Zhaohui Qin, PhD, MS

Research Program

Cell and Molecular Biology
Phone Number

404-712-9576
Email Address

zhaohui.qin@emory.edu

Biography

Zhaohui "Steve" Qin, PhD, MS, is an associate professor in the Department of Biostatistics and Bioinformatics at Rollins School of Public Health of Emory University. Dr. Qin is a member of the Cell and Molecular Biology Research Program at Winship.

Education

Dr. Qin earned his PhD and MS in Statistics from the University of Michigan. After obtaining his PhD, Dr. Qin completed a postdoctoral fellowship in Statistics at Harvard University.

Titles & Roles

Associate Professor, Department of Biostatistics and Bioinformatics

Rollins School of Public Health, Emory University

Research

Dr. Qin's research is in the areas of statistical genetics, genomics and bioinformatics. A major focus of Dr. Qin's research is on developing and evaluating model-based methods to analyze genetics and genomics data, in particular, next generation sequencing data, and on developing software so that the methods can be easily adopted by the research community.

Grants

View Grants

Grant Number	Title
5R01GM141392-04	Dissecting epitranscriptomic signal from complex tissues
5R01GM141392-05	Dissecting epitranscriptomic signal from complex tissues
7R01GM141392-03	Dissecting epitranscriptomic signal from complex tissues

