Published in Nucleic Acids Res on January 01, 2007
HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res (2008) 11.23
Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes. Nucleic Acids Res (2010) 5.23
Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes. Nucleic Acids Res (2008) 2.71
A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst Biol (2008) 1.81
Reconstruction of metabolic pathways for the cattle genome. BMC Syst Biol (2009) 1.63
PRODORIC (release 2009): a database and tool platform for the analysis of gene regulation in prokaryotes. Nucleic Acids Res (2008) 1.39
The Regulatory Network of Pseudomonas aeruginosa. Microb Inform Exp (2011) 0.91
Regulatory and metabolic networks for the adaptation of Pseudomonas aeruginosa biofilms to urinary tract-like conditions. PLoS One (2013) 0.87
Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions. Database (Oxford) (2010) 0.85
Clinical decision support systems for improving diagnostic accuracy and achieving precision medicine. J Clin Bioinforma (2015) 0.82
A combined computational-experimental analyses of selected metabolic enzymes in Pseudomonas species. Int J Biol Sci (2008) 0.79
MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89
EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet (2000) 69.26
From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res (2006) 44.35
Creating a bioinformatics nation. Nature (2002) 25.48
The ENZYME database in 2000. Nucleic Acids Res (2000) 23.85
The Jalview Java alignment editor. Bioinformatics (2004) 21.74
BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res (2004) 15.43
The Pathway Tools software. Bioinformatics (2002) 14.89
GenBank. Nucleic Acids Res (2006) 12.21
BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res (2004) 8.21
Establishment of Pseudomonas aeruginosa infection: lessons from a versatile opportunist. Microbes Infect (2000) 7.50
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res (2005) 7.13
DDBJ in preparation for overview of research activities behind data submissions. Nucleic Acids Res (2006) 6.02
RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. Nucleic Acids Res (2006) 5.57
EMBL Nucleotide Sequence Database: developments in 2005. Nucleic Acids Res (2006) 5.13
Integrating biological databases. Nat Rev Genet (2003) 4.41
Systems biology markup language: Level 2 and beyond. Biochem Soc Trans (2003) 4.11
Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes. Bioinformatics (2005) 2.82
PRODORIC: prokaryotic database of gene regulation. Nucleic Acids Res (2003) 2.81
Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation. Nucleic Acids Res (2005) 2.61
The University of Minnesota Biocatalysis/Biodegradation Database: the first decade. Nucleic Acids Res (2006) 2.52
Atlas - a data warehouse for integrative bioinformatics. BMC Bioinformatics (2005) 2.51
PathFinder: reconstruction and dynamic visualization of metabolic pathways. Bioinformatics (2002) 2.43
metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella. Nucleic Acids Res (2005) 2.21
PseudoCyc, a pathway-genome database for Pseudomonas aeruginosa. J Mol Microbiol Biotechnol (2003) 1.48
Anaerobic survival of Pseudomonas aeruginosa by pyruvate fermentation requires an Usp-type stress protein. J Bacteriol (2006) 1.34
BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res (2004) 8.21
Reductive glutamine metabolism by IDH1 mediates lipogenesis under hypoxia. Nature (2011) 7.94
BRENDA, enzyme data and metabolic information. Nucleic Acids Res (2002) 7.92
BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009. Nucleic Acids Res (2008) 4.75
IntEnz, the integrated relational enzyme database. Nucleic Acids Res (2004) 4.65
PrediSi: prediction of signal peptides and their cleavage positions. Nucleic Acids Res (2004) 3.93
QMEAN: A comprehensive scoring function for model quality assessment. Proteins (2008) 3.90
BRENDA, the enzyme information system in 2011. Nucleic Acids Res (2010) 3.83
GC-MS libraries for the rapid identification of metabolites in complex biological samples. FEBS Lett (2005) 3.29
Oncogenic K-Ras decouples glucose and glutamine metabolism to support cancer cell growth. Mol Syst Biol (2011) 3.15
Retracted Positive and negative roles of p85 alpha and p85 beta regulatory subunits of phosphoinositide 3-kinase in insulin signaling. J Biol Chem (2003) 3.06
BRENDA, AMENDA and FRENDA: the enzyme information system in 2007. Nucleic Acids Res (2007) 2.94
Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes. Bioinformatics (2005) 2.82
PRODORIC: prokaryotic database of gene regulation. Nucleic Acids Res (2003) 2.81
JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Res (2005) 2.60
RNA-dependent cysteine biosynthesis in archaea. Science (2005) 2.50
