Xiting Yan, PhD
Research & Publications
Biography
News
Research Summary
My current research focus on two parts: (1) developing novel statistical and computational models to analyze large scale omics and drug perturbation data to better understand disease pathogenesis, and (2) understanding the heterogeneity and pathogenesis of pulmonary diseases, such as asthma, idiopathic pulmonary fibrosis (IPF), sarcoidosis, pediatric cystic fibrosis and so on, by tailoring statistical and computational methods based on existing biological knowledge of the diseases.
My team has been involved in multiple transcriptomic studies of asthma, IPF, sarcoidosis, cystic fibrosis and lung injuries in pediatric patients undertaking cardio bypass procedure. My team have analyzed various types of large-scale transcriptomic data generated by these studies which include microarray gene expression data, bulk RNA sequencing data, single cell RNA sequencing data, T cell receptor repertoire data and 16s rRNA sequencing data. For each study, we tailed our computational and statistical analysis of the data based on existing biological knowledge of the corresponding disease or condition. These analyses have made various discoveries in heterogeneity in asthma pathogenesis, cell type specific changes in asthma patients, heterogeneity and molecular biomarker of sarcoidosis, rare cell populations specific to IPF and COPD, potential antigen specific T cell clones for SARS-CoV-2 infection (COVID19) in adults and so on. My team is currently working with physicians and basic scientists to make further and more translational discoveries for the aforementioned and more pulmonary diseases.
During our extensive analyses of various types of omics data generated by our collaborators, my team also identify computational and statistical needs and develop novel methods to address these needs. For example, in the analysis of single cell RNA sequencing data (scRNA-seq), we found prevalent dropout events and dominant subject variation in the data, which was not well addressed by existing differential expression (DE) methods designed for scRNA-seq data. We developed iDESC to identify cell type-specific differentially expressed genes from scRNA-seq data with multiple subjects. The development of these tools further boosted our capacity and ability to analyze different types of OMICS data to better understand disease pathogenesis.
Extensive Research Description
Analysis of one time-point microarray and longitudinal bulk RNA sequencing data from asthma patients;
Analysis of longitudinal microbiome sequencing data from children with cystic fibrosis;
Bulk RNA sequencing of IPF, A1AT and SARC patients using Ion Torrent technology;
Single cell RNA sequencing data analysis;
Spatial single cell RNA sequencing data analysis;
Coauthors
Research Interests
Genetics; Lung Diseases; Respiratory Hypersensitivity; Computational Biology; Genomics; Biostatistics; Molecular Medicine
Public Health Interests
Bioinformatics; Biomarkers; Genetics, Genomics, Epigenetics; Microbial Ecology; Modeling
Research Image
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Selected Publications
- Computational and Statistical Methods for Single-Cell RNA Sequencing DataWang Z, Yan X. Computational and Statistical Methods for Single-Cell RNA Sequencing Data 2022, 3-35. DOI: 10.1007/978-3-662-65902-1_1.
- Transcriptomics of bronchoalveolar lavage cells identifies new molecular endotypes of sarcoidosisVukmirovic M, Yan X, Gibson KF, Gulati M, Schupp JC, DeIuliis G, Adams TS, Hu B, Mihaljinec A, Woolard TN, Lynn H, Emeagwali N, Herzog EL, Chen ES, Morris A, Leader JK, Zhang Y, Garcia JGN, Maier LA, Collman RG, Drake WP, Becich MJ, Hochheiser H, Wisniewski SR, Benos PV, Moller DR, Prasse A, Koth LL, Kaminski N. Transcriptomics of bronchoalveolar lavage cells identifies new molecular endotypes of sarcoidosis European Respiratory Journal 2021, 58: 2002950. PMID: 34083402, PMCID: PMC9759791, DOI: 10.1183/13993003.02950-2020.
- G2S3: A gene graph-based imputation method for single-cell RNA sequencing dataWu W, Liu Y, Dai Q, Yan X, Wang Z. G2S3: A gene graph-based imputation method for single-cell RNA sequencing data PLOS Computational Biology 2021, 17: e1009029. PMID: 34003861, PMCID: PMC8189489, DOI: 10.1371/journal.pcbi.1009029.
- A novel pathway-based distance score enhances assessment of disease heterogeneity in gene expressionYan 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.
- Noninvasive Analysis of the Sputum Transcriptome Discriminates Clinical Phenotypes of AsthmaYan X, Chu JH, Gomez J, Koenigs M, Holm C, He X, Perez MF, Zhao H, Mane S, Martinez FD, Ober C, Nicolae DL, Barnes KC, London SJ, Gilliland F, Weiss ST, Raby BA, Cohn L, Chupp GL. Noninvasive Analysis of the Sputum Transcriptome Discriminates Clinical Phenotypes of Asthma American Journal Of Respiratory And Critical Care Medicine 2015, 191: 1116-1125. PMID: 25763605, PMCID: PMC4451618, DOI: 10.1164/rccm.201408-1440oc.
- Detecting functional rare variants by collapsing and incorporating functional annotation in Genetic Analysis Workshop 17 mini-exome dataYan X, Li L, Lee JS, Zheng W, Ferguson J, Zhao H. Detecting functional rare variants by collapsing and incorporating functional annotation in Genetic Analysis Workshop 17 mini-exome data BMC Proceedings 2011, 5: s27. PMID: 22373324, PMCID: PMC3287862, DOI: 10.1186/1753-6561-5-s9-s27.
- Detecting differentially expressed genes by relative entropyYan X, Deng M, Fung K, Qian M. Detecting differentially expressed genes by relative entropy Journal Of Theoretical Biology 2005, 234: 395-402. PMID: 15784273, DOI: 10.1016/j.jtbi.2004.11.039.
- Testing gene set enrichment for subset of genes: Sub-GSEYan 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.