Publications

Title/Journal	Authors	Publication Date
Inhibiting FAT1 Blocks Metabolic Bypass to Enhance Antitumor Efficacy of TCA Cycle Inhibition through Suppressing CPT1A-Dependent Fatty Acid Oxidation. Advanced science (Weinheim, Baden-Wurttemberg, Germany)	F Chen, J Yang, DO Popoola, F Yang, Y Liu, D Wang, ZS Qin, Z Chen, NF Saba, ZG Chen, Y Li, Y Teng	05/23/2025
MammOnc-DB, an integrative breast cancer data analysis platform for target discovery. NPJ breast cancer	SK Karthikeyan, DS Chandrashekar, S Sahai, S Shrestha, R Aneja, R Singh, CG Kleer, S Kumar, ZS Qin, H Nakshatri, U Manne, CJ Creighton, S Varambally	04/18/2025
Whole genome sequence-based association analysis of African American individuals with bipolar disorder and schizophrenia. medRxiv : the preprint server for health sciences	R Li, SAG Taliun, K Liao, M Flickinger, JL Sobell, G Genovese, AE Locke, RR Chiu, J LeFaive, J Wang, T Martins, S Chapman, A Neumann, RE Handsaker, DK Arnett, KC Barnes, E Boerwinkle, D Braff, BE Cade, M Fornage, RA Gibbs, KF Hoth, L Hou, C Kooperberg, RJF Loos, GA Metcalf, CG Montgomery, AC Morrison, ZS Qin, S Redline, AP Reiner, SS Rich, JI Rotter, KD Taylor, KA Viaud-Martinez, TB Bigdeli, S Gabriel, S Zollner, AV Smith, G Abecasis, S McCarroll, MT Pato, CN Pato, M Boehnke, J Knowles, HM Kang, RA Ophoff, J Ernst, LJ Scott	02/19/2025
Phenotypic Characterization of Subtype A and Recombinant AC Transmitted/Founder Viruses from a Rwandan HIV-1 Heterosexual Transmission Cohort. Viruses	L Yue, R Xu, S Mclnally, Q Qin, JW Rhodes, E Muok, G Umviligihozo, K Brooks, J Zhang, Z Qin, J Bizimana, J Hare, MA Price, SA Allen, E Karita, E Hunter	10/30/2024
Longitudinal multi-omics reveals pathogenic TSC2 variants disrupt developmental trajectories of human cortical organoids derived from Tuberous Sclerosis Complex. bioRxiv : the preprint server for biology	W Niu, S Yu, X Li, Z Wang, R Chen, C Michalski, A Jahangiri, Y Zohdy, JJ Chern, TJ Whitworth, J Wang, J Xu, Y Zhou, Z Qin, B Li, MJ Gambello, J Peng, Z Wen	10/11/2024
A novel classification framework for genome-wide association study of whole brain MRI images using deep learning. PLoS computational biology	S Yu, J Wu, Y Shao, D Qiu, ZS Qin	10/01/2024
MammOnc-DB, an integrative breast cancer data analysis platform for target discovery. Research square	S Varambally, SK Karthikeyan, D Chandrashekar, S Sahai, S Shrestha, R Aneja, R Singh, C Kleer, S Kumar, Z Qin, H Nakshatri, U Manne, C Creighton	09/26/2024
Obesity during preclinical Alzheimer's disease development exacerbates brain metabolic decline. Journal of neurochemistry	T Anderson, S Sharma, MA Kelberman, C Ware, N Guo, Z Qin, D Weinshenker, MB Parent	05/01/2024
Combined IL6 and CCR2 blockade potentiates antitumor activity of NK cells in HPV-negative head and neck cancer. Journal of experimental & clinical cancer research : CR	F Yang, C Yuan, F Chen, ZS Qin, NC Schmitt, GB Lesinski, NF Saba, Y Teng	03/12/2024
Editorial: Big data and artificial intelligence for genomics and therapeutics - Proceedings of the 19th Annual Meeting of the MidSouth Computational Biology and Bioinformatics Society (MCBIOS). Frontiers in bioinformatics	H Hong, I Toby-Ogundeji, RJ Doerksen, ZS Qin	01/01/2024
Role of TET1-mediated epigenetic modulation in Alzheimer's disease. Neurobiology of disease	MJ Armstrong, Y Jin, SM Vattathil, Y Huang, JP Schroeder, DA Bennet, ZS Qin, TS Wingo, P Jin	09/01/2023
Unsupervised Hierarchical Clustering of Head and Neck Cancer Patients by Pre-Treatment Plasma Metabolomics Creates Prognostic Metabolic Subtypes. Cancers	RC Eldridge, ZS Qin, NF Saba, MC Houser, DN Hayes, AH Miller, DW Bruner, DP Jones, C Xiao	06/14/2023
Identification of androgen response-related lncRNAs in prostate cancer. The Prostate	SK Karthikeyan, N Xu, JE Ferguson Rd, S Rais-Bahrami, ZS Qin, U Manne, GJ Netto, D S Chandrashekar, S Varambally	05/01/2023
