2024
Representing core gene expression activity relationships using the latent structure implicit in Bayesian networks
Gao J, Gerstein M. Representing core gene expression activity relationships using the latent structure implicit in Bayesian networks. Bioinformatics 2024, 40: btae463. PMID: 39051682, PMCID: PMC11316617, DOI: 10.1093/bioinformatics/btae463.Peer-Reviewed Original ResearchTranscriptional regulatory networksGene regulatory networksCo-expression networkGene expression activityChIP-seqGene conservationCluster genesSupplementary dataRegulatory networksBiological networksClearer clusteringCo-expressionExpression activityBioinformaticsGenesBiomedical studiesConservationExpressionClusters
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 ResearchConceptsTranscription 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