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 Metabolomics and Obesity Center

Contact: 
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:

  • Statistical Genetics: haplotype phasing, disease gene mapping
  • Computational Biology: transcription regulation network inference
  • Statistical Computing: Monte Carlo Methods

    • Teaching (Winter 2008):

  • BIOSTAT646 Data Analysis in Molecular Biology Winter 2008.
  • BIOSTAT682 Statistical Models and Numerical Methods in Human Genetics Winter 2008.

    • Past Teaching:

  • BIOSTAT601 Probability and Distribution Theory. Fall 2006.
  • 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.

    • Software developed and co-developed:

  • FESTA (tagSNP selection based on pairwise LD)
  • CRC and CRCView (Dirichelt Mixture model-based clustering of gene expression microarray data)
  • operonHMM (operon prediction based on DNA sequence data using HMM)
  • tripleM
  • 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:

    Ma J, Qin ZS (2007) Different normalization strategies for microarray gene expression traits affect the heritability estimation. BMC Proceedings. Accepted. 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.full paper supplementary material and download operonHMM.

    Qin ZS (2006) Clustering microarray gene expression data using weighted Chinese restaurant process. Bioinformatics. 22 1988-1997.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.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.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.full paper

    Qin ZS, Gopalakrishnan S, Abecasis G (2006) An efficient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria. Bioinformatics. 22. 220-5.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.full paper

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