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Kui Zhang, Ph.D.

Department of Biostatistics
Ryals Public Health Bldg, 317
University of Alabama at Birmingham
Birmingham, AL 35294
Phone: (205) 996-4094
Fax: (205) 975-2540
E-mail: kzhang@ms.soph.uab.edu

Full CV

 


Biography: Introduction for Dr. Kui Zhang and his research

Programs: Software packages developed by Kui Zhang's research group

Publications: Selected publications from Kui Zhang's research group

Teaching: A list of courses and their lecture notes

People: Members in Kui Zhang's research group
 

Biography


Dr. Kui Zhang obtained his PhD in probability and statistics from Peking University in 1999 and joined the section of statistical genetics of University of Alabama at Birmingham as a research assistant professor in 2003. He has two related but different research areas: (1) to develop a new methods and designing novel algorithms to locate complex disease genes in genetic linkage analysis and linkage disequilibrium analysis using both population-based and family-based data; (2) to develop computational tools to understand molecular functions combining different data such as gene expression microarray data and protein-protein interaction data. Currently, Dr. Zhang is continuing his methodology developments for linkage, disequilibrium, and haplotype analysis and microarray analysis. He is very interested in collaborating with other investigators to apply these methods to their projects.

For a detailed description of his research, please see his research statement (short version, full version)

For a detailed biography, please see his full CV and NIH Biosketch.

 

Programs

  • HapBlock: A set of dynamic programming algorithms for haplotype block partitioning and tag SNP selection using haplotype or genotype data
  • HAPLORE: A program for haplotype inference in general pedigrees without recombinants
  • HaploIHP: A program for haplotype inference for unrelated individuals using identified haplotypes and/or haplotype patterns.

Publications

  1. Kui Zhang, Hongyu Zhao. 2000. Assessing Reliability of Gene Clusters from Gene Expression Data. Functional & Integrative Genomics 1:156-173. [PMID: 11793234]
     
  2. Kui Zhang, Dayue Chen. 2001. The Probabilistic Study of d-SAT Problem. Advances in Mathematics (Chinese) 30: 231-237.
     
  3. Jinming Li, Dai Wang, Jianping Dong, Renfang Jiang, Kui Zhang, Shuanglin Zhang, Hongyu Zhao, Fengzhu Sun. 2001. The power of Transmission Disequilibrium Tests for Quantitative Traits. In: Wijsman EM, Almasy L, Amos CI, Borecki I, Falk CT, King TM, Martinez MM, Meyers D, Neuman R, Olson JM, Rich S, Spence MA, Thomas DC, Vieland VJ, Witte JS, MacCluer JW (Editors), Analysis of complex genetic traits: Applications to asthma and simulated data. In Genetic Epidemiology 21(Suppl 1): S632-S637. [PMID: 11793752]
     
  4. Shuanglin Zhang, Kui Zhang, Jinming Li, Fengzhu Sun, Hongyu Zhao. 2001. Test of Linkage and Association for Quantitative Traits in General Pedigrees: The Quantitative Pedigree Disequilibrium Test. In: Wijsman EM, Almasy L, Amos CI, Borecki I, Falk CT, King TM, Martinez MM, Meyers D, Neuman R, Olson JM, Rich S, Spence MA, Thomas DC, Vieland VJ, Witte JS, MacCluer JW (Editors), Analysis of complex genetic traits: Applications to asthma and simulated data. In Genetic Epidemiology 21(Suppl 1): S370-S375. [PMID: 11793701]
     
  5. Shuanglin Zhang, Kui Zhang, Jinming Li, Hongyu Zhao. 2002. On a Family-based Haplotype Pattern Mining Method for Linkage Disequilibrium Mapping. The Proceeding of Pacific Symposium on Biocomputing 7:100-111. [PMID: 11928467]
     
  6. Kui Zhang, Minghua Deng, Ting Chen, Michael S. Waterman, Fengzhu Sun. 2002. A Dynamical Programming Algorithm for Haplotype Block Partitioning. Proceedings of the National Academy of Sciences of the United States of America 99: 7335-7339. [PMID: 12032283]
     
  7. Kui Zhang, Peter Calabrese, Magnus Nordborg, Fengzhu Sun. 2002. Haplotype Structure and Its Applications to Association Studies: Power and Study Designs. The American Journal of Human Genetics 71: 1386-1394. [PMID: 12439824]
     
