Gene Ontology Annotation Database
Names
More detailed information about this field from each metasource.
Gene Ontology Annotation Database
metasource: Fairsharing.org
version: FAIRsharing.org: GOA; Gene Ontology Annotation Database; DOI: https://doi.org/10.25504/FAIRsharing.7zffgc; Last edited: March 9, 2021, 4:03 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
GOA
metasource: Fairsharing.org
version: FAIRsharing.org: GOA; Gene Ontology Annotation Database; DOI: https://doi.org/10.25504/FAIRsharing.7zffgc; Last edited: March 9, 2021, 4:03 p.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: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
goa
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
Names
More detailed information about this field from each metasource.
Gene Ontology Annotation Database
metasource: Fairsharing.orgversion: FAIRsharing.org: GOA; Gene Ontology Annotation Database; DOI: https://doi.org/10.25504/FAIRsharing.7zffgc; Last edited: March 9, 2021, 4:03 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
GOA
metasource: Fairsharing.orgversion: FAIRsharing.org: GOA; Gene Ontology Annotation Database; DOI: https://doi.org/10.25504/FAIRsharing.7zffgc; Last edited: March 9, 2021, 4:03 p.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: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
goa
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.116598
Names
More detailed information about this field from each metasource.
Gene Ontology Annotation Database
metasource: Fairsharing.orgversion: FAIRsharing.org: GOA; Gene Ontology Annotation Database; DOI: https://doi.org/10.25504/FAIRsharing.7zffgc; Last edited: March 9, 2021, 4:03 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
GOA
metasource: Fairsharing.orgversion: FAIRsharing.org: GOA; Gene Ontology Annotation Database; DOI: https://doi.org/10.25504/FAIRsharing.7zffgc; Last edited: March 9, 2021, 4:03 p.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: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
goa
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.116598
The GO Annotation Database (GOA) provides Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB), RNA molecules from RNACentral and protein complexes from the Complex Portal. GOA files contain a mixture of manual annotation supplied by members of the Gene Onotology Consortium and computationally assigned GO terms describing gene products. Annotation type is clearly indicated by associated evidence codes and there are links to the source data.
Description
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The GO Annotation Database (GOA) provides Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB), RNA molecules from RNACentral and protein complexes from the Complex Portal. GOA files contain a mixture of manual annotation supplied by members of the Gene Onotology Consortium and computationally assigned GO terms describing gene products. Annotation type is clearly indicated by associated evidence codes and there are links to the source data.
metasource: Fairsharing.orgversion: FAIRsharing.org: GOA; Gene Ontology Annotation Database; DOI: https://doi.org/10.25504/FAIRsharing.7zffgc; Last edited: March 9, 2021, 4:03 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
he Gene Onotology Annotation (GOA) database is maintained by the European Bioinformatics Institute (EBI) and aims to provide assignments of gene products to the Gene Ontology (GO) resource - a dynamic controlled vocabulary that encourages the consistent description of a protein's function, process and location of action. In the GOA project, this vocabulary is being applied to a non-redundant set of proteins described in the EBI's core genome and proteome databases (UniProt Knowledgebase, InterPro and Ensembl) that collectively provide complete and incomplete proteomes for human (GOA-Human), mouse (GOA-Mouse) and rat (GOA-Rat) as well as many other organisms (GOA-UniProt). GOA is produced by electronic and manual techniques and is updated monthly, in accordance with the latest data released by its core databases. The production of GOA-Human is in keeping with our GO Consortium agreement to fast track the functional annotation of the human proteome and with our Human Proteomics Initiative. The release of all our annotation (for >76,000 species) via GOA-UniProt has made the EBI one of the largest resources of GO annotation by providing nearly 5 million annotations (see Statistics on GOA home page). The GOA project also ensures maintenance and sharing of GO mappings to Swiss-Prot keywords and InterPro. These mappings provide a useful resource of functional information for the analysis of microarray and mass spectrometry data. The GOA project also ensures that at least some of the existing corpus of scientific knowledge in our core databases is converted into a computationally accessible form. By annotating all characterized proteins with GO terms and facilitating the transfer of this knowledge to similar uncharacterized proteins, we hope to contribute to a better understanding of all proteomes. The success and accuracy of our GO annotations rely on frequent electronic and manual checking. We actively encourage updates or corrections and new collaborations from the scientific community to improve this shared resource. For further information about how to use GOA please refer to our home page: http://www.ebi.ac.uk/GOA or contact us by e-mail to [email protected].
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
The UniProt GO annotation program aims to provide high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB). The assignment of GO terms to UniProt records is an integral part of UniProt biocuration. UniProt manual and electronic GO annotations are supplemented with manual annotations supplied by external collaborating GO Consortium groups, to ensure a comprehensive GO annotation dataset is supplied to users.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.116598
Webpage:
http://www.ebi.ac.uk/GOAWebpage
More detailed information about this field from each metasource.
http://www.ebi.ac.uk/GOA
metasource: Fairsharing.orgversion: FAIRsharing.org: GOA; Gene Ontology Annotation Database; DOI: https://doi.org/10.25504/FAIRsharing.7zffgc; Last edited: March 9, 2021, 4:03 p.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
http://www.ebi.ac.uk/GOA/
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.116598
Licence:
Name: Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0Licence name
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Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0
metasource: Fairsharing.orgversion: FAIRsharing.org: GOA; Gene Ontology Annotation Database; DOI: https://doi.org/10.25504/FAIRsharing.7zffgc; Last edited: March 9, 2021, 4:03 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Licence URL
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http://opendatacommons.org/licenses/pddl/1.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: GOA; Gene Ontology Annotation Database; DOI: https://doi.org/10.25504/FAIRsharing.7zffgc; Last edited: March 9, 2021, 4:03 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
The GOA database in 2009--an integrated Gene Ontology Annotation resource
PMID: 18957448
metasource: Fairsharing.org
version: FAIRsharing.org: GOA; Gene Ontology Annotation Database; DOI: https://doi.org/10.25504/FAIRsharing.7zffgc; Last edited: March 9, 2021, 4:03 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
The GOA database: gene Ontology annotation updates for 2015
PMID: 25378336
metasource: Fairsharing.org
version: FAIRsharing.org: GOA; Gene Ontology Annotation Database; DOI: https://doi.org/10.25504/FAIRsharing.7zffgc; Last edited: March 9, 2021, 4:03 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
The UniProt-GO Annotation database in 2011
PMID: 22123736
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
http://dx.doi.org/10.1093/nar/gku1113
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.
The GOA database in 2009--an integrated Gene Ontology Annotation resource
PMID: 18957448
metasource: Fairsharing.org
version: FAIRsharing.org: GOA; Gene Ontology Annotation Database; DOI: https://doi.org/10.25504/FAIRsharing.7zffgc; Last edited: March 9, 2021, 4:03 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
The GOA database: gene Ontology annotation updates for 2015
PMID: 25378336
metasource: Fairsharing.org
version: FAIRsharing.org: GOA; Gene Ontology Annotation Database; DOI: https://doi.org/10.25504/FAIRsharing.7zffgc; Last edited: March 9, 2021, 4:03 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
The UniProt-GO Annotation database in 2011
PMID: 22123736
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
http://dx.doi.org/10.1093/nar/gku1113
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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The GOA database in 2009--an integrated Gene Ontology Annotation resource
PubMed citations: 292.
