Zhaohui Steve Qin, PhD

Assistant Professor
Center for Statistical Genetics
Department of Biostatistics
School of Public Health

Affiliate Member
Center for Computational Medicine and Biology
Bioinformatics Graduate Program
Michigan Center for Translational Pathology
Michigan Metabolomics and Obesity Center


Department of Biostatistics  Tel: (734) 763-5965
University of Michigan Fax: (734) 763-2215
M4232 SPH II, 1420 Washington Heights Email: qin@umich.edu
Ann Arbor, MI 48109 Web: http://www-personal.umich.edu/~qin/

Research interests:

  • Computational Biology: high throughput genomics data analysis
  • Statistical Genetics: haplotype phasing, disease gene mapping
  • Statistical Computing: Monte Carlo Methods
  • Teaching (Fall 2009):

  • BIOSTAT601 Probability and Distribution Theory .
  • Past teaching:

  • BIOSTAT666 Statistical Models and Numerical Methods in Human Genetics. Winter 2008.
  • BIOSTAT601 Probability and Distribution Theory. Fall 2006, 2008.
  • BIOSTAT830 SNPs, Haplotypes and Association Studies. Winter 2006.
  • BIOSTAT682 Applied Bayesian Inference. Winter 2005, 2006.
  • BIOINFO 545/STAT545/BIOSTAT646 Data Anlysis in Molecular Biology Winter 2004, 2005, 2008, 2009.
  • Software developed and co-developed:

  • HMS (motif discovery using ChIP-Seq data).
  • BEST (for query large scale microarray compendium datasets).
  • FESTA (tagSNP selection based on pairwise LD).
  • CRC and CRCView (Dirichelt Mixture model-based clustering of gene expression microarray data and web server).
  • operonHMM (operon prediction based on DNA sequence data using HMM).
  • tripleM (extended PL-EM for phasing trios).
  • HapBlock (dynamic programming algorithms for haplotype block partitioning and tagSNPs selection).
  • EM-DeCODER (haplotype phasing using plain vanilla EM algorithm).
  • HAPLOTYPER (haplotype phasing using PL and Gibbs Sampler).
  • PL-EM (haplotype phasing using PL and EM algorithm).
  • BMC (putative motif clustering using Gibbs sampler algorithm).
  • Selected Publication:

    * -- trainee as first or co-first author.

    Breitkreutz A, *Choi H, Sharom J, Boucher L, Neduva V, Larsen B, Lin Z, Breitkreutz B, Stark C, Liu G , Ahn J, Dewar-Darch D, Qin ZS, Pawson T, Gingras A, Nesvizhskii AI, Tyers M. (2010) Global Architecture of the Yeast Kinome Interaction Network. Science. 328 1043-1046. abstract full paper.

    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) An Integrated Network of Androgen Receptor, Polycomb and TMPRSS2-ERG Gene Fusion in Prostate Cancer Progression. Cancer Cell. 17. 443-454. abstract full paper. On the cover.

    *Hu M, Yu J, Taylor, JMG, Chinnaiyan AM, Qin ZS. (2010) On the Detection and Refinement of Transcription Factor Binding Sites Using ChIP-Seq Data. Nucleic Acids Res. 38. 2154-2167. abstract full paper. supplementary material and download software HMS .

    *Choi H, Qin ZS, Ghosh D. (2010) A Double-layered Mixture Model for the Joint Analysis of DNA Copy Number and Gene Expression Data. J. Comput. Biol. 17. 121-137. abstract full paper.

    Gudjonsson JE, Ding J, Li X, Nair R, Tejasvi T, Qin ZS, Ghosh D, Aphale A, Gumucio DL, Voorhees JJ, Abecasis G, Elder JT. (2009) Global Gene Expression Analysis Reveals Evidence for Decreased Lipid Biosynthesis and Increased Innate Immunity in Uninvolved Psoriatic Skin. J. Invest. Dermatol. 129. 2795-2804. abstract full paper.

    *Chen Y, Lin G, Huo JS, Barney D, Wang ZN, Livshiz T, States DJ, Qin ZS, Schwartz J. (2009) Computational and functional analysis of growth hormone-regulated genes identifies the transcriptional repressor Bcl6 as a participant in GH-regulated transcription. Endocrinology. 150. 1645-1654. abstract full paper.

    *Zhou J, Qin ZS, Quinney KS, Kim S Wang Z, Hall S, Li L. (2009) Drug-Drug Interactions Prediction Assessment. J Biopharm Stat. 19. 641-657. full paper.

    *Choi H, Nesvizhskii A, Ghosh D, Qin ZS. (2009) Hierarchical Hidden Markov Model with Application to Joint Analysis of ChIP-chip and ChIP-seq Data. Bioinformatics. 25 1715-1721. abstract full paper. Our work is mentioned in this Feasure Story ChIP Goes Genome_Scale of the July issue of the Genome Technology magazine.

    *Hu M, Qin ZS. (2009) Apply Bayesian model selection to better query large scale microarray gene expression datasets. PLoS ONE. 4 e4495. abstract full paper. supplementary material and download software BEST .