- A novel Bayesian framework for harmonizing information across tissues and studies to increase cell type deconvolution accuracy.Deng W, Li B, Wang J, Jiang W, Yan X, Li N, Vukmirovic M, Kaminski N, Wang J, Zhao H. A novel Bayesian framework for harmonizing information across tissues and studies to increase cell type deconvolution accuracy. Briefings In Bioinformatics 2023, 24 PMID: 36631398, PMCID: PMC9851324, DOI: 10.1093/bib/bbac616.
- Leveraging Cell-Specific Disease Signatures to Predict New Drug Therapies for Idiopathic Pulmonary FibrosisAdams T, Song Q, Justet A, Mcdonough J, DeIuliis G, Yan X, Bar-Joseph Z, Kaminski N. Leveraging Cell-Specific Disease Signatures to Predict New Drug Therapies for Idiopathic Pulmonary Fibrosis 2022, a2318-a2318. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a2318.
- Decellularized Lung Tissue Proteomics Showed Decreased Surfactant and Increased Inflammatory Proteins in the Aged LungMcdonough J, Cosme Jr. C, Rupert C, Schupp J, Ahangari F, DeIuliis G, Yan X, Hagood J, Vanaudenaerde B, Niklason L, Hansen K, Kaminski N. Decellularized Lung Tissue Proteomics Showed Decreased Surfactant and Increased Inflammatory Proteins in the Aged Lung 2022, a3903-a3903. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a3903.
- Single Nuclei RNA Sequencing of Differentially Affected Regions in IPF Lungs Suggests a Central Role of Aberrant Basaloid Cells in Disease ProgressionSchupp J, Clair G, Adams T, Mcdonough J, Flint J, Kothapalli N, De Sadeleer L, Justet A, Melchior J, Paurus V, Olson H, Deluliis G, Ahangari F, Bar-Joseph Z, Yan X, Ding J, Wuyts W, Vanaudenaerde B, Kaminski N. Single Nuclei RNA Sequencing of Differentially Affected Regions in IPF Lungs Suggests a Central Role of Aberrant Basaloid Cells in Disease Progression 2022, a4975-a4975. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4975.
- Interactive Web-Based Lung Cell Atlases Lower Barriers to Transcriptomic Data Sharing, Mining and DisseminationCosme Jr. C, Flint J, Neumark N, Kothapalli N, Balayev A, Adams T, Schupp J, Mcdonough J, Yan X, Sauler M, Kaminski N. Interactive Web-Based Lung Cell Atlases Lower Barriers to Transcriptomic Data Sharing, Mining and Dissemination 2022, a4978-a4978. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4978.
- A Probabilistic Graphical Model for Understanding Cellular Dynamics in Idiopathic Pulmonary Fibrosis ProgressionDing J, Zheng Y, Schupp J, Adams T, Ahangari F, Yan X, Hasen P, Bar-Joseph Z, De Sadeleer L, Mcdonough J, Vanaudenaerde B, Wuyts W, Kaminski N. A Probabilistic Graphical Model for Understanding Cellular Dynamics in Idiopathic Pulmonary Fibrosis Progression 2022, a4986-a4986. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4986.
- Deconvolution of Spatial Transcriptomic Allows to Predict the Spatial Location of Each Cell Type of Interest in the Fibrotic LungJustet A, Adams T, Balayev A, Bärnthaler T, Cosme Jr C, Mcdonough J, Flint J, Schupp J, Zhao A, Deluliis J, Ahangari F, Yan X, Kaminski N. Deconvolution of Spatial Transcriptomic Allows to Predict the Spatial Location of Each Cell Type of Interest in the Fibrotic Lung 2022, a4991-a4991. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a4991.
- Single-Cell RNA Sequencing of Peripheral Blood Mononuclear Cells Reveals That T Cell Composition, Gene Expression, and Clonotype Significantly Distinguish Fibrotic Hypersensitivity Pneumonitis and Idiopathic Pulmonary FibrosisZhao A, Unterman A, Adams T, Yan X, Justet A, Deluliis G, Herzog E, Prasse A, Buendía-Roldán I, Pardo A, Selman M, Kaminski N. Single-Cell RNA Sequencing of Peripheral Blood Mononuclear Cells Reveals That T Cell Composition, Gene Expression, and Clonotype Significantly Distinguish Fibrotic Hypersensitivity Pneumonitis and Idiopathic Pulmonary Fibrosis 2022, a3522-a3522. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a3522.
- Changes in Immune Cell Populations in the Peripheral Blood of Individuals with Interstitial Lung AbnormalitiesZhao A, Unterman A, Adams T, Justet A, Yan X, Deluliis G, Herzog E, Prasse A, Buendia-Roldan I, Pardo A, Selman M, Kaminski N. Changes in Immune Cell Populations in the Peripheral Blood of Individuals with Interstitial Lung Abnormalities 2022, a5273-a5273. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a5273.
- The Integrated Stress Response Is Upregulated in Pulmonary Structural and Immune Cells After Cardiopulmonary Bypass in ChildrenHabet V, Li N, Charkoftaki G, Vasiliou V, Yan X, Dela Cruz C, Pierce R. The Integrated Stress Response Is Upregulated in Pulmonary Structural and Immune Cells After Cardiopulmonary Bypass in Children 2022, a5039-a5039. DOI: 10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a5039.
- Emerging insights in sarcoidosis: moving forward through reverse translational researchLiu A, Sharma L, Yan X, Dela Cruz CS, Herzog EL, Ryu C. Emerging insights in sarcoidosis: moving forward through reverse translational research American Journal Of Physiology - Lung Cellular And Molecular Physiology 2022, 322: l518-l525. PMID: 35196896, PMCID: PMC8957321, DOI: 10.1152/ajplung.00266.2021.
- Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19Unterman A, Sumida TS, Nouri N, Yan X, Zhao AY, Gasque V, Schupp JC, Asashima H, Liu Y, Cosme C, Deng W, Chen M, Raredon MSB, Hoehn KB, Wang G, Wang Z, DeIuliis G, Ravindra NG, Li N, Castaldi C, Wong P, Fournier J, Bermejo S, Sharma L, Casanovas-Massana A, Vogels CBF, Wyllie AL, Grubaugh ND, Melillo A, Meng H, Stein Y, Minasyan M, Mohanty S, Ruff WE, Cohen I, Raddassi K, Niklason L, Ko A, Montgomery R, Farhadian S, Iwasaki A, Shaw A, van Dijk D, Zhao H, Kleinstein S, Hafler D, Kaminski N, Dela Cruz C. Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19 Nature Communications 2022, 13: 440. PMID: 35064122, PMCID: PMC8782894, DOI: 10.1038/s41467-021-27716-4.
- Metagenomic sequencing of the bronchoalveolar lavage extracellular virome and cellular transcriptome of sarcoidosis patients does not detect rubella virusKeeler E, Vukmirovic M, Yan X, Gulino K, Ghedin E, Kaminski N, Sullivan K, Bushman F, Collman R, Rosenbach M. Metagenomic sequencing of the bronchoalveolar lavage extracellular virome and cellular transcriptome of sarcoidosis patients does not detect rubella virus Sarcoidosis, Vasculitis, And Diffuse Lung Diseases 2022, 39: e2022040. PMID: 36533601, PMCID: PMC9798337, DOI: 10.36141/svdld.v39i4.13407.
- Lung Microenvironments and Disease Progression in Fibrotic Hypersensitivity Pneumonitis.De Sadeleer LJ, McDonough JE, Schupp JC, Yan X, Vanstapel A, Van Herck A, Everaerts S, Geudens V, Sacreas A, Goos T, Aelbrecht C, Nawrot TS, Martens DS, Schols D, Claes S, Verschakelen JA, Verbeken EK, Ackermann M, Decottignies A, Mahieu M, Hackett TL, Hogg JC, Vanaudenaerde BM, Verleden SE, Kaminski N, Wuyts WA. Lung Microenvironments and Disease Progression in Fibrotic Hypersensitivity Pneumonitis. American Journal Of Respiratory And Critical Care Medicine 2022, 205: 60-74. PMID: 34724391, PMCID: PMC8865586, DOI: 10.1164/rccm.202103-0569oc.
- Openness Weighted Association Studies: Leveraging Personal Genome Information to Prioritize Noncoding VariantsSong S, Shan N, Wang G, Yan X, Liu JS, Hou L. Openness Weighted Association Studies: Leveraging Personal Genome Information to Prioritize Noncoding Variants Bioinformatics 2021, 37: btab514-. PMID: 34260700, PMCID: PMC8665759, DOI: 10.1093/bioinformatics/btab514.
- Integrated Single Cell Atlas of Endothelial Cells of the Human LungSchupp JC, Adams TS, Cosme C, Raredon MSB, Yuan Y, Omote N, Poli S, Chioccioli M, Rose KA, Manning EP, Sauler M, DeIuliis G, Ahangari F, Neumark N, Habermann AC, Gutierrez AJ, Bui LT, Lafyatis R, Pierce RW, Meyer KB, Nawijn MC, Teichmann SA, Banovich NE, Kropski JA, Niklason LE, Pe’er D, Yan X, Homer RJ, Rosas IO, Kaminski N. Integrated Single Cell Atlas of Endothelial Cells of the Human Lung Circulation 2021, 144: 286-302. PMID: 34030460, PMCID: PMC8300155, DOI: 10.1161/circulationaha.120.052318.
- Single Cell RNA Velocity Analysis of Aberrant Basaloid Cells in Pulmonary Fibrosis Reveals Trajectory Towards an Alveolar Type I Like Cell StateSchupp J, Adams T, Ahangari F, McDonough J, DeIuliis G, Poli S, Rosas I, Yan X, Kaminski N. Single Cell RNA Velocity Analysis of Aberrant Basaloid Cells in Pulmonary Fibrosis Reveals Trajectory Towards an Alveolar Type I Like Cell State 2021, a4350-a4350. DOI: 10.1164/ajrccm-conference.2021.203.1_meetingabstracts.a4350.
- Integrated scRNAseq Analysis of Murine Lung Fibrosis Reveals Patterns in Composition and Gene Expression of LymphocytesAdams T, Schupp J, Mcdonough J, Chioccioli M, Rose K, DeIuliis G, Yan X, Kaminski N. Integrated scRNAseq Analysis of Murine Lung Fibrosis Reveals Patterns in Composition and Gene Expression of Lymphocytes 2021, a4351-a4351. DOI: 10.1164/ajrccm-conference.2021.203.1_meetingabstracts.a4351.
- Comparative scRNA-seq Analysis of Peripheral Blood Mononuclear Cells from Patients with COVID-19 and Idiopathic Pulmonary Fibrosis Demonstrates Dissimilar Cell Shifts and Gene Expression ProfilesZhao A, Unterman A, Schupp J, Adams T, Sumida T, Ryu C, DeIuliis G, Yan X, Hafler D, Dela Cruz C, Herzog E, Kaminski N. Comparative scRNA-seq Analysis of Peripheral Blood Mononuclear Cells from Patients with COVID-19 and Idiopathic Pulmonary Fibrosis Demonstrates Dissimilar Cell Shifts and Gene Expression Profiles 2021, a4361-a4361. DOI: 10.1164/ajrccm-conference.2021.203.1_meetingabstracts.a4361.
- Single-cell characterization of a model of poly I:C-stimulated peripheral blood mononuclear cells in severe asthmaChen A, Diaz-Soto MP, Sanmamed MF, Adams T, Schupp JC, Gupta A, Britto C, Sauler M, Yan X, Liu Q, Nino G, Cruz CSD, Chupp GL, Gomez JL. Single-cell characterization of a model of poly I:C-stimulated peripheral blood mononuclear cells in severe asthma Respiratory Research 2021, 22: 122. PMID: 33902571, PMCID: PMC8074196, DOI: 10.1186/s12931-021-01709-9.