292 articles citing: The GOA database in 2009--an integrated Gene Ontology Annotation resource
Proteomic Exploration of Porcine Oocytes During Meiotic Maturation in vitro Using an Accurate TMT-Based Quantitative Approach. PMID:35198619
Protein Function Prediction Based on PPI Networks: Network Reconstruction vs Edge Enrichment. PMID:34970299
A machine learning framework for predicting drug-drug interactions. PMID:34475500
ECO-CollecTF: A Corpus of Annotated Evidence-Based Assertions in Biomedical Manuscripts. PMID:34327299
Iron insufficiency in floral buds impairs pollen development by disrupting tapetum function. PMID:34310779
Databases for Protein-Protein Interactions. PMID:34236665
Urine proteomics for profiling of mouse toxoplasmosis using liquid chromatography tandem mass spectrometry analysis. PMID:33879238
Towards FAIR protocols and workflows: the OpenPREDICT use case. PMID:33816932
Ensemble of Multiple Classifiers for Multilabel Classification of Plant Protein Subcellular Localization. PMID:33808227
Gene Duplication and Gain in the Trematode Atriophallophorus winterbourni Contributes to Adaptation to Parasitism. PMID:33484570
Proteomic Changes of Porcine Oocytes After Vitrification and Subsequent in vitro Maturation: A Tandem Mass Tag-Based Quantitative Analysis. PMID:33425922
Graph embeddings on gene ontology annotations for protein-protein interaction prediction. PMID:33323115
Comprehensive Proteomic Analysis of Lysine Ubiquitination in Seedling Leaves of Nicotiana tabacum. PMID:32832766
Computational Methods for Predicting Functions at the mRNA Isoform Level. PMID:32784445
Benchmarking gene ontology function predictions using negative annotations. PMID:32657372
UFO: A tool for unifying biomedical ontology-based semantic similarity calculation, enrichment analysis and visualization. PMID:32645039
Use of Chou's 5-steps rule to predict the subcellular localization of gram-negative and gram-positive bacterial proteins by multi-label learning based on gene ontology annotation and profile alignment. PMID:32598314
SDN2GO: An Integrated Deep Learning Model for Protein Function Prediction. PMID:32411695
De novo transcriptome sequencing and analysis of Anisakis pegreffii (Nematoda: Anisakidae) third-stage and fourth stage larvae. PMID:32298057
In silico unravelling pathogen-host signaling cross-talks via pathogen mimicry and human protein-protein interaction networks. PMID:31956393
Quantitative Proteomic Analysis Uncovers the Mediation of Endoplasmic Reticulum Stress-Induced Autophagy in DHAV-1-Infected DEF Cells. PMID:31817666
HisgAtlas 1.0: a human immunosuppression gene database. PMID:31725860
A Computational Framework for Predicting Direct Contacts and Substructures within Protein Complexes. PMID:31717703
Neglog: Homology-Based Negative Data Sampling Method for Genome-Scale Reconstruction of Human Protein-Protein Interaction Networks. PMID:31614890
A Multi-Label Learning Framework for Drug Repurposing. PMID:31505805
Seminal fluid compromises visual perception in honeybee queens reducing their survival during additional mating flights. PMID:31500699
RNA-seq data for olive flounder (Paralichthys olivaceus) according to water temperature. PMID:31489357
Advances in gene ontology utilization improve statistical power of annotation enrichment. PMID:31415589
Genetic and epigenetic regulation of human aging and longevity. PMID:31109447
Global Ubiquitome Profiling Revealed the Roles of Ubiquitinated Proteins in Metabolic Pathways of Tea Leaves in Responding to Drought Stress. PMID:30862833
Evolution of an X-Linked miRNA Family Predominantly Expressed in Mammalian Male Germ Cells. PMID:30649414
DeepIsoFun: a deep domain adaptation approach to predict isoform functions. PMID:30535380
Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy. PMID:30500839
Prioritising candidate genes causing QTL using hierarchical orthologous groups. PMID:30423067
PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information. PMID:30321395
Single-Run Mass Spectrometry Analysis Provides Deep Insight into E. coli Proteome. PMID:30259409
Dysregulation of the calcium handling protein, CCDC47, is associated with diabetic cardiomyopathy. PMID:30140426
DNA methylation associated with healthy aging of elderly twins. PMID:30136078
Automatic extraction of protein-protein interactions using grammatical relationship graph. PMID:30066644
Sex-Dependent Variation of Pumpkin (Cucurbita maxima cv. Big Max) Nectar and Nectaries as Determined by Proteomics and Metabolomics. PMID:30008725
Novel proteome and acetylome of Bemisia tabaci Q in response to Cardinium infection. PMID:29976144
Transferring knowledge of bacterial protein interaction networks to predict pathogen targeted human genes and immune signaling pathways: a case study on M. tuberculosis. PMID:29954330
Global assessment of its network dynamics reveals that the kinase Plk1 inhibits the phosphatase PP6 to promote Aurora A activity. PMID:29764989
Sensing the cilium, digital capture of ciliary data for comparative genomics investigations. PMID:29713460
HMMER Cut-off Threshold Tool (HMMERCTTER): Supervised classification of superfamily protein sequences with a reliable cut-off threshold. PMID:29579071
Aberrantly high expression of the CUB and zona pellucida-like domain-containing protein 1 (CUZD1) in mammary epithelium leads to breast tumorigenesis. PMID:29321207
Assessing the Performances of Protein Function Prediction Algorithms from the Perspectives of Identification Accuracy and False Discovery Rate. PMID:29316706
Characterization of plasma proteins in children of different Mycobacterium tuberculosis infection status using label-free quantitative proteomics. PMID:29262562
A framework for exploring associations between biomedical terms in PubMed. PMID:29262548
Human longevity: 25 genetic loci associated in 389,166 UK biobank participants. PMID:29227965
The Gene Ontology of eukaryotic cilia and flagella. PMID:29177046
A post-gene silencing bioinformatics protocol for plant-defence gene validation and underlying process identification: case study of the Arabidopsis thaliana NPR1. PMID:29169324
Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster. PMID:29045400
Mapping and comparative proteomic analysis of the starch biosynthetic pathway in rice by 2D PAGE/MS. PMID:28887709
Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing. PMID:28846689
A computational framework for distinguishing direct versus indirect interactions in human functional protein-protein interaction networks. PMID:28524201
COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information. PMID:28472402
The effects of shared information on semantic calculations in the gene ontology. PMID:28217262
SCALEUS: Semantic Web Services Integration for Biomedical Applications. PMID:28214993
Integrated proteomic and N-glycoproteomic analyses of doxorubicin sensitive and resistant ovarian cancer cells reveal glycoprotein alteration in protein abundance and glycosylation. PMID:28077793
PROPER: global protein interaction network alignment through percolation matching. PMID:27955623
The evolution of function within the Nudix homology clan. PMID:27936487
Multi-label ℓ2-regularized logistic regression for predicting activation/inhibition relationships in human protein-protein interaction networks. PMID:27819359
The Use of Signal-Transduction and Metabolic Pathways to Predict Human Disease Targets from Electric and Magnetic Fields Using in vitro Data in Human Cell Lines. PMID:27656641
TopoICSim: a new semantic similarity measure based on gene ontology. PMID:27473391
Computational discovery of Epstein-Barr virus targeted human genes and signalling pathways. PMID:27470517
DisSim: an online system for exploring significant similar diseases and exhibiting potential therapeutic drugs. PMID:27457921
Transcriptomic Analysis of the Endangered Neritid Species Clithon retropictus: De Novo Assembly, Functional Annotation, and Marker Discovery. PMID:27455329
Functional coherence metrics in protein families. PMID:27338101
Reactome from a WikiPathways Perspective. PMID:27203685
Contextualizing the Genes Altered in Bladder Neoplasms in Pediatric andTeen Patients Allows Identifying Two Main Classes of Biological ProcessesInvolved and New Potential Therapeutic Targets. PMID:27013923
A Protein Complex Map of Trypanosoma brucei. PMID:26991453
Data for global lysine-acetylation analysis in rice (Oryza sativa). PMID:26977447
Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing. PMID:26922242
Pyruvate Kinase M2 Activates mTORC1 by Phosphorylating AKT1S1. PMID:26876154
Multi-label multi-instance transfer learning for simultaneous reconstruction and cross-talk modeling of multiple human signaling pathways. PMID:26718335
Computational selection of antibody-drug conjugate targets for breast cancer. PMID:26700623
De novo and comparative transcriptome analysis of cultivated and wild spinach. PMID:26635144
Genes with stable DNA methylation levels show higher evolutionary conservation than genes with fluctuant DNA methylation levels. PMID:26515589
Integrative Genomics-Based Discovery of Novel Regulators of the Innate Antiviral Response. PMID:26485378
Experimental Evidence for a Revision in the Annotation of Putative Pyridoxamine 5'-Phosphate Oxidases P(N/M)P from Fungi. PMID:26327315
Urinary MicroRNA Profiling Predicts the Development of Microalbuminuria in Patients with Type 1 Diabetes. PMID:26239688
Knowledge transfer via classification rules using functional mapping for integrative modeling of gene expression data. PMID:26202217
PrOnto database : GO term functional dissimilarity inferred from biological data. PMID:26089836
SIFTER search: a web server for accurate phylogeny-based protein function prediction. PMID:25979264
Rv2031c of Mycobacterium tuberculosis: a master regulator of Rv2028-Rv2031 (HspX) operon. PMID:25964780
TermGenie - a web-application for pattern-based ontology class generation. PMID:25937883
ProtoBug: functional families from the complete proteomes of insects. PMID:25911153
Transcriptome characterization of three wild Chinese Vitis uncovers a large number of distinct disease related genes. PMID:25888081
Biochemical functional predictions for protein structures of unknown or uncertain function. PMID:25848497
dbPSP: a curated database for protein phosphorylation sites in prokaryotes. PMID:25841437
GRYFUN: a web application for GO term annotation visualization and analysis in protein sets. PMID:25794277
Shared resources, shared costs--leveraging biocuration resources. PMID:25776020
CD14 and complement crosstalk and largely mediate the transcriptional response to Escherichia coli in human whole blood as revealed by DNA microarray. PMID:25706641
A novel one-class SVM based negative data sampling method for reconstructing proteome-wide HTLV-human protein interaction networks. PMID:25620466
Finding gene regulatory network candidates using the gene expression knowledge base. PMID:25490885
Systematic analysis of the in situ crosstalk of tyrosine modifications reveals no additional natural selection on multiply modified residues. PMID:25476580
The GOA database: gene Ontology annotation updates for 2015. PMID:25378336
AdaBoost based multi-instance transfer learning for predicting proteome-wide interactions between Salmonella and human proteins. PMID:25330226