  8. Kui Zhang, Fengzhu Sun, Michael S. Waterman, Ting Chen. 2003. Haplotype Block Partitioning with Limited Resources and Applications to Human Chromosome 21 Haplotype Data. The American Journal of Human Genetics 73: 63-73. [PMID: 12802783]
     
  9. Sung Kim, Kui Zhang, Fengzhu Sun. 2003. Detecting Susceptibility Genes in Case-Control Studies Using Set Association Analysis. In: Almasy L, Amos CI, Bailey-Wilson JE, Cantor RM, Jaquish CE, Martinez M, Neuman RJ, Olson JM, Palmer LJ, Rich SS, Spence MA, MacCluer JW (Editors) Genetic Analysis Workshop 13: Analysis of Longitudinal Family Data for Complex Diseases and Related Risk Factors. BMC Genetics 2003, 4(Suppl 1): S9. [PMID: 14975077] [PMCID: 1866530]
     
  10. Minghua Deng, Kui Zhang, Shipra Mehta, Ting Chen, Fengzhu Sun. 2003. Prediction of Protein Function Using Protein-protein Interaction Data. Journal of Computational Biology 10: 947-960. [PMID: 14980019]
     
  11. Sung Kim, Kui Zhang, Fengzhu Sun. 2004. A Comparison of Different Strategies for Computing Confidence Intervals of the Linkage Disequilibrium Measure. The Proceeding of Pacific Symposium on Biocomputing 9: 128-139. [PMID: 14992498]
     
  12. Thomas G. Schulze, Kui Zhang, Yu-Sheng Chen, Nirmala Akula, Fengzhu Sun, Francis J. McMahon. 2004. Defining Haplotype Blocks and Tag Single-nucleotide Polymorphisms in the Human Genome. Human Molecular Genetics 35:335-342. [PMID: 14681300]
     
  13. Kui Zhang, Zhaohui Qin, Jun Liu, Ting Chen, Michael S. Waterman, Fengzhu Sun. 2004. Haplotype Block Partitioning and Tag SNP Selection Using Genotype Data and Their Applications to Association Studies. Genome Research 14: 908-916. [PMID: 15078859]
     
  14. Kui Zhang, Fengzhu Sun, Hongyu Zhao. 2005. HAPLORE: A Program for Haplotype Reconstruction in General Pedigrees without Recombination. Bioinformatics 21: 90-103. [PMID: 15231536]
     
  15. Kui Zhang, Zhaohui Qin, Ting Chen, Jun Liu, Michael Waterman, Fengzhu Sun. 2005. HapBlock: Haplotype Block Partitioning and Tag SNP Selection Software Using A Set of Dynamic Programming Algorithms. Bioinformatics 21: 131-134. [PMID: 15333454]
     
  16. T. Mark Beasley, Howard Wiener, Kui Zhang, Alfred A. Bartolucci, Christopher I. Amos, David Allison. 2005. Empirical Bayes Method for Incorporating Data from Multiple Genome Scans. Human Heredity 60: 36-42. [PMID: 16137992]
     
  17. Kui Zhang, Fengzhu Sun. 2005. Assessing the Power of Tag SNPs in Mapping of Quantitative Trait Loci (QTL) with Extremal and Random Samples. BMC Genetics 6: 51. [PMID: 16236175]
     
  18. Yao-Ting Huang, Kui Zhang, Ting Chen, Kun-Mao Chao. 2005. Selecting Additional Tag SNPs for Tolerating Missing Data in Genotyping. BMC Bioinformatics 6: 263. [PMID: 16259642] [PMCID: 1316880]
     
  19. Kui Zhang, Hongyu Zhao. 2006. A Comparison of Several Methods for Haplotype Frequency Estimation and Haplotype Reconstruction for Tightly Linked Markers from General Pedigrees. Genetic Epidemiology 30: 423-437. [PMID: 16685719]
     
  20. Kui Zhang, Howard Wiener, Marker Beasley, Varghese George, Christopher I. Amos, David Allison. 2006. An Empirical Bayes Method for Analysis of Quantitative-Trait Loci from Multiple Genome Scans. Genetics 173: 2283-2296. [PMID: 16751667]
     
