Published in BMC Bioinformatics on July 22, 2008
Ensembl 2009. Nucleic Acids Res (2008) 25.38
InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res (2011) 13.45
The SWISS-MODEL Repository and associated resources. Nucleic Acids Res (2008) 11.61
Rfam: updates to the RNA families database. Nucleic Acids Res (2008) 11.61
BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol (2009) 11.17
The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics (2009) 10.30
The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res (2011) 6.88
Ensembl Genomes: extending Ensembl across the taxonomic space. Nucleic Acids Res (2009) 5.09
VectorBase: a data resource for invertebrate vector genomics. Nucleic Acids Res (2008) 3.73
Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. Nucleic Acids Res (2011) 2.87
VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics. Nucleic Acids Res (2011) 2.45
Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases. BMC Med Genomics (2009) 2.36
The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics. BMC Bioinformatics (2013) 2.14
Dalliance: interactive genome viewing on the web. Bioinformatics (2011) 2.07
The Protein Model Portal. J Struct Funct Genomics (2008) 2.01
EMMA--mouse mutant resources for the international scientific community. Nucleic Acids Res (2009) 1.75
The InterPro BioMart: federated query and web service access to the InterPro Resource. Database (Oxford) (2011) 1.75
Visualizing next-generation sequencing data with JBrowse. Brief Bioinform (2012) 1.70
Dasty3, a WEB framework for DAS. Bioinformatics (2011) 1.67
DASMI: exchanging, annotating and assessing molecular interaction data. Bioinformatics (2009) 1.64
GenomeRNAi: a database for cell-based and in vivo RNAi phenotypes, 2013 update. Nucleic Acids Res (2012) 1.63
Next generation tools for genomic data generation, distribution, and visualization. BMC Bioinformatics (2010) 1.56
The Ensembl REST API: Ensembl Data for Any Language. Bioinformatics (2014) 1.43
Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research. J Proteomics (2010) 1.35
Choosing a genome browser for a Model Organism Database: surveying the maize community. Database (Oxford) (2010) 1.07
Taking the next step: building an Arabidopsis information portal. Plant Cell (2012) 1.06
Relax with CouchDB--into the non-relational DBMS era of bioinformatics. Genomics (2012) 1.02
Annotations for all by all - the BioSapiens network. Genome Biol (2009) 1.00
Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information. BMC Bioinformatics (2014) 0.98
AnnoTrack--a tracking system for genome annotation. BMC Genomics (2010) 0.98
DAS writeback: a collaborative annotation system. BMC Bioinformatics (2011) 0.95
VarioML framework for comprehensive variation data representation and exchange. BMC Bioinformatics (2012) 0.95
A web-based bioinformatics interface applied to the GENOSOJA Project: Databases and pipelines. Genet Mol Biol (2012) 0.95
openSNP--a crowdsourced web resource for personal genomics. PLoS One (2014) 0.95
myKaryoView: a light-weight client for visualization of genomic data. PLoS One (2011) 0.94
FeatureViewer, a BioJS component for visualization of position-based annotations in protein sequences. F1000Res (2014) 0.93
A quick guide to large-scale genomic data mining. PLoS Comput Biol (2010) 0.93
The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI. Nucleic Acids Res (2015) 0.91
Genome and network visualization facilitates the analyses of the effects of drugs and mutations on protein-protein and drug-protein networks. BMC Bioinformatics (2016) 0.90
pubmed2ensembl: a resource for mining the biological literature on genes. PLoS One (2011) 0.89
easyDAS: automatic creation of DAS servers. BMC Bioinformatics (2011) 0.88
Teaching the fundamentals of biological data integration using classroom games. PLoS Comput Biol (2012) 0.87
Annotation and visualization of endogenous retroviral sequences using the Distributed Annotation System (DAS) and eBioX. BMC Bioinformatics (2009) 0.85
GenExp: an interactive web-based genomic DAS client with client-side data rendering. PLoS One (2011) 0.82
Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases. Nucleic Acids Res (2011) 0.79
Personalized Oncology Suite: integrating next-generation sequencing data and whole-slide bioimages. BMC Bioinformatics (2014) 0.78
FISH Oracle 2: a web server for integrative visualization of genomic data in cancer research. J Clin Bioinforma (2014) 0.78
Review of the selected proceedings of the Fifth International Workshop on Data Integration in the Life Sciences 2008. BMC Bioinformatics (2008) 0.77
Current trends and new challenges of databases and web applications for systems driven biological research. Front Physiol (2010) 0.77
On an infrastructure to support sharing and aggregating pre- and post-publication systems biology research data. Syst Synth Biol (2012) 0.75
DASMIweb: online integration, analysis and assessment of distributed protein interaction data. Nucleic Acids Res (2009) 0.75
MyDas, an extensible Java DAS server. PLoS One (2012) 0.75
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
The distributed annotation system. BMC Bioinformatics (2001) 42.98
The Pfam protein families database. Nucleic Acids Res (2007) 30.53
Ensembl 2008. Nucleic Acids Res (2007) 20.67
The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol (2005) 18.20
Integrating sequence and structural biology with DAS. BMC Bioinformatics (2007) 5.12
Adding some SPICE to DAS. Bioinformatics (2005) 4.62
ProServer: a simple, extensible Perl DAS server. Bioinformatics (2007) 4.16
WormBase: new content and better access. Nucleic Acids Res (2006) 4.01
Dasty and UniProt DAS: a perfect pair for protein feature visualization. Bioinformatics (2005) 2.74
Integrating protein annotation resources through the Distributed Annotation System. Nucleic Acids Res (2005) 2.21
