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Research Articles (211)

Refereed Conference Articles (21)

Letters (3)

Journal Review Articles (10)

Book Chapters (21)

Books (2)



Research Articles



[211] H. Ma, H. Zhao (2012) FacPad: Bayesian sparse factor modeling for the inference of pathways responsive to drug treatment. Bioinformatics, in press.


[210] X. Ge, Y. Ren, O. Bartulos, M. Y. Lee, Z. Yue, K.-Y. Kim, W. Li, P. J. Amos, E. C. Bozkulak, A. Iyer, W. Zheng, H. Zhao, K. A. Martin, D. N. Kotton, G. Tellides, I.-H. Park, L. Yue, Y. Qyang (2012) Modeling Supravalvular Aortic Stenosis Syndrome Using Human Induced Pluripotent Stem Cells. Circulation, in press.  


[209] J. Ferguson, W. Wheeler, Y-P. Fu, L. Prokunina-Olsson, H. Zhao, J. Sampson (2012) Statistical tests for detecting associations with groups of genetic variants: generalization, evaluation, and implementation. European Journal of Human Genetics, in press.


[208] M. J. Stulberg, A. Lin, H. Zhao, S. A. Holley (2012) Crosstalk between Fgf and Wnt signaling in the zebrafish tailbud. Developmental Biology, in press


[207] X. Qi, H. Zhao (2012) Sparse Principal component analysis by choice of norm. Journal of Multivariate Statistics, in press.


[206] W. Zhang, J. Ferguson, S. M. Ng, K. Hui, G. Goh, A. Lin, E. Esplugues, R. A. Flavell, C. Abraham, H. Zhao, J. H. Cho (2012) Effector CD4+ T cell expression signatures and immune-mediated disease associated genes. PLoS One 7: e38510. [Pubmed]


[205] H. Zhang, A. I. Herman, H. R. Kranzler, R. F. Anton, H. Zhao, W. Zheng, J. Gelernter (2012) Array-based profiling of DNA methylation changes associated with alcohol dependence. Alcoholism: Clinical and Experimental Research, in press


[204] S. Zhang, H. Zhao (2012) Community identification in networks with unbalanced structure. Physical Review E, 85, 066114. [Linkout]


[203] T. Yuen, J. Iqbal, L.-L. Zhu, L. Sun, A. Lin, H. Zhao, J. Liu, P. K. Mistry, M. Zaidi (2012) Disease-drug pairs revealed by computational genomic connectivity mapping on GBA1 deficient, Gaucher disease mice. Biochemical and Biophysical Research Communications, 422(4): 573-7. [Pubmed]


[202] H. Ma, H. Zhao (2012) iFad: an integrative factor analysis model for drug-pathway association inference. Bioinformatics, 28(14):1911-8. [Pubmed]


[201] X. Chen, J. B. Listman, F. Slack, J. Gelernter, H. Zhao (2012) Biases and errors on allele frequency estimation and disease association tests of next generation sequencing of pooled samples. Genetic Epidemiology, in press.


[200] D. Li, H. Zhao, J. Gelernter (2012) Further clarification of the contribution of the ADH1C gene to vulnerability of alcoholism and selected liver diseases. Human Genetics, 131(8): 1361-74 [Pubmed]


[199] R. D. Beech, J. Qu, J. J. Leffert, A. Lin, K. A. Hong, J. Hansen, S. Umlauf, S. Mane, H. Zhao, R. Sinha (2012) Altered expression of cytokine signaling pathway genes in peripheral blood cells of alcohol dependent subjects: Preliminary Findings. Alcohol Clin Exp Res, in press.


[198] C. Heffelfinger, Z. Ouyang, A. Engberg, D. J. Leffell, A. M. Hanlon, P. B. Gordon, W. Zheng, H. Zhao, M. P. Snyder, A. E. Bale AE (2012) Correlation of global microRNA expression with basal cell carcinoma subtype. G3, 2: 279-286. [Pubmed]


[197] D. Chen, W. Zheng, A. Lin, K. Uyhazi, H. Zhao, H. Lin (2012) Pumilio 1 suppresses multiple activators of p53 to safeguard spermatogenesis. Current Biology, 22(5): 420-5. [Pubmed]


[196] C. K. Zhang, P. B. Stein, J. Liu, Z. Wang, R. Yang, J. H. Cho, P. K. Gregersen, J. M. Aerts, H. Zhao, G. M. Pastores, P. K. Mistry (2012) 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, 87(4): 377-83. [Pubmed]


[195] D. Li, H. Zhao, H. R. Kranzler, D. Oslin, R. F. Anton, L.A. Farrer, J. Gelernter (2012) Association of COL25A1 with Comorbid Antisocial Personality Disorder (ASPD) and Substance Dependence. Biological Psychiatry, 71(8):733-40. [Pubmed]


[194] K. Morino, K. F. Petersen, S. Sono, C. S. Choi, V. T. Samuel, A. Lin, A. Gallo, H. Zhao, A. Kashiwagi, I. J. Goldberg, H. Wang, R. H. Eckel, H. Maegawa, G. I. Shulman (2012) Regulation of mitochondrial biogenesis by lipoprotein lipase in muscle of insulin resistant offspring of parents with type 2 diabetes. Diabetes, 61(4): 877-87. [Pubmed]


[193] T. Tong, L. Chen, H. Zhao (2012) Improved mean estimation and its application to diagonal discriminant analysis. Bioinformatics, 28: 531-537. [Pubmed]


[192] G. Li, J. Gelernter, H. R. Kranzler, H. Zhao (2012) M3: An improved SNP calling algorithm for Illumina BeadArray Data. Bioinformatics, 28: 358-365. [Pubmed]


[191] D. Li, H. Zhao, J. Gelernter (2012) Strong protective effect of the aldehyde dehydrogenase gene (ALDH2) 504lys (*2) allele against alcoholism and alcohol-induced medical diseases in Asians. Human Genetics, 131:725-737. [Pubmed]


[190] Z. Wu, H. Zhao (2012) On model selection strategies to identify genes underlying binary traits using genome-wide association data. Statistica Sinica, in press


[189] N. Santoro, C. K. Zhang, H. Zhao, A. J. Pakstis, G. Kim, R. Kursawe, D. J. Dykas, A. E. Bale, C. Giannini, B. Pierpont, M. M. Shaw, L. Groop, S. Caprio (2012) A variant in the Glucokinase Regulatory Protein (GCKR) gene is associated with fatty liver in obese children and adolescents. Hepatology, 55: 781-789 [Pubmed]


[188] I. Kim, H. Pang, H. Zhao (2012) Bayesian semiparametric regression models for evaluating pathway effects on clinical continuous an binary outcomes. Statistics in Medicine, in press.


[187] L. Zuo, J. Gelernter, C. K. Zhang, H. Zhao, L. Lu, H. R. Kranzler, R. T. Malison, C. S. Li, F. Wang, X. Y. Zhang, H. W. Deng, J. H. Krystal, F. Zhang, X. Luo (2012) Genome-Wide Association Study of Alcohol Dependence Implicates KIAA0040 on Chromosome 1q. Neuropsychopharmacology, 37: 557-566. [Pubmed]


[186] B. Li, H. Chun, H. Zhao (2012) Sparse estimation of conditional graphical models with application to gene networks. Journal of American Statistical Association, in press.