A weighted multipath measurement based on gene ontology for estimating gene products similarity. PMID:25229994
Sequencing and de novo transcriptome assembly of Brachypodium sylvaticum (Poaceae). PMID:25202520
FSim: a novel functional similarity search algorithm and tool for discovering functionally related gene products. PMID:25184141
Transcriptomic dissection of the rice-Burkholderia glumae interaction. PMID:25183458
BC4GO: a full-text corpus for the BioCreative IV GO task. PMID:25070993
Computational reconstruction of proteome-wide protein interaction networks between HTLV retroviruses and Homo sapiens. PMID:25037487
A method for increasing expressivity of Gene Ontology annotations using a compositional approach. PMID:24885854
Biophysical constraints on the evolution of tissue structure and function. PMID:24882821
Computational prediction of protein function based on weighted mapping of domains and GO terms. PMID:24868539
De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum. PMID:24821410
Biofragments: an approach towards predicting protein function using biologically related fragments and its application to Mycobacterium tuberculosis CYP126. PMID:24677424
Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt. PMID:24641996
Integrative analysis of many RNA-seq datasets to study alternative splicing. PMID:24583115
GOLink: Finding Cooccurring Terms across Gene Ontology Namespaces. PMID:24524070
Global secretome characterization of A549 human alveolar epithelial carcinoma cells during Mycoplasma pneumoniae infection. PMID:24507763
High-resolution functional annotation of human transcriptome: predicting isoform functions by a novel multiple instance-based label propagation method. PMID:24369432
PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome. PMID:24275491
Probability weighted ensemble transfer learning for predicting interactions between HIV-1 and human proteins. PMID:24260261
A Signaling Network of Thyroid-Stimulating Hormone. PMID:24255551
Profiling of Parkin-binding partners using tandem affinity purification. PMID:24244333
Sequence signatures extracted from proximal promoters can be used to predict distal enhancers. PMID:24156763
Annotation extension through protein family annotation coherence metrics. PMID:24130572
Enrichment analysis applied to disease prognosis. PMID:24103636
Information content-based gene ontology semantic similarity approaches: toward a unified framework theory. PMID:24078912
DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures. PMID:24067102
Genome-wide gene expression profiling of stress response in a spinal cord clip compression injury model. PMID:23984903
Mass spectrometry-based analysis of rat liver and hepatocellular carcinoma Morris hepatoma 7777 plasma membrane proteome. PMID:23909495
Deep coverage of the Escherichia coli proteome enables the assessment of false discovery rates in simple proteogenomic experiments. PMID:23908556
Construction of gene clusters resembling genetic causal mechanisms for common complex disease with an application to young-onset hypertension. PMID:23879630
A guide to best practices for Gene Ontology (GO) manual annotation. PMID:23842463
FFPred 2.0: improved homology-independent prediction of gene ontology terms for eukaryotic protein sequences. PMID:23717476
Comparative proteomic analysis of supportive and unsupportive extracellular matrix substrates for human embryonic stem cell maintenance. PMID:23658023
Systematic analysis of experimental phenotype data reveals gene functions. PMID:23626672
Protein function prediction by massive integration of evolutionary analyses and multiple data sources. PMID:23514099
Predictability of gene ontology slim-terms from primary structure information in Embryophyta plant proteins. PMID:23441934
A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration. PMID:23425577
STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation. PMID:23409969
Identification of additional proteins in differential proteomics using protein interaction networks. PMID:23386401
Genomic analysis of the regulatory elements and links with intrinsic DNA structural properties in the shrunken genome of Buchnera. PMID:23375088
The evolutionary rate of antibacterial drug targets. PMID:23374913
SymGRASS: a database of sugarcane orthologous genes involved in arbuscular mycorrhiza and root nodule symbiosis. PMID:23368899
A large-scale evaluation of computational protein function prediction. PMID:23353650
Identification of new protein interactions between dengue fever virus and its hosts, human and mosquito. PMID:23326450
Phyletic profiling with cliques of orthologs is enhanced by signatures of paralogy relationships. PMID:23308060
Gene family matters: expanding the HGNC resource. PMID:23245209
The ortholog conjecture is untestable by the current gene ontology but is supported by RNA sequencing data. PMID:23209392
BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA. PMID:23203881
Accelerating cancer systems biology research through Semantic Web technology. PMID:23188758
DcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. PMID:23161684
Gene expression analysis of a murine model with pulmonary vascular remodeling compared to end-stage IPAH lungs. PMID:23157700
Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. PMID:23157382
Evolutionarily consistent families in SCOP: sequence, structure and function. PMID:23078280
GenoSets: visual analytic methods for comparative genomics. PMID:23056299
Specificity of linear motifs that bind to a common mitogen-activated protein kinase docking groove. PMID:23047924
The identification of candidate genes and SNP markers for classical bovine spongiform encephalopathy susceptibility. PMID:22918267
Assessment of community-submitted ontology annotations from a novel database-journal partnership. PMID:22859749
Mining GO annotations for improving annotation consistency. PMID:22848383
Function prediction and analysis of mycobacterium tuberculosis hypothetical proteins. PMID:22837694
The yeast magmas ortholog pam16 has an essential function in fermentative growth that involves sphingolipid metabolism. PMID:22808036
Novel pathways in the pathobiology of human abdominal aortic aneurysms. PMID:22797469
Genome plasticity and systems evolution in Streptomyces. PMID:22759432
Protein interactions with piALU RNA indicates putative participation of retroRNA in the cell cycle, DNA repair and chromatin assembly. PMID:22754750
The percentage of bacterial genes on leading versus lagging strands is influenced by multiple balancing forces. PMID:22735706
Multi-label multi-kernel transfer learning for human protein subcellular localization. PMID:22719847
Quality of computationally inferred gene ontology annotations. PMID:22693439
A topology-based metric for measuring term similarity in the gene ontology. PMID:22666244
VarioWatch: providing large-scale and comprehensive annotations on human genomic variants in the next generation sequencing era. PMID:22618869
Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs. PMID:22615551
Discovery of novel glucose-regulated proteins in isolated human pancreatic islets using LC-MS/MS-based proteomics. PMID:22578083
COFACTOR: an accurate comparative algorithm for structure-based protein function annotation. PMID:22570420
Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL. PMID:22541594
Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms. PMID:22536960
Exploring the transcriptome of Atlantic salmon (Salmo salar) skin, a major defense organ. PMID:22527268
Functional repertoire, molecular pathways and diseases associated with 3D domain swapping in the human proteome. PMID:22472218
High through-put sequencing of the Parhyale hawaiensis mRNAs and microRNAs to aid comparative developmental studies. PMID:22448274
CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. PMID:22434836
The automatic annotation of bacterial genomes. PMID:22408191
Extracting regulator activity profiles by integration of de novo motifs and expression data: characterizing key regulators of nutrient depletion responses in Streptomyces coelicolor. PMID:22406834
A Resource of Quantitative Functional Annotation for Homo sapiens Genes. PMID:22384401
User centered and ontology based information retrieval system for life sciences. PMID:22373375
On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report. PMID:22359495
BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins. PMID:22335941
Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. PMID:22301074
vHOG, a multispecies vertebrate ontology of homologous organs groups. PMID:22285560
Sequencing and comparative genomic analysis of 1227 Felis catus cDNA sequences enriched for developmental, clinical and nutritional phenotypes. PMID:22257742
IMID: integrated molecular interaction database. PMID:22238258
Systems analysis of the transcriptional response of human ileocecal epithelial cells to Clostridium difficile toxins and effects on cell cycle control. PMID:22225989
Similarity-based disease risk assessment for personal genomes: proof of concept. PMID:22195217
The impact of focused Gene Ontology curation of specific mammalian systems. PMID:22174742
Improving the extraction of complex regulatory events from scientific text by using ontology-based inference. PMID:22166672
Bioinformatic analysis and post-translational modification crosstalk prediction of lysine acetylation. PMID:22164248
Phosphorylation in protein-protein binding: effect on stability and function. PMID:22153503
neXtProt: a knowledge platform for human proteins. PMID:22139911
The UniProt-GO Annotation database in 2011. PMID:22123736
ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree. PMID:22121228
The IntAct molecular interaction database in 2012. PMID:22121220
Saccharomyces Genome Database: the genomics resource of budding yeast. PMID:22110037
GONUTS: the Gene Ontology Normal Usage Tracking System. PMID:22110029
ProRepeat: an integrated repository for studying amino acid tandem repeats in proteins. PMID:22102581
AnimalTFDB: a comprehensive animal transcription factor database. PMID:22080564
CADRE: the Central Aspergillus Data REpository 2012. PMID:22080563
SuperTarget goes quantitative: update on drug-target interactions. PMID:22067455
PomBase: a comprehensive online resource for fission yeast. PMID:22039153
Newt-omics: a comprehensive repository for omics data from the newt Notophthalmus viridescens. PMID:22039101
3DSwap: curated knowledgebase of proteins involved in 3D domain swapping. PMID:21959866
Interspecific proteomic comparisons reveal ash phloem genes potentially involved in constitutive resistance to the emerald ash borer. PMID:21949771
Quantification of protein group coherence and pathway assignment using functional association. PMID:21929787
The challenges of defining oral cancer: analysis of an ontological approach. PMID:21915705
GOMMA: a component-based infrastructure for managing and analyzing life science ontologies and their evolution. PMID:21914205
GO-based functional dissimilarity of gene sets. PMID:21884611
Gene expression profiling of Atlantic cod (Gadus morhua) embryogenesis using microarray. PMID:21833508
Tutorial videos of bioinformatics resources: online distribution trial in Japan named TogoTV. PMID:21803786
