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Hongyu Zhao

Research Profile

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Genes & Molecular Sequences

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Oligonucleotide Array Sequence Analysis

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Publications

TOP 3
Xiang Wan; Can Yang; Qiang Yang; Hongyu Zhao; Weichuan Yu
The complete compositional epistasis detection in genome-wide association studies.
John P Ferguson; Can Yang; Judy H Cho; Hongyu Zhao
Empirical Bayes correction for the Winner's Curse in genetic association studies.
Huiping Zhang; Hongyu Zhao; Wei Zheng; Raymond F Anton; Aryeh I Herman; Henry R Kranzler; Joel Gelernter
Array-based profiling of DNA methylation changes associated with alcohol dependence.

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All Publications

2013: Xiang Wan; Can Yang; Qiang Yang; Hongyu Zhao; Weichuan Yu
The complete compositional epistasis detection in genome-wide association studies.
BMC genetics 2013;14(1):7.
2013: John P Ferguson; Can Yang; Judy H Cho; Hongyu Zhao
Empirical Bayes correction for the Winner's Curse in genetic association studies.
Genetic epidemiology 2013;37(1):60-8.
2013: Huiping Zhang; Hongyu Zhao; Wei Zheng; Raymond F Anton; Aryeh I Herman; Henry R Kranzler; Joel Gelernter
Array-based profiling of DNA methylation changes associated with alcohol dependence.
Alcoholism, clinical and experimental research 2013;37 Suppl 1():E108-15.
2012: Haisu Ma; Hongyu Zhao
FacPad: Bayesian sparse factor modeling for the inference of pathways responsive to drug treatment.
Bioinformatics (Oxford, England) 2012;28(20):2662-70.
2012: Xin Ge; Amulya Iyer; Kun-Yong Kim; Darrell N Kotton; Min Young Lee; Wei Li; Kathleen A Martin; In-Hyun Park; Yongming Ren; George Tellides; Lixia Yue; Zhichao Yue; Hongyu Zhao; Wei Zheng; Peter J Amos; Oscar Bartulos; Esra Cagavi Bozkulak; Yibing Qyang
Modeling supravalvular aortic stenosis syndrome with human induced pluripotent stem cells.
Circulation 2012;126(14):1695-704.
2012: Michael J Stulberg; Hongyu Zhao; Aiping Lin; Scott A Holley
Crosstalk between Fgf and Wnt signaling in the zebrafish tailbud.
Developmental biology 2012;369(2):298-307.
2012: Xiaowei Chen; Joel Gelernter; Jennifer B Listman; Frank J Slack; Hongyu Zhao
Biases and errors on allele frequency estimation and disease association tests of next-generation sequencing of pooled samples.
Genetic epidemiology 2012;36(6):549-60.
2012: Robert D Beech; Julie Hansen; Kwangik A Hong; Janine J Leffert; Aiping Lin; Shrikant Mane; Jie Qu; Sheila Umlauf; Hongyu Zhao; Rajita Sinha
Altered expression of cytokine signaling pathway genes in peripheral blood cells of alcohol dependent subjects: preliminary findings.
Alcoholism, clinical and experimental research 2012;36(9):1487-96.
2012: Dawei Li; Hongyu Zhao; Joel Gelernter
Further clarification of the contribution of the ADH1C gene to vulnerability of alcoholism and selected liver diseases.
Human genetics 2012;131(8):1361-74.
2012: Haisu Ma; Hongyu Zhao
iFad: an integrative factor analysis model for drug-pathway association inference.
Bioinformatics (Oxford, England) 2012;28(14):1911-8.
2012: Dawei Li; Hongyu Zhao; Joel Gelernter
Strong protective effect of the aldehyde dehydrogenase gene (ALDH2) 504lys (*2) allele against alcoholism and alcohol-induced medical diseases in Asians.
Human genetics 2012;131(5):725-37.
2012: Dawei Li; David Oslin; Hongyu Zhao; Raymond F Anton; Lindsay A Farrer; Henry R Kranzler; Joel Gelernter
Association of COL25A1 with comorbid antisocial personality disorder and substance dependence.
Biological psychiatry 2012;71(8):733-40.
2012: Clarence K Zhang; Hongyu Zhao; Johannes M F G Aerts; Judy H Cho; Peter K Gregersen; Jun Liu; Gregory M Pastores; Philip B Stein; Zuoheng Wang; Ruhua Yang; Pramod K Mistry
Genome-wide association study of N370S homozygous Gaucher disease reveals the candidacy of CLN8 gene as a genetic modifier contributing to extreme phenotypic variation.
American journal of hematology 2012;87(4):377-83.
2012: Dong Chen; Aiping Lin; Katherine Uyhazi; Hongyu Zhao; Wei Zheng; Haifan Lin
Pumilio 1 suppresses multiple activators of p53 to safeguard spermatogenesis.
Current biology : CB 2012;22(5):420-5.