[185] J. Ferguson, J. Cho, H. Zhao (2012) A new approach for the joint analysis of multiple Chip-Seq libraries with application to Histone Modification. Statistical Applications in Genetics and Molecular Biology, 11, 3 (1-19). [Pubmed]




[184] L. Zuo, C. K. Zhang, F. Wang, C-S R. Li, H. Zhao, L. Lu, X-Y Zhang, L. Lu, H. Zhang, F. Zhang, J. H. Krystal, X. Luo (2011) A novel, functional and replicable risk gene region for alcohol dependence identified by genome-wide association study. PLoS One, e26726. [Pubmed]


[183] M. Kato, X. Chen, S. Inukai, H. Zhao, F. J. Slack (2011) Age-associated changes in expression of small, noncoding RNAs, including microRNAs, in C. elegans. RNA, 17: 1804-1820. [Pubmed]


[182] W. Zheng, L. Chung, H. Zhao (2011) Bias detection and correction in RNA-sequencing data. BMC Bioinformatics, 12: 290. [Pubmed]


[181] P. Xie P, H. R. Kranzler, M. Krauthammer, K. P. Cosgrove, D. Oslin, R. F. Anton, L. A. Farrer, M. R. Picciotto, J. H. Krystal, H. Zhao, J. Gelernter (2011) Rare nonsynonymous variants in alpha-4 nicotinic acetylcholine receptor gene protect against nicotine dependence. Biologial Psychiatry, 70: 528-536. [Pubmed]


[180] F. Qian, X. Wang, L. Zhang, A. Lin, H. Zhao, E. Fikrig, R. R. Montgomery (2011) Impaired interferon signaling in dendritic cells from older donors infected in vitro with West Nile virus. Journal of Infectious Disease 203: 1415-1424. [Pubmed]


[179] K. Wang, W-D Li, C.K. Zhang, Z. Wang, J. T. Glessner, S. F. A. Grant, H. Zhao, H. Hakonarson, R. A. Price (2011) A genome-wide association study on obesity and obesity-related traits. PLoS One, 6: e18939. [Pubmed]


[178] J. Kang, S. Kugathasan, M. Georges, H. Zhao, J. H. Cho; the NIDDK IBD Genetics Consortium (2011) Improved risk prediction for Crohn's disease with a multi-locus approach. Human Molecular Genetics, 20: 2435-2442. [Pubmed]


[177] Y. Lai, B. Wu, H. Zhao (2011) A permutation test approach to the choice of size k for the nearest neighbors classifier. Journal of Applied Statistics, 8: 2289-2302. [Linkout]


[176] N. Liu, H. Zhao, A. Patki, N. A. Limdi, D. B. Allison (2011) Controlling population structure in human genetic association studies with samples of unrelated individuals. Statistics and Its Interface, 4: 317-326. [PDF]


[175] J. Sampson, K. K. Kidd, J. R. Kidd, H. Zhao (2011) Select SNPs to identify ancestry. Annals of Human Genetics, 75: 539-553. [Pubmed]


[174] H. Chun, D. Ballard, J. Cho, H. Zhao (2011) Identification of association between disease and multiple markers via sparse partial least squares regression. Genetic Epidemiology, 35: 479-486. [Pubmed]


[173] T.N. Ferraro, G. G. Smith, D. Ballard, H. Zhao, C. L. Schwebel, A. Gupta, E. F. Rappaport, S. E. Ruiz, F. W. Lohoff, G. A. Doyle, W. H. Berrettini, R. J. Buono (2011) Quantitative trait loci for electrical seizure threshold mapped in C57BLKS/J and C57BL/10SnJ mice. Genes Brain Behavior, 10: 309-315. [Pubmed]


[172] J. S. Lee, M. Choi, X. Yan, R. P. Lifton, H. Zhao (2011) On optimal pooling designs to identify rare variants through massive resequencing. Genetic Epidemiology, 35: 139-147. [Pubmed]


[171] X. Chang, F. Liu, X. Wang, A. Lin, H. Zhao, B. Su (2011) The kinases MEKK2 and MEKK3 regulate transforming growth factor-β-mediated helper T cell differentiation. Immunity, 34: 201-212. [Pubmed]


[170] H. Ma, E. E. Schadt, L. M. Kaplan, H. Zhao (2011) COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method. Bioinformatics, 27: 1290-1298. [Pubmed]


[169] D. Li, H. Zhao, J. Gelernter (2011) Strong association of the Alcohol Dehydrogenase 1B Gene (ADH1B) with alcohol dependence and alcohol-induced medical diseases. Biological Psychiatry, 70: 504-512. [Pubmed]


[168] X. Qi, H. Zhao (2011) Some theoretical properties of Silverman's method for smoothed functional principal component analysis. Journal of Multivariate Analysis, 102: 741-767. [Pubmed]


[167] M. Chen, J. Cho, H. Zhao (2011) Incorporating biological pathways via a Markov random field model in genome-wide association studies. PLoS Genetics, 7: e1001353. [Pubmed]


[166] M. Chen, J. Cho, H. Zhao (2011) Detecting epistatic SNPs associated with complex diseases via a Bayesian classification tree search method. Annals of Human Genetics, 75: 112-121. [Pubmed]


[165] R. Luo, H. Zhao (2011) Bayesian hierarchical modeling for signaling pathway inference from single cell interventional data. Annals of Applied Statistics, 5: 725-745. [Linkout]




[164] R. D. Beech, L. Lowthert, J. J. Leffert, P. N. Mason, M. M. Taylor, S. Umlauf, A. Lin, J. Y. Lee, K. Maloney, A. Muralidharan, B. Lorberg, H. Zhao, S. S. Newton, S. Mane, C. N. Epperson, R. Sinha, H. Blumberg, Z. Bhagwagar. (2010) Increased peripheral blood expression of electron transport chain genes in bipolar depression. Bipolar Disorders, 12: 813-824. [Pubmed]


[163] P. K. Mistry, J. Liu, M. Yang, T. Nottoli, J. McGrath, D. Jain, K. Zhang, J. Keutzer, W-L Chuang, W. Z. Mehal, H. Zhao, A. Lin, S. Mane, X. Liu, Y. Z. Peng, J. H. Li, M. Agrawal, L-L Zhu, H. C. Blair, L. J. Robinson, J. Iqbal, L. Sun, M. Zaidi (2010) The GBA1 deficient mouse recapitulates Gaucher disease displaying system-wide cellular and molecular dysregulation beyond the macrophage. Proceedings of the National Academy of Sciences, 107: 19473-19478. [Pubmed]


[162] C. Berger, K. Hoffmann1, J. G. Vasquez, S. Mane, J. Lewis, R. Filler, A. Lin, H. Zhao, T. Durazzo, A. Baird, W. Lin, F. Foss, I. Christensen, M. Girardi, R. Tigelaar, R. Edelson (2010) Rapid generation of maturationally synchronized human dendritic cells: Contribution to the clinical efficacy of extracorporeal photochemotherapy. Blood, 116: 4838-4847. [Pubmed]


[161] N. Santoro, R. Kursawe, E. D’Adamo, D. J. Dykas, C. K. Zhang, A. E. Bale, A. M. Cali, D. Narayan, M. M. Shaw, B. Pierpont, M. Savoye, D. Lartaud, S. Eldrich, S. W. Cushman, H. Zhao, G. I. Shulman, S. Caprio (2010) A Common variant in the Patatin-Like Phopholipase 3 Gene (PNPLA3) is associated with fatty liver disease in obese children and adolescents. Hepatology, 52:1281-1290. [Pubmed]


[160] A. Davalos, C. Fernandez-Hernando, G. Sowa, B. Derakhshan, M. I. Lin, J. Y. Lee, H. Zhao, R. Luo, C. Colangelo, W. C. Sessa (2010) Quantitative proteomics of caveolin-1 regulated proteins: Characterization of PTRF/Cavin-1 in endothelial cells. Mol Cell Proteomics, 9:2109-2124. [Pubmed]


[159] D. Ballard, C. Abraham, J. Cho, H. Zhao (2010) Pathway analysis comparison using Crohn's disease GWAS. BMC Medical Genomics, 3, 25. [PDF]


[158] L. F. Mustavich, P. Miller, K. K. Kidd, H. Zhao (2010) Using a pharmacokinetic model to relate an individual's susceptibility to alcohol dependence to genotypes. Human Heredity, 70:177-193. [Pubmed]


[157] J. X. Hu, H. Zhao, H. H. Zhou (2010) False discovery rate control with groups. Journal of American Statistical Association, 105:1215-1227. [Pubmed]


[156] D. H .Ballard, J. Zhu, E. E. Schadt, H. Zhao (2010) Improving detection of genes associated with clinical traits using expression traits. International Journal of Systems and Synthetic Biology, in press.