A shortest-path graph kernel for estimating gene product semantic similarity. PMID:21801410
REVIGO summarizes and visualizes long lists of gene ontology terms. PMID:21789182
Genome-scale phylogenetic function annotation of large and diverse protein families. PMID:21784873
Integrated bio-entity network: a system for biological knowledge discovery. PMID:21738677
BioGraph: unsupervised biomedical knowledge discovery via automated hypothesis generation. PMID:21696594
Structural principles within the human-virus protein-protein interaction network. PMID:21680884
g:Profiler--a web server for functional interpretation of gene lists (2011 update). PMID:21646343
Genome-wide identification of conserved regulatory function in diverged sequences. PMID:21628450
Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis. PMID:21612636
Transcriptional double-autorepression feedforward circuits act for multicellularity and nervous system development. PMID:21569329
Extraction of consensus protein patterns in regions containing non-proline cis peptide bonds and their functional assessment. PMID:21569261
Genome analysis reveals interplay between 5'UTR introns and nuclear mRNA export for secretory and mitochondrial genes. PMID:21533221
GPS-CCD: a novel computational program for the prediction of calpain cleavage sites. PMID:21533053
Gene ontology function prediction in mollicutes using protein-protein association networks. PMID:21486441
The Protein Data Bank in Europe (PDBe): bringing structure to biology. PMID:21460450
UniProt Knowledgebase: a hub of integrated protein data. PMID:21447597
Predictive integration of gene functional similarity and co-expression defines treatment response of endothelial progenitor cells. PMID:21447198
Do two machine-learning based prognostic signatures for breast cancer capture the same biological processes? PMID:21423753
Comprehensive sequence analysis of 24,783 barley full-length cDNAs derived from 12 clone libraries. PMID:21415278
Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. PMID:21411447
Omics-based molecular target and biomarker identification. PMID:21370102
Protein function prediction: towards integration of similarity metrics. PMID:21353529
Protein expression profiles of C3H 10T1/2 murine fibroblasts and of isogenic cells transformed by the H1047R mutant of phosphoinositide 3-kinase (PI3K). PMID:21350335
B2G-FAR, a species-centered GO annotation repository. PMID:21335611
The what, where, how and why of gene ontology--a primer for bioinformaticians. PMID:21330331
PNAC: a protein nucleolar association classifier. PMID:21272300
Genome (re-)annotation and open-source annotation pipelines. PMID:21255336
A dual platform approach to transcript discovery for the planarian Schmidtea mediterranea to establish RNAseq for stem cell and regeneration biology. PMID:21179477
Accurate protein structure annotation through competitive diffusion of enzymatic functions over a network of local evolutionary similarities. PMID:21179190
Combined deletion of Fxr and Shp in mice induces Cyp17a1 and results in juvenile onset cholestasis. PMID:21123943
IntelliGO: a new vector-based semantic similarity measure including annotation origin. PMID:21122125
OMA 2011: orthology inference among 1000 complete genomes. PMID:21113020
AgBase: supporting functional modeling in agricultural organisms. PMID:21075795
SUPERFAMILY 1.75 including a domain-centric gene ontology method. PMID:21062816
CADgene: a comprehensive database for coronary artery disease genes. PMID:21045063
PDBe: Protein Data Bank in Europe. PMID:21045060
Transcriptome analysis of parallel-evolved Escherichia coli strains under ethanol stress. PMID:20955615
Shotgun proteomic analysis of Emiliania huxleyi, a marine phytoplankton species of major biogeochemical importance. PMID:20924652
The Renal Gene Ontology Annotation Initiative. PMID:20885853
DAnCER: disease-annotated chromatin epigenetics resource. PMID:20876685
Gene set enrichment; a problem of pathways. PMID:20861160
PeptideMine--a webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes. PMID:20858292
The Neural/Immune Gene Ontology: clipping the Gene Ontology for neurological and immunological systems. PMID:20831831
RoBuST: an integrated genomics resource for the root and bulb crop families Apiaceae and Alliaceae. PMID:20691054
Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept. PMID:20688752
Structural motif screening reveals a novel, conserved carbohydrate-binding surface in the pathogenesis-related protein PR-5d. PMID:20678238
Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization. PMID:20596258
Intrinsic disorder and protein multibinding in domain, terminal, and linker regions. PMID:20544079
Saliva Ontology: an ontology-based framework for a Salivaomics Knowledge Base. PMID:20525291
Re-annotation is an essential step in systems biology modeling of functional genomics data. PMID:20498845
agriGO: a GO analysis toolkit for the agricultural community. PMID:20435677
SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping. PMID:20377871
Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics. PMID:20350329
Genome-wide functional analysis of human 5' untranslated region introns. PMID:20222956
Pathway Palette: a rich internet application for peptide-, protein- and network-oriented analysis of MS data. PMID:20198642
Visualization of multiple alignments, phylogenies and gene family evolution. PMID:20195253
GOing Bayesian: model-based gene set analysis of genome-scale data. PMID:20172960
Advanced identification of proteins in uncharacterized proteomes by pulsed in vivo stable isotope labeling-based mass spectrometry. PMID:20139370
Functional characterization and topological modularity of molecular interaction networks. PMID:20122208
Proteomic analysis of peach fruit mesocarp softening and chilling injury using difference gel electrophoresis (DIGE). PMID:20082721
OLS dialog: an open-source front end to the ontology lookup service. PMID:20078892
From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase. PMID:20043185
Compounds from an unbiased chemical screen reverse both ER-to-Golgi trafficking defects and mitochondrial dysfunction in Parkinson's disease models. PMID:20038714
The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species. PMID:20003425
Codon usage is associated with the evolutionary age of genes in metazoan genomes. PMID:19995431
PDbase: a database of Parkinson's disease-related genes and genetic variation using substantia nigra ESTs. PMID:19958497
H-InvDB in 2009: extended database and data mining resources for human genes and transcripts. PMID:19933760
FunSimMat update: new features for exploring functional similarity. PMID:19923227
Representing ontogeny through ontology: a developmental biologist's guide to the gene ontology. PMID:19921742
MicrobesOnline: an integrated portal for comparative and functional genomics. PMID:19906701
Toward a quantitative theory of intrinsically disordered proteins and their function. PMID:19903882
HHMD: the human histone modification database. PMID:19892823
PDBe: Protein Data Bank in Europe. PMID:19858099
Software tool for researching annotations of proteins: open-source protein annotation software with data visualization. PMID:19839595
Structural and functional-annotation of an equine whole genome oligoarray. PMID:19811692
Integrating phenotype and gene expression data for predicting gene function. PMID:19811686
QuickGO: a web-based tool for Gene Ontology searching. PMID:19744993
Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention. PMID:19704032
OnEX: Exploring changes in life science ontologies. PMID:19678926
A systems biology network model for genetic association studies of nicotine addiction and treatment. PMID:19525886
The High Throughput Sequence Annotation Service (HT-SAS) - the shortcut from sequence to true Medline words. PMID:19445703 -
The GOA database: gene Ontology annotation updates for 2015
PubMed citations: 237.
237 articles citing: The GOA database: gene Ontology annotation updates for 2015
The Landscape of Virus-Host Protein-Protein Interaction Databases. PMID:35910656
Cardiomyocyte Cell-Cycle Regulation in Neonatal Large Mammals: Single Nucleus RNA-Sequencing Data Analysis via an Artificial-Intelligence-Based Pipeline. PMID:35860330
Increasing the throughput of sensitive proteomics by plexDIA. PMID:35835881
Chromosome-scale assembly and annotation of the perennial ryegrass genome. PMID:35831814
GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba. PMID:35758513
Proteomic Comparison of Ivermectin Sensitive and Resistant Staphylococcus aureus Clinical Isolates Reveals Key Efflux Pumps as Possible Resistance Determinants. PMID:35740165
Data Mining, Quality and Management in the Life Sciences. PMID:35507257
JaponicusDB: rapid deployment of a model organism database for an emerging model species. PMID:35380656
Current progress and open challenges for applying deep learning across the biosciences. PMID:35365602
Profiling and functional analysis of differentially expressed circular RNAs identified in foot-and-mouth disease virus infected PK-15 cells. PMID:35313983
Uncovering the genetic profiles underlying the intrinsic organization of the human cerebellum. PMID:35264730
Student biocuration projects as a learning environment. PMID:35211294
Wei2GO: weighted sequence similarity-based protein function prediction. PMID:35186498
Quantitative multiplexed proteomics analysis reveals reshaping of the lysine 2-hydroxyisobutyrylome in Fusarium graminearum by tebuconazole. PMID:35180840
Post-insemination selection dominates pre-insemination selection in driving rapid evolution of male competitive ability. PMID:35157717
CFTR interactome mapping using the mammalian membrane two-hybrid high-throughput screening system. PMID:35156780
PANDA2: protein function prediction using graph neural networks. PMID:35118378
ddRAD-seq reveals the genetic structure and detects signals of selection in Italian brown trout. PMID:35100964
FlyPhoneDB: an integrated web-based resource for cell-cell communication prediction in Drosophila. PMID:35100387
A novel gene functional similarity calculation model by utilizing the specificity of terms and relationships in gene ontology. PMID:35057740
Benchmark Evaluation of Protein-Protein Interaction Prediction Algorithms. PMID:35011283
Worldwide Protein Data Bank (wwPDB): A virtual treasure for research in biotechnology. PMID:34908533
Relation Extraction of Protein Complexes from Dynamic Protein-Protein Interaction Network. PMID:34904064
Endogenic upregulations of HIF/VEGF signaling pathway genes promote air breathing organ angiogenesis in bimodal respiration fish. PMID:34839401
PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions. PMID:34788826
Locally Adjust Networks Based on Connectivity and Semantic Similarities for Disease Module Detection. PMID:34759955
Co-evolution based machine-learning for predicting functional interactions between human genes. PMID:34753957
PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants. PMID:34747486
Hymenoptera Genome Database: new genomes and annotation datasets for improved go enrichment and orthologue analyses. PMID:34747465
Explainable machine learning predictions of dual-target compounds reveal characteristic structural features. PMID:34732806
