Hongyu Zhao, PhD

Research Interests

Genetics; Public Health; Computational Biology; Statistics; Genomics; Herbal Medicine; Proteomics; Biostatistics; Microbiota

Research Organizations

School of Public Health: YSPH Global Health Concentration

Cancer Genetics

Center for Polycystic Kidney Disease Research

Faculty Research

Keck: High Performance Computation | NIDA Neuroproteomics Center

Medical Informatics, Yale Center for

Obesity Research Working Group

Yale Cancer Center: Genomics, Genetics, and Epigenetics

Yale Institute for Global Health

Research Summary

Our research is driven by the need to analyze and interpret large and complex data sets in biomedical research. For example, in genome wide association studies involving thousands of individuals, millions of DNA variants are analyzed for each person. Such data offer people the opportunity to identify variants affecting disease susceptibility and develop risk prediction models to facilitate disease prevention and treatment. There are many statistical challenges arising from the analysis of such data, including the very high dimensionality, the relatively weak signals, and the need to incorporate prior knowledge and other data sets in analysis. Another example is the analysis of next generation sequence data which present even greater statistical and computational challenges. Our group has been developing statistical methods to address these challenges, such as empirical Bayes methods to borrow information across different data sets, different generalizations of Gaussian graphical models for network inference, Markov random field models for spatial and temporal modeling, and general machine learning methods for high dimensional data.

Specialized Terms: Statistical genomics and proteomics; Bioinformatics; Data integration; High dimensional data; Network and graphical models; Disease risk prediction; Herbal medicine; Microbiome

Extensive Research Description

• Genome Wide Associatio Studies: We are developing statisticla methods to integrate diverse data types and prior biological knowledge to identify genes for common diseases and risk prediction models. The diseases we work on include Crohn's disease, substance abuse, schizophrenia, bipolar, obesity, aneurysm, and autism.
• Network Modeling: We are developing statistical methods to model biological networks under the general framework of Gaussian and other graphical models. Specific networks we are working on include gene expression regulatory networks, signaling networks, and eQTL networks.
• Cancer Genomics: We are developing statistical and computational methods to analyze cancer genomics data, e.g. microarrays and next generation sequencing, to identify cancer subtypes, driver mutations, and appropriate treatments for cancer patients.
• Microbiome: We are developing modeling and analysis approaches for microbiome data generated from next generation sequencing data.
• Proteomics: Our current focus is on targeted proteomics, such as Multiple Reaction Monitoring.
• Herbal Medicine: Through systems biology approach, we are identifying tissue-specific target pathways of herbal medicine.

Selected Publications

• GPA: A statistical approach to prioritizing GWAS results by integrating pleiotropy and annotation

  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.

• On an additive semi-graphoid model for statistical networks with application to pathway analysis

  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.

• Guilt by Rewiring: Gene prioritization through network rewiring in genome wide association studies

  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.

• Improving genetic risk prediction by leveraging pleiotropy

  C. Li, C. Yang, J. Gelernter, H. Zhao (2014) Improving genetic risk prediction by leveraging pleiotropy. Human Genetics, 133: 639-650.

• Accounting for non-genetic factors by low-rank representation and sparse regression for eQTL mapping

  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.

• Sparse principal component analysis by choice of norm

  X. Qi, H. Zhao (2013) Sparse principal component analysis by choice of norm. Journal of Multivariate Analysis, 114: 127-160.

• Sparse estimation of conditional graphical models with application to gene networks

  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.

• iFad: an integrative factor analysis model for drug-pathway association inference

  H. Ma, H. Zhao (2012) iFad: an integrative factor analysis model for drug-pathway association inference. Bioinformatics, 28: 1911-1918.

• Bayesian hierarchical modeling for signaling pathway inference from single cell interventional data

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

• Incorporating biological pathways via a Markov random field model in genome-wide association studies

  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.

• Gene regulation network inference with joint sparse Gaussian graphical models

  H. Chun, X. Zhang, H. Zhao (2015) Gene regulation network inference with joint sparse Gaussian graphical models. Journal of Computational and Graphical Statistics, 24: 954–974.

• A statistical framework to predict functional non-coding regions in the human genome through integrated analysis of annotation data

  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.

• Pervasive pleiotropy between psychiatric disorders and immune disorders revealed by integrative analysis of multiple GWAS

  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.

