2019
Transcriptional regulatory model of fibrosis progression in the human lung
McDonough JE, Ahangari F, Li Q, Jain S, Verleden SE, Herazo-Maya J, Vukmirovic M, DeIuliis G, Tzouvelekis A, Tanabe N, Chu F, Yan X, Verschakelen J, Homer RJ, Manatakis DV, Zhang J, Ding J, Maes K, De Sadeleer L, Vos R, Neyrinck A, Benos PV, Bar-Joseph Z, Tantin D, Hogg JC, Vanaudenaerde BM, Wuyts WA, Kaminski N. Transcriptional regulatory model of fibrosis progression in the human lung. JCI Insight 2019, 4 PMID: 31600171, PMCID: PMC6948862, DOI: 10.1172/jci.insight.131597.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisAdvanced fibrosisAlveolar surface densityFibrosis progressionLung fibrosisHuman lungDynamic Regulatory Events MinerExtent of fibrosisIPF lungsPulmonary fibrosisControl lungsIPF tissueB lymphocytesFibrosisLungLinear mixed-effects modelsMixed-effects modelsGene expression changesSystems biology modelsDifferential gene expression analysisGene expression analysisProgressionGene expression networksRNA sequencingBiology models
2008
Nonlinear cooperation of p53-ING1-induced bax expression and protein S-nitrosylation in GSNO-induced thymocyte apoptosis: a quantitative approach with cross-platform validation
Duan S, Wan L, Fu WJ, Pan H, Ding Q, Chen C, Han P, Zhu X, Du L, Liu H, Chen Y, Liu X, Yan X, Deng M, Qian M. Nonlinear cooperation of p53-ING1-induced bax expression and protein S-nitrosylation in GSNO-induced thymocyte apoptosis: a quantitative approach with cross-platform validation. Apoptosis 2008, 14: 236. PMID: 19082896, DOI: 10.1007/s10495-008-0288-4.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsApoptosisBcl-2-Associated X ProteinDexamethasoneGene DosageGene Expression RegulationInhibitor of Growth Protein 1Intracellular Signaling Peptides and ProteinsMiceModels, BiologicalNeural Networks, ComputerNonlinear DynamicsNuclear ProteinsOligonucleotide Array Sequence AnalysisProtein BindingReproducibility of ResultsReverse Transcriptase Polymerase Chain ReactionS-NitrosoglutathioneThymus GlandTumor Suppressor Protein p53Tumor Suppressor ProteinsGenomic Androgen Receptor-Occupied Regions with Different Functions, Defined by Histone Acetylation, Coregulators and Transcriptional Capacity
Jia L, Berman BP, Jariwala U, Yan X, Cogan JP, Walters A, Chen T, Buchanan G, Frenkel B, Coetzee GA. Genomic Androgen Receptor-Occupied Regions with Different Functions, Defined by Histone Acetylation, Coregulators and Transcriptional Capacity. PLOS ONE 2008, 3: e3645. PMID: 18997859, PMCID: PMC2577007, DOI: 10.1371/journal.pone.0003645.Peer-Reviewed Original ResearchConceptsTranscription factorsChromatin immunoprecipitation-microarray analysisTarget gene expression levelsSame transcription factorHuman genomic DNAGene expression levelsChromatin structureSuch genesKnockout experimentsHistone acetylationTarget genesEnhancer activityTranscriptional capacityDNA locationsGenomic androgen receptorsGene expressionGenomic DNAMicroarray analysisProstate cancer cellsDifferential regulationGenesLuciferase reporterDiverse mechanismsHigh-throughput elucidationContinuous stretch
2006
MARD: a new method to detect differential gene expression in treatment-control time courses
Cheng C, Ma X, Yan X, Sun F, Li LM. MARD: a new method to detect differential gene expression in treatment-control time courses. Bioinformatics 2006, 22: 2650-2657. PMID: 16928738, DOI: 10.1093/bioinformatics/btl451.Peer-Reviewed Original Research