2012: Nicola Santoro; Melissa M Shaw; Clarence K Zhang; Hongyu Zhao; Daniel J Dykas; Cosimo Giannini; Leif Groop; Grace Kim; Romy Kursawe; Andrew J Pakstis; Bridget Pierpont; Allen E Bale; Sonia Caprio
Variant in the glucokinase regulatory protein (GCKR) gene is associated with fatty liver in obese children and adolescents.
Hepatology (Baltimore, Md.) 2012;55(3):781-9.
2012: Tiejun Tong; Liang Chen; Hongyu Zhao
Improved mean estimation and its application to diagonal discriminant analysis.
Bioinformatics (Oxford, England) 2012;28(4):531-7.
2012: Qing-Bin Gao; Xiaofei Ye; Hongyu Zhao; Jia He
Prediction of pattern recognition receptor family using pseudo-amino acid composition.
Biochemical and biophysical research communications 2012;417(1):73-7.
2012: Lori Lowthert; Kathleen Maloney; Shrikant Mane; Anjana Muralidharan; Rajita Sinha; Sheila Umlauf; Hongyu Zhao; Zubin Bhagwagar; Janine Leffert; Aiping Lin; Boris Lorberg; Robert Beech
Increased ratio of anti-apoptotic to pro-apoptotic Bcl2 gene-family members in lithium-responders one month after treatment initiation.
Biology of mood & anxiety disorders 2012;2(1):15.
2012: Wei Zhang; Hongyu Zhao; Clara Abraham; Enric Esplugues; John Ferguson; Richard A Flavell; Gerald Goh; Ken Hui; Aiping Lin; Sok Meng Ng; Judy H Cho
Effector CD4+ T cell expression signatures and immune-mediated disease associated genes.
PloS one 2012;7(6):e38510.
2012: John P Ferguson; Judy H Cho; Hongyu Zhao
A new approach for the joint analysis of multiple ChIP-seq libraries with application to histone modification.
Statistical applications in genetics and molecular biology 2012;11(3):Article 1.
2011: Wei Zheng; Hongyu Zhao; Tara A Gianoulis; Konrad Karczewski; Michael Snyder
Regulatory variation within and between species.
Annual review of genomics and human genetics 2011;12():327-46.
2011: Pingxing Xie; Hongyu Zhao; Raymond F Anton; Kelly P Cosgrove; Lindsay A Farrer; Henry R Kranzler; Michael Krauthammer; John H Krystal; David Oslin; Marina R Picciotto; Joel Gelernter
Rare nonsynonymous variants in alpha-4 nicotinic acetylcholine receptor gene protect against nicotine dependence.
Biological psychiatry 2011;70(6):528-36.
2011: Hyonho Chun; David H Ballard; Judy Cho; Hongyu Zhao
Identification of association between disease and multiple markers via sparse partial least-squares regression.
Genetic epidemiology 2011;35(6):479-86.
2011: Jia Kang; Subra Kugathasan; Hongyu Zhao; Judy H Cho; Michel Georges
Improved risk prediction for Crohn's disease with a multi-locus approach.
Human molecular genetics 2011;20(12):2435-42.
2011: Haisu Ma; Eric E Schadt; Lee M Kaplan; Hongyu Zhao
COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method.
Bioinformatics (Oxford, England) 2011;27(9):1290-8.
2011: Joon-Sang Lee; Murim Choi; Xiting Yan; Richard P Lifton; Hongyu Zhao
On optimal pooling designs to identify rare variants through massive resequencing.
Genetic epidemiology 2011;35(3):139-47.
2011: Gengxin Li; Lun Li; Xiting Yan; Xianghua Zhang; John Ferguson; Jia Kang; Joon-Sang Lee; Wei Zheng; Hongyu Zhao
Large-scale risk prediction applied to Genetic Analysis Workshop 17 mini-exome sequence data.
BMC proceedings 2011;5 Suppl 9():S46.
2011: Xiting Yan; John Ferguson; Joon-Sang Lee; Lun Li; Wei Zheng; Hongyu Zhao
Detecting functional rare variants by collapsing and incorporating functional annotation in Genetic Analysis Workshop 17 mini-exome data.
BMC proceedings 2011;5 Suppl 9():S27.
2011: Jia Kang; Joon-Sang Lee; Lun Li; Xiting Yan; Wei Zheng; Hongyu Zhao
Use of Bayesian networks to dissect the complexity of genetic disease: application to the Genetic Analysis Workshop 17 simulated data.
BMC proceedings 2011;5 Suppl 9():S37.
2011: Lingjun Zuo; John H Krystal; Chiang-Shan R Li; Lingeng Lu; Lin Lu; Fei Wang; Clarence K Zhang; Fengyu Zhang; Heping Zhang; Xiang-Yang Zhang; Hongyu Zhao; Xingguang Luo
A novel, functional and replicable risk gene region for alcohol dependence identified by genome-wide association study.
PloS one 2011;6(11):e26726.
2011: Wei Zheng; Lisa M Chung; Hongyu Zhao
Bias detection and correction in RNA-Sequencing data.
BMC bioinformatics 2011;12():290.