Dysregulation of Prefrontal Oligodendrocyte Lineage Cells Across Mouse Models of Adversity and Human Major Depressive Disorder Oligodendrocyte dysregulation in mouse models of stress and MDD. bioRxiv : the preprint server for biology	S Sharma, W Ma, KJ Ressler, T Anderson, DC Li, P Jin, SL Gourley, Z Qin	03/10/2023
Circadian rhythm sleep disorders and time-of-day-dependent memory deficiency in Presenilin1/2 conditional knockout mice with long noncoding RNA expression profiling changes. Sleep medicine	Y Si, J Chen, Y Shen, S Kubra, B Mei, ZS Qin, B Pan, B Meng	03/01/2023
Comprehensive 100-bp resolution genome-wide epigenomic profiling data for the hg38 human reference genome. Data in brief	RY Li, Y Huang, Z Zhao, ZS Qin	02/01/2023
Patterns of toxicity burden for FDA-approved immune checkpoint inhibitors in the United States. Journal of experimental & clinical cancer research : CR	F Yang, C Shay, M Abousaud, C Tang, Y Li, Z Qin, NF Saba, Y Teng	01/05/2023
Editorial: AI and data science in drug development and public health: Highlights from the MCBIOS 2022 conference. Frontiers in big data	R Homayouni, P Manda, AC Tan, ZS Qin	01/01/2023
Integrative Bayesian tensor regression for imaging genetics applications. Frontiers in neuroscience	Y Liu, N Chakraborty, ZS Qin, S Kundu	01/01/2023
NetAct: a computational platform to construct core transcription factor regulatory networks using gene activity. Genome biology	K Su, A Katebi, V Kohar, B Clauss, D Gordin, ZS Qin, RKM Karuturi, S Li, M Lu	12/27/2022
A clade C HIV-1 vaccine protects against heterologous SHIV infection by modulating IgG glycosylation and T helper response in macaques. Science immunology	A Sahoo, AT Jones, N Cheedarla, S Gangadhara, V Roy, TM Styles, A Shiferaw, KL Walter, LD Williams, X Shen, G Ozorowski, WH Lee, S Burton, L Yi, X Song, ZS Qin, CA Derdeyn, AB Ward, JD Clements, R Varadarajan, GD Tomaras, PA Kozlowski, G Alter, RR Amara	07/22/2022
Identification of PSMB5 as a genetic modifier of fragile X-associated tremor/ataxia syndrome. Proceedings of the National Academy of Sciences of the United States of America	HE Kong, J Lim, A Linsalata, Y Kang, I Malik, EG Allen, Y Cao, L Shubeck, R Johnston, Y Huang, Y Gu, X Guo, ME Zwick, Z Qin, TS Wingo, J Juncos, DL Nelson, MP Epstein, DJ Cutler, PK Todd, SL Sherman, ST Warren, P Jin	05/31/2022
LRcell: detecting the source of differential expression at the sub-cell-type level from bulk RNA-seq data. Briefings in bioinformatics	W Ma, S Sharma, P Jin, SL Gourley, ZS Qin	05/13/2022
A neutralizing antibody target in early HIV-1 infection was recapitulated in rhesus macaques immunized with the transmitted/founder envelope sequence. PLoS pathogens	S Welbourn, S Chakraborty, JE Yang, AS Gleinich, S Gangadhara, S Khan, C Ferrebee, B Yagnik, S Burton, T Charles, SA Smith, D Williams, R Mopuri, AA Upadhyay, J Thompson, MA Price, S Wang, Z Qin, X Shen, LD Williams, N Eisel, T Peters, L Zhang, W Kilembe, E Karita, GD Tomaras, SE Bosinger, RR Amara, P Azadi, ER Wright, S Gnanakaran, CA Derdeyn	05/01/2022
UALCAN: An update to the integrated cancer data analysis platform. Neoplasia (New York, N.Y.)	DS Chandrashekar, SK Karthikeyan, PK Korla, H Patel, AR Shovon, M Athar, GJ Netto, ZS Qin, S Kumar, U Manne, CJ Creighton, S Varambally	03/01/2022
ATAD3A mediates activation of RAS-independent mitochondrial ERK1/2 signaling, favoring head and neck cancer development. Journal of experimental & clinical cancer research : CR	L Lang, R Loveless, J Dou, T Lam, A Chen, F Wang, L Sun, J Juarez, ZS Qin, NF Saba, C Shay, Y Teng	01/29/2022
Disease category-specific annotation of variants using an ensemble learning framework. Briefings in bioinformatics	Z Cao, Y Huang, R Duan, P Jin, ZS Qin, S Zhang	01/17/2022
