2009
Identifying promoter features of co-regulated genes with similar network motifs
Harari O, del Val C, Romero-Zaliz R, Shin D, Huang H, Groisman EA, Zwir I. Identifying promoter features of co-regulated genes with similar network motifs. BMC Bioinformatics 2009, 10: s1. PMID: 19426448, PMCID: PMC2681069, DOI: 10.1186/1471-2105-10-s4-s1.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBinding SitesComputational BiologyDNA-Directed RNA PolymerasesEscherichia coliGene Expression Regulation, BacterialGene Regulatory NetworksGenome, BacterialMolecular Sequence DataPromoter Regions, GeneticRegulatory Sequences, Nucleic AcidSalmonella typhiTranscription FactorsConceptsTranscriptional regulatorsPromoter featuresNetwork motifsTranscription factorsTarget genesRegulatory proteinsPhoP/PhoQ regulatory systemExpression patternsGene expressionCo-regulated genesGroup of genesGene regulatory networksDifferential gene expressionCis-acting elementsDifferent expression patternsCharacteristic expression patternsSalmonella enterica serovar TyphimuriumProteobacterial genomesPhoP proteinEnterica serovar TyphimuriumRegulatory networksRNA polymeraseRegulatory regionsRepression siteMultiple promoters
2005
Analysis of differentially-regulated genes within a regulatory network by GPS genome navigation
Zwir I, Huang H, Groisman EA. Analysis of differentially-regulated genes within a regulatory network by GPS genome navigation. Bioinformatics 2005, 21: 4073-4083. PMID: 16159917, DOI: 10.1093/bioinformatics/bti672.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsArtificial IntelligenceCluster AnalysisComputational BiologyDatabases, GeneticEscherichia coliEscherichia coli ProteinsGene Expression RegulationGene Expression Regulation, BacterialGenomeGenomicsPromoter Regions, GeneticResponse ElementsSalmonella entericaSoftwareTranscription, GeneticConceptsPhoP proteinRegulatory featuresGene expressionEnteric bacteria Escherichia coliCis-regulatory featuresCo-regulated promotersPost-genomic eraTranscription initiationRegulatory networksRegulatory interactionsGene transcriptionNovel memberExpression patternsBacteria Escherichia coliGenesEscherichia coliSalmonella entericaMultiple mechanismsProteinFundamental mechanismsExpressionRegulonTranscriptionPromoterReduced dataset
1996
Mg2+ as an Extracellular Signal: Environmental Regulation of Salmonella Virulence
Véscovi E, Soncini F, Groisman E. Mg2+ as an Extracellular Signal: Environmental Regulation of Salmonella Virulence. Cell 1996, 84: 165-174. PMID: 8548821, DOI: 10.1016/s0092-8674(00)81003-x.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBacterial ProteinsBase SequenceCationsGene Expression Regulation, BacterialHydrogen-Ion ConcentrationKineticsMagnesiumMolecular Sequence DataMutationPeptidesPhenotypeProtein ConformationSalmonella typhimuriumSensitivity and SpecificitySignal TransductionTranscription FactorsVirulenceConceptsPhoP/PhoQ systemTranscription of PhoPSignal transduction cascadeVirulence regulatory systemGene expression patternsPeriplasmic domainWild-type SalmonellaExtracellular signalsTransduction cascadeSalmonella virulenceExpression patternsFirst messengersPhoPRegulatory systemGenesPhoQSalmonella typhimuriumPhysiological concentrationsDivalent cationsTranscriptionConcentration of Mg2LociMg2DomainVirulence