Kui Zhang

Summary

Affiliation: University of Alabama at Birmingham
Country: USA

Publications

  1. pmc Detecting epistatic interactions contributing to human gene expression using the CEPH family data
    Hua Li
    Bioinformatics Center, Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110, USA
    BMC Proc 1:S67. 2007
  2. pmc The role of the fat mass and obesity associated gene (FTO) in breast cancer risk
    Virginia Kaklamani
    Cancer Genetics Program, Division of Hematology Oncology, Department of Medicine and Robert H, Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, 676 N St Clair st suite 850, Chicago, IL 60611, USA
    BMC Med Genet 12:52. 2011
  3. pmc Detecting susceptibility genes in case-control studies using set association
    Sung Kim
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
    BMC Genet 4:S9. 2003
  4. pmc Selecting additional tag SNPs for tolerating missing data in genotyping
    Yao Ting Huang
    Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan
    BMC Bioinformatics 6:263. 2005
  5. pmc An empirical Bayes method for updating inferences in analysis of quantitative trait loci using information from related genome scans
    Kui Zhang
    Department of Biostatistics, Section of Statistical Genetics, University of Alabama, Birmingham 35294, USA
    Genetics 173:2283-96. 2006
  6. ncbi request reprint A comparison of several methods for haplotype frequency estimation and haplotype reconstruction for tightly linked markers from general pedigrees
    Kui Zhang
    Section on Statistical Genetics, Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama 35294 0022, USA
    Genet Epidemiol 30:423-37. 2006
  7. pmc Assessing the power of tag SNPs in the mapping of quantitative trait loci (QTL) with extremal and random samples
    Kui Zhang
    Department of Biostatistics, School of Public Health, University of Alabama, Birmingham, AL 35294, USA
    BMC Genet 6:51. 2005
  8. pmc The influence of human leukocyte antigen class I alleles and their population frequencies on human immunodeficiency virus type 1 control among African Americans
    Aleksandr Lazaryan
    University of Alabama at Birmingham, Birmingham, AL 35294 0022, USA
    Hum Immunol 72:312-8. 2011
  9. pmc 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
    Yongjun Liu
    Departments of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, USA
    Pharmacogenet Genomics 19:161-9. 2009
  10. pmc Genotype calling from next-generation sequencing data using haplotype information of reads
    Degui Zhi
    Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
    Bioinformatics 28:938-46. 2012

