Published in Nucleic Acids Res on January 01, 2002
The Pfam protein families database. Nucleic Acids Res (2004) 56.46
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res (2003) 52.80
Pfam: clans, web tools and services. Nucleic Acids Res (2006) 34.83
UniProt: the Universal Protein knowledgebase. Nucleic Acids Res (2004) 29.05
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
Rfam: an RNA family database. Nucleic Acids Res (2003) 22.93
PANTHER: a library of protein families and subfamilies indexed by function. Genome Res (2003) 21.64
SMART 4.0: towards genomic data integration. Nucleic Acids Res (2004) 19.37
InterProScan: protein domains identifier. Nucleic Acids Res (2005) 18.82
Database resources of the National Center for Biotechnology. Nucleic Acids Res (2003) 18.26
Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res (2003) 15.74
CDD: a curated Entrez database of conserved domain alignments. Nucleic Acids Res (2003) 14.38
CDART: protein homology by domain architecture. Genome Res (2002) 12.95
The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Res (2003) 12.81
A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. BMC Bioinformatics (2002) 10.84
Database resources of the National Center for Biotechnology Information: update. Nucleic Acids Res (2004) 9.85
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res (2003) 6.86
GlobPlot: Exploring protein sequences for globularity and disorder. Nucleic Acids Res (2003) 5.90
HMM Logos for visualization of protein families. BMC Bioinformatics (2004) 5.69
The ankyrin repeat as molecular architecture for protein recognition. Protein Sci (2004) 5.07
A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin. PLoS Biol (2004) 5.02
Update on XplorMed: A web server for exploring scientific literature. Nucleic Acids Res (2003) 4.42
Distribution and evolution of von Willebrand/integrin A domains: widely dispersed domains with roles in cell adhesion and elsewhere. Mol Biol Cell (2002) 4.27
Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world. Plant Cell (2003) 3.80
Accelerated evolution of the Prdm9 speciation gene across diverse metazoan taxa. PLoS Genet (2009) 3.60
The European Bioinformatics Institute's data resources. Nucleic Acids Res (2003) 3.34
Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS Biol (2005) 3.28
PKHD1, the polycystic kidney and hepatic disease 1 gene, encodes a novel large protein containing multiple immunoglobulin-like plexin-transcription-factor domains and parallel beta-helix 1 repeats. Am J Hum Genet (2002) 3.21
Cloning and characterization of two extracellular heparin-degrading endosulfatases in mice and humans. J Biol Chem (2002) 2.86
SeqHound: biological sequence and structure database as a platform for bioinformatics research. BMC Bioinformatics (2002) 2.84
The GAPs, GEFs, and GDIs of heterotrimeric G-protein alpha subunits. Int J Biol Sci (2005) 2.76
The role of saliva in tick feeding. Front Biosci (Landmark Ed) (2009) 2.73
MBGD: microbial genome database for comparative analysis. Nucleic Acids Res (2003) 2.60
Analysis of the small GTPase gene superfamily of Arabidopsis. Plant Physiol (2003) 2.45
The HSA domain binds nuclear actin-related proteins to regulate chromatin-remodeling ATPases. Nat Struct Mol Biol (2008) 2.26
MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress. BMC Genomics (2007) 2.19
Proteomic analysis of interchromatin granule clusters. Mol Biol Cell (2004) 2.12
FimX, a multidomain protein connecting environmental signals to twitching motility in Pseudomonas aeruginosa. J Bacteriol (2003) 2.07
Designed to be stable: crystal structure of a consensus ankyrin repeat protein. Proc Natl Acad Sci U S A (2003) 1.98
Common extracellular sensory domains in transmembrane receptors for diverse signal transduction pathways in bacteria and archaea. J Bacteriol (2003) 1.97
Mutations in MTMR13, a new pseudophosphatase homologue of MTMR2 and Sbf1, in two families with an autosomal recessive demyelinating form of Charcot-Marie-Tooth disease associated with early-onset glaucoma. Am J Hum Genet (2003) 1.96
The Nuclear Protein Database (NPD): sub-nuclear localisation and functional annotation of the nuclear proteome. Nucleic Acids Res (2003) 1.95
Structure and mechanism of ADP-ribose-1''-monophosphatase (Appr-1''-pase), a ubiquitous cellular processing enzyme. Protein Sci (2005) 1.95
