response to respiratory pathogens using microarray analysis. PMID:29884128
Differentiation in stem/progenitor cells along fetal or adult hepatic stages requires transcriptional regulators independently of oscillations in microRNA expression. PMID:29883712
Gene set analysis methods: a systematic comparison. PMID:29881462
MU-LOC: A Machine-Learning Method for Predicting Mitochondrially Localized Proteins in Plants. PMID:29875778
Meta-Analysis of Maternal and Fetal Transcriptomic Data Elucidates the Role of Adaptive and Innate Immunity in Preterm Birth. PMID:29867970
Tensor Decomposition-Based Unsupervised Feature Extraction Can Identify the Universal Nature of Sequence-Nonspecific Off-Target Regulation of mRNA Mediated by MicroRNA Transfection. PMID:29867052
REST, not REST4, is a risk factor associated with radiotherapy plus chemotherapy efficacy in glioma. PMID:29861627
Heterotroph Interactions Alter Prochlorococcus Transcriptome Dynamics during Extended Periods of Darkness. PMID:29854954
Identifying key genes, pathways and screening therapeutic agents for manganese-induced Alzheimer disease using bioinformatics analysis. PMID:29851783
A big data pipeline: Identifying dynamic gene regulatory networks from time-course Gene Expression Omnibus data with applications to influenza infection. PMID:29846143
Overactivated neddylation pathway in human hepatocellular carcinoma. PMID:29846044
Computational approaches for predicting key transcription factors in targeted cell reprogramming (Review). PMID:29845286
miR‑23a downregulation modulates the inflammatory response by targeting ATG12‑mediated autophagy. PMID:29845275
Identification of candidate biomarkers and pathways associated with SCLC by bioinformatics analysis. PMID:29845250
Identification of key genes and pathways in meningioma by bioinformatics analysis. PMID:29805558
The Cellosaurus, a Cell-Line Knowledge Resource. PMID:29805321
SMARTIV: combined sequence and structure de-novo motif discovery for in-vivo RNA binding data. PMID:29800452
GIANT 2.0: genome-scale integrated analysis of gene networks in tissues. PMID:29800226
Sex-Specific Transcriptome Differences in Substantia Nigra Tissue: A Meta-Analysis of Parkinson's Disease Data. PMID:29799491
Identification of genes involved in metabolism and signalling of abscisic acid and gibberellins during Epimedium pseudowushanense B.L.Guo seed morphophysiological dormancy. PMID:29796945
FAM188B enhances cell survival via interaction with USP7. PMID:29795372
Sphingosine-1-Phosphate Signaling and Metabolism Gene Signature in Pediatric Inflammatory Bowel Disease: A Matched-case Control Pilot Study. PMID:29788359
Archetypal transcriptional blocks underpin yeast gene regulation in response to changes in growth conditions. PMID:29785040
Computational identification of specific genes for glioblastoma stem-like cells identity. PMID:29773872
The relative resistance of children to sepsis mortality: from pathways to drug candidates. PMID:29773677
Methylation guide RNA evolution in archaea: structure, function and genomic organization of 110 C/D box sRNA families across six Pyrobaculum species. PMID:29771354
A comparative study of RNA-Seq and microarray data analysis on the two examples of rectal-cancer patients and Burkitt Lymphoma cells. PMID:29768462
Using ZFIN: Data Types, Organization, and Retrieval. PMID:29761463
Reuse of public, genome-wide, murine eosinophil expression data for hypotheses development. PMID:29758095
Integrative Bioinformatics and Functional Analyses of GEO, ENCODE, and TCGA Reveal FADD as a Direct Target of the Tumor Suppressor BRCA1. PMID:29757984
Decoding Common Features of Neurodegenerative Disorders: From Differentially Expressed Genes to Pathways. PMID:29755292
Integrated bioinformatics analysis reveals that the expression of cathepsin S is associated with lymph node metastasis and poor prognosis in papillary thyroid cancer. PMID:29749483
Automated transition analysis of activated gene regulation during diauxic nutrient shift in Escherichia coli and adipocyte differentiation in mouse cells. PMID:29745848
An integrated view of the role of miR-130b/301b miRNA cluster in prostate cancer. PMID:29744254
Paternal developmental toxicant exposure is associated with epigenetic modulation of sperm and placental Pgr and Igf2 in a mouse model. PMID:29741588
Meta-Analysis and Experimental Validation Identified FREM2 and SPRY1 as New Glioblastoma Marker Candidates. PMID:29734672
MSIQ: JOINT MODELING OF MULTIPLE RNA-SEQ SAMPLES FOR ACCURATE ISOFORM QUANTIFICATION. PMID:29731954
Identification of potential diagnostic and prognostic biomarkers in non-small cell lung cancer based on microarray data. PMID:29731852
Shared liver-like transcriptional characteristics in liver metastases and corresponding primary colorectal tumors. PMID:29721060
Genome-wide mapping of the RNA targets of the Pseudomonas aeruginosa riboregulatory protein RsmN. PMID:29718466
Low-level laser irradiation induces a transcriptional myotube-like profile in C2C12 myoblasts. PMID:29717386
Bioinformatics-based identification of potential microRNA biomarkers in frequent and non-frequent exacerbators of COPD. PMID:29713155
Structural and functional dissection of differentially expressed tomato WRKY transcripts in host defense response against the vascular wilt pathogen (Fusarium oxysporum f. sp. lycopersici). PMID:29709017
Identification of a five-lncRNA signature for predicting the risk of tumor recurrence in patients with breast cancer. PMID:29707762
DANUBE: Data-driven meta-ANalysis using UnBiased Empirical distributions-applied to biological pathway analysis. PMID:29706661
Aldolase B-Mediated Fructose Metabolism Drives Metabolic Reprogramming of Colon Cancer Liver Metastasis. PMID:29706565
Using 'collective omics data' for biomedical research training. PMID:29705995
Development of a computational promoter with highly efficient expression in tumors. PMID:29703163
Identification of Key Candidate Genes and Pathways in Endometrial Cancer by Integrated Bioinformatical Analysis. PMID:29693365
GEOMetaCuration: a web-based application for accurate manual curation of Gene Expression Omnibus metadata. PMID:29688376
Prevention of data duplication for high throughput sequencing repositories. PMID:29688363
EMUDRA: Ensemble of Multiple Drug Repositioning Approaches to improve prediction accuracy. PMID:29688306
The exon-intron gene structure upstream of the initiation codon predicts translation efficiency. PMID:29684192
Identification of homocysteine-suppressive mitochondrial ETC complex genes and tissue expression profile - Novel hypothesis establishment. PMID:29679893
Cholesterol metabolism promotes B-cell positioning during immune pathogenesis of chronic obstructive pulmonary disease. PMID:29674392
Identification of molecular target genes and key pathways in hepatocellular carcinoma by bioinformatics analysis. PMID:29670361
Integrated bioinformatic analysis unveils significant genes and pathways in the pathogenesis of supratentorial primitive neuroectodermal tumor. PMID:29670360
Transcription factors operate across disease loci, with EBNA2 implicated in autoimmunity. PMID:29662164
FAR2 is associated with kidney disease in mice and humans. PMID:29652635
A mega-analysis of expression quantitative trait loci (eQTL) provides insight into the regulatory architecture of gene expression variation in liver. PMID:29650998
MLL leukemia induction by t(9;11) chromosomal translocation in human hematopoietic stem cells using genome editing. PMID:29650777
A novel two-score system for interferon status segregates autoimmune diseases and correlates with clinical features. PMID:29643425
Condition-Specific Modeling of Biophysical Parameters Advances Inference of Regulatory Networks. PMID:29641998
The arachidonic acid metabolism protein-protein interaction network and its expression pattern in esophageal diseases. PMID:29636881
Comprehensive analysis of blood cells and plasma identifies tissue-specific miRNAs as potential novel circulating biomarkers in cattle. PMID:29636028
Dietary and Endocrine Regulation of Endogenous Hydrogen Sulfide Production: Implications for Longevity. PMID:29634343
Integrative analysis of Multiple Sclerosis using a systems biology approach. PMID:29618802
Differential expression of microRNAs and other small RNAs in muscle tissue of patients with ALS and healthy age-matched controls. PMID:29618798
Computational repositioning and preclinical validation of mifepristone for human vestibular schwannoma. PMID:29615643
HDAC genes play distinct and redundant roles in Cryptococcus neoformans virulence. PMID:29581526
Heparanase attenuates axon degeneration following sciatic nerve transection. PMID:29581478
Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites. PMID:29580379
Forniceal deep brain stimulation induces gene expression and splicing changes that promote neurogenesis and plasticity. PMID:29570050
Key genes and regulatory networks involved in the initiation, progression and invasion of colorectal cancer. PMID:29568567
Three-microRNA signature identified by bioinformatics analysis predicts prognosis of gastric cancer patients. PMID:29568201
Chromium disrupts chromatin organization and CTCF access to its cognate sites in promoters of differentially expressed genes. PMID:29561703
BTNET : boosted tree based gene regulatory network inference algorithm using time-course measurement data. PMID:29560827
Uncovering the regeneration strategies of zebrafish organs: a comprehensive systems biology study on heart, cerebellum, fin, and retina regeneration. PMID:29560825
Demethylator phenotypes in acute myeloid leukemia. PMID:29556023
Analysis of microRNA and Gene Expression Profiles in Alzheimer's Disease: A Meta-Analysis Approach. PMID:29555910
Could ALDH2*2 be the reason for low incidence and mortality of ovarian cancer for East Asia women? PMID:29552329
Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness. PMID:29549885
BIOPYDB: A Dynamic Human Cell Specific Biochemical Pathway Database with Advanced Computational Analyses Platform. PMID:29547394
Identification of prefrontal cortex protein alterations in Alzheimer's disease. PMID:29541381
The glycoprotein GPNMB attenuates astrocyte inflammatory responses through the CD44 receptor. PMID:29519253
Analysis of Gene Regulatory Networks of Maize in Response to Nitrogen. PMID:29518046
Identification of COL4A1 as a potential gene conferring trastuzumab resistance in gastric cancer based on bioinformatics analysis. PMID:29512712
Three unrelated protease inhibitors enhance accumulation of pharmaceutical recombinant proteins in Nicotiana benthamiana. PMID:29509983
Brain-specific functional relationship networks inform autism spectrum disorder gene prediction. PMID:29507298
Computational master-regulator search reveals mTOR and PI3K pathways responsible for low sensitivity of NCI-H292 and A427 lung cancer cell lines to cytotoxic action of p53 activator Nutlin-3. PMID:29504919
Identification of Shared Molecular Signatures Indicate the Susceptibility of Endometriosis to Multiple Sclerosis. PMID:29503661
Identification of long noncoding RNAs involved in muscle differentiation. PMID:29499054
Microbiological Sensing Technologies: A Review. PMID:29498670
From gene networks to drugs: systems pharmacology approaches for AUD. PMID:29497781
Computational de novo discovery of distinguishing genes for biological processes and cell types in complex tissues. PMID:29494600
Spatial specificity of auxin responses coordinates wood formation. PMID:29491423
Identification of relevant drugable targets in diffuse large B-cell lymphoma using a genome-wide unbiased CD20 guilt-by association approach. PMID:29489886
Investigation of hypoxia networks in ovarian cancer via bioinformatics analysis. PMID:29482638
Genome-wide Association Study Identifies a Regulatory Variant of RGMA Associated With Opioid Dependence in European Americans. PMID:29478698
Circular RNA GRB10 as a competitive endogenous RNA regulating nucleus pulposus cells death in degenerative intervertebral disk. PMID:29476072
Small RNA populations revealed by blocking rRNA fragments in Drosophila melanogaster reproductive tissues. PMID:29474379
Proteomic profiling of VCP substrates links VCP to K6-linked ubiquitylation and c-Myc function. PMID:29467282
Differentiated embryo chondrocyte plays a crucial role in DNA damage response via transcriptional regulation under hypoxic conditions. PMID:29466367
Boolean analysis identifies CD38 as a biomarker of aggressive localized prostate cancer. PMID:29464091
CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses. PMID:29458351
Dynamics of promoter bivalency and RNAP II pausing in mouse stem and differentiated cells. PMID:29458328
Identification of Key Pathways and Genes in the Dynamic Progression of HCC Based on WGCNA. PMID:29443924
Development of a primary human Small Intestine-on-a-Chip using biopsy-derived organoids. PMID:29440725
REST upregulates gremlin to modulate diffuse intrinsic pontine glioma vasculature. PMID:29435175
Downregulated cytoplasmic polyadenylation element-binding protein-4 is associated with the carcinogenesis of head and neck squamous cell carcinoma. PMID:29435062
Identification and analysis of key genes in osteosarcoma using bioinformatics. PMID:29435005
Identification of common key genes in breast, lung and prostate cancer and exploration of their heterogeneous expression. PMID:29434863
Comprehensive characterization of cancer genes in hepatocellular carcinoma genomes. PMID:29434842
microRNA-219 Reduces Viral Load and Pathologic Changes in Theiler's Virus-Induced Demyelinating Disease. PMID:29433936
MethCNA: a database for integrating genomic and epigenomic data in human cancer. PMID:29433427
Octopus-toolkit: a workflow to automate mining of public epigenomic and transcriptomic next-generation sequencing data. PMID:29420797
Bioinformatic analyses of microRNA-targeted genes and microarray-identified genes correlated with Barrett's esophagus. PMID:29417867
Regulation of insulin resistance and type II diabetes by hepatitis C virus infection: A driver function of circulating miRNAs. PMID:29411512
Region-Specific Methylation Profiling in Acute Myeloid Leukemia. PMID:29405013
Nc886 is epigenetically repressed in prostate cancer and acts as a tumor suppressor through the inhibition of cell growth. PMID:29394925
Network analysis revealed aurora kinase dysregulation in five gynecological types of cancer. PMID:29391900
Gene Expression Analysis Reveals Novel Shared Gene Signatures and Candidate Molecular Mechanisms between Pemphigus and Systemic Lupus Erythematosus in CD4+ T Cells. PMID:29387060
Germline contamination and leakage in whole genome somatic single nucleotide variant detection. PMID:29385983
Quantitative or qualitative transcriptional diagnostic signatures? A case study for colorectal cancer. PMID:29378509
The regulatory network analysis of long noncoding RNAs in human colorectal cancer. PMID:29374362
Bioinformatics-based identification of miR-542-5p as a predictive biomarker in breast cancer therapy. PMID:29371858
Moving towards a molecular taxonomy of autoimmune rheumatic diseases. PMID:29362467
Hippo signaling controls cell cycle and restricts cell plasticity in planarians. PMID:29357350
Reduced miR-105-1 levels are associated with poor survival of patients with non-small cell lung cancer. PMID:29344230
Large-scale comparative epigenomics reveals hierarchical regulation of non-CG methylation in Arabidopsis. PMID:29339507
Express: A database of transcriptome profiles encompassing known and novel transcripts across multiple development stages in eye tissues. PMID:29337142
Application of Weighted Gene Co-expression Network Analysis for Data from Paired Design. PMID:29330528
Systematic target function annotation of human transcription factors. PMID:29325558
Network perturbation analysis of gene transcriptional profiles reveals protein targets and mechanism of action of drugs and influenza A viral infection. PMID:29325153
ModuleDiscoverer: Identification of regulatory modules in protein-protein interaction networks. PMID:29323246
Dual inhibition of Wnt and Yes-associated protein signaling retards the growth of triple-negative breast cancer in both mesenchymal and epithelial states. PMID:29316250
Minimally invasive skin tape strip RNA sequencing identifies novel characteristics of the type 2-high atopic dermatitis disease endotype. PMID:29309794
Cattle infection response network and its functional modules. PMID:29301495
A novel prospective isolation of murine fetal liver progenitors to study in utero hematopoietic defects. PMID:29300724
ALE: automated label extraction from GEO metadata. PMID:29297276
Pseudogenes of annexin A2, novel prognosis biomarkers for diffuse gliomas. PMID:29291003
DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition. PMID:29284518
Integrated MicroRNA-mRNA Analysis Reveals miR-204 Inhibits Cell Proliferation in Gastric Cancer by Targeting CKS1B, CXCL1 and GPRC5A. PMID:29283424
Comparison of multiple transcriptomes exposes unified and divergent features of quiescent and activated skeletal muscle stem cells. PMID:29273087
A network-based meta-analysis for characterizing the genetic landscape of human aging. PMID:29270911
Enhancing the Promise of Drug Repositioning through Genetics. PMID:29270124
Prioritizing chronic obstructive pulmonary disease (COPD) candidate genes in COPD-related networks. PMID:29262568
Identification of key pathways and genes in Barrett's esophagus using integrated bioinformatics methods. PMID:29257318
A core program of gene expression characterizes cancer metastases. PMID:29254233
A family-based genome-wide association study of chronic rhinosinusitis with nasal polyps implicates several genes in the disease pathogenesis. PMID:29253858
Computational identification of microRNAs and their targets in liver cirrhosis. PMID:29250171
Co-expression Network Approach Reveals Functional Similarities among Diseases Affecting Human Skeletal Muscle. PMID:29249983
The Ability of Different Imputation Methods to Preserve the Significant Genes and Pathways in Cancer. PMID:29247873
Framework for reanalysis of publicly available Affymetrix® GeneChip® data sets based on functional regions of interest. PMID:29244006
Central role of the p53 pathway in the noncoding-RNA response to oxidative stress. PMID:29242407
Dosage-Dependent Expression Variation Suppressed on the Drosophila Male X Chromosome. PMID:29242386
Identification of Key Genes and Pathways in Tongue Squamous Cell Carcinoma Using Bioinformatics Analysis. PMID:29240723
Transcriptome-wide analysis of natural antisense transcripts shows their potential role in breast cancer. PMID:29234122
Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors. PMID:29234012
DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism. PMID:29233090
Query expansion using MeSH terms for dataset retrieval: OHSU at the bioCADDIE 2016 dataset retrieval challenge. PMID:29220467
Leveraging putative enhancer-promoter interactions to investigate two-way epistasis in Type 2 Diabetes GWAS. PMID:29218913
P4HB and PDIA3 are associated with tumor progression and therapeutic outcome of diffuse gliomas. PMID:29207176
Cross-Laboratory Analysis of Brain Cell Type Transcriptomes with Applications to Interpretation of Bulk Tissue Data. PMID:29204516
CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models. PMID:29192179
Genetic variation at the microRNA binding site of CAV1 gene is associated with lung cancer susceptibility. PMID:29190968
LncRNA H19 is a major mediator of doxorubicin chemoresistance in breast cancer cells through a cullin4A-MDR1 pathway. PMID:29190892
Integrative Bioinformatic Analysis of Transcriptomic Data Identifies Conserved Molecular Pathways Underlying Ionizing Radiation-Induced Bystander Effects (RIBE). PMID:29186820
SATORI: a system for ontology-guided visual exploration of biomedical data repositories. PMID:29186292
Selection of internal references for qRT-PCR assays of human hepatocellular carcinoma cell lines. PMID:29180379
Expression Atlas: gene and protein expression across multiple studies and organisms. PMID:29165655
FunCoup 4: new species, data, and visualization. PMID:29165593
MethBank 3.0: a database of DNA methylomes across a variety of species. PMID:29161430
DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA-gene interactions. PMID:29156006
Deep RNAseq indicates protective mechanisms of cold-tolerant indica rice plants during early vegetative stage. PMID:29151156
NONCODEV5: a comprehensive annotation database for long non-coding RNAs. PMID:29140524
Therapeutic target database update 2018: enriched resource for facilitating bench-to-clinic research of targeted therapeutics. PMID:29140520
CEACAM6 is a prognostic biomarker and potential therapeutic target for gastric carcinoma. PMID:29137373
Transcriptome dynamics along axolotl regenerative development are consistent with an extensive reduction in gene expression heterogeneity in dedifferentiated cells. PMID:29134148
ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments. PMID:29126285
miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions. PMID:29126174
Erythropoietin Increases Myelination in Oligodendrocytes: Gene Expression Profiling Reveals Early Induction of Genes Involved in Lipid Transport and Metabolism. PMID:29123527
Context-dependent compensation among phosphatidylserine-recognition receptors. PMID:29116131
Guanylate-binding protein-1 is a potential new therapeutic target for triple-negative breast cancer. PMID:29115931
Crosstalk between Receptor and Non-receptor Mediated Chemical Modes of Action in Rat Livers Converges through a Dysregulated Gene Expression Network at Tumor Suppressor Tp53. PMID:29114260
Overexpression of HS6ST2 is associated with poor prognosis in patients with gastric cancer. PMID:29113266
Beta-catenin represses protein kinase D1 gene expression by non-canonical pathway through MYC/MAX transcription complex in prostate cancer. PMID:29108267
lncRNAs PVT1 and HAR1A are prognosis biomarkers and indicate therapy outcome for diffuse glioma patients. PMID:29108264
Bioinformatic Analysis Identifies Three Potentially Key Differentially Expressed Genes in Peripheral Blood Mononuclear Cells of Patients with Takayasu's Arteritis. PMID:29105401
Cancer cell line specific co-factors modulate the FOXM1 cistrome. PMID:29100329
WebMeV: A Cloud Platform for Analyzing and Visualizing Cancer Genomic Data. PMID:29092929
HCMDB: the human cancer metastasis database. PMID:29088455
TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions. PMID:29087512
eQTLs Regulating Transcript Variations Associated with Rapid Internode Elongation in Deepwater Rice. PMID:29081784
SaVanT: a web-based tool for the sample-level visualization of molecular signatures in gene expression profiles. PMID:29070035
dreamBase: DNA modification, RNA regulation and protein binding of expressed pseudogenes in human health and disease. PMID:29059382
The SIN3A histone deacetylase complex is required for a complete transcriptional response to hypoxia. PMID:29059365
Xenbase: a genomic, epigenomic and transcriptomic model organism database. PMID:29059324
Transcriptional Activities of the Microbial Consortium Living with the Marine Nitrogen-Fixing Cyanobacterium Trichodesmium Reveal Potential Roles in Community-Level Nitrogen Cycling. PMID:29054872
Current Progress in EBV-Associated B-Cell Lymphomas. PMID:29052132
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
StemMapper: a curated gene expression database for stem cell lineage analysis. PMID:29045725
Evaluation of variable selection methods for random forests and omics data sets. PMID:29045534
PCSD: a plant chromatin state database. PMID:29040761
EpiDenovo: a platform for linking regulatory de novo mutations to developmental epigenetics and diseases. PMID:29040751
RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data. PMID:29040692
iSyTE 2.0: a database for expression-based gene discovery in the eye. PMID:29036527
ScanGEO: parallel mining of high-throughput gene expression data. PMID:29036513