• A Markov random field-based approach to characterizing human brain development using spatial-temporal transcriptome data

  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: 429–451.

• 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

  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.

• Predicting synergistic effects between compounds through their structural similarity and effects on transcriptomes

  Y. Liu, H. Zhao (2016) Predicting synergistic effects between compounds through their structural similarity and effects on transcriptomes. Bioinformatics, 32: 3782-3789.

• CCor: a whole genome network-based similarity measure between two genes

  Y. Hu, H. Zhao (2016) CCor: a whole genome network-based similarity measure between two genes. Biometrics, 72: 1216-1225.

• On high-dimensional misspecified mixed model analysis in genome-wide association study 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: 2127–2160.

Full List of PubMed Publications

• Zhang J, Li X, Hawley N, Zheng Z, Zou Z, Tan L, Chen Q, Shi H, Zhao H, Zhang Z: Trends in the Prevalence of Overweight and Obesity among Chinese School-Age Children and Adolescents from 2010 to 2015. Child Obes. 2018 Apr; 2018 Apr 5. PMID: 29620919
• Villarroel-Espindola F, Yu X, Datar I, Mani N, Sanmamed M, Velcheti V, Syrigos K, Toki M, Zhao H, Chen L, Herbst RS, Schalper KA: Spatially Resolved and Quantitative Analysis of VISTA/PD-1H as a Novel Immunotherapy Target in Human Non-Small Cell Lung Cancer. Clin Cancer Res. 2018 Apr 1; 2017 Dec 4. PMID: 29203588
• Gloria-Soria A, Dunn WA, Yu X, Vigneron A, Lee KY, Li M, Weiss BL, Zhao H, Aksoy S, Caccone A: Uncovering Genomic Regions Associated with Trypanosoma Infections in Wild Populations of the Tsetse Fly Glossina fuscipes. G3 (Bethesda). 2018 Mar 2; 2018 Mar 2. PMID: 29343494
• Park S, Zhao H: Spectral clustering based on learning similarity matrix. Bioinformatics. 2018 Feb 8; 2018 Feb 8. PMID: 29432517
• Kim HJ, Yu Z, Lawson A, Zhao H, Chung D, Stegle O: Improving SNP Prioritization and Pleiotropic Architecture Estimation by Incorporating Prior Knowledge Using graph-GPA. Bioinformatics. 2018 Feb 8; 2018 Feb 8. PMID: 29432514
• Sun J, Herazo-Maya JD, Huang X, Kaminski N, Zhao H: Distance-correlation based gene set analysis in longitudinal studies. Stat Appl Genet Mol Biol. 2018 Feb 5; 2018 Feb 5. PMID: 29397393
• Canli T, Yu L, Yu X, Zhao H, Fleischman D, Wilson RS, De Jager PL, Bennett DA: Loneliness 5 years ante-mortem is associated with disease-related differential gene expression in postmortem dorsolateral prefrontal cortex. Transl Psychiatry. 2018 Jan 10; 2018 Jan 10. PMID: 29317593
• Zhang X, Hu Y, Justice AC, Li B, Wang Z, Zhao H, Krystal JH, Xu K: DNA methylation signatures of illicit drug injection and hepatitis C are associated with HIV frailty. Nat Commun. 2017 Dec 21; 2017 Dec 21. PMID: 29269866
• Cui P, Zhong T, Wang Z, Wang T, Zhao H, Liu C, Lu H: Identification of human circadian genes based on time course gene expression profiles by using a deep learning method. Biochim Biophys Acta. 2017 Dec 12; 2017 Dec 12. PMID: 29241666
• Lu J, Lu Y, Wang X, Li X, Linderman GC, Wu C, Cheng X, Mu L, Zhang H, Liu J, Su M, Zhao H, Spatz ES, Spertus JA, Masoudi FA, Krumholz HM, Jiang L: Prevalence, awareness, treatment, and control of hypertension in China: data from 1·7 million adults in a population-based screening study (China PEACE Million Persons Project). Lancet. 2017 Dec 9; 2017 Nov 5. PMID: 29102084