Single-cell chromatin accessibility landscape in kidney identifies additional cell-of-origin in heterogenous papillary renal cell carcinoma. Nature communications	Q Wang, Y Zhang, B Zhang, Y Fu, X Zhao, J Zhang, K Zuo, Y Xing, S Jiang, Z Qin, E Li, H Guo, Z Liu, J Yang	01/10/2022
The novel BET degrader, QCA570, is highly active against the growth of human NSCLC cells and synergizes with osimertinib in suppressing osimertinib-resistant EGFR-mutant NSCLC cells. American journal of cancer research	C Liu, L Qian, KA Vallega, G Ma, D Zong, L Chen, S Wang, SR Ramalingam, Z Qin, SY Sun	01/01/2022
Extensive Chromatin Structure-Function Associations Revealed by Accurate 3D Compartmentalization Characterization. Frontiers in cell and developmental biology	Z Wen, W Zhang, Q Zhong, J Xu, C Hou, ZS Qin, L Li	01/01/2022
Plasma Metabolic Phenotypes of HPV-Associated versus Smoking-Associated Head and Neck Cancer and Patient Survival. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology	RC Eldridge, K Uppal, DN Hayes, MR Smith, X Hu, ZS Qin, JJ Beitler, AH Miller, EC Wommack, KA Higgins, DM Shin, B Ulrich, DC Qian, NF Saba, DW Bruner, DP Jones, C Xiao	10/01/2021
Pan-cancer analysis of pathway-based gene expression pattern at the individual level reveals biomarkers of clinical prognosis. Cell reports methods	K Su, Q Yu, R Shen, SY Sun, CS Moreno, X Li, ZS Qin	08/23/2021
A machine learning approach to brain epigenetic analysis reveals kinases associated with Alzheimer's disease. Nature communications	Y Huang, X Sun, H Jiang, S Yu, C Robins, MJ Armstrong, R Li, Z Mei, X Shi, ES Gerasimov, PL De Jager, DA Bennett, AP Wingo, P Jin, TS Wingo, ZS Qin	07/22/2021
Glucocorticoid receptor wields chromatin interactions to tune transcription for cytoskeleton stabilization in podocytes. Communications biology	H Wang, A Duan, J Zhang, Q Wang, Y Xing, Z Qin, Z Liu, J Yang	06/03/2021
Super-Enhancer-Associated Transcription Factors Maintain Transcriptional Regulation in Mature Podocytes. Journal of the American Society of Nephrology : JASN	J Yang, D Zhang, M Motojima, T Kume, Q Hou, Y Pan, A Duan, M Zhang, S Jiang, J Hou, J Shi, Z Qin, Z Liu	06/01/2021
Adolescent stress sensitizes the adult neuroimmune transcriptome and leads to sex-specific microglial and behavioral phenotypes. Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology	M Bekhbat, D Mukhara, MG Dozmorov, JC Stansfield, SD Benusa, MM Hyer, SA Rowson, SD Kelly, Z Qin, JL Dupree, GK Tharp, MG Tansey, GN Neigh	04/01/2021
Chromatin architecture reveals cell type-specific target genes for kidney disease risk variants. BMC biology	A Duan, H Wang, Y Zhu, Q Wang, J Zhang, Q Hou, Y Xing, J Shi, J Hou, Z Qin, Z Chen, Z Liu, J Yang	02/24/2021
Multiomics Analysis of Structural Magnetic Resonance Imaging of the Brain and Cerebrospinal Fluid Metabolomics in Cognitively Normal and Impaired Adults. Frontiers in aging neuroscience	RC Eldridge, K Uppal, M Shokouhi, MR Smith, X Hu, ZS Qin, DP Jones, I Hajjar	01/01/2021
Systematic Exploration in Tissue-Pathway Associations of Complex Traits Using Comprehensive eQTLs Catalog. Frontiers in big data	B Wang, J Yang, S Qiu, Y Bai, ZS Qin	01/01/2021
Systematic Evaluation of DNA Sequence Variations on in vivo Transcription Factor Binding Affinity. Frontiers in genetics	Y Jin, J Jiang, R Wang, ZS Qin	01/01/2021
Author Correction: Truncation of mutant huntingtin in knock-in mice demonstrates exon1 huntingtin is a key pathogenic form. Nature communications	H Yang, S Yang, L Jing, L Huang, L Chen, X Zhao, W Yang, Y Pan, P Yin, ZS Qin, B Tang, S Li, XJ Li	11/19/2020
An empirical bayesian approach for testing gene expression fold change and its application in detecting global dosage effects. NAR genomics and bioinformatics	Z Guo, Y Cui, X Shi, JA Birchler, I Albizua, SL Sherman, ZS Qin, T Ji	09/01/2020
