Published in Nucleic Acids Res on July 01, 2006
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res (2008) 54.83
PageMan: an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments. BMC Bioinformatics (2006) 3.34
Gene set enrichment analysis: performance evaluation and usage guidelines. Brief Bioinform (2011) 1.84
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments. Nucleic Acids Res (2008) 1.53
Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences. Bioinformatics (2008) 1.34
Analysis of temporal gene expression during Bacillus subtilis spore germination and outgrowth. J Bacteriol (2007) 1.24
Gene set analyses for interpreting microarray experiments on prokaryotic organisms. BMC Bioinformatics (2008) 1.11
Proinflammatory caspase-2-mediated macrophage cell death induced by a rough attenuated Brucella suis strain. Infect Immun (2011) 1.10
The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology. BMC Bioinformatics (2008) 1.01
Open source libraries and frameworks for biological data visualisation: a guide for developers. Proteomics (2015) 1.00
Dissecting complex transcriptional responses using pathway-level scores based on prior information. BMC Bioinformatics (2007) 1.00
Saccharomyces cerevisiae as a model organism: a comparative study. PLoS One (2011) 0.91
DISCLOSE : DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites. BMC Bioinformatics (2008) 0.91
Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks. Brief Bioinform (2008) 0.83
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46
Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A (2001) 132.88
Statistical significance for genomewide studies. Proc Natl Acad Sci U S A (2003) 88.64
PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet (2003) 53.59
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics (2004) 26.64
Multiple significance tests: the Bonferroni method. BMJ (1995) 23.46
The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res (2006) 22.70
GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol (2003) 22.63
GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics (2004) 20.23
The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Res (2003) 12.81
GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies. BMC Bioinformatics (2004) 11.23
PAGE: parametric analysis of gene set enrichment. BMC Bioinformatics (2005) 8.41
Significance analysis of functional categories in gene expression studies: a structured permutation approach. Bioinformatics (2005) 4.27
T-profiler: scoring the activity of predefined groups of genes using gene expression data. Nucleic Acids Res (2005) 2.88
PRODORIC: prokaryotic database of gene regulation. Nucleic Acids Res (2003) 2.81
Identifying subtle interrelated changes in functional gene categories using continuous measures of gene expression. Bioinformatics (2004) 2.47
GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms. Bioinformatics (2004) 1.83
Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information. Bioinformatics (2005) 1.82
GOAL: automated Gene Ontology analysis of expression profiles. Nucleic Acids Res (2004) 1.79
Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA. J Biol Chem (2005) 1.73
Reductive glutamine metabolism by IDH1 mediates lipogenesis under hypoxia. Nature (2011) 7.94
BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009. Nucleic Acids Res (2008) 4.75
Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis. Science (2012) 4.41
PrediSi: prediction of signal peptides and their cleavage positions. Nucleic Acids Res (2004) 3.93
BRENDA, the enzyme information system in 2011. Nucleic Acids Res (2010) 3.83
TRANSPATH: an integrated database on signal transduction and a tool for array analysis. Nucleic Acids Res (2003) 3.17
Oncogenic K-Ras decouples glucose and glutamine metabolism to support cancer cell growth. Mol Syst Biol (2011) 3.15
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
Increase of functional diversity by alternative splicing. Trends Genet (2003) 2.59
TRANSPATH: an information resource for storing and visualizing signaling pathways and their pathological aberrations. Nucleic Acids Res (2006) 2.55
RNA-dependent cysteine biosynthesis in archaea. Science (2005) 2.50
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
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
VBASE2, an integrative V gene database. Nucleic Acids Res (2005) 1.86
A Direct in vivo RNAi screen identifies MKK4 as a key regulator of liver regeneration. Cell (2013) 1.86
Genome sequences of the biotechnologically important Bacillus megaterium strains QM B1551 and DSM319. J Bacteriol (2011) 1.86
Bacillus megaterium--from simple soil bacterium to industrial protein production host. Appl Microbiol Biotechnol (2007) 1.85
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