• Lu Q, Li B, Ou D, Erlendsdottir M, Powles RL, Jiang T, Hu Y, Chang D, Jin C, Dai W, He Q, Liu Z, Mukherjee S, Crane PK, Zhao H: A Powerful Approach to Estimating Annotation-Stratified Genetic Covariance via GWAS Summary Statistics. Am J Hum Genet. 2017 Dec 7. PMID: 29220677
• Yan KK, Zhao H, Pang H: A comparison of graph- and kernel-based -omics data integration algorithms for classifying complex traits. BMC Bioinformatics. 2017 Dec 6; 2017 Dec 6. PMID: 29212468
• Zhu B, Song N, Shen R, Arora A, Machiela MJ, Song L, Landi MT, Ghosh D, Chatterjee N, Baladandayuthapani V, Zhao H: Integrating Clinical and Multiple Omics Data for Prognostic Assessment across Human Cancers. Sci Rep. 2017 Dec 5; 2017 Dec 5. PMID: 29209073
• Polimanti R, Zhao H, Farrer LA, Kranzler HR, Gelernter J: Ancestry-specific and sex-specific risk alleles identified in a genome-wide gene-by-alcohol dependence interaction study of risky sexual behaviors. Am J Med Genet B Neuropsychiatr Genet. 2017 Dec; 2017 Oct 9. PMID: 28990359
• Zhou H, Polimanti R, Yang BZ, Wang Q, Han S, Sherva R, Nuñez YZ, Zhao H, Farrer LA, Kranzler HR, Gelernter J: Genetic Risk Variants Associated With Comorbid Alcohol Dependence and Major Depression. JAMA Psychiatry. 2017 Dec 1. PMID: 29071344
• Polimanti R, Amstadter AB, Stein MB, Almli LM, Baker DG, Bierut LJ, Bradley B, Farrer LA, Johnson EO, King A, Kranzler HR, Maihofer AX, Rice JP, Roberts AL, Saccone NL, Zhao H, Liberzon I, Ressler KJ, Nievergelt CM, Koenen KC, Gelernter J, Psychiatric Genomics Consortium Posttraumatic Stress Disorder Workgroup.: A putative causal relationship between genetically determined female body shape and posttraumatic stress disorder. Genome Med. 2017 Nov 27; 2017 Nov 27. PMID: 29178946
• Zhang Y, Zhang D, Li X, Ip P, Ho F, Jiang Y, Sun W, Zhu Q, Zhu W, Zhang J, Zhao H, Wang G, Shen X, Jiang F: Daily Time-Use Patterns and Obesity and Mental Health among Primary School Students in Shanghai: A Population-Based Cross-Sectional Study. Sci Rep. 2017 Nov 23; 2017 Nov 23. PMID: 29170506
• Herazo-Maya JD, Sun J, Molyneaux PL, Li Q, Villalba JA, Tzouvelekis A, Lynn H, Juan-Guardela BM, Risquez C, Osorio JC, Yan X, Michel G, Aurelien N, Lindell KO, Klesen MJ, Moffatt MF, Cookson WO, Zhang Y, Garcia JGN, Noth I, Prasse A, Bar-Joseph Z, Gibson KF, Zhao H, Herzog EL, Rosas IO, Maher TM, Kaminski N: Validation of a 52-gene risk profile for outcome prediction in patients with idiopathic pulmonary fibrosis: an international, multicentre, cohort study. Lancet Respir Med. 2017 Nov; 2017 Sep 21. PMID: 28942086
• Jin SC, Homsy J, Zaidi S, Lu Q, Morton S, DePalma SR, Zeng X, Qi H, Chang W, Sierant MC, Hung WC, Haider S, Zhang J, Knight J, Bjornson RD, Castaldi C, Tikhonoa IR, Bilguvar K, Mane SM, Sanders SJ, Mital S, Russell MW, Gaynor JW, Deanfield J, Giardini A, Porter GA Jr, Srivastava D, Lo CW, Shen Y, Watkins WS, Yandell M, Yost HJ, Tristani-Firouzi M, Newburger JW, Roberts AE, Kim R, Zhao H, Kaltman JR, Goldmuntz E, Chung WK, Seidman JG, Gelb BD, Seidman CE, Lifton RP, Brueckner M: Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands. Nat Genet. 2017 Nov; 2017 Oct 9. PMID: 28991257
