Published in Nucleic Acids Res on October 27, 2013
BRENDA in 2015: exciting developments in its 25th year of existence. Nucleic Acids Res (2014) 1.64
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res (2015) 1.63
Big data and other challenges in the quest for orthologs. Bioinformatics (2014) 1.48
SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles. Bioinformatics (2015) 0.90
Genome sequence of Coxiella burnetii strain Namibia. Stand Genomic Sci (2014) 0.83
Globally distributed root endophyte Phialocephala subalpina links pathogenic and saprophytic lifestyles. BMC Genomics (2016) 0.75
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. Nucleic Acids Res (2017) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
The RAST Server: rapid annotations using subsystems technology. BMC Genomics (2008) 175.18
Identification of common molecular subsequences. J Mol Biol (1981) 130.53
The COG database: an updated version includes eukaryotes. BMC Bioinformatics (2003) 60.98
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics (2005) 46.40
STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res (2012) 18.26
Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol (1990) 17.64
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res (2011) 14.04
InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res (2011) 13.45
Ensembl 2013. Nucleic Acids Res (2012) 11.70
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2012) 8.41
Protein database searches using compositionally adjusted substitution matrices. FEBS J (2005) 8.14
GeneCards Version 3: the human gene integrator. Database (Oxford) (2010) 6.05
CYGD: the Comprehensive Yeast Genome Database. Nucleic Acids Res (2005) 5.25
CLANS: a Java application for visualizing protein families based on pairwise similarity. Bioinformatics (2004) 4.14
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res (2011) 3.94
Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. PLoS One (2009) 3.03
OMA 2011: orthology inference among 1000 complete genomes. Nucleic Acids Res (2010) 2.92
Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. Nucleic Acids Res (2011) 2.87
The predictive power of the CluSTr database. Bioinformatics (2005) 2.85
Nature of the protein universe. Proc Natl Acad Sci U S A (2009) 2.73
SIMAP: the similarity matrix of proteins. Nucleic Acids Res (2006) 2.26
The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions. Bioinformatics (2004) 2.08
PEDANT covers all complete RefSeq genomes. Nucleic Acids Res (2008) 1.78
SIMAP--the similarity matrix of proteins. Bioinformatics (2005) 1.62
SIMAP--a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters. Nucleic Acids Res (2009) 1.58
SIMAP--structuring the network of protein similarities. Nucleic Acids Res (2007) 1.37
KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters. Nucleic Acids Res (2012) 1.36
Pythoscape: a framework for generation of large protein similarity networks. Bioinformatics (2012) 1.15
ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree. Nucleic Acids Res (2011) 1.07
Rapid similarity search of proteins using alignments of domain arrangements. Bioinformatics (2013) 0.89
Pclust: protein network visualization highlighting experimental data. Bioinformatics (2013) 0.79
The Protein Information Resource: an integrated public resource of functional annotation of proteins. Nucleic Acids Res (2002) 12.20
The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol (2007) 8.24
MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res (2006) 7.75
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature (2006) 5.52
Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum. PLoS Genet (2008) 5.23
A genome-wide perspective of genetic variation in human metabolism. Nat Genet (2009) 5.00
The MIPS mammalian protein-protein interaction database. Bioinformatics (2004) 4.66
Gepard: a rapid and sensitive tool for creating dotplots on genome scale. Bioinformatics (2007) 4.45
The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization. Science (2007) 4.43
Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature (2006) 4.06
The dynamic genome of Hydra. Nature (2010) 4.00
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res (2011) 3.94
eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res (2013) 3.77
The PEDANT genome database. Nucleic Acids Res (2003) 3.47
Illuminating the evolutionary history of chlamydiae. Science (2004) 3.39
Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota. Trends Microbiol (2010) 2.84
Metabolic footprint of diabetes: a multiplatform metabolomics study in an epidemiological setting. PLoS One (2010) 2.84