2010: Robert D Beech; Lori Lowthert; Janine J Leffert; Portia N Mason; Mary M Taylor; Sheila Umlauf; Aiping Lin; Ji Young Lee; Kathleen Maloney; Anjana Muralidharan; Boris Lorberg; Hongyu Zhao; Samuel S Newton; Shrikant Mane; C Neill Epperson; Rajita Sinha; Hilary Blumberg; Zubin Bhagwagar
Increased peripheral blood expression of electron transport chain genes in bipolar depression.
Bipolar disorders 2010;12(8):813-24.
2010: Song Huang; Tiejun Tong; Hongyu Zhao
Bias-corrected diagonal discriminant rules for high-dimensional classification.
Biometrics 2010;66(4):1096-106.
2010: Pramod K Mistry; Jun Liu; Mei Yang; Timothy Nottoli; James McGrath; Dhanpat Jain; Kate Zhang; Joan Keutzer; Wei-Lien Chuang; Wajahat Z Mehal; Hongyu Zhao; Aiping Lin; Shrikant M Mane; Xuan Liu; Yuan Z Peng; Jian H Li; Manasi Agrawal; Ling-Ling Zhu; Harry C Blair; Lisa J Robinson; Jameel Iqbal; Li Sun; Wei-Lein Chuang; Mone Zaidi
Glucocerebrosidase gene-deficient mouse recapitulates Gaucher disease displaying cellular and molecular dysregulation beyond the macrophage.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(45):19473-8.
2010: Nicola Santoro; Romy Kursawe; Ebe D'Adamo; Daniel J Dykas; Clarence K Zhang; Allen E Bale; Anna M Calí; Deepak Narayan; Melissa M Shaw; Bridget Pierpont; Mary Savoye; Derek Lartaud; Samuel Eldrich; Samuel W Cushman; Hongyu Zhao; Gerald I Shulman; Sonia Caprio
A common variant in the patatin-like phospholipase 3 gene (PNPLA3) is associated with fatty liver disease in obese children and adolescents.
Hepatology (Baltimore, Md.) 2010;52(4):1281-90.
2010: Alberto Dávalos; Carlos Fernández-Hernando; Grzegorz Sowa; Derakhshan Behrad; Michelle I Lin; Ji Y Lee; Hongyu Zhao; Ruiyan Luo; Christopher M Colangelo; William C Sessa
Quantitative proteomics of caveolin-1-regulated proteins: characterization of polymerase i and transcript release factor/CAVIN-1 IN endothelial cells.
Molecular & cellular proteomics : MCP 2010;9(10):2109-24.
2010: David H Ballard; Judy Cho; Hongyu Zhao
Comparisons of multi-marker association methods to detect association between a candidate region and disease.
Genetic epidemiology 2010;34(3):201-12.
2010: Jia Kang; Judy Cho; Hongyu Zhao
Practical issues in building risk-predicting models for complex diseases.
Journal of biopharmaceutical statistics 2010;20(2):415-40.
2010: Laura F Mustavich; Perry Miller; Kenneth K Kidd; Hongyu Zhao
Using a pharmacokinetic model to relate an individual's susceptibility to alcohol dependence to genotypes.
Human heredity 2010;70(3):177-93.
2009: Ning Sun; Hongyu Zhao
Reconstructing transcriptional regulatory networks through genomics data.
Statistical methods in medical research 2009;18(6):595-617.
2009: Zheyang Wu; Hongyu Zhao
Statistical power of model selection strategies for genome-wide association studies.
PLoS genetics 2009;5(7):e1000582.
2009: Yuling Jiao; S Lori Tausta; Neeru Gandotra; Ning Sun; Tie Liu; Nicole K Clay; Teresa Ceserani; Meiqin Chen; Ligeng Ma; Matthew Holford; Hui-yong Zhang; Hongyu Zhao; Xing Wang Deng; Timothy Nelson
A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies.
Nature genetics 2009;41(2):258-63.
2009: David H Ballard; Chatchawit Aporntewan; Ji Young Lee; Joon-Sang Lee; Zheyang Wu; Hongyu Zhao
A pathway analysis applied to Genetic Analysis Workshop 16 genome-wide rheumatoid arthritis data.
BMC proceedings 2009;3 Suppl 7():S91.
2009: Zheyang Wu; Chatchawit Aporntewan; David H Ballard; Ji Young Lee; Joon-Sang Lee; Hongyu Zhao
Two-stage joint selection method to identify candidate markers from genome-wide association studies.
BMC proceedings 2009;3 Suppl 7():S29.
2009: Chatchawit Aporntewan; David H Ballard; Ji Young Lee; Joon-Sang Lee; Zheyang Wu; Hongyu Zhao
Gene hunting of the Genetic Analysis Workshop 16 rheumatoid arthritis data using rough set theory.
BMC proceedings 2009;3 Suppl 7():S126.
2009: Matthew E Holford; Haseena Rajeevan; Hongyu Zhao; Kenneth K Kidd; Kei-Hoi Cheung
Semantic Web-based integration of cancer pathways and allele frequency data.
Cancer informatics 2009;8():19-30.