Hedgehog-mesenchyme gene signature identifies bi-modal prognosis in luminal and basal breast cancer sub-types. PMID:29034935
Genomic insights into head and neck cancer. PMID:29034103
Single-cell RNA sequencing reveals developmental heterogeneity among early lymphoid progenitors. PMID:29030486
A strategy for evaluating pathway analysis methods. PMID:29029625
LiverWiki: a wiki-based database for human liver. PMID:29029599
Comparative analysis of differential gene expression tools for RNA sequencing time course data. PMID:29028903
Systematic, network-based characterization of therapeutic target inhibitors. PMID:29023443
RNA sequencing identifies novel non-coding RNA and exon-specific effects associated with cigarette smoking. PMID:28985737
Genome-wide identification of key modulators of gene-gene interaction networks in breast cancer. PMID:28984209
'Multi-omic' data analysis using O-miner. PMID:28981577
Viewing RNA-seq data on the entire human genome. PMID:28979763
A meta-analysis of transcriptomic characterization revealed extracellular matrix pathway involved in the H5N1 and H7N9 infections. PMID:28977969
AAgMarker 1.0: a resource of serological autoantigen biomarkers for clinical diagnosis and prognosis of various human diseases. PMID:28977551
Using neural networks for reducing the dimensions of single-cell RNA-Seq data. PMID:28973464
paraGSEA: a scalable approach for large-scale gene expression profiling. PMID:28973463
Statistically controlled identification of differentially expressed genes in one-to-one cell line comparisons of the CMAP database for drug repositioning. PMID:28962576
The Biofilm Inhibitor Carolacton Enters Gram-Negative Cells: Studies Using a TolC-Deficient Strain of Escherichia coli. PMID:28959742
RNA-sequencing reveals the complexities of the transcriptional response to lignocellulosic biofuel substrates in Aspergillus niger. PMID:28955445
Human hepatic gene expression signature of non-alcoholic fatty liver disease progression, a meta-analysis. PMID:28955037
Escape Excel: A tool for preventing gene symbol and accession conversion errors. PMID:28953918
Systematic Discovery of Archaeal Transcription Factor Functions in Regulatory Networks through Quantitative Phenotyping Analysis. PMID:28951888
Genomic characterization of tobacco/nut chewing HPV-negative early stage tongue tumors identify MMP10 asa candidate to predict metastases. PMID:28939077
Systematic integration of biomedical knowledge prioritizes drugs for repurposing. PMID:28936969
Light and Plastid Signals Regulate Different Sets of Genes in the Albino Mutant Pap7-1. PMID:28935841
De novo pathway-based biomarker identification. PMID:28934488
Identifying therapeutic targets by combining transcriptional data with ordinal clinical measurements. PMID:28931805
Screening of Critical Genes and MicroRNAs in Blood Samples of Patients with Ruptured Intracranial Aneurysms by Bioinformatic Analysis of Gene Expression Data. PMID:28930970
Screening of candidate key genes associated with human osteosarcoma using bioinformatics analysis. PMID:28928828
Overexpression and proliferation dependence of acyl-CoA thioesterase 11 and 13 in lung adenocarcinoma. PMID:28927126
Precision annotation of digital samples in NCBI's gene expression omnibus. PMID:28925997
Evolutionary history and functional divergence of the cytochrome P450 gene superfamily between Arabidopsis thaliana and Brassica species uncover effects of whole genome and tandem duplications. PMID:28923019
Cleaning by clustering: methodology for addressing data quality issues in biomedical metadata. PMID:28923003
De novo transcriptome of the cosmopolitan dinoflagellate Amphidinium carterae to identify enzymes with biotechnological potential. PMID:28916825
mmquant: how to count multi-mapping reads? PMID:28915787
Transcriptome analysis of developing lens reveals abundance of novel transcripts and extensive splicing alterations. PMID:28912564
Genome build information is an essential part of genomic track files. PMID:28911336
Web-based NGS data analysis using miRMaster: a large-scale meta-analysis of human miRNAs. PMID:28911107
Systematic analysis of coronary artery disease datasets revealed the potential biomarker and treatment target. PMID:28903366
Identification and characterization of preferred DNA-binding sites for the Thermus thermophilus transcriptional regulator FadR. PMID:28902898
Molecular mechanisms of pathogenesis in hepatocellular carcinoma revealed by RNA‑sequencing. PMID:28901494
Effects of Combined Low Glutathione with Mild Oxidative and Low Phosphorus Stress on the Metabolism of Arabidopsis thaliana. PMID:28894456
Expression of the ZIP/SLC39A transporters in β-cells: a systematic review and integration of multiple datasets. PMID:28893192
Integrated expression profiles analysis reveals novel predictive biomarker in pancreatic ductal adenocarcinoma. PMID:28881752
The landscape of DNA methylation-mediated regulation of long non-coding RNAs in breast cancer. PMID:28881636
Selection for energy efficiency drives strand-biased gene distribution in prokaryotes. PMID:28874819
FunctionAnnotator, a versatile and efficient web tool for non-model organism annotation. PMID:28874813
Chronic obstructive pulmonary disease candidate gene prioritization based on metabolic networks and functional information. PMID:28873096
New Genes and Functional Innovation in Mammals. PMID:28854603
RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes. PMID:28850115
Personalized identification of differentially expressed pathways in pediatric sepsis. PMID:28849000
Expression and Regulatory Network Analysis of miR-140-3p, a New Potential Serum Biomarker for Autism Spectrum Disorder. PMID:28848387
Repulsive Guidance Molecule a (RGMa) Induces Neuropathological and Behavioral Changes That Closely Resemble Parkinson's Disease. PMID:28842419
Identification of the Consistently Altered Metabolic Targets in Human Hepatocellular Carcinoma. PMID:28840186
Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse. PMID:28838066
Culture-induced recurrent epigenetic aberrations in human pluripotent stem cells. PMID:28837588
A regulation probability model-based meta-analysis of multiple transcriptomics data sets for cancer biomarker identification. PMID:28830341
Extracting replicable associations across multiple studies: Empirical Bayes algorithms for controlling the false discovery rate. PMID:28821015
Sources to variability in circulating human miRNA signatures. PMID:28820329
Dissecting the genomic activity of a transcriptional regulator by the integrative analysis of omics data. PMID:28819152
Biosemantics guided gene expression profiling of Sjögren's syndrome: a comparative analysis with systemic lupus erythematosus and rheumatoid arthritis. PMID:28818099
Crosstalk between diurnal rhythm and water stress reveals an altered primary carbon flux into soluble sugars in drought-treated rice leaves. PMID:28811563
Identification and characterization of a long non-coding RNA up-regulated during HIV-1 infection. PMID:28803142
Small secreted proteins from the necrotrophic conifer pathogen Heterobasidion annosum s.l. (HaSSPs) induce cell death in Nicotiana benthamiana. PMID:28801666
Analysis of salivary microRNA expression profiles and identification of novel biomarkers in esophageal cancer. PMID:28789354
Evolution of Daily Gene Co-expression Patterns from Algae to Plants. PMID:28751903
Prediction of novel target genes and pathways involved in irinotecan-resistant colorectal cancer. PMID:28749961
Bayesian association scan reveals loci associated with human lifespan and linked biomarkers. PMID:28748955
Root-Knot and Cyst Nematodes Activate Procambium-Associated Genes in Arabidopsis Roots. PMID:28747918
Exploring the cross talk between ER stress and inflammation in age-related macular degeneration. PMID:28742151
Using machine learning to identify air pollution exposure profiles associated with early cognitive skills among U.S. children. PMID:28732336
Identification of four prognostic LncRNAs for survival prediction of patients with hepatocellular carcinoma. PMID:28729955
Gene expression reversal toward pre-adult levels in the aging human brain and age-related loss of cellular identity. PMID:28724976
Identification of potential biomarkers and therapeutic targets for human IgA nephropathy and hypertensive nephropathy by bioinformatics analysis. PMID:28713898
Reduced Protein Expression in a Virus Attenuated by Codon Deoptimization. PMID:28698233
Ror2 Signaling and Its Relevance in Breast Cancer Progression. PMID:28695110
GeNNet: an integrated platform for unifying scientific workflows and graph databases for transcriptome data analysis. PMID:28695067
Differential co-expression analysis reveals a novel prognostic gene module in ovarian cancer. PMID:28694494
PDZK1 inhibits the development and progression of renal cell carcinoma by suppression of SHP-1 phosphorylation. PMID:28692056
Reorganization of gene network for degradation of polycyclic aromatic hydrocarbons (PAHs) in Pseudomonas aeruginosa PAO1 under several conditions. PMID:28685384
MicroRNA profiling in gingival crevicular fluid of periodontitis-a pilot study. PMID:28680811
Mechanisms of action of sacubitril/valsartan on cardiac remodeling: a systems biology approach. PMID:28649439
On the performance of de novo pathway enrichment. PMID:28649433
SBMLmod: a Python-based web application and web service for efficient data integration and model simulation. PMID:28646877
Predicting structured metadata from unstructured metadata. PMID:28637268
Predicting biomedical metadata in CEDAR: A study of Gene Expression Omnibus (GEO). PMID:28625880
MyGeneFriends: A Social Network Linking Genes, Genetic Diseases, and Researchers. PMID:28623182
Network Analysis Reveals a Common Host-Pathogen Interaction Pattern in Arabidopsis Immune Responses. PMID:28611808
PHF6 regulates phenotypic plasticity through chromatin organization within lineage-specific genes. PMID:28607179
Functional proteogenomics reveals biomarkers and therapeutic targets in lymphomas. PMID:28607076
Uniform neural tissue models produced on synthetic hydrogels using standard culture techniques. PMID:28599598
Gene and miRNA expression profiles of mouse Lewis lung carcinoma LLC1 cells following single or fractionated dose irradiation. PMID:28599420
A comparison of gene expression profiles in patients with coronary artery disease, type 2 diabetes, and their coexisting conditions. PMID:28595632
Analysis of Microarray-Identified Genes and MicroRNAs Associated with Idiopathic Pulmonary Fibrosis. PMID:28588348
PA3225 Is a Transcriptional Repressor of Antibiotic Resistance Mechanisms in Pseudomonas aeruginosa. PMID:28584154
DrugSig: A resource for computational drug repositioning utilizing gene expression signatures. PMID:28562632
Profile and functional analysis of small RNAs derived from Aspergillus fumigatus infected with double-stranded RNA mycoviruses. PMID:28558690
On the effects of alternative optima in context-specific metabolic model predictions. PMID:28557990
Extensive phenotypic characterization of a new transgenic mouse reveals pleiotropic perturbations in physiology due to mesenchymal hGH minigene expression. PMID:28546545
Interleukin-like EMT inducer regulates partial phenotype switching in MITF-low melanoma cell lines. PMID:28545079
Gene signature associated with benign neurofibroma transformation to malignant peripheral nerve sheath tumors. PMID:28542306
Large-scale transcriptome analysis reveals arabidopsis metabolic pathways are frequently influenced by different pathogens. PMID:28540497
Circadian networks in human embryonic stem cell-derived cardiomyocytes. PMID:28536247
MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive. PMID:28535296
Matrix Mechanosensing: From Scaling Concepts in 'Omics Data to Mechanisms in the Nucleus, Regeneration, and Cancer. PMID:28532215
Bioinformatics and in vitro experimental analyses identify the selective therapeutic potential of interferon gamma and apigenin against cervical squamous cell carcinoma and adenocarcinoma. PMID:28526810
Prediction of NSCLC recurrence from microarray data with GEP. PMID:28518058
A Web Service Framework for Interactive Analysis of Metabolomics Data. PMID:28514166
The Transcriptome of Type I Murine Astrocytes under Interferon-Gamma Exposure and Remyelination Stimulus. PMID:28505143
Expression of the filaggrin gene in umbilical cord blood predicts eczema risk in infancy: A birth cohort study. PMID:28502108
RegulatorTrail: a web service for the identification of key transcriptional regulators. PMID:28472408
Gene set selection via LASSO penalized regression (SLPR). PMID:28472344
EnHERV: Enrichment analysis of specific human endogenous retrovirus patterns and their neighboring genes. PMID:28472109
Interactive Toxicogenomics: Gene set discovery, clustering and analysis in Toxygates. PMID:28469246
Pervasive Behavioral Effects of MicroRNA Regulation in Drosophila. PMID:28468905
Computational modeling of the cell-autonomous mammalian circadian oscillator. PMID:28466791
Zipper plot: visualizing transcriptional activity of genomic regions. PMID:28464823
Investigation of differentially-expressed microRNAs and genes in cervical cancer using an integrated bioinformatics analysis. PMID:28454467
CHK2 is involved in the p53-independent radiosensitizing effects of valproic acid. PMID:28454438
Metabolic control of primed human pluripotent stem cell fate and function by the miR-200c-SIRT2 axis. PMID:28436968
Genomic responses to the socio-sexual environment in male Drosophila melanogaster exposed to conspecific rivals. PMID:28428330
High-fat diet induced leptin and Wnt expression: RNA-sequencing and pathway analysis of mouse colonic tissue and tumors. PMID:28426873
Integrated analysis of genes associated with poor prognosis of patients with colorectal cancer liver metastasis. PMID:28424419
Reduced changes in protein compared to mRNA levels across non-proliferating tissues. PMID:28420336
The E. coli molecular phenotype under different growth conditions. PMID:28417974
Transcriptional networks are associated with resistance to Mycobacterium tuberculosis infection. PMID:28414762
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
Highly accessible AU-rich regions in 3' untranslated regions are hotspots for binding of regulatory factors. PMID:28410363
miRCat2: accurate prediction of plant and animal microRNAs from next-generation sequencing datasets. PMID:28407097
Omicseq: a web-based search engine for exploring omics datasets. PMID:28402462
Changes in circulating microRNA levels can be identified as early as day 8 of pregnancy in cattle. PMID:28380001
Drug repurposing from the perspective of pharmaceutical companies. PMID:28369768
Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment. PMID:28351423
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
C9ORF135 encodes a membrane protein whose expression is related to pluripotency in human embryonic stem cells. PMID:28345668
In silico search for modifier genes associated with pancreatic and liver disease in Cystic Fibrosis. PMID:28339466
Melting temperature highlights functionally important RNA structure and sequence elements in yeast mRNA coding regions. PMID:28335026
RCAS: an RNA centric annotation system for transcriptome-wide regions of interest. PMID:28334930
BCIP: a gene-centered platform for identifying potential regulatory genes in breast cancer. PMID:28327601
Exploring the nature of prediagnostic blood transcriptome markers of chronic lymphocytic leukemia by assessing their overlap with the transcriptome at the clinical stage. PMID:28320322
Identification and interaction analysis of key genes and microRNAs in hepatocellular carcinoma by bioinformatics analysis. PMID:28302149
Systems-level understanding of ethanol-induced stresses and adaptation in E. coli. PMID:28300180
Comprehensive processing of high-throughput small RNA sequencing data including quality checking, normalization, and differential expression analysis using the UEA sRNA Workbench. PMID:28289155
Support for phosphoinositol 3 kinase and mTOR inhibitors as treatment for lupus using in-silico drug-repurposing analysis. PMID:28284231
ELF-MF exposure affects the robustness of epigenetic programming during granulopoiesis. PMID:28266526
Gene expression profiles reveal key pathways and genes associated with neuropathic pain in patients with spinal cord injury. PMID:28260076
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
Personalized chemotherapy selection for breast cancer using gene expression profiles. PMID:28256629
ZEB1 regulates glioma stemness through LIF repression. PMID:28246407
RNA-Sequencing data supports the existence of novel VEGFA splicing events but not of VEGFAxxxb isoforms. PMID:28246395
Identification of miRNA-mRNA crosstalk in CD4+ T cells during HIV-1 infection by integrating transcriptome analyses. PMID:28222782
Blood transcriptome based biomarkers for human circadian phase. PMID:28218891
FocusHeuristics - expression-data-driven network optimization and disease gene prediction. PMID:28205611
An approach to infer putative disease-specific mechanisms using neighboring gene networks. PMID:28200075
Analysis of miRNA, mRNA, and TF interactions through network-based methods. PMID:28194173
A feature selection method based on multiple kernel learning with expression profiles of different types. PMID:28184251
Reduced mitochondrial activity in colonocytes facilitates AMPKα2-dependent inflammation. PMID:28183804
Large-scale analysis of microRNA expression, epi-transcriptomic features and biogenesis. PMID:28180281
Genome-wide exonic small interference RNA-mediated gene silencing regulates sexual reproduction in the homothallic fungus Fusarium graminearum. PMID:28146558
Metabox: A Toolbox for Metabolomic Data Analysis, Interpretation and Integrative Exploration. PMID:28141874
Association of microRNA-33a Molecular Signature with Non-Small Cell Lung Cancer Diagnosis and Prognosis after Chemotherapy. PMID:28141816
Prostatic compensation of the vitamin D axis in African American men. PMID:28138564
Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization. PMID:28133571
Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy. PMID:28132844
IC-Finder: inferring robustly the hierarchical organization of chromatin folding. PMID:28130423
Expression of Calgranulin Genes S100A8, S100A9 and S100A12 Is Modulated by n-3 PUFA during Inflammation in Adipose Tissue and Mononuclear Cells. PMID:28125622
Underexpression of Specific Interferon Genes Is Associated with Poor Prognosis of Melanoma. PMID:28114321
RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets. PMID:28108657
Using Network Extracted Ontologies to Identify Novel Genes with Roles in Appressorium Development in the Rice Blast Fungus Magnaporthe oryzae. PMID:28106722
Molecular Characterization of Pediatric Restrictive Cardiomyopathy from Integrative Genomics. PMID:28098235
MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration. PMID:28095799
Genome-wide expression profiling in muscle and subcutaneous fat of lambs in response to the intake of concentrate supplemented with vitamin E. PMID:28095783
ARA-PEPs: a repository of putative sORF-encoded peptides in Arabidopsis thaliana. PMID:28095775
Direct Heme Uptake by Phytoplankton-Associated Roseobacter Bacteria. PMID:28083564
Personalized Prediction of Proliferation Rates and Metabolic Liabilities in Cancer Biopsies. PMID:28082911
Establishment of a integrative multi-omics expression database CKDdb in the context of chronic kidney disease (CKD). PMID:28079125
A CpG island methylator phenotype in acute myeloid leukemia independent of IDH mutations and associated with a favorable outcome. PMID:28074068
A review of connectivity map and computational approaches in pharmacogenomics. PMID:28069634
Enumerateblood - an R package to estimate the cellular composition of whole blood from Affymetrix Gene ST gene expression profiles. PMID:28061752
LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells. PMID:28056766
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
Mechanosensing by the nucleus: From pathways to scaling relationships. PMID:28043971
Androgen receptor transcriptionally regulates semaphorin 3C in a GATA2-dependent manner. PMID:28038451
Robust transcriptional tumor signatures applicable to both formalin-fixed paraffin-embedded and fresh-frozen samples. PMID:28036264
Fetal and adult progenitors give rise to unique populations of CD8+ T cells. PMID:28034872
HEDD: the human epigenetic drug database. PMID:28025347
VaProS: a database-integration approach for protein/genome information retrieval. PMID:28012137
Daxx inhibits hypoxia-induced lung cancer cell metastasis by suppressing the HIF-1α/HDAC1/Slug axis. PMID:28004751
Cytoplasm-Translocated Ku70/80 Complex Sensing of HBV DNA Induces Hepatitis-Associated Chemokine Secretion. PMID:27994596
Pan- and core- network analysis of co-expression genes in a model plant. PMID:27982071
Integrating Epigenomics into the Understanding of Biomedical Insight. PMID:27980397
Performance Evaluation and Online Realization of Data-driven Normalization Methods Used in LC/MS based Untargeted Metabolomics Analysis. PMID:27958387
GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments. PMID:27924024
Identification of candidate genes in osteoporosis by integrated microarray analysis. PMID:27908864
Function-driven discovery of disease genes in zebrafish using an integrated genomics big data resource. PMID:27903883
Identification of laryngeal cancer prognostic biomarkers using an inflammatory gene-related, competitive endogenous RNA network. PMID:27902487
DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database. PMID:27899673
jPOSTrepo: an international standard data repository for proteomes. PMID:27899654
The dbGaP data browser: a new tool for browsing dbGaP controlled-access genomic data. PMID:27899644
TFBSbank: a platform to dissect the big data of protein-DNA interaction in human and model species. PMID:27899608
Accelerated placental aging in early onset preeclampsia pregnancies identified by DNA methylation. PMID:27894195
Proteomic profiling of NCI-60 extracellular vesicles uncovers common protein cargo and cancer type-specific biomarkers. PMID:27894104
EWAS: epigenome-wide association studies software 1.0 - identifying the association between combinations of methylation levels and diseases. PMID:27892496
Diet-Microbiota Interactions Mediate Global Epigenetic Programming in Multiple Host Tissues. PMID:27889451
Interactive cooperation and hierarchical operation of microRNA and transcription factor crosstalk in human transcriptional regulatory network. PMID:27879476
Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer. PMID:27876760
Conservation of immune gene signatures in solid tumors and prognostic implications. PMID:27871313
Insights into the human mesenchymal stromal/stem cell identity through integrative transcriptomic profiling. PMID:27871224
Unmasking ultradian rhythms in gene expression. PMID:27871062
The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data. PMID:27863463
Changes in Communication between Muscle Stem Cells and their Environment with Aging. PMID:27858742
Gene expression profiling of breast cancer in Lebanese women. PMID:27857161
Identification of transcription factors (TFs) and targets involved in the cholangiocarcinoma (CCA) by integrated analysis. PMID:27857060
Identification of an Efficient Gene Expression Panel for Glioblastoma Classification. PMID:27855170
Identification of potential genes for human ischemic cardiomyopathy based on RNA-Seq data. PMID:27852050
GEN3VA: aggregation and analysis of gene expression signatures from related studies. PMID:27846806
Proliferation rates and gene expression profiles in human lymphoblastoid cell lines from patients with depression characterized in response to antidepressant drug therapy. PMID:27845776
Integrative analysis of genetic data sets reveals a shared innate immune component in autism spectrum disorder and its co-morbidities. PMID:27842596
