Featured Publications
A novel pathway-based distance score enhances assessment of disease heterogeneity in gene expression
Yan X, Liang A, Gomez J, Cohn L, Zhao H, Chupp GL. A novel pathway-based distance score enhances assessment of disease heterogeneity in gene expression. BMC Bioinformatics 2017, 18: 309. PMID: 28637421, PMCID: PMC5480187, DOI: 10.1186/s12859-017-1727-4.Peer-Reviewed Original ResearchTesting gene set enrichment for subset of genes: Sub-GSE
Yan X, Sun F. Testing gene set enrichment for subset of genes: Sub-GSE. BMC Bioinformatics 2008, 9: 362. PMID: 18764941, PMCID: PMC2543030, DOI: 10.1186/1471-2105-9-362.Peer-Reviewed Original Research
2024
Biomarkers and molecular endotypes of sarcoidosis: lessons from omics and non-omics studies
Ji H, Xi N, Mohan C, Yan X, Jain K, Zang Q, Gahtan V, Zhao R. Biomarkers and molecular endotypes of sarcoidosis: lessons from omics and non-omics studies. Frontiers In Immunology 2024, 14: 1342429. PMID: 38250062, PMCID: PMC10797773, DOI: 10.3389/fimmu.2023.1342429.Peer-Reviewed Original ResearchConceptsMolecular endotypesChronic granulomatous disorderSarcoidosis biomarkersTNF blockadeDifferentiate sarcoidosisGranulomatous disorderSarcoidosisAdvanced omics approachesHealthy controlsDisease heterogeneityEndotypesDocumented biomarkerBiomarker profilesPersonalized medicineBiomarkersOmics approachesOmics studiesDiseaseDiagnosisTargeted studiesOmicsBlockadePrognosisTherapyEtiology
2020
Latent-space embedding of expression data identifies gene signatures from sputum samples of asthmatic patients
Lou S, Li T, Spakowicz D, Yan X, Chupp GL, Gerstein M. Latent-space embedding of expression data identifies gene signatures from sputum samples of asthmatic patients. BMC Bioinformatics 2020, 21: 457. PMID: 33059594, PMCID: PMC7560063, DOI: 10.1186/s12859-020-03785-y.Peer-Reviewed Original Research
2012
Modeling RNA degradation for RNA-Seq with applications
Wan L, Yan X, Chen T, Sun F. Modeling RNA degradation for RNA-Seq with applications. Biostatistics 2012, 13: 734-747. PMID: 22353193, PMCID: PMC3616752, DOI: 10.1093/biostatistics/kxs001.Peer-Reviewed Original Research
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 Proteins
2007
Inferring activity changes of transcription factors by binding association with sorted expression profiles
Cheng C, Yan X, Sun F, Li LM. Inferring activity changes of transcription factors by binding association with sorted expression profiles. BMC Bioinformatics 2007, 8: 452. PMID: 18021409, PMCID: PMC2194743, DOI: 10.1186/1471-2105-8-452.Peer-Reviewed Original ResearchConceptsTranscription factorsExpression profilesMicroarray dataTarget gene selectionPost-transcriptional modificationsChIP-chip dataMicroarray expression profilesExpression differentiationLow expression levelsProfile of expressionTarget genesRegulatory mechanismsGene expressionBiological processesMicroarray studiesAffinity dataGene selectionSame machineryExpression levelsGenesActivity changesSignificance cutoffDifferentiationMeaningful hypothesesAffinity scores
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