Published in Nucleic Acids Res on December 01, 2007
The Pfam protein families database. Nucleic Acids Res (2009) 37.98
Ensembl 2009. Nucleic Acids Res (2008) 25.38
GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol (2010) 16.72
Ensembl 2014. Nucleic Acids Res (2013) 12.62
Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res (2011) 11.32
genenames.org: the HGNC resources in 2011. Nucleic Acids Res (2010) 5.77
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res (2011) 3.94
Ensembl 2016. Nucleic Acids Res (2015) 3.61
The UCSC genome browser and associated tools. Brief Bioinform (2012) 3.29
FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data. Genome Biol (2010) 2.79
Parameters for accurate genome alignment. BMC Bioinformatics (2010) 2.78
Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nat Genet (2013) 2.76
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs. Nucleic Acids Res (2012) 2.68
eHive: an artificial intelligence workflow system for genomic analysis. BMC Bioinformatics (2010) 2.52
Conservation of an RNA regulatory map between Drosophila and mammals. Genome Res (2010) 2.43
Berkeley PHOG: PhyloFacts orthology group prediction web server. Nucleic Acids Res (2009) 2.35
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. Nucleic Acids Res (2010) 2.22
De novo analysis of transcriptome dynamics in the migratory locust during the development of phase traits. PLoS One (2010) 2.19
modMine: flexible access to modENCODE data. Nucleic Acids Res (2011) 2.18
Computational methods for Gene Orthology inference. Brief Bioinform (2011) 2.16
OrthoList: a compendium of C. elegans genes with human orthologs. PLoS One (2011) 2.05
OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011. Nucleic Acids Res (2010) 2.02
Databases of homologous gene families for comparative genomics. BMC Bioinformatics (2009) 2.01
YeastMine--an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit. Database (Oxford) (2012) 1.92
A comprehensive gene expression atlas of sex- and tissue-specificity in the malaria vector, Anopheles gambiae. BMC Genomics (2011) 1.88
Jamb and jamc are essential for vertebrate myocyte fusion. PLoS Biol (2011) 1.76
GIGA: a simple, efficient algorithm for gene tree inference in the genomic age. BMC Bioinformatics (2010) 1.69
PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome. Nucleic Acids Res (2013) 1.69
IUPHAR-DB: updated database content and new features. Nucleic Acids Res (2012) 1.66
Genome and transcriptome analysis of the fungal pathogen Fusarium oxysporum f. sp. cubense causing banana vascular wilt disease. PLoS One (2014) 1.64
MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score. Nucleic Acids Res (2010) 1.59
Orthology prediction methods: a quality assessment using curated protein families. Bioessays (2011) 1.56
Reassessing domain architecture evolution of metazoan proteins: major impact of gene prediction errors. Genes (Basel) (2011) 1.56
The tree versus the forest: the fungal tree of life and the topological diversity within the yeast phylome. PLoS One (2009) 1.53
The locust genome provides insight into swarm formation and long-distance flight. Nat Commun (2014) 1.42
Ultra-fast sequence clustering from similarity networks with SiLiX. BMC Bioinformatics (2011) 1.40
Evolution and function of CAG/polyglutamine repeats in protein-protein interaction networks. Nucleic Acids Res (2012) 1.38
Genomes of the rice pest brown planthopper and its endosymbionts reveal complex complementary contributions for host adaptation. Genome Biol (2014) 1.34
Quantifying the mechanisms of domain gain in animal proteins. Genome Biol (2010) 1.32
Genome-wide dFOXO targets and topology of the transcriptomic response to stress and insulin signalling. Mol Syst Biol (2011) 1.32
PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees. BMC Bioinformatics (2009) 1.32
OrthoSelect: a protocol for selecting orthologous groups in phylogenomics. BMC Bioinformatics (2009) 1.29
TreeFam v9: a new website, more species and orthology-on-the-fly. Nucleic Acids Res (2013) 1.29
Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis. BMC Res Notes (2012) 1.24
InterMOD: integrated data and tools for the unification of model organism research. Sci Rep (2013) 1.23
APPRIS: annotation of principal and alternative splice isoforms. Nucleic Acids Res (2012) 1.21
Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE. BMC Genomics (2013) 1.18
FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies. Nucleic Acids Res (2011) 1.17
Quickly finding orthologs as reciprocal best hits with BLAT, LAST, and UBLAST: how much do we miss? PLoS One (2014) 1.16
CentrosomeDB: a human centrosomal proteins database. Nucleic Acids Res (2008) 1.16
The Chicken Gene Nomenclature Committee report. BMC Genomics (2009) 1.15
Analysis of the disintegrin-metalloproteinases family reveals ADAM29 and ADAM7 are often mutated in melanoma. Hum Mutat (2011) 1.14
SysZNF: the C2H2 zinc finger gene database. Nucleic Acids Res (2008) 1.13
Evolution of vertebrate rod and cone phototransduction genes. Philos Trans R Soc Lond B Biol Sci (2009) 1.10
Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies. PLoS Comput Biol (2012) 1.09