A Multi-Marker Test for Analyzing Paired Genetic Data in Transplantation. PMID:34721531
PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies. PMID:34718760
Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO). PMID:34710081
Proteomic and lipidomic profiling of demyelinating lesions identifies fatty acids as modulators in lesion recovery. PMID:34706241
Gene Ontology curation of the blood-brain barrier to improve the analysis of Alzheimer's and other neurological diseases. PMID:34697638
Navigating the amino acid sequence space between functional proteins using a deep learning framework. PMID:34616884
Challenges and opportunities in the study of extracellular vesicles: Global institutional context and national state of the art. PMID:34559503
Functionathon: a manual data mining workflow to generate functional hypotheses for uncharacterized human proteins and its application by undergraduate students. PMID:34318869
Early-life social experience affects offspring DNA methylation and later life stress phenotype. PMID:34285226
The Infectious Disease Ontology in the age of COVID-19. PMID:34275487
DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction. PMID:34252926
Attenuation of clinical and immunological outcomes during SARS-CoV-2 infection by ivermectin. PMID:34170074
FINER: enhancing the prediction of tissue-specific functions of isoforms by refining isoform interaction networks. PMID:34169280
Genome-Wide Screening of Oxidizing Agent Resistance Genes in Escherichia coli. PMID:34072091
NetGO 2.0: improving large-scale protein function prediction with massive sequence, text, domain, family and network information. PMID:34038555
PredictProtein - Predicting Protein Structure and Function for 29 Years. PMID:33999203
COVID-19-related anosmia is associated with viral persistence and inflammation in human olfactory epithelium and brain infection in hamsters. PMID:33941622
Transcriptome sequencing revealed the mechanism of promoting floret opening by exogenous methyl jasmonate in sorghum. PMID:33927972
Nusinersen Modulates Proteomics Profiles of Cerebrospinal Fluid in Spinal Muscular Atrophy Type 1 Patients. PMID:33919289
Research on the Interaction Mechanism Between α Mino-Phosphonate Derivative Q-R and Harpin-Binding Protein 1 in Tobacco (Nicotiana tabacum) Plants. PMID:33868188
Application and evaluation of knowledge graph embeddings in biomedical data. PMID:33816992
The Redox Proteome of Thiol Proteins in the Rice Blast Fungus Magnaporthe oryzae. PMID:33776980
Embeddings from deep learning transfer GO annotations beyond homology. PMID:33441905
Evolution and diversification of the nuclear envelope. PMID:33435791
Intracellular and Extracellular Markers of Lethality in Osteogenesis Imperfecta: A Quantitative Proteomic Approach. PMID:33406681
Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome. PMID:33393786
Multi-resolution visualization and analysis of biomolecular networks through hierarchical community detection and web-based graphical tools. PMID:33351828
Transcriptional Landscape of Waddlia chondrophila Aberrant Bodies Induced by Iron Starvation. PMID:33255276
A thorough analysis of the contribution of experimental, derived and sequence-based predicted protein-protein interactions for functional annotation of proteins. PMID:33237964
CATH: increased structural coverage of functional space. PMID:33237325
A network-based comparative framework to study conservation and divergence of proteomes in plant phylogenies. PMID:33219668
In Silico Identification of SOX1 Post-Translational Modifications Highlights a Shared Protein Motif. PMID:33202879
MaizeMine: A Data Mining Warehouse for the Maize Genetics and Genomics Database. PMID:33193550
A six-amino-acid motif is a major determinant in functional evolution of HOX1 proteins. PMID:33184220
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. PMID:33170273
Integrated analysis of phosphoproteome and ubiquitylome in epididymal sperm of buffalo (Bubalus bubalis). PMID:33140506
The relationship between protein domains and homopeptides in the Plasmodium falciparum proteome. PMID:33062426
Predicting candidate genes from phenotypes, functions and anatomical site of expression. PMID:33051643
Aggregation and disaggregation features of the human proteome. PMID:33022891
CMNPD: a comprehensive marine natural products database towards facilitating drug discovery from the ocean. PMID:32986829
Cytokines mapping for tissue-specific expression, eQTLs and GWAS traits. PMID:32895400
Resolution of polycistronic RNA by SL2 trans-splicing is a widely conserved nematode trait. PMID:32887788
Profiling and bioinformatics analyses reveal differential circular RNA expression in NK/T-cell lymphoma-associated hemophagocytic syndrome. PMID:32856037
N-glycosylation of the human β1,4-galactosyltransferase 4 is crucial for its activity and Golgi localization. PMID:32827291
iPSC-derived progenitor stromal cells provide new insights into aberrant musculoskeletal development and resistance to cancer in down syndrome. PMID:32764607
Genomic analyses of a livestock pest, the New World screwworm, find potential targets for genetic control programs. PMID:32753684
Comparative transcriptomics of primary cells in vertebrates. PMID:32718981
AXL confers cell migration and invasion by hijacking a PEAK1-regulated focal adhesion protein network. PMID:32681075
Proteome-wide analysis of a malaria vaccine study reveals personalized humoral immune profiles in Tanzanian adults. PMID:32662772
A trafficome-wide RNAi screen reveals deployment of early and late secretory host proteins and the entire late endo-/lysosomal vesicle fusion machinery by intracellular Salmonella. PMID:32658937
The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction. PMID:32657391
Benchmarking gene ontology function predictions using negative annotations. PMID:32657372
Transcriptome Analysis of Wounding in the Model Grass Lolium temulentum. PMID:32580425
Automated generation of gene summaries at the Alliance of Genome Resources. PMID:32559296
Dynamic rewiring of the human interactome by interferon signaling. PMID:32539747
Integrated omics in Drosophila uncover a circadian kinome. PMID:32483184
Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons. PMID:32470107
Ubiquitome analysis reveals the involvement of lysine ubiquitination in the spermatogenesis process of adult buffalo (Bubalus bubalis) testis. PMID:32469046
Extracellular Vesicles in Renal Cell Carcinoma: Multifaceted Roles and Potential Applications Identified by Experimental and Computational Methods. PMID:32457844
An Integrated Proteomic and Transcriptomic Analysis Reveals the Venom Complexity of the Bullet Ant Paraponera clavata. PMID:32422990
Detection of superoxide dismutase (Cu-Zn) isoenzymes in leaves and pseudobulbs of Bulbophyllum morphologlorum Kraenzl orchid by comparative proteomic analysis. PMID:32395639
QuartataWeb: Integrated Chemical-Protein-Pathway Mapping for Polypharmacology and Chemogenomics. PMID:32221612
KCML: a machine-learning framework for inference of multi-scale gene functions from genetic perturbation screens. PMID:32141232
Genome sequencing of gut symbiotic Bacillus velezensis LC1 for bioethanol production from bamboo shoots. PMID:32140179
Classification of Trispanins: A Diverse Group of Proteins That Function in Membrane Synthesis and Transport Mechanisms. PMID:32039202
Extinction of chromosomes due to specialization is a universal occurrence. PMID:32034231
Mutation Enrichment and Transcriptomic Activation Signatures of 419 Molecular Pathways in Cancer. PMID:31979117
The proteome of IVF-induced aberrant embryo-maternal crosstalk by implantation stage in ewes. PMID:31956410
Evolving knowledge graph similarity for supervised learning in complex biomedical domains. PMID:31900127
A novel algorithm for alignment of multiple PPI networks based on simulated annealing. PMID:31881842
Formal axioms in biomedical ontologies improve analysis and interpretation of associated data. PMID:31821406
Graph-based information diffusion method for prioritizing functionally related genes in protein-protein interaction networks. PMID:31797617
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. PMID:31744546
Discovery of disease- and drug-specific pathways through community structures of a literature network. PMID:31738408
The neXtProt knowledgebase in 2020: data, tools and usability improvements. PMID:31724716
Cisplatin-resistant triple-negative breast cancer subtypes: multiple mechanisms of resistance. PMID:31684899
Bovine Genome Database: new annotation tools for a new reference genome. PMID:31647100
Computational methods and tools for binding site recognition between proteins and small molecules: from classical geometrical approaches to modern machine learning strategies. PMID:31628659
Challenges in the annotation of pseudoenzymes in databases: the UniProtKB approach. PMID:31618524
Differential gene expression during substrate probing in larvae of the Caribbean coral Porites astreoides. PMID:31596993
Molecular phenotyping using networks, diffusion, and topology: soft tissue sarcoma. PMID:31562358
DIFFUSE: predicting isoform functions from sequences and expression profiles via deep learning. PMID:31510699
Resources to Discover and Use Short Linear Motifs in Viral Proteins. PMID:31427097
Toxoplasma gondii effector TgIST blocks type I interferon signaling to promote infection. PMID:31413201
ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity. PMID:31406507
Analysis of Protein-Protein Functional Associations by Using Gene Ontology and KEGG Pathway. PMID:31396531
Using deep maxout neural networks to improve the accuracy of function prediction from protein interaction networks. PMID:31335894
Redox signals at the ER-mitochondria interface control melanoma progression. PMID:31304984
Harnessing Human Microphysiology Systems as Key Experimental Models for Quantitative Systems Pharmacology. PMID:31201557
NetGO: improving large-scale protein function prediction with massive network information. PMID:31106361
INGA 2.0: improving protein function prediction for the dark proteome. PMID:31073595
Improved annotation of the domestic pig genome through integration of Iso-Seq and RNA-seq data. PMID:31064321
Molecular convergence and positive selection associated with the evolution of symbiont transmission mode in stony corals. PMID:30991927
Genome-wide association study of an unusual dolphin mortality event reveals candidate genes for susceptibility and resistance to cetacean morbillivirus. PMID:30976305
Genomic subtyping and therapeutic targeting of acute erythroleukemia. PMID:30926971
Identification of prognostic biomarkers in colorectal cancer using a long non-coding RNA-mediated competitive endogenous RNA network. PMID:30854042
Annotation of gene product function from high-throughput studies using the Gene Ontology. PMID:30715275
Towards comprehensive annotation of Drosophila melanogaster enzymes in FlyBase. PMID:30689844
Classifying mild traumatic brain injuries with functional network analysis. PMID:30577783
Integrating Multiple Interaction Networks for Gene Function Inference. PMID:30577643
Clinically Relevant Post-Translational Modification Analyses-Maturing Workflows and Bioinformatics Tools. PMID:30577541
Proteome modifications on tomato under extreme high light induced-stress. PMID:30534005
