Published in Methods Mol Biol on January 01, 2007
PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res (2012) 8.54
The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet (2010) 8.07
Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation. BMC Bioinformatics (2009) 2.74
A beginner's guide to eukaryotic genome annotation. Nat Rev Genet (2012) 2.67
A computational genomics pipeline for prokaryotic sequencing projects. Bioinformatics (2010) 2.63
Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat Biotechnol (2012) 2.45
The Protein Feature Ontology: a tool for the unification of protein feature annotations. Bioinformatics (2008) 2.33
Molecular genetics of addiction and related heritable phenotypes: genome-wide association approaches identify "connectivity constellation" and drug target genes with pleiotropic effects. Ann N Y Acad Sci (2008) 1.69
Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling. Microbiome (2013) 1.69
Identification and characterization of novel human tissue-specific RFX transcription factors. BMC Evol Biol (2008) 1.62
ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii. BMC Genomics (2009) 1.58
The 2008 update of the Aspergillus nidulans genome annotation: a community effort. Fungal Genet Biol (2008) 1.56
Comparative genome analysis of Trichophyton rubrum and related dermatophytes reveals candidate genes involved in infection. MBio (2012) 1.55
The automatic annotation of bacterial genomes. Brief Bioinform (2012) 1.50
De novo transcriptome sequence assembly and analysis of RNA silencing genes of Nicotiana benthamiana. PLoS One (2013) 1.48
Architecture and gene repertoire of the flexible genome of the extreme acidophile Acidithiobacillus caldus. PLoS One (2013) 1.47
ESG: extended similarity group method for automated protein function prediction. Bioinformatics (2009) 1.46
Genome sequence of the pathogenic intestinal spirochete brachyspira hyodysenteriae reveals adaptations to its lifestyle in the porcine large intestine. PLoS One (2009) 1.41
Generation and analysis of blueberry transcriptome sequences from leaves, developing fruit, and flower buds from cold acclimation through deacclimation. BMC Plant Biol (2012) 1.41
Genomic analysis of the multidrug-resistant Acinetobacter baumannii strain MDR-ZJ06 widely spread in China. Antimicrob Agents Chemother (2011) 1.40
miRNA Repertoires of Demosponges Stylissa carteri and Xestospongia testudinaria. PLoS One (2016) 1.38
Rapid annotation of anonymous sequences from genome projects using semantic similarities and a weighting scheme in gene ontology. PLoS One (2009) 1.26
The draft genome sequence of European pear (Pyrus communis L. 'Bartlett'). PLoS One (2014) 1.23
ANNIE: integrated de novo protein sequence annotation. Nucleic Acids Res (2009) 1.19
New assembly, reannotation and analysis of the Entamoeba histolytica genome reveal new genomic features and protein content information. PLoS Negl Trop Dis (2010) 1.17
Genome annotation and intraviral interactome for the Streptococcus pneumoniae virulent phage Dp-1. J Bacteriol (2010) 1.12
Real-time ligand binding pocket database search using local surface descriptors. Proteins (2010) 1.12
Discovery and annotation of small proteins using genomics, proteomics, and computational approaches. Genome Res (2011) 1.06
Comparative genomics reveals insight into virulence strategies of plant pathogenic oomycetes. PLoS One (2013) 1.05
Small RNA and transcriptome deep sequencing proffers insight into floral gene regulation in Rosa cultivars. BMC Genomics (2012) 1.03
Phylum-wide comparative genomics unravel the diversity of secondary metabolism in Cyanobacteria. BMC Genomics (2014) 1.02
OKCAM: an ontology-based, human-centered knowledgebase for cell adhesion molecules. Nucleic Acids Res (2008) 1.01
Genome sequence of the Asian Tiger mosquito, Aedes albopictus, reveals insights into its biology, genetics, and evolution. Proc Natl Acad Sci U S A (2015) 1.01
Evolutionary history and stress regulation of the lectin superfamily in higher plants. BMC Evol Biol (2010) 0.98