2009: Joshua N Sampson; Hongyu Zhao
Genotyping and inflated type I error rate in genome-wide association case/control studies.
BMC bioinformatics 2009;10():68.
2009: Debayan Datta; Hongyu Zhao
Effect of false positive and false negative rates on inference of binding target conservation across different conditions and species from ChIP-chip data.
BMC bioinformatics 2009;10():23.
2008: Stephane Budel; Thihan Padukkavidana; Betty P Liu; Zeny Feng; Fenghua Hu; Sam Johnson; Juha Lauren; James H Park; Aaron W McGee; Ji Liao; Althea Stillman; Ji-Eun Kim; Bao-Zhu Yang; Stefano Sodi; Joel Gelernter; Hongyu Zhao; Fuki M Hisama; Amy F T Arnsten; Stephen M Strittmatter
Genetic variants of Nogo-66 receptor with possible association to schizophrenia block myelin inhibition of axon growth.
The Journal of neuroscience : the official journal of the Society for Neuroscience 2008;28(49):13161-72.
2008: Bao-Zhu Yang; Henry R Kranzler; Hongyu Zhao; Jeffrey R Gruen; Xingguang Luo; Joel Gelernter
Haplotypic variants in DRD2, ANKK1, TTC12, and NCAM1 are associated with comorbid alcohol and drug dependence.
Alcoholism, clinical and experimental research 2008;32(12):2117-27.
2008: Bixia Xiang; Ao Li; Dinu Valentin; Norma J Nowak; Hongyu Zhao; Peining Li
Analytical and clinical validity of whole-genome oligonucleotide array comparative genomic hybridization for pediatric patients with mental retardation and developmental delay.
American journal of medical genetics. Part A 2008;146A(15):1942-54.
2008: Weizhen Ji; Jia Nee Foo; Brian J O'Roak; Hongyu Zhao; Martin G Larson; DB Simon; Christopher Newton-Cheh; Sate Matthew; Daniel Levy; Richard P Lifton
Rare independent mutations in renal salt handling genes contribute to blood pressure variation.
Nature genetics 2008;40(5):592-9.
2008: Debayan Datta; Hongyu Zhao
Statistical methods to infer cooperative binding among transcription factors in Saccharomyces cerevisiae.
Bioinformatics (Oxford, England) 2008;24(4):545-52.
2008: Stephane Budel; Sang-Ohk Shim; Zeny Feng; Hongyu Zhao; Fuki Hisama; Stephen M Strittmatter
No association between schizophrenia and polymorphisms of the PlexinA2 gene in Chinese Han Trios.
Schizophrenia research 2008;99(1-3):365-6.
2008: Herbert Pang; Hongyu Zhao
Building pathway clusters from Random Forests classification using class votes.
BMC bioinformatics 2008;9():87.
2007: Bao-Zhu Yang; Henry R Kranzler; Hongyu Zhao; Jeffrey R Gruen; Xingguang Luo; Joel Gelernter
Association of haplotypic variants in DRD2, ANKK1, TTC12 and NCAM1 to alcohol dependence in independent case control and family samples.
Human molecular genetics 2007;16(23):2844-53.
2007: valentin dinu; Hongyu Zhao; Perry L Miller
Integrating domain knowledge with statistical and data mining methods for high-density genomic SNP disease association analysis.
Journal of biomedical informatics 2007;40(6):750-60.
2007: Inyoung Kim; Yin Liu; Hongyu Zhao
Bayesian methods for predicting interacting protein pairs using domain information.
Biometrics 2007;63(3):824-33.
2007: valentin dinu; Perry L Miller; Hongyu Zhao
Evidence for association between multiple complement pathway genes and AMD.
Genetic epidemiology 2007;31(3):224-37.
2007: Jungeun Lee; Kun He; Viktor Stolc; Horim Lee; Pablo Figueroa; Ying Gao; Waraporn Tongprasit; Hongyu Zhao; Ilha Lee; Xing Wang Deng
Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development.
The Plant cell 2007;19(3):731-49.
2007: Song Huang; David Ballard; Hongyu Zhao
The role of heritability in mapping expression quantitative trait loci.
BMC proceedings 2007;1 Suppl 1():S86.
2007: Tih-Shih Lee; Shrikant M Mane; Tore Eid; Hongyu Zhao; Aiping Lin; Zhong Guan; Jung H Kim; Jeffrey Schweitzer; David King-Stevens; Peter Weber; Susan S Spencer; Dennis D Spencer; Nihal C de Lanerolle
Gene expression in temporal lobe epilepsy is consistent with increased release of glutamate by astrocytes.
Molecular medicine (Cambridge, Mass.) 2007;13(1-2):1-13.
2006: Sou-Pan Wu; Lin Leng; Zeny Feng; Nianjun Liu; Hongyu Zhao; Courtney McDonald; Annette Lee; Frank C Arnett; Peter K Gregersen; MD Mayes; Richard Bucala
Macrophage migration inhibitory factor promoter polymorphisms and the clinical expression of scleroderma.
Arthritis and rheumatism 2006;54(11):3661-9.