RSK2 activity mediates glioblastoma invasiveness and is a potential target for new therapeutics. PMID:27829215
Transcriptomic Biomarkers for Tuberculosis: Evaluation of DOCK9. EPHA4, and NPC2 mRNA Expression in Peripheral Blood. PMID:27826286
Cathelicidin Insufficiency in Patients with Fatal Leptospirosis. PMID:27812211
Large-scale gene co-expression network as a source of functional annotation for cattle genes. PMID:27806696
Unveiling DNA structural features of promoters associated with various types of TSSs in prokaryotic transcriptomes and their role in gene expression. PMID:27803028
Rawcopy: Improved copy number analysis with Affymetrix arrays. PMID:27796336
Molecular mechanisms underlying COPD-muscle dysfunction unveiled through a systems medicine approach. PMID:27794560
NGSmethDB 2017: enhanced methylomes and differential methylation. PMID:27794041
Large Scale Gene Expression Meta-Analysis Reveals Tissue-Specific, Sex-Biased Gene Expression in Humans. PMID:27790248
Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse. PMID:27789702
Using Big Data to Discover Diagnostics and Therapeutics for Gastrointestinal and Liver Diseases. PMID:27773806
Incorporating topological information for predicting robust cancer subnetwork markers in human protein-protein interaction network. PMID:27766944
Alternative Polyadenylation in Triple-Negative Breast Tumors Allows NRAS and c-JUN to Bypass PUMILIO Posttranscriptional Regulation. PMID:27758885
Identification of candidate biomarkers and analysis of prognostic values in ovarian cancer by integrated bioinformatics analysis. PMID:27757782
Comparative Transcriptomic Analysis of Two Brassica napus Near-Isogenic Lines Reveals a Network of Genes That Influences Seed Oil Accumulation. PMID:27746810
Relevance of Tumor-Infiltrating Immune Cell Composition and Functionality for Disease Outcome in Breast Cancer. PMID:27737921
Computational methods for direct cell conversion. PMID:27736295
CNARA: reliability assessment for genomic copy number profiles. PMID:27733115
Differential Coexpression Analysis Reveals Extensive Rewiring of Arabidopsis Gene Coexpression in Response to Pseudomonas syringae Infection. PMID:27721457
Novel microRNA discovery using small RNA sequencing in post-mortem human brain. PMID:27716130
Landscape of Genomic Alterations in Pituitary Adenomas. PMID:27707790
Genome-wide compendium and functional assessment of in vivo heart enhancers. PMID:27703156
hemaClass.org: Online One-By-One Microarray Normalization and Classification of Hematological Cancers for Precision Medicine. PMID:27701436
Celecoxib exhibits an anti-gastric cancer effect by targeting focal adhesion and leukocyte transendothelial migration-associated genes. PMID:27698798
Survey of Genes Involved in Biosynthesis, Transport, and Signaling of Phytohormones with Focus on Solanum lycopersicum. PMID:27695302
Genome-wide identification and characterization of tRNA-derived RNA fragments in land plants. PMID:27681945
Characterization and phosphoproteomic analysis of a human immortalized podocyte model of Fabry disease generated using CRISPR/Cas9 technology. PMID:27681560
Integrated RNA-seq and sRNA-seq analysis reveals miRNA effects on secondary metabolism in Solanum tuberosum L. PMID:27679507
COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH). PMID:27679477
Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd. PMID:27667448
Identification of Transcribed Enhancers by Genome-Wide Chromatin Immunoprecipitation Sequencing. PMID:27662872
Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms. PMID:27654999
The application of transcriptomic data in the authentication of beef derived from contrasting production systems. PMID:27654331
CardioTF, a database of deconstructing transcriptional circuits in the heart system. PMID:27635320
Differential expression analysis for individual cancer samples based on robust within-sample relative gene expression orderings across multiple profiling platforms. PMID:27634898
THBS2 is a Potential Prognostic Biomarker in Colorectal Cancer. PMID:27632935
Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos. PMID:27626379
Systems Medicine as an Emerging Tool for Cardiovascular Genetics. PMID:27626034
Positive Selection Linked with Generation of Novel Mammalian Dentition Patterns. PMID:27613398
Meta-Analysis of Parkinson's Disease Transcriptome Data Using TRAM Software: Whole Substantia Nigra Tissue and Single Dopamine Neuron Differential Gene Expression. PMID:27611585
Plasma exosome microRNAs are indicative of breast cancer. PMID:27608715
Profiling Pre-MicroRNA and Mature MicroRNA Expressions Using a Single Microarray and Avoiding Separate Sample Preparation. PMID:27605179
Temporal dynamics of the developing lung transcriptome in three common inbred strains of laboratory mice reveals multiple stages of postnatal alveolar development. PMID:27602285
Meta-analysis of clinical metabolic profiling studies in cancer: challenges and opportunities. PMID:27601137
"Upstream Analysis": An Integrated Promoter-Pathway Analysis Approach to Causal Interpretation of Microarray Data. PMID:27600225
Data sources for in vivo molecular profiling of human phenotypes. PMID:27599755
Effects of Gene Dose, Chromatin, and Network Topology on Expression in Drosophila melanogaster. PMID:27599372
Order restricted inference for oscillatory systems for detecting rhythmic signals. PMID:27596593
Explore Small Molecule-induced Genome-wide Transcriptional Profiles for Novel Inflammatory Bowel Disease Drug. PMID:27570643
Microarray-based identification of genes associated with cancer progression and prognosis in hepatocellular carcinoma. PMID:27567667
Large-Scale Public Transcriptomic Data Mining Reveals a Tight Connection between the Transport of Nitrogen and Other Transport Processes in Arabidopsis. PMID:27563305
EpiTracer - an algorithm for identifying epicenters in condition-specific biological networks. PMID:27556637
Reconstructing directed gene regulatory network by only gene expression data. PMID:27556418
A molecular conundrum involving hypothalamic responses to and roles of long non-coding RNAs following food deprivation. PMID:27555291
Gene name errors are widespread in the scientific literature. PMID:27552985
Serum neutrophil gelatinase-associated lipocalin and resistin are associated with dengue infection in adults. PMID:27549428
EnhancerAtlas: a resource for enhancer annotation and analysis in 105 human cell/tissue types. PMID:27515742
Databases and tools for constructing signal transduction networks in cancer. PMID:27502015
Decreased LIPF expression is correlated with DGKA and predicts poor outcome of gastric cancer. PMID:27498782
Modeling protein-DNA binding via high-throughput in vitro technologies. PMID:27497616
Disrupted cooperation between transcription factors across diverse cancer types. PMID:27496222
SoyNet: a database of co-functional networks for soybean Glycine max. PMID:27492285
Achiasmy: Male Fruit Flies Are Not Ready to Mix. PMID:27486580
Effect of a diet enriched with omega-6 and omega-3 fatty acids on the pig liver transcriptome. PMID:27482299
Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder. PMID:27479844
Genome-wide identification and expression analysis of sulfate transporter (SULTR) genes in potato (Solanum tuberosum L.). PMID:27473680
The effects of lymph node status on predicting outcome in ER+ /HER2- tamoxifen treated breast cancer patients using gene signatures. PMID:27469239
Structural basis for LIN54 recognition of CHR elements in cell cycle-regulated promoters. PMID:27465258
Integrative Analysis of Microarray Data to Reveal Regulation Patterns in the Pathogenesis of Hepatocellular Carcinoma. PMID:27458175
Predicting associations between microRNAs and target genes in breast cancer by bioinformatics analyses. PMID:27446395
Gene Expression Music Algorithm-Based Characterization of the Ewing Sarcoma Stem Cell Signature. PMID:27446218
Integration and Visualization of Translational Medicine Data for Better Understanding of Human Diseases. PMID:27441714
Comparison of In Vivo Gene Expression Profiling of RPE/Choroid following Intravitreal Injection of Dexamethasone and Triamcinolone Acetonide. PMID:27429799
Research Resource: A Reference Transcriptome for Constitutive Androstane Receptor and Pregnane X Receptor Xenobiotic Signaling. PMID:27409825
A systems-oriented analysis of the grapevine R2R3-MYB transcription factor family uncovers new insights into the regulation of stilbene accumulation. PMID:27407139
Obtaining Human Ischemic Stroke Gene Expression Biomarkers from Animal Models: A Cross-species Validation Study. PMID:27407070
Overcoming the matched-sample bottleneck: an orthogonal approach to integrate omic data. PMID:27403564
Screening Driving Transcription Factors in the Processing of Gastric Cancer. PMID:27403158
FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki. PMID:27402679
Non-myogenic tumors display altered expression of dystrophin (DMD) and a high frequency of genetic alterations. PMID:27391342
Systematic Identification of Anti-Fungal Drug Targets by a Metabolic Network Approach. PMID:27379244
Profiling networks of distinct immune-cells in tumors. PMID:27377892
BcCluster: A Bladder Cancer Database at the Molecular Level. PMID:27376128
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
FOXR2 Interacts with MYC to Promote Its Transcriptional Activities and Tumorigenesis. PMID:27346356
The space of enzyme regulation in HeLa cells can be inferred from its intracellular metabolome. PMID:27335086
multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome Profiles. PMID:27330269
A crowdsourcing approach for reusing and meta-analyzing gene expression data. PMID:27323300
Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families. PMID:27322404
Identification of Cancer Related Genes Using a Comprehensive Map of Human Gene Expression. PMID:27322383
Meta-Analysis of Differential Connectivity in Gene Co-Expression Networks in Multiple Sclerosis. PMID:27314336
GON4L Drives Cancer Growth through a YY1-Androgen Receptor-CD24 Axis. PMID:27312530
Heat shock protein 90 is required for sexual and asexual development, virulence, and heat shock response in Fusarium graminearum. PMID:27306495
Extracting a low-dimensional description of multiple gene expression datasets reveals a potential driver for tumor-associated stroma in ovarian cancer. PMID:27287041
Integration of TP53, DREAM, MMB-FOXM1 and RB-E2F target gene analyses identifies cell cycle gene regulatory networks. PMID:27280975
Diagnostic value of microRNAs in asbestos exposure and malignant mesothelioma: systematic review and qualitative meta-analysis. PMID:27259231
Torn apart and reunited: impact of a heterotroph on the transcriptome of Prochlorococcus. PMID:27258949
Common Marker Genes Identified from Various Sample Types for Systemic Lupus Erythematosus. PMID:27257790
Embracing an integromic approach to tissue biomarker research in cancer: Perspectives and lessons learned. PMID:27255914
SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis. PMID:27255077
EGFR Signal-Network Reconstruction Demonstrates Metabolic Crosstalk in EMT. PMID:27253373
VESPUCCI: Exploring Patterns of Gene Expression in Grapevine. PMID:27242836
Coronary artery disease susceptibility gene ADTRP regulates cell cycle progression, proliferation, and apoptosis by global gene expression regulation. PMID:27235449
Cogena, a novel tool for co-expressed gene-set enrichment analysis, applied to drug repositioning and drug mode of action discovery. PMID:27234029
Glucocorticoid receptor isoforms direct distinct mitochondrial programs to regulate ATP production. PMID:27226058
Deficiency of myeloid-related proteins 8 and 14 (Mrp8/Mrp14) does not block inflammaging but prevents steatosis. PMID:27224926
Abundance and Temperature Dependency of Protein-Protein Interaction Revealed by Interface Structure Analysis and Stability Evolution. PMID:27220911
Transcriptomic network analyses of leaf dehydration responses identify highly connected ABA and ethylene signaling hubs in three grapevine species differing in drought tolerance. PMID:27215785
A gene expression microarray for Nicotiana benthamiana based on de novo transcriptome sequence assembly. PMID:27213006
DIANA-mirExTra v2.0: Uncovering microRNAs and transcription factors with crucial roles in NGS expression data. PMID:27207881
Prevention of antipsychotic-induced hyperglycaemia by vitamin D: a data mining prediction followed by experimental exploration of the molecular mechanism. PMID:27199286
Venus flytrap carnivorous lifestyle builds on herbivore defense strategies. PMID:27197216
Whole-transcriptome analysis of UUO mouse model of renal fibrosis reveals new molecular players in kidney diseases. PMID:27189340
Improving microRNA target prediction with gene expression profiles. PMID:27189211
CTLPScanner: a web server for chromothripsis-like pattern detection. PMID:27185889
LOGIQA: a database dedicated to long-range genome interactions quality assessment. PMID:27185059
Utilization of a Conidia-Deficient Mutant to Study Sexual Development in Fusarium graminearum. PMID:27175901
Microarray Gene Expression Analysis to Evaluate Cell Type Specific Expression of Targets Relevant for Immunotherapy of Hematological Malignancies. PMID:27171398
Practical Approaches for Mining Frequent Patterns in Molecular Datasets. PMID:27168722
Inferring gene targets of drugs and chemical compounds from gene expression profiles. PMID:27153589
DrugGenEx-Net: a novel computational platform for systems pharmacology and gene expression-based drug repurposing. PMID:27151405
How Hepatitis C Virus Leads to Hepatocellular Carcinoma: A Network-Based Study. PMID:27148389
PPARgene: A Database of Experimentally Verified and Computationally Predicted PPAR Target Genes. PMID:27148361
Data-based Reconstruction of Gene Regulatory Networks of Fungal Pathogens. PMID:27148247
The extracellular interactome of the human adenovirus family reveals diverse strategies for immunomodulation. PMID:27145901
Identifying Network Perturbation in Cancer. PMID:27145341
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. PMID:27141961
Conserved Senescence Associated Genes and Pathways in Primary Human Fibroblasts Detected by RNA-Seq. PMID:27140416
Cassava (Manihot esculenta) transcriptome analysis in response to infection by the fungus Colletotrichum gloeosporioides using an oligonucleotide-DNA microarray. PMID:27138000
G-DOC Plus - an integrative bioinformatics platform for precision medicine. PMID:27130330
OM-FBA: Integrate Transcriptomics Data with Flux Balance Analysis to Decipher the Cell Metabolism. PMID:27100883
Loss of Panx1 Impairs Mammary Gland Development at Lactation: Implications for Breast Tumorigenesis. PMID:27099931
g:Profiler-a web server for functional interpretation of gene lists (2016 update). PMID:27098042
A new molecular signature method for prediction of driver cancer pathways from transcriptional data. PMID:27098033
Peak-valley-peak pattern of histone modifications delineates active regulatory elements and their directionality. PMID:27095194
Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources. PMID:27092246
Human induced pluripotent stem cell-derived cardiomyocytes recapitulate the predilection of breast cancer patients to doxorubicin-induced cardiotoxicity. PMID:27089514
Identification and Evolutionary Analysis of Potential Candidate Genes in a Human Eating Disorder. PMID:27088090
The immunology of host defence peptides: beyond antimicrobial activity. PMID:27087664
NPInter v3.0: an upgraded database of noncoding RNA-associated interactions. PMID:27087310
HIC1 Expression Distinguishes Intestinal Carcinomas Sensitive to Chemotherapy. PMID:27084425
Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system. PMID:27078110
Data set for transcriptional response to depletion of the Shoc2 scaffolding protein. PMID:27077079
DNA hypomethylation upregulates expression of the MGAT3 gene in HepG2 cells and leads to changes in N-glycosylation of secreted glycoproteins. PMID:27073020
Identification of colorectal cancer-restricted microRNAs and their target genes based on high-throughput sequencing data. PMID:27069368
Contrasting invertebrate immune defense behaviors caused by a single gene, the Caenorhabditis elegans neuropeptide receptor gene npr-1. PMID:27066825
Immunological metagene signatures derived from immunogenic cancer cell death associate with improved survival of patients with lung, breast or ovarian malignancies: A large-scale meta-analysis. PMID:27057433
Identification of Differentially Expressed Genes through Integrated Study of Alzheimer's Disease Affected Brain Regions. PMID:27050411
A Novel Prioritization Method in Identifying Recurrent Venous Thromboembolism-Related Genes. PMID:27050193
Long non-coding RNA Databases in Cardiovascular Research. PMID:27049585
Transcriptomics resources of human tissues and organs. PMID:27044256
Ang-2/VEGF bispecific antibody reprograms macrophages and resident microglia to anti-tumor phenotype and prolongs glioblastoma survival. PMID:27044098
isomiR-SEA: an RNA-Seq analysis tool for miRNAs/isomiRs expression level profiling and miRNA-mRNA interaction sites evaluation. PMID:27036505
In Silico Analysis of Arabidopsis thaliana Peroxisomal 6-Phosphogluconate Dehydrogenase. PMID:27034898
An integrated analysis tool for analyzing hybridization intensities and genotypes using new-generation population-optimized human arrays. PMID:27029637
Expansion Mechanisms and Evolutionary History on Genes Encoding DNA Glycosylases and Their Involvement in Stress and Hormone Signaling. PMID:27026054
Can data repositories help find effective treatments for complex diseases? PMID:27018167
A blood RNA signature for tuberculosis disease risk: a prospective cohort study. PMID:27017310
Androgen deprivation therapy sensitizes triple negative breast cancer cells to immune-mediated lysis through androgen receptor independent modulation of osteoprotegerin. PMID:27015557
Condensin I and II behaviour in interphase nuclei and cells undergoing premature chromosome condensation. PMID:27008552
The Gene Expression Omnibus Database. PMID:27008011
Abscisic acid transcriptomic signaling varies with grapevine organ. PMID:27001301
MOL1 is required for cambium homeostasis in Arabidopsis. PMID:26991973
Transcriptional profile of immediate response to ionizing radiation exposure. PMID:26981369
Whole transcriptome profiling of patient-derived xenograft models as a tool to identify both tumor and stromal specific biomarkers. PMID:26980748
Principles of metadata organization at the ENCODE data coordination center. PMID:26980513
Spatiotemporal variation of mammalian protein complex stoichiometries. PMID:26975353
A rank-based transcriptional signature for predicting relapse risk of stage II colorectal cancer identified with proper data sources. PMID:26967049
12-HETER1/GPR31, a high-affinity 12(S)-hydroxyeicosatetraenoic acid receptor, is significantly up-regulated in prostate cancer and plays a critical role in prostate cancer progression. PMID:26965684
Combining Human Disease Genetics and Mouse Model Phenotypes towards Drug Repositioning for Parkinson's disease. PMID:26958284
Transcriptomes of Plant Gametophytes Have a Higher Proportion of Rapidly Evolving and Young Genes than Sporophytes. PMID:26956888
A Human "eFP" Browser for Generating Gene Expression Anatograms. PMID:26954504
Drug Repositioning for Cancer Therapy Based on Large-Scale Drug-Induced Transcriptional Signatures. PMID:26954019
Gene expression variability in mammalian embryonic stem cells using single cell RNA-seq data. PMID:26951854
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
PRAME as an Independent Biomarker for Metastasis in Uveal Melanoma. PMID:26933176
Genome-Wide Transcriptional Response of Saccharomyces cerevisiae to Stress-Induced Perturbations. PMID:26925399
The Human Toxome Collaboratorium: A Shared Environment for Multi-Omic Computational Collaboration within a Consortium. PMID:26924983
Analysis of transcripts differentially expressed between fruited and deflowered 'Gala' adult trees: a contribution to biennial bearing understanding in apple. PMID:26924309
Reduced-representation Phosphosignatures Measured by Quantitative Targeted MS Capture Cellular States and Enable Large-scale Comparison of Drug-induced Phenotypes. PMID:26912667
Revealing the role of VEGFA in clear cell sarcoma of the kidney by protein-protein interaction network and significant pathway analysis. PMID:26893674
Early developmental gene enhancers affect subcortical volumes in the adult human brain. PMID:26890892
A novel transcription factor gene FHS1 is involved in the DNA damage response in Fusarium graminearum. PMID:26888604
MIrExpress: A Database for Gene Coexpression Correlation in Immune Cells Based on Mutual Information and Pearson Correlation. PMID:26881263
Seqinspector: position-based navigation through the ChIP-seq data landscape to identify gene expression regulators. PMID:26868127
Temporal Genetic Modifications after Controlled Cortical Impact--Understanding Traumatic Brain Injury through a Systematic Network Approach. PMID:26861311
ksRepo: a generalized platform for computational drug repositioning. PMID:26860211
Integrative Genomic Analyses Yield Cell-Cycle Regulatory Programs with Prognostic Value. PMID:26856934
Dictyocaulus viviparus genome, variome and transcriptome elucidate lungworm biology and support future intervention. PMID:26856411
NABIC: A New Access Portal to Search, Visualize, and Share Agricultural Genomics Data. PMID:26848255
"Hit-and-Run" transcription: de novo transcription initiated by a transient bZIP1 "hit" persists after the "run". PMID:26843062
Benchmarking Procedures for High-Throughput Context Specific Reconstruction Algorithms. PMID:26834640
A genomics-based framework for identifying biomarkers of human neurodevelopmental toxicity. PMID:26827931
Drug repositioning for non-small cell lung cancer by using machine learning algorithms and topological graph theory. PMID:26817825
Novel Neuroprotective Multicomponent Therapy for Amyotrophic Lateral Sclerosis Designed by Networked Systems. PMID:26807587
Microarray Meta-Analysis Focused on the Response of Genes Involved in Redox Homeostasis to Diverse Abiotic Stresses in Rice. PMID:26793229
TRANS PROF DB: A new resource for sharing translational profiles. PMID:26779411
SEPARATING THE CAUSES AND CONSEQUENCES IN DISEASE TRANSCRIPTOME. PMID:26776202
Oncogenic CARMA1 couples NF-κB and β-catenin signaling in diffuse large B-cell lymphomas. PMID:26776161
New players in heterochromatin silencing: histone variant H3.3 and the ATRX/DAXX chaperone. PMID:26773061
Drosophila Mitf regulates the V-ATPase and the lysosomal-autophagic pathway. PMID:26761346
Identifying and functionally characterizing tissue-specific and ubiquitously expressed human lncRNAs. PMID:26760768
Combining location-and-scale batch effect adjustment with data cleaning by latent factor adjustment. PMID:26753519
Network-Based Comparative Analysis of Arabidopsis Immune Responses to Golovinomyces orontii and Botrytis cinerea Infections. PMID:26750561
Improving microRNA target prediction by modeling with unambiguously identified microRNA-target pairs from CLIP-ligation studies. PMID:26743510
Transcriptional profiling and muscle cross-section analysis reveal signs of ischemia reperfusion injury following total knee arthroplasty with tourniquet. PMID:26733251
Multiple Transcriptome Data Analysis Reveals Biologically Relevant Atopic Dermatitis Signature Genes and Pathways. PMID:26717000
Blood transcriptomics and metabolomics for personalized medicine. PMID:26702339
Computational selection of antibody-drug conjugate targets for breast cancer. PMID:26700623
Profiling of Sox4-dependent transcriptome in skin links tumour suppression and adult stem cell activation. PMID:26697322
Enhanced degradation of softwood versus hardwood by the white-rot fungus Pycnoporus coccineus. PMID:26692083
Identification of epistatic interactions through genome-wide association studies in sporadic medullary and juvenile papillary thyroid carcinomas. PMID:26690675
Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders. PMID:26690135
Biogenesis and growth phase-dependent alteration of 5-methoxycarbonylmethoxyuridine in tRNA anticodons. PMID:26681692
Fundamentals of protein interaction network mapping. PMID:26681426
Investigation of microRNAs in mouse macrophage responses to lipopolysaccharide-stimulation by combining gene expression with microRNA-target information. PMID:26680554
Screening of potential biomarkers for cholangiocarcinoma by integrated analysis of microarray data sets. PMID:26679756
Identification of network-based biomarkers of cardioembolic stroke using a systems biology approach with time series data. PMID:26679092
Gene signature combinations improve prognostic stratification of multiple myeloma patients. PMID:26669975
ChromContact: A web tool for analyzing spatial contact of chromosomes from Hi-C data. PMID:26666652
Identification of a Stelar-Localized Transport Protein That Facilitates Root-to-Shoot Transfer of Chloride in Arabidopsis. PMID:26662602
In search of underlying mechanisms and potential drugs of melphalan-induced vascular toxicity through retinal endothelial cells using bioinformatics approach. PMID:26662105
HRGRN: A Graph Search-Empowered Integrative Database of Arabidopsis Signaling Transduction, Metabolism and Gene Regulation Networks. PMID:26657893
iTAP: integrated transcriptomics and phenotype database for stress response of Escherichia coli and Saccharomyces cerevisiae. PMID:26653323
ALCOdb: Gene Coexpression Database for Microalgae. PMID:26644461
Detecting Protein Complexes in Protein Interaction Networks Modeled as Gene Expression Biclusters. PMID:26641660
RBP-Var: a database of functional variants involved in regulation mediated by RNA-binding proteins. PMID:26635394
MERAV: a tool for comparing gene expression across human tissues and cell types. PMID:26626150
Screening of potential biomarkers for chemoresistant ovarian carcinoma with miRNA expression profiling data by bioinformatics approach. PMID:26622864
Database resources of the National Center for Biotechnology Information. PMID:26615191
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. PMID:26615188
DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts. PMID:26612864
The sialyl-glycolipid stage-specific embryonic antigen 4 marks a subpopulation of chemotherapy-resistant breast cancer cells with mesenchymal features. PMID:26607327
Integrated network model provides new insights into castration-resistant prostate cancer. PMID:26603105
Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells. PMID:26602695
Lynx: a knowledge base and an analytical workbench for integrative medicine. PMID:26590263
COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses. PMID:26586805
DIANA-miRGen v3.0: accurate characterization of microRNA promoters and their regulators. PMID:26586797
WeGET: predicting new genes for molecular systems by weighted co-expression. PMID:26582928
CpG island erosion, polycomb occupancy and sequence motif enrichment at bivalent promoters in mammalian embryonic stem cells. PMID:26582124
SEA: a super-enhancer archive. PMID:26578594
Identification of potential biomarkers to differentially diagnose solid pseudopapillary tumors and pancreatic malignancies via a gene regulatory network. PMID:26578390
Mining for novel candidate clock genes in the circadian regulatory network. PMID:26576534
NRP1 is targeted by miR-130a and miR-130b, and is associated with multidrug resistance in epithelial ovarian cancer based on integrated gene network analysis. PMID:26573160
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
From System-Wide Differential Gene Expression to Perturbed Regulatory Factors: A Combinatorial Approach. PMID:26562430
Essentiality drives the orientation bias of bacterial genes in a continuous manner. PMID:26560889
Profiling of Discrete Gynecological Cancers Reveals Novel Transcriptional Modules and Common Features Shared by Other Cancer Types and Embryonic Stem Cells. PMID:26559525
A network-based method to evaluate quality of reproducibility of differential expression in cancer genomics studies. PMID:26556852
Integrative enrichment analysis: a new computational method to detect dysregulated pathways in heterogeneous samples. PMID:26556243
DASHR: database of small human noncoding RNAs. PMID:26553799
ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression. PMID:26546318
A measure of the impact of CV incompleteness on prediction error estimation with application to PCA and normalization. PMID:26537575
MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebrates. PMID:26527726
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond. PMID:26527724
Tamoxifen therapy benefit predictive signature coupled with prognostic signature of post-operative recurrent risk for early stage ER+ breast cancer. PMID:26527319
An mRNA expression signature for prognostication in de novo acute myeloid leukemia patients with normal karyotype. PMID:26517675
Integrated interactions database: tissue-specific view of the human and model organism interactomes. PMID:26516188
Genes with stable DNA methylation levels show higher evolutionary conservation than genes with fluctuant DNA methylation levels. PMID:26515589
Novel gene sets improve set-level classification of prokaryotic gene expression data. PMID:26511329
Inferring Infection Patterns Based on a Connectivity Map of Host Transcriptional Responses. PMID:26508266
Construction of citrus gene coexpression networks from microarray data using random matrix theory. PMID:26504573
Characterization of whole-genome autosomal differences of DNA methylation between men and women. PMID:26500701
FXYD5 is a Marker for Poor Prognosis and a Potential Driver for Metastasis in Ovarian Carcinomas. PMID:26494976
DNA Methylation Landscapes of Human Fetal Development. PMID:26492326
COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access. PMID:26491418
FAS Death Receptor: A Breast Cancer Subtype-Specific Radiation Response Biomarker and Potential Therapeutic Target. PMID:26488758
Integrative Genomics-Based Discovery of Novel Regulators of the Innate Antiviral Response. PMID:26485378
Integrated Analysis Reveals together miR-182, miR-200c and miR-221 Can Help in the Diagnosis of Prostate Cancer. PMID:26484677
Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants. PMID:26481351
Computational Systems Biology of Psoriasis: Are We Ready for the Age of Omics and Systems Biomarkers? PMID:26480058
Concordance between RNA-sequencing data and DNA microarray data in transcriptome analysis of proliferative and quiescent fibroblasts. PMID:26473061
A novel bi-level meta-analysis approach: applied to biological pathway analysis. PMID:26471455
Multipotent luminal mammary cancer stem cells model tumor heterogeneity. PMID:26467658
Public data and open source tools for multi-assay genomic investigation of disease. PMID:26463000
The folate-coupled enzyme MTHFD2 is a nuclear protein and promotes cell proliferation. PMID:26461067
Genome-wide ChIP-seq analysis of human TOP2B occupancy in MCF7 breast cancer epithelial cells. PMID:26459242
Broad-spectrum antibodies against self-antigens and cytokines in RAG deficiency. PMID:26457731
Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology. PMID:26454094
An Independent Filter for Gene Set Testing Based on Spectral Enrichment. PMID:26451820
The Hox cluster microRNA miR-615: a case study of intronic microRNA evolution. PMID:26451238
Identification of cellular microRNA-136 as a dual regulator of RIG-I-mediated innate immunity that antagonizes H5N1 IAV replication in A549 cells. PMID:26450567
Exploring the potential of public proteomics data. PMID:26449181
A cross-cancer differential co-expression network reveals microRNA-regulated oncogenic functional modules. PMID:26448606
Meta-Analysis of Multiple Sclerosis Microarray Data Reveals Dysregulation in RNA Splicing Regulatory Genes. PMID:26437396
Biofilm Formation Mechanisms of Pseudomonas aeruginosa Predicted via Genome-Scale Kinetic Models of Bacterial Metabolism. PMID:26431398
Dynamics in Transcriptomics: Advancements in RNA-seq Time Course and Downstream Analysis. PMID:26430493
Integrated analysis of gene expression and genomic aberration data in osteosarcoma (OS). PMID:26427513
DMAP: a connectivity map database to enable identification of novel drug repositioning candidates. PMID:26423722
miR-134 in extracellular vesicles reduces triple-negative breast cancer aggression and increases drug sensitivity. PMID:26416415
Cancer associated fibroblasts have phenotypic and functional characteristics similar to the fibrocytes that represent a novel MDSC subset. PMID:26405600
Transcriptomics Profiling of Alzheimer's Disease Reveal Neurovascular Defects, Altered Amyloid-β Homeostasis, and Deregulated Expression of Long Noncoding RNAs. PMID:26402107
Integrative analysis of human protein, function and disease networks. PMID:26399914
Automated Identification of Core Regulatory Genes in Human Gene Regulatory Networks. PMID:26393364
A constitutive active MAPK/ERK pathway due to BRAFV600E positively regulates AHR pathway in PTC. PMID:26392334
Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data. PMID:26363020
Deciphering Seed Sequence Based Off-Target Effects in a Large-Scale RNAi Reporter Screen for E-Cadherin Expression. PMID:26361354
Genome instability model of metastatic neuroblastoma tumorigenesis by a dictionary learning algorithm. PMID:26358114
Integrated Analyses of Gene Expression Profiles Digs out Common Markers for Rheumatic Diseases. PMID:26352601
New Technologies for Studying Biofilms. PMID:26350329
Meta-Analysis of Large-Scale Toxicogenomic Data Finds Neuronal Regeneration Related Protein and Cathepsin D to Be Novel Biomarkers of Drug-Induced Toxicity. PMID:26335687
Comparative Analysis of Label-Free and 8-Plex iTRAQ Approach for Quantitative Tissue Proteomic Analysis. PMID:26331617
Integrative analysis of multi-omics data for identifying multi-markers for diagnosing pancreatic cancer. PMID:26328610
Integrated analysis of differential gene expression profiles in hippocampi to identify candidate genes involved in Alzheimer's disease. PMID:26324066
RNASeqMetaDB: a database and web server for navigating metadata of publicly available mouse RNA-Seq datasets. PMID:26323714
Prior knowledge driven Granger causality analysis on gene regulatory network discovery. PMID:26316173
Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana. PMID:26305463
Systems Genetics Reveals the Functional Context of PCOS Loci and Identifies Genetic and Molecular Mechanisms of Disease Heterogeneity. PMID:26305227
Integrated Transcriptomics Establish Macrophage Polarization Signatures and have Potential Applications for Clinical Health and Disease. PMID:26302899
Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment. PMID:26298294
FBG1 Is the Final Arbitrator of A1AT-Z Degradation. PMID:26295339
The Absence of Pupylation (Prokaryotic Ubiquitin-Like Protein Modification) Affects Morphological and Physiological Differentiation in Streptomyces coelicolor. PMID:26283768
Arid1a inactivation in an Apc- and Pten-defective mouse ovarian cancer model enhances epithelial differentiation and prolongs survival. PMID:26279473
Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation. PMID:26275208
Drosophila Shep and C. elegans SUP-26 are RNA-binding proteins that play diverse roles in nervous system development. PMID:26271810
Modulator of apoptosis 1 (MOAP-1) is a tumor suppressor protein linked to the RASSF1A protein. PMID:26269600
Transcription Factor Repertoire of Homeostatic Eosinophilopoiesis. PMID:26268651
Distilling a Visual Network of Retinitis Pigmentosa Gene-Protein Interactions to Uncover New Disease Candidates. PMID:26267445
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
Analysis of microarray-identified genes and microRNAs associated with drug resistance in ovarian cancer. PMID:26261572
Proteogenomic analysis of psoriasis reveals discordant and concordant changes in mRNA and protein abundance. PMID:26251673
Potential roles of microRNA-29a in the molecular pathophysiology of T-cell acute lymphoblastic leukemia. PMID:26251039
Oligonucleotide gap-fill ligation for mutation detection and sequencing in situ. PMID:26240388
Identification and functional analysis of early gene expression induced by circadian light-resetting in Drosophila. PMID:26231660
Integrated genomic analyses identify KDM1A's role in cell proliferation via modulating E2F signaling activity and associate with poor clinical outcome in oral cancer. PMID:26225839
An Integrative Approach for Mapping Differentially Expressed Genes and Network Components Using Novel Parameters to Elucidate Key Regulatory Genes in Colorectal Cancer. PMID:26222778
Network analysis of temporal functionalities of the gut induced by perturbations in new-born piglets. PMID:26220188
Coordination between Drosophila Arc1 and a specific population of brain neurons regulates organismal fat. PMID:26209258
Transferring genomics to the clinic: distinguishing Burkitt and diffuse large B cell lymphomas. PMID:26207141
Coexpression Network Analysis of Macronutrient Deficiency Response Genes in Rice. PMID:26206757
Polymorphisms in Genes Involved in EGFR Turnover Are Predictive for Cetuximab Efficacy in Colorectal Cancer. PMID:26206335
Associations of SNPs located at candidate genes to bovine growth traits, prioritized with an interaction networks construction approach. PMID:26198337
The Interferon-Inducible Mouse Apolipoprotein L9 and Prohibitins Cooperate to Restrict Theiler's Virus Replication. PMID:26196674
Choriodecidual Group B Streptococcal Infection Induces miR-155-5p in the Fetal Lung in Macaca nemestrina. PMID:26195546
Increased H3K9me3 drives dedifferentiated phenotype via KLF6 repression in liposarcoma. PMID:26193637
Downregulation of long noncoding RNA MALAT1 induces epithelial-to-mesenchymal transition via the PI3K-AKT pathway in breast cancer. PMID:26191181
miR-23a impairs bone differentiation in osteosarcoma via down-regulation of GJA1. PMID:26191074
A cross-species genetic analysis identifies candidate genes for mouse anxiety and human bipolar disorder. PMID:26190982
Screening of potential target genes for cataract by analyzing mRNA expression profile of mouse Hsf4-null lens. PMID:26187041
Combined Analysis of SNP Array Data Identifies Novel CNV Candidates and Pathways in Ependymoma and Mesothelioma. PMID:26185765
Comparative Correlation Structure of Colon Cancer Locus Specific Methylation: Characterisation of Patient Profiles and Potential Markers across 3 Array-Based Datasets. PMID:26185542
Integrated network analysis and logistic regression modeling identify stage-specific genes in Oral Squamous Cell Carcinoma. PMID:26179909
Exosome-mediated microRNA signaling from breast cancer cells is altered by the anti-angiogenesis agent docosahexaenoic acid (DHA). PMID:26178901
Meta-Analysis of Placental Transcriptome Data Identifies a Novel Molecular Pathway Related to Preeclampsia. PMID:26171964
Differential and coherent processing patterns from small RNAs. PMID:26166713
DAPIT Over-Expression Modulates Glucose Metabolism and Cell Behaviour in HEK293T Cells. PMID:26161955
SEEK: a systems biology data and model management platform. PMID:26160520
A reproducible approach to high-throughput biological data acquisition and integration. PMID:26157642
Using gene expression signatures to identify novel treatment strategies in gulf war illness. PMID:26156520
The Convergence of Systems and Reductionist Approaches in Complex Trait Analysis. PMID:26140590
Identification of thiostrepton as a novel therapeutic agent that targets human colon cancer stem cells. PMID:26136074
Integrative Analysis Reveals Regulatory Programs in Endometriosis. PMID:26134036
A systematic analysis of human lipocalin family and its expression in esophageal carcinoma. PMID:26131602
A second trigeminal CGRP receptor: function and expression of the AMY1 receptor. PMID:26125036
MSL: A Measure to Evaluate Three-dimensional Patterns in Gene Expression Data. PMID:26124630
A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal. PMID:26122086
Pioglitazone Identifies a New Target for Aneurysm Treatment: Role of Egr1 in an Experimental Murine Model of Aortic Aneurysm. PMID:26113112
Molecular Features of Triple Negative Breast Cancer: Microarray Evidence and Further Integrated Analysis. PMID:26103053
Publisher’s Note:Abstraction for data integration:Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction. PMID:26101093
Deep sequencing, profiling and detailed annotation of microRNAs in Takifugu rubripes. PMID:26078057
Defining the Human Brain Proteome Using Transcriptomics and Antibody-Based Profiling with a Focus on the Cerebral Cortex. PMID:26076492
Constraint programming based biomarker optimization. PMID:26075274
Unravelling personalized dysfunctional gene network of complex diseases based on differential network model. PMID:26070628
Computational prediction of miRNAs and their targets in Phaseolus vulgaris using simple sequence repeat signatures. PMID:26067253
TRRUST: a reference database of human transcriptional regulatory interactions. PMID:26066708
C/EBPα-p30 protein induces expression of the oncogenic long non-coding RNA UCA1 in acute myeloid leukemia. PMID:26053097
An integrated genomic analysis of papillary renal cell carcinoma type 1 uncovers the role of focal adhesion and extracellular matrix pathways. PMID:26051997
Revealing protein-lncRNA interaction. PMID:26041786
Novel Biological Substrates of Human Kallikrein 7 Identified through Degradomics. PMID:26032414
Hidden among the crowd: differential DNA methylation-expression correlations in cancer occur at important oncogenic pathways. PMID:26029238
The Homeobox Genes of Caenorhabditis elegans and Insights into Their Spatio-Temporal Expression Dynamics during Embryogenesis. PMID:26024448
Databases for Microbiologists. PMID:26013493
CEMP1 Induces Transformation in Human Gingival Fibroblasts. PMID:26011628
SPECTRA: An Integrated Knowledge Base for Comparing Tissue and Tumor-Specific PPI Networks in Human. PMID:26005672
Gene set enrichment analysis of pathways and transcription factors associated with diabetic retinopathy using a microarray dataset. PMID:25997411
StarScan: a web server for scanning small RNA targets from degradome sequencing data. PMID:25990732
PALM-IST: Pathway Assembly from Literature Mining--an Information Search Tool. PMID:25989388
ImmuSort, a database on gene plasticity and electronic sorting for immune cells. PMID:25988315
DNA methylation changes in the placenta are associated with fetal manganese exposure. PMID:25982381
Small molecule inhibition of Axl receptor tyrosine kinase potently suppresses multiple malignant properties of glioma cells. PMID:25980499
Cell Cycle Control by the Master Regulator CtrA in Sinorhizobium meliloti. PMID:25978424
A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis. PMID:25977815
IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. PMID:25969450
Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea. PMID:25952370
FlyNet: a versatile network prioritization server for the Drosophila community. PMID:25943544
Identification and validation of a two-gene expression index for subtype classification and prognosis in Diffuse Large B-Cell Lymphoma. PMID:25940947
FNTM: a server for predicting functional networks of tissues in mouse. PMID:25940632
NFFinder: an online bioinformatics tool for searching similar transcriptomics experiments in the context of drug repositioning. PMID:25940629
GXD: a community resource of mouse Gene Expression Data. PMID:25939429
Dysregulated mechanisms underlying Duchenne muscular dystrophy from co-expression network preservation analysis. PMID:25935398
Understanding multicellular function and disease with human tissue-specific networks. PMID:25915600
Gene expression profile analysis of colorectal cancer to investigate potential mechanisms using bioinformatics. PMID:25914544
A dominant role for the methyl-CpG-binding protein Mbd2 in controlling Th2 induction by dendritic cells. PMID:25908537
Identification of commonly dysregulated genes in colorectal cancer by integrating analysis of RNA-Seq data and qRT-PCR validation. PMID:25908452
mBISON: Finding miRNA target over-representation in gene lists from ChIP-sequencing data. PMID:25889572
Effects of statin on circulating microRNAome and predicted function regulatory network in patients with unstable angina. PMID:25889164
ColoWeb: a resource for analysis of colocalization of genomic features. PMID:25887597
NMF-mGPU: non-negative matrix factorization on multi-GPU systems. PMID:25887585
Circulating miR-200c and miR-141 and outcomes in patients with breast cancer. PMID:25885099
Nasal mucosal microRNA expression in children with respiratory syncytial virus infection. PMID:25884957
The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community. PMID:25883147
REGULATOR: a database of metazoan transcription factors and maternal factors for developmental studies. PMID:25880930
Identification of important interacting proteins (IIPs) in Plasmodium falciparum using large-scale interaction network analysis and in-silico knock-out studies. PMID:25879642
GWAS for executive function and processing speed suggests involvement of the CADM2 gene. PMID:25869804
Prediction of cancer proteins by integrating protein interaction, domain frequency, and domain interaction data using machine learning algorithms. PMID:25866773
What to compare and how: Comparative transcriptomics for Evo-Devo. PMID:25864439
Retinoic acid-independent expression of Meis2 during autopod patterning in the developing bat and mouse limb. PMID:25861444
The recently identified modifier of murine metastable epialleles, Rearranged L-Myc Fusion, is involved in maintaining epigenetic marks at CpG island shores and enhancers. PMID:25857663
Transcript and protein expression decoupling reveals RNA binding proteins and miRNAs as potential modulators of human aging. PMID:25853883
Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy. PMID:25853550
Wnt directs the endosomal flux of LDL-derived cholesterol and lipid droplet homeostasis. PMID:25851648
Robust meta-analysis of gene expression using the elastic net. PMID:25829177
Human gastroenteropancreatic expression of melatonin and its receptors MT1 and MT2. PMID:25822611
Activation of an endogenous retrovirus-associated long non-coding RNA in human adenocarcinoma. PMID:25821520
Isoflavones in soy flour diet have different effects on whole-genome expression patterns than purified isoflavone mix in human MCF-7 breast tumors in ovariectomized athymic nude mice. PMID:25820259
BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis. PMID:25819073
Genome-wide identification, evolutionary, and expression analyses of histone H3 variants in plants. PMID:25815311
RiceNet v2: an improved network prioritization server for rice genes. PMID:25813048
Characterization of resistance to rhabdovirus and retrovirus infection in a human myeloid cell line. PMID:25811758
Genomic profiling in locally advanced and inflammatory breast cancer and its link to DCE-MRI and overall survival. PMID:25811737
Test set bias affects reproducibility of gene signatures. PMID:25788628
Deciphering deterioration mechanisms of complex diseases based on the construction of dynamic networks and systems analysis. PMID:25788156
A gene-based information gain method for detecting gene-gene interactions in case-control studies. PMID:25758991
Tracking the best reference genes for RT-qPCR data normalization in filamentous fungi. PMID:25757610
Toxicogenomics profiling of bone marrow from rats treated with topotecan in combination with oxaliplatin: a mechanistic strategy to inform combination toxicity. PMID:25729387
EXPath: a database of comparative expression analysis inferring metabolic pathways for plants. PMID:25708775
Analysis of the Bovine Monocyte-Derived Macrophage Response to Mycobacterium avium Subspecies Paratuberculosis Infection Using RNA-seq. PMID:25699042
