Zhaohui S Qin

Summary

Affiliation: University of Michigan
Country: USA

Publications

  1. pmc Query large scale microarray compendium datasets using a model-based bayesian approach with variable selection
    Ming Hu
    Department of Biostatistics, Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
    PLoS ONE 4:e4495. 2009
  2. pmc On the detection and refinement of transcription factor binding sites using ChIP-Seq data
    Ming Hu
    Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
    Nucleic Acids Res 38:2154-67. 2010
  3. pmc Different normalization strategies for microarray gene expression traits affect the heritability estimation
    Jun Ma
    Department of Molecular Cellular and Developmental Biology, University of Michigan, 210 Washtenaw Avenue, LSI 6026, Ann Arbor, Michigan 48109 2216, USA
    BMC Proc 1:S154. 2007
  4. pmc HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data
    Zhaohui S Qin
    Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, 48109 2029, USA
    BMC Bioinformatics 11:369. 2010
  5. ncbi request reprint Clustering microarray gene expression data using weighted Chinese restaurant process
    Zhaohui S Qin
    Center for Statistical Genetics, Department of Biostatistics, School of Public Health, University of Michigan 1420 Washington Heights, Ann Arbor, MI 48109 2029, USA
    Bioinformatics 22:1988-97. 2006
  6. ncbi request reprint An efficient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria
    Zhaohui S Qin
    Center for Statistical Genetics, Department of Biostatistics, School of Public Health, University of Michigan 1420 Washington Heights, Ann Arbor, MI 48109 2029, USA
    Bioinformatics 22:220-5. 2006
  7. ncbi request reprint CRCView: a web server for analyzing and visualizing microarray gene expression data using model-based clustering
    Zuoshuang Xiang
    Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, USA
    Bioinformatics 23:1843-5. 2007
  8. pmc Structural comparison of metabolic networks in selected single cell organisms
    Dongxiao Zhu
    Bioinformatics Program, University of Michigan, Ann Arbor, MI 48109, USA
    BMC Bioinformatics 6:8. 2005
  9. pmc Global gene expression analysis reveals evidence for decreased lipid biosynthesis and increased innate immunity in uninvolved psoriatic skin
    Johann E Gudjonsson
    Department of Dermatology, University of Michigan, 1910 Taubman Center, Ann Arbor, Michigan 48109, USA
    J Invest Dermatol 129:2795-804. 2009
  10. pmc SAINT: probabilistic scoring of affinity purification-mass spectrometry data
    Hyungwon Choi
    Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
    Nat Methods 8:70-3. 2011