• Streicher SA, Klein AP, Olson SH, Amundadottir LT, DeWan AT, Zhao H, Risch HA: Impact of Sixteen Established Pancreatic Cancer Susceptibility Loci in American Jews. Cancer Epidemiol Biomarkers Prev. 2017 Oct; 2017 Jul 28. PMID: 28754795
• Charkoftaki G, Chen Y, Han M, Sandoval M, Yu X, Zhao H, Orlicky DJ, Thompson DC, Vasiliou V: Transcriptomic analysis and plasma metabolomics in Aldh16a1-null mice reveals a potential role of ALDH16A1 in renal function. Chem Biol Interact. 2017 Oct 1; 2017 Feb 28. PMID: 28254523
• Sun J, Herazo-Maya JD, Kaminski N, Zhao H, Warren JL: A Dirichlet process mixture model for clustering longitudinal gene expression data. Stat Med. 2017 Sep 30; 2017 Jun 15. PMID: 28620908
• Richardson JB, Lee KY, Mireji P, Enyaru J, Sistrom M, Aksoy S, Zhao H, Caccone A: Genomic analyses of African Trypanozoon strains to assess evolutionary relationships and identify markers for strain identification. PLoS Negl Trop Dis. 2017 Sep; 2017 Sep 29. PMID: 28961238
• Wang T, Zhao H: A Dirichlet-tree multinomial regression model for associating dietary nutrients with gut microorganisms. Biometrics. 2017 Sep; 2017 Jan 23. PMID: 28112797
• Lin Z, Wang T, Yang C, Zhao H: On joint estimation of Gaussian graphical models for spatial and temporal data. Biometrics. 2017 Sep; 2017 Jan 18. PMID: 28099997
• Lu Q, Powles RL, Abdallah S, Ou D, Wang Q, Hu Y, Lu Y, Liu W, Li B, Mukherjee S, Crane PK, Zhao H: Systematic tissue-specific functional annotation of the human genome highlights immune-related DNA elements for late-onset Alzheimer's disease. PLoS Genet. 2017 Jul; 2017 Jul 24. PMID: 28742084
• Fang H, Huang C, Zhao H, Deng M: gCoda: Conditional Dependence Network Inference for Compositional Data. J Comput Biol. 2017 Jul; 2017 May 10. PMID: 28489411
• Williams KR, Colangelo CM, Hou L, Chung L, Belcher JM, Abbott T, Hall IE, Zhao H, Cantley LG, Parikh CR: Use of a Targeted Urine Proteome Assay (TUPA) to identify protein biomarkers of delayed recovery after kidney transplant. Proteomics Clin Appl. 2017 Jul; 2017 Mar 31. PMID: 28261998
• Klein MI, Stern DF, Zhao H: GRAPE: a pathway template method to characterize tissue-specific functionality from gene expression profiles. BMC Bioinformatics. 2017 Jun 26; 2017 Jun 26. PMID: 28651562
• Goffredo M, Santoro N, Tricò D, Giannini C, D'Adamo E, Zhao H, Peng G, Yu X, Lam TT, Pierpont B, Caprio S, Herzog RI: A Branched-Chain Amino Acid-Related Metabolic Signature Characterizes Obese Adolescents with Non-Alcoholic Fatty Liver Disease. Nutrients. 2017 Jun 22; 2017 Jun 22. PMID: 28640216
• Yan X, Liang A, Gomez J, Cohn L, Zhao H, Chupp GL: A novel pathway-based distance score enhances assessment of disease heterogeneity in gene expression. BMC Bioinformatics. 2017 Jun 20; 2017 Jun 20. PMID: 28637421
• Hu Y, Lu Q, Liu W, Zhang Y, Li M, Zhao H: Joint modeling of genetically correlated diseases and functional annotations increases accuracy of polygenic risk prediction. PLoS Genet. 2017 Jun; 2017 Jun 9. PMID: 28598966
• Hu Y, Lu Q, Powles R, Yao X, Yang C, Fang F, Xu X, Zhao H: Leveraging functional annotations in genetic risk prediction for human complex diseases. PLoS Comput Biol. 2017 Jun; 2017 Jun 8. PMID: 28594818
• Fragoso CA, Moreno M, Wang Z, Heffelfinger C, Arbelaez LJ, Aguirre JA, Franco N, Romero LE, Labadie K, Zhao H, Dellaporta SL, Lorieux M: Genetic Architecture of a Rice Nested Association Mapping Population. G3 (Bethesda). 2017 Jun 7; 2017 Jun 7. PMID: 28450374