EnzML: multi-label prediction of enzyme classes using InterPro signatures. BMC Bioinformatics (2012) 0.97
Systematic analysis of GT factor family of rice reveals a novel subfamily involved in stress responses. Mol Genet Genomics (2009) 0.97
Candidate genes that may be responsible for the unusual resistances exhibited by Bacillus pumilus SAFR-032 spores. PLoS One (2013) 0.96
An expression database for roots of the model legume Medicago truncatula under salt stress. BMC Genomics (2009) 0.95
Comparative genomics of Helicobacter pylori and the human-derived Helicobacter bizzozeronii CIII-1 strain reveal the molecular basis of the zoonotic nature of non-pylori gastric Helicobacter infections in humans. BMC Genomics (2011) 0.95
Genome duplication and mutations in ACE2 cause multicellular, fast-sedimenting phenotypes in evolved Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2013) 0.93
Comparative analysis of serine/arginine-rich proteins across 27 eukaryotes: insights into sub-family classification and extent of alternative splicing. PLoS One (2011) 0.92
Recombinant human cytomegalovirus (HCMV) RL13 binds human immunoglobulin G Fc. PLoS One (2012) 0.92
Meta-analysis and genome-wide interpretation of genetic susceptibility to drug addiction. BMC Genomics (2011) 0.91
Identification of differentially expressed genes of Trichinella spiralis larvae after exposure to host intestine milieu. PLoS One (2013) 0.91
LRRML: a conformational database and an XML description of leucine-rich repeats (LRRs). BMC Struct Biol (2008) 0.91
Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals. BMC Genomics (2013) 0.91
From sequence to enzyme mechanism using multi-label machine learning. BMC Bioinformatics (2014) 0.90
Prediction of enzyme function by combining sequence similarity and protein interactions. BMC Bioinformatics (2008) 0.90
Genomic analysis reveals multiple [FeFe] hydrogenases and hydrogen sensors encoded by treponemes from the H(2)-rich termite gut. Microb Ecol (2011) 0.89
Revisiting the missing protein-coding gene catalog of the domestic dog. BMC Genomics (2009) 0.89
Neisseria Base: a comparative genomics database for Neisseria meningitidis. Database (Oxford) (2011) 0.88
Expansion mechanisms and functional annotations of hypothetical genes in the rice genome. Plant Physiol (2009) 0.87
Draft genome of a commonly misdiagnosed multidrug resistant pathogen Candida auris. BMC Genomics (2015) 0.87
Transcriptome analysis of Taenia solium cysticerci using Open Reading Frame ESTs (ORESTES). Parasit Vectors (2009) 0.87
Identification and characterization of potential therapeutic candidates in emerging human pathogen Mycobacterium abscessus: a novel hierarchical in silico approach. PLoS One (2013) 0.87
Genome-wide characterization and analysis of bZIP transcription factor gene family related to abiotic stress in cassava. Sci Rep (2016) 0.87
Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host. Nucleic Acids Res (2015) 0.86
Analysis of Babesia bovis infection-induced gene expression changes in larvae from the cattle tick, Rhipicephalus (Boophilus) microplus. Parasit Vectors (2012) 0.86
Phylogenetic Profiles Reveal Structural and Functional Determinants of Lipid-binding. J Proteomics Bioinform (2009) 0.86
Acquisition through horizontal gene transfer of plasmid pSMA198 by Streptococcus macedonicus ACA-DC 198 points towards the dairy origin of the species. PLoS One (2015) 0.86
Evidence of probabilistic behaviour in protein interaction networks. BMC Syst Biol (2008) 0.86
Developmental regulation of ecdysone receptor (EcR) and EcR-controlled gene expression during pharate-adult development of honeybees (Apis mellifera). Front Genet (2014) 0.86
MorusDB: a resource for mulberry genomics and genome biology. Database (Oxford) (2014) 0.86
The Scutellaria baicalensis R2R3-MYB transcription factors modulates flavonoid biosynthesis by regulating GA metabolism in transgenic tobacco plants. PLoS One (2013) 0.85
Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP. BMC Bioinformatics (2010) 0.85
Analysis of the canine brain transcriptome with an emphasis on the hypothalamus and cerebral cortex. Mamm Genome (2013) 0.85
