Q. Lu, R. L. Powles, S. Abdallah, D. Ou, Q. Wang, Y. Hu, Y. Lu, W. Liu, B. Li, S. Mukherjee, P. K. Crane, H. Zhao (2017) Systematic tissue-specific functional annotation of the human genome highlights immune-related DNA elements for late-onset Alzheimerís disease. PLOS Genetics.
 S. A. Streicher, A. P. Klein, S. H. Olson, L. T. Amundadottir, A. T. DeWan, H. Zhao, H. A. Risch (2017) Impact of sixteen established pancreatic cancer susceptibility loci in American Jews. Cancer Epidemiology, Biomarkers & Prevention.
 L. Zhu, J. Zhao, H. Zhao (2017) Pivotal variable detection of the covariance matrix and its application to high dimensional factor models. Statistics and Computing.
 Y. Liu, H. Zhao (2017) Variable importance-weighted random forests. Quantitative Biology.
 J. Sun, J. D. Herazo-Mayab, N. Kaminski, H. Zhao, J. L. Warrena (2017) A Dirichlet process mixture model for clustering longitudinal gene expression data. Statistics in Medicine.
 Y. Wang, H. Zhao, M. Deng, H. Fang, D. Yang (2017) Network clustering analysis using mixture exponential-family random graph models and its application in genetic interaction data. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
 H. Fang, C. Huang, H. Zhao, M. Deng (2017) gCoda: Conditional dependence network inference for compositional data. Journal of Computational Biology.
 Y. Zhang, M. H. Linder, A. Shojaie, Z. Ouyang, R. Shen, K. A. Baggerly, V. Baladandayuthapani, H. Zhao (2017) Dissecting pathway disturbances using network topology and multi-platform genomics data. Statistics in Biosciences.
 N. Rauniyar, G. Peng, T. T. Lam, H. Zhao, G. Mor, K. R. Williams (2017) Data-Independent Acquisition (DIA) and Parallel Reaction Monitoring (PRM) mass spectrometry identification of serum biomarkers for ovarian cancer. Biomarker Insights.
 K. R. Williams, C. M. Colangelo, L. Hou, L. Chung, J. M. Belcher, T. Abbott, I. E. Hall, H. Zhao, L. G. Cantley, C. R. Parikh (2017) Use of a Targeted Urine Proteome Assay (TUPA) to identify protein biomarkers of delayed recovery after kidney transplant. Proteomics Clinical Applications.
 K. Koenen, L. Duncan, A. Ratanatharathorn, A. Aiello, L. Almli, A. Amstadter, A. Koch, D. Baker, J. Beckham, L. Bierut, J. Bisson, B. Bradley-Davino, C.-Y. Chen, S. Dalvie, L. Farrer, S. Galea, M. Garrett, J. Gelernter, G. Guffanti, M. Hauser, E. Johnson, R. Kessler, N. Kimbrel, A. King, N. Koen, H. Kranzler, M. Logue, A. Maihofer, A. Martin, M. Miller, R. Morey, N. Nugent, J. Rice, S. Ripke, A. Roberts, N. Saccone, J. Smoller, D. Stein, M. Stein, J. Sumner, M. Uddin, R. Ursano, D. Wildman, R. Yehuda, H. Zhao, M. Daly, I. Liberzon, K. Ressler, C. Nievergelt (2017) Largest GWAS of PTSD (N=20,070) yields genetic overlap with schizophrenia and sex differences in heritability. Molecular Psychiatry.
 R. Polimanti, J. Kaufman, H. Zhao, H. Kranzler, R. Ursano, R. Kessler, J. Gelernter, M. Stein (2017) A genome-wide gene-by-trauma interaction study of alcohol misuse in two independent cohorts identifies PRKG1 as a risk locus. Molecular Psychiatry.
analysis. Annals of Applied Statistics.
 T. Wang, H. Zhao (2017) Structured subcomposition selection in regression and its application to microbiome data
 T. Wang, H. Zhao (2017) A Dirichlet-tree multinomial regression model for associating dietary nutrients with gut microorganisms. Biometrics.
 Z. Lin, T. Wang, C. Yang, H. Zhao (2017) On joint estimation of Gaussian graphical models for spatial and temporal data. Biometrics.
 T. Wang, H. Zhao (2017) Constructing predictive microbial signatures at multiple taxonomic levels. Journal of the American Statistical Association.
 T. Wang, H. Zhao, M. Chen, L. Zhu (2017) Estimating a sparse reduction for general regression in high dimensions. Statistics and Computing.
 Q. Lu, C. Jin, J. Sun, R. Bowler, K. Kechris, N. Kaminski, H. Zhao (2017) Post-GWAS prioritization through data integration provides novel insights on chronic obstructive pulmonary disease. Statistics in Biosciences.
 G. Charkoftaki, Y. Chen, M. Han, M. Sandoval, X. Yu, H. Zhao, D. J. Orlicky, D. C. Thompson, V. Vasiliou (2017) Transcriptomic analysis and plasma metabolomics in Aldh16a1-null mice reveals a potential role of ALDH16A1 in renal function. Chem Biol Interact.
 M. I. Klein, D. F. Stern, H. Zhao (2017) GRAPE: A pathway template method to characterize tissue-specific functionality from gene expression profiles. BMC Bioinformatics, 18: 317.
 X. Yan, A. Liang, J. Gomez, L. Cohn, H. Zhao, G. L. Chupp (2017) A novel pathway-based distance score enhances assessment of disease heterogeneity in gene expression. BMC Bioinformatics, 18: 309.
 M. Goffredo, N. Santoro, D. TricÚ, C. Giannini, E. D'Adamo, H. Zhao, G. Peng, X. Yu, T. T. Lam, B. Pierpont, S. Caprio, R. I. Herzog (2017) A branched-chain amino acid-related metabolic signature characterizes obese adolescents with non-alcoholic fatty liver disease. Nutrients, 9, 642.
 Y. Hu, Q. Lu, W. Liu, Y. Zhang, M. Li, H. Zhao (2017) Joint modeling of genetically correlated diseases and functional annotations increases accuracy of polygenic risk prediction. PLOS Genetics, 13: e1006836.
 Y. Hu, Q. Lu, R. Powles, X. Yao, C. Yang, F. Fang, X. Xu, H. Zhao (2017) Leveraging functional annotations in genetic risk prediction for human complex diseases. PLOS Computational Biology, 13: e1005589.
 C. A. Fragoso, M. Moreno, Z. Wang, C. Heffelfinger, L. J. Arbelaez, J. A. Aguirre, N. Franco, L. E. Romero, K. Labadie, H. Zhao, S. L. Dellaporta, M. Lorieux (2017) Genetic architecture of a rice nested association mapping population. G3: Genes, Genomes, Genetics, 7: 1913-1926.
 J. Sun, J. Warren, H. Zhao (2017) A Bayesian semiparametric factor analysis model for subtype identification. Statistical Application in Genetics and Molecular Biology, 16: 145-158.
 Y. Zhang, Z. Ouyang, H. Zhao (2017) A statistical framework for data integration through graphical models with application to cancer genomics. Annals of Applied Statistics, 11: 161-184.
 R. Zhu, Y.-Q. Zhao, G. Chen, S. Ma, H. Zhao (2017) Greedy outcome weighted tree learning of optimal personalized treatment rules. Biometrics, 73: 391-400.
 R. Polimanti, H. Zhang, A. H. Smith, H. Zhao, L. A. Farrer, H. R. Kranzler, J. Gelernter (2017) Genome-wide association study of body mass index in subjects with alcohol dependence. Addiction Biology, 22: 535-549.
 A. C. Justice, K. A. McGinnis, J. Tate, K. Xu, W. C. Becker, H. Zhao, J. Gelernter, H. R. Kranzler (2017) Validating harmful alcohol use as a phenotype for genetic discovery using phosphatidylethanol and a polymorphism in ADH1B. Alcoholism: Clinical and Experimental Research, 41: 998-1003.
 A. Adkins, L. Hack, T. Bigdeli, V. Williamson, G. McMichael, M. Mamdani, A. Edwards, F. Aliev, R. Chan, P. Bhandari, R. Rabbe, J. Alaimo, G. Blackwell, A. Moscati, R. Poland, B. Rood, D. Patterson, D. Walsh, of Alcohol Dependence, Collaborative Study of the Genetics; J. Whitfield, G. Zhu, G. Montgomery, A. Henders, N. Martin, A. Heath, P. Madden, J. Frank, M. Ridinger, N. Wodarz, M. Soyka, P. Zill, M. Ising, M. NŲthen, F. Kiefer, M. Rietschel, of Addiction Consortium, The German Study of the Genetics; J. Gelernter, R. Sherva, R. Koesterer, L. Almasy, H. Zhao, H. Kranzler, L. Farrer, B. Maher, C. Prescott, D. Dick, S.-A. Bacanu, L. Mathies, A. Davies, V. Vladimirov, M. Grotewiel, M. Bowers, J. Bettinger, B. Webb, M. Miles, K. Kendler, B. Riley (2017) Genomewide Association Study of Alcohol Dependence Identifies Risk Loci Altering Ethanol-response Behaviors in Model Organisms. Alcoholism: Clinical and Experimental Research, 41: 911-928.
 D. Chung, H. J. Kim, H. Zhao (2017) graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture. PLOS Computational Biology, 13: e1005388.
 R. Polimanti, H. Zhao, H. Kranzler, J. Gelernter (2017) S100A10 identified in a genome-wide gene-by-cannabis dependence interaction analysis of risky sexual behaviors. Journal of Psychiatry and Neuroscience, 42: 160189.
 B. Zhao, Q. Lu, Y. Cheng, J. M. Belcher, E. D. Siew, D. E. Leaf, S. C. Body, A. A. Fox, S. W. Waikar, C. D. Collard, H. Thiessen-Philbrook, T. Alp Ikizler, L. B. Ware, C. Edelstein, A. X. Garg, M. Choi, J. Schaub, H. Zhao, R. P. Lifton, C. R. Parikh for the TRIBE-AKI Consortium (2017) A genome-wide association study to identify single nucleotide polymorphisms for acute kidney injury. American Journal of Respiratory and Critical Care Medicine, 195: 482-490.