Exome sequencing identifies ACAD9 mutations as a cause of complex I deficiency. Nat Genet (2010) 2.81
Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts. Environ Microbiol (2009) 2.68
Sequence-based prediction of type III secreted proteins. PLoS Pathog (2009) 2.58
Exon discovery by genomic sequence alignment. Bioinformatics (2002) 2.38
A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. Proc Natl Acad Sci U S A (2010) 2.25
Molecular evolution of eukaryotic genomes: hemiascomycetous yeast spliceosomal introns. Nucleic Acids Res (2003) 2.21
amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions. Environ Microbiol (2011) 2.02
MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics. Nucleic Acids Res (2004) 1.97
The PEDANT genome database in 2005. Nucleic Acids Res (2005) 1.88
probeCheck--a central resource for evaluating oligonucleotide probe coverage and specificity. Environ Microbiol (2008) 1.85
Complete genome sequence of Cronobacter turicensis LMG 23827, a food-borne pathogen causing deaths in neonates. J Bacteriol (2010) 1.83
PEDANT covers all complete RefSeq genomes. Nucleic Acids Res (2008) 1.78
Bioinformatics analysis of targeted metabolomics--uncovering old and new tales of diabetic mice under medication. Endocrinology (2008) 1.75
SIMAP--the similarity matrix of proteins. Bioinformatics (2005) 1.62
Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling. Genome Biol (2013) 1.62
SIMAP--a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters. Nucleic Acids Res (2009) 1.58
B2G-FAR, a species-centered GO annotation repository. Bioinformatics (2011) 1.53
FGDB: a comprehensive fungal genome resource on the plant pathogen Fusarium graminearum. Nucleic Acids Res (2006) 1.49
Unity in variety--the pan-genome of the Chlamydiae. Mol Biol Evol (2011) 1.47
The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations. Environ Microbiol (2012) 1.42
Development of a Fusarium graminearum Affymetrix GeneChip for profiling fungal gene expression in vitro and in planta. Fungal Genet Biol (2006) 1.41
The genome of the amoeba symbiont "Candidatus Amoebophilus asiaticus" reveals common mechanisms for host cell interaction among amoeba-associated bacteria. J Bacteriol (2009) 1.36
FGDB: revisiting the genome annotation of the plant pathogen Fusarium graminearum. Nucleic Acids Res (2010) 1.35
Metatranscriptomics of the marine sponge Geodia barretti: tackling phylogeny and function of its microbial community. Environ Microbiol (2012) 1.32
Sputnik: a database platform for comparative plant genomics. Nucleic Acids Res (2003) 1.32
The Negatome database: a reference set of non-interacting protein pairs. Nucleic Acids Res (2009) 1.32
Can we estimate the accuracy of ADME-Tox predictions? Drug Discov Today (2006) 1.30
SNAPper: gene order predicts gene function. Bioinformatics (2002) 1.27
Approaching clinical proteomics: current state and future fields of application in fluid proteomics. Clin Chem Lab Med (2009) 1.27
The sufficient minimal set of miRNA seed types. Bioinformatics (2011) 1.25
Effective--a database of predicted secreted bacterial proteins. Nucleic Acids Res (2010) 1.23
PEDANT genome database: 10 years online. Nucleic Acids Res (2006) 1.20
Independent evolution of the core domain and its flanking sequences in small heat shock proteins. FASEB J (2010) 1.20
Impact of natural genetic variation on the transcriptome of autotetraploid Arabidopsis thaliana. Proc Natl Acad Sci U S A (2010) 1.20
MIPS: curated databases and comprehensive secondary data resources in 2010. Nucleic Acids Res (2010) 1.19
The genome of the obligate intracellular parasite Trachipleistophora hominis: new insights into microsporidian genome dynamics and reductive evolution. PLoS Pathog (2012) 1.16
Cloning and characterization of Enterobacter sakazakii pigment genes and in situ spectroscopic analysis of the pigment. FEMS Microbiol Lett (2006) 1.15
Phage morphology recapitulates phylogeny: the comparative genomics of a new group of myoviruses. PLoS One (2012) 1.14
The Genome of Nitrospina gracilis Illuminates the Metabolism and Evolution of the Major Marine Nitrite Oxidizer. Front Microbiol (2013) 1.14
Effects of season and experimental warming on the bacterial community in a temperate mountain forest soil assessed by 16S rRNA gene pyrosequencing. FEMS Microbiol Ecol (2012) 1.11
The evolutionary dynamics of protein-protein interaction networks inferred from the reconstruction of ancient networks. PLoS One (2013) 1.11
How can we deliver the large plant genomes? Strategies and perspectives. Curr Opin Plant Biol (2002) 1.10