Insights into the genome sequence of a free-living Kinetoplastid: Bodo saltans (Kinetoplastida: Euglenozoa). BMC Genomics (2008) 0.85
PoGO: Prediction of Gene Ontology terms for fungal proteins. BMC Bioinformatics (2010) 0.85
Gut transcriptome of replete adult female cattle ticks, Rhipicephalus (Boophilus) microplus, feeding upon a Babesia bovis-infected bovine host. Parasitol Res (2013) 0.85
Transcriptome analysis of the Cryptocaryon irritans tomont stage identifies potential genes for the detection and control of cryptocaryonosis. BMC Genomics (2010) 0.84
Identification of microRNAs in the coral Stylophora pistillata. PLoS One (2014) 0.83
Genome comparison of human and non-human malaria parasites reveals species subset-specific genes potentially linked to human disease. PLoS Comput Biol (2011) 0.83
Diversity and dispersal of a ubiquitous protein family: acyl-CoA dehydrogenases. Nucleic Acids Res (2009) 0.83
The box H/ACA snoRNP assembly factor Shq1p is a chaperone protein homologous to Hsp90 cochaperones that binds to the Cbf5p enzyme. J Mol Biol (2009) 0.83
The Levels of a Universally Conserved tRNA Modification Regulate Cell Growth. J Biol Chem (2015) 0.82
Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species. Genome Biol (2014) 0.82
Origins of Myc proteins--using intrinsic protein disorder to trace distant relatives. PLoS One (2013) 0.82
TollML: a database of toll-like receptor structural motifs. J Mol Model (2010) 0.82
Evidence for a novel gene associated with human influenza A viruses. Virol J (2009) 0.81
Beyond genomic variation--comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage. BMC Genomics (2014) 0.81
TRUNCATULIX--a data warehouse for the legume community. BMC Plant Biol (2009) 0.80
The Eimeria transcript DB: an integrated resource for annotated transcripts of protozoan parasites of the genus Eimeria. Database (Oxford) (2013) 0.80
Vaccinia virus G8R protein: a structural ortholog of proliferating cell nuclear antigen (PCNA). PLoS One (2009) 0.79
Tree shrew database (TreeshrewDB): a genomic knowledge base for the Chinese tree shrew. Sci Rep (2014) 0.79
Genome-Wide Identification and Expression Analyses of Aquaporin Gene Family during Development and Abiotic Stress in Banana. Int J Mol Sci (2015) 0.79
Short toxin-like proteins attack the defense line of innate immunity. Toxins (Basel) (2013) 0.79
Representative transcript sets for evaluating a translational initiation sites predictor. BMC Bioinformatics (2009) 0.78
Meta4: a web application for sharing and annotating metagenomic gene predictions using web services. Front Genet (2013) 0.78
Bacterial clade with the ribosomal RNA operon on a small plasmid rather than the chromosome. Proc Natl Acad Sci U S A (2015) 0.78
High-throughput sequencing and de novo transcriptome assembly of Swertia japonica to identify genes involved in the biosynthesis of therapeutic metabolites. Plant Cell Rep (2016) 0.77
A "footprint" of plant carbon fixation cycle functions during the development of a heterotrophic fungus. Sci Rep (2015) 0.77
Transcriptome analysis elucidates key developmental components of bryozoan lophophore development. Sci Rep (2014) 0.77
bex-db: Bioinformatics workbench for comprehensive analysis of barley-expressed genes. Breed Sci (2013) 0.77
Expansion of tandem repeats in sea anemone Nematostella vectensis proteome: A source for gene novelty? BMC Genomics (2009) 0.77
The Chloroplast Genome of Utricularia reniformis Sheds Light on the Evolution of the ndh Gene Complex of Terrestrial Carnivorous Plants from the Lentibulariaceae Family. PLoS One (2016) 0.76
MediPlEx - a tool to combine in silico & experimental gene expression profiles of the model legume Medicago truncatula. BMC Res Notes (2010) 0.76
Enzyme informatics. Curr Top Med Chem (2012) 0.76
Transcriptome and proteome dynamics in larvae of the barnacle Balanus Amphitrite from the Red Sea. BMC Genomics (2015) 0.76
The ERF transcription factor family in cassava: genome-wide characterization and expression analyses against drought stress. Sci Rep (2016) 0.76