- Immune dysregulation and autoreactivity correlate with disease severity in SARS-CoV-2-associated multisystem inflammatory syndrome in childrenRamaswamy A, Brodsky NN, Sumida TS, Comi M, Asashima H, Hoehn KB, Li N, Liu Y, Shah A, Ravindra NG, Bishai J, Khan A, Lau W, Sellers B, Bansal N, Guerrerio P, Unterman A, Habet V, Rice AJ, Catanzaro J, Chandnani H, Lopez M, Kaminski N, Dela Cruz CS, Tsang JS, Wang Z, Yan X, Kleinstein SH, van Dijk D, Pierce RW, Hafler DA, Lucas CL. Immune dysregulation and autoreactivity correlate with disease severity in SARS-CoV-2-associated multisystem inflammatory syndrome in children Immunity 2021, 54: 1083-1095.e7. PMID: 33891889, PMCID: PMC8043654, DOI: 10.1016/j.immuni.2021.04.003.
- Post-infectious inflammatory disease in MIS-C features elevated cytotoxicity signatures and autoreactivity that correlates with severity.Ramaswamy A, Brodsky NN, Sumida TS, Comi M, Asashima H, Hoehn KB, Li N, Liu Y, Shah A, Ravindra NG, Bishai J, Khan A, Lau W, Sellers B, Bansal N, Guerrerio P, Unterman A, Habet V, Rice AJ, Catanzaro J, Chandnani H, Lopez M, Kaminski N, Dela Cruz CS, Tsang JS, Wang Z, Yan X, Kleinstein SH, van Dijk D, Pierce RW, Hafler DA, Lucas CL. Post-infectious inflammatory disease in MIS-C features elevated cytotoxicity signatures and autoreactivity that correlates with severity. MedRxiv : The Preprint Server For Health Sciences 2021 PMID: 33300011, PMCID: PMC7724682, DOI: 10.1101/2020.12.01.20241364.
- MicroRNA miR-24-3p reduces DNA damage responses, apoptosis, and susceptibility to chronic obstructive pulmonary diseaseNouws J, Wan F, Finnemore E, Roque W, Kim SJ, Bazan IS, Li CX, Sköld C, Dai Q, Yan X, Chioccioli M, Neumeister V, Britto CJ, Sweasy J, Bindra RS, Wheelock ÅM, Gomez JL, Kaminski N, Lee PJ, Sauler M. MicroRNA miR-24-3p reduces DNA damage responses, apoptosis, and susceptibility to chronic obstructive pulmonary disease JCI Insight 2021, 6: e134218. PMID: 33290275, PMCID: PMC7934877, DOI: 10.1172/jci.insight.134218.
- Toward a Cell Atlas of the Human AirwaySchupp JC, Yan X, Kaminski N. Toward a Cell Atlas of the Human Airway American Journal Of Respiratory And Critical Care Medicine 2020, 202: 1611-1612. PMID: 32841575, PMCID: PMC7737583, DOI: 10.1164/rccm.202007-2977ed.
- Gene coexpression networks reveal novel molecular endotypes in alpha-1 antitrypsin deficiencyChu JH, Zang W, Vukmirovic M, Yan X, Adams T, DeIuliis G, Hu B, Mihaljinec A, Schupp JC, Becich MJ, Hochheiser H, Gibson KF, Chen ES, Morris A, Leader JK, Wisniewski SR, Zhang Y, Sciurba FC, Collman RG, Sandhaus R, Herzog EL, Patterson KC, Sauler M, Strange C, Kaminski N. Gene coexpression networks reveal novel molecular endotypes in alpha-1 antitrypsin deficiency Thorax 2020, 76: 134-143. PMID: 33303696, DOI: 10.1136/thoraxjnl-2019-214301.
- Regulation and characterization of tumor-infiltrating immune cells in breast cancerDai Q, Wu W, Amei A, Yan X, Lu L, Wang Z. Regulation and characterization of tumor-infiltrating immune cells in breast cancer International Immunopharmacology 2020, 90: 107167. PMID: 33223469, PMCID: PMC7855363, DOI: 10.1016/j.intimp.2020.107167.
- Single-Cell Transcriptional Archetypes of Airway Inflammation in Cystic Fibrosis.Schupp JC, Khanal S, Gomez JL, Sauler M, Adams TS, Chupp GL, Yan X, Poli S, Zhao Y, Montgomery RR, Rosas IO, Dela Cruz CS, Bruscia EM, Egan ME, Kaminski N, Britto CJ. Single-Cell Transcriptional Archetypes of Airway Inflammation in Cystic Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2020, 202: 1419-1429. PMID: 32603604, PMCID: PMC7667912, DOI: 10.1164/rccm.202004-0991oc.
- Latent-space embedding of expression data identifies gene signatures from sputum samples of asthmatic patientsLou 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.
- Severe respiratory viral infection induces procalcitonin in the absence of bacterial pneumoniaGautam S, Cohen AJ, Stahl Y, Toro P, Young GM, Datta R, Yan X, Ristic NT, Bermejo SD, Sharma L, Restrepo M, Dela Cruz CS. Severe respiratory viral infection induces procalcitonin in the absence of bacterial pneumonia Thorax 2020, 75: 974-981. PMID: 32826284, DOI: 10.1136/thoraxjnl-2020-214896.
- Interplay of tRNA-Derived Fragments and T Cell Activation in Breast Cancer Patient SurvivalShan N, Li N, Dai Q, Hou L, Yan X, Amei A, Lu L, Wang Z. Interplay of tRNA-Derived Fragments and T Cell Activation in Breast Cancer Patient Survival Cancers 2020, 12: 2230. PMID: 32785169, PMCID: PMC7466003, DOI: 10.3390/cancers12082230.