2006: Herbert Pang; Aiping Lin; Matthew Holford; Bradley E Enerson; Bin Lu; Michael P Lawton; Eugenia Floyd; Hongyu Zhao
Pathway analysis using random forests classification and regression.
Bioinformatics (Oxford, England) 2006;22(16):2028-36.
2006: Tomomi Tsubouchi; Hongyu Zhao; G Shirleen Roeder
The meiosis-specific zip4 protein regulates crossover distribution by promoting synaptonemal complex formation together with zip2.
Developmental cell 2006;10(6):809-19.
2006: Ning Sun; Raymond J Carroll; Hongyu Zhao
Bayesian error analysis model for reconstructing transcriptional regulatory networks.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(21):7988-93.
2006: Xin You; Meng Pan; Wenli Gao; Her-Shyong Shiah; Jian Tao; Dongqing Zhang; Fotios Koumpouras; Shuang Wang; Hongyu Zhao; Joseph A Madri; David Baker; Yung-Chi Cheng; Zhinan Yin
Effects of a novel tylophorine analog on collagen-induced arthritis through inhibition of the innate immune response.
Arthritis and rheumatism 2006;54(3):877-86.
2006: Weichuan Yu; Baolin Wu; Ning Lin; Kathy Stone; Kenneth Williams; Hongyu Zhao
Detecting and aligning peaks in mass spectrometry data with applications to MALDI.
Computational biology and chemistry 2006;30(1):27-38.
2006: Samuel Shao-Min Zhang; Xuming Xu; Mu-Gen Liu; Hongyu Zhao; M Bento Soares; Colin J Barnstable; Xin-Yuan Fu
A biphasic pattern of gene expression during mouse retina development.
BMC developmental biology 2006;6():48.
2006: Weichuan Yu; Baolin Wu; Junfeng Liu; Xiaoye Li; Kathy Stone; Kenneth R Williams; Hongyu Zhao
MALDI-MS data analysis for disease biomarker discovery.
Methods in molecular biology (Clifton, N.J.) 2006;328():199-216.
2006: Bradley E Enerson; Aiping Lin; Bin Lu; Hongyu Zhao; Michael P Lawton; Eugenia Floyd
Acute drug-induced vascular injury in beagle dogs: pathology and correlating genomic expression.
Toxicologic pathology 2006;34(1):27-32.
2005: Liang Chen; Hongyu Zhao
Negative correlation between compositional symmetries and local recombination rates.
Bioinformatics (Oxford, England) 2005;21(21):3951-8.
2005: Tao Huang; Baolin Wu; Paul Lizardi; Hongyu Zhao
Detection of DNA copy number alterations using penalized least squares regression.
Bioinformatics (Oxford, England) 2005;21(20):3811-7.
2005: Yin Liu; Nianjun Liu; Hongyu Zhao
Inferring protein-protein interactions through high-throughput interaction data from diverse organisms.
Bioinformatics (Oxford, England) 2005;21(15):3279-85.
2005: Erol E Gulcicek; Christopher M Colangelo; Walter McMurray; Kathryn Stone; Kenneth Williams; Terence Wu; Hongyu Zhao; Heidi Spratt; Alexander Kurosky; Baolin Wu
Proteomics and the analysis of proteomic data: an overview of current protein-profiling technologies.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2005;Chapter 13():Unit 13.1.
2005: Guohua Zou; Hongyu Zhao
Family-based association tests for different family structures using pooled DNA.
Annals of human genetics 2005;69(Pt 4):429-42.
2005: Yuling Jiao; Peixin Jia; xiangfeng wang; Ning Su; Shuliang Yu; Dongfen Zhang; Ligeng Ma; Qi Feng; Zhaoqing Jin; Lei Li; Yongbiao Xue; Zhukuan Cheng; Hongyu Zhao; Bin Han; Xing Wang Deng
A tiling microarray expression analysis of rice chromosome 4 suggests a chromosome-level regulation of transcription.
The Plant cell 2005;17(6):1641-57.
2005: Gil Mor; Irene Visintin; Yinglei Lai; Hongyu Zhao; Peter Schwartz; Thomas Rutherford; Luo Yue; Patricia Bray-Ward; David C Ward
Serum protein markers for early detection of ovarian cancer.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(21):7677-82.
2005: Bao-Zhu Yang; Hongyu Zhao; Henry R Kranzler; Joel Gelernter
Practical population group assignment with selected informative markers: characteristics and properties of Bayesian clustering via STRUCTURE.
Genetic epidemiology 2005;28(4):302-12.
2005: Matthew Holford; Naixin Li; Prakash M Nadkarni; Hongyu Zhao
VitaPad: visualization tools for the analysis of pathway data.
Bioinformatics (Oxford, England) 2005;21(8):1596-602.
2005: Song Huang; Shuang Wang; Nianjun Liu; Liang Chen; Cheongeun Oh; Hongyu Zhao
Whole-genome association analysis to identify markers associated with recombination rates using single-nucleotide polymorphisms and microsatellites.
BMC genetics 2005;6 Suppl 1():S51.