 R. Polimanti, Q. Wang, S. Meda, K. Patel, G. Pearlson, H. Zhao, L. Farrer, H. Kranzler, J. Gelernter (2017) The interplay between risky sexual behaviors and alcohol dependence: genome-wide association and neuroimaging support for LHPP as a risk gene. Neuropsychopharmacology, 42: 598-605.
 Q. Wang, R. Polimanti, H. R. Kranzler, L. A. Farrer, H. Zhao, J. Gelernter (2017) Genetic factor common to schizophrenia and HIV infection is associated with risky sexual behavior. Human Genetics, 136: 75-83.
 C. Heit, S. Marshall, S. Singh, X. Yu, G. Charkoftaki, H. Zhao, D. J. Orlicky, K. S. Fritz, D. C. Thompson, V. Vasiliou (2017) Catalase deletion promotes prediabetic phenotype in mice. Free Radic Biol Med 103: 48-56.
 F. Hong, S. M. Rachidi, D. Lundgren, D. Han, X. Huang, H. Zhao, Y. Kimura, H. Hirano, O. Ohara, H. Udono, S. Meng, B. Liu, Z. Li (2017) Mapping the client network of a major mammalian endoplasmic reticulum heat shock protein 90 reveals its roles in innate immunity, Wnt signaling and organ development. PLOS One, 12: e0169260
 L. Hou, N. Sun, S. Mane, F. Sayward, N. Rajeevan, K.-H. Cheung, K. Cho, S. Pyarajan, M. Aslan, P. Miller, P. D. Harvey, J. M. Gaziano, J. Concato, H. Zhao (2017) Impacts of genotyping errors on statistical power of association tests in genomic analyses: a case study. Genetic Epidemiology, 41: 152-162.
 K. Lee, B. Li, H. Zhao (2016) On an additive partial correlation operator and nonparametric estimation of graphical models. Biometrika, 103: 513-530.
 Z. Lin, C. Yang, Y. Zhu, J. C. Duchi, Y. Fu, Y. Wang, B. Jiang, M. Zamanighomi, X. Xu, M. Li, N. Sestan, H. Zhao, W. H. Wong (2016) AC-PCA: simultaneous dimension reduction and adjustment for confounding variation. Proceedings of the National Academy of Sciences, 113: 14662-14667.
 R. Zhu, Q. Zhao, H. Zhao, S. Ma (2016) Integrating multidimensional omics data for cancer outcome. Biostatistics, 17: 605-618.
 Y. Hu, H. Zhao (2016) CCor: a whole genome network-based similarity measure between two genes. Biometrics, 72: 1216-1225.
 Y. Liu, H. Zhao (2016) Predicting synergistic effects between compounds through their structural similarity and effects on transcriptomes. Bioinformatics, Bioinformatics, 32: 3782-3789.
 A. T. Timberlake, J. Choi, S. Zaidi, Q. Lu, C. Nelson-Williams, E. D. Brooks, K. Bilguvar, I. Tikhonova, S. Mane, J. F. Yang, R. Sawh-Martinez, S. Persing, E. G. Zellner, E. Loring, C. Chuang, A. Galm, P. W. Hashim, D. M. Steinbacher, M. L. DiLuna, C. C. Duncan, K. A. Pelphrey, H. Zhao, J. A. Persing, R. P. Lifton (2016) Digenic inheritance of non-syndromic midline craniosynostosis via rare SMAD6 and common BMP2 alleles. eLife, 5: e20125.
 K. Dong, H. Zhao, T. Tong, X. Wan (2016) NBLDA: Negative Binomial Linear Discriminant Analysis for RNA-Seq Data. BMC Bioinformatics, 17: 369.
 K. Lee, B. Li, H. Zhao (2016) Variable selection via additive conditional independence. Journal of the Royal Statistical Society - Series B, 78: 1037-1055.
 R. Polimanti, B. Z. Yang, H. Zhao, J. Gelernter (2016) Evidence of polygenic adaptation in the systems genetics of anthropometric traits. PLOS One, 11: e0160654.
 L. S. Chuang, N. Villaverde, K. Y. Hui, A. Mortha, A. Rahman, A. P. Levine, T. Haritunians, S. M. Ng, W. Zhang, N. Y. Hsu, J. A. Facey, T. Luong, H. Fernandez-Hernandez, D. Li, M. Rivas, E. R. Schiff, A. Gusev, L. P. Schumm, B. M. Bowen, Y. Sharma, K. Ning, R. Remark, S. Gnjatic, P. Legnani, J. George, B. E. Sands, J. M. Stempak, L. W. Datta, S. Lipka, S. Katz, A. S. Cheifetz, N. Barzilai, N. Pontikos, C. Abraham, M. J. Dubinsky, S. Targan, K. Taylor, J. I. Rotter, E. J. Scherl, R. J. Desnick, M. T. Abreu, H. Zhao, G. Atzmon, I. Pe'er, S. Kugathasan, H. Hakonarson, J. L. McCauley, T. Lencz, A. Darvasi, V. Plagnol, M. S. Silverberg, A. M. Muise, S. R. Brant, M. J. Daly, A. W. Segal, R. H. Duerr, M. Merad, D. P. McGovern, I. Peter, J. H. Cho (2016) A Frameshift in CSF2RB predominant among Ashkenazi Jews increases risk for Crohn's disease and reduces monocyte signaling via GMCSF. Gastroenterology. pii: S0016-5085(16): 34717-34725.
 N. Li, L. Subrahmanyan, E. Smith E, X. Yu, S. Zaidi, M. Choi, S. Mane, C. Nelson-Williams, M. Bahjati, M. Kazemi, M. Hashemi, M. Fathzadeh, A. Narayanan, L. Tian, F. Montazeri, M. Mani, M. L. Begleiter, B. G. Coon, H. T. Lynch, E. N. Olson, H. Zhao, J. Ruland, R. P. Lifton, A. Mani (2016) Mutations in the Histone Modifier PRDM6 Are Associated with Isolated Nonsyndromic Patent Ductus Arteriosus. Am J Hum Genet, 98: 1082-1091.
 Z. Xie, D. Zhang, D. Chung, Z. Tang, H. Huang, L. Dai, S. Qi, J. Li, G. Colak, Y. Chen, C. Xia, C. Peng, H. Ruan, M. Kirkey, D. Wang, L. M. Jensen, S. D. Pletcher, M. Tan, D. B. Lombard, K. P. White, H. Zhao, J. Li, R. G. Roeder, X. Yang, Y. Zhao (2016) Metabolic regulation of gene expression by histone lysine ÔĀĘ-hydroxybutyrylation. Molecular Cell, 62: 194-206.
 J. Liu, C. Yang, X. Shi, C. Li, J. Huang, H. Zhao, Shuangge Ma (2016) Analyzing association mapping in pedigree-based GWAS using a penalized multi-trait mixed model. Genetic Epidemiology, 40: 382-393.
 Q. Lu, R. Powles, Q. Wang, J. He, H. Zhao (2016) Integrative tissue-specific functional annotations in the human genome provide novel insights on many complex traits and improve signal prioritization in genome wide association studies. PLOS Genetics, 12: e1005947.
 G. Ryslik, Y. Cheng, Y. Modis. H. Zhao (2016) Leveraging protein quaternary structure to identify oncogenic driver mutations. BMC Bioinformatics, 17: 137.
 Z. Lin, M. Li, N. Sestan, H. Zhao (2016) A Markov Random Field-based approach for joint estimation of differentially expressed genes in mouse transcriptome data. Statistical Applications in Molecular Biology and Genetics, 15: 139-150.
 M. Chen. H. Lin, H. Zhao (2016) Change point analysis of histone modifications reveals epidenteic blocks with distinct regulatory activity and biological functions. Annals of Applied Statistics, 10: 506-526.
 R. Sherva, Q. Wang, H. Kranzler, H. Zhao, R. Koesterer, A. Herman, L. Farrer, J. Gelernter (2016) Genome wide association study of cannabis dependence severity reveals novel risk variants, genes previously implicated in schizophrenia risk, and shared risk with major depressive disorder. JAMA Psychiatry, 73: 472-480.
 X. Huang, D. Stern, H. Zhao (2016) Transcriptional profiles from paired normal samples offer complementary information on cancer patient survival -- Evidence from TCGA Pan-Cancer Data. Scientific Reports, 6: 20567.
 M. Goffredo, S. Caprio, A. Feldstein, E. D‚ÄôAdamo, M. M. Shaw, B. Pierpont, M. Savoye, H. Zhao, A. E. Bale, N. Santoro (2016) Role of the TM6SF2 rs58542926 in the pathogenesis of pediatric fatty liver disease (NAFLD): a multiethnic study. Hepatology, 63: 117-125.
 P. Harvey, M. Aslan, M. Du, H. Zhao, L. Siever, A. Pulver, J. M. Gaziano, J. Concato (2016) Factor structure of cognition and functional capacity in two studies of schizophrenia and bipolar disorder: Implications for genomic studies. Neuropsychology, 30: 28-39.
 C. A. Fragoso, C. Heffelfinger, H. Zhao, S. L. Dellaporta (2016) Imputing genotypes in biallelic populations from low-coverage sequence data. Genetics, 202: 487-495.
 F. Wang, H. Xu, H. Zhao, J. Gelernter, H. Zhang (2016) DNA co-methylation modules in postmortem prefrontal cortex tissues of European Australians with alcohol use disorders. Scientific Reports, 6: 19430.
 J. Jiang, C. Li, D. Paul, C. Yang, H. Zhao (2016) On high-dimensional misspecified mixed model analysis in genome-wide association study. Annals of Statistics, 44: 2127‚Äď2160.
