Published in Nucleic Acids Res on November 27, 2012
eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res (2013) 3.77
OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software. Nucleic Acids Res (2014) 1.73
Alterations of immune response of Non-Small Cell Lung Cancer with Azacytidine. Oncotarget (2013) 1.44
Oncofinder, a new method for the analysis of intracellular signaling pathway activation using transcriptomic data. Front Genet (2014) 1.22
Quickly finding orthologs as reciprocal best hits with BLAT, LAST, and UBLAST: how much do we miss? PLoS One (2014) 1.16
The OncoFinder algorithm for minimizing the errors introduced by the high-throughput methods of transcriptome analysis. Front Mol Biosci (2014) 1.04
TFClass: a classification of human transcription factors and their rodent orthologs. Nucleic Acids Res (2014) 1.01
MetaRef: a pan-genomic database for comparative and community microbial genomics. Nucleic Acids Res (2013) 0.93
SIMAP--the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage. Nucleic Acids Res (2013) 0.91
Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano. Proc Natl Acad Sci U S A (2015) 0.87
FireDB: a compendium of biological and pharmacologically relevant ligands. Nucleic Acids Res (2013) 0.87
KCF-S: KEGG Chemical Function and Substructure for improved interpretability and prediction in chemical bioinformatics. BMC Syst Biol (2013) 0.86
Phylogenomic reconstruction of archaeal fatty acid metabolism. Environ Microbiol (2014) 0.84
A comparative metagenome survey of the fecal microbiota of a breast- and a plant-fed Asian elephant reveals an unexpectedly high diversity of glycoside hydrolase family enzymes. PLoS One (2014) 0.83
Comparative analysis of sugarcane bagasse metagenome reveals unique and conserved biomass-degrading enzymes among lignocellulolytic microbial communities. Biotechnol Biofuels (2015) 0.83
HoPaCI-DB: host-Pseudomonas and Coxiella interaction database. Nucleic Acids Res (2013) 0.82
Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm. Front Plant Sci (2015) 0.82
High-Quality Genome Assembly and Annotation for Plasmodium coatneyi, Generated Using Single-Molecule Real-Time PacBio Technology. Genome Announc (2016) 0.81
Metagenome survey of a multispecies and alga-associated biofilm revealed key elements of bacterial-algal interactions in photobioreactors. Appl Environ Microbiol (2013) 0.80
Transcription factor and microRNA-regulated network motifs for cancer and signal transduction networks. BMC Syst Biol (2015) 0.79
Elucidation of the evolutionary expansion of phosphorylation signaling networks using comparative phosphomotif analysis. BMC Genomics (2014) 0.78
Comparative genome analyses of Serratia marcescens FS14 reveals its high antagonistic potential. PLoS One (2015) 0.78
Boolean network model for GPR142 against Type 2 diabetes and relative dynamic change ratio analysis using systems and biological circuits approach. Syst Synth Biol (2015) 0.76
Large-scale analysis of the evolutionary histories of phosphorylation motifs in the human genome. Gigascience (2015) 0.75
HieranoiDB: a database of orthologs inferred by Hieranoid. Nucleic Acids Res (2016) 0.75
Data aggregation at the level of molecular pathways improves stability of experimental transcriptomic and proteomic data. Cell Cycle (2017) 0.75
Global Transcriptome Profiling of Xanthomonas oryzae pv. oryzae under in planta Growth and in vitro Culture Conditions. Plant Pathol J (2017) 0.75
Identification of common molecular subsequences. J Mol Biol (1981) 130.53
The COG database: an updated version includes eukaryotes. BMC Bioinformatics (2003) 60.98
The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res (2004) 54.37
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KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res (2011) 30.20
KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res (2007) 29.46
KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res (2009) 28.60
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OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res (2006) 11.43
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res (2009) 5.90
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res (2011) 5.79
Empirical statistical estimates for sequence similarity searches. J Mol Biol (1998) 4.14
Automatic clustering of orthologs and inparalogs shared by multiple proteomes. Bioinformatics (2006) 3.98
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res (2011) 3.94
Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA). Genome Res (2002) 3.93
OMA 2011: orthology inference among 1000 complete genomes. Nucleic Acids Res (2010) 2.92
MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups. Nucleic Acids Res (2006) 2.30
Roundup 2.0: enabling comparative genomics for over 1800 genomes. Bioinformatics (2012) 1.29