Research Grants

Collaborators

Detail Information

Publications32

  1. pmc Query large scale microarray compendium datasets using a model-based bayesian approach with variable selection
    Ming Hu
    Department of Biostatistics, Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
    PLoS ONE 4:e4495. 2009
    ..When we apply this new method to the Escherichia coli microarray compendium data, it identifies a majority of known regulons as well as novel potential target genes of numerous key transcription factors...
  2. pmc On the detection and refinement of transcription factor binding sites using ChIP-Seq data
    Ming Hu
    Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
    Nucleic Acids Res 38:2154-67. 2010
    ..These findings may offer new biological insights into the mechanisms of transcription factor regulation...
  3. pmc Different normalization strategies for microarray gene expression traits affect the heritability estimation
    Jun Ma
    Department of Molecular Cellular and Developmental Biology, University of Michigan, 210 Washtenaw Avenue, LSI 6026, Ann Arbor, Michigan 48109 2216, USA
    BMC Proc 1:S154. 2007
    ..Analysis of their annotation indicates different types of genes were enriched in this group compared to genes showing strong heritability...
  4. pmc HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data
    Zhaohui S Qin
    Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, 48109 2029, USA
    BMC Bioinformatics 11:369. 2010
    ..In order to realize the full potential of this technique, increasingly sophisticated statistical algorithms have been developed to analyze the massive amount of data generated by this method...
  5. ncbi request reprint Clustering microarray gene expression data using weighted Chinese restaurant process
    Zhaohui S Qin
    Center for Statistical Genetics, Department of Biostatistics, School of Public Health, University of Michigan 1420 Washington Heights, Ann Arbor, MI 48109 2029, USA
    Bioinformatics 22:1988-97. 2006
    ..However, substantial fluctuation contained in microarray data, lack of knowledge on the number of clusters and complex regulatory mechanisms underlying biological systems make the clustering problems tremendously challenging...
  6. ncbi request reprint An efficient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria
    Zhaohui S Qin
    Center for Statistical Genetics, Department of Biostatistics, School of Public Health, University of Michigan 1420 Washington Heights, Ann Arbor, MI 48109 2029, USA
    Bioinformatics 22:220-5. 2006
    ..The goal is to minimize the number of markers selected for genotyping in a particular platform and therefore reduce genotyping cost while simultaneously maximizing the information content provided by selected markers...
  7. ncbi request reprint CRCView: a web server for analyzing and visualizing microarray gene expression data using model-based clustering
    Zuoshuang Xiang
    Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, USA
    Bioinformatics 23:1843-5. 2007
    ..It allows flexible input data format, rich graphical illustration as well as integrated GO term based annotation/interpretation of clustering results. Availability: http://helab.bioinformatics.med.umich.edu/crcview/...
  8. pmc Structural comparison of metabolic networks in selected single cell organisms
    Dongxiao Zhu
    Bioinformatics Program, University of Michigan, Ann Arbor, MI 48109, USA
    BMC Bioinformatics 6:8. 2005
    ....
  9. pmc Global gene expression analysis reveals evidence for decreased lipid biosynthesis and increased innate immunity in uninvolved psoriatic skin
    Johann E Gudjonsson
    Department of Dermatology, University of Michigan, 1910 Taubman Center, Ann Arbor, Michigan 48109, USA
    J Invest Dermatol 129:2795-804. 2009
    ..Taken together, our results identify a "pre-psoriatic" gene expression signature, suggesting decreased lipid biosynthesis and increased innate immunity in uninvolved psoriatic skin...
  10. pmc SAINT: probabilistic scoring of affinity purification-mass spectrometry data
    Hyungwon Choi
    Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
    Nat Methods 8:70-3. 2011
    ..We show that SAINT is applicable to data of different scales and protein connectivity and allows transparent analysis of AP-MS data...
  11. pmc A double-layered mixture model for the joint analysis of DNA copy number and gene expression data
    Hyungwon Choi
    Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
    J Comput Biol 17:121-37. 2010
    ....
  12. ncbi request reprint High throughput screening of co-expressed gene pairs with controlled false discovery rate (FDR) and minimum acceptable strength (MAS)
    Dongxiao Zhu
    Bioinformatics Program, University of Michigan, Ann Arbor, MI 48109, USA
    J Comput Biol 12:1029-45. 2005
    ..The method has been implemented in an R package "GeneNT" that is freely available from the Comprehensive R Archive Network (CRAN): www.cran.r-project.org/...
  13. pmc Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer
    Jung H Kim
    Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    Genome Res 21:1028-41. 2011
    ..This comprehensive methylome map will further our understanding of epigenetic regulation in prostate cancer progression...
  14. pmc An integrated network of androgen receptor, polycomb, and TMPRSS2-ERG gene fusions in prostate cancer progression
    Jindan Yu
    Michigan Center for Translational Pathology, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    Cancer Cell 17:443-54. 2010
    ..These findings provide a working model in which TMPRSS2-ERG plays a critical role in cancer progression by disrupting lineage-specific differentiation of the prostate and potentiating the EZH2-mediated dedifferentiation program...
  15. pmc Characterization of the EZH2-MMSET histone methyltransferase regulatory axis in cancer
    Irfan A Asangani
    Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    Mol Cell 49:80-93. 2013
    ..Together, these results suggest that the EZH2-MMSET HMTase axis coordinately functions as a master regulator of transcriptional repression, activation, and oncogenesis and may represent an attractive therapeutic target in cancer...