[155] W. Zheng, H. Zhao, E. Mancera, L. Steinmetz, M. Snyder  (2010) Genetic analysis of variation in transcription factor binding in yeast. Nature, 464: 1187-1191. [PDF]


[154] H. Pang, D. Datta, H. Zhao (2010) Pathway analysis using random forests with bivariate node-split for survival outcomes. Bioinformatics, 26: 250-258. [PDF]


[153] S. Huang, T. Tong, H. Zhao (2010) Bias-corrected diagonal discriminant rules for high-dimensional classification. Biometrics, 66:1096-1106. [Pubmed]


[152] R. Luo, C. M. Colangelo, W. C. Sessa, H. Zhao (2010) Bayesian analysis of iTRAQ data with nonrandom missingness: Identification of differentially expressed proteins. Statistics in BioSciences, 1: 228-245. [PDF]


[151] J. Kang, J. Cho, H. Zhao (2010) Practical issues in building risk predicting models for complex diseases. Journal of Biopharmaceutical Statistics, 20: 415-440. [PDF]


[150] D. Ballard, J. Cho, H. Zhao (2010) Comparisons of multi-marker association methods to detect association between a candidate region and disease. Genetic Epidemiology, 34: 201-212. [PDF]


[149] X. Qi, H. Zhao (2010) Asymptotic efficiency and finite-sample properties of the generalized profiling estimation of the parameters in ordinary differential equations. Annals of Statistics, 38: 435-481. [PDF]




[148] J. Liu, L. Chen, H. Zhao, D. F. Moore, Y. Lin, W. J. Shi (2009) On calculating the probability of a set of orthologous sequences. Journal of Advances and Applications in Bioinformatics and Chemistry, 2: 37-48. [PDF]


[147] J. Sampson, H. Zhao (2009) Identifying individuals in complex mixture of DNA with unknown ancestry. Statistical Applications in Genetics and Molecular Biology, 8, Article 37. [PDF]


[146] Z. Wu, H. Zhao (2009) Statistical power of model selection strategies for genome-wide association studies. PLoS Genetics, 5: e1000582. [PDF]


[145] K. He, X. Li, J. Zhou, XW Deng, H. Zhao, J. Luo J (2009) NTAP: For NimbleGen tiling array ChIP-chip data analysis. Bioinformatics, 25: 1838-1840. [PDF]


[144] N. Papeta, K. T. Chan, S. Prakash, J. Martino, K. Kiryluk, D. Ballard, L. A. Bruggeman, R. Frankel, Z. Zheng, P. E. Klotman, H. Zhao, V. D. D'Agati, R. P. Lifton, A. G. Gharavi (2009) Susceptibility loci for murine HIV-associated nephropathy encode trans-regulators of podocyte gene expression. J Clin Invest, 119: 1178-1188. [PDF]


[143] X. Li, H. Zhao (2009) Weighted random subspace method for high dimensional data classification. Statistics and Its Interface, 2: 153-159. [PDF]


[142] J. Sampson, H. Zhao (2009) Genotyping and inflated type I error rate in genome-wide association case/control studies. BMC Bioinformatics, 10, 68. [PDF]


[141] H. R. Kranzler, J. Gelernter, R. F. Anton, A. J. Arias, A. Herman, H. Zhao, L. Burian, J. Covault (2009) Association of markers in the 3’ region of the GluR5 kainate receptor subunit gene (GRIK1) to alcohol dependence. Alcoholism: Clinical and Experimental Research, 33: 925-930. [PDF]


[140] D. Datta, H. Zhao (2009) 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, 10, 23. [PDF]


[139] N. Liu, R. Bucala, H. Zhao (2009) Modeling informatively missing genotypes in haplotype analysis. Communications in Statistics - Theory and Methods, 38(18): 3445-3460. [PDF]


[138] H. Pang, T. Tong, H. Zhao (2009) Shrinkage-based diagonal discriminant analysis and its applications in high-dimensional data. Biometrics, 65: 1021-1029. [PDF]


[137] M. E. Holford, H. Rajeevan, H. Zhao, K. K. Kidd, K-H Cheung (2009) Semantic web-based integration of cancer pathways and allele frequency data.  Cancer Informatics, 8: 19-30. [PDF]


[136] B. Z. Yang, H. R. Kranzler, H. Zhao, J. R. Gruen, X. Luo, J. Gelernter (2008) Haplotypic variants in DRD2, ANKK1, TTC12, and NCAM1 are associated with comorbid alcohol and drug dependence. Alcohol Clin Exp Res, 32: 2117-2127. [PDF]


[135] N. Liu, D. Zhang, H. Zhao (2009) Genotyping error detection in samples of unrelated individuals without replicate genotyping. Human Heredity, 67: 154-162. [PDF]


[134] Y Jiao, S. L. Tausta, N. Gandotra, N. Sun, T. Liu, N. Clay, T. Ceserani, M. Chen, L. Ma, M. Holford, H. Zhao, X. Deng, T. Nelson (2009) A transcriptome atlas of rice cell types reveals cellular, functional and developmental hierarchies. Nature Genetics, 41: 258-263. [PDF]




[133] S. Budel, T. Padukkavidana, B. Liu, Z. Feng, F. Hu, S. Johnson, J. Lauren, J. Park, A. McGee, J. Liao, A. Stillman, J-E Kim, S. Sodi, B-Z Yang, J. Gelernter, H. Zhao, F. Hisama, A. Arnsten, S. Strittmatter (2008) Genetic variants of Nogo-66 Receptor with possible association to schizophrenia block myelin inhibition of axon growth.  Journal of Neuroscience, 28: 13161-13172. [PDF]


[132] B. Xiang, A. Li, D. Valentin, N. J. Nowak, H. Zhao, P. Li (2008) Analytical and clinical validity of whole-genome oligonucleotide array comparative genomic hybridization for pediatric patients with mental retardation and developmental delay. Am J Med Genet A. 146A: 1942-1954. [PDF]


[131] L. Chen, T. Tong, H. Zhao (2008) Considering dependence among genes and markers for false discovery control in eQTL mapping. Bioinformatics, 24: 2015-2022. [PDF]


[130] J. Cao, H. Zhao (2008) Estimating dynamic models for gene regulation networks. Bioinformatics, 24: 1619-1624. [PDF]


[129] W. Ji, J. N. Foo, B. J. O’Roak, H. Zhao, M. G. Larson, D. B. Simon, C. Newton-Cheh, M. W. State, D. Levy, R. P. Lifton (2008) Rare independent mutations in renal salt handling genes contribute to blood pressure variation. Nature Genetics, 40: 592-599. [PDF]


[128] H. Pang, H. Zhao (2008) Building pathway clusters from Random Forests classification using class votes. BMC Bioinformatics, 9, 87. [PDF]


[127] R. A. Price, W.-D. Li, H. Zhao (2008) FTO gene associated with extreme obesity in cases, controls and extremely discordant sister pairs. BMC Medical Genetics, 9, 4. [PDF]


[126] J. Liu, H. Zhao, J. Tan, D. Luo, W. Yu, E. J. Harner (2008) Is subcellular localization informative for modeling protein-protein interaction signal? Research Letters in Signal Processing, Volume 2008, Issue 1, Article 2. [PDF]


[125] T. Tong, H. Zhao (2008) Practical guidelines for assessing power and false discovery rate for a fixed sample size in microarray experiments. Statistics in Medicine, 27: 1960-1972. [PDF]


[124] J. Liu, W. Yu, B. Wu, H. Zhao (2008) Bayesian mass spectra peak alignment from mass charge ratios. Cancer Informatics, 4: 217-241. [PDF]


[123] W. Yu, Z. He, J. Liu, H. Zhao (2008) Improving mass spectrometry peak detection using multiple peak alignment results. Journal of Proteome Research, 7: 123-129. [PDF]


[122] S. Budel, S-O Shim, Z. Feng, H. Zhao, F. Hisama, S. M. Strittmatter (2008) No association between schizophrenia and polymorphisms of the PlexinA2 gene in Chinese Han Trios. Schizophrenia Research, 99: 365-366. [PDF]


[121] Y. Zuo, G. Zou, J. Wang, H. Zhao, H. Liang (2008) Optimal two-stage design for case-control association analysis incorporating genotyping errors. Annals of Human Genetics, 72: 375-387. [PDF]


[120] D. Datta, H. Zhao (2008) Statistical methods to infer cooperative binding among transcription factors in Saccharomyces cerevisiae. Bioinformatics, 24: 545-552. [PDF]


[119] Z. Guan, B. Wu, H. Zhao (2008) Nonparametric estimator of false discovery rate based on Bernstein polynomials. Statistica Sinica, 18: 905-923. [PDF]




[118] B. Z. Yang, H. R. Kranzler, H. Zhao, J. R. Gruen, X. Luo, J. Gelernter (2007) Association of haplotypic variants in DRD2, ANKK1, TTC12 and NCAM1 to alcohol dependence in independent case-control and family samples. Hum Mol Genet. 16: 2844-2853. [PDF]


[117] V. Dinu, H. Zhao, P. Miller (2007) Integrating domain knowledge with statistical and data mining methods for high density genomic SNP disease association analysis. Journal of Biomedical Informatics, 40: 750-760.[PDF]