Application of Petri net based analysis techniques to signal transduction pathways. BMC Bioinformatics (2006) 1.68
Long-term anaerobic survival of the opportunistic pathogen Pseudomonas aeruginosa via pyruvate fermentation. J Bacteriol (2004) 1.63
Atypical chronic myeloid leukemia as defined in the WHO classification is a JAK2 V617F negative neoplasm. Leuk Res (2008) 1.62
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
SYSTOMONAS--an integrated database for systems biology analysis of Pseudomonas. Nucleic Acids Res (2007) 1.55
The biochemistry of heme biosynthesis. Arch Biochem Biophys (2008) 1.53
Structure and function of enzymes in heme biosynthesis. Protein Sci (2010) 1.48
PRODORIC (release 2009): a database and tool platform for the analysis of gene regulation in prokaryotes. Nucleic Acids Res (2008) 1.39
Model validation of biological pathways using Petri nets--demonstrated for apoptosis. Biosystems (2004) 1.36
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
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
Complexome profiling identifies TMEM126B as a component of the mitochondrial complex I assembly complex. Cell Metab (2012) 1.29
Coexpression of cyclooxygenases (COX-1, COX-2) and vascular endothelial growth factors (VEGF-A, VEGF-C) in esophageal adenocarcinoma. Cancer Res (2005) 1.25
Anaerobic adaptation in Pseudomonas aeruginosa: definition of the Anr and Dnr regulons. Environ Microbiol (2010) 1.24
Anaerobic physiology of Pseudomonas aeruginosa in the cystic fibrosis lung. Int J Med Microbiol (2010) 1.23
Oxygen-independent coproporphyrinogen-III oxidase HemN from Escherichia coli. J Biol Chem (2002) 1.22
Different mechanisms of cyclin D1 overexpression in multiple myeloma revealed by fluorescence in situ hybridization and quantitative analysis of mRNA levels. Blood (2004) 1.20
Pathways for phosphatidylcholine biosynthesis in bacteria. Microbiology (2003) 1.20
ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks. Nucleic Acids Res (2008) 1.18
Petri net modelling of gene regulation of the Duchenne muscular dystrophy. Biosystems (2008) 1.18
Gene expression changes in the host response between resistant and susceptible inbred mouse strains after influenza A infection. Microbes Infect (2010) 1.18
The induction of cytochrome P450 3A5 (CYP3A5) in the human liver and intestine is mediated by the xenobiotic sensors pregnane X receptor (PXR) and constitutively activated receptor (CAR). J Biol Chem (2004) 1.16
A short story about a big magic bug. Bioeng Bugs (2010) 1.16
Structure and function of radical SAM enzymes. Curr Opin Chem Biol (2004) 1.16
Characterization of JG024, a pseudomonas aeruginosa PB1-like broad host range phage under simulated infection conditions. BMC Microbiol (2010) 1.15
Production and secretion of recombinant Leuconostoc mesenteroides dextransucrase DsrS in Bacillus megaterium. Biotechnol Bioeng (2005) 1.14
ADAM17 regulates epidermal growth factor receptor expression through the activation of Notch1 in non-small cell lung cancer. Cancer Res (2010) 1.14
omiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data. Bioinformatics (2013) 1.13
Identification and functional analysis of enzymes required for precorrin-2 dehydrogenation and metal ion insertion in the biosynthesis of sirohaem and cobalamin in Bacillus megaterium. Biochem J (2003) 1.13
Steady state analysis of metabolic pathways using Petri nets. In Silico Biol (2003) 1.12
A multifaceted study of Pseudomonas aeruginosa shutdown by virulent podovirus LUZ19. MBio (2013) 1.11
Crystal structure of the nitrogenase-like dark operative protochlorophyllide oxidoreductase catalytic complex (ChlN/ChlB)2. J Biol Chem (2010) 1.11
Characterization of a new type of phosphopantetheinyl transferase for fatty acid and siderophore synthesis in Pseudomonas aeruginosa. J Biol Chem (2002) 1.10
An improved Escherichia coli donor strain for diparental mating. FEMS Microbiol Lett (2009) 1.10
A biomolecular isolation framework for eco-systems biology. ISME J (2012) 1.10
MetaQuant: a tool for the automatic quantification of GC/MS-based metabolome data. Bioinformatics (2006) 1.10
Molecular mechanisms of polymorphic CYP3A7 expression in adult human liver and intestine. J Biol Chem (2002) 1.10
Gli1 mediates lung cancer cell proliferation and Sonic Hedgehog-dependent mesenchymal cell activation. PLoS One (2013) 1.08
Genetic tools for the investigation of Roseobacter clade bacteria. BMC Microbiol (2009) 1.07
Bacillus subtilis Fnr senses oxygen via a [4Fe-4S] cluster coordinated by three cysteine residues without change in the oligomeric state. Mol Microbiol (2006) 1.06
Complexity of dopamine metabolism. Cell Commun Signal (2013) 1.06
Sequencing and characterization of Pseudomonas aeruginosa phage JG004. BMC Microbiol (2011) 1.04
Structural and functional comparison of HemN to other radical SAM enzymes. Biol Chem (2005) 1.04