ODB: a database for operon organizations, 2011 update. Nucleic Acids Res (2010) 1.03
GENIES: gene network inference engine based on supervised analysis. Nucleic Acids Res (2012) 0.95
CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality. Nucleic Acids Res (2010) 0.84
The KEGG resource for deciphering the genome. Nucleic Acids Res (2004) 53.05
KEGG for linking genomes to life and the environment. Nucleic Acids Res (2007) 49.37
From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res (2006) 44.35
The KEGG databases at GenomeNet. Nucleic Acids Res (2002) 33.68
KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res (2011) 30.20
KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res (2007) 29.46
KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res (2009) 28.60
Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. J Am Chem Soc (2003) 15.30
Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res (2013) 15.13
LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res (2002) 13.61
A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature (2012) 11.68
Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions. J Am Chem Soc (2004) 11.50
KEGG as a glycome informatics resource. Glycobiology (2005) 11.05
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
Network-based analysis and characterization of adverse drug-drug interactions. J Chem Inf Model (2011) 7.92
Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways. J Chem Inf Model (2007) 7.70
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
Comprehensive analysis of distinctive polyketide and nonribosomal peptide structural motifs encoded in microbial genomes. J Mol Biol (2007) 6.59
Prediction of glycan structures from gene expression data based on glycosyltransferase reactions. Bioinformatics (2005) 5.76
The commonality of protein interaction networks determined in neurodegenerative disorders (NDDs). Bioinformatics (2007) 5.63
AAindex: amino acid index database, progress report 2008. Nucleic Acids Res (2007) 4.21
KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res (2008) 4.14
iPath: interactive exploration of biochemical pathways and networks. Trends Biochem Sci (2008) 4.03
BioRuby: bioinformatics software for the Ruby programming language. Bioinformatics (2010) 3.85
Modular architecture of metabolic pathways revealed by conserved sequences of reactions. J Chem Inf Model (2013) 3.58
BioMart Central Portal: an open database network for the biological community. Database (Oxford) (2011) 3.03
Prediction of drug-target interaction networks from the integration of chemical and genomic spaces. Bioinformatics (2008) 2.96
E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs. Bioinformatics (2009) 2.88
The repertoire of desaturases and elongases reveals fatty acid variations in 56 eukaryotic genomes. J Lipid Res (2007) 2.65
iPath2.0: interactive pathway explorer. Nucleic Acids Res (2011) 2.50
Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs. Bioinformatics (2003) 2.45
Comprehensive analysis of glycosyltransferases in eukaryotic genomes for structural and functional characterization of glycans. Carbohydr Res (2009) 2.40
Extraction and analysis of chemical modification patterns in drug development. J Chem Inf Model (2009) 2.28
Towards zoomable multidimensional maps of the cell. Nat Biotechnol (2007) 2.20
Supervised prediction of drug-target interactions using bipartite local models. Bioinformatics (2009) 2.20
VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. Nucleic Acids Res (2007) 2.17
Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework. Bioinformatics (2010) 2.14
Identification of a new cryptochrome class. Structure, function, and evolution. Mol Cell (2003) 2.11
Gene annotation and pathway mapping in KEGG. Methods Mol Biol (2007) 2.09
High incidence of ICA anterior wall aneurysms in patients with an anomalous origin of the ophthalmic artery: possible relevance to the pathogenesis of aneurysm formation. J Neurosurg (2013) 2.03
Global analysis of circadian expression in the cyanobacterium Synechocystis sp. strain PCC 6803. J Bacteriol (2005) 1.80
EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. Nucleic Acids Res (2006) 1.75
The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships. Bioinformatics (2005) 1.75
Alteration of gene expression in human hepatocellular carcinoma with integrated hepatitis B virus DNA. Clin Cancer Res (2005) 1.64
ODB: a database of operons accumulating known operons across multiple genomes. Nucleic Acids Res (2006) 1.58
Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol (2015) 1.58
Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics. Bioinformatics (2012) 1.52
Genome sequence of the cat pathogen, Chlamydophila felis. DNA Res (2006) 1.50
PathPred: an enzyme-catalyzed metabolic pathway prediction server. Nucleic Acids Res (2010) 1.49