2005: Nianjun Liu; Liang Chen; Shuang Wang; Cheongeun Oh; Hongyu Zhao
Comparison of single-nucleotide polymorphisms and microsatellites in inference of population structure.
BMC genetics 2005;6 Suppl 1():S26.
2005: Liang Chen; Nianjun Liu; Shuang Wang; Cheongeun Oh; Nicholas J Carriero; Hongyu Zhao
Whole-genome association studies on alcoholism comparing different phenotypes using single-nucleotide polymorphisms and microsatellites.
BMC genetics 2005;6 Suppl 1():S130.
2005: Cheongeun Oh; Shuang Wang; Nianjun Liu; Liang Chen; Hongyu Zhao
A Bayesian genome screening of maximum number of drinks as an alcoholism phenotype with the new Haseman-Elston method.
BMC genetics 2005;6 Suppl 1():S116.
2005: Bao-Zhu Yang; Hongyu Zhao; Henry R Kranzler; Joel Gelernter
Characterization of a likelihood based method and effects of markers informativeness in evaluation of admixture and population group assignment.
BMC genetics 2005;6():50.
2005: Liang Chen; Hongyu Zhao
Gene expression analysis reveals that histone deacetylation sites may serve as partitions of chromatin gene expression domains.
BMC genomics 2005;6():44.
2005: Samuel Shao-Min Zhang; Xuming Xu; Jinming Li; Mu-Gen Liu; Hongyu Zhao; M Bento Soares; Colin J Barnstable; Xin-Yuan Fu
Comprehensive in silico functional specification of mouse retina transcripts.
BMC genomics 2005;6():40.
2005: Nicholas Carriero; Michael V Osier; Kei-Hoi Cheung; Perry L Miller; Mark Gerstein; Hongyu Zhao; Baolin Wu; Scott Rifkin; Joseph Chang; Heping Zhang; Kevin White; Kenneth Williams; Martin Schultz
A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studies.
Journal of the American Medical Informatics Association : JAMIA 2005;12(1):90-8.
2004: Nianjun Liu; Sarah L Sawyer; Namita Mukherjee; Andrew J Pakstis; Judith R Kidd; Kenneth K Kidd; Anthony J Brookes; Hongyu Zhao
Haplotype block structures show significant variation among populations.
Genetic epidemiology 2004;27(4):385-400.
2004: Yinglei Lai; Baolin Wu; Liang Chen; Hongyu Zhao
A statistical method for identifying differential gene-gene co-expression patterns.
Bioinformatics (Oxford, England) 2004;20(17):3146-55.
2004: Frederick H Wilson; Ali Hariri; anita farhi; Hongyu Zhao; Kitt Falk Petersen; Hakan R Toka; Carol Nelson-Williams; Khalid M Raja; Michael Kashgarian; Gerald I Shulman; Steven J Scheinman; Richard P Lifton
A cluster of metabolic defects caused by mutation in a mitochondrial tRNA.
Science (New York, N.Y.) 2004;306(5699):1190-4.
2004: Yin Liu; Hongyu Zhao
A computational approach for ordering signal transduction pathway components from genomics and proteomics Data.
BMC bioinformatics 2004;5():158.
2004: Michael V Osier; Hongyu Zhao; Kei-Hoi Cheung
Handling multiple testing while interpreting microarrays with the Gene Ontology Database.
BMC bioinformatics 2004;5():124.
2004: Keith Hoek; David L Rimm; Kenneth R Williams; Hongyu Zhao; Stephan Ariyan; Aiping Lin; Harriet M Kluger; Aaron J Berger; Elaine Cheng; Eduardo S. Trombetta; Terence Wu; Michio Niinobe; Kazuaki Yoshikawa; Gregory E Hannigan; Ruth Halaban
Expression profiling reveals novel pathways in the transformation of melanocytes to melanomas.
Cancer research 2004;64(15):5270-82.
2004: Rajendra Marathe; Zhong Guan; Radhamani Anandalakshmi; Hongyu Zhao; Savithramma P Dinesh-Kumar
Study of Arabidopsis thaliana resistome in response to cucumber mosaic virus infection using whole genome microarray.
Plant molecular biology 2004;55(4):501-20.
2004: Guohua Zou; Hongyu Zhao
The estimation of sibling genetic risk parameters revisited.
Genetic epidemiology 2004;26(4):286-93.
2004: Ning Sun; Hongyu Zhao
Genomic approaches in dissecting complex biological pathways.
Pharmacogenomics 2004;5(2):163-79.
2004: Chern-Sing Goh; Ning Lan; Shawn Douglas; Baolin Wu; Nathaniel Echols; Andrew Smith; Duncan Milburn; Gaetano T Montelione; Hongyu Zhao; Mark Gerstein
Mining the structural genomics pipeline: identification of protein properties that affect high-throughput experimental analysis.
Journal of molecular biology 2004;336(1):115-30.
2004: Yu Xia; Haiyuan Yu; Ronald Jansen; Michael Seringhaus; Sarah Baxter; Dov Greenbaum; Hongyu Zhao; Mark Gerstein
Analyzing cellular biochemistry in terms of molecular networks.