Identification of novel candidate genes involved in the progression of emphysema by bioinformatic methods. PMID:30532529
Improving the Gene Ontology Resource to Facilitate More Informative Analysis and Interpretation of Alzheimer's Disease Data. PMID:30501127
NeVOmics: An Enrichment Tool for Gene Ontology and Functional Network Analysis and Visualization of Data from OMICs Technologies. PMID:30477135
SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins. PMID:30445541
The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions. PMID:30418645
ECO, the Evidence & Conclusion Ontology: community standard for evidence information. PMID:30407590
ConnectedAlign: a PPI network alignment method for identifying conserved protein complexes across multiple species. PMID:30367584
Aberrant PRDM9 expression impacts the pan-cancer genomic landscape. PMID:30341163
Genome-Wide Quantification of the Effect of Gene Overexpression on Escherichia coli Growth. PMID:30115866
Functional insights into the infective larval stage of Anisakis simplex s.s., Anisakis pegreffii and their hybrids based on gene expression patterns. PMID:30086708
HPO2GO: prediction of human phenotype ontology term associations for proteins using cross ontology annotation co-occurrences. PMID:30083448
Epigenetic regulation of brain region-specific microglia clearance activity. PMID:30038282
Enumerating consistent sub-graphs of directed acyclic graphs: an insight into biomedical ontologies. PMID:29949985
Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits. PMID:29945546
Predicting human protein function with multi-task deep neural networks. PMID:29889900
Expanding the horizons of microRNA bioinformatics. PMID:29871895
deepNF: deep network fusion for protein function prediction. PMID:29868758
RepTB: a gene ontology based drug repurposing approach for tuberculosis. PMID:29785561
Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes. PMID:29761466
Using ZFIN: Data Types, Organization, and Retrieval. PMID:29761463
In silico epigenetics of metal exposure and subclinical atherosclerosis in middle aged men: pilot results from the Aragon Workers Health Study. PMID:29685964
MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein-Protein Network Mapping. PMID:29534977
Identification and comparative analysis of microRNAs from tomato varieties showing contrasting response to ToLCV infections. PMID:29515314
In silico structural and functional prediction of African swine fever virus protein-B263R reveals features of a TATA-binding protein. PMID:29492339
Quantitative Proteomics of Synaptosomal Fractions in a Rat Overexpressing Human DISC1 Gene Indicates Profound Synaptic Dysregulation in the Dorsal Striatum. PMID:29467617
Pi-Pi contacts are an overlooked protein feature relevant to phase separation. PMID:29424691
The genomes of two Eutrema species provide insight into plant adaptation to high altitudes. PMID:29394339
HMG-box transcription factor 1: a positive regulator of the G1/S transition through the Cyclin-CDK-CDKI molecular network in nasopharyngeal carcinoma. PMID:29367693
Cattle infection response network and its functional modules. PMID:29301495
Revealing protein functions based on relationships of interacting proteins and GO terms. PMID:29297388
Reduced Levels of the Synaptic Functional Regulator FMRP in Dentate Gyrus of the Aging Sprague-Dawley Rat. PMID:29218006
Gene gravity-like algorithm for disease gene prediction based on phenotype-specific network. PMID:29212543
The Gene Ontology of eukaryotic cilia and flagella. PMID:29177046
Phosphoproteomics of cAMP signaling of Bordetella adenylate cyclase toxin in mouse dendritic cells. PMID:29176673
A post-gene silencing bioinformatics protocol for plant-defence gene validation and underlying process identification: case study of the Arabidopsis thaliana NPR1. PMID:29169324
Genome-wide identification of miRNAs and lncRNAs in Cajanus cajan. PMID:29141604
Proteomics analysis of bladder cancer invasion: Targeting EIF3D for therapeutic intervention. PMID:29050215
Systematic integration of biomedical knowledge prioritizes drugs for repurposing. PMID:28936969
Rat Genome and Model Resources. PMID:28838068
Identification of Nidogen 1 as a lung metastasis protein through secretome analysis. PMID:28827399
Functional determinants of protein assembly into homomeric complexes. PMID:28694495
Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction. PMID:28651538
Establishment of a 3D cell culture model of primary bovine mammary epithelial cells extracted from fresh milk. PMID:28643224
MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome. PMID:28502612
Mining Exosomal Genes for Pancreatic Cancer Targets. PMID:28446531
CDCA2 promotes lung adenocarcinoma cell proliferation and predicts poor survival in lung adenocarcinoma patients. PMID:28423619
Circular RNA alterations are involved in resistance to avian leukosis virus subgroup-J-induced tumor formation in chickens. PMID:28415618
Biocuration in the structure-function linkage database: the anatomy of a superfamily. PMID:28365730
RNA Editing During Sexual Development Occurs in Distantly Related Filamentous Ascomycetes. PMID:28338982
Functional proteomic analysis of corticosteroid pharmacodynamics in rat liver: Relationship to hepatic stress, signaling, energy regulation, and drug metabolism. PMID:28315483
Systemic QSAR and phenotypic virtual screening: chasing butterflies in drug discovery. PMID:28274840
Semi-quantitative proteomics of mammalian cells upon short-term exposure to non-ionizing electromagnetic fields. PMID:28234898
From the research laboratory to the database: the Caenorhabditis elegans kinome in UniProtKB. PMID:28159896
The integration of weighted human gene association networks based on link prediction. PMID:28137253
An advanced reference genome of Trifolium subterraneum L. reveals genes related to agronomic performance. PMID:28111887
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
The neXtProt knowledgebase on human proteins: 2017 update. PMID:27899619
PROSNET: INTEGRATING HOMOLOGY WITH MOLECULAR NETWORKS FOR PROTEIN FUNCTION PREDICTION. PMID:27896959
A New Chicken Genome Assembly Provides Insight into Avian Genome Structure. PMID:27852011
Large-scale gene co-expression network as a source of functional annotation for cattle genes. PMID:27806696
CGDB: a database of circadian genes in eukaryotes. PMID:27789706
Gold Nanoparticle Reprograms Pancreatic Tumor Microenvironment and Inhibits Tumor Growth. PMID:27758098
Exploring human disease using the Rat Genome Database. PMID:27736745
The rules and impact of nonsense-mediated mRNA decay in human cancers. PMID:27618451
An expanded evaluation of protein function prediction methods shows an improvement in accuracy. PMID:27604469
FFPred 3: feature-based function prediction for all Gene Ontology domains. PMID:27561554
Missing gene identification using functional coherence scores. PMID:27552989
Eliciting the Functional Taxonomy from protein annotations and taxa. PMID:27534507
Identification of compound-protein interactions through the analysis of gene ontology, KEGG enrichment for proteins and molecular fragments of compounds. PMID:27530612
Disrupted cooperation between transcription factors across diverse cancer types. PMID:27496222
SoyNet: a database of co-functional networks for soybean Glycine max. PMID:27492285
Unfoldomics of prostate cancer: on the abundance and roles of intrinsically disordered proteins in prostate cancer. PMID:27453073
Comparative transcriptomic analysis of human and Drosophila extracellular vesicles. PMID:27282340
Abasy Atlas: a comprehensive inventory of systems, global network properties and systems-level elements across bacteria. PMID:27242034
Peptide-based systems analysis of inflammation induced myeloid-derived suppressor cells reveals diverse signaling pathways. PMID:27193397
The Chinchilla Research Resource Database: resource for an otolaryngology disease model. PMID:27173523
PepPSy: a web server to prioritize gene products in experimental and biocuration workflows. PMID:27173522
APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks. PMID:27131791
Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host. PMID:27127642
A molecular classification of human mesenchymal stromal cells. PMID:27042394
Contextualizing the Genes Altered in Bladder Neoplasms in Pediatric andTeen Patients Allows Identifying Two Main Classes of Biological ProcessesInvolved and New Potential Therapeutic Targets. PMID:27013923
KinetochoreDB: a comprehensive online resource for the kinetochore and its related proteins. PMID:26989151
Pipeline for the identification and classification of ion channels in parasitic flatworms. PMID:26983991
REGene: a literature-based knowledgebase of animal regeneration that bridge tissue regeneration and cancer. PMID:26975833
Efficient and biologically relevant consensus strategy for Parkinson's disease gene prioritization. PMID:26961748
MiR-708 promotes steroid-induced osteonecrosis of femoral head, suppresses osteogenic differentiation by targeting SMAD3. PMID:26932538
An Atlas of the Human Kinome Reveals the Mutational Landscape Underlying Dysregulated Phosphorylation Cascades in Cancer. PMID:26921330
Operon Gene Order Is Optimized for Ordered Protein Complex Assembly. PMID:26804901
CSGene: a literature-based database for cell senescence genes and its application to identify critical cell aging pathways and associated diseases. PMID:26775705
Plasma Proteome Biomarkers of Inflammation in School Aged Children in Nepal. PMID:26636573
From Single Variants to Protein Cascades: MULTISCALE MODELING OF SINGLE NUCLEOTIDE VARIANT SETS IN GENETIC DISORDERS. PMID:26601959
COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses. PMID:26586805
GO-PCA: An Unsupervised Method to Explore Gene Expression Data Using Prior Knowledge. PMID:26575370
Organic and inorganic mercurials have distinct effects on cellular thiols, metal homeostasis, and Fe-binding proteins in Escherichia coli. PMID:26498643
Integrated analysis of miRNA and mRNA paired expression profiling of prenatal skeletal muscle development in three genotype pigs. PMID:26496978
A-DaGO-Fun: an adaptable Gene Ontology semantic similarity-based functional analysis tool. PMID:26476781
Release of Small RNA-containing Exosome-like Vesicles from the Human Filarial Parasite Brugia malayi. PMID:26401956
Co-Inheritance Analysis within the Domains of Life Substantially Improves Network Inference by Phylogenetic Profiling. PMID:26394049
Application of comparative biology in GO functional annotation: the mouse model. PMID:26141960
ZFIN, The zebrafish model organism database: Updates and new directions. PMID:26097180
dictyBase 2015: Expanding data and annotations in a new software environment. PMID:26088819
Region Evolution eXplorer - A tool for discovering evolution trends in ontology regions. PMID:26034559
Global alterations of the transcriptional landscape during yeast growth and development in the absence of Ume6-dependent chromatin modification. PMID:25957495
Widespread macromolecular interaction perturbations in human genetic disorders. PMID:25910212
Origin and evolution of metabolic sub-cellular compartmentalization in eukaryotes. PMID:25869000 -
The UniProt-GO Annotation database in 2011
PubMed citations: 193.