[116] W. Yu, J. Liu, C. Colangelo, E. Gulcicek, H. Zhao (2007) A new protocol of analyzing isotope coded affinity tag data from high resolution LC-MS spectrometry. Computational Biology and Chemistry, 31: 215-221.[PDF]


[115] S. Wang, H. Zhao (2007) Sample size needed to detect gene-gene interactions using linkage analysis. Annals of Human Genetics, 71: 828-842.[PDF]


[114] J. Lee, K. He, V. Stolc, H. Lee, P. Figueroa, Y. Gao, W. Tongprasit, H. Zhao, I. Lee, X. W. Deng (2007) Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development. Plant Cell, 19: 731-749.[PDF]


[113] T-S Lee, S. Mane, T. Eid, H. Zhao, A. Lin, Z. Guan, J. H. Kim, J. Schweitzer, D. King-Stevens, P. Weber, S. S. Spencer, D. D. Spencer, N. C. De Lanerolle. (2007) Gene expression in temporal lobe epilepsy is consistent with increased release of glutamate by astrocytes. Molecular Medicine 13: 1-13. [PDF]


[112] V. Dinu, P. Miller, H. Zhao. (2007) Evidence for association between multiple complement pathway genes and AMD. Genetic Epidemiology, 31: 224-237. [PDF]


[111] I. Kim, Y. Liu, H. Zhao. (2007) Bayesian methods for predicting interacting protein pairs using domain information. Biometrics, 63: 824-833. [PDF]




[110] S. P. Wu, L. Leng, Z. Feng, N. Liu, H. Zhao, C. McDonald, A. Lee, F. C. Arnett, P. K. Gregersen, M. D. Mayes, R. Bucala R (2006) Macrophage migration inhibitory factor promoter polymorphisms and the clinical expression of scleroderma. Arthritis & Rheumatism 54: 3661-3669. [PDF]


[109] S. S. Zhang, X. Xu, M. G. Liu, H. Zhao, M. B. Soares, C. J. Barnstable, X. Y. Fu (2006) A biphasic pattern of gene expression during mouse retina development. BMC Developmental Biology 6: 48. [PDF]


[108] H. Pang, A. Lin, M. Holford, B. E. Enerson, B. Lu, M. P. Lawton, E. Floyd, H. Zhao (2006) Pathway analysis using random forests classification and regression. Bioinformatics, 22: 2028-2036. [PDF]


[107] B. Wu, N. Liu, H. Zhao (2006) PSMIX: an R package for population stratification inference via maximum likelihood method. BMC Bioinformatics, 7: 317. [PDF]


[106] N. Liu, H. Zhao (2006) A nonparametric approach for population structure inference using multilocus genotypes. Human Genomics, 2: 353-364. [PDF]


[105] X. You, M. Pan, W. Gao, H. S. Shiah, J. Tao, D. Zhang, F. Koumpouras, S. Wang, H. Zhao, J. A. Madri, D. Baker, Y. C. Cheng, Z. Yin (2006) Effects of a novel tylophorine analog on collagen-induced arthritis through inhibition of the innate immune response. Arthritis & Rheumatism 54: 877-886. [PDF]


[104] T. Tsubouchi, H. Zhao, G. S. Roeder (2006) Crossover distribution by promoting synaptonemal complex formation together with Zip2. Developmental Cell, 10: 809-819. [PDF]


[103] Y. Zuo, G. Zou, H. Zhao (2006) Two-stage designs in case-control association analysis. Genetics, 173: 1747-1760. [PDF]


[102] N. Sun, R. Carroll, H. Zhao (2006) Bayesian Error Analysis Model (BEAM) for reconstructing transcriptional regulatory networks. Proceedings of the National Academy of Sciences 103: 7988-7993. [PDF]


[101] K. Zhang, H. 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. [PDF]


[100] B. E. Enerson, A. Lin, B. Lu, H. Zhao, M. P. Lawton, E. Floyd (2006) Acute drug-induced vascular injury in beagle dogs: pathology and correlating genomic expression. Toxicology Pathology, 34: 27-32. [PDF]


[99] J. Gelernter, C. Panhuysen, M. Wilcox, V. Hesselbrock, B. Rounsaville, J. Poling, R. Weiss, S. Sonne, H. Zhao, L. Farrer, H. R. Kranzler (2006) Genomewide linkage scan for opioid dependence and related traits. American Journal of Human Genetics, 78: 759-769. [PDF]


[98] N. Liu, I. Beerman, R. Lifton, H. Zhao (2006) Haplotype analysis in the presence of informatively missing genotype data. Genetic Epidemiology, 30: 290-300. [PDF]


[97] B. Wu, Z. Guan, H. Zhao (2006) Parametric and nonparametric FDR estimation revisited. Biometrics, 62: 735-744. [PDF]


[96] S. Wang, S. Huang, L. Zheng, H. Zhao (2006) Mapping quantitative trait loci in non-inbred mosquito crosses.  Genetics, 172: 2293-2308. [PDF]


[95] W. Yu, X. Li, J. Liu, B. Wu, K. Williams, H. Zhao (2006) Multiple peak alignment in sequential data analysis: A scale-space based approach. IEEE/ACM Trans. Computational Biology and Bioinformatics 3: 208-219. [PDF]


[94] W. Yu, B. Wu, N. Lin, K. Stone, K. Williams, H. Zhao (2006) Detecting and aligning peaks in mass spectrometry data with applications to MALDI. Computational Biology and Chemistry, 30: 27-38. [PDF]


[93] B. Wu, T. Abbott, D. Fishman, W. McMurray, G. Mor, K. Stone, D. Ward, K. Williams, H. Zhao (2006) Ovarian cancer classification based on mass spectrometry analysis of sera. Cancer Informatics, 2: 123-132. [PDF]




[92] L. Ma, C. Chen, X. Liu, Y. Jiao, N. Su, L. Li, X. Wang, M. Cao, N. Sun, X. Zhang, J. Bao, J. Li, S. Pedersen, L. Bolund, H. Zhao, L. Yuan, G. K-S Wong, J. Wang, X. W. Deng, J. Wang (2005) A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. Genome Research, 15: 1274-1283. [PDF] 


[91] B-Z Yang, H. Zhao, H. R. Kranzler, J. Gelernter (2005) Characterization of a likelihood based method and effects of markers informativeness in evaluation of admixture and population group assignment. BMC Genetics, 6:50. [PDF]


[90] T. Huang, B. Wu, P. Lizardi, H. Zhao (2005) Detection of DNA copy number alterations using penalized least squares regression. Bioinformatics, 21: 3811-3817. [PDF]


[89] L. Chen, H. Zhao (2005) Negative correlation between compositional symmetries and local recombination rates. Bioinformatics, 21: 3951-1958. [PDF]


[88] F. W. Lohoff, T. N. Ferraro, T. Sander, H. Zhao, J. P. Dahl, W. H. Berrettini, R. J. Buono (2005) No association between common variations in the human alpha 2 subunit gene (ATP1A2) of the sodium-potassium-transporting ATPase and idiopathic generalized epilepsy. Neuroscience Letters 382:33-38. [PDF]


[87] L. Ma, N. Sun, X. Liu, Y. Jiao, H. Zhao, X. W. Deng (2005) Organ-specific expression of Arabidopsis genome during development. Plant Physiology, 138: 80-91. [PDF]


[86] Y. Liu, N. Liu, H. Zhao (2005) Inferring protein-protein interactions through high throughput interaction data from diverse organisms. Bioinformatics, 21: 3279-3285. [PDF]


[85] N. Lin, H. Zhao (2005) Are scale-free networks robust to measurement errors? BMC Bioinformatics 6: 119. [PDF]


[84] Y. Jiao, P. Jia, X. Wang, N. Su, S. Yu, D. Zhang, L. Ma, Q. Feng, Z. Jin, L. Li, Y. Xue, Z. Cheng, H. Zhao, B. Han, X. W. Deng (2005) A tiling microarray expression analysis of rice chromosome 4 suggests a chromosomal level regulation of transcription. Plant Cell, 17: 1641-1657. [PDF]


[83] G. Mor, I. Visintin, Y. Lai , H. Zhao, P. Schwartz, T. Rutherford, L. Yue, P. Bray-Ward, D. Ward (2005) Serum protein markers for early detection of ovarian cancer.  Proceedings of the National Academy of Sciences, 102: 7677-7682. [PDF]


[82] L. Chen, H. Zhao (2005) Gene expression analysis reveals that histone deacetylation sites may serve as partitions of chromatin gene expression domains. BMC Genomics 6: 44. [PDF]