TarO: a target optimisation system for structural biology. Nucleic Acids Res (2008) 1.89
Identification of new flagellar genes of Salmonella enterica serovar Typhimurium. J Bacteriol (2006) 1.89
Brugia malayi excreted/secreted proteins at the host/parasite interface: stage- and gender-specific proteomic profiling. PLoS Negl Trop Dis (2009) 1.88
From endonucleases to transcription factors: evolution of the AP2 DNA binding domain in plants. Plant Cell (2004) 1.87
Diversity in nucleotide binding site-leucine-rich repeat genes in cereals. Genome Res (2002) 1.84
SPD--a web-based secreted protein database. Nucleic Acids Res (2005) 1.75
Late cytoplasmic maturation of the small ribosomal subunit requires RIO proteins in Saccharomyces cerevisiae. Mol Cell Biol (2003) 1.72
NEAT: a domain duplicated in genes near the components of a putative Fe3+ siderophore transporter from Gram-positive pathogenic bacteria. Genome Biol (2002) 1.72
Structural basis of the interaction between the AAA ATPase p97/VCP and its adaptor protein p47. EMBO J (2004) 1.68
A Phytophthora infestans cystatin-like protein targets a novel tomato papain-like apoplastic protease. Plant Physiol (2006) 1.67
Computational identification and characterization of novel genes from legumes. Plant Physiol (2004) 1.67
Phylogenetic analysis of Sec7-domain-containing Arf nucleotide exchangers. Mol Biol Cell (2004) 1.66
An argonaute-like protein is required for meiotic silencing. Genetics (2003) 1.61
Novel domains and orthologues of eukaryotic transcription elongation factors. Nucleic Acids Res (2002) 1.60
The GATA family of transcription factors in Arabidopsis and rice. Plant Physiol (2004) 1.58
Cluster II che genes from Pseudomonas aeruginosa are required for an optimal chemotactic response. J Bacteriol (2002) 1.58
Overexpression of GLUTAMINE DUMPER1 leads to hypersecretion of glutamine from Hydathodes of Arabidopsis leaves. Plant Cell (2004) 1.54
Modeling the evolution of protein domain architectures using maximum parsimony. J Mol Biol (2006) 1.53
VSIG4, a B7 family-related protein, is a negative regulator of T cell activation. J Clin Invest (2006) 1.51
Identifying DNA-binding proteins using structural motifs and the electrostatic potential. Nucleic Acids Res (2004) 1.50
Progress towards mapping the universe of protein folds. Genome Biol (2004) 1.41
A death-associated protein kinase (DAPK)-interacting protein, DIP-1, is an E3 ubiquitin ligase that promotes tumor necrosis factor-induced apoptosis and regulates the cellular levels of DAPK. J Biol Chem (2002) 1.41
Structural basis for SH3 domain-mediated high-affinity binding between Mona/Gads and SLP-76. EMBO J (2003) 1.38
An insight into the sialome of Anopheles funestus reveals an emerging pattern in anopheline salivary protein families. Insect Biochem Mol Biol (2006) 1.37
Minimotif miner 2nd release: a database and web system for motif search. Nucleic Acids Res (2008) 1.36
Type-B response regulators display overlapping expression patterns in Arabidopsis. Plant Physiol (2004) 1.35
New knowledge from old: in silico discovery of novel protein domains in Streptomyces coelicolor. BMC Microbiol (2003) 1.33
Large-scale exploration of growth inhibition caused by overexpression of genomic fragments in Saccharomyces cerevisiae. Genome Biol (2004) 1.33
Alternative splicing of mouse transcription factors affects their DNA-binding domain architecture and is tissue specific. Genome Biol (2004) 1.30
Pseudomonas aeruginosa fimL regulates multiple virulence functions by intersecting with Vfr-modulated pathways. Mol Microbiol (2005) 1.29
The salivary gland transcriptome of the neotropical malaria vector Anopheles darlingi reveals accelerated evolution of genes relevant to hematophagy. BMC Genomics (2009) 1.28
An insight into the sialome of the blood-sucking bug Triatoma infestans, a vector of Chagas' disease. Insect Biochem Mol Biol (2007) 1.26
RanBP2/Nup358 provides a major binding site for NXF1-p15 dimers at the nuclear pore complex and functions in nuclear mRNA export. Mol Cell Biol (2004) 1.26
Sulfolobus tengchongensis spindle-shaped virus STSV1: virus-host interactions and genomic features. J Virol (2005) 1.26
A virulence factor of myxoma virus colocalizes with NF-kappaB in the nucleus and interferes with inflammation. J Virol (2004) 1.26