 Q. Lu, X. Yao, Y. Hu, H. Zhao (2016) GenoWAP: GWAS signal prioritization through integrated analysis of genomic functional annotation. Bioinformatics, 32: 542-548.
 T. Wang, M. Chen, H. Zhao (2016) Estimating DNA methylation levels by joint modeling of multiple methylation profiles from microarray data. Biometrics, 72: 354-363.
 M. Chen, C. Gao, H. Zhao (2016) Posterior contraction rates of the phylogenetic Indian buffet processes. Bayesian Analysis, 11: 477-497.
 C. Li, C. Yang, G. Hather, R. Liu, H. Zhao (2016) Efficient drug-pathway association analysis via integrative penalized matrix decomposition. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 13: 531-540.
 M. Chen, Z. Ren, H. Zhao, H. Zhou (2015) Asymptotically normal and efficient estimation of covariate-adjusted Gaussian graphical model. Journal of American Statistical Association, 111: 394-406.
 G. Li, H. Zhao (2015) M3-S: a genotype calling method incorporating information from samples with known genotypes. BMC Bioinformatics, 16:403.
 G. Li, Y. Cui, H. Zhao (2015) An Empirical Bayes risk prediction model using multiple traits for sequencing data. Statistical Applications in Genetics and Molecular Biology, 14: 551-573.
 H. Fang, C. Huang, H. Zhao, M. Deng (2015) CCLasso: Correlation inference for compositional data through Lasso. Bioinformatics, 31: 3172-3180.
 R. Polimanti, C. Yang, H. Zhao, J. Gelernter (2015) Dissecting ancestry genomic background in substance dependence genome-wide association studies. Pharmacogenomics, 16: 1487-1498.
 Q. Wang, C. Yang, J. Gelernter, H. Zhao (2015) Pervasive pleiotropy between psychiatric disorders and immune disorders revealed by integrative analysis of multiple GWAS. Human Genetics, 134: 1195-1209.
 L. Zuo, C. K Zhang, F. G. Sayward, K.-H. Cheung, K. Wang, J. H Krystal, H. Zhao, X. Luo (2015) Gene-based and pathway-based genome-wide association study of alcohol dependence. Shanghai Archives of Psychiatry, 27: 111-118.
 Y. Xie, Y. Jin, B. L. Merenick, M. Ding, K. M. Fetalvero, R. J. Wagner, A. Mai, S. Gleim, D. Tucker, M. J. Birnbaum, B. A. Ballif, A. K. Luciano, W. C. Sessa, E. M. Rzucidlo, R. J. Powell, L. Hou, H. Zhao, J. Yu, J. Hwa, K. A. Martin (2015) Phosphorylation of GATA-6 is required for vascular smooth muscle cell differentiation after mTORC1 inhibition. Science Signaling, 8(376): ra44.
 Q. Lu, Y. Hu, J. Sun, Y. Cheng, K.-H. Cheung, H. Zhao (2015) A statistical framework to predict functional non-coding regions in the human genome through integrated analysis of annotation data. Scientific Reports, 5: 10576.
 P. Goyette, G. Boucher, D. Mallon, E. Ellinghaus, L. Jostins, H. Huang, S. Ripke, E. S. Gusareva, V. Annese, S. L. Hauser, J. R. Oksenberg, I. Thomsen, S. Leslie; International Inflammatory Bowel Disease Genetics Consortium; Australia and New Zealand IBDGC; Belgium IBD Genetics Consortium; Italian Group for IBD Genetics Consortium; NIDDK Inflammatory Bowel Disease Genetics Consortium; United Kingdom IBDGC; Wellcome Trust Case Control Consortium; Quebec IBD Genetics Consortium, M. J. Daly, K. Van Steen, R. H. Duerr, J. C. Barrett, D. P. McGovern, L. P. Schumm, J. A. Traherne, M. N. Carrington, V. Kosmoliaptsis, T. H. Karlsen, A. Franke, J. D. Rioux (2015) High-density mapping of the MHC identifies a shared role for HLA-DRB1*01:03 in inflammatory bowel diseases and heterozygous advantage in ulcerative colitis. Nature Genetics, 47: 172-179.
 K. Xu, H. R. Kranzler, R. Sherva, C. E. Sartor, L. Almasy, R. Koesterer, H. Zhao, L. A. Farrer, J. Gelernter (2015) Genome-wide association study for maximum number of alcohol drinks in European Americans and African Americans. Alcoholism: Clinical and Experimental Research, 39: 1137-1147.
 G. Stefani, X. Chen, H. Zhao, F. J. Slack (2015) A novel mechanism of LIN-28 regulation of let-7 microRNA expression revealed by in vivo HITS-CLIP in C. elegans. RNA, 21: 985-996.
 X. Yan, J.-H. Chu, J. Gomez, M. Koenigs, C. Holm, X. He, M. F. Perez, H. Zhao, S. Mane, F. D. Martinez, C. Ober, D. L. Nicolae, K. C. Barnes, S. J. London, F. Gilliland, S. T. Weiss, B. A. Raby, L. Cohn, G. L. Chupp (2015) Non-invasive analysis of the sputum transcriptome discriminates clinical phenotypes of asthma. American Journal of Respiratory and Critical Care Medicine, 191(10):1116-1125.
 B. R. Evans, A. Gloria-Soria, L. Hou, C. McBride, M. Bonizzoni, H. Zhao, J. R. Powell (2015) A multipurpose high throughput SNP chip for the dengue and yellow fever mosquito, Aedes aegypti. G3 g3.114.016196.
 W. Lam, Z. Jiang, F. Guan, X. Huang, R. Hu, J. Wang, S. Bussom, S.-H. Liu, H. Zhao, Y. Yen, Y.-C. Cheng (2015) PHY906(KD018), an adjuvant based on a 1800-year-old Chinese medicine, enhanced the anti-tumor activity of Sorafenib by changing the tumor microenvironment. Scientific Reports, 5: 9384.
 A. M. B. Tadeu, S. Lin, L. Hou, L. Chung, M. Zhong, H. Zhao, V. Horsley (2015) Transcriptional profiling of ectoderm specification to keratinocyte fate in human embryonic stem cells. PLOS One, 10: e0122493.
 Z. Lin, S. Sanders, M. Li, N. Sestan, M. State, H. Zhao (2015) A Markov random field-based approach to characterizing human brain development using spatial-temporal transcriptome data. Annals of Applied Statistics, 9: 429‚Äď451.
 S. Zhang, H. Zhao, M. K. Ng (2015) Functional module analysis for¬ gene coexpression networks with network integration. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 12: 1146 ‚Äď 1160.
 C. Zheng, C. D. Man, C. Cobelli, L. Groop, H. Zhao, A. E. Bale, M. Shaw, E. Duran, B. Pierpont, S. Caprio, N. Santoro (2015) A common variant in the MTNR1B gene is associated with increased risk of impaired fasting glucose (IFG) in obese youth. Obesity, 23: 1022-1029.
 E. F. Foxman, J. A. Storer, K. Vanaja, B. R. Wasik, L. Hou, H. Zhao, P. E. Turner, A. Levchenko, A. Iwasaki (2015) Temperature-dependent innate defense against the common cold virus limits viral replication at warm temperature in mouse airway cells. Proc Natl Acad Sci USA, 112: 827-32.
 J. Sun, H. Zhao (2015) The application of sparse estimation of covariance matrix to quadratic discriminant analysis. BMC Bioinformatics, 16:48.
 H. Chun, X. Zhang, H. Zhao (2015) Gene regulation network inference with joint sparse Gaussian graphical models. Journal of Computational and Graphical Statistics, 24: 954‚Äď974.
 X. Qi, R. Luo, R. Carroll, H. Zhao (2015) Sparse regression by projection and sparse discriminant analysis. Journal of Computational and Graphical Statistics, 24: 416-438.
 H. Pang, I. Kim. H. Zhao (2015) Random effects model for multiple pathway analysis with applications to type II diabetes microarray data. Statistics in Biosciences, 7: 167‚Äď186.
 X. Chen, T. Paranjape, C. Stahlhut, T. McVeigh, F. Keane, S. Nallur, N. Miller, M. Kerin, Y. Deng, X. Yao, H. Zhao, J. Weidhaas, F. Slack (2015) Targeted resequencing of the microRNAome and 3'UTRome reveals functional germline DNA variants with altered prevalence in epithelial ovarian cancer. Oncogene, 34: 2125-2137.
 X. Chen, D. Chung, G. Stefani, F. J. Slack, H. Zhao (2015) Statistical issues in binding site identification through CLIP-seq. Statistics and Its Interface, 8: 419‚Äď436.
 J. Gelernter, H. R. Kranzler, R. Sherva, L. Almasy, A. I. Herman, R. Koesterer, H. Zhao, L. A. Farrer (2015) Genomewide association study of nicotine dependence in American populations: identification of novel risk loci in both African- and European-Americans. Biological Psychiatry, 77: 493-503.
 D. Li, H. Zhao, H. R. Kranzler, M. D. Li, K. P. Jensen, T. Zayats, L. A. Farrer, J. Gelernter (2015) Genome-wide association study of copy number variations (CNVs) with opioid dependence. Neuropsychopharmacology, 40: 1016-1026.
 C. Heffelfinger, C. A. Fragoso, M. A. Moreno, J. D. Overton, J. P. Mottinger, H. Zhao, J. Tohme, S. L. Dellaporta (2014) Flexible and scalable genotyping-by-sequencing strategies for population studies. BMC Genomics 15: 979.
 D. Chung, C. Yang, C. Li, J. Gelernter, H. Zhao (2014) GPA: A statistical approach to prioritizing GWAS results by integrating pleiotropy and annotation. PLOS Genetics, 10: e1004787.
 J. E. Gallagher, W. Zheng, X. Rong, N. Miranda, Z. Lin, B. Dunn, H. Zhao, M. P. Snyder (2014) Divergence in a master variator generates distinct phenotypes and transcriptional responses. Genes Dev 28: 409-421.