[81] S. S. Zhang, X. Xu, J. Li, M. G. Liu, H. Zhao, M. B. Soares, C. J. Barnstable, X. Y. Fu (2005) Comprehensive in silico functional specification of mouse retina transcripts. BMC Genomics, 6: 40. [PDF]


[80] B. Z. Yang, H. Zhao, H. R. Kranzler, J. Gelernter (2005) Practical population group assignment with selected informative markers: Characteristics and properties of Bayesian clustering via STRUCTURE. Genet Epidemiology, 28: 302-312. [PDF]


[79] Y. Lai, H. Zhao (2005) A statistical method to detect chromosomal regions with DNA copy number alterations using SNP-array-based CGH data. Computational Biology and Chemistry, 29: 47-54. [PDF]


[78] B. S. Kennedy, S. V. Kasl, J. Lichtman, H. Zhao (2005) Predicting readmission stroke type among blacks and whites in California. Journal of Stroke and Cerebrovascular Disease, 14: 251-260. [PDF]


[77] M. Holford, N. Li, P. Nadkarni, H. Zhao (2005) VitaPad: visualization tools for the analysis of pathway data. Bioinformatics, 21: 1596-1602. [PDF]


[76] L. Chen, H. Zhao (2005) Integrating mRNA decay information into co-regulation study. Journal of Computer Science and Technology, 20: 434-438. [PDF]


[75] Z. Guan, H. Zhao (2005) A semiparametric approach for marker gene selection based on gene expression data. Bioinformatics, 21: 529-536. [PDF]


[74] G. Zou, H. Zhao (2005) Family-based association tests for different family structures using pooled DNA. Annals of Human Genetics, 69: 429-442. [PDF]


[73] K. Zhang, F. Sun, H. Zhao. (2005) HAPLORE: A program for haplotype reconstruction in general pedigrees without recombination. Bioinformatics, 21: 90-103. [PDF]


[72] N. Carriero, M. V. Osier, K-H Cheung, P. L. Miller, M. Gerstein, H. Zhao, B. Wu, S. Rifkin, J. Chang, H. Zhang, K. White, K. Williams, M. Schultz (2005) A 'High Productivity/Low Maintenance' approach to high performance computation for biomedicine: Four Case Studies. Journal of American Medical Informatics Association, 12: 90-98.[PDF]




[71] F. H. Wilson, A. Hariri, A. Farhi, H. Zhao, K. F. Petersen, H. R. Toka, C. Nelson-Williams, K. M. Raja, M. Kashgarian, G. I. Shulman, S. J. Scheinman, R. P. Lifton RP (2004) A cluster of metabolic defects caused by mutation in a mitochondrial tRNA. Science, 306: 1190-1194. [PDF]


[70] Y. Liu, H. Zhao (2004) A computational approach for ordering signal transduction pathway components from genomics and proteomics data. BMC Bioinformatics, 5, 158. [PDF]


[69] N. Lin, B. Wu, R. Jansen, M. Gerstein, H. Zhao (2004) Information assessment on predicting protein-protein interactions. BMC Bioinformatics, 5, 154.[PDF]


[68] M. V. Osier, H. Zhao, K-H Cheung (2004) Handling multiple testing while interpreting microarrays with the gene ontology database. BMC Bioinformatics, 5, 124. [PDF]


[67] Y. Gao, J. Li, E. Strickland, S. Hua, H. Zhao, Z. Chen, L. Qu, X. W. Deng (2004) An Arabidopsis promoter microarray and its initial usage in the identification of HY5 binding targets in Vitro. Plant Molecular Biology, 54: 683-699.[PDF]


[66] N. Liu, S. L. Sawyer, N. Mukherjee, A. J. Pakstis, J. R. Kidd, K. K. Kidd, A. J.Brookes, H. Zhao (2004) Haplotype block structures show significant variation among populations. Genetic Epidemiology, 27: 385-400.[PDF]


[65] Y. Lai, B. Wu, L. Chen, H. Zhao (2004) Statistical method for identifying differential gene-gene coexpression patterns. Bioinformatics, 20: 3146-3155.[PDF]


[64] Hoek, K., Rimm, D.L., Williams, K.R., Zhao, H., Ariyan, S., Lin, A., Kluger, H.M., Berger, A.J., Cheng, E., Trombetta, E.S.,Wu, T., Niinobe, M., Yoshikawa, K., Hannigan, G.E., Halaban, R. (2004) Expression profiling reveals novel pathways in the transformation of melanocytes to melanomas. Cancer Research, 64: 5270-5282. [PDF]


[63] R. Marathe, Z. Guan, R. Anandalakshmi, H. Zhao, S. Dinesh-Kumar (2004) Study of Arabidopsis thaliana resistome in response to cucumber mosaic virus infection using whole genome microarray. Plant Molecular Biology, 55: 501-520. [PDF]


[62] R. J. Buono , F. W. Lohoff, T. Sander, M. R. Sperling, M. J. O'Connor, D. J. Dlugos, S. G. Ryan, G. T. Golden, H. Zhao, T. M. Scattergood, W. H. Berrettini, T. N. Ferraro. (2004) Association between variation in the human KCNJ10 potassium ion channel gene and seizure susceptibility. Epilepsy Research, 58: 175-183. [PDF]


[61] W. D. Li, C. Dong, D. Li, H. Zhao, R. A. Price. (2004) An obesity-related locus in chromosome region 12q23-24. Diabetes 53: 812-820. [PDF]


[60] G. Zou, H. Zhao. (2004) The estimation of sibling genetic risk parameters revisited. Genetic Epidemiology, 26: 286-293. [PDF]


[59] X. Sun, J. C. Stephens, H. Zhao. (2004) The impact of sample size and marker selection on the study of haplotype structures. Human Genomics, 1: 179-193. [PDF]


[58] C.-S. Goh, N. Lan, S. Douglas, B. Wu, N. Echols, A. Smith, D. Milburn, G. T. Montelione, H. Zhao, M. Gerstein. (2004) Mining the structural genomics pipeline: Identification of protein properties that affect high-throughput experimental analysis. Journal of Molecular Biology, 336: 115-130. [PDF]


[57] T. N. Ferraro, G. T. Golden, G. G. Smith, J. F. Martin, F. W. Lohoff, T. A. Gieringer, D. Zamboni, C. L. Schwebel1, D. M. Press, S. O. Kratzer, H. Zhao, W. H. Berrettini, R. J. Buono. (2004) Fine mapping of a seizure susceptibility locus on mouse chromosome 1: Nomination of Kcnj10 as a causative gene. Mammalian Genome, 15: 239-251. [PDF]


[56] W. Zhao, J. Wang, X. He, X. Huang, Y. Jiao, M. Dai, S. Wei, J. Fu, Y. Chen, X. Ren, Y. Zhang, P. Ni, J. Zhang, S. Li, J. Wang, G. Wong, H. Zhao, J. Yu, H. Yang, J. Wang. (2004) BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics. Nucleic Acid Research, 32: D377-382. [PDF]


[55] G. Zou, H. Zhao. (2004) The impacts of errors in individual genotyping and DNA pooling on association studies. Genetic Epidemiology, 26: 1-10. [PDF]




[54] N. Sun, L. Ma, D. Pan, H. Zhao, X-W Deng. (2003) Evaluation of regulatory potential of Calvin cycle pathway steps based on large-scale gene expression profiling data. Plant Molecular Biology, 53: 467-478. [PDF]


[53] D. Pan, N. Sun, K-H Cheung, Z. Guan, L. Ma, M. Holford, X-W Deng, H. Zhao (2003) PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis. BMC Bioinformatics, 4:56. [PDF]


[52] L. Zheng, S. Wang, P. Romans, H. Zhao, C. Luna, M. Q. Benedict (2003) Quantitative trait loci in Anopheles gambiae controlling the encapsulation response against Plasmodium cynomolgi Ceylon. BMC Genetics 2003, 4:16 [PDF]


[51] Y. Jiao, H. Yang, L. Ma, N. Sun, H. Yu, T. Liu, Y. Gao, H. Gu, Z. Chen, M. Wada, M. Gerstein, H. Zhao, L. Qu, X. W. Deng. (2003) A genome wide analysis of blue light regulation of Arabidopsis transcription factor gene expression during seedling development. Plant Physiology, 133: 1480-1493. [PDF]