CUPSAT: prediction of protein stability upon point mutations. Nucleic Acids Res (2006) 2.38
BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA. Nucleic Acids Res (2012) 2.33
MetaboliteDetector: comprehensive analysis tool for targeted and nontargeted GC/MS based metabolome analysis. Anal Chem (2009) 2.17
The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea. ISME J (2009) 2.00
Crystal structure of coproporphyrinogen III oxidase reveals cofactor geometry of Radical SAM enzymes. EMBO J (2003) 1.98
Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5'- and 3'-halves. Nature (2005) 1.97
BRENDA: a resource for enzyme data and metabolic information. Trends Biochem Sci (2002) 1.97
VBASE2, an integrative V gene database. Nucleic Acids Res (2005) 1.86
Genome sequences of the biotechnologically important Bacillus megaterium strains QM B1551 and DSM319. J Bacteriol (2011) 1.86
Hormonal regulation of adiponectin gene expression in 3T3-L1 adipocytes. Biochem Biophys Res Commun (2002) 1.86
Bacillus megaterium--from simple soil bacterium to industrial protein production host. Appl Microbiol Biotechnol (2007) 1.85
Adiponectin gene expression and secretion is inhibited by interleukin-6 in 3T3-L1 adipocytes. Biochem Biophys Res Commun (2003) 1.82
Crystal structure of 5-aminolevulinate synthase, the first enzyme of heme biosynthesis, and its link to XLSA in humans. EMBO J (2005) 1.74
The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources. Nucleic Acids Res (2010) 1.71
JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information. Nucleic Acids Res (2006) 1.69
Alternative mRNA splicing produces a novel biologically active short isoform of PGC-1alpha. J Biol Chem (2009) 1.67
Long-term anaerobic survival of the opportunistic pathogen Pseudomonas aeruginosa via pyruvate fermentation. J Bacteriol (2004) 1.63
The structure of an inverting GH43 beta-xylosidase from Geobacillus stearothermophilus with its substrate reveals the role of the three catalytic residues. J Mol Biol (2006) 1.63
Immune-responsive gene 1 protein links metabolism to immunity by catalyzing itaconic acid production. Proc Natl Acad Sci U S A (2013) 1.62
RhlR expression in Pseudomonas aeruginosa is modulated by the Pseudomonas quinolone signal via PhoB-dependent and -independent pathways. J Bacteriol (2006) 1.59
Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC). Bioinformatics (2004) 1.56
The biochemistry of heme biosynthesis. Arch Biochem Biophys (2008) 1.53
Structure and function of enzymes in heme biosynthesis. Protein Sci (2010) 1.48
Similarity and differences in the Lactobacillus acidophilus group identified by polyphasic analysis and comparative genomics. J Bacteriol (2006) 1.46
Piezosurgery: an ultrasound device for cutting bone and its use and limitations in maxillofacial surgery. Br J Oral Maxillofac Surg (2004) 1.44
Fast and robust registration of PET and MR images of human brain. Neuroimage (2004) 1.41
PRODORIC (release 2009): a database and tool platform for the analysis of gene regulation in prokaryotes. Nucleic Acids Res (2008) 1.39
Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase. EMBO J (2003) 1.35
AAV6.βARKct cardiac gene therapy ameliorates cardiac function and normalizes the catecholaminergic axis in a clinically relevant large animal heart failure model. Eur Heart J (2012) 1.35
The substrate specificity-determining amino acid code of 4-coumarate:CoA ligase. Proc Natl Acad Sci U S A (2003) 1.35
Anaerobic survival of Pseudomonas aeruginosa by pyruvate fermentation requires an Usp-type stress protein. J Bacteriol (2006) 1.34
JVirGel: Calculation of virtual two-dimensional protein gels. Nucleic Acids Res (2003) 1.33
Biochemical characterization and identification of the catalytic residues of a family 43 beta-D-xylosidase from Geobacillus stearothermophilus T-6. Biochemistry (2005) 1.29
The Fnr regulon of Bacillus subtilis. J Bacteriol (2006) 1.29
The anaerobic regulatory network required for Pseudomonas aeruginosa nitrate respiration. J Bacteriol (2007) 1.29
The importance of uniformity in reporting protein-function data. Trends Biochem Sci (2005) 1.27
Observing local and global properties of metabolic pathways: 'load points' and 'choke points' in the metabolic networks. Bioinformatics (2006) 1.26
Atomic resolution structures of R-specific alcohol dehydrogenase from Lactobacillus brevis provide the structural bases of its substrate and cosubstrate specificity. J Mol Biol (2005) 1.25
The complex methylome of the human gastric pathogen Helicobacter pylori. Nucleic Acids Res (2013) 1.25
Anaerobic adaptation in Pseudomonas aeruginosa: definition of the Anr and Dnr regulons. Environ Microbiol (2010) 1.24