Specific interaction with the nuclear transporter importin α2 can modulate paraspeckle protein 1 delivery to nuclear paraspeckles. PMID:25694451
Identification of potential transcriptomic markers in developing ankylosing spondylitis: a meta-analysis of gene expression profiles. PMID:25688367
Whole blood gene expression profiles distinguish clinical phenotypes of venous thromboembolism. PMID:25684211
Large scale aggregate microarray analysis reveals three distinct molecular subclasses of human preeclampsia. PMID:25679511
Gene expression changes during retinal development and rod specification. PMID:25678762
FlowerNet: a gene expression correlation network for anther and pollen development. PMID:25667314
Hidden Markov Model-Based CNV Detection Algorithms for Illumina Genotyping Microarrays. PMID:25657572
Expression and regulation of long noncoding RNAs in TLR4 signaling in mouse macrophages. PMID:25652569
EcoliNet: a database of cofunctional gene network for Escherichia coli. PMID:25650278
Discovery of Protein-lncRNA Interactions by Integrating Large-Scale CLIP-Seq and RNA-Seq Datasets. PMID:25642422
Identification of differentially expressed genes in pituitary adenomas by integrating analysis of microarray data. PMID:25642247
Prioritizing causal disease genes using unbiased genomic features. PMID:25633252
A gene mapping bottleneck in the translational route from zebrafish to human. PMID:25628646
Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA. PMID:25622106
Computational deconvolution of genome wide expression data from Parkinson's and Huntington's disease brain tissues using population-specific expression analysis. PMID:25620908
3USS: a web server for detecting alternative 3'UTRs from RNA-seq experiments. PMID:25617413
CD95 promotes metastatic spread via Sck in pancreatic ductal adenocarcinoma. PMID:25613377
Comparative computational analysis of pluripotency in human and mouse stem cells. PMID:25604210
Biological interpretation of genome-wide association studies using predicted gene functions. PMID:25597830
Specific and redundant activities of ETV1 and ETV4 in prostate cancer aggressiveness revealed by co-overexpression cellular contexts. PMID:25595908
A multi-gene signature predicts outcome in patients with pancreatic ductal adenocarcinoma. PMID:25587357
Sparse expression bases in cancer reveal tumor drivers. PMID:25583238
Prediction of mature microRNA and piwi-interacting RNA without a genome reference or precursors. PMID:25580537
Protein interactome of muscle invasive bladder cancer. PMID:25569276
Mouse-human experimental epigenetic analysis unmasks dietary targets and genetic liability for diabetic phenotypes. PMID:25565211
β-Catenin is central to DUX4-driven network rewiring in facioscapulohumeral muscular dystrophy. PMID:25551153
Analysis of the basal chordate Botryllus schlosseri reveals a set of genes associated with fertility. PMID:25542255
RNase L targets distinct sites in influenza A virus RNAs. PMID:25540362
Sex- and tissue-specific functions of Drosophila doublesex transcription factor target genes. PMID:25535918
Systems genomics evaluation of the SH-SY5Y neuroblastoma cell line as a model for Parkinson's disease. PMID:25528190
Identification of differentially expressed genes regulated by transcription factors in glioblastomas by bioinformatics analysis. PMID:25514975
Identifying and validating a combined mRNA and microRNA signature in response to imatinib treatment in a chronic myeloid leukemia cell line. PMID:25506832
miR30a inhibits LOX expression and anaplastic thyroid cancer progression. PMID:25488748
The extraembryonic serosa is a frontier epithelium providing the insect egg with a full-range innate immune response. PMID:25487990
Accounting for eXentricities: analysis of the X chromosome in GWAS reveals X-linked genes implicated in autoimmune diseases. PMID:25479423
linkedISA: semantic representation of ISA-Tab experimental metadata. PMID:25472428
Systems Medicine: from molecular features and models to the clinic in COPD. PMID:25471042
Self-pMHCII complexes are variably expressed in the thymus and periphery independent of mRNA expression but dependent on the activation state of the APCs. PMID:25451972
High dimensional biological data retrieval optimization with NoSQL technology. PMID:25435347
Analysis of the protein-protein interaction networks of differentially expressed genes in pulmonary embolism. PMID:25434468
Identification of 4438 novel lincRNAs involved in mouse pre-implantation embryonic development. PMID:25428585
Identification and molecular characterization of tissue-preferred rice genes and their upstream regularly sequences on a genome-wide level. PMID:25428432
arrayMap 2014: an updated cancer genome resource. PMID:25428357
DoRiNA 2.0--upgrading the doRiNA database of RNA interactions in post-transcriptional regulation. PMID:25416797
Comparative functional genomics and the bovine macrophage response to strains of the mycobacterium genus. PMID:25414700
ProteomeScout: a repository and analysis resource for post-translational modifications and proteins. PMID:25414335
Identification of common gene networks responsive to radiotherapy in human cancer cells. PMID:25412644
Expression of human skin-specific genes defined by transcriptomics and antibody-based profiling. PMID:25411189
Beyond protein expression, MOPED goes multi-omics. PMID:25404128
Database resources of the National Center for Biotechnology Information. PMID:25398906
DDMGD: the database of text-mined associations between genes methylated in diseases from different species. PMID:25398897
Molecular toolbox for genetic manipulation of the stalked budding bacterium Hyphomonas neptunium. PMID:25398860
PubAngioGen: a database and knowledge for angiogenesis and related diseases. PMID:25392416
Sustained β-catenin activity in dermal fibroblasts promotes fibrosis by up-regulating expression of extracellular matrix protein-coding genes. PMID:25385294
miRNA Temporal Analyzer (mirnaTA): a bioinformatics tool for identifying differentially expressed microRNAs in temporal studies using normal quantile transformation. PMID:25379175
Human cancer databases (review). PMID:25369839
Fingerprints of a message: integrating positional information on the transcriptome. PMID:25364746
Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress. PMID:25362847
ArrayExpress update--simplifying data submissions. PMID:25361974
A common gene expression signature in Huntington's disease patient brain regions. PMID:25358814
AraNet v2: an improved database of co-functional gene networks for the study of Arabidopsis thaliana and 27 other nonmodel plant species. PMID:25355510
Expression and evolution of the Tiki1 and Tiki2 genes in vertebrates. PMID:25354456
STRING v10: protein-protein interaction networks, integrated over the tree of life. PMID:25352553
Oncogenic Ras inhibits IRF1 to promote viral oncolysis. PMID:25347735
A GRHL3-regulated repair pathway suppresses immune-mediated epidermal hyperplasia. PMID:25347468
Analysis of gene expression in induced pluripotent stem cell-derived human neurons exposed to botulinum neurotoxin A subtype 1 and a type A atoxic derivative. PMID:25337697
Computational Methods for CLIP-seq Data Processing. PMID:25336930
Vitamin D receptor and RXR in the post-genomic era. PMID:25335912
Mouse Tumor Biology (MTB): a database of mouse models for human cancer. PMID:25332399
ImmuCo: a database of gene co-expression in immune cells. PMID:25326331
Neural network cascade optimizes microRNA biomarker selection for nasopharyngeal cancer prognosis. PMID:25310846
Sphingomyelin phosphodiesterase acid-like 3A (SMPDL3A) is a novel nucleotide phosphodiesterase regulated by cholesterol in human macrophages. PMID:25288789
Joint genetic analysis of hippocampal size in mouse and human identifies a novel gene linked to neurodegenerative disease. PMID:25280473
CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities. PMID:25270877
Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets. PMID:25270025
A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing. PMID:25266672
GeneMANIA: Fast gene network construction and function prediction for Cytoscape. PMID:25254104
Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease. PMID:25252782
Transcription start site associated RNAs (TSSaRNAs) are ubiquitous in all domains of life. PMID:25238539
Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli. PMID:25237058
Translating bioinformatics in oncology: guilt-by-profiling analysis and identification of KIF18B and CDCA3 as novel driver genes in carcinogenesis. PMID:25236463
Unlocking the mystery of the hard-to-sequence phage genome: PaP1 methylome and bacterial immunity. PMID:25233860
Primate-specific miR-576-3p sets host defense signalling threshold. PMID:25232931
The Digital Ageing Atlas: integrating the diversity of age-related changes into a unified resource. PMID:25232097
WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions. PMID:25231498
Characterization of chemically induced liver injuries using gene co-expression modules. PMID:25226513
Drug repositioning discovery for early- and late-stage non-small-cell lung cancer. PMID:25210704
LCK: a new biomarker candidate for the early diagnosis of acute myocardial infarction. PMID:25209966
NF-κB directly mediates epigenetic deregulation of common microRNAs in Epstein-Barr virus-mediated transformation of B-cells and in lymphomas. PMID:25200074
Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records. PMID:25197497
Bcl-6 directly represses the gene program of the glycolysis pathway. PMID:25194422
Transcriptome profiling of spinal muscular atrophy motor neurons derived from mouse embryonic stem cells. PMID:25191843
Gene co-expression network analysis in Rhodobacter capsulatus and application to comparative expression analysis of Rhodobacter sphaeroides. PMID:25164283
Personalized identification of altered pathways in cancer using accumulated normal tissue data. PMID:25161229
Grape seed procyanidin supplementation to rats fed a high-fat diet during pregnancy and lactation increases the body fat content and modulates the inflammatory response and the adipose tissue metabolism of the male offspring in youth. PMID:25152240
Studying the complex expression dependences between sets of coexpressed genes. PMID:25147825
Mining 3D patterns from gene expression temporal data: a new tricluster evaluation measure. PMID:25143987
Primary transcriptome map of the hyperthermophilic archaeon Thermococcus kodakarensis. PMID:25127548
Lean Big Data integration in systems biology and systems pharmacology. PMID:25109570
Bioinformatic approaches to augment study of epithelial-to-mesenchymal transition in lung cancer. PMID:25096367
Enrichment Map - a Cytoscape app to visualize and explore OMICs pathway enrichment results. PMID:25075306
Selective clearance of aberrant tau proteins and rescue of neurotoxicity by transcription factor EB. PMID:25069841
Glycosylation-related genes in NS0 cells are insensitive to moderately elevated ammonium concentrations. PMID:25062658
Genome-wide prediction of cancer driver genes based on SNP and cancer SNV data. PMID:25057442
Prioritizing uncharacterized genes in the search for glioma biomarkers. PMID:25055012
Codon-by-codon modulation of translational speed and accuracy via mRNA folding. PMID:25051069
Data integration in the era of omics: current and future challenges. PMID:25032990
Wnt signaling inhibits adrenal steroidogenesis by cell-autonomous and non-cell-autonomous mechanisms. PMID:25029241
yStreX: yeast stress expression database. PMID:25024351
Meta-analysis of differentially expressed genes in osteosarcoma based on gene expression data. PMID:25023069
Comprehensive identification of essential pathways and transcription factors related to epilepsy by gene set enrichment analysis on microarray datasets. PMID:25016997
An integrative analysis of meningioma tumors reveals the determinant genes and pathways of malignant transformation. PMID:25003081
Integrative analysis of independent transcriptome data for rare diseases. PMID:24981076
Bacterial siderophores that evade or overwhelm lipocalin 2 induce hypoxia inducible factor 1α and proinflammatory cytokine secretion in cultured respiratory epithelial cells. PMID:24980968
The inferred cardiogenic gene regulatory network in the mammalian heart. PMID:24971943
The gene expression database for mouse development (GXD): putting developmental expression information at your fingertips. PMID:24958384
Midkine expression in high grade gliomas: Correlation of this novel marker with proliferation and survival in human gliomas. PMID:24949221
Early aberrant DNA methylation events in a mouse model of acute myeloid leukemia. PMID:24944583
Interruption of KLF5 acetylation converts its function from tumor suppressor to tumor promoter in prostate cancer cells. PMID:24931571
Improving functional annotation for industrial microbes: a case study with Pichia pastoris. PMID:24929579
dbCerEx: a web-based database for the analysis of cervical cancer transcriptomes. PMID:24918550
REGNET: mining context-specific human transcription networks using composite genomic information. PMID:24912499
MOPED 2.5--an integrated multi-omics resource: multi-omics profiling expression database now includes transcriptomics data. PMID:24910945
Network Assessor: an automated method for quantitative assessment of a network's potential for gene function prediction. PMID:24904632
Structural bioinformatics of the interactome. PMID:24895853
DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections. PMID:24895436
Longissimus dorsi transcriptome analysis of purebred and crossbred Iberian pigs differing in muscle characteristics. PMID:24885501
Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells. PMID:24885402
Vitamin D and the RNA transcriptome: more than mRNA regulation. PMID:24860511
Cross-platform toxicogenomics for the prediction of non-genotoxic hepatocarcinogenesis in rat. PMID:24830643
OTX2 duplication is implicated in hemifacial microsomia. PMID:24816892
WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans. PMID:24813450
Integrating omics technologies to study pulmonary physiology and pathology at the systems level. PMID:24802001
The role of carbon starvation in the induction of enzymes that degrade plant-derived carbohydrates in Aspergillus niger. PMID:24792495
Identification of a BRCA1-mRNA splicing complex required for efficient DNA repair and maintenance of genomic stability. PMID:24746700
Correlating histone modification patterns with gene expression data during hematopoiesis. PMID:24743998
CMT: a constrained multi-level thresholding approach for ChIP-Seq data analysis. PMID:24736605
Identification of mRNAs and lincRNAs associated with lung cancer progression using next-generation RNA sequencing from laser micro-dissected archival FFPE tissue specimens. PMID:24735754
Two-stage, in silico deconvolution of the lymphocyte compartment of the peripheral whole blood transcriptome in the context of acute kidney allograft rejection. PMID:24733377
'In silico expression analysis', a novel PathoPlant web tool to identify abiotic and biotic stress conditions associated with specific cis-regulatory sequences. PMID:24727366
What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins. PMID:24723265
Evidence for the biogenesis of more than 1,000 novel human microRNAs. PMID:24708865
Precise genetic mapping and integrative bioinformatics in Diversity Outbred mice reveals Hydin as a novel pain gene. PMID:24700285
Hypermethylation in the ZBTB20 gene is associated with major depressive disorder. PMID:24694013
Bi-Force: large-scale bicluster editing and its application to gene expression data biclustering. PMID:24682815
SLC25A1, or CIC, is a novel transcriptional target of mutant p53 and a negative tumor prognostic marker. PMID:24681808
Clinical proteomic biomarkers: relevant issues on study design & technical considerations in biomarker development. PMID:24679154
Transcriptome analysis reveals differential splicing events in IPF lung tissue. PMID:24647608
Genomic convergence and network analysis approach to identify candidate genes in Alzheimer's disease. PMID:24628925
p53 haploinsufficiency and functional abnormalities in multiple myeloma. PMID:24625551
Transglutaminase 2 inhibitor abrogates renal cell carcinoma in xenograft models. PMID:24610445
BioPlat: a software for human cancer biomarker discovery. PMID:24574115
A networks method for ranking microRNA dysregulation in cancer. PMID:24564923
The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again. PMID:24564732
Systematically profiling and annotating long intergenic non-coding RNAs in human embryonic stem cell. PMID:24564552
The future of whole-cell modeling. PMID:24556244
BiNA: a visual analytics tool for biological network data. PMID:24551056
Evaluation of rice promoters conferring pollen-specific expression in a heterologous system, Arabidopsis. PMID:24550073
Systems analysis of transcriptional data provides insights into muscle's biological response to botulinum toxin. PMID:24536034
Ribonuclease L and metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs. PMID:24500209
ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa. PMID:24498971
A GNAS mutation found in pancreatic intraductal papillary mucinous neoplasms induces drastic alterations of gene expression profiles with upregulation of mucin genes. PMID:24498386
The interplay of light and oxygen in the reactive oxygen stress response of Chlamydomonas reinhardtii dissected by quantitative mass spectrometry. PMID:24482124
Transcriptome analysis of Vibrio parahaemolyticus in type III secretion system 1 inducing conditions. PMID:24478989
Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens. PMID:24476156
Composition of seed sequence is a major determinant of microRNA targeting patterns. PMID:24470575
Pathway analysis for drug repositioning based on public database mining. PMID:24460210
Toward more transparent and reproducible omics studies through a common metadata checklist and data publications. PMID:24456465
Characterizing and controlling the inflammatory network during influenza A virus infection. PMID:24445954
An interactive Bayesian model for prediction of lymph node ratio and survival in pancreatic cancer patients. PMID:24444460
Bidirectional promoters are the major source of gene activation-associated non-coding RNAs in mammals. PMID:24438357
Pharmacological characterisation of ligand- and voltage-gated ion channels expressed in human iPSC-derived forebrain neurons. PMID:24429870
Constitutive patterns of gene expression regulated by RNA-binding proteins. PMID:24401680
Identification of biomarkers for esophageal squamous cell carcinoma using feature selection and decision tree methods. PMID:24396308
Identification of metastasis-associated genes in colorectal cancer through an integrated genomic and transcriptomic analysis. PMID:24385689
The global translation profile in a ribosomal protein mutant resembles that of an eIF3 mutant. PMID:24377433
Integration of miRNA and protein profiling reveals coordinated neuroadaptations in the alcohol-dependent mouse brain. PMID:24358208
DPRP: a database of phenotype-specific regulatory programs derived from transcription factor binding data. PMID:24302579
starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. PMID:24297251
Comparative transcript profiling by SuperSAGE identifies novel candidate genes for controlling potato quantitative resistance to late blight not compromised by late maturity. PMID:24294214
PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools. PMID:24285306
miRBase: annotating high confidence microRNAs using deep sequencing data. PMID:24275495
Abnormalities in glycogen metabolism in a patient with alpers' syndrome presenting with hypoglycemia. PMID:24272679
Network portal: a database for storage, analysis and visualization of biological networks. PMID:24271392
NGSmethDB: an updated genome resource for high quality, single-cytosine resolution methylomes. PMID:24271385
The UCSC Genome Browser database: 2014 update. PMID:24270787
Database resources of the National Center for Biotechnology Information. PMID:24259429
miRNEST 2.0: a database of plant and animal microRNAs. PMID:24243848
Means to an end: mechanisms of alternative polyadenylation of messenger RNA precursors. PMID:24243805
PATRIC, the bacterial bioinformatics database and analysis resource. PMID:24225323
Progenetix: 12 years of oncogenomic data curation. PMID:24225322
Reconstruction and analysis of human kidney-specific metabolic network based on omics data. PMID:24222897
COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia. PMID:24214998
CellFateScout - a bioinformatics tool for elucidating small molecule signaling pathways that drive cells in a specific direction. PMID:24206562
Functional analysis of microRNA and transcription factor synergistic regulatory network based on identifying regulatory motifs in non-small cell lung cancer. PMID:24200043
Bivalve omics: state of the art and potential applications for the biomonitoring of harmful marine compounds. PMID:24189277
WetA is required for conidiogenesis and conidium maturation in the ascomycete fungus Fusarium graminearum. PMID:24186953
BloodChIP: a database of comparative genome-wide transcription factor binding profiles in human blood cells. PMID:24185696
The Database of Genomic Variants: a curated collection of structural variation in the human genome. PMID:24174537
GeneProf data: a resource of curated, integrated and reusable high-throughput genomics experiments. PMID:24174536
The mouse Gene Expression Database (GXD): 2014 update. PMID:24163257
Lessons from postgenome-wide association studies: functional analysis of cancer predisposition loci. PMID:24127939
The effect of carbonic anhydrase IX on focal contacts during cell spreading and migration. PMID:24101905
Genomic pathway analysis reveals that EZH2 and HDAC4 represent mutually exclusive epigenetic pathways across human cancers. PMID:24079712
Ultrasonic incisions produce less inflammatory mediator response during early healing than electrosurgical incisions. PMID:24058457
A quality control system for profiles obtained by ChIP sequencing. PMID:24038469
Manteia, a predictive data mining system for vertebrate genes and its applications to human genetic diseases. PMID:24038354
The relationship between gene isoform multiplicity, number of exons and protein divergence. PMID:24023641
Drug repurposing: a better approach for infectious disease drug discovery? PMID:24011665
Ontology based molecular signatures for immune cell types via gene expression analysis. PMID:24004649
Genome-wide analyses of Shavenbaby target genes reveals distinct features of enhancer organization. PMID:23972280
Bidirectional processing of pri-miRNAs with branched terminal loops by Arabidopsis Dicer-like1. PMID:23934148
Transcriptional abundance is not the single force driving the evolution of bacterial proteins. PMID:23914835
Analysis of the transcriptome in molecular epidemiology studies. PMID:23907930
Browsing (Epi)genomes: a guide to data resources and epigenome browsers for stem cell researchers. PMID:23827707
EMMPRIN expression positively correlates with WHO grades of astrocytomas and meningiomas. PMID:23817808
Inferring the functional effect of gene expression changes in signaling pathways. PMID:23748960
Comprehensive functional annotation of seventy-one breast cancer risk Loci. PMID:23717510
User-friendly solutions for microarray quality control and pre-processing on ArrayAnalysis.org. PMID:23620278
Computational solutions for omics data. PMID:23594911
GATA-1 genome-wide occupancy associates with distinct epigenetic profiles in mouse fetal liver erythropoiesis. PMID:23519611
New insights from existing sequence data: generating breakthroughs without a pipette. PMID:23438857
Database resources of the National Center for Biotechnology Information. PMID:23193264 -
NCBI GEO: archive for functional genomics data sets--10 years on
PubMed citations: 587.
