Research Topics
Genomes and Genes
| Kui ZhangSummaryAffiliation: University of Alabama at Birmingham Country: USA Publications
Research Grants
| Collaborators
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Detail Information
Publications
Detecting epistatic interactions contributing to human gene expression using the CEPH family dataHua 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)...- The role of the fat mass and obesity associated gene (FTO) in breast cancer riskVirginia 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... - Detecting susceptibility genes in case-control studies using set associationSung 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... - Selecting additional tag SNPs for tolerating missing data in genotypingYao 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... - An empirical Bayes method for updating inferences in analysis of quantitative trait loci using information from related genome scansKui 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... 
A comparison of several methods for haplotype frequency estimation and haplotype reconstruction for tightly linked markers from general pedigreesKui 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...- Assessing the power of tag SNPs in the mapping of quantitative trait loci (QTL) with extremal and random samplesKui 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... 
The influence of human leukocyte antigen class I alleles and their population frequencies on human immunodeficiency virus type 1 control among African AmericansAleksandr 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...- Pharmacogenetic association of the APOA1/C3/A4/A5 gene cluster and lipid responses to fenofibrate: the genetics of lipid-lowering drugs and diet network studyYongjun 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... - Genotype calling from next-generation sequencing data using haplotype information of readsDegui 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... - HAPLORE: a program for haplotype reconstruction in general pedigrees without recombinationKui Zhang
Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, AL 35294, USA
Bioinformatics 21:90-103. 2005..AVAILABILITY: The program can be downloaded from http://bioinformatics.med.yale.edu... - Empirical bayes method for incorporating data from multiple genome scansT 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... - HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithmsKui Zhang
Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
Bioinformatics 21:131-4. 2005..g. non-synonymous SNPs) as tag SNPs. AVAILABILITY: The HapBlock program and its supplemental documents can be downloaded from the website http://www.cmb.usc.edu/~msms/HapBlock... - Similarity-based multimarker association tests for continuous traitsWan 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... - Genome-wide association studies of rheumatoid arthritis data via multiple hypothesis testing methods for correlated testsGuolian 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... - Haplotype-association analysisNianjun 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... - Length bias correction for RNA-seq data in gene set analysesLiyan 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... - Temporal characteristics of cold pain perceptionMichael 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... - GJB2 and GJB6 mutations in children with congenital cytomegalovirus infectionShannon 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... - Juxtatumoral stromal reactions in uterine endometrioid adenocarcinoma and their prognostic significanceShi 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... - Smooth muscle cell-specific runx2 deficiency inhibits vascular calcificationYong 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... - Altered DNA methylation profile in idiopathic pulmonary fibrosisYan 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)... - Constitutively decreased TGFBR1 allelic expression is a common finding in colorectal cancer and is associated with three TGFBR1 SNPsBoris 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... - Haplotype inference for present-absent genotype data using previously identified haplotypes and haplotype patternsYun Joo Yoo
Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
Bioinformatics 23:2399-406. 2007.... - A Bayesian hierarchical model for detecting haplotype-haplotype and haplotype-environment interactions in genetic association studiesJun 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... - Stem cell pathways contribute to clinical chemoresistance in ovarian cancerAdam 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... - Case-control association analysis of rheumatoid arthritis with candidate genes using related casesYun 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... - Application of imputation methods to the analysis of rheumatoid arthritis data in genome-wide association studiesDouglas 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... - Human leukocyte antigen class I supertypes and HIV-1 control in African AmericansAleksandr 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... - Genes and biochemical pathways in human skeletal muscle affecting resting energy expenditure and fuel partitioningXuxia 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... - The SCARB1 gene is associated with lipid response to dietary and pharmacological interventionsYongjun 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... - Effect of sedation on pain perceptionMichael A Frölich
Department of Anesthesiology, University of Alabama at Birmingham, Birmingham, Alabama 35249 6810, USA
Anesthesiology 118:611-21. 2013.... - What factors affect intrapartum maternal temperature? A prospective cohort study: maternal intrapartum temperatureMichael 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... - 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... - 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.... - Microarray analysisGrier 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... - Haplotype block structure and its applications to association studies: power and study designsKui 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... - Defining haplotype blocks and tag single-nucleotide polymorphisms in the human genomeThomas 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... - A family-based association study of the MOG gene with schizophrenia in the Chinese populationXinmin 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... - Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studiesKui 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... - No association between PPP3CC and schizophrenia in the Chinese populationZhengrui Xi
Schizophr Res 90:357-9. 2007 - A dynamic programming algorithm for haplotype block partitioningKui 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... - Prediction of protein function using protein-protein interaction dataMinghua 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... - Prediction of protein function using protein-protein interaction dataMinghua 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... - [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... - MAASE: an alternative splicing database designed for supporting splicing microarray applicationsChristina 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... - Haplotype block partition with limited resources and applications to human chromosome 21 haplotype dataKui 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...
Research Grants
- Haplotype Analysis in Linkage Disequilibrium MappingKui 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. ..
- Haplotype Analysis in Linkage Disequilibrium MappingKui 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. ..
- Haplotype analysis of population and pedigree data in association studiesKui Zhang; Fiscal Year: 2007..The meeting will take place in December of 2007 and be attended by scientists from academia, government, and industry. ..
- Haplotype Analysis in Linkage Disequilibrium MappingKui 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. ..