Molecular characterization of the evolution of phagosomes. Mol Syst Biol (2010) 1.08
Mitotic spindle proteomics in Chinese hamster ovary cells. PLoS One (2011) 1.08
RFX2 is broadly required for ciliogenesis during vertebrate development. Dev Biol (2011) 1.06
Selectome: a database of positive selection. Nucleic Acids Res (2008) 1.02
Maximum likelihood models and algorithms for gene tree evolution with duplications and losses. BMC Bioinformatics (2011) 1.02
PhyloPars: estimation of missing parameter values using phylogeny. Nucleic Acids Res (2009) 1.02
PhyloExplorer: a web server to validate, explore and query phylogenetic trees. BMC Evol Biol (2009) 1.01
Genome sequencing of the perciform fish Larimichthys crocea provides insights into molecular and genetic mechanisms of stress adaptation. PLoS Genet (2015) 1.01
Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment. Gigascience (2014) 1.00
A manual collection of Syt, Esyt, Rph3a, Rph3al, Doc2, and Dblc2 genes from 46 metazoan genomes--an open access resource for neuroscience and evolutionary biology. BMC Genomics (2010) 0.99
Highly expressed and slowly evolving proteins share compositional properties with thermophilic proteins. Mol Biol Evol (2009) 0.99
Troponin T is essential for sarcomere assembly in zebrafish skeletal muscle. J Cell Sci (2011) 0.97
Human monogenic disease genes have frequently functionally redundant paralogs. PLoS Comput Biol (2013) 0.97
AGR2 gene function requires a unique endoplasmic reticulum localization motif. J Biol Chem (2011) 0.97
Systematic Phenomics Analysis Deconvolutes Genes Mutated in Intellectual Disability into Biologically Coherent Modules. Am J Hum Genet (2016) 0.96
Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes. Genome Biol (2009) 0.96
What evidence is there for the homology of protein-protein interactions? PLoS Comput Biol (2012) 0.95
PRISM offers a comprehensive genomic approach to transcription factor function prediction. Genome Res (2013) 0.94
AMN directs endocytosis of the intrinsic factor-vitamin B(12) receptor cubam by engaging ARH or Dab2. Traffic (2010) 0.93
Assessing the genetic diversity of rice originating from Bangladesh, Assam and West Bengal. Rice (N Y) (2015) 0.91
The apoptotic engulfment protein Ced-6 participates in clathrin-mediated yolk uptake in Drosophila egg chambers. Mol Biol Cell (2012) 0.88
On the origin and evolutionary history of NANOG. PLoS One (2014) 0.88
A clathrin coat assembly role for the muniscin protein central linker revealed by TALEN-mediated gene editing. Elife (2014) 0.87
Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. BMC Bioinformatics (2013) 0.87
Developing a community-based genetic nomenclature for anole lizards. BMC Genomics (2011) 0.86
Polytomy identification in microbial phylogenetic reconstruction. BMC Syst Biol (2011) 0.85
Identification of the Schistosoma mansoni TNF-alpha receptor gene and the effect of human TNF-alpha on the parasite gene expression profile. PLoS Negl Trop Dis (2009) 0.84
Reassessing domain architecture evolution of metazoan proteins: major impact of errors caused by confusing paralogs and epaktologs. Genes (Basel) (2011) 0.84
PhyleasProg: a user-oriented web server for wide evolutionary analyses. Nucleic Acids Res (2011) 0.84
A meta-approach for improving the prediction and the functional annotation of ortholog groups. BMC Genomics (2014) 0.84
Disruption of POGZ Is Associated with Intellectual Disability and Autism Spectrum Disorders. Am J Hum Genet (2016) 0.83
Information Commons for Rice (IC4R). Nucleic Acids Res (2015) 0.83
PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood. Nucleic Acids Res (2008) 0.83
A survey of putative secreted and transmembrane proteins encoded in the C. elegans genome. BMC Genomics (2012) 0.83
Towards an evolutionary model of transcription networks. PLoS Comput Biol (2011) 0.82
Programmed ribosomal frameshifting in the expression of the regulator of intestinal stem cell proliferation, adenomatous polyposis coli (APC). RNA Biol (2011) 0.81
A tale of two drug targets: the evolutionary history of BACE1 and BACE2. Front Genet (2013) 0.81
A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation. PLoS One (2014) 0.81
The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome. PLoS Biol (2015) 0.81
Complementing the Eukaryotic Protein Interactome. PLoS One (2013) 0.81
Cetaceans evolution: insights from the genome sequences of common minke whales. BMC Genomics (2015) 0.80
The DAF-16 FOXO transcription factor regulates natc-1 to modulate stress resistance in Caenorhabditis elegans, linking insulin/IGF-1 signaling to protein N-terminal acetylation. PLoS Genet (2014) 0.80
Sex-biased expression of microRNAs in Drosophila melanogaster. Open Biol (2014) 0.80
Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies. J Mol Biol (2015) 0.79
Drosophila Rbp6 is an orthologue of vertebrate Msi-1 and Msi-2, but does not function redundantly with dMsi to regulate germline stem cell behaviour. PLoS One (2012) 0.79
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol (2003) 102.57
The COG database: an updated version includes eukaryotes. BMC Bioinformatics (2003) 60.98
MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics (2004) 50.89
A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78
Distinguishing homologous from analogous proteins. Syst Zool (1970) 25.10
The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res (2006) 22.70
Ensembl 2007. Nucleic Acids Res (2006) 20.10
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2006) 18.84
The UCSC genome browser database: update 2007. Nucleic Acids Res (2006) 13.04
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res (2006) 11.43
Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res (2005) 9.90
TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res (2006) 8.83
Orthologs, paralogs, and evolutionary genomics. Annu Rev Genet (2005) 8.62
FlyBase: genomes by the dozen. Nucleic Acids Res (2006) 6.96
GeneDB: a resource for prokaryotic and eukaryotic organisms. Nucleic Acids Res (2004) 6.30
PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways. Nucleic Acids Res (2006) 6.20
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. BMC Biol (2005) 4.18
WormBase: new content and better access. Nucleic Acids Res (2006) 4.01
The HUGO Gene Nomenclature Committee (HGNC). Hum Genet (2001) 3.89
The human phylome. Genome Biol (2007) 3.81
Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases. Bioinformatics (2005) 3.62
Functional classification using phylogenomic inference. PLoS Comput Biol (2006) 2.88
A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database. BMC Bioinformatics (2006) 2.39
PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification. Genome Biol (2006) 2.27
Schistosoma mansoni genome: closing in on a final gene set. Exp Parasitol (2007) 1.57
The SYSTERS Protein Family Database in 2005. Nucleic Acids Res (2005) 1.49
The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39
Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (2009) 190.94
Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res (2008) 157.44
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
SOAP: short oligonucleotide alignment program. Bioinformatics (2008) 68.13
The Pfam protein families database. Nucleic Acids Res (2004) 56.46
Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics (2010) 52.01
Model-based analysis of ChIP-Seq (MACS). Genome Biol (2008) 51.63
The Pfam protein families database. Nucleic Acids Res (2002) 51.34
The diploid genome sequence of an Asian individual. Nature (2008) 46.29
De novo assembly of human genomes with massively parallel short read sequencing. Genome Res (2009) 45.91
Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet (2008) 43.63
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78
SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics (2009) 39.47
Pfam: clans, web tools and services. Nucleic Acids Res (2006) 34.83
Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature (2003) 26.58
The variant call format and VCFtools. Bioinformatics (2011) 25.88
The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res (2003) 24.72
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
Enterotypes of the human gut microbiome. Nature (2011) 24.36
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol (2008) 21.72
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience (2012) 20.89
Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res (2008) 20.59
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A (2002) 20.48
The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol (2005) 18.20
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
GeneWise and Genomewise. Genome Res (2004) 17.87
InterPro, progress and status in 2005. Nucleic Acids Res (2005) 17.53
SNP detection for massively parallel whole-genome resequencing. Genome Res (2009) 15.96
The sequence and de novo assembly of the giant panda genome. Nature (2009) 15.76
A large genome center's improvements to the Illumina sequencing system. Nat Methods (2008) 15.56
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
Ensembl 2012. Nucleic Acids Res (2011) 14.55
The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol (2003) 13.32
WEGO: a web tool for plotting GO annotations. Nucleic Acids Res (2006) 13.06
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res (2008) 12.72
Mapping copy number variation by population-scale genome sequencing. Nature (2011) 12.55
A systematic survey of loss-of-function variants in human protein-coding genes. Science (2012) 12.25
Prepublication data sharing. Nature (2009) 12.24
Population genomics of domestic and wild yeasts. Nature (2009) 11.79
A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature (2012) 11.68
Sequencing of 50 human exomes reveals adaptation to high altitude. Science (2010) 11.27
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
Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature (2010) 9.95
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
QuickTree: building huge Neighbour-Joining trees of protein sequences. Bioinformatics (2002) 9.36
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13
Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature (2010) 8.99
TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res (2006) 8.83