Annual review of biochemistry 2004;73():1051-87.
2004: Guohua Zou; Hongyu Zhao
The impacts of errors in individual genotyping and DNA pooling on association studies.
Genetic epidemiology 2004;26(1):1-10.
2003: Deyun Pan; Ning Sun; Kei-Hoi Cheung; Zhong Guan; Ligeng Ma; Matthew Holford; Xingwang Deng; Hongyu Zhao
PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis.
BMC bioinformatics 2003;4():56.
2003: Ning Sun; Ligeng Ma; Deyun Pan; Hongyu Zhao; Xing Wang Deng
Evaluation of light regulatory potential of Calvin cycle steps based on large-scale gene expression profiling data.
Plant molecular biology 2003;53(4):467-78.
2003: Shuang Wang; Hongyu Zhao
Sample size needed to detect gene-gene interactions using association designs.
American journal of epidemiology 2003;158(9):899-914.
2003: Liangbiao Zheng; Shuang Wang; Patricia Romans; Hongyu Zhao; Coralia Luna; Mark Q Benedict
Quantitative trait loci in Anopheles gambiae controlling the encapsulation response against Plasmodium cynomolgi Ceylon.
BMC genetics 2003;4():16.
2003: Baolin Wu; Tom Abbott; David Fishman; Walter McMurray; Gil Mor; Kathryn Stone; David Ward; Kenneth Williams; Hongyu Zhao
Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data.
Bioinformatics (Oxford, England) 2003;19(13):1636-43.
2003: Ginesa Garcia-Rostan; Hongyu Zhao; Robert L Camp; Marina Pollan; Agustin Herrero; Javier Pardo; Ran Wu; Maria Luisa Carcangiu; Jose Costa; Giovanni Tallini
ras mutations are associated with aggressive tumor phenotypes and poor prognosis in thyroid cancer.
Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2003;21(17):3226-35.
2003: Ling V Sun; Liang Chen; Frauke Greil; Nicolas Negre; Tong-Ruei Li; Giacomo Cavalli; Hongyu Zhao; Bas van Steensel; Kevin P White
Protein-DNA interaction mapping using genomic tiling path microarrays in Drosophila.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(16):9428-33.
2003: Guohua Zou; Deyun Pan; Hongyu Zhao
Genotyping error detection through tightly linked markers.
Genetics 2003;164(3):1161-73.
2003: Xingguang Luo; Henry R Kranzler; Hongyu Zhao; Joel Gelernter
Haplotypes at the OPRM1 locus are associated with susceptibility to substance dependence in European-Americans.
American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2003;120B(1):97-108.
2003: Hongyu Zhao; Ruth Pfeiffer; Mitchell H Gail
Haplotype analysis in population genetics and association studies.
Pharmacogenomics 2003;4(2):171-8.
2003: Guohua Zou; Hongyu Zhao
Haplotype frequency estimation in the presence of genotyping errors.
Human heredity 2003;56(1-3):131-8.
2003: Shuang Wang; Kenneth K Kidd; Hongyu Zhao
On the use of DNA pooling to estimate haplotype frequencies.
Genetic epidemiology 2003;24(1):74-82.
2003: Shuanglin Zhang; Xiaofeng Zhu; Hongyu Zhao
On a semiparametric test to detect associations between quantitative traits and candidate genes using unrelated individuals.
Genetic epidemiology 2003;24(1):44-56.
2002: Haiyang Wang; Ligeng Ma; Jessica Habashi; Jinming Li; Hongyu Zhao; Xing Wang Deng
Analysis of far-red light-regulated genome expression profiles of phytochrome A pathway mutants in Arabidopsis.
The Plant journal : for cell and molecular biology 2002;32(5):723-33.
2002: Arya Mani; Seyed-Mahmoud Meraji; Roozbeh Houshyar; Jayaram Radhakrishnan; Alaleh Mani; Mehrabeh Ahangar; Tayebeh M Rezaie; Mohammad-Ali Taghavinejad; Behrooz Broumand; Hongyu Zhao; Carol Nelson-Williams; Richard P Lifton
Finding genetic contributions to sporadic disease: a recessive locus at 12q24 commonly contributes to patent ductus arteriosus.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(23):15054-9.
2002: Guanqing Wu; Xin Tian; Sayoko Nishimura; Glen S Markowitz; Vivette D'Agati; Jong Hoon Park; Lili Yao; Li Li; Lin Geng; Hongyu Zhao; Winfried Edelmann; Stefan Somlo
Trans-heterozygous Pkd1 and Pkd2 mutations modify expression of polycystic kidney disease.
Human molecular genetics 2002;11(16):1845-54.
2002: Kei-Hoi Cheung; Kevin White; Janet Hager; Mark Gerstein; Valerie Reinke; Kenneth Nelson; Peter Masiar; Ranjana Srivastava; Yuli Li; Jinming Li; Hongyu Zhao; Jinming Li; David Allison; Michael Snyder; Perry Miller; Kenneth Williams
YMD: a microarray database for large-scale gene expression analysis.