 H. Pang, H. Zhao (2014) Stratified pathway analysis for heterogeneity among the samples. Cancer Informatics, 13(Suppl 4): 73-78.
 L. Hou, T. Ma, H. Zhao (2014) Incorporating functional annotation information in prioritizing disease associated SNPs from genome wide association studies. Science China Life Sciences, 57: 1072-1079.
 R. D. Beech, J. J. Leffert, A. Lin, K. A. Hong, J. Hansen, S. Umlauf, S. Mane, H. Zhao, R. Sinha (2014) Stress-related alcohol consumption in heavy drinkers correlates with expression of miR-10a, miR-21 and components of the TAR-RNA binding protein (TRBP)-associated complex. Alcoholism: Clinical and Experimental Research, 38: 2743-2753.
 H. Zhang, F. Wang, J. Liu, H. Zhao, J. Gelernter (2014) Differentially co-expressed genes in postmortem prefrontal cortex tissues of individuals with alcohol use disorders. Human Genetics, 133: 1383-1394.
 D. Della-Morte, L. Wang, A. Beecham, S. H. Blanton, H. Zhao, R. L. Sacco, T. Rundek, C. Dong (2014) Novel genetic variants modify the effect of smoking on carotid plaque burden in Hispanics. J Neurol Sci, 344: 27-31.
 P. D. Harvey, L. J. Siever, G. D. Huang, S. Muralidhar, H. Zhao, P. Miller, M. Aslan, S. Mane, M. McNamara, T. Gleason, M. Brophy, R. Przygodszki, T. J. O‚ÄôLeary, M. Gaziano, J. Concato (2014) The genetics of functional disability in schizophrenia and bipolar illness: Methods and initial results for VA cooperative study #572. Am J Med Genet B Neuropsychiatr Genet 165: 381-389.
 G. A. Ryslik, Y. Cheng, K.-H. Cheung, R. D. Bjornson, D. Zelterman, Y. Modis, H. Zhao (2014) A spatial simulation approach to account for protein structure when identifying non-random somatic mutations. BMC Bioinformatics, 15: 231.
 H. Zhang, F. Wang, C. Yang, H. Xu, Z. Wang, H. Zhao, J. Gelernter (2014) Identification of methylation quantitative trait loci (mQTLs) influencing DNA methylation in the promoter regions of alcohol dependence risk genes. Human Genetics, 133: 1093-1104.
 S. A. Nish, D. Schenten, T. Wunderlich, S. D. Pope, Y. Gao, N. Hoshi, S. Yu, X. Yan, H. K. Lee, L. Pasman, I. Brodsky, B. Yordy, H. Zhao, J. Br√ľning, R. Medzhitov (2014) T cell-intrinsic role of IL-6 signaling in primary and memory responses. Elife. 2014 May 19:e01949.
 L. Chung, C. Colangelo, H. Zhao (2014) Data pre-processing for label-free multiple reaction monitoring (MRM) experiments. Biology, 3: 383-402.
 J. Gelernter, H. R. Kranzler, R. Sherva, R. Koesterer, L. Almasy, H. Zhao, L. A. Farrer LA (2014) Genome-wide association study of opioid dependence: multiple associations mapped to calcium and potassium pathways. Biol Psychiatry, 76: 66-74.
 C. Giannini, C. D. Man, L. Groop, C. Cobelli, H. Zhao, M. M. Shaw, E. Duran, B. Pierpont, A. E. Bale, S. Caprio, N. Santoro (2014) The co-occurrence of risk alleles in or near genes modulating insulin secretion predisposes obese youth to prediabetes. Diabetes Care, 37: 475-482.
 J. Gelernter, R. Sherva, R. Koesterer, L. Almasy, H. Zhao, H. R. Kranzler, L. Farrer (2014) Genome-wide association study of cocaine dependence and related traits: FAM53B identified as a risk gene. Mol Psychiatry, 19: 41-49.
 D. N. Assis, L. Leng, X. Du, C. K. Zhang, G. Grieb, M. Merk, A. B. Garcia, C. McCrann, J. Chapiro, A. Meinhardt, Y. Mizue, D. J. Nikolic-Paterson, J. Bernhagen, M. M. Kaplan, H. Zhao, J. L. Boyer, R. Bucala (2014) The role of macrophage migration inhibitory factor (MIF) in autoimmune liver disease. Hepatology, 59: 580-591.
 P. Xie, H. R. Kranzler, J. H. Krystal, L. A. Farrer, H. Zhao, J. Gelernter (2014) Deep resequencing of 17 glutamate system genes identifies rare variants in DISC1 and GRIN2B affecting risk of opioid dependence. Addict Biol, 19: 955-964.
 A. R. Gupta, M. Pirruccello, F. Cheng, H. J. Kang, T. V. Fernandez, J. M. Baskin, M. Choi, L. Liu, A. G. Ercan-Sencicek, J. D. Murdoch, L. Klei, B. M. Neale, D. Franjic, M. J. Daly, R. P. Lifton, P. De Camilli, H. Zhao, N. Sestan, M. W. State (2014) Rare deleterious mutations of the gene EFR3A in autism spectrum disorders. Molecular Autism, 5:31.
 G. A. Ryslik, Y. Cheng, K.-H. Cheung, Y. Modis, H. Zhao (2014) A graph theoretic approach to utilizing protein structure to identify non-random somatic mutations. BMC Bioinformatics, 15: 86.
 Brownstein et al. (2014) An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome Biology, 15: R53.
 R. Zhu, H. Zhao, S. Ma (2014) Identifying gene-environment and gene-gene interactions using a progressive penalization approach. Genetic Epidemiology, 38:353-368.
 Z. Wu, Y. Sun, S. He, J. Cho, H. Zhao, J. Jin (2014) Detection boundary and higher criticism approach for rare and weak genetic effects. Annals of Applied Statistics, 8: 824-851.
 D. Schenten, S. A. Nish, S. Yu, X. Yan, H. K. Lee, I. Brodsky, L. Pasman, B. Yordy, F. T. Wunderlich, J. C. Br√ľning, H. Zhao, R. Medzhitov (2014) Signaling through the Adaptor Molecule MyD88 in CD4(+) T Cells Is Required to Overcome Suppression by Regulatory T Cells. Immunity 40: 78-90.
 M. Kim, X. Chen, L. Chin, T. Paranjape, W. Speed, K. K. Kidd, H. Zhao, J. B. Weidhaas, F. J. Slack FJ (2014) Extensive sequence variation in the 3‚Ä≤ untranslated region of the KRAS gene in lung and ovarian cancer cases. Cell Cycle, 13: 1030-1040.
 F. Xu, L. Li, P. V. Schulz, G. P. Gallagher, B. Xiang, H. Zhao, P. Li (2014) Cytogenomic mapping and bioinformatic mining reveal interacting brain expressed genes for intellectual disability. Molecular Cytogenetics, 7:4.
 B. Li, H. Chun, H. Zhao (2014) On an additive semi-graphoid model for statistical networks with application to pathway analysis. Journal of American Statistical Association, 109: 1188-1204.
 L. Hou, M. Chen, C. K. Zhang, J. Cho, H. Zhao (2014) Guilt by Rewiring: Gene prioritization through network rewiring in genome wide association studies. Human Molecular Genetics, 23: 2780-2790.
 D. Li, A. Sulovari, C. Cheng, H. Zhao, H. R. Kranzler, J. Gelernter (2014) Association of gamma-aminobutyric acid A receptor őĪ2 gene (GABRA2) with alcohol use disorder. Neuropsychopharmacology, 39: 907-918.
 J. E. Brown, B. R. Evans, W. Zheng, V. Obas, L. Barrera-Martinez, A. Egizi, H. Zhao, A. Caccone, J. R. Powell (2014) Human impacts have shaped historical and recent evolution in aedes aegypti, the Dengue and Yellow Fever mosquito. Evolution, 68: 514-525.
 L. Wang, T. Rundek, A. Beecham, B. Hudson, S. H. Blanton, H. Zhao, R. L. Sacco, C. Dong (2014) Genome-wide interaction study identifies RCBTB1 as a modifier for smoking effect on carotid intima-media thickness. Arterioscler Thromb Vasc Biol, 34: 219-225.
 C. Li, C. Yang, J. Gelernter, H. Zhao (2014) Improving genetic risk prediction by leveraging pleiotropy. Human Genetics, 133: 639-650.
 C. Yang, C. Li, H. R. Kranzler, L. A. Farrer, H. Zhao, J. Gelernter (2014) Exploring the genetic architecture of alcohol dependence in African-Americans via analysis of a genomewide set of common variants. Human Genetics, 133: 617-624.
 R. D. Beech, J. J. Leffert, A. Lin, L. G. Sylvia, S. Umlauf, S. Mane, H. Zhao, C. Bowden, J. R. Calabrese, E. S. Friedman, T. A. Ketter, D. V. Iosifescu, N. A. Reilly-Harrington, M. Ostacher, M. E. Thase, A. Nierenberg (2014) Gene-expression differences in peripheral blood between lithium responders and non-responders in the Lithium Treatment-Moderate dose Use Study (LiTMUS). Pharmacogenomics J., 14: 182-191.
 S. Oh, S. Song, G. Grabowski, H. Zhao, J. P. Noonan (2013) Time series expression analyses using RNA-seq: A statistical approach. BioMed Research International, 2013: 203681.
 M. Chen, M. Gunel, H. Zhao (2013) SomatiCA: Identifying, Characterizing and Quantifying Somatic Copy Number Aberrations from Cancer Genome Sequencing Data. PLoS One, 8: e78143.
 S. Han, B-Z Yang, H. R. Kranzler, X. Liu, H. Zhao, L. A. Farrer, E. Boerwinkle, J. Potash, J. Gelernter (2013) Integrating GWAS and human protein interaction network identifies a gene sub-network underlying alcohol dependence. Am J Hum Genet, 93: 1027-1034.