- Approaches for integrating heterogeneous RNA-seq data reveal cross-talk between microbes and genes in asthmatic patientsSpakowicz D, Lou S, Barron B, Gomez JL, Li T, Liu Q, Grant N, Yan X, Hoyd R, Weinstock G, Chupp GL, Gerstein M. Approaches for integrating heterogeneous RNA-seq data reveal cross-talk between microbes and genes in asthmatic patients Genome Biology 2020, 21: 150. PMID: 32571363, PMCID: PMC7310008, DOI: 10.1186/s13059-020-02033-z.
- Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosisAdams TS, Schupp JC, Poli S, Ayaub EA, Neumark N, Ahangari F, Chu SG, Raby BA, DeIuliis G, Januszyk M, Duan Q, Arnett HA, Siddiqui A, Washko GR, Homer R, Yan X, Rosas IO, Kaminski N. Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis Science Advances 2020, 6: eaba1983. PMID: 32832599, PMCID: PMC7439502, DOI: 10.1126/sciadv.aba1983.
- A Network of Sputum MicroRNAs is Associated with Neutrophilic Airway Inflammation in AsthmaGomez JL, Chen A, Diaz MP, Zirn N, Gupta A, Britto C, Sauler M, Yan X, Stewart E, Santerian K, Grant N, Liu Q, Fry R, Rager J, Cohn L, Alexis N, Chupp GL. A Network of Sputum MicroRNAs is Associated with Neutrophilic Airway Inflammation in Asthma American Journal Of Respiratory And Critical Care Medicine 2020, 0: 51-64. PMID: 32255668, PMCID: PMC7328332, DOI: 10.1164/rccm.201912-2360oc.
- Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis.Adams TS, Schupp JC, Poli S, Ayaub EA, Neumark N, Ahangari F, Chu SG, Raby BA, DeIuliis G, Januszyk M, Duan Q, Arnett HA, Siddiqui A, Washko GR, Homer R, Yan X, Rosas IO, Kaminski N. Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis. Science Advances 2020, 6 PMID: 32937511, DOI: 10.1126/sciadv.aba1983.
- Low Surfactant Type II Alveolar Epithelial Cells Are an Enriched Cell Population in the Aged LungMcDonough J, Adams T, Schupp J, DeIuliis G, Yan X, Cosme jr C, Kaminski N. Low Surfactant Type II Alveolar Epithelial Cells Are an Enriched Cell Population in the Aged Lung 2020, a4390-a4390. DOI: 10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a4390.
- Deconvolution of Bulk RNAseq Datasets Confirms Substantial Cellular Population Shifts in the Distal Lung in IPFAdams T, Schupp J, McDonough J, Ahangari F, DeIuliis G, Yan X, Rosas I, Kaminski N. Deconvolution of Bulk RNAseq Datasets Confirms Substantial Cellular Population Shifts in the Distal Lung in IPF 2020, a2248-a2248. DOI: 10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a2248.
- Gene Expression Patterns Distinctly Characterize Differentially Affected Regions in Human Fibrotic Hypersensitivity Pneumonitis LungsDe Sadeleer L, McDonough J, Schupp J, Yan X, Vanaudenaerde B, Verleden S, Kaminski N, Wuyts W. Gene Expression Patterns Distinctly Characterize Differentially Affected Regions in Human Fibrotic Hypersensitivity Pneumonitis Lungs 2020, a2262-a2262. DOI: 10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a2262.
- Single Cell Transcriptomics Reveals Novel COL15A1+ Endothelial Population in Pulmonary Fibrosis and Lung CancerSchupp J, Adams T, Ahangari F, Poli De Frias S, DeIuliis G, Yan X, Rosas I, Homer R, Kaminski N. Single Cell Transcriptomics Reveals Novel COL15A1+ Endothelial Population in Pulmonary Fibrosis and Lung Cancer 2020, a6142-a6142. DOI: 10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a6142.
- Severe Respiratory Viral Infection Increases Procalcitonin in the Absence of Bacterial PneumoniaGautam S, Cohen A, Stahl Y, Valda Toro P, Young G, Yan X, Kunitomo Y, Card M, Tsang D, Dela Cruz C. Severe Respiratory Viral Infection Increases Procalcitonin in the Absence of Bacterial Pneumonia 2020, a6232-a6232. DOI: 10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a6232.
- Dexmedetomidine-Induced Thermodysregulation in the Intensive Care UnitCohen A, Valda Toro P, Kahn P, Yan X, Card M, Kunitomo Y, Lee S, Young G, Tsang D, Gautam S, Dela Cruz C. Dexmedetomidine-Induced Thermodysregulation in the Intensive Care Unit 2020, a6310-a6310. DOI: 10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a6310.
- Characterization of Sputum Single Cell Transcriptomes in AsthmaYan X, Liu Q, Adams T, Schupp J, Grant N, Gomez J, Cohn L, Chupp G. Characterization of Sputum Single Cell Transcriptomes in Asthma 2020, a3046-a3046. DOI: 10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a3046.
- Whole Exome Sequencing of Severe Asthma Identifies Novel Gene Association CandidatesWang Z, Shan N, Yan X, Mane S, Gomez J, Chupp G. Whole Exome Sequencing of Severe Asthma Identifies Novel Gene Association Candidates 2020, a1336-a1336. DOI: 10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a1336.
- Transcriptional regulatory model of fibrosis progression in the human lungMcDonough 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.
- Integrating multiomics longitudinal data to reconstruct networks underlying lung developmentDing J, Ahangari F, Espinoza CR, Chhabra D, Nicola T, Yan X, Lal CV, Hagood JS, Kaminski N, Bar-Joseph Z, Ambalavanan N. Integrating multiomics longitudinal data to reconstruct networks underlying lung development American Journal Of Physiology - Lung Cellular And Molecular Physiology 2019, 317: l556-l568. PMID: 31432713, PMCID: PMC6879899, DOI: 10.1152/ajplung.00554.2018.