Integrating biological data through the genome. Hum Mol Genet (2006) 2.12
Integrating electron microscopy information into existing Distributed Annotation Systems. J Struct Biol (2007) 1.69
Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res (2008) 151.16
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
The Bioperl toolkit: Perl modules for the life sciences. Genome Res (2002) 58.63
The Pfam protein families database. Nucleic Acids Res (2004) 56.46
The Pfam protein families database. Nucleic Acids Res (2002) 51.34
Patterns of somatic mutation in human cancer genomes. Nature (2007) 38.41
A census of human cancer genes. Nat Rev Cancer (2004) 36.20
The Pfam protein families database. Nucleic Acids Res (2011) 33.46
The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol (2008) 31.04
InterPro: the integrative protein signature database. Nucleic Acids Res (2008) 25.07
Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics (2005) 24.54
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol (2008) 21.72
The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36
International network of cancer genome projects. Nature (2010) 20.35
A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature (2009) 18.39
SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res (2002) 18.11
EnsMart: a generic system for fast and flexible access to biological data. Genome Res (2004) 17.64
Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21
Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res (2008) 15.69
SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res (2004) 15.21
A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat Genet (2006) 15.14
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res (2009) 14.90
Ensembl 2011. Nucleic Acids Res (2010) 14.68
The International Protein Index: an integrated database for proteomics experiments. Proteomics (2004) 14.67
Ensembl 2012. Nucleic Acids Res (2011) 14.55
InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res (2011) 13.45
Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res (2007) 13.44
Reactome: a knowledge base of biologic pathways and processes. Genome Biol (2007) 13.36
The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res (2012) 13.14
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol (2008) 12.96
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res (2008) 12.72
Ensembl 2014. Nucleic Acids Res (2013) 12.62
Prepublication data sharing. Nature (2009) 12.24
Ensembl 2013. Nucleic Acids Res (2012) 11.70
Rfam: updates to the RNA families database. Nucleic Acids Res (2008) 11.61
A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol (2004) 11.42
Optimized design and assessment of whole genome tiling arrays. Bioinformatics (2007) 11.38
Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res (2010) 11.23
Ensembl's 10th year. Nucleic Acids Res (2009) 10.82
Mouse genomic variation and its effect on phenotypes and gene regulation. Nature (2011) 10.66
An overview of Ensembl. Genome Res (2004) 10.35
The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol (2007) 10.24
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics (2012) 9.68
Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science (2002) 9.43
Genome sequence of Aedes aegypti, a major arbovirus vector. Science (2007) 9.19
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics (2006) 8.68
A high-resolution map of human evolutionary constraint using 29 mammals. Nature (2011) 8.67
The Reactome pathway knowledgebase. Nucleic Acids Res (2013) 8.56
The zebrafish reference genome sequence and its relationship to the human genome. Nature (2013) 8.52
The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24
Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet (2009) 8.11
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol (2007) 8.03
Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res (2002) 7.89
Clinical presentation, etiology, and outcome of infective endocarditis in the 21st century: the International Collaboration on Endocarditis-Prospective Cohort Study. Arch Intern Med (2009) 7.82
PRIDE: the proteomics identifications database. Proteomics (2005) 7.52
The IntAct molecular interaction database in 2012. Nucleic Acids Res (2011) 7.49
Staphylococcus aureus endocarditis: a consequence of medical progress. JAMA (2005) 7.41
Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Res (2008) 7.35
The Ensembl core software libraries. Genome Res (2004) 7.30
The HGNC Database in 2008: a resource for the human genome. Nucleic Acids Res (2007) 7.29
Calling on a million minds for community annotation in WikiProteins. Genome Biol (2008) 7.11
EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol (2006) 7.06
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res (2007) 7.05
Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Res (2010) 6.58
The European Nucleotide Archive. Nucleic Acids Res (2010) 6.48
Challenges and standards in integrating surveys of structural variation. Nat Genet (2007) 6.05
Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database (Oxford) (2011) 6.04
Heritable individual-specific and allele-specific chromatin signatures in humans. Science (2010) 5.94
Genome analysis of the platypus reveals unique signatures of evolution. Nature (2008) 5.74
The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Res (2007) 5.67
Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation. PLoS One (2011) 5.64
A guide to the Proteomics Identifications Database proteomics data repository. Proteomics (2009) 5.63
Efficient storage of high throughput DNA sequencing data using reference-based compression. Genome Res (2011) 5.60
Immunity-related genes and gene families in Anopheles gambiae. Science (2002) 5.47
Computing topological parameters of biological networks. Bioinformatics (2007) 5.36