  16. pmc Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data
    Hyungwon Choi
    Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
    Bioinformatics 25:1715-21. 2009
    ..Therefore, it is of interest to see whether the two data sources can be combined to enhance the detection of TFBS...
  17. pmc C/EBPβ mediates growth hormone-regulated expression of multiple target genes
    Tracy X Cui
    Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan 48109 5622, USA
    Mol Endocrinol 25:681-93. 2011
    ..Overall, these studies suggest that C/EBPβ, like the signal transducer and activator of transcription proteins, regulates multiple genes in response to GH...
  18. pmc FOXP3 orchestrates H4K16 acetylation and H3K4 trimethylation for activation of multiple genes by recruiting MOF and causing displacement of PLU-1
    Hiroto Katoh
    Division of Immunotherapy, Department of Surgery, University of Michigan School of Medicine and Cancer Center, Ann Arbor, MI 48109, USA
    Mol Cell 44:770-84. 2011
    ....
  19. ncbi request reprint Improved classification of mass spectrometry database search results using newer machine learning approaches
    Peter J Ulintz
    National Resource for Proteomics and Pathways, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, USA
    Mol Cell Proteomics 5:497-509. 2006
    ..Performance was evaluated using publically available electrospray data and a new collection of MALDI data generated from purified human reference proteins...
  20. pmc Operon prediction for sequenced bacterial genomes without experimental information
    Nicholas H Bergman
    University of Michigan Medical School, Bioinformatics Program and Department of Microbiology and Immunology, 6605H Medical Sciences Bldg II, 1150 W Medical Center Dr, Ann Arbor, MI 48109 0620, USA
    Appl Environ Microbiol 73:846-54. 2007
    ....
  21. doi request reprint Targeting MLL1 H3K4 methyltransferase activity in mixed-lineage leukemia
    Fang Cao
    Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
    Mol Cell 53:247-61. 2014
    ..We envision broad applications for MM-401 in basic and translational research. ..
  22. pmc Computational and functional analysis of growth hormone (GH)-regulated genes identifies the transcriptional repressor B-cell lymphoma 6 (Bc16) as a participant in GH-regulated transcription
    Yili Chen
    Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan 48109 5622
    Endocrinology 150:3645-54. 2009
    ..Together these analyses identify Bcl6 as a participant in GH-regulated gene expression and suggest an interplay between the repressor Bcl6 and the activator Stat5 in regulating genes, which contribute to GH responses...
  23. pmc Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq
    Ming Hu
    Department of Statistics, Harvard University, Cambridge, MA 02138, USA
    Bioinformatics 28:63-8. 2012
    ..In particular, large base-specific variation and between-base dependence make simple approaches, such as those that use averaging to normalize RNA-Seq data and quantify gene expressions, ineffective...
  24. doi request reprint The central role of EED in the orchestration of polycomb group complexes
    Qi Cao
    1 Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA 2 Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA 3 Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, Texas 77030, USA 4 Cancer Center, Houston Methodist Research Institute, Houston, Texas 77030, USA
    Nat Commun 5:3127. 2014
    ..EED functions to recruit PRC1 to H3K27me3 loci and enhances PRC1-mediated H2A ubiquitin E3 ligase activity. Taken together, we suggest an integral role for EED as an epigenetic exchange factor coordinating the activities of PRC1 and 2. ..
  25. pmc A comparison of phasing algorithms for trios and unrelated individuals
    Jonathan Marchini
    Department of Statistics, University of Oxford, Oxford OX1 3TG, United Kingdom
    Am J Hum Genet 78:437-50. 2006
    ..Finally, we evaluated methods of estimating the value of r(2) between a pair of SNPs and concluded that all methods estimated r(2) well when the estimated value was >or=0.8...
  26. pmc Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies
    Kui Zhang
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089 1113, USA
    Genome Res 14:908-16. 2004
    ..The power of association studies based on tag SNPs using genotype data is similar to that using haplotype data...
  27. pmc Incorporating genotyping uncertainty in haplotype inference for single-nucleotide polymorphisms
    Hosung Kang
    Department of Statistics, Harvard University, Cambridge, MA 02138, USA
    Am J Hum Genet 74:495-510. 2004
    ....
  28. pmc Statistical resynchronization and Bayesian detection of periodically expressed genes
    Xin Lu
    Department of Statistics, Harvard University, Cambridge, MA 02138, USA
    Nucleic Acids Res 32:447-55. 2004
    ....
  29. ncbi request reprint Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites
    Zhaohui S Qin
    Department of Statistics, Harvard University, Cambridge, MA 02138, USA
    Nat Biotechnol 21:435-9. 2003
    ....
  30. pmc Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms
    Zhaohui S Qin
    Am J Hum Genet 71:1242-7. 2002
  31. pmc Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms
    Tianhua Niu
    Program for Population Genetics, Harvard School of Public Health, Boston, MA, USA
    Am J Hum Genet 70:157-69. 2002
    ....
  32. pmc Family-based SNP association study on 8q24 in bipolar disorder
    Peter P Zandi
    Department of Mental Health, Johns Hopkins School of Public Health, Baltimore, Maryland 21205, USA
    Am J Med Genet B Neuropsychiatr Genet 147:612-8. 2008
    ..These findings with ADCY8 and ST3GAL1 warrant further investigation in order to confirm the observed associations and their functional significance for BP susceptibility...

Research Grants1

  1. Model-Based Methods for Analyzing ChIP Sequencing Data
    Zhaohui Qin; Fiscal Year: 2009
    ..The development of statistical and computational strategies proposed here will help us gain in-depth understanding of mechanisms mediating transcriptional regulation in prostate cancer progression. ..