- Whole Lung Single Cell RNAseq Reveals a Unique IPF-Specific Epithelial Cell PopulationSchupp J, Adams T, Neumark N, Poli De Frias S, Ahangari F, Omote N, Chioccioli M, Xylourgidis N, DeIuliis G, Chu S, Yan X, Rosas I, Kaminski N. Whole Lung Single Cell RNAseq Reveals a Unique IPF-Specific Epithelial Cell Population 2019, a4017-a4017. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a4017.
- Archetype Analysis Reveals Distinct Disease-Specific Archetypes of Fibroblast and Myofibroblast Co-Occurring Within the IPF LungAdams T, Schupp J, Neumark N, Poli De Frias S, Ahangari F, DeIuliis G, Chu S, Raredon M, Yan X, Rosas I, Kaminski N. Archetype Analysis Reveals Distinct Disease-Specific Archetypes of Fibroblast and Myofibroblast Co-Occurring Within the IPF Lung 2019, a4018-a4018. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a4018.
- Viral Pneumonia Is an Independent Risk Factor for Pulmonary Fibrosis: Results of Large-Scale Longitudinal Population-Level DataShojaee A, Kaminski N, Siner J, Aryan Y, Yan X, Dela Cruz C. Viral Pneumonia Is an Independent Risk Factor for Pulmonary Fibrosis: Results of Large-Scale Longitudinal Population-Level Data 2019, a4213-a4213. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a4213.
- Macrophage Programs in BAL and Lung Parenchyma of the Healthy and in IPF PatientsSchupp J, Adams T, Neumark N, Poli De Frias S, Ahangari F, DeIuliis G, Chu S, Yan X, Kaminski N, Prasse A, Rosas I. Macrophage Programs in BAL and Lung Parenchyma of the Healthy and in IPF Patients 2019, a5247-a5247. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a5247.
- Alveolar and Fibroblast Foci Specific Genome-Wide Gene Expression Profiling Identifies Common Dysregulated Expression of CREB1, a Regulator Across Cell Types, in IPFVukmirovic M, Brereton C, Yan X, Xylourgidis N, Deluliis G, Woolard T, Hu B, Mihaljinec A, Homer R, Maya J, Ahangari F, Fabre A, Smart D, Conforti F, Marshall B, Alzetani A, Davies D, Richeldi L, Kaminski N, Jones M. Alveolar and Fibroblast Foci Specific Genome-Wide Gene Expression Profiling Identifies Common Dysregulated Expression of CREB1, a Regulator Across Cell Types, in IPF 2019, a5262-a5262. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a5262.
- A Novel Interface for Sharing the Human Cell IPF AtlasNeumark N, Adams T, Schupp J, Yan X, Poli De Frias S, Kaminski N. A Novel Interface for Sharing the Human Cell IPF Atlas 2019, a6076-a6076. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a6076.
- MicroRNA miR-223 Is Associated with Lung Function Impairment and TH17 Inflammation in AsthmaGomez J, Chen A, Yan X, Cohn L, Chupp G. MicroRNA miR-223 Is Associated with Lung Function Impairment and TH17 Inflammation in Asthma 2019, a2929-a2929. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a2929.
- Cell Lineage Defined by Single Cell Transcriptomics of the Sputum in AsthmaYan X, Liu Q, Mihaljinec A, Gomez J, Cohn L, Chupp G. Cell Lineage Defined by Single Cell Transcriptomics of the Sputum in Asthma 2019, a6085-a6085. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a6085.
- Integration of Sputum eQTL and GWAS Indicates IL-27/EBI3 Pathway Is Associated with Severe AsthmaChu J, Yan X, Liang A, Hu B, Gomez J, Chupp G. Integration of Sputum eQTL and GWAS Indicates IL-27/EBI3 Pathway Is Associated with Severe Asthma 2019, a6088-a6088. DOI: 10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a6088.
- Genomic Comparison Among Global Isolates of L. interrogans Serovars Copenhageni and Icterohaemorrhagiae Identified Natural Genetic Variation Caused by an IndelSantos LA, Adhikarla H, Yan X, Wang Z, Fouts DE, Vinetz JM, Alcantara LCJ, Hartskeerl RA, Goris MGA, Picardeau M, Reis MG, Townsend JP, Zhao H, Ko AI, Wunder EA. Genomic Comparison Among Global Isolates of L. interrogans Serovars Copenhageni and Icterohaemorrhagiae Identified Natural Genetic Variation Caused by an Indel Frontiers In Cellular And Infection Microbiology 2018, 8: 193. PMID: 29971217, PMCID: PMC6018220, DOI: 10.3389/fcimb.2018.00193.
- Characterisation of asthma subgroups associated with circulating YKL-40 levelsGomez JL, Yan X, Holm CT, Grant N, Liu Q, Cohn L, Nezgovorova V, Meyers DA, Bleecker ER, Crisafi GM, Jarjour NN, Rogers L, Reibman J, Chupp GL. Characterisation of asthma subgroups associated with circulating YKL-40 levels European Respiratory Journal 2017, 50: 1700800. PMID: 29025889, PMCID: PMC5967238, DOI: 10.1183/13993003.00800-2017.
- Polysomnographic phenotypes and their cardiovascular implications in obstructive sleep apnoeaZinchuk AV, Jeon S, Koo BB, Yan X, Bravata DM, Qin L, Selim BJ, Strohl KP, Redeker NS, Concato J, Yaggi HK. Polysomnographic phenotypes and their cardiovascular implications in obstructive sleep apnoea Thorax 2017, 73: 472. PMID: 28935698, PMCID: PMC6693344, DOI: 10.1136/thoraxjnl-2017-210431.