Proceedings of the 2019 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC bioinformatics	JD Wren, Y Bai, ZS Qin, D Yan, R Homayouni	07/06/2020
Truncation of mutant huntingtin in knock-in mice demonstrates exon1 huntingtin is a key pathogenic form. Nature communications	H Yang, S Yang, L Jing, L Huang, L Chen, X Zhao, W Yang, Y Pan, P Yin, ZS Qin, B Tang, S Li, XJ Li	05/22/2020
Application of topic models to a compendium of ChIP-Seq datasets uncovers recurrent transcriptional regulatory modules. Bioinformatics (Oxford, England)	G Yang, A Ma, ZS Qin, L Chen	04/15/2020
Lack of RAN-mediated toxicity in Huntington's disease knock-in mice. Proceedings of the National Academy of Sciences of the United States of America	S Yang, H Yang, L Huang, L Chen, Z Qin, S Li, XJ Li	02/25/2020
Regulatory annotation of genomic intervals based on tissue-specific expression QTLs. Bioinformatics (Oxford, England)	T Xu, P Jin, ZS Qin	02/01/2020
A comprehensive review of computational prediction of genome-wide features. Briefings in bioinformatics	T Xu, X Zheng, B Li, P Jin, Z Qin, H Wu	01/17/2020
DeconPeaker, a Deconvolution Model to Identify Cell Types Based on Chromatin Accessibility in ATAC-Seq Data of Mixture Samples. Frontiers in genetics	H Li, A Sharma, K Luo, ZS Qin, X Sun, H Liu	01/01/2020
Signatures of somatic mutations and gene expression from p16INK4A positive head and neck squamous cell carcinomas (HNSCC). PloS one	NF Saba, AR Dinasarapu, KR Magliocca, B Dwivedi, S Seby, ZS Qin, M Patel, CC Griffith, X Wang, M El-Deiry, CE Steuer, J Kowalski, DM Shin, ME Zwick, ZG Chen	01/01/2020
Author Correction: Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations. Nature communications	M Daya, N Rafaels, TM Brunetti, S Chavan, AM Levin, A Shetty, CR Gignoux, MP Boorgula, G Wojcik, M Campbell, C Vergara, DG Torgerson, VE Ortega, A Doumatey, HR Johnston, N Acevedo, MI Araujo, PC Avila, G Belbin, E Bleecker, C Bustamante, L Caraballo, A Cruz, GM Dunston, C Eng, MU Faruque, TS Ferguson, C Figueiredo, JG Ford, W Gan, PA Gourraud, NN Hansel, RD Hernandez, EF Herrera-Paz, S Jiménez, EE Kenny, J Knight-Madden, R Kumar, LA Lange, EM Lange, A Lizee, P Maul, T Maul, A Mayorga, D Meyers, DL Nicolae, TD O'Connor, RR Oliveira, CO Olopade, O Olopade, ZS Qin, C Rotimi, N Vince, H Watson, RJ Wilks, JG Wilson, S Salzberg, C Ober, EG Burchard, LK Williams, TH Beaty, MA Taub, I Ruczinski, RA Mathias, KC Barnes	09/04/2019
Rapid Irreversible Transcriptional Reprogramming in Human Stem Cells Accompanied by Discordance between Replication Timing and Chromatin Compartment. Stem cell reports	V Dileep, KA Wilson, C Marchal, X Lyu, PA Zhao, B Li, A Poulet, DA Bartlett, JC Rivera-Mulia, ZS Qin, AJ Robins, TC Schulz, MJ Kulik, RP McCord, J Dekker, S Dalton, VG Corces, DM Gilbert	07/09/2019
RT States: systematic annotation of the human genome using cell type-specific replication timing programs. Bioinformatics (Oxford, England)	A Poulet, B Li, T Dubos, JC Rivera-Mulia, DM Gilbert, ZS Qin	07/01/2019
Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations. Nature communications	M Daya, N Rafaels, TM Brunetti, S Chavan, AM Levin, A Shetty, CR Gignoux, MP Boorgula, G Wojcik, M Campbell, C Vergara, DG Torgerson, VE Ortega, A Doumatey, HR Johnston, N Acevedo, MI Araujo, PC Avila, G Belbin, E Bleecker, C Bustamante, L Caraballo, A Cruz, GM Dunston, C Eng, MU Faruque, TS Ferguson, C Figueiredo, JG Ford, W Gan, PA Gourraud, NN Hansel, RD Hernandez, EF Herrera-Paz, S Jiménez, EE Kenny, J Knight-Madden, R Kumar, LA Lange, EM Lange, A Lizee, P Maul, T Maul, A Mayorga, D Meyers, DL Nicolae, TD O'Connor, RR Oliveira, CO Olopade, O Olopade, ZS Qin, C Rotimi, N Vince, H Watson, RJ Wilks, JG Wilson, S Salzberg, C Ober, EG Burchard, LK Williams, TH Beaty, MA Taub, I Ruczinski, RA Mathias, KC Barnes	02/20/2019