 W. D. Li, H. Jiao, K. Wang, C. K. Zhang, J. T. Glessner, S. F. Grant, H. Zhao, H. Hakonarson, A. R. Price (2013) A genome wide association study of plasma uric acid levels in obese cases and never-overweight controls. Obesity, 21: E490-494.
 S. Zhang, H. Zhao (2013) Normalized modularity optimization method for community identification with degree adjustment. Physical Review E, 88, 052802
 W. Chen, C. K. Zhang, Y. Cheng, S. Zhang, H. Zhao (2013) A comparison of methods for clustering 16S rRNA sequences into OTUs. PLoS One, 8: e70837
 W. Chen, Y. Cheng, C. Zhang, S. Zhang, H. Zhao (2013) MSClust: A Multi-Seeds based Clustering algorithm for microbiome profiling using 16S rRNA sequence. Journal of Microbiological Methods, 94: 347-355.
 H. Zhu, F. Hu, H. Zhao (2013) Adaptive clinical trial designs to detect interaction between treatment and a dichotomous biomarker. Canadian Journal of Statistics, 41: 525-539.
 J. Gelernter, H. R. Kranzler, R. Sherva, L. Almasy, R. Koesterer, A. H. Smith, R. Anton, U. W. Preuss, M. Ridinger, D. Rujescu, N. Wodarz, P. Zill, H. Zhao, L. A. Farrer (2013) Genome-wide association study of alcohol dependence: significant findings in African- and European-Americans including novel risk loci. Mol Psychiatry, 19: 41-49.
 Y. Gao, S. A. Nish, R. Jiang, L. Hou, P. Licona-Lim√≥n, J. S. Weinstein, H. Zhao, R. Medzhitov (2013) Control of T helper 2 responses by transcription factor IRF4-dependent dendritic cells. Immunity, 39: 722-732.
 F. Qian, L. Chung, W. Zheng, V. Bruno, R. P. Alexander, Z. Wang, X. Wang, S. Kurscheid, H. Zhao, E. Fikrig, M. Gerstein, M. Snyder, R. R. Montgomery (2013) Identification of genes critical for resistance to infection by West Nile virus using RNA-Seq analysis. Viruses, 5: 1664-1681.
 H. Zhang, F. Wang, H. R. Kranzler, H. Zhao, J. Gelernter J (2013) Profiling of childhood adversity-associated DNA methylation changes in alcoholic patients and healthy controls. PLoS One, 8: e65648.
 X. Chen, F. J. Slack, H. Zhao (2013) Joint analysis of expression profiles from multiple cancers improves the identification of microRNA-gene interactions. Bioinformatics, 29: 2137-2145.
 G. A. Ryslik, Y. Cheng, K. H. Cheung, Y. Modis, H. Zhao (2013) Utilizing protein structure to identify non-random somatic mutations. BMC Bioinformatics, 14: 190.
 P. Xie, H. R. Kranzler, C. Yang, H. Zhao, L. A. Farrer, J. Gelernter (2013) Genome-wide association study identifies new susceptibility loci for posttraumatic stress disorder. Biol Psychiatry, 74: 656-663.
 J. P. Saxe, M. Chen, H. Zhao, H. Lin (2013) Tdrkh is essential for spermatogenesis and participates in primary piRNA biogenesis in the germline. EMBO J., 32: 1869-1885.
 C. K. Zhang, J. Hewett, J. Hemming, T. Grant, H. Zhao, C. Abraham, I. Oikonomou, M. Kanakia, J. H. Cho, D. D. Proctor (2013) The influence of depression on quality of life in patients with inflammatory bowel disease. Inflamm Bowel Dis., 19: 1732-1739.
 S. Zaidi, M. Choi, H. Wakimoto, L. Ma, J. Jiang, J. D. Overton, A. Romano-Adesman, R. D. Bjornson, R. E. Breitbart, K. K. Brown, N. J. Carriero, Y. H. Cheung, J. Deanfield, S. DePalma, K. A. Fakhro, J. Glessner, H. Hakonarson, M. J. Italia, J. R. Kaltman, J. Kaski, R. Kim, J. K. Kline, T. Lee, J. Leipzig, A. Lopez, S. M. Mane, L. E. Mitchell, J. W. Newburger, M. Parfenov, I. Pe'er, G. Porter, A. E. Roberts, R. Sachidanandam, S. J. Sanders, H. S. Seiden, M. W. State, S. Subramanian, I. R. Tikhonova, W. Wang, D. Warburton, P. S. White, I. A. Williams, H. Zhao, J. G. Seidman, M. Brueckner, W. K. Chung, B. D. Gelb, E. Goldmuntz, C. E. Seidman, R. P. Lifton (2013) De novo mutations in histone-modifying genes in congenital heart disease. Nature, 498: 220-223.
 W. Zhang, K. Y. Hui, A. Gusev, N. Warner, S. M. Ng, J. Ferguson, M. Choi, A. Burberry, C. Abraham, L. Mayer, R. J. Desnick, C. J. Cardinale, H. Hakonarson, M. Waterman, Y. Chowers, A. Karban, S. R. Brant, M. S. Silverberg, P. K. Gregersen, S. Katz, R. P. Lifton, H. Zhao, G. Nu√Īez, I. Pe'er, I. Peter, J. H. Cho (2013) Extended haplotype association study in Crohn's disease identifies a novel, Ashkenazi Jewish-specific missense mutation in the NF-őļB pathway gene, HEATR3. Genes Immun 14: 310-316.
 L. M. Chung, J. P. Ferguson, W. Zheng, F. Qian, V. Bruno, R. R. Montgomery, H. Zhao (2013) Differential expression analysis for paired RNA-Seq data. BMC Bioinformatics, 14: 110.
 W. Zheng, H. Zhao (2013) Studying the evolution of transcription factor binding events using multi-species ChIP-Seq data. Stat Appl Genet Mol Biol, 2013 12: 1-15.
 T. Tong, Z. Feng, J. S. Hilton, H. Zhao (2013) Estimating the proportion of true null hypotheses using the pattern of observed p-values. Journal of Applied Statistics, 40: 1949-1964.
 J. S. Lee, H. Zhao (2013) On estimation of allele frequencies via next-generation DNA resequencing with barcoding. Statistics in BioSciences, 5: 26-53.
 L. Wang, W. Zheng, H. Zhao, M. Deng (2013) Statistical analysis reveals co-expression patterns of many pairs of genes in yeast are jointly regulated by interacting loci. PLoS Genetics, 9: e1003414.
 C. Yang, L. Wang, S. Zhang, H. Zhao (2013) Accounting for non-genetic factors by low-rank representation and sparse regression for eQTL mapping. Bioinformatics, 29: 1026-1034.
 X. Wan, C. Yang, Q. Yang, H. Zhao, W. Yu (2013) The complete compositional epistasis detection in genome-wide association studies. BMC Genetics, 14:7.
 L. Wang, Y. Jiao, Y.¬ Huang, X. Liu, G.¬ Gibson, B.¬ Bennett, K.M.¬ Hamre, D. Li, H.¬ Zhao, J.¬ Gelernter, H.¬ Kranzler, L.¬ Farrer, L. Lu, R.¬ Williams, Y.¬ Wang,¬ W. Gu (2013) A critical evaluation of the transcription factor, Atf2, as a candidate modulator of alcohol preference in mouse and human populations. Genetics and Molecular Research, 12: 5992-6005.
 X. Wan, C. Yang, Q. Yang, H. Zhao, W. Yu (2013) HapBoost: A fast approach to boosting haplotype association analyses in genome-wide association studies. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10: 207-212.
 F. Qian, C. Bolen, C. Jing, X. Wang, W. Zheng, H. Zhao, E. Fikrig, R. Bruce, S. Kleinstein, R. Montgomery (2013) Impaired TLR3-mediated immune responses from macrophages of patients chronically infected with Hepatitis C virus. Clinical and Vaccine Immunology, 20: 146-155.
 X. Zhou, C. Yang, X. Wan, H. Zhao, W. Yu (2013) Multi-sample aCGH data analysis via total variation and spectral regularization. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10: 230-235.
 J. Ferguson, W. Wheeler, Y-P. Fu, L. Prokunina-Olsson, H. Zhao, J. Sampson (2013) Statistical tests for detecting associations with groups of genetic variants: generalization, evaluation, and implementation. European Journal of Human Genetics, 21: 680-686.
 I. Kim, H. Pang, H. Zhao (2013) Statistical properties on semiparametric regression for evaluating pathway effects. Journal of Statistical Planning and Inference 143: 745-763.
 J. Ferguson, C. Yang, J. Cho, H. Zhao (2013) Empirical Bayes correction for the winner's curse in genetic association studies. Genetic Epidemiology, 37: 60-68.
 X. Qi, H. Zhao (2013) Sparse principal component analysis by choice of norm. Journal of Multivariate Analysis, 114: 127-160. ¬
 H. Zhang, A. I. Herman, H. R. Kranzler, R. F. Anton, H. Zhao, W. Zheng, J. Gelernter (2013) Array-based profiling of DNA methylation changes associated with alcohol dependence. Alcoholism: Clinical and Experimental Research, 37 Suppl 1:E108-15.