  21. Jessica M. Grunda, L. Burton Nabors, Cheryl A. Palmer, David C. Chhieng, Adam D. Steg, Tom Mikkelsen, Robert B. Diasio, Kui Zhang, David Allison, William E. Grizzle, Wenquan Wang, Yancey Gillespie, Martin R. Johnson. 2006. Increased Expression of Thymidylate Synthetase (TS), Ubiquitin Specific Protease 10 (USP10) and Survivin Associated with Poor Survival in Glioblastoma Multiforme (GBM). Journal of Neuro-Oncology 80: 261-274. [PMID: 16773218]
     
  22. Shannon A. Ross, Zdenek Novak, Rekha A. Kumbla, Kui Zhang, Karen B. Fowler, Suresh Boppana. 2007. GJB2 and GJB6 Mutations in Children with Congenital Cytomegalovirus. Pediatric Research 61: 687-691. [PMID: 17426645]
     
  23. Hua Li, Guimin Gao, Jian Li, Grier P. Page, Kui Zhang. 2007. Detecting Epistatic Interactions Contributing to Human Gene Expression Using the CEPH Family Data. BMC Proceeding 2007, 1 (Suppl 1): S33. [PMID: 18466568] [PMCID: 2367573]
     
  24. Yun Joo Yoo, Guimin Gao, Kui Zhang. 2007. Case-control association analysis of rheumatoid arthritis with candidate genes using related cases. BMC Proceeding 2007, 1(Suppl 1): S67. [PMID: 18466531].
     
  25. Yun Joo Yoo, Jianming Tang, Richard A. Kaslow, Kui Zhang. 2007. Haplotype Inference for Present-absent Genotype Using Previously Identified Haplotypes and Haplotype Patterns. Bioinformatics 23: 2399-2406. [PMID: 17644820]
     
  26. Nianjun Liu, Kui Zhang, Hongyu Zhao. 2008. Haplotype-Association Analysis. D.C. Rao and C. Charles Gu (Editors): Genetic Dissection of Complex Traits. Advances in Genetics 60: 335-405. [PMID: 18358327]
     
  27. Yong-Jun Liu, Jose M. Ordovas, Guimin Gao, Michael Province, Robert J. Straka, Michael Y. Tsai, Chao-Qiang Lai, Kui Zhang, Ingrid Borecki, James E. Hixson, David B. Allison, Donna K. Arnett. 2008. The SCARB1 gene is Associated with Lipid Response to Dietary and Pharmacological Interventions. The Journal of Human Genetics 53: 709-717. [PMID: 18542840]
     
  28. Yong-Jun Liu, Jose M. Ordovas, Guimin Gao, Michael Province, Robert J. Straka, Michael Y. Tsai, Chao-Qiang Lai, Kui Zhang, Ingrid Borecki, James E. Hixson, David B. Allison, Donna K. Arnett. 2009. Pharmacogenetic Association of the APOA1/C3/A4/A5 Gene Cluster and Lipid Responses to Fenofibrate - The Genetics of Lipid Lowering Drugs and Diet Network Study. Pharmacogenetics and Genomics 19: 161-169. [PMID: 19057464] [PMCID: 2733171]
     
  29. Zhe Lei, Reng-Yun Liu, Jun Zhao, Zeyi Liu, Xiefang Jiang, Weiming You, Xiao-Feng Chen, Xia Liu, Kui Zhang, Boris Pasche, Hong-Tao Zhang. 2009. TGFBR1 Haplotypes and Risk of Non-small Cell Lung Cancer. Cancer Research 69:7046-7052. [PMID: 19690145] [PMCID: 2737098].
     
  30. Douglas K. Childers, Guolian Kang, Nianjun Liu, Guimin Gao, Kui Zhang. 2009. Application of Imputation Methods to the Analysis of Rheumatoid Arthritis Data in Genome-Wide Association Studies. BMC Proceedings 3 (Suppl 7): S24. [PMID: 20018014] [PMCID: 2795921].
     
