Published in Nucleic Acids Res on January 01, 2006
Operon prediction using both genome-specific and general genomic information. Nucleic Acids Res (2006) 4.41
DOOR: a database for prokaryotic operons. Nucleic Acids Res (2008) 3.50
Ten years of bacterial genome sequencing: comparative-genomics-based discoveries. Funct Integr Genomics (2006) 1.86
Quantitative assessment of protein function prediction from metagenomics shotgun sequences. Proc Natl Acad Sci U S A (2007) 1.47
DOOR 2.0: presenting operons and their functions through dynamic and integrated views. Nucleic Acids Res (2013) 1.26
Short Promoters in Viral Vectors Drive Selective Expression in Mammalian Inhibitory Neurons, but do not Restrict Activity to Specific Inhibitory Cell-Types. Front Neural Circuits (2009) 1.08
Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli. BMC Genomics (2007) 1.05
ODB: a database for operon organizations, 2011 update. Nucleic Acids Res (2010) 1.03
Large-scale analysis of gene clustering in bacteria. Genome Res (2008) 0.97
Transcriptional profile of Pseudomonas syringae pv. phaseolicola NPS3121 in response to tissue extracts from a susceptible Phaseolus vulgaris L. cultivar. BMC Microbiol (2009) 0.90
MycoperonDB: a database of computationally identified operons and transcriptional units in Mycobacteria. BMC Bioinformatics (2006) 0.90
Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions. Database (Oxford) (2010) 0.85
Binary particle swarm optimization for operon prediction. Nucleic Acids Res (2010) 0.84
Multiple independent fusions of glucose-6-phosphate dehydrogenase with enzymes in the pentose phosphate pathway. PLoS One (2011) 0.84
Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum. Nucleic Acids Res (2015) 0.83
Crystal structures, dynamics and functional implications of molybdenum-cofactor biosynthesis protein MogA from two thermophilic organisms. Acta Crystallogr Sect F Struct Biol Cryst Commun (2010) 0.77
Shewregdb: database and visualization environment for experimental and predicted regulatory information in Shewanella oneidensis mr-1. Bioinformation (2009) 0.77
Two-way AIC: detection of differentially expressed genes from large scale microarray meta-dataset. BMC Genomics (2013) 0.75
Elucidation of operon structures across closely related bacterial genomes. PLoS One (2014) 0.75
Parkinson's disease-related DJ-1 functions in thiol quality control against aldehyde attack in vitro. Sci Rep (2017) 0.75
The KEGG resource for deciphering the genome. Nucleic Acids Res (2004) 53.05
The use of gene clusters to infer functional coupling. Proc Natl Acad Sci U S A (1999) 16.35
STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res (2005) 10.44
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RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucleic Acids Res (2004) 5.73
A global analysis of Caenorhabditis elegans operons. Nature (2002) 5.29
Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res (2000) 5.14
A novel method for accurate operon predictions in all sequenced prokaryotes. Nucleic Acids Res (2005) 4.68
A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters. Nucleic Acids Res (2000) 4.53
Prediction of operons in microbial genomes. Nucleic Acids Res (2001) 4.44
Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes. Genome Res (2003) 3.10
Modeling and predicting transcriptional units of Escherichia coli genes using hidden Markov models. Bioinformatics (1999) 2.89
Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes. Mol Biol Evol (1999) 2.68
DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics. Nucleic Acids Res (2004) 2.61
Co-expression pattern from DNA microarray experiments as a tool for operon prediction. Nucleic Acids Res (2002) 2.50
Conserved clusters of functionally related genes in two bacterial genomes. J Mol Evol (1997) 2.39
Computational identification of operons in microbial genomes. Genome Res (2002) 2.35
Predicting the operon structure of Bacillus subtilis using operon length, intergene distance, and gene expression information. Pac Symp Biocomput (2004) 1.94
A Bayesian network approach to operon prediction. Bioinformatics (2003) 1.57
Conservation of gene co-regulation in prokaryotes and eukaryotes. Trends Biotechnol (2002) 1.55
Predicting bacterial transcription units using sequence and expression data. Bioinformatics (2003) 1.48
A probabilistic learning approach to whole-genome operon prediction. Proc Int Conf Intell Syst Mol Biol (2000) 1.47
Inferring gene regulatory networks from time-ordered gene expression data of Bacillus subtilis using differential equations. Pac Symp Biocomput (2003) 1.34
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
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
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
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
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
DNA microarray analysis of redox-responsive genes in the genome of the cyanobacterium Synechocystis sp. strain PCC 6803. J Bacteriol (2003) 1.46
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. J Biomed Semantics (2013) 1.44
KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains. Nucleic Acids Res (2004) 1.43
The genome of the heartworm, Dirofilaria immitis, reveals drug and vaccine targets. FASEB J (2012) 1.40
Positive regulation of sugar catabolic pathways in the cyanobacterium Synechocystis sp. PCC 6803 by the group 2 sigma factor sigE. J Biol Chem (2005) 1.40
KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters. Nucleic Acids Res (2012) 1.36
The KEGG databases and tools facilitating omics analysis: latest developments involving human diseases and pharmaceuticals. Methods Mol Biol (2012) 1.33
Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009. Nucleic Acids Res (2008) 1.32
Extracting active pathways from gene expression data. Bioinformatics (2003) 1.31
Supervised enzyme network inference from the integration of genomic data and chemical information. Bioinformatics (2005) 1.28
Community-driven development for computational biology at Sprints, Hackathons and Codefests. BMC Bioinformatics (2014) 1.27
Drug target prediction using adverse event report systems: a pharmacogenomic approach. Bioinformatics (2012) 1.27
Using the KEGG database resource. Curr Protoc Bioinformatics (2005) 1.25
Extraction of phylogenetic network modules from the metabolic network. BMC Bioinformatics (2006) 1.23
CyanoBase and RhizoBase: databases of manually curated annotations for cyanobacterial and rhizobial genomes. Nucleic Acids Res (2013) 1.20
Using the KEGG database resource. Curr Protoc Bioinformatics (2012) 1.19
Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis. BMC Bioinformatics (2006) 1.18
Domain shuffling and the evolution of vertebrates. Genome Res (2009) 1.18
Extraction of leukemia specific glycan motifs in humans by computational glycomics. Carbohydr Res (2005) 1.17