I have extensive experience in statistical modeling and computing with applications to statistical genetics and genomics. My recent research is focused on developing Bayesian model-based methods to analyze data generated from applications of next-generation sequencing technologies such as ChIP-seq, RNA-seq, Hi-C, WGBS, resequencing, and on developing software so that the methods can be easily adopted by the research community. I am also actively collaborating with biomedical scientists and clinicians on projects that utilize next-generation sequencing technologies to better understand genomics and epigenomics.
Contact Information
1518 Clifton Road NE ,
Atlanta , GA 30322-4201
Phone: (404) 712-9576
Fax: (404)727-1370
Email: zhaohui.qin@emory.edu
Areas of Interest
- Bayesian Analysis
- Bioinformatics
- Epigenetics
- Genetics
- Genomics
- Machine Learning
- Statistical Modeling
Education
- PhD 2000, University of Michigan, Ann Arbor, MI
- BS 1994, Peking University, Beijing, China
Courses Taught
- BIOS 799R: Dissertation
- BIOS 795R: Pre-Candidacy Research
- BIOS 534: Machine Learning
Affiliations & Activities
Department of Biomedical Informatics, Emory University School of Medicine
Department of Computer Science, Emory University
Publications
- Cao Z, Huang Y, Duan R, Jin P, Qin ZS, Zhang S, 2022, Disease Category-specific Annotation of Variants Using an Ensemble Learning Framework, Briefings in Bioinformatics, 23, bbab438
- Ma W, Sharma S, Jin P, Gourley SL, Qin ZS, 2022, LRcell: detecting the source of differential expression at the sub-cell type level from bulk RNA-seq data, Briefings in Bioinformatics, , bbac063
- Jin Y, Jiang J, Wang R, Qin ZS , 2022, Systematic Evaluation of DNA Sequence Variations on in vivo Transcription Factor Binding Affinity, Frontiers in Genetics, 12, 667866
- Huang Y, Sun X, Jiang H, Yu S, Robins C, Armstrong JM, Li R, Mei Z, Shi X, Gerasimov ES, De Jager PL, Bennett DA, Wingo AP, Jin P, Wingo TS, Qin ZS , 2021, A machine learning approach to brain epigenetics analysis reveals kinases associated with Alzheimer’s dis-ease. , Nature Communications, 12, 4472
- Su K, Yu Q, Shen R, Sun SY, Moreno CS, Li X, Qin ZS , 2021, Pan-cancer analysis of pathway-based gene expression pattern at the individual level reveals novel bi-omarkers of clinical prognosis. , Cell Reports Methods, 1, 100050
- Guo Z, Cui Y, Shi X, Birchler JA, Albizua I, Sherman SL, Qin ZS, Ji T. , 2020, An Empirical Bayesian Approach for Testing Gene Expression Fold Change and Its Application in Detecting Global Dosage Effects, Nucleic Acids Research Genomics and Bioinformatics, 2, lqaa072
- Yang G, Ma A, Qin ZS, Chen L, 2020, Application of Topic Models to a Compendium of ChIP-Seq Datasets Uncovers Recurrent Transcriptional Regulatory Modules, Bioinformatics, 36, 2352-2358
- Xu T, Jin P, Qin ZS, 2020, Regulatory annotation of genomic intervals based on tissue-specific expression QTLs., Bioinformatics, 36, 690-697
- Poulet A, Li B, Dubos T, Rivera-Mulia JC, Gilbert DM, Qin ZS, 2019, RT States: systematic annotation of the human genome using cell type-specific replication timing programs, Bioinformatics, 35, 2167-2176
- Sun X, Gao J, Jin P, Eng C, Burchard EG, Beaty TH, Ruczinski I, Mathias RA, Barnes KC, Wang F, Qin ZS on behalf of CAAPA consortium , 2018, Optimized Distributed Systems Achieve Significant Performance Improvement on Sorted Merging of Massive VCF Files, Gigascience, 7, giy052
- Sun X, Pittard WS, Xu T, Chen L, Zwick ME, Jiang X, Wang F, Qin ZS, 2017, Omicseq: A web-based search engine for exploring omics datasets, Nucleic Acids Research, 45, W445-W452
- Chen L, Jin P, Qin ZS, 2016, DIVAN: accurate identification of non-coding disease-specific risk variants using multi-omics profiles. , Genoem Biology, 12, 252
- Chen L, Wang C, Qin ZS, Wu H., 2015, A novel statistical method for quantitative comparison of multiple ChIP-seq datasets. , Bioinformatics, 31, 1889-1896
- Xu T, Li B, Zhao M, Szulwach KE, Street RC, Lin L, Yao B, Zhang F, Jin P, Wu H, Qin ZS., 2015, Base-resolution methylation patterns accurately predict transcription factor bindings in vivo. , Nucleic Acids Research. , 43, 2757-2766
- Li B, He Q, Sun Z, Zhu Y, Qin ZS, 2015, Bayesian inference with historical data-based informative priors improves detection of differentially expressed genes. , Bioinformatics, 32, 682-689
- Yuan S, Johnston HR, Zhang G, Li Y, Hu Y-J, Qin ZS. , 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 , 11, e1004448
- Chen L, Qin ZS, 2015, traseR: an R package for performing trait-associated SNP enrichment analysis in genomic intervals., Bioinformatics, 32, 1214-1216
- Li L, Lyu X, Hou C, Takenaka N, Ong CT, Cubeñas-Potts C, Hu M, Lei EP, Bosco G, Qin ZS, Corces, VG, 2015, Widespread Rearrangement of 3D Chromatin Organization Underlies Polycomb-Mediated Stress-Induced Silencing, Mol Cell, 58, 216-231
- Hu M, Deng K, Qin ZS, Dixon J, Selvaraj S, Fang J, Ren B, Liu JS. , 2013, Bayesian inference of three-dimensional chromosomal organization. , PLoS Comput Biol. , 9, e1002893
- Choi H, Fermin D, Nesvizhskii AI, Ghosh D, Qin ZS., 2013, Sparsely-correlated Hidden Markov Models with Application to Genome-wide Location Studies. , Bioinformatics, 29, 533-541
- Hou C, Li L, Qin ZS, Corces, VG, 2012, Gene Density, Transcription and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains. , Mol Cell, 48, 471-484
- Li X, Li L, Byun JS, Pandey R, Gardner K, Qin ZS, Dou Y., 2012, The histone acetyltransferase MOF is a key regulator of the embryonic stem cell core transcriptional network., Cell Stem Cell, 11, 163-178
- Hu M, Zhu Y, Taylor JMG, Liu JS, Qin ZS , 2012, Using Poisson mixed-effects model to quantify exon-level gene expression in RNA-seq. , Bioinformatics, 28, 63-68
- Yu J, Yu J, Mani R, Cao X, Cao Q, Brenner CJ, Cao X, Wang GX, Wu L, Li J, *Hu M, Gong Y, Cheng H, Laxman B, Vellaichamy A, Shankar S, Li Y, Dhanasekaran SM, Morey R, Barrette T, Lonigro RJ, Tomlins SA, Varambally S, Qin ZS, Chinnaiyan, AM, 2010, Integrated Network of Androgen Receptor, Polycomb and TMPRSS2-ERG Gene Fusion in Prostate Cancer Progression. , Cancer Cell, 17, 443
- Hu M, Yu J, Taylor, JM, Chinnaiyan AM, Qin ZS, 2010, On the Detection and Refinement of Transcription Factor Binding Sites Using ChIP-Seq Data. , Nucleic Acids Res. , 38, 2154