Collaborators

Detail Information

Publications49

  1. pmc Detecting epistatic interactions contributing to human gene expression using the CEPH family data
    Hua Li
    Bioinformatics Center, Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110, USA
    BMC Proc 1:S67. 2007
    ..We evaluated the power of the method by simulation studies and applied this method to the analysis of the Centre d'Etude du Polymorphisme Humain family gene expression data provided by Genetics Analysis Workshop 15 (GAW15)...
  2. pmc The role of the fat mass and obesity associated gene (FTO) in breast cancer risk
    Virginia Kaklamani
    Cancer Genetics Program, Division of Hematology Oncology, Department of Medicine and Robert H, Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, 676 N St Clair st suite 850, Chicago, IL 60611, USA
    BMC Med Genet 12:52. 2011
    ..Our objective was to evaluate tissue expression of FTO in breast and the role of FTO SNPs in predicting breast cancer risk...
  3. pmc Detecting susceptibility genes in case-control studies using set association
    Sung Kim
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
    BMC Genet 4:S9. 2003
    ..This is due to the wide spacing between the markers and the lack of association between the marker loci and the simulated phenotype...
  4. pmc Selecting additional tag SNPs for tolerating missing data in genotyping
    Yao Ting Huang
    Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan
    BMC Bioinformatics 6:263. 2005
    ..In reality, some tag SNPs may be missing, and we may fail to distinguish two distinct haplotypes due to the ambiguity caused by missing data...
  5. pmc An empirical Bayes method for updating inferences in analysis of quantitative trait loci using information from related genome scans
    Kui Zhang
    Department of Biostatistics, Section of Statistical Genetics, University of Alabama, Birmingham 35294, USA
    Genetics 173:2283-96. 2006
    ..In the face of marked heterogeneity among studies, the empirical Bayes method outperforms the comparator...
  6. ncbi request reprint A comparison of several methods for haplotype frequency estimation and haplotype reconstruction for tightly linked markers from general pedigrees
    Kui Zhang
    Section on Statistical Genetics, Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama 35294 0022, USA
    Genet Epidemiol 30:423-37. 2006
    ..Among four haplotyping methods capable of analyzing general pedigrees, HAPLORE and MERLIN have comparable performance and outperform the other two methods in almost all situations...
  7. pmc Assessing the power of tag SNPs in the mapping of quantitative trait loci (QTL) with extremal and random samples
    Kui Zhang
    Department of Biostatistics, School of Public Health, University of Alabama, Birmingham, AL 35294, USA
    BMC Genet 6:51. 2005
    ..It is also important to know how much power is gained when tag SNPs instead of the same number of randomly chosen SNPs are used...
  8. pmc The influence of human leukocyte antigen class I alleles and their population frequencies on human immunodeficiency virus type 1 control among African Americans
    Aleksandr Lazaryan
    University of Alabama at Birmingham, Birmingham, AL 35294 0022, USA
    Hum Immunol 72:312-8. 2011
    ..Certain HLA class I associations with control of HIV-1 infection cross the boundaries of race and viral subtype, whereas others appear confined within one or the other of those boundaries...
  9. pmc 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
    Yongjun Liu
    Departments of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, USA
    Pharmacogenet Genomics 19:161-9. 2009
    ..The apolipoproteins (APOA1/C3/A4/A5) are key components in modulating lipoprotein metabolism. It is unknown whether variants at the APOA1/C3/A4/A5 gene cluster are associated with lipid response to pharmacologic intervention...
  10. pmc Genotype calling from next-generation sequencing data using haplotype information of reads
    Degui Zhi
    Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
    Bioinformatics 28:938-46. 2012
    ..Current LD-based methods use read counts or genotype likelihoods at individual potential polymorphic sites (PPSs). Reads that span multiple PPSs (jumping reads) can provide additional haplotype information overlooked by current methods...
  11. ncbi request reprint Empirical bayes method for incorporating data from multiple genome scans
    T Mark Beasley
    Department of Biostatistics, Section of Statistical Genetics, The University of Alabama at Birmingham, 35294, USA
    Hum Hered 60:36-42. 2005
    ..This EB method for incorporating data from multiple studies into genome scan analyses seems promising...
  12. ncbi request reprint HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms
    Kui Zhang
    Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
    Bioinformatics 21:131-4. 2005
    ..Finally, the programs provide flexibility to include specific SNPs (e.g. non-synonymous SNPs) as tag SNPs...
  13. ncbi request reprint HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination
    Kui Zhang
    Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, AL 35294, USA