587 articles citing: NCBI GEO: archive for functional genomics data sets--10 years on
Assessing author willingness to enter study information into structured data templates as part of the manuscript submission process: A pilot study. PMID:35846467
Supervised Machine Learning Empowered Multifactorial Genetic Inheritance Disorder Prediction. PMID:35685134
Esrrb Regulates Specific Feed-Forward Loops to Transit From Pluripotency Into Early Stages of Differentiation. PMID:35652095
Identifying the shared genes and KEGG pathways of Resolvin D1-targeted network and osteoarthritis using bioinformatics. PMID:35436417
Identification and Verification of Potential Hub Genes in Amphetamine-Type Stimulant (ATS) and Opioid Dependence by Bioinformatic Analysis. PMID:35432486
Development of a prognostic metabolic signature in stomach adenocarcinoma. PMID:35355155
The ability to classify patients based on gene-expression data varies by algorithm and performance metric. PMID:35275931
The intrinsically disordered TSSC4 protein acts as a helicase inhibitor, placeholder and multi-interaction coordinator during snRNP assembly and recycling. PMID:35188580
TRmir: A Comprehensive Resource for Human Transcriptional Regulatory Information of MiRNAs. PMID:35186035
BIRC5 promotes cancer progression and predicts prognosis in laryngeal squamous cell carcinoma. PMID:35178302
Mechanisms and Molecular Targets of BuShenHuoXue Formula for Osteoarthritis. PMID:35155962
Predicting Drosha and Dicer Cleavage Sites with DeepMirCut. PMID:35141278
Screening of hub genes associated with prognosis in non-small cell lung cancer by integrated bioinformatics analysis. PMID:35117319
Cysteine cathepsin C: a novel potential biomarker for the diagnosis and prognosis of glioma. PMID:35109832
Comprehensive Analysis of Pertinent Genes and Pathways in Atrial Fibrillation. PMID:35003319
TF-Marker: a comprehensive manually curated database for transcription factors and related markers in specific cell and tissue types in human. PMID:34986601
ELK3: A New Molecular Marker for the Diagnosis and Prognosis of Glioma. PMID:34976781
High Expression of PDE8B and DUOX2 Associated with Ability of Metastasis in Thyroid Carcinoma. PMID:34966441
Bioinformatics analysis of candidate genes and potential therapeutic drugs targeting adipose tissue in obesity. PMID:34964707
MCAM is associated with metastasis and poor prognosis in osteosarcoma by modulating tumor cell migration. PMID:34961985
A Bioinformatics Approach to Identifying Potential Biomarkers for Cryptosporidium parvum: A Coccidian Parasite Associated with Fetal Diarrhea. PMID:34960172
Identification and Clinical Validation of Key Extracellular Proteins as the Potential Biomarkers in Relapsing-Remitting Multiple Sclerosis. PMID:34950135
hnRNPA1/UP1 Unfolds KRAS G-Quadruplexes and Feeds a Regulatory Axis Controlling Gene Expression. PMID:34926957
A Novel In Silico Benchmarked Pipeline Capable of Complete Protein Analysis: A Possible Tool for Potential Drug Discovery. PMID:34827106
Exploring the mechanism of Yixinyin for myocardial infarction by weighted co-expression network and molecular docking. PMID:34799616
Meta-Analysis of Esophageal Cancer Transcriptomes Using Independent Component Analysis. PMID:34795689
HFIP: an integrated multi-omics data and knowledge platform for the precision medicine of heart failure. PMID:34791105
Deep Learning in Cancer Diagnosis and Prognosis Prediction: A Minireview on Challenges, Recent Trends, and Future Directions. PMID:34754327
MVIP: multi-omics portal of viral infection. PMID:34718748
Identification of Key eRNAs for Spinal Cord Injury by Integrated Multinomial Bioinformatics Analysis. PMID:34708039
A brain-specific pgc1α fusion transcript affects gene expression and behavioural outcomes in mice. PMID:34649938
Simplifying the development of portable, scalable, and reproducible workflows. PMID:34643507
POU class 2 homeobox associating factor 1 (POU2AF1) participates in abdominal aortic aneurysm enlargement based on integrated bioinformatics analysis. PMID:34637689
CKAP2L, as an Independent Risk Factor, Closely Related to the Prognosis of Glioma. PMID:34631884
VCAM1 expression in the myocardium is associated with the risk of heart failure and immune cell infiltration in myocardium. PMID:34593936
scMethBank: a database for single-cell whole genome DNA methylation maps. PMID:34570235
Immune-Related Genes Are Prognostic Markers for Prostate Cancer Recurrence. PMID:34490029
The Fibrosis-Targeted Collagen/Integrins Gene Profile Predicts Risk of Metastasis in Pulmonary Neuroendocrine Neoplasms. PMID:34458147
C-X-C motif chemokine ligand 12: a potential therapeutic target in Duchenne muscular dystrophy. PMID:34424816
Gene Expression Meta-Analysis Reveals Interferon-Induced Genes Associated With SARS Infection in Lungs. PMID:34367154
SeqNet: An R Package for Generating Gene-Gene Networks and Simulating RNA-Seq Data. PMID:34321962
Potential therapeutic target genes for systemic lupus erythematosus: a bioinformatics analysis. PMID:34180358
Identification of candidate targets for the diagnosis and treatment of atherosclerosis by bioinformatics analysis. PMID:34150004
Bioinformatics-based Identification of Key Pathways and Hub Genes of Traumatic Brain Injury in a Rat Model. PMID:34047944
Genome-wide analysis of microRNA156 and its targets, the genes encoding SQUAMOSA promoter-binding protein-like (SPL) transcription factors, in the grass family Poaceae. PMID:33973419
Screening and identification of LMNB1 and DLGAP5, two key biomarkers in gliomas. PMID:33956061
Prognostic and immunological potential of PPM1G in hepatocellular carcinoma. PMID:33952716
Identification and validation of the prognostic value of cyclic GMP-AMP synthase-stimulator of interferon (cGAS-STING) related genes in gastric cancer. PMID:33843442
CHRNA5 belongs to the secondary estrogen signaling network exhibiting prognostic significance in breast cancer. PMID:33469842
Identification of potential biomarkers of peripheral blood mononuclear cell in hepatocellular carcinoma using bioinformatic analysis: A protocol for systematic review and meta-analysis. PMID:33466191
Unbiased RNA-Seq-driven identification and validation of reference genes for quantitative RT-PCR analyses of pooled cancer exosomes. PMID:33407103
An Educational Bioinformatics Project to Improve Genome Annotation. PMID:33365016
Correlation of carbonic anhydrase 9 (CA9) with pathological T-stage and prognosis in patients with oral tongue squamous cell carcinoma. PMID:33313266
Identifying a Potential Key Gene, TIMP1, Associated with Liver Metastases of Uveal Melanoma by Weight Gene Co-Expression Network Analysis. PMID:33239893
A Distance-Based Framework for the Characterization of Metabolic Heterogeneity in Large Sets of Genome-Scale Metabolic Models. PMID:33205127
MADA: a web service for analysing DNA methylation array data. PMID:33203349
deepBase v3.0: expression atlas and interactive analysis of ncRNAs from thousands of deep-sequencing data. PMID:33175131
Identification of key genes and biological pathways in lung adenocarcinoma via bioinformatics analysis. PMID:33130972
ATACdb: a comprehensive human chromatin accessibility database. PMID:33125076
Finding disease modules for cancer and COVID-19 in gene co-expression networks with the Core&Peel method. PMID:33077837
Reduced Expression of hsa-miR-338-3p Contributes to the Development of Glioma Cells by Targeting Mitochondrial 3-Oxoacyl-ACP Synthase (OXSM) in Glioblastoma (GBM). PMID:33061435
LncSEA: a platform for long non-coding RNA related sets and enrichment analysis. PMID:33045741
In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm. PMID:33006999
Application of Transcriptional Gene Modules to Analysis of Caenorhabditis elegans' Gene Expression Data. PMID:32759329
RORα phosphorylation by casein kinase 1α as glucose signal to regulate estrogen sulfation in human liver cells. PMID:32686824
Identification of differentially expressed metastatic genes and their signatures to predict the overall survival of uveal melanoma patients by bioinformatics analysis. PMID:32685390
Comparative analysis of metabolic and transcriptomic features of Nothobranchius furzeri. PMID:32603650
Minichromosome maintenance 6 complex component identified by bioinformatics analysis and experimental validation in esophageal squamous cell carcinoma. PMID:32583000
Transcriptional repression of Myc underlies the tumour suppressor function of AGO1 in Drosophila. PMID:32527935
Bioinformatics Analysis based on Multiple Databases Identifies Hub Genes Associated with Hepatocellular Carcinoma. PMID:32476992
Comparative functional genomic analysis of Alzheimer's affected and naturally aging brains. PMID:32219020
Identification of hub genes associated with outcome of clear cell renal cell carcinoma. PMID:32218839
Semi-CAM: A semi-supervised deconvolution method for bulk transcriptomic data with partial marker gene information. PMID:32214192
Molecular Mechanism of Aflatoxin-Induced Hepatocellular Carcinoma Derived from a Bioinformatics Analysis. PMID:32210020
Upregulated Seizure-Related 6 Homolog-Like 2 Is a Prognostic Predictor of Hepatocellular Carcinoma. PMID:32148567
Prediction of Alzheimer's disease using blood gene expression data. PMID:32103140
Transcriptional insights into the CD8+ T cell response in mono-HIV and HCV infection. PMID:32093694
CSA: a web service for the complete process of ChIP-Seq analysis. PMID:31874601
Identification of Transcriptional Metabolic Dysregulation in Subtypes of Pituitary Adenoma by Integrated Bioinformatics Analysis. PMID:31819570
Distinct gene expression characteristics in epithelial cell-Porphyromonas gingivalis interactions by integrating transcriptome analyses. PMID:31692996
Prediction of a miRNA-mRNA functional synergistic network for cervical squamous cell carcinoma. PMID:31642613
miRWoods: Enhanced precursor detection and stacked random forests for the sensitive detection of microRNAs. PMID:31596843
Identification of key gene modules and transcription factors for human osteoarthritis by weighted gene co-expression network analysis. PMID:31572500
Prospects of genomic resources available at the global databases for the flora of United Arab Emirates. PMID:31475085
Assessment of network module identification across complex diseases. PMID:31471613
EdgeScaping: Mapping the spatial distribution of pairwise gene expression intensities. PMID:31386677
Gene Expression Analyses in Breast Cancer: Sample Matters. PMID:31360851
Upregulation of nucleoprotein AHNAK is associated with poor outcome of pancreatic ductal adenocarcinoma prognosis via mediating epithelial-mesenchymal transition. PMID:31333803
A Novel Genes Signature Associated with the Progression of Polycystic Ovary Syndrome. PMID:31278444
Mr.Vc: a database of microarray and RNA-seq of Vibrio cholerae. PMID:31231774
Aspergillus fumigatus Challenged by Human Dendritic Cells: Metabolic and Regulatory Pathway Responses Testify a Tight Battle. PMID:31192161
Using literature-based discovery to identify candidate genes for the interaction between myocardial infarction and depression. PMID:31185929
A web-based tool for the prediction of rice transcription factor function. PMID:31169887
Mitochondrial Adaptations in Elderly and Young Men Skeletal Muscle Following 2 Weeks of Bed Rest and Rehabilitation. PMID:31118897
FAM111B, a direct target of p53, promotes the malignant process of lung adenocarcinoma. PMID:31114230
Ten simple rules for carrying out and writing meta-analyses. PMID:31095553
SEanalysis: a web tool for super-enhancer associated regulatory analysis. PMID:31028388
Comparison of multi-tissue aging between human and mouse. PMID:30996271
Investigation of molecular biomarker candidates for diagnosis and prognosis of chronic periodontitis by bioinformatics analysis of pooled microarray gene expression datasets in Gene Expression Omnibus (GEO). PMID:30922293
Phenotypic subgrouping and multi-omics analyses reveal reduced diazepam-binding inhibitor (DBI) protein levels in autism spectrum disorder with severe language impairment. PMID:30921354
Adapting Community Detection Algorithms for Disease Module Identification in Heterogeneous Biological Networks. PMID:30918511
Diagnostic and prognostic value of CEP55 in clear cell renal cell carcinoma as determined by bioinformatics analysis. PMID:30896867
Multiomics analysis profile acute liver injury module clusters to compare the therapeutic efficacy of bifendate and muaddil sapra. PMID:30867448
Using Openly Accessible Resources to Strengthen Causal Inference in Epigenetic Epidemiology of Neurodevelopment and Mental Health. PMID:30832291
Integrative Analysis Revealing Human Adipose-Specific Genes and Consolidating Obesity Loci. PMID:30816281
Identification of special key genes for alcohol-related hepatocellular carcinoma through bioinformatic analysis. PMID:30755830
Lysophosphatidic Acid Receptor 6 (LPAR6) Expression and Prospective Signaling Pathway Analysis in Breast Cancer. PMID:30694446
Restructured GEO: restructuring Gene Expression Omnibus metadata for genome dynamics analysis. PMID:30649296
Leveraging Multilayered "Omics" Data for Atopic Dermatitis: A Road Map to Precision Medicine. PMID:30631320
Network-based logistic regression integration method for biomarker identification. PMID:30598085
The Prognostic Value of Cell Cycle Gene Expression Signatures in Muscle Invasive, High-Grade Bladder Cancer. PMID:30561442
A data citation roadmap for scientific publishers. PMID:30457573
SEdb: a comprehensive human super-enhancer database. PMID:30371817
Transcriptional repressor GATA binding 1-mediated repression of SRY-box 2 expression suppresses cancer stem cell functions and tumor initiation. PMID:30315105
MicroRNA therapeutics: design of single-stranded miR-216b mimics to target KRAS in pancreatic cancer cells. PMID:30306823
Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism. PMID:30275053
Extensive evaluation of the generalized relevance network approach to inferring gene regulatory networks. PMID:30239704
Bioinformatics analyses of significant genes, related pathways and candidate prognostic biomarkers in glioblastoma. PMID:30132538
Physio-Genetic Dissection of Dark-Induced Leaf Senescence and Timing Its Reversal in Barley. PMID:30126868
Machine Learning Based Toxicity Prediction: From Chemical Structural Description to Transcriptome Analysis. PMID:30103448
A merged lung cancer transcriptome dataset for clinical predictive modeling. PMID:30040079
The calcium channel proteins ORAI3 and STIM1 mediate TGF-β induced Snai1 expression. PMID:30034631
Random Matrix Analysis for Gene Interaction Networks in Cancer Cells. PMID:30006574
C-terminal truncation of IFN-γ inhibits proinflammatory macrophage responses and is deficient in autoimmune disease. PMID:29925830
A gene interaction network‑based method to measure the common and heterogeneous mechanisms of gynecological cancer. PMID:29749503
Prevention of data duplication for high throughput sequencing repositories. PMID:29688363
Integrated genome-wide Alu methylation and transcriptome profiling analyses reveal novel epigenetic regulatory networks associated with autism spectrum disorder. PMID:29686828
Curated compendium of human transcriptional biomarker data. PMID:29664470
Role of COL6A3 in colorectal cancer. PMID:29620224
Gene Expression Meta-Analysis of Seven Candidate Gene Sets for Diabetes Traits Following a GWAS Pathway Study. PMID:29503662
UBASH3B promotes tamoxifen resistance and could be negatively regulated by ESR1. PMID:29492198
Mutational Pleiotropy and the Strength of Stabilizing Selection Within and Between Functional Modules of Gene Expression. PMID:29437825
Principal metabolic flux mode analysis. PMID:29420676
Use of methylation profiling to identify significant differentially methylated genes in bone marrow mesenchymal stromal cells from acute myeloid leukemia. PMID:29207054
Integrating sequence and gene expression information predicts genome-wide DNA-binding proteins and suggests a cooperative mechanism. PMID:29186632
Identification of potential therapeutic targets for gliomas by bioinformatics analysis. PMID:29113156
MGA repository: a curated data resource for ChIP-seq and other genome annotated data. PMID:29069466
A sequential Monte Carlo approach to gene expression deconvolution. PMID:29049343
Incorporating genomic, transcriptomic and clinical data: a prognostic and stem cell-like MYC and PRC imbalance in high-risk neuroblastoma. PMID:28984200
Functional Impact of Chromatin Remodeling Gene Mutations and Predictive Signature for Therapeutic Response in Bladder Cancer. PMID:28970362
Molecular mechanisms underlying gliomas and glioblastoma pathogenesis revealed by bioinformatics analysis of microarray data. PMID:28952134
Precision annotation of digital samples in NCBI's gene expression omnibus. PMID:28925997
Cleaning by clustering: methodology for addressing data quality issues in biomedical metadata. PMID:28923003
Transcriptomic meta-analysis identifies gene expression characteristics in various samples of HIV-infected patients with nonprogressive disease. PMID:28899396
Genome-wide DNA methylation analysis in blood cells from patients with Werner syndrome. PMID:28861129
Global analysis of gene expression in maize leaves treated with low temperature. II. Combined effect of severe cold (8 °C) and circadian rhythm. PMID:28828699
Discovering Condition-Specific Gene Co-Expression Patterns Using Gaussian Mixture Models: A Cancer Case Study. PMID:28819158
From Saccharomyces cerevisiae to human: The important gene co-expression modules. PMID:28804628
Expression changes in pelvic organ prolapse: a systematic review and in silico study. PMID:28794464
Consensus strategy in genes prioritization and combined bioinformatics analysis for preeclampsia pathogenesis. PMID:28789679
Using omics approaches to understand pulmonary diseases. PMID:28774304
CLIC, a tool for expanding biological pathways based on co-expression across thousands of datasets. PMID:28719601
Genome-Wide Identification and Analysis of Genes, Conserved between japonica and indica Rice Cultivars, that Respond to Low-Temperature Stress at the Vegetative Growth Stage. PMID:28713404
Prognostic and functional role of subtype-specific tumor-stroma interaction in breast cancer. PMID:28672102
System Level Meta-analysis of Microarray Datasets for Elucidation of Diabetes Mellitus Pathobiology. PMID:28659725
Cross-species gene modules emerge from a systems biology approach to osteoarthritis. PMID:28649440
The potential regulatory mechanisms of the gonadotropin-releasing hormone in gonadotropin transcriptions identified with bioinformatics analyses. PMID:28623929
Recent computational developments on CLIP-seq data analysis and microRNA targeting implications. PMID:28605404
Identification of gene markers associated with metastasis in clear cell renal cell carcinoma. PMID:28599476
DTWscore: differential expression and cell clustering analysis for time-series single-cell RNA-seq data. PMID:28535748
Reproducible RNA-seq analysis using recount2. PMID:28398307
Personalized Identification of Differentially Expressed Modules in Osteosarcoma. PMID:28190021
MicroRNA and mRNA Transcriptome Profiling in Primary Human Astrocytes Infected with Borrelia burgdorferi. PMID:28135303
Tissue Non-Specific Genes and Pathways Associated with Diabetes: An Expression Meta-Analysis. PMID:28117714
The protein level and transcription activity of activating transcription factor 1 is regulated by prolyl isomerase Pin1 in nasopharyngeal carcinoma progression. PMID:28032861
Prediction of Possible Biomarkers and Novel Pathways Conferring Risk to Post-Traumatic Stress Disorder. PMID:27997584
EP-DNN: A Deep Neural Network-Based Global Enhancer Prediction Algorithm. PMID:27929098
ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data. PMID:27924033
Long intergenic non-coding RNA expression signature in human breast cancer. PMID:27897201
A meta-analysis of public microarray data identifies gene regulatory pathways deregulated in peripheral blood mononuclear cells from individuals with Systemic Lupus Erythematosus compared to those without. PMID:27846842
snpGeneSets: An R Package for Genome-Wide Study Annotation. PMID:27807048
Genome-Wide Interaction Analyses between Genetic Variants and Alcohol Consumption and Smoking for Risk of Colorectal Cancer. PMID:27723779
Genome-Wide Characterization and Expression Analysis of the Germin-Like Protein Family in Rice and Arabidopsis. PMID:27669230
Diverse fates of uracilated HIV-1 DNA during infection of myeloid lineage cells. PMID:27644592
Integrated Analysis of DNA Methylation and mRNA Expression Profiles Data to Identify Key Genes in Lung Adenocarcinoma. PMID:27610375
Tissue of origin dictates branched-chain amino acid metabolism in mutant Kras-driven cancers. PMID:27609895
Integrating Colon Cancer Microarray Data: Associating Locus-Specific Methylation Groups to Gene Expression-Based Classifications. PMID:27600244
Data Integration for Microarrays: Enhanced Inference for Gene Regulatory Networks. PMID:27600224
Stromal Activation by Tumor Cells: An in Vitro Study in Breast Cancer. PMID:27600076
An Osteopontin/CD44 Axis in RhoGDI2-Mediated Metastasis Suppression. PMID:27593345
Network pharmacology dissection of multiscale mechanisms of herbal medicines in stage IV gastric adenocarcinoma treatment. PMID:27583849
Updated Rice Kinase Database RKD 2.0: enabling transcriptome and functional analysis of rice kinase genes. PMID:27540739
Evaluation of Normalization Methods for RNA-Seq Gene Expression Estimation. PMID:27532058
Opening up the blackbox: an interpretable deep neural network-based classifier for cell-type specific enhancer predictions. PMID:27490187
A Mechanistic Beta-Binomial Probability Model for mRNA Sequencing Data. PMID:27326762
Differences in DNA Repair Capacity, Cell Death and Transcriptional Response after Irradiation between a Radiosensitive and a Radioresistant Cell Line. PMID:27245205
Decreased Expression of EHD2 Promotes Tumor Metastasis and Indicates Poor Prognosis in Hepatocellular Carcinoma. PMID:27221498
Cartography of Pathway Signal Perturbations Identifies Distinct Molecular Pathomechanisms in Malignant and Chronic Lung Diseases. PMID:27200087
OM-FBA: Integrate Transcriptomics Data with Flux Balance Analysis to Decipher the Cell Metabolism. PMID:27100883
Computational Reconstruction of NFκB Pathway Interaction Mechanisms during Prostate Cancer. PMID:27078000
Requirements for the formal representation of pathophysiology mechanisms by clinicians. PMID:27051514
A molecular classification of human mesenchymal stromal cells. PMID:27042394
Differential network analysis reveals the genome-wide landscape of estrogen receptor modulation in hormonal cancers. PMID:26972162
Efficient and biologically relevant consensus strategy for Parkinson's disease gene prioritization. PMID:26961748
shRNA target prediction informed by comprehensive enquiry (SPICE): a supporting system for high-throughput screening of shRNA library. PMID:26941783
GEMINI: a computationally-efficient search engine for large gene expression datasets. PMID:26911289
ePIANNO: ePIgenomics ANNOtation tool. PMID:26859295
CressInt: a user-friendly web resource for genome-scale exploration of gene regulation in Arabidopsis thaliana. PMID:26855883
Diversity of Gene Expression in Hepatocellular Carcinoma Cells. PMID:26779818
COMPUTATIONAL APPROACHES TO STUDY MICROBES AND MICROBIOMES. PMID:26776218
The leukemogenic fusion gene MLL-AF9 alters microRNA expression pattern and inhibits monoblastic differentiation via miR-511 repression. PMID:26762252
A Computational Pipeline for Cross-Species Analysis of RNA-seq Data Using R and Bioconductor. PMID:26692761
Integrative genomic analysis reveals functional diversification of APOBEC gene family in breast cancer. PMID:26682542
iTAP: integrated transcriptomics and phenotype database for stress response of Escherichia coli and Saccharomyces cerevisiae. PMID:26653323
Semi-Supervised Multi-View Learning for Gene Network Reconstruction. PMID:26641091
Lupus Nephritis IgG Induction of Calcium/Calmodulin-Dependent Protein Kinase IV Expression in Podocytes and Alteration of Their Function. PMID:26636664
Prioritizing and selecting likely novel miRNAs from NGS data. PMID:26635395