An Integrated System Biology Approach Yields Drug Repositioning Candidates for the Treatment of Heart Failure. Frontiers in genetics	G Yang, A Ma, ZS Qin	01/01/2019
EWS/ETS-Driven Ewing Sarcoma Requires BET Bromodomain Proteins. Cancer research	PN Gollavilli, A Pawar, K Wilder-Romans, R Natesan, CG Engelke, VL Dommeti, PM Krishnamurthy, A Nallasivam, IJ Apel, T Xu, ZS Qin, FY Feng, IA Asangani	08/15/2018
Optimized distributed systems achieve significant performance improvement on sorted merging of massive VCF files. GigaScience	X Sun, J Gao, P Jin, C Eng, EG Burchard, TH Beaty, I Ruczinski, RA Mathias, K Barnes, F Wang, ZS Qin	06/01/2018
Probabilistic and machine learning-based retrieval approaches for biomedical dataset retrieval. Database : the journal of biological databases and curation	P Karisani, ZS Qin, E Agichtein	01/01/2018
Using DIVAN to assess disease/trait-associated single nucleotide variants in genome-wide scale. BMC research notes	L Chen, ZS Qin	10/30/2017
Omicseq: a web-based search engine for exploring omics datasets. Nucleic acids research	X Sun, WS Pittard, T Xu, L Chen, ME Zwick, X Jiang, F Wang, ZS Qin	07/03/2017
CRISPR/Cas9-mediated gene editing ameliorates neurotoxicity in mouse model of Huntington's disease. The Journal of clinical investigation	S Yang, R Chang, H Yang, T Zhao, Y Hong, HE Kong, X Sun, Z Qin, P Jin, S Li, XJ Li	06/30/2017
Ten-eleven translocation 2 interacts with forkhead box O3 and regulates adult neurogenesis. Nature communications	X Li, B Yao, L Chen, Y Kang, Y Li, Y Cheng, L Li, L Lin, Z Wang, M Wang, F Pan, Q Dai, W Zhang, H Wu, Q Shu, Z Qin, C He, M Xu, P Jin	06/29/2017
Improving Hierarchical Models Using Historical Data with Applications in High-Throughput Genomics Data Analysis. Statistics in biosciences	B Li, Y Li, ZS Qin	06/01/2017
Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome. Scientific reports	HR Johnston, YJ Hu, J Gao, TD O'Connor, GR Abecasis, GL Wojcik, CR Gignoux, PA Gourraud, A Lizee, M Hansen, R Genuario, D Bullis, C Lawley, EE Kenny, C Bustamante, TH Beaty, RA Mathias, KC Barnes, ZS Qin	04/21/2017
An approach of identifying differential nucleosome regions in multiple samples. BMC genomics	L Liu, J Xie, X Sun, K Luo, ZS Qin, H Liu	02/07/2017
Computationally Tractable Multivariate HMM in Genome-Wide Mapping Studies. Methods in molecular biology (Clifton, N.J.)	H Choi, D Ghosh, Z Qin	01/01/2017
DIVAN: accurate identification of non-coding disease-specific risk variants using multi-omics profiles. Genome biology	L Chen, P Jin, ZS Qin	12/06/2016
Molecular signatures associated with ZIKV exposure in human cortical neural progenitors. Nucleic acids research	F Zhang, C Hammack, SC Ogden, Y Cheng, EM Lee, Z Wen, X Qian, HN Nguyen, Y Li, B Yao, M Xu, T Xu, L Chen, Z Wang, H Feng, WK Huang, KJ Yoon, C Shan, L Huang, Z Qin, KM Christian, PY Shi, M Xu, M Xia, W Zheng, H Wu, H Song, H Tang, GL Ming, P Jin	10/14/2016
A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome. Nature communications	RA Mathias, MA Taub, CR Gignoux, W Fu, S Musharoff, TD O'Connor, C Vergara, DG Torgerson, M Pino-Yanes, SS Shringarpure, L Huang, N Rafaels, MP Boorgula, HR Johnston, VE Ortega, AM Levin, W Song, R Torres, B Padhukasahasram, C Eng, DA Mejia-Mejia, T Ferguson, ZS Qin, AF Scott, M Yazdanbakhsh, JG Wilson, J Marrugo, LA Lange, R Kumar, PC Avila, LK Williams, H Watson, LB Ware, C Olopade, O Olopade, R Oliveira, C Ober, DL Nicolae, D Meyers, A Mayorga, J Knight-Madden, T Hartert, NN Hansel, MG Foreman, JG Ford, MU Faruque, GM Dunston, L Caraballo, EG Burchard, E Bleecker, MI Araujo, EF Herrera-Paz, K Gietzen, WE Grus, M Bamshad, CD Bustamante, EE Kenny, RD Hernandez, TH Beaty, I Ruczinski, J Akey, KC Barnes	10/11/2016