193 articles citing: The UniProt-GO Annotation database in 2011
Loci underlying leaf agronomic traits identified by re-sequencing celery accessions based on an assembled genome. PMID:35784787
A chromosome-level genome assembly of Artocarpus nanchuanensis (Moraceae), an extremely endangered fruit tree. PMID:35701376
Chromosome-scale genome assembly of an important medicinal plant honeysuckle. PMID:35610245
Chromosome-level genome assembly of the diploid blueberry Vaccinium darrowii provides insights into its subtropical adaptation and cuticle synthesis. PMID:35605198
Mapping and Validation of scRNA-Seq-Derived Cell-Cell Communication Networks in the Tumor Microenvironment. PMID:35572582
Qualitative Proteome-Wide Analysis Reveals the Diverse Functions of Lysine Crotonylation in Dendrobium huoshanense. PMID:35251091
Zebrafish information network, the knowledgebase for Danio rerio research. PMID:35166825
Transcriptome analysis of gibberellins and abscisic acid during the flooding response in Fokienia hodginsii. PMID:35148337
Chromosome-level genome assembly of the fully mycoheterotrophic orchid Gastrodia elata. PMID:35100375
Chromosome-level genome assembly of Bactrocera dorsalis reveals its adaptation and invasion mechanisms. PMID:35017661
Chromosome-level genome assembly of Zizania latifolia provides insights into its seed shattering and phytocassane biosynthesis. PMID:35017643
A Chromosome-Level Genome Assembly of the Pygmy Mole Cricket Xya riparia. PMID:34999819
Chromosome Genome Assembly of Cromileptes altivelis Reveals Loss of Genome Fragment in Cromileptes Compared with Epinephelus Species. PMID:34946822
Chromosome-Level Genome Assembly of the Burbot (Lota lota) Using Nanopore and Hi-C Technologies. PMID:34887901
Morus alba L. Leaves - Integration of Their Transcriptome and Metabolomics Dataset: Investigating Potential Genes Involved in Flavonoid Biosynthesis at Different Harvest Times. PMID:34868120
The Genetic Relatedness and Antimicrobial Resistance Patterns of Mastitis-Causing Staphylococcus aureus Strains Isolated from New Zealand Dairy Cattle. PMID:34822660
Genome and systems biology of Melilotus albus provides insights into coumarins biosynthesis. PMID:34717292
Global analysis of lysine acetylation in soybean leaves. PMID:34504199
Transcriptomic responses to drought stress among natural populations provide insights into local adaptation of weeping forsythia. PMID:34130656
nhKcr: a new bioinformatics tool for predicting crotonylation sites on human nonhistone proteins based on deep learning. PMID:34002774
Genome-wide analyses of the relict gull (Larus relictus): insights and evolutionary implications. PMID:33926388
The draft genome of the specialist flea beetle Altica viridicyanea (Coleoptera: Chrysomelidae). PMID:33827435
Comparative analysis of drought-responsive and -adaptive genes in Chinese wingnut (Pterocarya stenoptera C. DC). PMID:33663380
Genome survey sequencing and genetic diversity of cultivated Akebia trifoliata assessed via phenotypes and SSR markers. PMID:33400074
System, Method and Software for Calculation of a Cannabis Drug Efficiency Index for the Reduction of Inflammation. PMID:33396562
Chromosomal-Level Genome Assembly of Silver Sillago (Sillago sihama). PMID:33367716
Genome sequencing and phylogenetic analysis of allotetraploid Salix matsudana Koidz. PMID:33328474
The genome and transcriptome analysis of snake gourd provide insights into its evolution and fruit development and ripening. PMID:33328440
Chromosomal assembly of the Antarctic toothfish ( Dissostichus mawsoni) genome using third-generation DNA sequencing and Hi-C technology. PMID:33258338
Epigenetic Studies Revealed a Ghost Proteome in PC1/3 KD Macrophages under Antitumoral Resistance Induced by IL-10. PMID:33163760
The genome of Chinese flowering cherry (Cerasus serrulata) provides new insights into Cerasus species. PMID:33082971
Significant reductions in apoptosis-related proteins (HSPA6, HSPA8, ITGB3, YWHAH, and PRDX6) are involved in immune thrombocytopenia. PMID:33047245
High quality genome of Erigeron breviscapus provides a reference for herbal plants in Asteraceae. PMID:32985109
A mini foxtail millet with an Arabidopsis-like life cycle as a C4 model system. PMID:32868891
Positive Selection and Gene Expression Analyses from Salivary Glands Reveal Discrete Adaptations within the Ecologically Diverse Bat Family Phyllostomidae. PMID:32697843
SuccSite: Incorporating Amino Acid Composition and Informative k-spaced Amino Acid Pairs to Identify Protein Succinylation Sites. PMID:32592791
The New Biomarker for Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (CESC) Based on Public Database Mining. PMID:32351997
The chromosome-scale assembly of the willow genome provides insight into Salicaceae genome evolution. PMID:32257231
iMarmot: an integrative platform for comparative and functional genomics of marmots. PMID:32228437
SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics. PMID:32196115
Proteomic Analysis of Salmonella-modified Membranes Reveals Adaptations to Macrophage Hosts. PMID:32102972
Machine learning approaches and databases for prediction of drug-target interaction: a survey paper. PMID:31950972
The pomegranate (Punica granatum L.) draft genome dissects genetic divergence between soft- and hard-seeded cultivars. PMID:31549477
A chromosome-level draft genome of the grain aphid Sitobion miscanthi. PMID:31430367
Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C. PMID:31289832
Pseudomolecule-level assembly of the Chinese oil tree yellowhorn (Xanthoceras sorbifolium) genome. PMID:31241154
Evaluating measures of association for single-cell transcriptomics. PMID:30962620
Long Noncoding RNA and Protein Interactions: From Experimental Results to Computational Models Based on Network Methods. PMID:30875752
Genomic data integration systematically biases interactome mapping. PMID:30332399
Integrated systems analysis reveals conserved gene networks underlying response to spinal cord injury. PMID:30277459
Protein lysine acetylation plays a regulatory role in Bacillus subtilis multicellularity. PMID:30265683
SDADB: a functional annotation database of protein structural domains. PMID:29961821
Comparative transcriptome analysis of Haematococcus pluvialis on astaxanthin biosynthesis in response to irradiation with red or blue LED wavelength. PMID:29916185
Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology. PMID:29440116
Comparative analysis of the genomes of Stylophora pistillata and Acropora digitifera provides evidence for extensive differences between species of corals. PMID:29242500
Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium. PMID:29220487
MatureP: prediction of secreted proteins with exclusive information from their mature regions. PMID:28607462
The effects of DLEU1 gene expression in Burkitt lymphoma (BL): potential mechanism of chemoimmunotherapy resistance in BL. PMID:28427156
Transcriptome Analysis Reveals Candidate Genes Related to Color Fading of 'Red Bartlett' (Pyrus communis L.). PMID:28408914
Preprotein mature domains contain translocase targeting signals that are essential for secretion. PMID:28404644
Drug-screening and genomic analyses of HER2-positive breast cancer cell lines reveal predictors for treatment response. PMID:28356768
Systematic protein-protein interaction mapping for clinically relevant human GPCRs. PMID:28298427
Using predictive specificity to determine when gene set analysis is biologically meaningful. PMID:28204549
Global Lysine Acetylome Analysis of Desiccated Somatic Embryos of Picea asperata. PMID:28066480
Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle. PMID:28004835
The evolution of function within the Nudix homology clan. PMID:27936487
Expansion of the Gene Ontology knowledgebase and resources. PMID:27899567
The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations. PMID:27812948
Silencing of Profilin-1 suppresses cell adhesion and tumor growth via predicted alterations in integrin and Ca2+ signaling in T24M-based bladder cancer models. PMID:27683119
Functional characterization of the Arabidopsis transcription factor bZIP29 reveals its role in leaf and root development. PMID:27660483
Increased Intestinal Microbial Diversity Following Fecal Microbiota Transplant for Active Crohn's Disease. PMID:27542133
Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. PMID:27535938
Twenty-six circulating antigens and two novel diagnostic candidate molecules identified in the serum of canines with experimental acute toxoplasmosis. PMID:27357215
Network motif-based method for identifying coronary artery disease. PMID:27347046
Integrative analysis of extracellular and intracellular bladder cancer cell line proteome with transcriptome: improving coverage and validity of -omics findings. PMID:27167498
UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB. PMID:27153729
Generation and gene expression profiling of 48 transcription-factor-inducible mouse embryonic stem cell lines. PMID:27150017
Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. PMID:27126040
Standardized benchmarking in the quest for orthologs. PMID:27043882
Genome and network visualization facilitates the analyses of the effects of drugs and mutations on protein-protein and drug-protein networks. PMID:26961139
Protein functional analysis data in support of comparative proteomics of the pathogenic black yeast Exophiala dermatitidis under different temperature conditions. PMID:26958594
Ensembl comparative genomics resources. PMID:26896847
ChemProt-3.0: a global chemical biology diseases mapping. PMID:26876982
Gene Expression Variation Resolves Species and Individual Strains among Coral-Associated Dinoflagellates within the Genus Symbiodinium. PMID:26868597
KNOWLEDGE DRIVEN BINNING AND PHEWAS ANALYSIS IN MARSHFIELD PERSONALIZED MEDICINE RESEARCH PROJECT USING BIOBIN. PMID:26776191
Integration of a Decrescent Transcriptome and Metabolomics Dataset of Peucedanum praeruptorum to Investigate the CYP450 and MDR Genes Involved in Coumarins Biosynthesis and Transport. PMID:26697023
Finding New Order in Biological Functions from the Network Structure of Gene Annotations. PMID:26588252
The effect of microbial colonization on the host proteome varies by gastrointestinal location. PMID:26574685
PDBe: improved accessibility of macromolecular structure data from PDB and EMDB. PMID:26476444
Global analysis of lysine acetylation in strawberry leaves. PMID:26442052
Quantitative analysis of the murine lipid droplet-associated proteome during diet-induced hepatic steatosis. PMID:26416795
ExAtlas: An interactive online tool for meta-analysis of gene expression data. PMID:26223199
Direct Estimates of the Genomic Contributions to Blood Pressure Heritability within a Population-Based Cohort (ARIC). PMID:26162070
Better prediction of functional effects for sequence variants. PMID:26110438
Functional Operons in Secondary Metabolic Gene Clusters in Glarea lozoyensis (Fungi, Ascomycota, Leotiomycetes). PMID:26081635
Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea. PMID:25952370
MicroRNA Expression Profile of Neural Progenitor-Like Cells Derived from Rat Bone Marrow Mesenchymal Stem Cells under the Influence of IGF-1, bFGF and EGF. PMID:25938966
NeuroPep: a comprehensive resource of neuropeptides. PMID:25931458
Fasting induces anti-Warburg effect that increases respiration but reduces ATP-synthesis to promote apoptosis in colon cancer models. PMID:25909219
Fasting induces anti-Warburg effect that increases respiration but reduces ATP-synthesis to promote apoptosis in colon cancer models. PMID:25909219
ANDSystem: an Associative Network Discovery System for automated literature mining in the field of biology. PMID:25881313
Construction of an ortholog database using the semantic web technology for integrative analysis of genomic data. PMID:25875762
Exosomes released from breast cancer carcinomas stimulate cell movement. PMID:25798887
Malleable nature of mRNA-protein compositional complementarity and its functional significance. PMID:25753660
Network-assisted genetic dissection of pathogenicity and drug resistance in the opportunistic human pathogenic fungus Cryptococcus neoformans. PMID:25739925
The roles of post-translational modifications in the context of protein interaction networks. PMID:25692714
PhenomeExpress: a refined network analysis of expression datasets by inclusion of known disease phenotypes. PMID:25631385
The neXtProt knowledgebase on human proteins: current status. PMID:25593349
Global coordination in adaptation to gene rewiring. PMID:25564530
Transcriptome sequencing reveals the virulence and environmental genetic programs of Vibrio vulnificus exposed to host and estuarine conditions. PMID:25489854
Genomic characterisation of an endometrial pathogenic Escherichia coli strain reveals the acquisition of genetic elements associated with extra-intestinal pathogenicity. PMID:25481482