Genomic profiling screens small molecules of metastatic prostate carcinoma. PMID:26622681
BioGPS: building your own mash-up of gene annotations and expression profiles. PMID:26578587
FXYD5 is a Marker for Poor Prognosis and a Potential Driver for Metastasis in Ovarian Carcinomas. PMID:26494976
Time course transcriptional profiling of senescing barley leaves. PMID:26484183
Genome-wide identification and functional analysis of lincRNAs acting as miRNA targets or decoys in maize. PMID:26470872
Genome-Wide Detection and Analysis of Multifunctional Genes. PMID:26436655
Gene expression profiling of the inner ear. PMID:26403558
Integrated gene and miRNA expression analysis of prostate cancer associated fibroblasts supports a prominent role for interleukin-6 in fibroblast activation. PMID:26375444
Gene expression meta-analysis reveals immune response convergence on the IFNγ-STAT1-IRF1 axis and adaptive immune resistance mechanisms in lymphoma. PMID:26362649
Phenotype-Dependent Coexpression Gene Clusters: Application to Normal and Premature Ageing. PMID:26357076
Geroprotectors.org: a new, structured and curated database of current therapeutic interventions in aging and age-related disease. PMID:26342919
EphA2 Expression Is a Key Driver of Migration and Invasion and a Poor Prognostic Marker in Colorectal Cancer. PMID:26283684
Network-Based Association Study of Obesity and Type 2 Diabetes with Gene Expression Profiles. PMID:26273637
Phylogenomics databases for facilitating functional genomics in rice. PMID:26223238
ExAtlas: An interactive online tool for meta-analysis of gene expression data. PMID:26223199
A reproducible approach to high-throughput biological data acquisition and integration. PMID:26157642
Comprehensive comparison of large-scale tissue expression datasets. PMID:26157623
Protein functional features are reflected in the patterns of mRNA translation speed. PMID:26155933
Reconstruction and validation of a constraint-based metabolic network model for bone marrow-derived mesenchymal stem cells. PMID:26132591
An online tool for evaluating diagnostic and prognostic gene expression biomarkers in bladder cancer. PMID:26126604
Nicotinate O-Glucosylation Is an Evolutionarily Metabolic Trait Important for Seed Germination under Stress Conditions in Arabidopsis thaliana. PMID:26116607
MiRBooking simulates the stoichiometric mode of action of microRNAs. PMID:26089388
An interactive web application for the dissemination of human systems immunology data. PMID:26088622
piRNA-like small RNAs mark extended 3'UTRs present in germ and somatic cells. PMID:26076733
miR-30e* is an independent subtype-specific prognostic marker in breast cancer. PMID:26057454
BioMiner: Paving the Way for Personalized Medicine. PMID:26005322
ImmuSort, a database on gene plasticity and electronic sorting for immune cells. PMID:25988315
Integrative meta-analysis of differentially expressed genes in osteoarthritis using microarray technology. PMID:25975828
Prediction of intracellular metabolic states from extracellular metabolomic data. PMID:25972769
Comparison of merging and meta-analysis as alternative approaches for integrative gene expression analysis. PMID:25937953
Transcriptomic Analysis of Drought Stress Responses in Ammopiptanthus mongolicus Leaves Using the RNA-Seq Technique. PMID:25923822
Methylation array data can simultaneously identify individuals and convey protected health information: an unrecognized ethical concern. PMID:25859287
The promise of multi-omics and clinical data integration to identify and target personalized healthcare approaches in autism spectrum disorders. PMID:25831060
Isoflavones in soy flour diet have different effects on whole-genome expression patterns than purified isoflavone mix in human MCF-7 breast tumors in ovariectomized athymic nude mice. PMID:25820259
Analytical methods in untargeted metabolomics: state of the art in 2015. PMID:25798438
Arabidopsis flower specific defense gene expression patterns affect resistance to pathogens. PMID:25750645
Selection of reference genes for qPCR- and ddPCR-based analyses of gene expression in Senescing Barley leaves. PMID:25723393
Biological databases for human research. PMID:25712261
Techniques for transferring host-pathogen protein interactions knowledge to new tasks. PMID:25699028
Systems approaches to predict the functions of glycoside hydrolases during the life cycle of Aspergillus niger using developmental mutants ∆brlA and ∆flbA. PMID:25629352
A metabolic signature of colon cancer initiating cells. PMID:25571056
Delayed inflammatory and cell death responses are associated with reduced pathogenicity in Lujo virus-infected cynomolgus macaques. PMID:25520505
Deciphering miRNA transcription factor feed-forward loops to identify drug repurposing candidates for cystic fibrosis. PMID:25484921
Identification of several hub-genes associated with periodontitis using integrated microarray analysis. PMID:25483140
Estimation and Testing of Gene Expression Heterosis. PMID:25435758
Bootstrap-based differential gene expression analysis for RNA-Seq data with and without replicates. PMID:25435284
Toward computational cumulative biology by combining models of biological datasets. PMID:25427176
The evolutionary fate of the horizontally transferred agrobacterial mikimopine synthase gene in the genera Nicotiana and Linaria. PMID:25420106
Differential temporal expression of milk miRNA during the lactation cycle of the marsupial tammar wallaby (Macropus eugenii). PMID:25417092
Multi-omic landscape of rheumatoid arthritis: re-evaluation of drug adverse effects. PMID:25414848
Revealing the potential pathogenesis of glioma by utilizing a glioma associated protein-protein interaction network. PMID:25410026
Genome-wide identification and analysis of Catharanthus roseus RLK1-like kinases in rice. PMID:25399351
Systematic analysis of new drug indications by drug-gene-disease coherent subnetworks. PMID:25390685
A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana. PMID:25361952
Small RNAs from plants, bacteria and fungi within the order Hypocreales are ubiquitous in human plasma. PMID:25344700
Measuring the effect of inter-study variability on estimating prediction error. PMID:25330348
Transcriptomic analysis unveils correlations between regulative apoptotic caspases and genes of cholesterol homeostasis in human brain. PMID:25330190
Integration of heterogeneous molecular networks to unravel gene-regulation in Mycobacterium tuberculosis. PMID:25279447
ExpressionData - A public resource of high quality curated datasets representing gene expression across anatomy, development and experimental conditions. PMID:25228922
RNA-seq Transcriptional Profiling of Peripheral Blood Leukocytes from Cattle Infected with Mycobacterium bovis. PMID:25206354
A novel binary T-vector with the GFP reporter gene for promoter characterization. PMID:25197968
Conserved temporal patterns of microRNA expression in Drosophila support a developmental hourglass model. PMID:25169982
Synovial phenotypes in rheumatoid arthritis correlate with response to biologic therapeutics. PMID:25167216
In-silico prediction of key metabolic differences between two non-small cell lung cancer subtypes. PMID:25093336
Integrating biological pathways and genomic profiles with ChiBE 2. PMID:25086704
IL-10-producing NKT10 cells are a distinct regulatory invariant NKT cell subset. PMID:25061873
A dedicated database system for handling multi-level data in systems biology. PMID:25053973
Nfkb1 is a haploinsufficient DNA damage-specific tumor suppressor. PMID:25043302
High resolution mapping of modified DNA nucleobases using excision repair enzymes. PMID:25015380
Peripheral blood cells inform on the presence of breast cancer: a population-based case-control study. PMID:24931809
A homolog of lariat-debranching enzyme modulates turnover of branched RNA. PMID:24919400
Genome-wide identification of heat shock proteins (Hsps) and Hsp interactors in rice: Hsp70s as a case study. PMID:24884676
Co-expression network analysis identifies transcriptional modules in the mouse liver. PMID:24816893
categoryCompare, an analytical tool based on feature annotations. PMID:24808906
Involvement of endocytosis and alternative splicing in the formation of the pathological process in the early stages of Parkinson's disease. PMID:24804238
Pleiotropic mutations are subject to strong stabilizing selection. PMID:24793289
Regulation of the gut microbiota by the mucosal immune system in mice. PMID:24792038
Transcriptional dissection of pancreatic tumors engrafted in mice. PMID:24739241
Chromatin landscapes of retroviral and transposon integration profiles. PMID:24721906
Seminal plasma as a diagnostic fluid for male reproductive system disorders. PMID:24709963
Gene expression profile analysis of Manila clam (Ruditapes philippinarum) hemocytes after a Vibrio alginolyticus challenge using an immune-enriched oligo-microarray. PMID:24708293
Navigating and mining modENCODE data. PMID:24636835
Exploring the molecular causes of hepatitis B virus vaccination response: an approach with epigenomic and transcriptomic data. PMID:24612962
Meta-analysis of gene expression profiles to predict response to biologic agents in rheumatoid arthritis. PMID:24595895
MGDB: crossing the marker genes of a user microarray with a database of public-microarrays marker genes. PMID:24574116
Weighted set enrichment of gene expression data. PMID:24565001
Co-expression network analysis identifies Spleen Tyrosine Kinase (SYK) as a candidate oncogenic driver in a subset of small-cell lung cancer. PMID:24564859
MaTSE: the gene expression time-series explorer. PMID:24564291
Integration of transcription and flux data reveals molecular paths associated with differences in oxygen-dependent phenotypes of Saccharomyces cerevisiae. PMID:24528924
Integration of high-volume molecular and imaging data for composite biomarker discovery in the study of melanoma. PMID:24527435
Translational Bioinformatics Approaches to Drug Development. PMID:24527359
High-Throughput Single-Cell Analysis for Wound Healing Applications. PMID:24527358
RNAi-mediated silencing of MLL-AF9 reveals leukemia-associated downstream targets and processes. PMID:24517546
5β-Reduced steroids and human Δ(4)-3-ketosteroid 5β-reductase (AKR1D1). PMID:24513054
DRUGSURV: a resource for repositioning of approved and experimental drugs in oncology based on patient survival information. PMID:24503543
Accurate data processing improves the reliability of Affymetrix gene expression profiles from FFPE samples. PMID:24489733
A comprehensive look at transcription factor gene expression changes in colorectal adenomas. PMID:24472434
Robust prognostic gene expression signatures in bladder cancer and lung adenocarcinoma depend on cell cycle related genes. PMID:24465512
In Vitro Global Gene Expression Analyses Support the Ethnopharmacological Use of Achyranthes aspera. PMID:24454496
Determinants of expression variability. PMID:24435799
A field guide to genomics research. PMID:24409093
The nature and extent of mutational pleiotropy in gene expression of male Drosophila serrata. PMID:24402375
Characterization of the yehUT two-component regulatory system of Salmonella enterica Serovar Typhi and Typhimurium. PMID:24386394
Guilt by rewiring: gene prioritization through network rewiring in genome wide association studies. PMID:24381306
B-cell lymphoma gene regulatory networks: biological consistency among inference methods. PMID:24379827
An emerging picture of the seed desiccome: confirmed regulators and newcomers identified using transcriptome comparison. PMID:24376450
TIPMaP: a web server to establish transcript isoform profiles from reliable microarray probes. PMID:24373374
VTCdb: a gene co-expression database for the crop species Vitis vinifera (grapevine). PMID:24341535
PaGenBase: a pattern gene database for the global and dynamic understanding of gene function. PMID:24312499
A multi-level multi-scale approach to study essential genes in Mycobacterium tuberculosis. PMID:24308365
Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments. PMID:24304889
Late-replicating CNVs as a source of new genes. PMID:24285712
Genome-wide identification and analysis of Japonica and Indica cultivar-preferred transcripts in rice using 983 Affymetrix array data. PMID:24280533
Integrating in silico resources to map a signaling network. PMID:24233784
Co-expression network analysis and genetic algorithms for gene prioritization in preeclampsia. PMID:24219996
AXL is a key regulator of inherent and chemotherapy-induced invasion and predicts a poor clinical outcome in early-stage colon cancer. PMID:24170546
Experimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive. PMID:24167589
The Ets transcription factor EHF as a regulator of cornea epithelial cell identity. PMID:24142692
Simple topological features reflect dynamics and modularity in protein interaction networks. PMID:24130468
A robust prognostic signature for hormone-positive node-negative breast cancer. PMID:24112773
Making open data work for plant scientists. PMID:24043847
Microarray profiling of mononuclear peripheral blood cells identifies novel candidate genes related to chemoradiation response in rectal cancer. PMID:24040155
Long non-coding RNA identification over mouse brain development by integrative modeling of chromatin and genomic features. PMID:24038472
Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies. PMID:24037214
Mapping yeast transcriptional networks. PMID:24018767
Using molecular features of xenobiotics to predict hepatic gene expression response. PMID:24010729
Aurora kinases in head and neck cancer. PMID:23993387
Construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research. PMID:23986771
ESTOOLS Data@Hand: human stem cell gene expression resource. PMID:23985726
Combining docking site and phosphosite predictions to find new substrates: identification of smoothelin-like-2 (SMTNL2) as a c-Jun N-terminal kinase (JNK) substrate. PMID:23981301
Differential expression analysis with global network adjustment. PMID:23968143
A Bacteriophage tailspike domain promotes self-cleavage of a human membrane-bound transcription factor, the myelin regulatory factor MYRF. PMID:23966832
An integrative computational analysis provides evidence for FBN1-associated network deregulation in trisomy 21. PMID:23951402
Systematic review of genome-wide gene expression studies of bipolar disorder. PMID:23945090
Upstream mononucleotide A-repeats play a cis-regulatory role in mammals through the DICER1 and Ago proteins. PMID:23935075
Analysis of the transcriptome in molecular epidemiology studies. PMID:23907930
Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data. PMID:23895370
Summarizing cellular responses as biological process networks. PMID:23895181
REACTIN: regulatory activity inference of transcription factors underlying human diseases with application to breast cancer. PMID:23885756
High-throughput identification of reference genes for research and clinical RT-qPCR analysis of breast cancer samples. PMID:23876162
A systems-genetics approach and data mining tool to assist in the discovery of genes underlying complex traits in Oryza sativa. PMID:23874666
NanoMiner - integrative human transcriptomics data resource for nanoparticle research. PMID:23874618
GStream: improving SNP and CNV coverage on genome-wide association studies. PMID:23844243
DBATE: database of alternative transcripts expression. PMID:23842462
Connectivity Mapping for Candidate Therapeutics Identification Using Next Generation Sequencing RNA-Seq Data. PMID:23840550
Multitask learning for host-pathogen protein interactions. PMID:23812987
A comparative analysis of transcription factor expression during metazoan embryonic development. PMID:23799133
Combined small RNA and degradome sequencing reveals novel miRNAs and their targets in response to low nitrate availability in maize. PMID:23788746
Analysis and prediction of pathways in HeLa cells by integrating biological levels of organization with systems-biology approaches. PMID:23785426
bioNerDS: exploring bioinformatics' database and software use through literature mining. PMID:23768135
INMEX--a web-based tool for integrative meta-analysis of expression data. PMID:23766290
Alternative splicing tends to avoid partial removals of protein-protein interaction sites. PMID:23758645
Effect of normalization on statistical and biological interpretation of gene expression profiles. PMID:23755061
Loss of caveolin-1 in prostate cancer stroma correlates with reduced relapse-free survival and is functionally relevant to tumour progression. PMID:23729330
Sensitive and specific detection of mosaic chromosomal abnormalities using the Parent-of-Origin-based Detection (POD) method. PMID:23724825
Integrated analysis of recurrent properties of cancer genes to identify novel drivers. PMID:23718799
Enhancer networks revealed by correlated DNAse hypersensitivity states of enhancers. PMID:23700312
Probiotics VSL#3 protect against development of visceral pain in murine model of irritable bowel syndrome. PMID:23691109
A20 restricts wnt signaling in intestinal epithelial cells and suppresses colon carcinogenesis. PMID:23671587
Transcription factors that convert adult cell identity are differentially polycomb repressed. PMID:23650565
A new 12-gene diagnostic biomarker signature of melanoma revealed by integrated microarray analysis. PMID:23638386
Candidate cancer-targeting agents identified by expression-profiling arrays. PMID:23637543
Chapter 15: disease gene prioritization. PMID:23633938
Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq. PMID:23629695
Transcriptional feedback in the insulin signalling pathway modulates ageing in both Caenorhabditis elegans and Drosophila melanogaster. PMID:23624434
When is hub gene selection better than standard meta-analysis? PMID:23613865
Heterogeneity of tumor-induced gene expression changes in the human metabolic network. PMID:23604282
MERTK receptor tyrosine kinase is a therapeutic target in melanoma. PMID:23585477
Metabolomics identifies pyrimidine starvation as the mechanism of 5-aminoimidazole-4-carboxamide-1-β-riboside-induced apoptosis in multiple myeloma cells. PMID:23585020
Probabilistic error correction for RNA sequencing. PMID:23558750
Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq. PMID:23555231
Strong EGFR signaling in cell line models of ERBB2-amplified breast cancer attenuates response towards ERBB2-targeting drugs. PMID:23552733
Transcriptome Profiling Following Neuronal and Glial Expression of ALS-Linked SOD1 in Drosophila. PMID:23550139
Cancer genome landscapes. PMID:23539594
Genes associated with the cis-regulatory functions of intragenic LINE-1 elements. PMID:23530910
Network pharmacology strategies toward multi-target anticancer therapies: from computational models to experimental design principles. PMID:23530504
Global gene expression profiling reveals SPINK1 as a potential hepatocellular carcinoma marker. PMID:23527199
A conserved upstream motif orchestrates autonomous, germline-enriched expression of Caenorhabditis elegans piRNAs. PMID:23516384
Uncovering hidden duplicated content in public transcriptomics data. PMID:23487185
Next generation sequencing reveals the expression of a unique miRNA profile in response to a gram-positive bacterial infection. PMID:23472090
Identity-by-descent mapping to detect rare variants conferring susceptibility to multiple sclerosis. PMID:23472070
Whole genome gene expression meta-analysis of inflammatory bowel disease colon mucosa demonstrates lack of major differences between Crohn's disease and ulcerative colitis. PMID:23468882
1918 Influenza virus hemagglutinin (HA) and the viral RNA polymerase complex enhance viral pathogenicity, but only HA induces aberrant host responses in mice. PMID:23449804
Fast probabilistic file fingerprinting for big data. PMID:23445565
A novel method for cross-species gene expression analysis. PMID:23444967
Profiling and identification of small rDNA-derived RNAs and their potential biological functions. PMID:23418607
canEvolve: a web portal for integrative oncogenomics. PMID:23418540
Stallion sperm transcriptome comprises functionally coherent coding and regulatory RNAs as revealed by microarray analysis and RNA-seq. PMID:23409192
Massive-scale gene co-expression network construction and robustness testing using random matrix theory. PMID:23409071
Description of plant tRNA-derived RNA fragments (tRFs) associated with argonaute and identification of their putative targets. PMID:23402430
Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework. PMID:23383610
Specificity and heterogeneity of terahertz radiation effect on gene expression in mouse mesenchymal stem cells. PMID:23378916
Genome-wide identification and analysis of the B3 superfamily of transcription factors in Brassicaceae and major crop plants. PMID:23377560
Improved moderation for gene-wise variance estimation in RNA-Seq via the exploitation of external information. PMID:23368783
The genome-defence gene Tex19.1 suppresses LINE-1 retrotransposons in the placenta and prevents intra-uterine growth retardation in mice. PMID:23364048
Evaluation of methods for modeling transcription factor sequence specificity. PMID:23354101
Partial AUC maximization for essential gene prediction using genetic algorithms. PMID:23351383
Comprehensive meta-analysis of Signal Transducers and Activators of Transcription (STAT) genomic binding patterns discerns cell-specific cis-regulatory modules. PMID:23324445
STIFDB2: an updated version of plant stress-responsive transcription factor database with additional stress signals, stress-responsive transcription factor binding sites and stress-responsive genes in Arabidopsis and rice. PMID:23314754
Transcriptome-wide expansion of non-coding regulatory switches: evidence from co-occurrence of Alu exonization, antisense and editing. PMID:23303787
Integrated analysis of gene expression profiles associated with response of platinum/paclitaxel-based treatment in epithelial ovarian cancer. PMID:23300757
The human brain online: an open resource for advancing brain research. PMID:23300378
MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data. PMID:23300135
Upstream distal regulatory elements contact the Lmo2 promoter in mouse erythroid cells. PMID:23285212
An integrative approach to inferring gene regulatory module networks. PMID:23285197
Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function. PMID:23284291
Genomewide analysis of intronic microRNAs in rice and Arabidopsis. PMID:23271017
Reuse of public genome-wide gene expression data. PMID:23269463
The yeast eukaryotic translation initiation factor 2B translation initiation complex interacts with the fatty acid synthesis enzyme YBR159W and endoplasmic reticulum membranes. PMID:23263984
ellipsoidFN: a tool for identifying a heterogeneous set of cancer biomarkers based on gene expressions. PMID:23262226
Unlocking the potential of publicly available microarray data using inSilicoDb and inSilicoMerging R/Bioconductor packages. PMID:23259851
Cutoff Finder: a comprehensive and straightforward Web application enabling rapid biomarker cutoff optimization. PMID:23251644
ChIP-on-chip analysis identifies IL-22 as direct target gene of ectopically expressed FOXP3 transcription factor in human T cells. PMID:23244505
CancerMA: a web-based tool for automatic meta-analysis of public cancer microarray data. PMID:23241162
Dissection of a quantitative trait locus for PR interval duration identifies Tnni3k as a novel modulator of cardiac conduction. PMID:23236294
Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE. PMID:23234303
Multiscale integration of -omic, imaging, and clinical data in biomedical informatics. PMID:23231990
The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes. PMID:23209799
dNTP Supply Gene Expression Patterns after P53 Loss. PMID:23205301
OrysPSSP: a comparative platform for small secreted proteins from rice and other plants. PMID:23203890
YM500: a small RNA sequencing (smRNA-seq) database for microRNA research. PMID:23203880
BSRD: a repository for bacterial small regulatory RNA. PMID:23203879
Whole miRNome-wide differential co-expression of microRNAs. PMID:23200138
Finding microRNA targets in plants: current status and perspectives. PMID:23200136