OTOF mutations revealed by genetic analysis of hearing loss families including a potential temperature sensitive auditory neuropathy allele. J Med Genet (2005) 1.24
Identification and functional characterization of chicken toll-like receptor 5 reveals a fundamental role in the biology of infection with Salmonella enterica serovar typhimurium. Infect Immun (2005) 1.24
Molecular modeling of the chromatosome particle. Nucleic Acids Res (2003) 1.22
Sequence-based prediction of protein domains. Nucleic Acids Res (2004) 1.21
Folding of a designed simple ankyrin repeat protein. Protein Sci (2004) 1.20
Membrane-bound progesterone receptors contain a cytochrome b5-like ligand-binding domain. Genome Biol (2002) 1.20
Regulation of cellular homeostasis by galectins. Glycoconj J (2004) 1.20
Gene expression profiles of microdissected pancreatic ductal adenocarcinoma. Virchows Arch (2003) 1.18
Interactions between the PAS and HAMP domains of the Escherichia coli aerotaxis receptor Aer. J Bacteriol (2004) 1.18
VMD: a community annotation database for oomycetes and microbial genomes. Nucleic Acids Res (2006) 1.18
A complex prediction: three-dimensional model of the yeast exosome. EMBO Rep (2002) 1.18
Interactions between plant RING-H2 and plant-specific NAC (NAM/ATAF1/2/CUC2) proteins: RING-H2 molecular specificity and cellular localization. Biochem J (2003) 1.18
Refining multiple sequence alignments with conserved core regions. Nucleic Acids Res (2006) 1.15
PAS domain of the Aer redox sensor requires C-terminal residues for native-fold formation and flavin adenine dinucleotide binding. J Bacteriol (2004) 1.15
eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity. Nucleic Acids Res (2005) 1.14
An Rpb4/Rpb7-like complex in yeast RNA polymerase III contains the orthologue of mammalian CGRP-RCP. Mol Cell Biol (2003) 1.14
A novel firmicute protein family related to the actinobacterial resuscitation-promoting factors by non-orthologous domain displacement. BMC Genomics (2005) 1.13
KinG: a database of protein kinases in genomes. Nucleic Acids Res (2004) 1.13
Graph theoretical insights into evolution of multidomain proteins. J Comput Biol (2006) 1.12
The TC10-interacting protein CIP4/2 is required for insulin-stimulated Glut4 translocation in 3T3L1 adipocytes. Proc Natl Acad Sci U S A (2002) 1.12
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
The sequence of the human genome. Science (2001) 101.55
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res (2000) 67.44
Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol (2001) 66.87
RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res (2001) 45.29
Predicting coiled coils from protein sequences. Science (1991) 38.18
SMART, a simple modular architecture research tool: identification of signaling domains. Proc Natl Acad Sci U S A (1998) 36.83
The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res (2001) 24.45
SMART: a web-based tool for the study of genetically mobile domains. Nucleic Acids Res (2000) 17.77
AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinformatics (2001) 4.79
Accurate formula for P-values of gapped local sequence and profile alignments. J Mol Biol (2000) 3.51
CHROMA: consensus-based colouring of multiple alignments for publication. Bioinformatics (2001) 3.30
Evolution of domain families. Adv Protein Chem (2000) 2.98
Cadherin superfamily proteins in Caenorhabditis elegans and Drosophila melanogaster. J Mol Biol (2001) 2.64
Exon structure conservation despite low sequence similarity: a relic of dramatic events in evolution? EMBO J (2001) 2.50
Sequence variation and disease in the wake of the draft human genome. Hum Mol Genet (2001) 2.07
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
A method and server for predicting damaging missense mutations. Nat Methods (2010) 78.53
Human non-synonymous SNPs: server and survey. Nucleic Acids Res (2002) 50.45
Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature (2002) 45.19
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
Comparative metagenomics of microbial communities. Science (2005) 25.88
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
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
Comparative assessment of large-scale data sets of protein-protein interactions. Nature (2002) 24.25
Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature (2005) 23.04
Proteome survey reveals modularity of the yeast cell machinery. Nature (2006) 20.77
STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res (2008) 20.62
The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36
SMART 4.0: towards genomic data integration. Nucleic Acids Res (2004) 19.37
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res (2010) 18.73
STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res (2012) 18.26
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
InterPro, progress and status in 2005. Nucleic Acids Res (2005) 17.53
SMART 5: domains in the context of genomes and networks. Nucleic Acids Res (2006) 17.13
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol (2004) 16.08
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics (2006) 14.96
Toward automatic reconstruction of a highly resolved tree of life. Science (2006) 14.96
Functional impact of global rare copy number variation in autism spectrum disorders. Nature (2010) 14.66
InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res (2011) 13.45
New developments in the InterPro database. Nucleic Acids Res (2007) 12.49
STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic Acids Res (2006) 12.16
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res (2011) 10.82
Mouse genomic variation and its effect on phenotypes and gene regulation. Nature (2011) 10.66
STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res (2005) 10.44
Genome-wide genetic association of complex traits in heterogeneous stock mice. Nat Genet (2006) 9.87
The obesity-associated FTO gene encodes a 2-oxoglutarate-dependent nucleic acid demethylase. Science (2007) 9.86
SMART 6: recent updates and new developments. Nucleic Acids Res (2008) 9.80
STRING: a database of predicted functional associations between proteins. Nucleic Acids Res (2003) 9.45
Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science (2002) 9.43
The Collaborative Cross, a community resource for the genetic analysis of complex traits. Nat Genet (2004) 9.37
Drug target identification using side-effect similarity. Science (2008) 9.24
SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res (2011) 9.15
Bioinformatics in the post-sequence era. Nat Genet (2003) 8.83
mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes. Genes Dev (2006) 8.78
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res (2006) 8.36
Literature mining for the biologist: from information retrieval to biological discovery. Nat Rev Genet (2006) 8.23
Protein disorder prediction: implications for structural proteomics. Structure (2003) 7.93
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature (2007) 7.91
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol (2011) 7.53
Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res (2007) 7.34
Alternative splicing and genome complexity. Nat Genet (2001) 7.30
The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc Natl Acad Sci U S A (2002) 7.21
A first-generation linkage disequilibrium map of human chromosome 22. Nature (2002) 7.03
Systematic discovery of in vivo phosphorylation networks. Cell (2007) 6.94
Richness of human gut microbiome correlates with metabolic markers. Nature (2013) 6.93
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res (2003) 6.86
A side effect resource to capture phenotypic effects of drugs. Mol Syst Biol (2010) 6.75
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature (2008) 6.69
The ecoresponsive genome of Daphnia pulex. Science (2011) 6.55
The genome of the model beetle and pest Tribolium castaneum. Nature (2008) 6.50
A RING-type ubiquitin ligase family member required to repress follicular helper T cells and autoimmunity. Nature (2005) 6.31
The genome of a songbird. Nature (2010) 5.90
Association of genes to genetically inherited diseases using data mining. Nat Genet (2002) 5.78
Genome analysis of the platypus reveals unique signatures of evolution. Nature (2008) 5.74
Strategies for mapping and cloning quantitative trait genes in rodents. Nat Rev Genet (2005) 5.57
Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science (2010) 5.56
Immunity-related genes and gene families in Anopheles gambiae. Science (2002) 5.47
Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biol (2009) 5.45
Mutations in genes encoding ribonuclease H2 subunits cause Aicardi-Goutières syndrome and mimic congenital viral brain infection. Nat Genet (2006) 5.26