    Bioinformatics 21:90-103. 2005
    ....
  14. pmc Similarity-based multimarker association tests for continuous traits
    Wan Yu Lin
    Department of Biostatistics, University of Alabama at Birmingham, USA
    Ann Hum Genet 76:246-60. 2012
    ..3). Our SIMp test outperforms other tests when the causal variant was introduced at common haplotypes (the maximum frequency of risk haplotypes >0.4). We also applied our two tests to an adiposity data set to show their utility...
  15. doi request reprint Structure of tumor necrosis factor-alpha haploblocks in European populations
    Aimee M Merino
    Department of Medicine, University of Alabama, Birmingham, AL, USA
    Immunogenetics 65:543-52. 2013
    ..We also found that the ancestral haplotype 8.1 shares a TNF block haplotype with HLA-B*4402. HLA-B*5701, a known protective allele in HIV-1 pathogenesis, occurred in a unique TNF block haplotype...
  16. pmc Genome-wide association studies of rheumatoid arthritis data via multiple hypothesis testing methods for correlated tests
    Guolian Kang
    Section on Statistical Genetics, Department of Biostatistics, The University of Alabama at Birmingham, 1665 University Boulevard, Birmingham, Alabama 35294, USA
    BMC Proc 3:S38. 2009
    ..Simulation studies demonstrate that the MC method may have slightly higher power than the p-values adjusted for correlated tests method...
  17. pmc Length bias correction for RNA-seq data in gene set analyses
    Liyan Gao
    Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
    Bioinformatics 27:662-9. 2011
    ..Since transcript length is not related to gene expression, adjusting for such length dependency in GSA becomes necessary...
  18. doi request reprint Haplotype-association analysis
    Nianjun Liu
    Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
    Adv Genet 60:335-405. 2008
    ..We then cover a number of statistical methods that employ haplotype information in association analysis. In addition, we discuss the advantages and limitations of different methods...
  19. pmc Temporal characteristics of cold pain perception
    Michael A Frölich
    Department of Anesthesiology and Center for the Development of Functional Imaging CDFI, University of Alabama at Birmingham UAB, United States
    Neurosci Lett 480:12-5. 2010
    ..This may be important when looking for the physiological correlates of perception as opposed to the presence of a stimulus per se...
  20. doi request reprint Juxtatumoral stromal reactions in uterine endometrioid adenocarcinoma and their prognostic significance
    Shi Wei
    Department of Pathology, Division of Anatomic Pathology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35249 7331, USA
    Int J Gynecol Pathol 29:562-7. 2010
    ..This is even more important in those cases where no staging procedure was performed and in cases where the tumor was an incidental finding...
  21. ncbi request reprint GJB2 and GJB6 mutations in children with congenital cytomegalovirus infection
    Shannon A Ross
    Department of Pediatrics, The University of Alabama at Birmingham, Birmingham, Alabama 35233, USA
    Pediatr Res 61:687-91. 2007
    ..Although GJB2 mutations were detected in children with and without CMV-related hearing loss, those with hearing loss had a higher frequency of GJB2 mutations...
  22. pmc Smooth muscle cell-specific runx2 deficiency inhibits vascular calcification
    Yong Sun
    Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
    Circ Res 111:543-52. 2012
    ..We have previously reported that the osteogenic transcription factor Runx2 is an essential and sufficient regulator of calcification of vascular smooth muscle cells (VSMC) in vitro...
  23. pmc Altered DNA methylation profile in idiopathic pulmonary fibrosis
    Yan Y Sanders
    Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, 901 19th Street South, BMRII Room 408, Birmingham, AL 35294, USA
    Am J Respir Crit Care Med 186:525-35. 2012
    ..It is likely that epigenetic alterations contribute to pathogenesis in idiopathic pulmonary fibrosis (IPF)...
  24. pmc Constitutively decreased TGFBR1 allelic expression is a common finding in colorectal cancer and is associated with three TGFBR1 SNPs
    Boris Pasche
    Division of Hematology Oncology, The University of Alabama at Birmingham and UAB Comprehensive Cancer Center, Birmingham, AL 35203, USA
    J Exp Clin Cancer Res 29:57. 2010
    ..This phenotype was first observed in mice, then in lymphoblastoid cell lines from patients with microsatellite stable colorectal tumors...
  25. ncbi request reprint Haplotype inference for present-absent genotype data using previously identified haplotypes and haplotype patterns
    Yun Joo Yoo
    Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
    Bioinformatics 23:2399-406. 2007
    ....
  26. pmc A Bayesian hierarchical model for detecting haplotype-haplotype and haplotype-environment interactions in genetic association studies
    Jun Li
    Department of Biostatistics, Section on Statistical Genetics, University of Alabama at Birmingham, Birmingham, AL 35294 0022, USA
    Hum Hered 71:148-60. 2011