    *Zhou J, Qin ZS, Kim S, Wang Z, Yu M, Chien JY, Lucksiri A, Li L. (2009) A New Probabilistic Rule for Drug-Drug Interaction Prediction. Journal of Pharmacokinetics and Pharmacodynamics. 36 1-18. abstract full paper.

    Qin ZS, Zhu J, Ulintz PJ, Andrews PC. (2008) Machine learning approaches for peptide identification based on mass spectrometry database search results. Introduction to Machine Learning and Bioinformatis. CRC Press.

    *Ma J, Qin ZS (2007) Different normalization strategies for microarray gene expression traits affect the heritability estimation. BMC Proceedings. 1(Suppl 1):S154. abstract full paper.

    Bommer GT, Gerin I, Feng Y, Kaczorowski AJ, Kuick R, Love RE, Zhai Y, Giordano TJ, Qin ZS, Moore BB, MacDougald OA, Cho KR, Fearon ER. (2007) p53-mediated Activation of miRNA34 Candidate Tumor-suppressor Genes. Curr Biol. 17 1298-1307. abstract full paper.

    Xiang Z, Qin ZS, He Y. (2007) CRCView: A web server for analyzing and visualizing microarray gene expression data using model-based clustering. Bioinformatics. 23, 1843-1845. abstract full paper CRCView web server .

    Bergmen NH, Karla D. Passalacqua, Philip C. Hanna, Qin ZS. (2007) Operon prediction in sequenced bacterial genomes without experimental Information. Applied Environmental Microbiology. 73 846-854. abstract full paper supplementary material and download operonHMM.

    Qin ZS (2006) Clustering microarray gene expression data using weighted Chinese restaurant process. Bioinformatics. 22 1988-1997. abstract full paper supplementary material and download CRC.

    *Gopalakrishnan S, Qin ZS (2006) TagSNP Selection Based on Pairwise LD Criteria and Power Analysis in Association Studies. Pacific Symposium on Biocomputing. 11. 511-522. abstract full paper.

    Marchini J, Cutler D, Patterson N, Stephens M, Eskin E, Halperin E, Lin S, Qin ZS, Munro HM, Abecasis GR, Donnelly P; International HapMap Consortium. (2006) A comparison of phasing algorithms for trios and unrelated individuals. Am J Hum Genet. 78 437-450. abstract full paper download tripleM.

    *Ulintz PJ, Zhu J, Qin ZS, Andrews PC. (2006) Improved classification of mass spectrometry database search results using newer machine learning approaches. Mol Cell Proteomics. 5. 497-509. abstract full paper.

    Qin ZS, Gopalakrishnan S, Abecasis G (2006) An efficient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria. Bioinformatics. 22. 220-225. abstract full paper supplementary material and download FESTA.

    *Zhu D, Hero AO, Qin ZS and Swaroop A (2005) High throughput screening of co-expressed gene pairs with controlled False Discovery Rate (FDR) and Minimum Acceptable Strength (MAS). J. Comput. Biol. 12. 1029-45. abstract full paper

    *Zhu D, Qin ZS (2005) Structure comparison of metabolic networks in selected single cell organisms. BMC Bioinformatics. 6: 8. abstract full paper

    Zhang K, Qin ZS, Chen T, Liu JS, Waterman MS, Sun F (2004) HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms. Bioinformatics. 21 131-134. abstract full paper download HapBlock.

    Zhang K, Qin ZS, Liu JS, Chen T, Waterman MS, Sun, F (2004) Haplotype Block partitioning and Tag SNP Selection Using Genotype Data and Their Applications to Association Studies. Genome Res. 14 908-916. abstract full paper

    Kang H, Qin ZS, Niu T, Liu JS (2004) Incorporating Genotyping Uncertainty in Haplotype Inference for Single-Nucleotide Polymorphisms. Am. J. Hum. Genet. 74 495-510. abstract full paper

    Lu, X., Zhang, W., Qin, Z.S., Kwast, K.E., Liu, J.S. (2004) Statistical Resynchronization and Bayesian Detection of Periodically Expressed Genes. Nucleic Acids Res. 32 447-455. abstract full paper

    Qin ZS, McCue LA, Thompson W, Mayerhoffer L, Lawrence CE and Liu JS (2003) Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites. Nat Biotechnol. 21 435-9. abstract full paper supplementary material and download BMC.

    Qin ZS, Niu T and Liu JS (2002) Partition-Ligation EM Algorithm for Haplotype Inference with Single Nucleotide Polymorphisms. Am. J. Hum. Genet. 71 1242-7. abstract full paper supplementary material and download PLEM.

    Niu T, Qin ZS, Xu X and Liu JS (2002) Bayesian haplotype inference for multiple linked single nucleotide polymorphisms. Am. J. Hum. Genet. 70 157-69. abstract full paper supplementary material and download HAPLOTYPER.

    Qin ZS and Liu JS (2001) Multi-Point Metropolis method with application to hybrid Monte Carlo. J. Comp. Phys., 172:827-40. full paper

    Chen L, Qin ZS, and Liu JS (2001) Exploring Hybrid Monte Carlo in Bayesian Computation. Proceedings of ISBA 2000 - The Sixth World Meeting of the International Society for Bayesian Analysis. 2001 full paper