A chemical proteomics approach for the search of pharmacological targets of the antimalarial clinical candidate albitiazolium in Plasmodium falciparum using photocrosslinking and click chemistry. PMID:25470252
Gene Ontology Consortium: going forward. PMID:25428369
Community structure detection for overlapping modules through mathematical programming in protein interaction networks. PMID:25412367
The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. PMID:25399418
Whole Genome Sequencing Reveals a Chromosome 9p Deletion Causing DOCK8 Deficiency in an Adult Diagnosed with Hyper IgE Syndrome Who Developed Progressive Multifocal Leukoencephalopathy. PMID:25388448
The GOA database: gene Ontology annotation updates for 2015. PMID:25378336
RNA-seq analysis and de novo transcriptome assembly of Jerusalem artichoke (Helianthus tuberosus Linne). PMID:25375764
AraNet v2: an improved database of co-functional gene networks for the study of Arabidopsis thaliana and 27 other nonmodel plant species. PMID:25355510
Proteomes of host cell membranes modified by intracellular activities of Salmonella enterica. PMID:25348832
UniProt: a hub for protein information. PMID:25348405
Genetic resources for advanced biofuel production described with the Gene Ontology. PMID:25346727
A 3D cellular context for the macromolecular world. PMID:25289590
Integration of heterogeneous molecular networks to unravel gene-regulation in Mycobacterium tuberculosis. PMID:25279447
A high-resolution network model for global gene regulation in Mycobacterium tuberculosis. PMID:25232098
Proteome-wide subcellular topologies of E. coli polypeptides database (STEPdb). PMID:25210196
FSim: a novel functional similarity search algorithm and tool for discovering functionally related gene products. PMID:25184141
The use of semantic similarity measures for optimally integrating heterogeneous Gene Ontology data from large scale annotation pipelines. PMID:25147557
Protein localization analysis of essential genes in prokaryotes. PMID:25105358
A PWWP domain-containing protein targets the NuA3 acetyltransferase complex via histone H3 lysine 36 trimethylation to coordinate transcriptional elongation at coding regions. PMID:25104842
In vivo mRNA profiling of uropathogenic Escherichia coli from diverse phylogroups reveals common and group-specific gene expression profiles. PMID:25096872
Standardized description of scientific evidence using the Evidence Ontology (ECO). PMID:25052702
Hijacking of host cellular functions by an intracellular parasite, the microsporidian Anncaliia algerae. PMID:24967735
Insights into pathophysiology of dystropy through the analysis of gene networks: an example of bronchial asthma and tuberculosis. PMID:24954693
Improving functional annotation for industrial microbes: a case study with Pichia pastoris. PMID:24929579
A method for increasing expressivity of Gene Ontology annotations using a compositional approach. PMID:24885854
BioCreative-IV virtual issue. PMID:24852177
LocTree3 prediction of localization. PMID:24848019
Large-scale determination of sequence, structure, and function relationships in cytosolic glutathione transferases across the biosphere. PMID:24756107
Identification of microRNAs in the coral Stylophora pistillata. PMID:24658574
Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt. PMID:24641996
A second-generation protein-protein interaction network of Helicobacter pylori. PMID:24627523
Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data. PMID:24622611
From the environment to the host: re-wiring of the transcriptome of Pseudomonas aeruginosa from 22°C to 37°C. PMID:24587139
Analysis of the transcriptome of adult Dictyocaulus filaria and comparison with Dictyocaulus viviparus, with a focus on molecules involved in host-parasite interactions. PMID:24487001
Predicting human protein subcellular locations by the ensemble of multiple predictors via protein-protein interaction network with edge clustering coefficients. PMID:24466278
Low frequency variants, collapsed based on biological knowledge, uncover complexity of population stratification in 1000 genomes project data. PMID:24385916
PDBe: Protein Data Bank in Europe. PMID:24288376
Proteomic analysis of membrane proteins of vero cells: exploration of potential proteins responsible for virus entry. PMID:24286161
Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis. PMID:24270792
PANADA: protein association network annotation, determination and analysis. PMID:24265686
Growth rate-coordinated transcriptome reorganization in bacteria. PMID:24252326
COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia. PMID:24214998
The functional therapeutic chemical classification system. PMID:24177719
Quantification of the impact of PSI:Biology according to the annotations of the determined structures. PMID:24139526
Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals. PMID:24119094
Identification and characterization of long non-coding RNAs related to mouse embryonic brain development from available transcriptomic data. PMID:23967161
BGDB: a database of bivalent genes. PMID:23894186
TCW: transcriptome computational workbench. PMID:23874959
Structural disorder provides increased adaptability for vesicle trafficking pathways. PMID:23874186
A novel function prediction approach using protein overlap networks. PMID:23866986
Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution. PMID:23829427
BioBin: a bioinformatics tool for automating the binning of rare variants using publicly available biological knowledge. PMID:23819467
Biases in the experimental annotations of protein function and their effect on our understanding of protein function space. PMID:23737737
A task-based approach for Gene Ontology evaluation. PMID:23734599
PlantLoc: an accurate web server for predicting plant protein subcellular localization by substantiality motif. PMID:23729470
Characterizing the state of the art in the computational assignment of gene function: lessons from the first critical assessment of functional annotation (CAFA). PMID:23630983
The challenge of increasing Pfam coverage of the human proteome. PMID:23603847
Identification and analysis of red sea mangrove (Avicennia marina) microRNAs by high-throughput sequencing and their association with stress responses. PMID:23593307
Discovery-2: an interactive resource for the rational selection and comparison of putative drug target proteins in malaria. PMID:23537208
Protein function prediction using domain families. PMID:23514456
hTERT extends the life of human fibroblasts without compromising type I interferon signaling. PMID:23472163
Expression divergence between Escherichia coli and Salmonella enterica serovar Typhimurium reflects their lifestyles. PMID:23427276
Using BioBin to explore rare variant population stratification. PMID:23424138
Identification and analysis of a novel dimerization domain shared by various members of c-Jun N-terminal kinase (JNK) scaffold proteins. PMID:23341463
Disruption of the S41 peptidase gene in mycoplasma mycoides capri impacts proteome profile, H(2)O(2) production, and sensitivity to heat shock. PMID:23300541
Adding protein context to the human protein-protein interaction network to reveal meaningful interactions. PMID:23300433
The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes. PMID:23209799
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. PMID:23203869
EcoGene 3.0. PMID:23197660
HAMAP in 2013, new developments in the protein family classification and annotation system. PMID:23193261
ChemProt-2.0: visual navigation in a disease chemical biology database. PMID:23185041
The draft genome of sweet orange (Citrus sinensis). PMID:23179022
The mouse genome database: genotypes, phenotypes, and models of human disease. PMID:23175610
Update on activities at the Universal Protein Resource (UniProt) in 2013. PMID:23161681
Genome reduction promotes increase in protein functional complexity in bacteria. PMID:23114380
SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models. PMID:23110173
BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions. PMID:23087378
Sequencing and analysis of full-length cDNAs, 5'-ESTs and 3'-ESTs from a cartilaginous fish, the elephant shark (Callorhinchus milii). PMID:23056606
The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data. PMID:22961259
Endosomal crosstalk: meeting points for signaling pathways. PMID:22796207
CombFunc: predicting protein function using heterogeneous data sources. PMID:22641853
The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. PMID:22144685 - http://dx.doi.org/10.1093/nar/gku1113
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annotation
metasource: Fairsharing.org
version: FAIRsharing.org: GOA; Gene Ontology Annotation Database; DOI: https://doi.org/10.25504/FAIRsharing.7zffgc; Last edited: March 9, 2021, 4:03 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
gene
metasource: Fairsharing.org
version: FAIRsharing.org: GOA; Gene Ontology Annotation Database; DOI: https://doi.org/10.25504/FAIRsharing.7zffgc; Last edited: March 9, 2021, 4:03 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
gene ontology enrichment
metasource: Fairsharing.org
version: FAIRsharing.org: GOA; Gene Ontology Annotation Database; DOI: https://doi.org/10.25504/FAIRsharing.7zffgc; Last edited: March 9, 2021, 4:03 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: GOA; Gene Ontology Annotation Database; DOI: https://doi.org/10.25504/FAIRsharing.7zffgc; Last edited: March 9, 2021, 4:03 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein-containing complex
metasource: Fairsharing.org
version: FAIRsharing.org: GOA; Gene Ontology Annotation Database; DOI: https://doi.org/10.25504/FAIRsharing.7zffgc; Last edited: March 9, 2021, 4:03 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: GOA; Gene Ontology Annotation Database; DOI: https://doi.org/10.25504/FAIRsharing.7zffgc; Last edited: March 9, 2021, 4:03 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
genomics databases (non-vertebrate)
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
genome annotation terms, ontologies and nomenclature
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
model organisms
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
ontology and terminology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
data submission, annotation and curation
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
plant biology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
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annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: GOA; Gene Ontology Annotation Database; DOI: https://doi.org/10.25504/FAIRsharing.7zffgc; Last edited: March 9, 2021, 4:03 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
gene
metasource: Fairsharing.orgversion: FAIRsharing.org: GOA; Gene Ontology Annotation Database; DOI: https://doi.org/10.25504/FAIRsharing.7zffgc; Last edited: March 9, 2021, 4:03 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
gene ontology enrichment
metasource: Fairsharing.orgversion: FAIRsharing.org: GOA; Gene Ontology Annotation Database; DOI: https://doi.org/10.25504/FAIRsharing.7zffgc; Last edited: March 9, 2021, 4:03 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: GOA; Gene Ontology Annotation Database; DOI: https://doi.org/10.25504/FAIRsharing.7zffgc; Last edited: March 9, 2021, 4:03 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
protein-containing complex
metasource: Fairsharing.orgversion: FAIRsharing.org: GOA; Gene Ontology Annotation Database; DOI: https://doi.org/10.25504/FAIRsharing.7zffgc; Last edited: March 9, 2021, 4:03 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
ribonucleic acid
metasource: Fairsharing.orgversion: FAIRsharing.org: GOA; Gene Ontology Annotation Database; DOI: https://doi.org/10.25504/FAIRsharing.7zffgc; Last edited: March 9, 2021, 4:03 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
genomics databases (non-vertebrate)
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
genome annotation terms, ontologies and nomenclature
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
model organisms
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.116598
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.116598
ontology and terminology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.116598
data submission, annotation and curation
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.116598
plant biology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:13.116598
gene gene ontology enrichment protein protein-containing complex rna genomics genome annotation terms, ontologies and nomenclature model organisms ontology and terminology data submission, annotation and curation plant biology
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