 L. Jostins, S. Ripke, R. K. Weersma, R. H. Duerr, D. P. McGovern, K. Y. Hui, J. C. Lee, L. P. Schumm, Y. Sharma, C. A. Anderson, J. Essers, M. Mitrovic, K. Ning, I. Cleynen, E. Theatre, S. L. Spain, S. Raychaudhuri, P. Goyette, Z. Wei, C. Abraham, J. P. Achkar, T. Ahmad, L. Amininejad, A. N. Ananthakrishnan, V. Andersen, J. M. Andrews, L. Baidoo, T. Balschun, P. A. Bampton, A. Bitton, G. Boucher, S. Brand, C. B√ľning, A. Cohain, S. Cichon, M. D'Amato, D. De Jong, K. L. Devaney, M. Dubinsky, C. Edwards, D. Ellinghaus, L. R. Ferguson, D. Franchimont, K. Fransen, R. Gearry, M. Georges, C. Gieger, J. Glas, T. Haritunians, A. Hart, C. Hawkey, M. Hedl, X. Hu, T. H. Karlsen, L. Kupcinskas, S. Kugathasan, A. Latiano, D. Laukens, I. C. Lawrance, C. W. Lees, E. Louis, G. Mahy, J. Mansfield, A. R. Morgan, C. Mowat, W. Newman, O. Palmieri, C. Y. Ponsioen, U. Potocnik, N. J. Prescott, M. Regueiro, J. I. Rotter, R. K. Russell, J. D. Sanderson, M. Sans, J. Satsangi, S. Schreiber, L. A. Simms, J. Sventoraityte, S. R. Targan, K. D. Taylor, M. Tremelling, H. W. Verspaget, M. De Vos, C. Wijmenga, D. C. Wilson, J. Winkelmann, R. J. Xavier, S. Zeissig, B. Zhang, C. K. Zhang, H. Zhao; International IBD Genetics Consortium (IIBDGC), M. S. Silverberg, V. Annese, H. Hakonarson, S. R. Brant, G. Radford-Smith, C. G. Mathew, J. D. Rioux, E. E. Schadt, M. J. Daly, A. Franke, M. Parkes, S. Vermeire, J. C. Barrett, J. H. Cho (2012) Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature, 491: 119-124.
 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: 573-577.
 C. Ram√≠rez, Y. D√≠az-Toro, J. Tellez, T. M. Castilho, R. Rojas, N. A. Ettinger, I. Tikhonova, N. D. Alexander, L. Valderrama, J. Hager, M. E. Wilson, A. Lin, H. Zhao, N. G. Saravia, D. McMahon-Pratt (2012) Human Macrophage Response to L. (Viannia) panamensis: Microarray Evidence for an Early Inflammatory Response. PLoS Negl Trop Dis. 6: e1866.
 L. Lowthert, J. J. Leffert, A. Lin, S. Umlauf, K. Maloney, A. Muralidharan, B. Lorberg, S. Mane, H. Zhao, R. Sinha, Z. Bhagwagar, R. D. Beech (2012) Increased ratio of anti-apoptotic to pro-apoptotic Bcl2 gene-family members in lithium-responders one month after treatment initiation. Biology of Mood and Anxiety Disorders, 2:15.
 H. Ma, H. Zhao (2012) FacPad: Bayesian sparse factor modeling for the inference of pathways responsive to drug treatment. Bioinformatics, 28: 2662-2670.
 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, 126: 1695-1704.
 M. J. Stulberg, A. Lin, H. Zhao, S. A. Holley (2012) Crosstalk between Fgf and Wnt signaling in the zebrafish tailbud. Dev Biol, 369: 298-307.
 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.
 S. Zhang, H. Zhao (2012) Community identification in networks with unbalanced structure. Physical Review E, 85: 066114. ¬
 T. Yuen, J. Iqbal, L.-L. Zhu, L. Sun, A. Lin, H. Zhao, J. Liu, P. K. Mistry (2012) Disease-drug pairs revealed by computational genomic connectivity mapping on GBA1 deficient, Gaucher disease mice. Biochemical and Biophysical Research Communications, 422: 573-577.
 H. Ma, H. Zhao (2012) iFad: an integrative factor analysis model for drug-pathway association inference. Bioinformatics, 28: 1911-1918.
 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, 36: 549-560.
 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: 1361-1374.
 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, 36: 1487-1496.
 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.
 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: 420-425.
 C. K. Zhang, P. B. Stein, J. Liu, G. M. Pastores, Z. Wang, R. Yang, J. H. Cho, P. K. Gregersen, J. M. F. G. Aerts, H. Zhao, 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: 377-383.
 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: 733-740.
 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: 877-887.
 T. Tong, L. Chen, H. Zhao (2012) Improved mean estimation and its application to diagonal discriminant analysis. Bioinformatics, 28: 531-537.
 G. Li, J. Gelernter, H. R. Kranzler, H. Zhao (2012) M3: An improved SNP calling algorithm for Illumina BeadArray Data. Bioinformatics, 28: 358-365.
 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. Hum Genetics, 131: 725-737.
 Z. Wu, H. Zhao (2012) On model selection strategies to identify genes underlying binary traits using genome-wide association data. Statistica Sinica, 22: 1041-1074.
 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.
 I. Kim, H. Pang, H. Zhao (2012) Bayesian semiparametric regression models for evaluating pathway effects on clinical continuous and binary outcomes. Statistics in Medicine, 31: 1633-1651.
 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.
 B. Li, H. Chun, H. Zhao (2012) Sparse estimation of conditional graphical models with application to gene networks. Journal of American Statistical Association, 107: 152-167.
 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).
 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.
 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.
 W. Zheng, L. Chung, H. Zhao (2011) Bias detection and correction in RNA-sequencing data. BMC Bioinformatics, 12: 290.
 P. Xie, 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. Biological Psychiatry, 70: 528-536
 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.
 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.
 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.
 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.
 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.
 J. Sampson, K. K. Kidd, J. R. Kidd, H. Zhao (2011) Select SNPs to identify ancestry. Annals of Human Genetics, 75: 539-553.
 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.
 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.
 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.
 X. Chang, F. Liu, X. Wang, A. Lin, H. Zhao, B. Su (2011) The kinases MEKK2 and MEKK3 regulate transforming growth factor-ő≤-mediated helper T cell differentiation. Immunity, 34: 201-212.
 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.
 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.
 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.
 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.
 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.
 R. Luo, H. Zhao (2011) Bayesian hierarchical modeling for signaling pathway inference from single cell interventional data. Annals of Applied Statistics, 5: 725‚Äď745.
 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.
 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.
 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.
 N. Santoro, R. Kursawe, E. D‚ÄôAdamo, 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.
 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.
 D. Ballard, C. Abraham, J. Cho, H. Zhao (2010) Pathway analysis comparison using Crohn's disease GWAS. BMC Medical Genomics, 3, 25.
 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.
 J. X. Hu, H. Zhao, H. H. Zhou (2010) False discovery rate control with groups. Journal of American Statistical Association, 105: 1215‚Äď1227.
 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.
 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.
 H. Pang, D. Datta, H. Zhao (2010) Pathway analysis using random forests with bivariate node-split for survival outcomes. Bioinformatics, 26: 250-258.
 S. Huang, T. Tong, H. Zhao (2010) Bias-corrected diagonal discriminant rules for high-dimensional classification. Biometrics, 66: 1096-1106.
 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.
 J. Kang, J. Cho, H. Zhao (2010) Practical issues in building risk predicting models for complex diseases. Journal of Biopharmaceutical Statistics, 20: 415-440.
 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.
 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.
 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.
 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.
 Z. Wu, H. Zhao (2009) Statistical power of model selection strategies for genome-wide association studies. PLoS Genetics, 5: e1000582.
 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.
 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. Journal of Clinical Investigation, 119: 1178-1188.
 X. Li, H. Zhao (2009) Weighted random subspace method for high dimensional data classification. Statistics and Its Interface, 2: 153-159.
 J. Sampson, H. Zhao (2009) Genotyping and inflated type I error rate in genome-wide association case/control studies. BMC Bioinformatics, 10, 68.
 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‚Äô region of the GluR5 kainate receptor subunit gene (GRIK1) to alcohol dependence. Alcoholism: Clinical and Experimental Research, 33: 925-930.
 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.
 N. Liu, R. Bucala, H. Zhao (2009) Modeling informatively missing genotypes in haplotype analysis. Communications in Statistics - Theory and Methods, 38: 3445-3460.
 H. Pang, T. Tong, H. Zhao (2009) Shrinkage-based diagonal discriminant analysis and its applications in high-dimensional data. Biometrics, 65: 1021-1029.
 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.
 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. Alcoholism: Clinical and Experimental Research, 32: 2117-2127.
 N. Liu, D. Zhang, H. Zhao (2009) Genotyping error detection in samples of unrelated individuals without replicate genotyping. Human Heredity, 67: 154-162.
 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.
 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.
 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. American Journal of Medical Genetics A. 146A: 1942-1954.
 L. Chen, T. Tong, H. Zhao (2008) Considering dependence among genes and markers for false discovery control in eQTL mapping. Bioinformatics, 24: 2015-2022.
 J. Cao, H. Zhao (2008) Estimating dynamic models for gene regulation networks. Bioinformatics, 24: 1619-1624.
 W. Ji, J. N. Foo, B. J. O‚ÄôRoak, 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.
 H. Pang, H. Zhao (2008) Building pathway clusters from Random Forests classification using class votes. BMC Bioinformatics, 9, 87.
 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.
 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.
 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.
 J. Liu, W. Yu, B. Wu, H. Zhao (2008) Bayesian mass spectra peak alignment from mass charge ratios. Cancer Informatics, 4: 217-241.
 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.
 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.
 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.
 D. Datta, H. Zhao (2008) Statistical methods to infer cooperative binding among transcription factors in Saccharomyces cerevisiae. Bioinformatics, 24: 545-552.
 Z. Guan, B. Wu, H. Zhao (2008) Nonparametric estimator of false discovery rate based on Bernstein polynomials. Statistica Sinica, 18: 905-923.
 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. Human Molecular Genetics, 16: 2844-2853.
 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.
 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.
 S. Wang, H. Zhao (2007) Sample size needed to detect gene-gene interactions using linkage analysis. Annals of Human Genetics, 71: 828-842.
 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.
 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.
 V. Dinu, P. Miller, H. Zhao. (2007) Evidence for association between multiple complement pathway genes and AMD. Genetic Epidemiology, 31: 224-237.
 I. Kim, Y. Liu, H. Zhao. (2007) Bayesian methods for predicting interacting protein pairs using domain information. Biometrics, 63: 824-833.
 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.
 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.
 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.
 B. Wu, N. Liu, H. Zhao (2006) PSMIX: an R package for population stratification inference via maximum likelihood method. BMC Bioinformatics, 7: 317.