Using genome-wide expression profiling to define gene networks relevant to the study of complex traits: from RNA integrity to network topology. PMID:23195313
MiRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting. PMID:23193297
ENCODE data in the UCSC Genome Browser: year 5 update. PMID:23193274
EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era. PMID:23193273
ArrayExpress update--trends in database growth and links to data analysis tools. PMID:23193272
NCBI GEO: archive for functional genomics data sets--update. PMID:23193258
OikoBase: a genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica. PMID:23185044
RiceFREND: a platform for retrieving coexpressed gene networks in rice. PMID:23180784
RiceXPro version 3.0: expanding the informatics resource for rice transcriptome. PMID:23180765
BioGPS and MyGene.info: organizing online, gene-centric information. PMID:23175613
A ν-support vector regression based approach for predicting imputation quality. PMID:23173775
Identifying stage-specific protein subnetworks for colorectal cancer. PMID:23173715
Association of genes with physiological functions by comparative analysis of pooled expression microarray data. PMID:23170034
ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. PMID:23161675
First survey and functional annotation of prohormone and convertase genes in the pig. PMID:23153308
PMRD: a curated database for genes and mutants involved in plant male reproduction. PMID:23153247
Dynamic protein-protein interaction subnetworks of lung cancer in cases with smoking history. PMID:23149315
Theory on the coupled stochastic dynamics of transcription and splice-site recognition. PMID:23133354
A role for transcription factor GTF2IRD2 in executive function in Williams-Beuren syndrome. PMID:23118870
CellLineNavigator: a workbench for cancer cell line analysis. PMID:23118487
A Neuronal Transcriptome Response Involving Stress Pathways is Buffered by Neuronal microRNAs. PMID:23115547
Application of genomic tools in plant breeding. PMID:23115520
Selective gene-expression profiling of migratory tumor cells in vivo predicts clinical outcome in breast cancer patients. PMID:23113900
Cancer module genes ranking using kernelized score functions. PMID:23095178
Porcine tissue-specific regulatory networks derived from meta-analysis of the transcriptome. PMID:23049964
The transcription factor Th-POK negatively regulates Th17 differentiation in Vα14i NKT cells. PMID:23034280
Structure-based prediction of protein-protein interactions on a genome-wide scale. PMID:23023127
The bioinformatics analysis of miRNAs signatures differentially expressed in HER2(+) versus HER2(-) breast cancers. PMID:23009584
Tuning the engine: an introduction to resources on post-transcriptional regulation of gene expression. PMID:22995832
Transcriptional expression patterns triggered by chemically distinct neuroprotective molecules. PMID:22986168
Online tools for bioinformatics analyses in nutrition sciences. PMID:22983844
A pathway-based classification of breast cancer integrating data on differentially expressed genes, copy number variations and microRNA target genes. PMID:22983731
Estrogen-induced upregulation and 3'-UTR shortening of CDC6. PMID:22977174
AbsIDconvert: an absolute approach for converting genetic identifiers at different granularities. PMID:22967011
Techniques to cope with missing data in host-pathogen protein interaction prediction. PMID:22962468
Proteomic profiling identifies dysregulated pathways in small cell lung cancer and novel therapeutic targets including PARP1. PMID:22961666
A single-sample microarray normalization method to facilitate personalized-medicine workflows. PMID:22959562
Mechanisms of dietary response in mice and primates: a role for EGR1 in regulating the reaction to human-specific nutritional content. PMID:22937124
SNP microarray analyses reveal copy number alterations and progressive genome reorganization during tumor development in SVT/t driven mice breast cancer. PMID:22935085
Neurofunctional imaging of β-cell dynamics. PMID:22928569
CDS: a fold-change based statistical test for concomitant identification of distinctness and similarity in gene expression analysis. PMID:22917185
Gene expression and epigenetic discovery screen reveal methylation of SFRP2 in prostate cancer. PMID:22915211
Optimizing the GATA-3 position weight matrix to improve the identification of novel binding sites. PMID:22913572
A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers. PMID:22909066
Changes in the Staphylococcus aureus transcriptome during early adaptation to the lung. PMID:22876285
Assessing numerical dependence in gene expression summaries with the jackknife expression difference. PMID:22876276
The carbon starvation response of Aspergillus niger during submerged cultivation: insights from the transcriptome and secretome. PMID:22873931
Preeclampsia: a bioinformatics approach through protein-protein interaction networks analysis. PMID:22873350
Identification of CBX3 and ABCA5 as putative biomarkers for tumor stem cells in osteosarcoma. PMID:22870217
Expression analysis of macrodactyly identifies pleiotrophin upregulation. PMID:22848377
BioGPS and GXD: mouse gene expression data-the benefits and challenges of data integration. PMID:22847375
A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs. PMID:22836136
Studying and modelling dynamic biological processes using time-series gene expression data. PMID:22805708
Wisdom of crowds for robust gene network inference. PMID:22796662
Microarray test results should not be compensated for multiplicity of gene contents. PMID:22784577
Integration of biological networks and pathways with genetic association studies. PMID:22777728
Viral perturbations of host networks reflect disease etiology. PMID:22761553
Conserved rules govern genetic interaction degree across species. PMID:22747640
Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation. PMID:22735334
DEFOG: discrete enrichment of functionally organized genes. PMID:22706384
Identification of metagenes and their interactions through large-scale analysis of Arabidopsis gene expression data. PMID:22694750
Detection and correction of probe-level artefacts on microarrays. PMID:22647057
Integrative analysis of gene and miRNA expression profiles with transcription factor-miRNA feed-forward loops identifies regulators in human cancers. PMID:22645320
SLocX: Predicting Subcellular Localization of Arabidopsis Proteins Leveraging Gene Expression Data. PMID:22639594
Analyzing large biological datasets with association networks. PMID:22638576
arrayMap: a reference resource for genomic copy number imbalances in human malignancies. PMID:22629346
Biomedical application of fuzzy association rules for identifying breast cancer biomarkers. PMID:22622817
Transcriptome-based identification of antioxidative gene expression after fish oil supplementation in normo- and dyslipidemic men. PMID:22621246
MGEx-Udb: a mammalian uterus database for expression-based cataloguing of genes across conditions, including endometriosis and cervical cancer. PMID:22606288
O-miner: an integrative platform for automated analysis and mining of -omics data. PMID:22600742
Extent, causes, and consequences of small RNA expression variation in human adipose tissue. PMID:22589741
Systematic identification of functional plant modules through the integration of complementary data sources. PMID:22589469
Organizational structure and the periphery of the gene regulatory network in B-cell lymphoma. PMID:22583750
Microarray analysis of LTR retrotransposon silencing identifies Hdac1 as a regulator of retrotransposon expression in mouse embryonic stem cells. PMID:22570599
GPSy: a cross-species gene prioritization system for conserved biological processes--application in male gamete development. PMID:22570409
Defining the limits of physiological plasticity: how gene expression can assess and predict the consequences of ocean change. PMID:22566679
A review of spatial computational models for multi-cellular systems, with regard to intestinal crypts and colorectal cancer development. PMID:22565629
Quantitatively integrating molecular structure and bioactivity profile evidence into drug-target relationship analysis. PMID:22559876
Digital gene expression analysis based on integrated de novo transcriptome assembly of sweet potato [Ipomoea batatas (L.) Lam]. PMID:22558397
Integration of MicroRNA databases to study MicroRNAs associated with multiple sclerosis. PMID:22549745
Prognostic gene signatures for patient stratification in breast cancer: accuracy, stability and interpretability of gene selection approaches using prior knowledge on protein-protein interactions. PMID:22548963
Erythroid-specific transcriptional changes in PBMCs from pulmonary hypertension patients. PMID:22545094
Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features. PMID:22537144
How can microarrays unlock asthma? PMID:22500180
CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human. PMID:22495751
System approaches reveal the molecular networks involved in neural stem cell differentiation. PMID:22492180
Population differences in transcript-regulator expression quantitative trait loci. PMID:22479588
PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing. PMID:22467211
Comparative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of miRNAs. PMID:22457063
Making sense out of massive data by going beyond differential expression. PMID:22447773
Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report. PMID:22434826
Sleeping Beauty mutagenesis reveals cooperating mutations and pathways in pancreatic adenocarcinoma. PMID:22421440
How much can we learn about the function of bacterial rRNA modification by mining large-scale experimental datasets? PMID:22411911
Deriving transcriptional programs and functional processes from gene expression databases. PMID:22408194
Global gene expression and systems biology analysis of bovine monocyte-derived macrophages in response to in vitro challenge with Mycobacterium bovis. PMID:22384131
Assessing the utility of gene co-expression stability in combination with correlation in the analysis of protein-protein interaction networks. PMID:22369639
Generation of mouse ES cell lines engineered for the forced induction of transcription factors. PMID:22355682
The human lung adenocarcinoma cell line EKVX produces an infectious xenotropic murine leukemia virus. PMID:22355448
The latent membrane protein 1 (LMP1) oncogene of Epstein-Barr virus can simultaneously induce and inhibit apoptosis in B cells. PMID:22318153
Exploring tomato gene functions based on coexpression modules using graph clustering and differential coexpression approaches. PMID:22307966
Markov Chain Ontology Analysis (MCOA). PMID:22300537
Deep sequencing reveals predominant expression of miR-21 amongst the small non-coding RNAs in retinal microvascular endothelial cells. PMID:22298343
SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data. PMID:22293517
TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks. PMID:22292669
IntegromeDB: an integrated system and biological search engine. PMID:22260095
Use of intercellular washing fluid to investigate the secreted proteome of the rice-Magnaporthe interaction. PMID:22246111
Molecular bioelectricity in developmental biology: new tools and recent discoveries: control of cell behavior and pattern formation by transmembrane potential gradients. PMID:22237730
Tramtrack is genetically upstream of genes controlling tracheal tube size in Drosophila. PMID:22216153
K12/SECTM1, an interferon-γ regulated molecule, synergizes with CD28 to costimulate human T cell proliferation. PMID:22184754
Genome-wide transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis reveals suppression of host immune genes. PMID:22182502
HOMER: a human organ-specific molecular electronic repository. PMID:22165817
Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases. PMID:22151178
Database resources of the National Center for Biotechnology Information. PMID:22140104
BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata. PMID:22139929
MOPED: Model Organism Protein Expression Database. PMID:22139914
Small RNA profiling in two Brassica napus cultivars identifies microRNAs with oil production- and development-correlated expression and new small RNA classes. PMID:22138974
RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.). PMID:22136458
miRNEST database: an integrative approach in microRNA search and annotation. PMID:22135287
Synergy analysis reveals association between insulin signaling and desmoplakin expression in palmitate treated HepG2 cells. PMID:22132232
GeneSigDB: a manually curated database and resource for analysis of gene expression signatures. PMID:22110038
The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments. PMID:22110025
TopFIND 2.0--linking protein termini with proteolytic processing and modifications altering protein function. PMID:22102574
The BioSample Database (BioSD) at the European Bioinformatics Institute. PMID:22096232
ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets. PMID:22087737
PLEXdb: gene expression resources for plants and plant pathogens. PMID:22084198
modMine: flexible access to modENCODE data. PMID:22080565
The UCSC Archaeal Genome Browser: 2012 update. PMID:22080555
The International Nucleotide Sequence Database Collaboration. PMID:22080546
WormBase 2012: more genomes, more data, new website. PMID:22067452
Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments. PMID:22064864
Glycosylation and post-translational modification gene expression analysis by DNA microarrays for cultured mammalian cells. PMID:22033470
Transcriptomic characterization of a synergistic genetic interaction during carpel margin meristem development in Arabidopsis thaliana. PMID:22031826
Hormone receptor and ERBB2 status in gene expression profiles of human breast tumor samples. PMID:22022496
A framework to select clinically relevant cancer cell lines for investigation by establishing their molecular similarity with primary human cancers. PMID:22012889
The Sequence Read Archive: explosive growth of sequencing data. PMID:22009675
A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. PMID:22000014
Chipster: user-friendly analysis software for microarray and other high-throughput data. PMID:21999641
Expression of FACT in mammalian tissues suggests its role in maintaining of undifferentiated state of cells. PMID:21998152
Human cancer long non-coding RNA transcriptomes. PMID:21991387
PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species. PMID:21896772
The integrated web service and genome database for agricultural plants with biotechnology information. PMID:21887015
FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context. PMID:21884636
The real cost of sequencing: higher than you think! PMID:21867570
Computational approach to identify enzymes that are potential therapeutic candidates for psoriasis. PMID:21822480
Efficient overproduction of membrane proteins in Lactococcus lactis requires the cell envelope stress sensor/regulator couple CesSR. PMID:21818275
The reconstruction of condition-specific transcriptional modules provides new insights in the evolution of yeast AP-1 proteins. PMID:21695268
PILGRM: an interactive data-driven discovery platform for expert biologists. PMID:21653547
Comparative genomic analysis of the hexuronate metabolism genes and their regulation in gammaproteobacteria. PMID:21622752
Identification of an imprinted master trans regulator at the KLF14 locus related to multiple metabolic phenotypes. PMID:21572415
Translational bioinformatics: linking knowledge across biological and clinical realms. PMID:21561873
Inference of the transcriptional regulatory network in Staphylococcus aureus by integration of experimental and genomics-based evidence. PMID:21531804
Complex modulation of androgen responsive gene expression by methoxyacetic acid. PMID:21453523
Rice-Map: a new-generation rice genome browser. PMID:21450055
Global landscape of a co-expressed gene network in barley and its application to gene discovery in Triticeae crops. PMID:21441235
QiSampler: evaluation of scoring schemes for high-throughput datasets using a repetitive sampling strategy on gold standards. PMID:21388526
Profiling spermatogenic failure in adult testes bearing Sox9-deficient Sertoli cells identifies genes involved in feminization, inflammation and stress. PMID:21182756 -
Submission of microarray data to public repositories
PubMed citations: 37.
37 articles citing: Submission of microarray data to public repositories
Responsible, practical genomic data sharing that accelerates research. PMID:32694666
Common Gene Expression Patterns in Environmental Model Organisms Exposed to Engineered Nanomaterials: A Meta-Analysis. PMID:31752483
Predictability of human differential gene expression. PMID:30846554
How Many Lymph Nodes Are Enough? Assessing the Adequacy of Lymph Node Yield for Papillary Thyroid Cancer. PMID:27528716
From System-Wide Differential Gene Expression to Perturbed Regulatory Factors: A Combinatorial Approach. PMID:26562430
Databases for Microbiologists. PMID:26013493
The molecular components of the extracellular protein-degradation pathways of the ectomycorrhizal fungus Paxillus involutus. PMID:23902518
Using genome-wide expression profiling to define gene networks relevant to the study of complex traits: from RNA integrity to network topology. PMID:23195313
How can microarrays unlock asthma? PMID:22500180
Knowledge sharing and collaboration in translational research, and the DC-THERA Directory. PMID:21969471
The need for the pathology community to sponsor a whole slide imaging repository with technical guidance from the pathology informatics community. PMID:21845229
Who shares? Who doesn't? Factors associated with openly archiving raw research data. PMID:21765886
Using DNA microarrays to assay part function. PMID:21601083
Conceptual aspects of large meta-analyses with publicly available microarray data: a case study in oncology. PMID:21423405
Public sharing of research datasets: a pilot study of associations. PMID:21339841
The role of gene expression in ecological speciation. PMID:20860685
The filamentous fungal gene expression database (FFGED). PMID:20025988
A novel information retrieval model for high-throughput molecular medicine modalities. PMID:19458790
Repeatability of published microarray gene expression analyses. PMID:19174838
Key issues in conducting a meta-analysis of gene expression microarray datasets. PMID:18767902
MIFlowCyt: the minimum information about a Flow Cytometry Experiment. PMID:18752282
Navigating public microarray databases. PMID:18629145
Discovery of agents that eradicate leukemia stem cells using an in silico screen of public gene expression data. PMID:18305216
Genetic and molecular epidemiology. PMID:17699527
ArrayExpress--a public database of microarray experiments and gene expression profiles. PMID:17132828
The single extracytoplasmic-function sigma factor of Xylella fastidiosa is involved in the heat shock response and presents an unusual regulatory mechanism. PMID:17098905
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. PMID:17087822
MicroArray Facility: a laboratory information management system with extended support for Nylon based technologies. PMID:16987406
Global gene expression analysis of the heat shock response in the phytopathogen Xylella fastidiosa. PMID:16885450
Standardizing the standards. PMID:16738556
Whose data set is it anyway? Sharing raw data from randomized trials. PMID:16704733
ITTACA: a new database for integrated tumor transcriptome array and clinical data analysis. PMID:16381943
Storage and retrieval of microarray data and open source microarray database software. PMID:15988049
Global transcription profiling reveals comprehensive insights into hypoxic response in Arabidopsis. PMID:15734912
ArrayExpress--a public repository for microarray gene expression data at the EBI. PMID:15608260
The European Bioinformatics Institute's data resources: towards systems biology. PMID:15608238
DDBJ in collaboration with mass-sequencing teams on annotation. PMID:15608189 - http://dx.doi.org/10.1093/nar/gks1193
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dna microarray
metasource: Fairsharing.org
version: FAIRsharing.org: GEO; Gene Expression Omnibus; DOI: https://doi.org/10.25504/FAIRsharing.5hc8vt; Last edited: April 26, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
gene expression data
metasource: Fairsharing.org
version: FAIRsharing.org: GEO; Gene Expression Omnibus; DOI: https://doi.org/10.25504/FAIRsharing.5hc8vt; Last edited: April 26, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
genome
metasource: Fairsharing.org
version: FAIRsharing.org: GEO; Gene Expression Omnibus; DOI: https://doi.org/10.25504/FAIRsharing.5hc8vt; Last edited: April 26, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
microarray data and other gene expression databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
covid-19
metasource: re3data.org
version: re3data.org: Gene Expression Omnibus; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R33P44 last accessed: 2022-11-04
gene expression
metasource: re3data.org
version: re3data.org: Gene Expression Omnibus; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R33P44 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:16.605798
genetic regulation
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version: re3data.org: Gene Expression Omnibus; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R33P44 last accessed: 2022-11-04
genomics data
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version: re3data.org: Gene Expression Omnibus; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R33P44 last accessed: 2022-11-04
microarray experiment
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version: extracted_at: 2022-11-04T11:32:16.605798
experimental design and studies
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version: extracted_at: 2022-11-04T11:32:16.605798
probes and primers
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Tags
More detailed information about this field from each metasource.
dna microarray
metasource: Fairsharing.orgversion: FAIRsharing.org: GEO; Gene Expression Omnibus; DOI: https://doi.org/10.25504/FAIRsharing.5hc8vt; Last edited: April 26, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
gene expression data
metasource: Fairsharing.orgversion: FAIRsharing.org: GEO; Gene Expression Omnibus; DOI: https://doi.org/10.25504/FAIRsharing.5hc8vt; Last edited: April 26, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
genome
metasource: Fairsharing.orgversion: FAIRsharing.org: GEO; Gene Expression Omnibus; DOI: https://doi.org/10.25504/FAIRsharing.5hc8vt; Last edited: April 26, 2021, 11:57 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
microarray data and other gene expression databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
covid-19
metasource: re3data.orgversion: re3data.org: Gene Expression Omnibus; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R33P44 last accessed: 2022-11-04
gene expression
metasource: re3data.orgversion: re3data.org: Gene Expression Omnibus; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R33P44 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:16.605798
genetic regulation
metasource: re3data.orgversion: re3data.org: Gene Expression Omnibus; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R33P44 last accessed: 2022-11-04
genomics data
metasource: re3data.orgversion: re3data.org: Gene Expression Omnibus; editing status 2021-09-02; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R33P44 last accessed: 2022-11-04
microarray experiment
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:16.605798
experimental design and studies
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:16.605798
probes and primers
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:16.605798
dna microarray gene expression genome microarray data and other gene expression covid-19 gene expression genetic regulation genomics data microarray experiment experimental design and studies probes and primers
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