  31. Guolian Kang, Douglas K. Childers, Nianjun Liu, Kui Zhang, Guimin Gao. 2009. Genome-wide Association studies of Rheumatoid Arthritis Data via Multiple Hypothesis Testing Methods for Correlated Tests. BMC Proceedings 3 (Suppl 7): S38. [PMID: 20018029] [PMCID: 2795936]
     
  32. Aleksandr Lazaryan, Wei Song, Elena Lobashevsky, Jianming Tang, Sadeep Shrestha, Kui Zhang, Lytt I. Gardner, Craig M. Wilson, Richard A. Kaslow. 2010. Human leukocyte antigen class I supertypes and HIV-1 control in African-Americans. Journal of Virology 84: 2610-2617. [PMID: 20032191]
     
  33. Li Ma, Yan Xiao, Hui Huang, Weinian Rao, Qingwei Wang, Yue Feng, Kui Zhang, Qing Song. 2010. Direct Determination of Molecular Haplotypes by Chromosome Microdissection. Nature Methods 7: 299-301. [PMID: 20305652]
     
  34. Michael A. Frolich, Mark S. Bolding, Gary R. Cutter, Timothy H Ness, Kui Zhang. 2010. Temporal Characteristics of Cold Pain Perception. Neuroscience Letters 480: 12-15. [PMID: 20493237]
     
  35. Boris Pasche, Kari B. Wisinski, Maureen Sadim, Virginia Kaklamani, Michael Pennison, Qinghua Zeng, Naresh Bellam, Jacquelyn Zimmerman, Nengjun Yi, Kui Zhang, John Baron, Daniel O. Stram, M. Geoffrey Hayes. 2010. Constitutively decreased TGFBR1 allelic expression is a common finding in colorectal cancer and is associated with three TGFBR1 SNPs. Journal of Experimental & Clinical Cancer Research 29: 57. [PMID: 20500843]
     
  36. Shi Wei, Michael G. Conner, Kui Zhang, Gene P. Siegal, Lea Novak. 2010. Juxtatumoral Stromal Reactions in Uterine Endometrioid Adenocarcinoma and Their Prognostic Significance. International Journal of Gynecological Pathology 29: 562-567. [PMID: 20881855]
     
  37. Xuxia Wu, Amit Patki, Cristina Lara-Castro, Xiangqin Cui, Kui Zhang, R. Grace Walton, Michael V Osier, Gary L. Gadbury, David B. Allison, Mitchell Martin, W. Timothy Garvey. 2011. Genes and Biochemical Pathways in Human Skeletal Muscle Affecting Resting Energy Expenditure and Fuel Partitioning. Journal of Applied Physiology. Accepted.
     
  38. Gu Jing, Kaiyu Yuan, Amy Turk, Nirag Jhala, Juan Arnoletti, Kui Zhang, Jay McDonald, Yabing Chen. 2011. Tamoxifen enhances therapeutic effects of gemcitabine on cholangiocarcinoma tumorigenesis. Laboratory Investigation. Accepted.
     
  39. Gao L, Fang Z, Zhang K, Zhi D, Cui X. Length Bias Correction for RNA-seq Data in Gene Set Analyses. Bioinformatics. 2011 Jan 19. [Epub ahead of print] [PMID: 21252076]
     
  40. Boshao Zhang, Degui Zhi, Kui Zhang, Guimin Gao, Nita N. Limdi, Nianjun Liu. 2011. Practical Consideration of Genotype Imputation: Sample Size, Window Size, Reference Choice, and Untyped Rate. Statistics and Its Inference. Accepted.
     
  41. Aleksandr Lazaryan, Wei Song, Elena Lobashevsky, Jianming Tang, Sadeep Shrestha, Kui Zhang, Janet M. McNicholl, Lytt I. Gardner, Craig M. Wilson, Robert S. Klein, Anne Rompalo, Kenneth Mayer, Jack Sobel, Richard A. Kaslow for the HIV Epidemiology Research Study Group and Reaching for Excellence in Adolescent Care and Health Study Group. 2011. The Influence of HLA Class I Alleles and Their Population Frequencies on HIV-1 Control Among African Americans. Human Immunology. 72(4):312-8. [PMID: 21262311] [doi:10.1016/j.humimm.2011.01.003]
     
  42. Virginia Kalamani, Nengjun Yi, Kui Zhang, Maureen Sadim, Kenneth Offit, Carole Oddoux, Harry Ostrer, Christos Mantzoros, Boris Pasche. 2011. Polymorphisms of ADIPOQ and ADIPOR1 and Prostate Cancer Risk. Metabolism. [PMID: 21397927]
     

Teaching

People


Webpage last updated: Feb 02, 2011