 N. Liu, H. Zhao (2006) A nonparametric approach for population structure inference using multilocus genotypes. Human Genomics, 2: 353-364.
 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.
 T. Tsubouchi, H. Zhao, G. S. Roeder (2006) Crossover distribution by promoting synaptonemal complex formation together with Zip2. Developmental Cell, 10: 809-819.
 Y. Zuo, G. Zou, H. Zhao (2006) Two-stage designs in case-control association analysis. Genetics, 173: 1747-1760.
 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.
 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.
 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.
 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.
 N. Liu, I. Beerman, R. Lifton, H. Zhao (2006) Haplotype analysis in the presence of informatively missing genotype data. Genetic Epidemiology, 30: 290-300.
 B. Wu, Z. Guan, H. Zhao (2006) Parametric and nonparametric FDR estimation revisited. Biometrics, 62: 735-744.
 S. Wang, S. Huang, L. Zheng, H. Zhao (2006) Mapping quantitative trait loci in non-inbred mosquito crosses. Genetics, 172: 2293-2308.
 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.
 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.
 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.
 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.
 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.
 T. Huang, B. Wu, P. Lizardi, H. Zhao (2005) Detection of DNA copy number alterations using penalized least squares regression. Bioinformatics, 21: 3811-3817.
 L. Chen, H. Zhao (2005) Negative correlation between compositional symmetries and local recombination rates. Bioinformatics, 21: 3951-1958.
 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.
 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.
 Y. Liu, N. Liu, H. Zhao (2005) Inferring protein-protein interactions through high throughput interaction data from diverse organisms. Bioinformatics, 21: 3279-3285.
 N. Lin, H. Zhao (2005) Are scale-free networks robust to measurement errors? BMC Bioinformatics, 6: 119.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 M. Holford, N. Li, P. Nadkarni, H. Zhao (2005) VitaPad: visualization tools for the analysis of pathway data. Bioinformatics, 21: 1596-1602.
 L. Chen, H. Zhao (2005) Integrating mRNA decay information into co-regulation study. Journal of Computer Science and Technology, 20: 434-438.
 Z. Guan, H. Zhao (2005) A semiparametric approach for marker gene selection based on gene expression data. Bioinformatics, 21: 529-536.
 G. Zou, H. Zhao (2005) Family-based association tests for different family structures using pooled DNA. Annals of Human Genetics, 69: 429-442.
 K. Zhang, F. Sun, H. Zhao. (2005) HAPLORE: A program for haplotype reconstruction in general pedigrees without recombination. Bioinformatics, 21: 90-103.
 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.
 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.
 Y. Liu, H. Zhao (2004) A computational approach for ordering signal transduction pathway components from genomics and proteomics data. BMC Bioinformatics, 5, 158.
 N. Lin, B. Wu, R. Jansen, M. Gerstein, H. Zhao (2004) Information assessment on predicting protein-protein interactions. BMC Bioinformatics, 5, 154.
 M. V. Osier, H. Zhao, K-H Cheung (2004) Handling multiple testing while interpreting microarrays with the gene ontology database. BMC Bioinformatics, 5, 124.
 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.
 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.
 Y. Lai, B. Wu, L. Chen, H. Zhao (2004) Statistical method for identifying differential gene-gene coexpression patterns. Bioinformatics, 20: 3146-3155.
 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.
 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.
 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.
 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.
 G. Zou, H. Zhao. (2004) The estimation of sibling genetic risk parameters revisited. Genetic Epidemiology, 26: 286-293.
 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.
 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.
 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.
 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.
 G. Zou, H. Zhao. (2004) The impacts of errors in individual genotyping and DNA pooling on association studies. Genetic Epidemiology, 26: 1-10.
 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.
 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.
 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
 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.
 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.
 G. Zou, H. Zhao. (2003) Haplotype frequency estimation in the presence of genotyping errors. Human Heredity, 56: 131-138.
 L. V. Sun, L. Chen, F. Greil, N. Negre, T.-R. Li, G. Cavalli, H. Zhao, B. Van Steensel, K. P. White (2003) DNA‚Äďprotein interaction mapping using genomic tiling path microarrays in Drosophila. Proceedings of the National Academy of Sciences, 100: 9428-9433.
 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.
 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.
 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‚Äď7q35. Diabetes, 52: 1557-1561.
 S. Wang, H. Zhao. (2003) Sample size to detect gene-gene interactions using association designs. American Journal of Epidemiology, 158: 899-914.
 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.
 G. Zou, D. Pan, H. Zhao. (2003) Genotyping error detection through tightly linked markers. Genetics, 164: 1161-1173.
 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.
 L. Ma, H. Zhao, X-W 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.
 S. Wang, K. K. Kidd, H. Zhao. (2003) On the use of DNA pooling to estimate haplotype frequencies. Genetic Epidemiology, 24: 74-82.
 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.
 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.
 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.
 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.
 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.
 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.
 X. Zhu, S. Zhang, H. Zhao, R. S. Cooper. (2002) Association mapping using a mixture model for complex traits. Genetic Epidemiology, 23: 181-196.
 S. Zhang, H. Zhao. (2002) Linkage disequilibrium mapping with genotype data. Genetic Epidemiology, 22: 66-77.
 S. Zhang, K. K. Kidd, H. Zhao. (2002) Detecting genetic association in case-control studies using similarity-based association tests. Statistica Sinica, 12: 337-359.
 J. Li, S. Sherman, N. Lamb, H. Zhao. (2001) Multipoint genetic mapping with trisomy data. American Journal of Human Genetics, 69: 1255-1265.
 H. Wang, L. Ma, J. Li, H. Zhao, X-W Deng. (2001) Direct interaction of Arabidopsis Cryptochromes with COP1 in light control¬ development. Science, 294: 154-158.
 L. Ma, J. Li, J. Hager, L. Qu, Z. Chen, H. Zhao, X-W Deng. (2001) Light control of Arabidopsis development entails co-ordinated regulation of genome expression and cellular pathways. Plant Cell, 13: 2589-2607.
 S. Zhang, A. J. Pakstis, K. K. Kidd, 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.
 S. Zhang, H. Zhao. (2001) Quantitative similarity-based association test using population samples. American Journal of Human Genetics, 69: 601-614.
 H. Zhao, J. Li, W. P. Robinson. (2001) Statistical analysis of uniparental disomy data using hidden Markov models. Biometrics, 57: 1074-1079.
 H. Zhao, F. Liang. (2001) On relationship inference using continuous gamete identity by descent data. Journal of Computational Biology, 8: 191-200.
 A. Kamina, R. W. Makuch, H. Zhao. (2001) Stochastic modeling of early HIV-1 population dynamics. Mathematical Biosciences, 170: 187-198.
 H. Zhao, S. Zhang, K. R. Merikangas, M. Trixler, D. Wildenaur, F. Sun, K. K. Kidd. (2000) Transmission/disequilibrium tests using multiple tightly linked markers. American Journal of Human Genetics, 67: 936-946.
 H. Zhao, J. Li, W. P. Robinson. (2000) Multipoint genetic mapping with uniparental disomy data. American Journal of Human Genetics, 67: 851-861.
 F. Sun, W. D. Flanders, Q. Yang, H. Zhao. (2000) Transmission/disequilibrium tests for quantitative traits. Annals of Human Genetics, 64: 555-565.
 K. Zhang, H. Zhao. (2000) Assessing reliability of gene clusters from gene expression data. Functional and Integrative Genomics, 1: 156-173.
 S. Zhang, 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.
 J. R. Kidd, A. J. Pakstis, H. Zhao, R.-B. Lu, F. E. Okonofua, A. Odunsi, E. Grigorenko, B. Bonne-Tamir, J. Friedlaender, L. O. Schulz, J. Parnas, K. K. Kidd. (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.
 H. Zhao, K. R. Merikangas, K. K. Kidd. (1999) On a randomization test in linkage analysis. American Journal of Human Genetics, 65: 1449-1456.
 H. Zhao, A. J. Pakstis, J. R. Kidd, K. K. Kidd. (1999) Assessing linkage disequilibrium in a complex genetic system. Annals of Human Genetics, 63: 167-179.
 H. Zhao, T. P. Speed. (1998) Statistical analysis of half-tetrads. Genetics, 150: 473-485.
 H. Zhao, T. P. Speed. (1998) Statistical analysis of ordered tetrads. Genetics, 150: 459-472.
 H. Zhao, T. P. Speed. (1998) Stochastic modeling of the crossover process during meiosis. Communications in Statistics, Theory and Methods, 27: 1557-1580.
 K. K. Kidd, B. Morar, C. M. Castiglione, H. Zhao, A. J. Pakstis, W. C. Speed, B. Bonne-Tamir, R.-B. Lu, D. Goldman, C. Lee, Y. S. Nam, D. K. Grandy, T. Jenkins, J. R. Kidd. (1998) A global survey of haplotype frequencies and linkage disequilibrium at the DRD2 locus. Human Genetics, 103: 211-227.
 H. Zhao, H. Zhang, J. I. Rotter. (1997) Cost-effective sib-pair designs in the mapping quantitative-trait loci. American Journal of Human Genetics, 60: 1211-1221.
 D. R. Goldstein, H. Zhao, T. P. Speed. (1997) The effects of genotyping errors and interference on estimation of genetic distance. Human Heredity, 47: 86-100.
 K. Lange, H. Zhao, T. P. Speed. (1997) Modeling chiasma interference using the Poisson-skip model. Annals of Applied Probability, 7: 299-313.
 J. D. Ohmen, H. Y. Yang, K. K. Yamamoto, H. Zhao, Y. Ma, L. G. Bentley, Z. Huang, S. Gerwehr, S. Pressman, C. McElree, S. Targan, J. I. Rotter, N. Fischel-Ghodsian (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.
 H. Zhao, T. P. Speed. (1996) On genetic map functions. Genetics, 142: 1369-1377.
 D. R. Goldstein, H. Zhao, T. P. Speed. (1995) Relative efficiencies of several statistical models of recombination for exclusion mapping and gene ordering. Genomics, 27: 265-273.
