2006
Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights
Kim PM, Lu LJ, Xia Y, Gerstein MB. Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights. Science 2006, 314: 1938-1941. PMID: 17185604, DOI: 10.1126/science.1136174.Peer-Reviewed Original ResearchGenomic analysis of the hierarchical structure of regulatory networks
Yu H, Gerstein M. Genomic analysis of the hierarchical structure of regulatory networks. Proceedings Of The National Academy Of Sciences Of The United States Of America 2006, 103: 14724-14731. PMID: 17003135, PMCID: PMC1595419, DOI: 10.1073/pnas.0508637103.Peer-Reviewed Original ResearchConceptsTranscription factorsMaster transcription factorRegulatory networksRegulatory hierarchyProtein-protein interaction networkMost transcription factorsExpression of thousandsExpression level changesGenomic analysisProtein interactionsInteraction networksTarget genesDirect targetGenesEukaryotesProkaryotesCellsFundamental questionsBiologyTargetExpression
2004
Genomic analysis of regulatory network dynamics reveals large topological changes
Luscombe NM, Madan Babu M, Yu H, Snyder M, Teichmann SA, Gerstein M. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 2004, 431: 308-312. PMID: 15372033, DOI: 10.1038/nature02782.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsCell CycleGene Expression ProfilingGene Expression Regulation, FungalGenomicsModels, BiologicalSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsSoftwareTranscription FactorsConceptsTranscription factorsActive transcription factorRegulatory network dynamicsBiological networksHigher eukaryotesLarge-scale topological changesGenomic scaleGenomic analysisCell cycleDiverse stimuliEnvironmental responsesMolecular biologyFast signal propagationTwo-tiered hierarchyNetwork analysisGlobal topological measuresLocal motifsSub-network structureEukaryotesTemporal progression