Detection of an Escherichia coli ST167 strain with two tandem copies of blaNDM-1 encoded in the chromosome. J Clin Microbiol (2016) 0.76
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res (2003) 52.80
InterPro: the integrative protein signature database. Nucleic Acids Res (2008) 25.07
The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res (2003) 24.72
The Universal Protein Resource (UniProt). Nucleic Acids Res (2005) 23.66
The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res (2006) 22.70
The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res (2004) 18.75
InterPro, progress and status in 2005. Nucleic Acids Res (2005) 17.53
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol (2004) 16.08
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics (2009) 15.08
IntAct: an open source molecular interaction database. Nucleic Acids Res (2004) 15.02
The International Protein Index: an integrated database for proteomics experiments. Proteomics (2004) 14.67
InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res (2011) 13.45
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol (2008) 12.96
The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Res (2003) 12.81
New developments in the InterPro database. Nucleic Acids Res (2007) 12.49
Prepublication data sharing. Nature (2009) 12.24
UniProt archive. Bioinformatics (2004) 11.92
A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol (2004) 11.42
The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol (2007) 10.24
The GOA database in 2009--an integrated Gene Ontology Annotation resource. Nucleic Acids Res (2008) 10.21
EMBL Nucleotide Sequence Database in 2006. Nucleic Acids Res (2006) 9.72
The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics (2006) 8.68
The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol (2007) 8.03
PRIDE: the proteomics identifications database. Proteomics (2005) 7.52
The EMBL Nucleotide Sequence Database. Nucleic Acids Res (2005) 7.18
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
The EMBL Nucleotide Sequence Database. Nucleic Acids Res (2004) 6.72
An evaluation of GO annotation retrieval for BioCreAtIvE and GOA. BMC Bioinformatics (2005) 6.58
The EBI SRS server-new features. Bioinformatics (2002) 6.38
The UniProt-GO Annotation database in 2011. Nucleic Acids Res (2011) 5.19
EMBL Nucleotide Sequence Database: developments in 2005. Nucleic Acids Res (2006) 5.13
High-quality protein knowledge resource: SWISS-PROT and TrEMBL. Brief Bioinform (2002) 4.95
UniProtJAPI: a remote API for accessing UniProt data. Bioinformatics (2008) 4.88
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. Nucleic Acids Res (2008) 4.73
IntEnz, the integrated relational enzyme database. Nucleic Acids Res (2004) 4.65
The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res (2007) 4.23
PRIDE: a public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res (2006) 4.19
Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. Nucleic Acids Res (2005) 4.15
The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases. BMC Bioinformatics (2007) 3.97
Evidence standards in experimental and inferential INSDC Third Party Annotation data. OMICS (2006) 3.97
The Gene Ontology Annotation (GOA) Database--an integrated resource of GO annotations to the UniProt Knowledgebase. In Silico Biol (2003) 3.86
Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database. Nucleic Acids Res (2007) 3.84
The proteomics standards initiative. Proteomics (2003) 3.78
Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles. J Proteome Res (2009) 3.77
The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible. Expert Rev Proteomics (2006) 3.74
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nat Biotechnol (2007) 3.55
UniSave: the UniProtKB sequence/annotation version database. Bioinformatics (2006) 3.38
QuickGO: a web-based tool for Gene Ontology searching. Bioinformatics (2009) 3.36
The European Bioinformatics Institute's data resources. Nucleic Acids Res (2003) 3.34