[50] G. Garcia-Rostan, H. Zhao, M. Pollan, A. Herrero, R. L. Camp, J. Pardo, R. Wu, J. Costa, M. L. Carcangiu, G. Tallini. (2003) Ras mutations are associated with aggressive tumor phenotypes and poor prognosis in thyroid cancer. Journal of Clinical Oncology, 21: 3226-3235. [PDF]


[49] G. Zou, H. Zhao. (2003) Haplotype frequency estimation in the presence of genotyping errors. Human Heredity, 56: 131-138. [PDF]


[48] L. V. Sun, L. Chen, F. Greil, N. Negre, T.-R. Li, G. Cavalli, H. Zhao, B. Van Steensel, K. P. White (2003) DNA–protein interaction mapping using genomic tiling path microarrays in Drosophila. Proceedings of the National Academy of Sciences, 100: 9428-9433. [PDF]


[47] X. Luo, H. R. Kranzler, H. Zhao, J. Gelernter. (2003) Haplotypes at the OPRM1 locus are associated with susceptibility to substance dependence in European-Americans. American Journal of Medical Genetics 120B: 97-108. [PDF]


[46] N. M. Wikonkal, E. Remenyik, D. Knezevic, W. Zhang, M. Liu, H. Zhao, T. R. Berton, D. G. Johnson, D. E. Brash. (2003) Inactivating E2f1 reverts apoptosis resistance and cancer sensitivity in Trp53-deficient mice. Nature Cell Biology 5: 655-660. [PDF]


[45] W-D Li, D. Li, S. Wang, S. Zhang, H. Zhao, R. A. Price. (2003) Linkage and linkage disequilibrium mapping of genes influencing human obesity in chromosome region 7q22.1–7q35. Diabetes, 52: 1557-1561. [PDF]


[44] S. Wang, H. Zhao. (2003) Sample size to detect gene-gene interactions using association designs. American Journal of Epidemiology, 158: 899-914. [PDF]


[43] B. Wu, T. Abbott, D. Fishman, W. McMurray, G. Mor, K. Stone, D. Ward, K. Williams, H. Zhao. (2003) Comparison of statistical methods for classification of ovarian cancer using a proteomics dataset. Bioinformatics, 19: 1636-1643. [PDF]


[42] G. Zou, D. Pan, H. Zhao. (2003) Genotyping error detection through tightly linked markers.  Genetics, 164: 1161-1173. [PDF]


[41] H-S Chen, X. Zhu, H. Zhao, S. Zhang. (2003) Qualitative semi-parametric test to detect genetic association in case-control design under structured population.  Annals of Human Genetics, 67: 250-264. [PDF]


[40] L. Ma, H. Zhao, XW Deng (2003) Analysis of the mutational effects of the COP/DET/FUS loci on genome expression profiles reveals their overlapping yet not identical roles in regulating Arabidopsis seedling development. Development, 130: 969-981. [PDF]


[39] S. Wang, K. K. Kidd, H. Zhao. (2003) On the use of DNA pooling to estimate haplotype frequencies. Genetic Epidemiology, 24: 74-82. [PDF]


[38] S. Zhang, X. Zhu, H. Zhao. (2003) On a semi-parametric test to detect associations between quantitative traits and candidate genes using unrelated individuals. Genetic Epidemiology, 24: 44-56. [PDF]


[37] C. Dong, S. Wang, W-D Li, H. Zhao, R. A. Price. (2003) Interacting genetic loci in chromosome regions 20q and 10q influence extreme human obesity. American Journal of Human Genetics, 72: 115-124. [PDF]




[36] H. Wang, L. Ma, J. Haboshi, J. Li, H. Zhao, X-W Deng. (2002) Analysis of far-red light regulated genome expression profiles of phytochrome A pathway mutants in Arabidopsis. Plant Journal, 32: 723-733. [PDF]


[35] L. Ma, Y. Gao, L. Qu, Z. Chen, J. Li, H. Zhao, X-W Deng. (2002) Genomic evidence for COP1 as a repressor of light-regulated gene expression and development in Arabidopsis. Plant Cell, 14: 2383-2398. [PDF]


[34] G. Wu, X. Tian, S. Nishimura, G. S. Markowitz, V. D'Agati, J. H. Park, L. Yao, L. Li, L. Geng, H. Zhao, W. Edelmann, S. Somlo. (2002) Trans-heterozygous Pkd1 and Pkd2 mutations modify expression of polycystic kidney disease. Human Molecular Genetics, 16: 1845-1854. [PDF]


[33] A. Mani, S. M. Meraji, R. Houshyar, J. Radhakrishnan, A. Mani, M. Ahangar, T. M. Rezaie, M. A. Taghavinejad, B. Broumand, H. Zhao, C. Nelson-Williams, R. P. Lifton. (2002) Finding genetic contributions to sporadic disease: A recessive locus at 12q24 commonly contributes to patent ductus arteriosus. Proceedings of the National Academy of Sciences, 99: 15054-15059. [PDF]


[32] X. Zhu, S. Zhang, H. Zhao, R. S. Cooper. (2002) Association mapping using a mixture model for complex traits. Genetic Epidemiology, 23: 181-196. [PDF]


[31] S. Zhang and H. Zhao. (2002) Linkage disequilibrium mapping with genotype data. Genetic Epidemiology, 22: 66-77. [PDF]


[30] S. Zhang, K. K. Kidd, and H. Zhao. (2002) Detecting genetic association in case-control studies using similarity-based association tests. Statistica Sinica, 12: 337-359. [PDF]




[29] J. Li, S. Sherman, N. Lamb, and H. Zhao. (2001) Multipoint genetic mapping with trisomy data. American Journal of Human Genetics, 69: 1255-1265. [PDF]


[28] H. Wang, L. Ma, J. Li, H. Zhao, and X-W Deng. (2001) Direct interaction of Arabidopsis Cryptochromes with COP1 in light control development. Science, 294: 154-158. [PDF]


[27] L. Ma, J. Li, J. Hager, L. Qu, Z. Chen, H. Zhao, and X-W Deng. (2001) Light control of Arabidopsis development entails co-ordinated regulation of genome expression and cellular pathways. Plant Cell, 13: 2589-2607. [PDF]


[26] S. Zhang, A. J. Pakstis, K. K. Kidd, and H. Zhao. (2001) Comparisons of two methods for haplotype reconstruction and haplotype frequency estimates from population data. American Journal of Human Genetics, 69: 906-912. [PDF]


[25] S. Zhang and H. Zhao. (2001) Quantitative similarity-based association test using population samples. American Journal of Human Genetics, 69: 601-614. [PDF]


[24] H. Zhao, J. Li, and W. P. Robinson. (2001) Statistical analysis of uniparental disomy data using hidden Markov models. Biometrics, 57: 1074-1079. [PDF]


[23] H. Zhao and F. Liang. (2001) On relationship inference using continuous gamete identity by descent data. Journal of Computational Biology, 8: 191-200. [PDF]


[22] A. Kamina, R. W. Makuch, and H. Zhao. (2001) A stochastic modeling of early HIV-1 population dynamics. Mathematical Biosciences, 170: 187-198. [PDF]




[21] H. Zhao, S. Zhang, K. R. Merikangas, M. Trixler, D. Wildenaur, F. Sun, and K. K. Kidd. (2000) Transmission/disequilibrium tests using multiple tightly linked markers. American Journal of Human Genetics, 67: 936-946. [PDF]


[20] H. Zhao, J. Li, and W. P. Robinson. (2000) Multipoint genetic mapping with uniparental disomy data. American Journal of Human Genetics, 67: 851-861. [PDF]


[19] F. Sun, W. D. Flanders, Q. Yang, and H. Zhao. (2000) Transmission/disequilibrium tests for quantitative traits. Annals of Human Genetics, 64: 555-565. [PDF]


[18] K. Zhang and H. Zhao. (2000) Assessing reliability of gene clusters from gene expression data. Functional and Integrative Genomics, 1: 156-173. [PDF]


[17] S. Zhang and H. Zhao. (2000) Linkage disequilibrium mapping in populations of variable size using the decay of haplotype sharing and a stepwise-mutation model. Genetic Epidemiology, 19: S99-S105. [PDF]


[16] J. R. Kidd, A. J. Pakstis, H. Zhao, R-B Lu, and others. (2000) Haplotypes and linkage disequilibrium at the phenylalanine hydroxylase locus (PAH) in a global representation of populations. American Journal of Human Genetics, 66: 1882-1899. [PDF]




[15] H. Zhao, K. R. Merikangas, and K. K. Kidd. (1999) On a randomization test in linkage analysis. American Journal of Human Genetics, 65: 1449-1456. [PDF]