Identification of enzymes involved in anaerobic benzene degradation by a strictly anaerobic iron-reducing enrichment culture. Environ Microbiol (2010) 1.09
Large scale application of neural network based semantic role labeling for automated relation extraction from biomedical texts. PLoS One (2009) 1.05
Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes. Genome Biol (2009) 1.04
Super paramagnetic clustering of protein sequences. BMC Bioinformatics (2005) 1.02
Functional characterization of two clusters of Brachypodium distachyon UDP-glycosyltransferases encoding putative deoxynivalenol detoxification genes. Mol Plant Microbe Interact (2013) 1.01
Molecular recognition determinants for type IV secretion of diverse families of conjugative relaxases. Mol Microbiol (2010) 1.00
The DICS repository: module-assisted analysis of disease-related gene lists. Bioinformatics (2009) 1.00
The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context. Nucleic Acids Res (2006) 0.99
NxrB encoding the beta subunit of nitrite oxidoreductase as functional and phylogenetic marker for nitrite-oxidizing Nitrospira. Environ Microbiol (2013) 0.97
Targeting effectors: the molecular recognition of Type III secreted proteins. Microbes Infect (2010) 0.97
Shotgun sequencing of Yersinia enterocolitica strain W22703 (biotype 2, serotype O:9): genomic evidence for oscillation between invertebrates and mammals. BMC Genomics (2011) 0.95
Molecular characterization of the alpha-glucosidase activity in Enterobacter sakazakii reveals the presence of a putative gene cluster for palatinose metabolism. Syst Appl Microbiol (2006) 0.93
Combined genomic and proteomic approaches identify gene clusters involved in anaerobic 2-methylnaphthalene degradation in the sulfate-reducing enrichment culture N47. J Bacteriol (2010) 0.93
DNA damage-induced expression of p53 suppresses mitotic checkpoint kinase hMps1: the lack of this suppression in p53MUT cells contributes to apoptosis. J Biol Chem (2006) 0.92
Comprehensive in silico prediction and analysis of chlamydial outer membrane proteins reflects evolution and life style of the Chlamydiae. BMC Genomics (2009) 0.90
Complete genome sequences of Desulfosporosinus orientis DSM765T, Desulfosporosinus youngiae DSM17734T, Desulfosporosinus meridiei DSM13257T, and Desulfosporosinus acidiphilus DSM22704T. J Bacteriol (2012) 0.90
Separation of sequences from host-pathogen interface using triplet nucleotide frequencies. Fungal Genet Biol (2007) 0.86
Approaching clinical proteomics: current state and future fields of application in cellular proteomics. Cytometry A (2009) 0.86
Beyond the 'best' match: machine learning annotation of protein sequences by integration of different sources of information. Bioinformatics (2008) 0.86
Draft genome sequence of Lactobacillus casei W56. J Bacteriol (2012) 0.85
Network-based SNP meta-analysis identifies joint and disjoint genetic features across common human diseases. BMC Genomics (2012) 0.85
An environmental perspective on large-scale genome clustering based on metabolic capabilities. Bioinformatics (2008) 0.84
Signature protein of the PVC superphylum. Appl Environ Microbiol (2013) 0.84
Phenotypic and transcriptomic analyses of Sigma L-dependent characteristics in Listeria monocytogenes EGD-e. Food Microbiol (2012) 0.83
Spatiotemporal expression control correlates with intragenic scaffold matrix attachment regions (S/MARs) in Arabidopsis thaliana. PLoS Comput Biol (2006) 0.82
pH as a Driver for Ammonia-Oxidizing Archaea in Forest Soils. Microb Ecol (2014) 0.82
A novel putative miRNA target enhancer signal. PLoS One (2009) 0.81
Cellulose as an extracellular matrix component present in Enterobacter sakazakii biofilms. J Food Prot (2008) 0.81
Genomic insights into the metabolic potential of the polycyclic aromatic hydrocarbon degrading sulfate-reducing Deltaproteobacterium N47. Environ Microbiol (2010) 0.81
Comparative analysis of benzoxazinoid biosynthesis in monocots and dicots: independent recruitment of stabilization and activation functions. Plant Cell (2012) 0.81
Prediction of microbial phenotypes based on comparative genomics. BMC Bioinformatics (2015) 0.80
Metagenomics of Kamchatkan hot spring filaments reveal two new major (hyper)thermophilic lineages related to Thaumarchaeota. Res Microbiol (2013) 0.80
Rare variants in LRRK1 and Parkinson's disease. Neurogenetics (2013) 0.78
Exploiting scale-free information from expression data for cancer classification. Comput Biol Chem (2005) 0.78
Complete Genome Sequence of Listeria monocytogenes LL195, a Serotype 4b Strain from the 1983-1987 Listeriosis Epidemic in Switzerland. Genome Announc (2013) 0.78