- Validation of a 52-gene risk profile for outcome prediction in patients with idiopathic pulmonary fibrosis: an international, multicentre, cohort studyHerazo-Maya JD, Sun J, Molyneaux PL, Li Q, Villalba JA, Tzouvelekis A, Lynn H, Juan-Guardela BM, Risquez C, Osorio JC, Yan X, Michel G, Aurelien N, Lindell KO, Klesen MJ, Moffatt MF, Cookson WO, Zhang Y, Garcia JGN, Noth I, Prasse A, Bar-Joseph Z, Gibson KF, Zhao H, Herzog EL, Rosas IO, Maher TM, Kaminski N. Validation of a 52-gene risk profile for outcome prediction in patients with idiopathic pulmonary fibrosis: an international, multicentre, cohort study The Lancet Respiratory Medicine 2017, 5: 857-868. PMID: 28942086, PMCID: PMC5677538, DOI: 10.1016/s2213-2600(17)30349-1.
- Identification and validation of differentially expressed transcripts by RNA-sequencing of formalin-fixed, paraffin-embedded (FFPE) lung tissue from patients with Idiopathic Pulmonary FibrosisVukmirovic M, Herazo-Maya JD, Blackmon J, Skodric-Trifunovic V, Jovanovic D, Pavlovic S, Stojsic J, Zeljkovic V, Yan X, Homer R, Stefanovic B, Kaminski N. Identification and validation of differentially expressed transcripts by RNA-sequencing of formalin-fixed, paraffin-embedded (FFPE) lung tissue from patients with Idiopathic Pulmonary Fibrosis BMC Pulmonary Medicine 2017, 17: 15. PMID: 28081703, PMCID: PMC5228096, DOI: 10.1186/s12890-016-0356-4.
- MAPKAP kinase 2(MK2) expression is associated with severe asthmaChupp G, Yan X, Nezgovorova V, Grant N, Bradford W, Brophy C, Cohn L. MAPKAP kinase 2(MK2) expression is associated with severe asthma 2016, pa4649. DOI: 10.1183/13993003.congress-2016.pa4649.
- Sputum Gene Expression of IL-13 Receptor α2 Chain Correlates with Airflow Obstruction and Helper T-Cell Type 2 Inflammation in AsthmaNezgovorova V, Liu Q, Hu B, Villalobos JL, Yan X, Niu N, Holm C, Grant NP, Marone S, Ravage-Mass L, Lee CG, Elias JA, Cohn L, Chupp GL. Sputum Gene Expression of IL-13 Receptor α2 Chain Correlates with Airflow Obstruction and Helper T-Cell Type 2 Inflammation in Asthma Annals Of The American Thoracic Society 2016, 13 Suppl 1: s96-7. PMID: 27027964, PMCID: PMC5015742, DOI: 10.1513/annalsats.201509-611mg.
- Noninvasive Analysis of the Sputum Transcriptome Discriminates Clinical Phenotypes of AsthmaYan X, Chu JH, Gomez J, Koenigs M, Holm C, He X, Perez MF, Zhao H, Mane S, Martinez FD, Ober C, Nicolae DL, Barnes KC, London SJ, Gilliland F, Weiss ST, Raby BA, Cohn L, Chupp GL. Noninvasive Analysis of the Sputum Transcriptome Discriminates Clinical Phenotypes of Asthma Annals Of The American Thoracic Society 2016, 13 Suppl 1: s104-5. PMID: 27027945, PMCID: PMC5015745, DOI: 10.1513/annalsats.201510-681mg.
- Signaling through the Adaptor Molecule MyD88 in CD4+ T Cells Is Required to Overcome Suppression by Regulatory T CellsSchenten D, Nish S, Yu S, Yan X, Lee H, Brodsky I, Pasman L, Yordy B, Wunderlich F, Brüning J, Zhao H, Medzhitov R. Signaling through the Adaptor Molecule MyD88 in CD4+ T Cells Is Required to Overcome Suppression by Regulatory T Cells Immunity 2014, 40: 814. DOI: 10.1016/j.immuni.2014.04.012.
- An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY ChallengeBrownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie Jr D, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, de Bakker P, Duzkale H, Dworzyński P, Fairbrother W, Francioli L, Funke BH, Giovanni MA, Handsaker RE, Lage K, Lebo MS, Lek M, Leshchiner I, MacArthur DG, McLaughlin HM, Murray MF, Pers TH, Polak PP, Raychaudhuri S, Rehm HL, Soemedi R, Stitziel NO, Vestecka S, Supper J, Gugenmus C, Klocke B, Hahn A, Schubach M, Menzel M, Biskup S, Freisinger P, Deng M, Braun M, Perner S, Smith R, Andorf JL, Huang J, Ryckman K, Sheffield VC, Stone EM, Bair T, Black-Ziegelbein EA, Braun TA, Darbro B, DeLuca AP, Kolbe DL, Scheetz TE, Shearer AE, Sompallae R, Wang K, Bassuk AG, Edens E, Mathews K, Moore SA, Shchelochkov OA, Trapane P, Bossler A, Campbell CA, Heusel JW, Kwitek A, Maga T, Panzer K, Wassink T, Van Daele D, Azaiez H, Booth K, Meyer N, Segal MM, Williams MS, Tromp G, White P, Corsmeier D, Fitzgerald-Butt S, Herman G, Lamb-Thrush D, McBride KL, Newsom D, Pierson CR, Rakowsky AT, Maver A, Lovrečić L, Palandačić A, Peterlin B, Torkamani A, Wedell A, Huss M, Alexeyenko A, Lindvall JM, Magnusson M, Nilsson D, Stranneheim H, Taylan F, Gilissen C, Hoischen A, van Bon B, Yntema H, Nelen M, Zhang W, Sager J, Zhang L, Blair K, Kural D, Cariaso M, Lennon GG, Javed A, Agrawal S, Ng PC, Sandhu KS, Krishna S, Veeramachaneni V, Isakov O, Halperin E, Friedman E, Shomron N, Glusman G, Roach JC, Caballero J, Cox HC, Mauldin D, Ament SA, Rowen L, Richards DR, Lucas F, Gonzalez-Garay ML, Caskey CT, Bai Y, Huang Y, Fang F, Zhang Y, Wang Z, Barrera J, Garcia-Lobo JM, González-Lamuño D, Llorca J, Rodriguez MC, Varela I, Reese MG, De La Vega FM, Kiruluta E, Cargill M, Hart RK, Sorenson JM, Lyon GJ, Stevenson DA, Bray BE, Moore BM, Eilbeck K, Yandell M, Zhao H, Hou L, Chen X, Yan X, Chen M, Li C, Yang C, Gunel M, Li P, Kong Y, Alexander AC, Albertyn ZI, Boycott KM, Bulman DE, Gordon P, Innes AM, Knoppers BM, Majewski J, Marshall CR, Parboosingh JS, Sawyer SL, Samuels ME, Schwartzentruber J, Kohane IS, Margulies DM. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge Genome Biology 2014, 15: r53. PMID: 24667040, PMCID: PMC4073084, DOI: 10.1186/gb-2014-15-3-r53.