    ..Furthermore, methods for detecting the association between rare haplotypes and disease have not kept pace with their counterpart of common haplotypes...
  27. pmc Stem cell pathways contribute to clinical chemoresistance in ovarian cancer
    Adam D Steg
    Department of Obstetrics, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
    Clin Cancer Res 18:869-81. 2012
    ..However, whether these populations are more capable of surviving chemotherapy in de novo tumors is unknown...
  28. pmc Case-control association analysis of rheumatoid arthritis with candidate genes using related cases
    Yun Joo Yoo
    Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, 1665 University Boulevard, Ryals Building 327H, Birmingham, Alabama 35294, USA
    BMC Proc 1:S33. 2007
    ..These results, together with the results, based on simulated data, showed that higher power could be achieved using all related cases...
  29. pmc Application of imputation methods to the analysis of rheumatoid arthritis data in genome-wide association studies
    Douglas K Childers
    Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
    BMC Proc 3:S24. 2009
    ..We found some untyped SNP that showed significant association with rheumatoid arthritis. Among them, a few of these were not located near any typed SNP that was found to be significant and thus may be worth further investigation...
  30. pmc Genes and biochemical pathways in human skeletal muscle affecting resting energy expenditure and fuel partitioning
    Xuxia Wu
    Dept of Nutrition Sciences, The Univ of Alabama at Birmingham, 1675 University Blvd, Birmingham, AL 35294 3360, USA
    J Appl Physiol 110:746-55. 2011
    ..Individual variations in whole body REE and RQ are regulated by differential expressions of specific genes and pathways intrinsic to skeletal muscle...
  31. doi request reprint The SCARB1 gene is associated with lipid response to dietary and pharmacological interventions
    Yongjun Liu
    Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
    J Hum Genet 53:709-17. 2008
    ..In summary, our study suggested that the SCARB1 gene may serve as a useful marker that predicts variation in baseline lipid levels, postprandial lipid response, and response to fenofibrate intervention...
  32. pmc Human leukocyte antigen class I supertypes and HIV-1 control in African Americans
    Aleksandr Lazaryan
    University of Alabama at Birmingham, Birmingham, Alabama 35294 0022, USA
    J Virol 84:2610-7. 2010
    ..The study demonstrated the dominant role of HLA-B supertypes in HIV-1 clade B-infected African Americans and further dissected the contributions of individual class I alleles and their population frequencies to the supertype effects...
  33. pmc Multiple hits for the association of uterine fibroids on human chromosome 1q43
    Brahim Aissani
    Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
    PLoS ONE 8:e58399. 2013
    ..With the high potential for occult tumors in common conditions such as fibroids, validation of our data in family-based studies is needed...
  34. pmc Effect of sedation on pain perception
    Michael A Frölich
    Department of Anesthesiology, University of Alabama at Birmingham, Birmingham, Alabama 35249 6810, USA
    Anesthesiology 118:611-21. 2013
    ....
  35. doi request reprint What factors affect intrapartum maternal temperature? A prospective cohort study: maternal intrapartum temperature
    Michael A Frölich
    Department of Anesthesiology, University of Alabama, Birmingham, AL, USA
    Anesthesiology 117:302-8. 2012
    ..To investigate the potential causes of noninfectious maternal temperature changes during labor, we conducted a prospective cohort study in women scheduled for labor induction...
  36. pmc Calmodulin mediates Fas-induced FADD-independent survival signaling in pancreatic cancer cells via activation of Src-extracellular signal-regulated kinase (ERK)
    Kaiyu Yuan
    Departments of Pathology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
    J Biol Chem 286:24776-84. 2011
    ..Understanding the molecular mechanisms responsible for the resistance of pancreatic cells to apoptosis induced by Fas-death receptor signaling may provide molecular insights into designing novel therapies to treat pancreatic tumors...
  37. ncbi request reprint Increased expression of thymidylate synthetase (TS), ubiquitin specific protease 10 (USP10) and survivin is associated with poor survival in glioblastoma multiforme (GBM)
    Jessica M Grunda
    Departments of Pharmacology and Toxicology, Division of Clinical Pharmacology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
    J Neurooncol 80:261-74. 2006
    ....
  38. ncbi request reprint Microarray analysis
    Grier P Page
    Department of Biostatistics, University of Alabama at Birmingham, Hoover, AL, USA
    Methods Mol Biol 404:409-30. 2007
    ..These steps include a clearly stated biological question, experimental design, careful experimental conduct, complete statistical analysis, validation/verification of results, and dissemination of the data...
  39. ncbi request reprint Defining haplotype blocks and tag single-nucleotide polymorphisms in the human genome
    Thomas G Schulze