 H. Zhao, M. S. McPeek, T. P. Speed. (1995) Statistical analysis of chromatid interference. Genetics, 139: 1057-1065.
 H. Zhao, M. S. McPeek, T. P. Speed. (1995) Statistical analysis of crossover interference using the chi-square model. Genetics, 139: 1045-1056.
 K. Doksum, S. Blyth, E. Bradlow, X. L. Meng, H. Zhao. (1994) Correlation curves as local measures of variance explained by regression. Journal of American Statistical Association, 89: 571-583.
 M. Chen, C. Yang, C. Li, L. Hou, X. Chen, H. Zhao (2014) Admixture mapping analysis in the context of GWAS with GAW18 data. The Proceedings of Genetic Analysis Workshop 18, BMC Proceedings, 8(Suppl 1): S3.
 C. Li, C. Yang, M. Chen, X. Chen, L. Hou, H. Zhao (2014) Adjustment of familial relatedness in association test for rare variants. The Proceedings of Genetic Analysis Workshop 18, BMC Proceedings, 8(Suppl 1): S39.
 C. Yang, C. Li, M. Chen, X. Chen, L. Hou, H. Zhao (2014) A penalized linear mixed model for genomic prediction using pedigree structures. The Proceedings of Genetic Analysis Workshop 18, BMC Proceedings, 8(Suppl 1): S67.
 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, 5 Supplement 9: S37.
 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, 5 Supplement 9: S117.
 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, 5 Supplement 9: S27.
 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, 5 Supplement 9: S46.
 Z. He, H. Zhao, W. Yu (2011) Score regularization for peptide identification. BMC Bioinformatics, 12 Supplement 1: S2.
 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.
 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.
 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.
 S. Huang, D. Ballard, H. Zhao (2007) The role of heritability in mapping expression quantitative trait loci. BMC Proceedings, 1: S86.
 L. A. Cupples, J. Bailey, K. C. Cartier, C. T. Falk, K-Y Liu, Y. Ye, R. Yu, H. Zhao (2005) Group 14: Data Mining. Genetic Epidemiology, 29 Suppl 1: S103-9.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 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.
 N. Sun, H. Zhao (2014) Putting things in order. Proc Natl Acad Sci USA 111: 16236-16237.
 H. Zhao, K. R. Merikangas, and K. K. Kidd. (2000) Reply to Kong and Nicolae. American Journal of Human Genetics, 67: 1355-1356.
 H. Zhao. (1999) The interpretation of the parameters in the transmission/disequilibrium test. American Journal of Human Genetics, 64: 326-328.
 C. Yang, C. Li, Q. Wang, D. Chung, H. Zhao (2015) Implications of pleiotropy: Challenges and opportunities for mining Big Data in Biomedicine. Frontiers in Genetics (Applied Genetic Epidemiology), 6: 229.
 Q. Wang, Q. Lv, H. Zhao (2015) A review of study designs and statistical methods for genomic epidemiology studies using next generation sequencing. Frontiers in Genetics (Applied Genetic Epidemiology), 6: 149.
 X. Zhou, C. Yang, H. Zhao, W. Yu (2014) Low-rank modeling and its applications in image analysis. ACM Computing Surveys, 47: 36.¬
 H. Chun, M. Chen, B. Li, H. Zhao (2013) Network inference via conditional graphical models with multiple sources of genomic data. Frontiers in Genetics (Bioinformatics and Computational Biology), 4: 294.
 H. Lin, H. Zhao (2013) A Review of post-GWAS prioritization approaches. Frontiers in Genetics (Statistical Genetics and Methodology), 4: 280.
 H. Ma, H. Zhao (2013) Drug target inference through pathway analysis of genomics data. Advanced Drug Delivery Reviews, 65: 966-972.
 L. Li, X. Zhang, H. Zhao (2012) eQTL. Methods in Molecular Biology, 871: 265-279.
 R. Luo, H. Zhao (2012) Protein quantitation using iTRAQ: Review on the sources of variations and analysis of nonrandom missingness. Statistics and Its Interface, 5: 99-107.
 J. Cao, X. Qi, H. Zhao (2012) Modelling gene regulation networks using ordinary differential equations. Methods in Molecular Biology, 802: 185-197.
 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.
 N. Sun, H. Zhao (2009) Reconstructing transcriptional regulatory networks through genomics data. Statistical Methods in Medical Research, 18: 595-617.
 Y. Liu, I. Kim, H. Zhao (2008) Protein interaction predictions from diverse sources. Drug Discovery Today, 13: 409-416.
 N. Liu, K. Zhang, H. Zhao (2008) Haplotype Association Analysis. Advances in Genetics, 60: 335-405.
 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.
 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.
 N. Sun, H. Zhao. (2004) Genomic approaches in dissecting complex biological pathways. Pharmacogenomics, 5: 163-179.
 H. Zhao, R. Pfiffer, M. H. Gail. (2003) Haplotype analysis in population genetics and association studies. Phamacogenomics, 4: 171-178.
 H. Zhao. (2000) Family-based association studies. Statistical Methods in Medical Research, 9: 563-587.
 H. Zhang, H. Zhao, and K. R. Merikangas. (1997) Strategies to identify genes for complex diseases. Annals of Medicine, 29: 493-498.
 H. H-S Lu, B. Sch√∂lkopf, H. Zhao (eds) (2011) Handbook of Computational Statistics: Statistical Bioinformatics, Springer.
 S. Lin, H. Zhao (eds) (2009) Handbook of Statistical Genetics. Springer-Verlag Berlin Heidelberg.
 M. Chen, C. Yang, C. Li, H. Zhao (2016) eQTL mapping. Genome-Wide Association Studies: From Polymorphism to Personalized Medicine. Edited by Appasani K, Cambridge University Press, 208-228.
 C. Yang, C. Li, D. Chung, M. Chen, H. Zhao (2016) Introduction to statistical methods in genomewide association studies. Genome-Wide Association Studies: From Polymorphism to Personalized Medicine. Edited by Appasani K, Cambridge University Press, 26-52.
 C. Li, C. Yang, G. Hather, R. Liu, H. Zhao (2015) Data integration and drug discovery: pathway-based approaches. Integrating Omics Data, edited by G. C. Tseng, X. J. Zhou and D. Ghosh, Cambridge University Press, 425-444.
 N. Sun, H. Zhao (2015) Data integration methods in genome wide association studies. Advanced Medical Statistics (2nd edition), edited by Y. Lu, L. Tian, J. Fan, H. Jin, World Scientific Publishing Company, 961-976.
 M. Chen, L. Hou, H. Zhao (2014) Statistical methods for the analysis of next generation sequence data from paired tumor-normal samples. Statistical Analysis of Next Generation Sequencing Data, Edited by Datta S, Nettleton D, Springer, 379-404.
 M. Chen, H. Zhao (2014) Graphical modeling of biological pathways in genome-wide association studies. Probabilistic Graphical Models for Genetics, Genomics and Postgenomics, edited by Christine Sinoquet and Rapha√ęl Mourad, Oxford University Press, 294-317.
 H. Ma, H. Zhao (2013) Application of Bayesian sparse factor analysis models in bioinformatics. Statistical Bioinformatics, edited by K.-A. Do, S. Qin, and M. Vannucci, Cambridge University Press, 350-365.
 H. Chun, J. Kang, X. Zhang, M. Deng, H. Ma, H. Zhao (2011) 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. Sch√∂lkopf, and H. Zhao, Springer, 461-478.
 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.
 K. Zhang, H. Zhao (2010) Family based association studies. Handbook of Statistical Genetics, edited by S. Lin and H. Zhao, Springer-Verlag Berlin Heidelberg, 191-240.
 X. Zhang, H. Zhao (2010) 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.
 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.
 I. Kim, Y. Liu, H. Zhao (2010) Sparsity priors for protein-protein interaction predictions. Bayesian Modeling in Bioinformatics, edited by D. Dey, S. Ghosh, and B. Mallick, Chapman & Hall, 255-269.
 Y. Liu, I. Kim, H. Zhao (2009) 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.
 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.
 J. Wang, G. Zou, H. Zhao (2007) DNA pooling: Methods and applications in association studies. Current Topics in Human Genetics, Studies in Human Diseases, edited by HW Deng, H. Shen, Y-J Liu, H. Hu, 179-208.
 S. Huang, D. Ballard, Z. Wu, H. Zhao (2007) Expression quantitative trait loci mapping. Current Topics in Human Genetics, Studies in Human Diseases, edited by HW Deng, H. Shen, Y-J Liu, H. Hu, 397-431.
 Z. Feng, N. Liu, H. Zhao (2007) Haplotype inference and association analysis in unrelated samples. Current Topics in Human Genetics, Studies in Human Diseases, edited by HW Deng, H. Shen, Y-J Liu, H. Hu, 123-159.
 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.
 N. Sun, H. Zhao (2006) A misclassification model for inferring transcriptional regulatory networks. Bayesian Inference for Gene Expression and Proteomics, edited by K-A Do, P. Mueller and M. Vannucci, 347-365.
 W. Yu, B. Wu, T. Huang, X. Li, K. Williams, H. Zhao (2006) Statistical methods in proteomics. Springer Handbook of Engineering Statistics, edited by H. Pham, Springer, 623-638.
 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.
 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, Chapter 13.
 H. Zhao, B. Wu, N. Sun. (2003) DNA-protein binding and gene expression patterns. In Science and Statistics: A Festschrift for Terry Speed. IMS Lecture Notes-Monograph Series, edited by D. R. Goldstein, Vol 40, pp 259-274.
 T. P. Speed and H. Zhao (2001) Chromosome maps. Handbook of Statistical Genetics, Chapter 1: 3-39.
 H. Zhao and T. P. Speed. (1999) On a Markov model for chromatid interference. Statistics in Molecular Biology (IMS Lecture Notes 33), 1-20.