The Proteome Analysis database: a tool for the in silico analysis of whole proteomes. Nucleic Acids Res (2003) 3.29
Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Res (2007) 3.13
Research capacity. Enabling the genomic revolution in Africa. Science (2014) 3.05
The EBI SRS server--recent developments. Bioinformatics (2002) 3.04
The Integr8 project--a resource for genomic and proteomic data. In Silico Biol (2005) 3.03
Applications of InterPro in protein annotation and genome analysis. Brief Bioinform (2002) 3.03
The predictive power of the CluSTr database. Bioinformatics (2005) 2.85
Clinical proteomics: A need to define the field and to begin to set adequate standards. Proteomics Clin Appl (2007) 2.84
Dasty and UniProt DAS: a perfect pair for protein feature visualization. Bioinformatics (2005) 2.74
ASTD: The Alternative Splicing and Transcript Diversity database. Genomics (2008) 2.72
InterPro: an integrated documentation resource for protein families, domains and functional sites. Brief Bioinform (2002) 2.66
Increase of functional diversity by alternative splicing. Trends Genet (2003) 2.59
The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI). OMICS (2006) 2.38
The use of common ontologies and controlled vocabularies to enable data exchange and deposition for complex proteomic experiments. Pac Symp Biocomput (2005) 2.29
The Gene Ontology Annotation (GOA) Project--Application of GO in SWISS-PROT, TrEMBL and InterPro. Comp Funct Genomics (2003) 1.93
MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data. Genome Biol (2008) 1.76
Finding one's way in proteomics: a protein species nomenclature. Chem Cent J (2009) 1.75
Cardiovascular GO annotation initiative year 1 report: why cardiovascular GO? Proteomics (2008) 1.72
Common interchange standards for proteomics data: Public availability of tools and schema. Proteomics (2004) 1.68
Dasty3, a WEB framework for DAS. Bioinformatics (2011) 1.67
GOAnnotator: linking protein GO annotations to evidence text. J Biomed Discov Collab (2006) 1.66
Recommendations for biomarker identification and qualification in clinical proteomics. Sci Transl Med (2010) 1.59
Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Database (Oxford) (2012) 1.56
Further steps towards data standardisation: the Proteomic Standards Initiative HUPO 3(rd) annual congress, Beijing 25-27(th) October, 2004. Proteomics (2005) 1.54
Systematic comparison of the human saliva and plasma proteomes. Proteomics Clin Appl (2009) 1.51
Systematic characterization of the murine mitochondrial proteome using functionally validated cardiac mitochondria. Proteomics (2008) 1.51
Use of Gene Ontology Annotation to understand the peroxisome proteome in humans. Database (Oxford) (2013) 1.48
Best practices in bioinformatics training for life scientists. Brief Bioinform (2013) 1.45
The InterPro database and tools for protein domain analysis. Curr Protoc Bioinformatics (2008) 1.43
Phosphoproteome analysis reveals regulatory sites in major pathways of cardiac mitochondria. Mol Cell Proteomics (2010) 1.41
Analyzing large-scale proteomics projects with latent semantic indexing. J Proteome Res (2007) 1.39
Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB "complete proteome" sets. Proteomics (2011) 1.31
The importance of uniformity in reporting protein-function data. Trends Biochem Sci (2005) 1.27
The speciation of the proteome. Chem Cent J (2008) 1.21
Further steps in standardisation. Report of the second annual Proteomics Standards Initiative Spring Workshop (Siena, Italy 17-20th April 2005). Proteomics (2005) 1.20
Progress in Establishing Common Standards for Exchanging Proteomics Data: The Second Meeting of the HUPO Proteomics Standards Initiative. Comp Funct Genomics (2003) 1.18
The European Bioinformatics Institute's data resources 2014. Nucleic Acids Res (2013) 1.17
The EMBL Nucleotide Sequence and Genome Reviews Databases. Methods Mol Biol (2007) 1.17
Altered proteome biology of cardiac mitochondria under stress conditions. J Proteome Res (2008) 1.16
From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems. Bioinformatics (2011) 1.15