    Dicvision of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health ZI, 68159 Mannheim, Germany
    Hum Mol Genet 13:335-42. 2004
    ..More information is needed to guide the choice of method, marker allele frequencies, and parameters in the development of a haplotype map...
  40. pmc A dynamic programming algorithm for haplotype block partitioning
    Kui Zhang
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, 1042 West 36th Place, DRB142, Los Angeles, CA 90089 1113, USA
    Proc Natl Acad Sci U S A 99:7335-9. 2002
    ..We also apply the dynamic programming algorithm to the same data set based on haplotype diversity. A total of 3,982 representative SNPs and 1,884 blocks are identified to account for 95% of the haplotype diversity in each block...
  41. 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...
  42. ncbi request reprint A family-based association study of the MOG gene with schizophrenia in the Chinese population
    Xinmin Liu
    Bio X Life Science Research Center, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, P R China
    Schizophr Res 73:275-80. 2005
    ..01982). Our results would indicate that the MOG gene may play a significant role in schizophrenia in the Han Chinese. However, further study is required using other methods and involving other populations...
  43. ncbi request reprint No association between PPP3CC and schizophrenia in the Chinese population
    Zhengrui Xi
    Schizophr Res 90:357-9. 2007
  44. pmc Haplotype block structure and its applications to association studies: power and study designs
    Kui Zhang
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles 90089, USA
    Am J Hum Genet 71:1386-94. 2002
    ..Our study also indicates that haplotype-based analysis can be much more powerful than marker-by-marker analysis...
  45. ncbi request reprint Prediction of protein function using protein-protein interaction data
    Minghua Deng
    Program in Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089 1113, USA
    J Comput Biol 10:947-60. 2003
    ..gsf.de). We show that our approach outperforms other available methods for function prediction based on protein interaction data. The supplementary data is available at www-hto.usc.edu/~msms/ProteinFunction...
  46. ncbi request reprint Prediction of protein function using protein-protein interaction data
    Minghua Deng
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089 1113, USA
    Proc IEEE Comput Soc Bioinform Conf 1:197-206. 2002
    ..gsf.de). We show that our approach outperforms other available methods for function prediction based on protein interaction data...
  47. pmc Haplotype block partition with limited resources and applications to human chromosome 21 haplotype data
    Kui Zhang
    Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, 1042 W 36th Place DRB 290, Los Angeles, CA 90089 1113, USA
    Am J Hum Genet 73:63-73. 2003
    ..We also calculate the distribution of block break points in intergenic regions, genes, exons, and coding regions and do not find any significant differences...
  48. ncbi request reprint [Development of software system of medical monitoring equipment in spacecraft]
    Ming Wei
    Institute of Space Medico Engineering, Beijing, China
    Space Med Med Eng (Beijing) 16:500-3. 2003
    ..To develop a software system that can gather, manage and transmit signals of electrocardiograms, respiration, body temperature and blood pressure at real time, in order to monitor physiological signals of astronauts...
  49. pmc MAASE: an alternative splicing database designed for supporting splicing microarray applications
    Christina L Zheng
    Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA 92093 0651, USA
    RNA 11:1767-76. 2005
    ..We provide a detailed introduction and a step-by-step user guide to the MAASE database system to facilitate future large-scale annotation efforts, integration with other alternative splicing databases, and splicing array fabrication...

Research Grants6

  1. Haplotype Analysis in Linkage Disequilibrium Mapping
    Kui Zhang; Fiscal Year: 2006
    ..4) Release user-friendly software to the scientific community. The proposed methods are expected to aid the discovery of genes that are responsible for complex human diseases and finally enhance our ability to understand them. ..
  2. Haplotype Analysis in Linkage Disequilibrium Mapping
    Kui Zhang; Fiscal Year: 2007
    ..4) Release user-friendly software to the scientific community. The proposed methods are expected to aid the discovery of genes that are responsible for complex human diseases and finally enhance our ability to understand them. ..
  3. Haplotype analysis of population and pedigree data in association studies
    Kui Zhang; Fiscal Year: 2007
    ..The meeting will take place in December of 2007 and be attended by scientists from academia, government, and industry. ..
  4. Haplotype Analysis in Linkage Disequilibrium Mapping
    Kui Zhang; Fiscal Year: 2010
    ..4) Release user-friendly software to the scientific community. The proposed methods are expected to aid the discovery of genes that are responsible for complex human diseases and finally enhance our ability to understand them. ..