[14] H. Zhao, A. J. Pakstis, J. R. Kidd, and K. K. Kidd. (1999) Assessing linkage disequilibrium in a complex genetic system. Annals of Human Genetics, 63: 167-179. [PDF] 




[13] H. Zhao and T. P. Speed. (1998) Statistical analysis of half-tetrads. Genetics, 150: 473-485. [PDF]


[12] H. Zhao and T. P. Speed. (1998) Statistical analysis of ordered tetrads. Genetics, 150: 459-472. [PDF]


[11] H. Zhao and T. P. Speed. (1998) Stochastic modeling of the crossover process during meiosis. Communications in Statistics, Theory and Methods, 27: 1557-1580. [PDF]


[10] K. K. Kidd, B. Morar, C. M. Castiglione, H. Zhao, and others. (1998) A global survey of haplotype frequencies and linkage disequilibrium at the DRD2 locus. Human Genetics, 103: 211-227. [PDF]




[9] H. Zhao, H. Zhang, and J. I. Rotter. (1997) Cost-effective sib-pair designs in the mapping quantitative-trait loci. American Journal of Human Genetics, 60: 1211-1221. [PDF]


[8] D. R. Goldstein, H. Zhao, and T. P. Speed. (1997) The effects of genotyping errors and interference on estimation of genetic distance. Human Heredity, 47: 86-100.


[7] K. Lange, H. Zhao, and T. P. Speed. (1997) Modeling chiasma interference using the Poisson-skip model. Annals of Applied Probability, 7: 299-313. [PDF]




[6] J. D. Ohmen, H. Y. Yang, K. K. Yamamoto, H. Zhao, and others. (1996) Susceptibility locus for inflammatory bowel disease on chromosome 16 has a role in Crohns disease, but not in Ulcerative Colotis. Human Molecular Genetics, 5: 1679-1683. [PDF]


[5] H. Zhao and T. P. Speed. (1996) On genetic map functions. Genetics, 142: 1369-1377. [PDF]




[4] D. R. Goldstein, H. Zhao, and T. P. Speed. (1995) Relative efficiencies of several statistical models of recombination for exclusion mapping and gene ordering. Genomics, 27: 265-273. [PDF]


[3] H. Zhao, M. S. McPeek, and T. P. Speed. (1995) Statistical analysis of chromatid interference. Genetics, 139: 1057-1065. [PDF]


[2] H. Zhao, M. S. McPeek, and T. P. Speed. (1995) Statistical analysis of crossover interference using the chi-square model. Genetics, 139: 1045-1056. [PDF]




[1] K. Doksum, S. Blyth, E. Bradlow, X. L. Meng, and H. Zhao. (1994) Correlation curves as local measures of variance explained by regression. Journal of American Statistical Association, 89: 571-583. [PDF]



Refereed Conference Articles

[21] J. Kang, W. Zheng, L. Li, J. S. Lee, X. Yan, H. Zhao (2011) Utilization of Bayesian Network to dissect the complexity of genetic disease: Application to the GAW17 Simulated Data. BMC Proceedings, in press.


[20] L. Li, W. Zheng, J. S. Lee, X. Zhang, J. Ferguson, X. Yan, H. Zhao (2011) Collapsing-based and kernel-based single gene analyses applied to Genetic Analysis Workshop 17 mini-exome data. BMC Proceedings, in press.


[19] X. Yan, L. Li, J. S. Lee, W. Zheng, J. Ferguson, H. Zhao (2011) Detecting functional rare variants by collapsing and incorporating functional annotation in Genetic Analysis Workshop 17 mini-exome data. BMC Proceedings, in press.


[18] G. Li, J. Ferguson, W. Zheng, J. S. Lee, X. Zhang, L. Li, J. Kang, X. Yan, H. Zhao (2011) Large-scale risk prediction applied to Genetic Analysis Workshop 17 mini-exome sequence data. BMC Proceedings, in press.


[17] Z. He, H. Zhao, W. Yu (2011) Score regularization for peptide identification. BMC Bioinformatics, 12 Supplement 1:S2. [Pubmed]


[16] D. H. Ballard, C. Aporntewan, J. Y. Lee, J. S. Lee, Z. Wu, H. Zhao (2009) A pathway analysis applied to GAW 16 genome wide rheumatoid arthritis data. BMC Proceedings, Supplement 7: S91. [PDF]


[15] Z. Wu, C. Aporntewan, D. H. Ballard, J. Y. Lee, J. S. Lee, H. Zhao (2009) Two-stage joint selection method to identify potential candidate markers from genome-wide association studies. BMC Proceedings, Supplement 7: S29. [PDF]


[14] C. Aporntewan, D. H. Ballard, J. Y. Lee, J. S. Lee, Z. Wu, H. Zhao (2009) Gene hunting of the GAW16 rheumatoid arthritis data using rough set theory. BMC Proceedings, Supplement 7: S126. [PDF]


[13] S. Huang, D. Ballard, H. Zhao (2007) The role of heritability in mapping expression quantitative trait loci. BMC Proceedings, 1: S86. [PDF]


[12] L. A. Cupples, J. Bailey, K. C. Cartier, C. T. Falk, K-Y Liu, Y. Ye, R. Yu, H. Zhao (2005) GAW14 Workshop: Data Mining. Genetic Epidemiology, 29 Suppl 1:S103-9. [PDF]


[11] L. Chen, N. Liu, S. Wang, C. Oh, N. J. Carriero, H. Zhao (2005) Whole genome association studies on alcoholism comparing different phenotypes using single nucleotide polymorphisms and microsatellites. BMC Genetics, 6(Suppl 1): S130. [PDF]


[10] S. Huang, S. Wang, N. Liu, L. Chen, C. Oh, H. Zhao (2005) Whole-genome association analysis to identify markers associated with recombination rates using single nucleotide polymorphisms and microsatellites. BMC Genetics, 6(Suppl 1): S51. [PDF]


[9] N. Liu, L. Chen, S. Wang, C. Oh, H. Zhao (2005) Comparison of single nucleotide polymorphisms and microsatellites in inference of population structure. BMC Genetics, 6(Suppl 1): S26.[PDF]


[8] C. Oh, S. Wang, N. Liu, L. Chen, H. Zhao (2005) A Bayesian genome screening of maximum number of drinks as an alcoholism phenotype with the new Haseman-Elston method. BMC Genetics, 6(Suppl 1): S116. [PDF]


[7] S. Wang, S. Huang, N. Liu, L. Chen, C. Oh, H. Zhao (2005) Whole-genome linkage analysis in mapping alcoholism genes using single nucleotide polymorphisms and microsatellites. BMC Genetics, 6(Suppl 1): S28. [PDF]


[6] K. H. Cheung, K. White, J. Hager, M. Gerstein, V. Reinke, K. Nelson, P. Masiar, R. Srivastava, Y. Li, J. Li, J. M. Li, H. Zhao, D. B. Allison, M. Snyder, P. Miller, K. Williams. (2002) YMD: A microarray Database for Large-scale Gene Expression Analysis. Proceedings of AMIA Symposium 140-144. [PDF]


[5] S. Zhang, K. Zhang, J. Li, and H. Zhao. (2002) On a family-based haplotype pattern mining method for linkage disequilirbium mapping. Pacific Symposium on Biocomputing, 100-111. [PDF]


[4] J. Li, D. Wang, J. Dong, R. Jiang, K. Zhang, S. Zhang, H. Zhao, and F. Sun. (2001) The power of transmission disequilibrium tests for quantitative traits. Genetic Epidemiology, 21: S632-S637. [PDF]


[3] S. Zhang, K. Zhang, J. Li, F. Sun, and H. Zhao. (2001) Test of association for quantitative traits in general pedigrees: the quantitative pedigree disequilibrium test. Genetic Epidemiology, 21: S370-S375. [PDF]


[2] L. J. Sheffield, M. P. Knauert, A. J. Pakstis, H. Zhao, and K. K. Kidd. (1999) Analyses of the COGA data set in one ethnic group with examinations of alternative definitions of alcoholism. Genetic Epidemiology, 17, S319-S324.[PDF]


[1] H. Zhao, L. J. Sheffield, A. J. Pakstis, M. P. Knauert, and K. K. Kidd. (1999) A more powerful method to evaluate p-values in GENEHUNTER. Genetic Epidemiology, 17: S415-S420. [PDF]