- Signaling through the Adaptor Molecule MyD88 in CD4+ T Cells Is Required to Overcome Suppression by Regulatory T CellsSchenten D, Nish SA, Yu S, Yan X, Lee HK, Brodsky I, Pasman L, Yordy B, Wunderlich FT, Brüning JC, Zhao H, Medzhitov R. Signaling through the Adaptor Molecule MyD88 in CD4+ T Cells Is Required to Overcome Suppression by Regulatory T Cells Immunity 2014, 40: 78-90. PMID: 24439266, PMCID: PMC4445716, DOI: 10.1016/j.immuni.2013.10.023.
- T cell-intrinsic role of IL-6 signaling in primary and memory responsesNish SA, Schenten D, Wunderlich FT, Pope SD, Gao Y, Hoshi N, Yu S, Yan X, Lee HK, Pasman L, Brodsky I, Yordy B, Zhao H, Brüning J, Medzhitov R. T cell-intrinsic role of IL-6 signaling in primary and memory responses ELife 2014, 3: e01949. PMID: 24842874, PMCID: PMC4046568, DOI: 10.7554/elife.01949.
- Plasmacytoid dendritic cells, interferon signaling, and FcγR contribute to pathogenesis and therapeutic response in childhood immune thrombocytopenia.Sehgal K, Guo X, Koduru S, Shah A, Lin A, Yan X, Dhodapkar KM. Plasmacytoid dendritic cells, interferon signaling, and FcγR contribute to pathogenesis and therapeutic response in childhood immune thrombocytopenia. Science Translational Medicine 2013, 5: 193ra89. PMID: 23843450, DOI: 10.1126/scitranslmed.3006277.
- Modeling RNA degradation for RNA-Seq with applicationsWan 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.
- Collapsing-based and kernel-based single-gene analyses applied to Genetic Analysis Workshop 17 mini-exome dataLi L, Zheng W, Lee JS, Zhang X, Ferguson J, Yan X, Zhao H. Collapsing-based and kernel-based single-gene analyses applied to Genetic Analysis Workshop 17 mini-exome data BMC Proceedings 2011, 5: s117. PMID: 22373309, PMCID: PMC3287841, DOI: 10.1186/1753-6561-5-s9-s117.
- Large-scale risk prediction applied to Genetic Analysis Workshop 17 mini-exome sequence dataLi G, Ferguson J, Zheng W, Lee JS, Zhang X, Li L, Kang J, Yan X, Zhao H. Large-scale risk prediction applied to Genetic Analysis Workshop 17 mini-exome sequence data BMC Proceedings 2011, 5: s46. PMID: 22373389, PMCID: PMC3287883, DOI: 10.1186/1753-6561-5-s9-s46.
- Dealing with high dimensionality for the identification of common and rare variants as main effects and for gene‐environment interactionBickeböller H, Houwing‐Duistermaat J, Wang X, Yan X. Dealing with high dimensionality for the identification of common and rare variants as main effects and for gene‐environment interaction Genetic Epidemiology 2011, 35: s35-s40. PMID: 22128056, DOI: 10.1002/gepi.20647.
- Use of Bayesian networks to dissect the complexity of genetic disease: application to the Genetic Analysis Workshop 17 simulated dataKang J, Zheng W, Li L, Lee JS, Yan X, Zhao H. Use of Bayesian networks to dissect the complexity of genetic disease: application to the Genetic Analysis Workshop 17 simulated data BMC Proceedings 2011, 5: s37. PMID: 22373110, PMCID: PMC3287873, DOI: 10.1186/1753-6561-5-s9-s37.
- On optimal pooling designs to identify rare variants through massive resequencingLee JS, Choi M, Yan X, Lifton RP, Zhao H. On optimal pooling designs to identify rare variants through massive resequencing Genetic Epidemiology 2011, 35: 139-147. PMID: 21254222, PMCID: PMC3176340, DOI: 10.1002/gepi.20561.
- Nonlinear cooperation of p53-ING1-induced bax expression and protein S-nitrosylation in GSNO-induced thymocyte apoptosis: a quantitative approach with cross-platform validationDuan 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.
- Genomic Androgen Receptor-Occupied Regions with Different Functions, Defined by Histone Acetylation, Coregulators and Transcriptional CapacityJia 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.
- Progressive recruitment of Runx2 to genomic targets despite decreasing expression during osteoblast differentiationPregizer S, Baniwal SK, Yan X, Borok Z, Frenkel B. Progressive recruitment of Runx2 to genomic targets despite decreasing expression during osteoblast differentiation Journal Of Cellular Biochemistry 2008, 105: 965-970. PMID: 18821584, PMCID: PMC2591066, DOI: 10.1002/jcb.21900.
- Inferring activity changes of transcription factors by binding association with sorted expression profilesCheng 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.
- MARD: a new method to detect differential gene expression in treatment-control time coursesCheng 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.