Statistical challenges in analyzing methylation and long-range chromosomal interaction data. Statistics in biosciences	Z Qin, B Li, KN Conneely, H Wu, M Hu, D Ayyala, Y Park, VX Jin, F Zhang, H Zhang, L Li, S Lin	10/01/2016
Heat Shock Protein Beta-1 Modifies Anterior to Posterior Purkinje Cell Vulnerability in a Mouse Model of Niemann-Pick Type C Disease. PLoS genetics	C Chung, MJ Elrick, JM Dell'Orco, ZS Qin, S Kalyana-Sundaram, AM Chinnaiyan, VG Shakkottai, AP Lieberman	05/01/2016
Gene integrated set profile analysis: a context-based approach for inferring biological endpoints. Nucleic acids research	J Kowalski, B Dwivedi, S Newman, JM Switchenko, R Pauly, DA Gutman, J Arora, K Gandhi, K Ainslie, G Doho, Z Qin, CS Moreno, MR Rossi, PM Vertino, S Lonial, L Bernal-Mizrachi, LH Boise	04/20/2016
traseR: an R package for performing trait-associated SNP enrichment analysis in genomic intervals. Bioinformatics (Oxford, England)	L Chen, ZS Qin	04/15/2016
A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data. Bioinformatics (Oxford, England)	Z Xu, G Zhang, F Jin, M Chen, TS Furey, PF Sullivan, Z Qin, M Hu, Y Li	03/01/2016
Bayesian inference with historical data-based informative priors improves detection of differentially expressed genes. Bioinformatics (Oxford, England)	B Li, Z Sun, Q He, Y Zhu, ZS Qin	03/01/2016
MLL1 and MLL1 fusion proteins have distinct functions in regulating leukemic transcription program. Cell discovery	J Xu, L Li, J Xiong, A denDekker, A Ye, H Karatas, L Liu, H Wang, ZS Qin, S Wang, Y Dou	01/01/2016
The single-species metagenome: subtyping Staphylococcus aureus core genome sequences from shotgun metagenomic data. PeerJ	SJ Joseph, B Li, RA Petit Iii, ZS Qin, L Darrow, TD Read	01/01/2016
Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates. Nucleic acids research	H Wu, T Xu, H Feng, L Chen, B Li, B Yao, Z Qin, P Jin, KN Conneely	12/02/2015
Combined Loss of Tet1 and Tet2 Promotes B Cell, but Not Myeloid Malignancies, in Mice. Cell reports	Z Zhao, L Chen, MM Dawlaty, F Pan, O Weeks, Y Zhou, Z Cao, H Shi, J Wang, L Lin, S Chen, W Yuan, Z Qin, H Ni, SD Nimer, FC Yang, R Jaenisch, P Jin, M Xu	11/24/2015
Cell-Cycle Control of Bivalent Epigenetic Domains Regulates the Exit from Pluripotency. Stem cell reports	AM Singh, Y Sun, L Li, W Zhang, T Wu, S Zhao, Z Qin, S Dalton	09/08/2015
One Size Doesn't Fit All - RefEditor: Building Personalized Diploid Reference Genome to Improve Read Mapping and Genotype Calling in Next Generation Sequencing Studies. PLoS computational biology	S Yuan, HR Johnston, G Zhang, Y Li, YJ Hu, ZS Qin	08/01/2015
A novel statistical method for quantitative comparison of multiple ChIP-seq datasets. Bioinformatics (Oxford, England)	L Chen, C Wang, ZS Qin, H Wu	06/15/2015
Widespread rearrangement of 3D chromatin organization underlies polycomb-mediated stress-induced silencing. Molecular cell	L Li, X Lyu, C Hou, N Takenaka, HQ Nguyen, CT Ong, C Cubeñas-Potts, M Hu, EP Lei, G Bosco, ZS Qin, VG Corces	04/16/2015
Base-resolution methylation patterns accurately predict transcription factor bindings in vivo. Nucleic acids research	T Xu, B Li, M Zhao, KE Szulwach, RC Street, L Lin, B Yao, F Zhang, P Jin, H Wu, ZS Qin	03/11/2015
Reciprocal occupancy of BCL6 and STAT5 on Growth Hormone target genes: contrasting transcriptional outcomes and promoter-specific roles of p300 and HDAC3. Molecular and cellular endocrinology	G Lin, CR LaPensee, ZS Qin, J Schwartz	09/01/2014
H2B ubiquitylation promotes RNA Pol II processivity via PAF1 and pTEFb. Molecular cell	L Wu, L Li, B Zhou, Z Qin, Y Dou	06/19/2014
Therapeutic targeting of BET bromodomain proteins in castration-resistant prostate cancer. Nature	IA Asangani, VL Dommeti, X Wang, R Malik, M Cieslik, R Yang, J Escara-Wilke, K Wilder-Romans, S Dhanireddy, C Engelke, MK Iyer, X Jing, YM Wu, X Cao, ZS Qin, S Wang, FY Feng, AM Chinnaiyan	06/12/2014