[3] X. Luo, J. Gelernter, H. Zhao, H.R. Kranzler. (2005) Response to Dr. Kopke's comments on haplotypes at the DPRM1 locus. American Journal of Medical Genetics, 135B:102. [PDF]


[2] H. Zhao, K. R. Merikangas, and K. K. Kidd. (2000) Reply to Kong and Nicolae. American Journal of Human Genetics, 67: 1355-1356. [PDF]


[1] H. Zhao. (1999) The interpretation of the parameters in the transmission/disequilibrium test. American Journal of Human Genetics, 64: 326-328. [PDF]



Journal Review Articles

[10] W. Zheng, T. A. Gianoulis, K. J. Karczewski, H. Zhao, M. Snyder (2011) Regulatory variation within and between species. Annual Reviews of Genomics and Human Genetics, 12: 327-346. [Pubmed]


[9] N. Sun, H. Zhao (2009) Reconstructing transcriptional regulatory networks through genomics data. Statistical Methods in Medical Research, 18: 595-617. [PDF]


[8] Y. Liu, I. Kim, H. Zhao (2008) Protein interaction predictions from diverse sources. Drug Discovery Today, 13: 409-416. [PDF]


[7] N. Liu, K. Zhang, H. Zhao (2008) Haplotype Association Analysis. Advances in Genetics, 60: 335-405. [PDF]


[6] Stone KL, Bjornson RD, Blasko GG, Bruce C, Cofrancesco R, Carriero NJ, Colangelo CM, Crawford JK, Crawford JM, Dasilva NC, Deluca JD, Elliott JI, Elliott MM, Flory PJ, Folta-Stogniew EJ, Gulcicek E, Kong Y, Lam TT, Lee JY, Lin A, Lopresti MB, Mane SM, McMurray WJ, Tikhonova IR, Westman S, Williams NA, Wu TL, Zhao H, Williams KR. (2007) Keck foundation biotechnology resource laboratory, Yale university. Yale J Biol Med. 80: 195-211. [PDF]


[5] Y. Xia, H. Yu, R. Jansen, M. Seringhaus, S. Baxter, D. Greenbaum, H. Zhao, M. Gerstein. (2004) Analyzing cellular biochemistry in terms of molecular networks. Annual Review of Biochemistry, 73: 1051-1087. [PDF]


[4] N. Sun, H. Zhao. (2004) Genomic approaches in dissecting complex biological pathways. Pharmacogenomics, 5: 163-179. [PDF]


[3] H. Zhao, R. Pfiffer, M. H. Gail.  (2003) Haplotype analysis in population genetics and association studies. Phamacogenomics, 4: 171-178. [PDF]


[2] H. Zhao. (2000) Family-based association studies. Statistical Methods in Medical Research, 9: 563-587. [PDF]


[1] H. Zhang, H. Zhao, and K. R. Merikangas. (1997) Strategies to identify genes for complex diseases. Annals of Medicine, 29: 493-498.



Book Chapters

[21] L. Li, X. Zhang, H. Zhao (2011) eQTL. Topics for Methods in Molecular Biology: QTL analysis, edited by S. Rifkin, in press.


[20] J. Cao, X. Qi, H. Zhao (2011) Modelling gene regulation networks using ordinary differential equations. Next Generation Microarray Bioinformatics, a volume in the Methods in Molecular Biology, edited by J. Wang, T. Aik-Choon and T. Tian, Humana Press, Springer, in press.


[19] H. Chun, J. Kang, X. Zhang, M. Deng, H. Ma, H. Zhao (2010) Reverse engineering of gene regulation networks with an application to the DREAM4 in silico network challenge. Handbook of Computational Statistics: Statistical Bioinformatics, Edited by H. H-S Lu, B. Schölkopf, and H. Zhao, Springer, 461-478.


[18] N. Sun, H. Zhao (2010) Bayesian methods in genomics and proteomics studies. Knowledge-Based Bioinformatics, edited by M. Ramoni and G. Alterovitz, Wiley, 125-136.


[17] K. Zhang, H. Zhao (2010) Family based association studies. Handbook of Statistical Genetics, 191-240. Springer-Verlag Berlin Heidelberg, 191-240.


[16] X. Zhang, H. Zhao (2009) An evaluation of gene module concepts in the interpretation of gene expression data. Frontiers in Computational and Systems Biology, edited by J. Feng, W. Fu, F. Sun, Springer-Verlag, London, 331-349.


[15] N. Sun, H. Zhao (2009) Current trends and statistical issues in genome wide association studies. Statistical Bioinformatics, edited by J. Lee, Wiley-Blackwell, 283-308.


[14] I. Kim, Y. Liu, H. Zhao (2009) Sparsity priors for protein-protein interaction predictions. In: Bayesian Modeling in Bioinformatics edited by D. Dey, S. Ghosh, and B. Mallick, Chapman & Hall, 255-269.


[13] Y. Liu, I. Kim, H. Zhao (2008) Protein interaction predictions from diverse sources. New Developments in Biostatistics and Bioinformatics, edited by J. Fan, X. Lin and J. S. Liu, World Scientific, New Jersey, 159-178.


[12] H. Pang, I. Kim, H. Zhao (2008) Pathway-based methods for analyzing microarray data. Analysis of Microarray Data: Network based Approaches, edited by F. Emmert-Streib and M. Dehmer, Wiley-VCH, Weinheim, Germany, 355-384.


[11] J. Wang, G. Zou, H. Zhao (2007) DNA pooling: Methods and applications in association studies. In Current Topics in Human Genetics, Studies in Human Diseases edited by HW Deng, H. Shen, Y-J Liu, H. Hu, 179-208.


[10] S. Huang, D. Ballard, Z. Wu, H. Zhao (2007) Expression quantitative trait loci mapping. In Current Topics in Human Genetics, Studies in Human Diseases edited by HW Deng, H. Shen, Y-J Liu, H. Hu, 397-431.


[9] Z. Feng, N. Liu, H. Zhao (2007) Haplotype inference and association analysis in unrelated samples. In Current Topics in Human Genetics, Studies in Human Diseases edited by HW Deng, H. Shen, Y-J Liu, H. Hu, 123-159.


[8] Y. Liu, N. Sun, J. Liu, L. Chen, M. McIntosh, L. Zheng, H. Zhao (2007) Identifying stage-specific genes by combining information from two different types of oligonucleotide arrays. Methods of Microarray Data Analysis V, edited by P. McConnell, S. Lin and P. Hurban, 59-74.


[7] N. Sun, H. Zhao (2006) A misclassification model for inferring transcriptional regulatory networks. Bayesian Inference for Gene Expression and Proteomics. Editors: Kim-Anh Do, Peter Mueller, Marina Vannucci. 347-365.


[6] W. Yu, B. Wu, T. Huang, X. Li, K. Williams, H. Zhao (2006) Statistical methods in proteomics. Springer Handbook of Engineering Statistics, 623-638.  


[5] W. Yu, B. Wu, J. Liu, X. Li, K. Stone, K. Williams, H. Zhao (2006) MALDI-MS Data Analysis for Disease Biomarker Discovery. Methods in Molecular Biology, New and Emerging Proteomics Techniques, edited by D. Nedelkov and R. W. Nelson. Humana Press, 328: 199-216.


[4] E. Gulcicek, C. Colangelo, W. McMurray, K. Stone, B. Wu, T. Wu, H. Spratt, A. Kurosky, H. Zhao, K. Williams (2005) Proteomics and the Analysis of Proteomic Data. Current Protocols in Bioinformatics (Davison, D., Page, R., Petsko, G., Stormo, G., and Stein, L. eds) John Wiley and Sons, Indianapolis, IN, in press.


[3] H. Zhao, B. Wu, N. Sun. (2003) DNA-protein binding and gene expression patterns. In: Goldstein DR (ed) Science and Statistics: A Festschrift for Terry Speed. IMS Lecture Notes-Monograph Series, Vol 40, pp 259-274. [PDF]


[2] T. P. Speed and H. Zhao (2001) Chromosome maps. Handbook of Statistical Genetics, 3-39. [PDF]


[1] H. Zhao and T. P. Speed. (1999) On a Markov model for chromatid interference. Statistics in Molecular Biology (IMS Lecture Notes 33), 1-20. [PDF]





[2] H. H-S Lu, B. Scholkopf, and H. Zhao (eds) (2010) Handbook of Computational Statistics: Statistical Bioinformatics, Springer, in press.


[1] S. Lin, H. Zhao (eds) (2009) Handbook of Statistical Genetics. Springer-Verlag Berlin Heidelberg.