Proceedings / AMIA ... Annual Symposium. AMIA Symposium 2002;():140-4.
2002: Shuanglin Zhang; Kui Zhang; Jinming Li; Hongyu Zhao
On a family-based haplotype pattern mining method for linkage disequilibrium mapping.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2002;():100-11.
2002: Shuanglin Zhang; Hongyu Zhao
Linkage disequilibrium mapping with genotype data.
Genetic epidemiology 2002;22(1):66-77.
2001: Hongyu Zhao; J Li; W P Robinson
Statistical analysis of uniparental disomy data using hidden Markov models.
Biometrics 2001;57(4):1074-9.
2001: Jinming Li; Stephanie L Sherman; Neil E Lamb; Hongyu Zhao
Multipoint genetic mapping with trisomy data.
American journal of human genetics 2001;69(6):1255-65.
2001: S Zhang; Hongyu Zhao
Quantitative similarity-based association tests using population samples.
American journal of human genetics 2001;69(3):601-14.
2001: Jinming Li; D Wang; J Dong; R Jiang; Kui Zhang; Shuanglin Zhang; Hongyu Zhao; F Sun
The power of transmission disequilibrium tests for quantitative traits.
Genetic epidemiology 2001;21 Suppl 1():S632-7.
2001: Shuanglin Zhang; Kui Zhang; Jinming Li; F Sun; Hongyu Zhao
Test of association for quantitative traits in general pedigrees: the quantitative pedigree disequilibrium test.
Genetic epidemiology 2001;21 Suppl 1():S370-5.
2001: Hongyu Zhao; F Liang
On relationship inference using gamete identity by descent data.
Journal of computational biology : a journal of computational molecular cell biology 2001;8(2):191-200.
2000: K Zhang; Hongyu Zhao
Assessing reliability of gene clusters from gene expression data.
Functional & integrative genomics 2000;1(3):156-73.
2000: Hongyu Zhao; S Zhang; Kathleen Ries Merikangas; Mátyás Trixler; Dieter B Wildenauer; F Sun; Kenneth K Kidd
Transmission/disequilibrium tests using multiple tightly linked markers.
American journal of human genetics 2000;67(4):936-46.
2000: Hongyu Zhao; Jinming Li; W P Robinson
Multipoint genetic mapping with uniparental disomy data.
American journal of human genetics 2000;67(4):851-61.
2000: Judith R Kidd; Andrew J Pakstis; Hongyu Zhao; Ru-Band Lu; Friday Okonofua; Adekunle Odunsi; Elena L Grigorenko; B B Tamir; J Friedlaender; Leslie O Schulz; Josef Parnas; Kenneth K Kidd
Haplotypes and linkage disequilibrium at the phenylalanine hydroxylase locus, PAH, in a global representation of populations.
American journal of human genetics 2000;66(6):1882-99.
2000: Shuanglin Zhang; Hongyu Zhao
Linkage disequilibrium mapping in populations of variable size using the decay of haplotype sharing and a stepwise-mutation model.
Genetic epidemiology 2000;19 Suppl 1():S99-105.
1999: Hongyu Zhao; Kathleen Ries Merikangas; Kenneth K Kidd
On a randomization procedure in linkage analysis.
American journal of human genetics 1999;65(5):1449-56.
1999: Hongyu Zhao; Andrew J Pakstis; Judith R Kidd; Kenneth K Kidd
Assessing linkage disequilibrium in a complex genetic system. I. Overall deviation from random association.
Annals of human genetics 1999;63(Pt 2):167-79.
1999: Hongyu Zhao; L J Sheffield; Andrew J Pakstis; Melissa P Knauert; Kenneth K Kidd
A more powerful method to evaluate p-values in GENEHUNTER.
Genetic epidemiology 1999;17 Suppl 1():S415-20.
1999: L J Sheffield; Melissa P Knauert; Andrew J Pakstis; Hongyu Zhao; Kenneth K Kidd
Analyses of the COGA data set in one ethnic group with examinations of alternative definitions of alcoholism.
Genetic epidemiology 1999;17 Suppl 1():S319-24.
1998: Hongyu Zhao; T P Speed
Statistical analysis of half-tetrads.
Genetics 1998;150(1):473-85.
1998: Hongyu Zhao; T P Speed
Statistical analysis of ordered tetrads.
Genetics 1998;150(1):459-72.
1998: Hongyu Zhao; Lidija Ivic; Joji M Otaki; M Hashimoto; K Mikoshiba; Stuart Firestein
Functional expression of a mammalian odorant receptor.
Science (New York, N.Y.) 1998;279(5348):237-42.
1997: Hongyu Zhao; Heping Zhang; J I Rotter
Cost-effective sib-pair designs in the mapping of quantitative-trait loci.
American journal of human genetics 1997;60(5):1211-21.
1993: Clare M Bergson; Hongyu Zhao; K Saijoh; Ronald S Duman; Eric J Nestler
Ezrin and osteonectin, two proteins associated with cell shape and growth, are enriched in the locus coeruleus.
Molecular and cellular neurosciences 1993;4(1):64-73.