EgoNet: identification of human disease ego-network modules. BMC genomics	R Yang, Y Bai, Z Qin, T Yu	04/28/2014
Targeting MLL1 H3K4 methyltransferase activity in mixed-lineage leukemia. Molecular cell	F Cao, EC Townsend, H Karatas, J Xu, L Li, S Lee, L Liu, Y Chen, P Ouillette, J Zhu, JL Hess, P Atadja, M Lei, ZS Qin, S Malek, S Wang, Y Dou	01/23/2014
Integrated analysis of whole-genome paired-end and mate-pair sequencing data for identifying genomic structural variations in multiple myeloma. Cancer informatics	R Yang, L Chen, S Newman, K Gandhi, G Doho, CS Moreno, PM Vertino, L Bernal-Mizarchi, S Lonial, LH Boise, M Rossi, J Kowalski, ZS Qin	01/01/2014
The central role of EED in the orchestration of polycomb group complexes. Nature communications	Q Cao, X Wang, M Zhao, R Yang, R Malik, Y Qiao, A Poliakov, AK Yocum, Y Li, W Chen, X Cao, X Jiang, A Dahiya, C Harris, FY Feng, S Kalantry, ZS Qin, SM Dhanasekaran, AM Chinnaiyan	01/01/2014
Direct amplification, sequencing and profiling of Chlamydia trachomatis strains in single and mixed infection clinical samples. PloS one	SJ Joseph, B Li, T Ghonasgi, CP Haase, ZS Qin, D Dean, TD Read	01/01/2014
Understanding spatial organizations of chromosomes via statistical analysis of Hi-C data. Quantitative biology (Beijing, China)	M Hu, K Deng, Z Qin, JS Liu	06/01/2013
Exploring the cooccurrence patterns of multiple sets of genomic intervals. BioMed research international	H Wu, ZS Qin	01/01/2013
MotifOrganizer: a scalable model-based motif clustering tool for mammalian genomes. Frontiers in bioscience (Elite edition)	ZS Qin, M Bilenky, G Su, SJ Jones	01/01/2013
HiCNorm: removing biases in Hi-C data via Poisson regression. Bioinformatics (Oxford, England)	M Hu, K Deng, S Selvaraj, Z Qin, B Ren, JS Liu	12/01/2012
Gene density, transcription, and insulators contribute to the partition of the Drosophila genome into physical domains. Molecular cell	C Hou, L Li, ZS Qin, VG Corces	11/09/2012
Read-mapping using personalized diploid reference genome for RNA sequencing data reduced bias for detecting allele-specific expression. IEEE International Conference on Bioinformatics and Biomedicine workshops. IEEE International Conference on Bioinformatics and Biomedicine	S Yuan, Z Qin	10/01/2012
The histone acetyltransferase MOF is a key regulator of the embryonic stem cell core transcriptional network. Cell stem cell	X Li, L Li, R Pandey, JS Byun, K Gardner, Z Qin, Y Dou	08/03/2012
GPUmotif: an ultra-fast and energy-efficient motif analysis program using graphics processing units. PloS one	P Zandevakili, M Hu, Z Qin	01/01/2012
FOXP3 orchestrates H4K16 acetylation and H3K4 trimethylation for activation of multiple genes by recruiting MOF and causing displacement of PLU-1. Molecular cell	H Katoh, ZS Qin, R Liu, L Wang, W Li, X Li, L Wu, Z Du, R Lyons, CG Liu, X Liu, Y Dou, P Zheng, Y Liu	12/09/2011
Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer. Genome research	JH Kim, SM Dhanasekaran, JR Prensner, X Cao, D Robinson, S Kalyana-Sundaram, C Huang, S Shankar, X Jing, M Iyer, M Hu, L Sam, C Grasso, CA Maher, N Palanisamy, R Mehra, HD Kominsky, J Siddiqui, J Yu, ZS Qin, AM Chinnaiyan	07/01/2011
C/EBPβ mediates growth hormone-regulated expression of multiple target genes. Molecular endocrinology (Baltimore, Md.)	TX Cui, G Lin, CR LaPensee, AA Calinescu, M Rathore, C Streeter, G Piwien-Pilipuk, N Lanning, H Jin, C Carter-Su, ZS Qin, J Schwartz	04/01/2011
SAINT: probabilistic scoring of affinity purification-mass spectrometry data. Nature methods	H Choi, B Larsen, ZY Lin, A Breitkreutz, D Mellacheruvu, D Fermin, ZS Qin, M Tyers, AC Gingras, AI Nesvizhskii	01/01/2011
Statistical Issues in the Analysis of ChIP-Seq and RNA-Seq Data. Genes	D Ghosh, ZS Qin	09/27/2010