• Rauniyar N, Peng G, Lam TT, Zhao H, Mor G, Williams KR: Data-Independent Acquisition and Parallel Reaction Monitoring Mass Spectrometry Identification of Serum Biomarkers for Ovarian Cancer. Biomark Insights. 2017; 2017 Jun 5. PMID: 28615921
• Zhu R, Zhao YQ, Chen G, Ma S, Zhao H: Greedy outcome weighted tree learning of optimal personalized treatment rules. Biometrics. 2017 Jun; 2016 Oct 4. PMID: 27704531
• Polimanti R, Meda SA, Pearlson GD, Zhao H, Sherva R, Farrer LA, Kranzler HR, Gelernter J: S100A10 identified in a genome-wide gene × cannabis dependence interaction analysis of risky sexual behaviours. J Psychiatry Neurosci. 2017 Jun. PMID: 28418321
• Justice AC, McGinnis KA, Tate JP, Xu K, Becker WC, Zhao H, Gelernter J, Kranzler HR: Validating Harmful Alcohol Use as a Phenotype for Genetic Discovery Using Phosphatidylethanol and a Polymorphism in ADH1B. Alcohol Clin Exp Res. 2017 May; 2017 Apr 10. PMID: 28295416
• Adkins AE, Hack LM, Bigdeli TB, Williamson VS, McMichael GO, Mamdani M, Edwards AC, Aliev F, Chan RF, Bhandari P, Raabe RC, Alaimo JT, Blackwell GG, Moscati A, Poland RS, Rood B, Patterson DG, Walsh D, Collaborative Study of the Genetics of Alcoholism Consortium., Whitfield JB, Zhu G, Montgomery GW, Henders AK, Martin NG, Heath AC, Madden PAF, Frank J, Ridinger M, Wodarz N, Soyka M, Zill P, Ising M, Nöthen MM, Kiefer F, Rietschel M, German Study of the Genetics of Addiction Consortium., Gelernter J, Sherva R, Koesterer R, Almasy L, Zhao H, Kranzler HR, Farrer LA, Maher BS, Prescott CA, Dick DM, Bacanu SA, Mathies LD, Davies AG, Vladimirov VI, Grotewiel M, Bowers MS, Bettinger JC, Webb BT, Miles MF, Kendler KS, Riley BP: Genomewide Association Study of Alcohol Dependence Identifies Risk Loci Altering Ethanol-Response Behaviors in Model Organisms. Alcohol Clin Exp Res. 2017 May; 2017 Mar 30. PMID: 28226201
• Polimanti R, Zhang H, Smith AH, Zhao H, Farrer LA, Kranzler HR, Gelernter J: Genome-wide association study of body mass index in subjects with alcohol dependence. Addict Biol. 2017 Mar; 2015 Oct 12. PMID: 26458734
• Chung D, Kim HJ, Zhao H: graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture. PLoS Comput Biol. 2017 Feb; 2017 Feb 17. PMID: 28212402
• Zhao B, Lu Q, Cheng Y, Belcher JM, Siew ED, Leaf DE, Body SC, Fox AA, Waikar SS, Collard CD, Thiessen-Philbrook H, Ikizler TA, Ware LB, Edelstein CL, Garg AX, Choi M, Schaub JA, Zhao H, Lifton RP, Parikh CR, TRIBE-AKI Consortium * .: A Genome-Wide Association Study to Identify Single-Nucleotide Polymorphisms for Acute Kidney Injury. Am J Respir Crit Care Med. 2017 Feb 15. PMID: 27576016
• Heit C, Marshall S, Singh S, Yu X, Charkoftaki G, Zhao H, Orlicky DJ, Fritz KS, Thompson DC, Vasiliou V: Catalase deletion promotes prediabetic phenotype in mice. Free Radic Biol Med. 2017 Feb; 2016 Dec 8. PMID: 27939935
• Hou L, Sun N, Mane S, Sayward F, Rajeevan N, Cheung KH, Cho K, Pyarajan S, Aslan M, Miller P, Harvey PD, Gaziano JM, Concato J, Zhao H: Impact of genotyping errors on statistical power of association tests in genomic analyses: A case study. Genet Epidemiol. 2017 Feb; 2016 Dec 26. PMID: 28019059
• Polimanti R, Wang Q, Meda SA, Patel KT, Pearlson GD, Zhao H, Farrer LA, Kranzler HR, Gelernter J: The Interplay Between Risky Sexual Behaviors and Alcohol Dependence: Genome-Wide Association and Neuroimaging Support for LHPP as a Risk Gene. Neuropsychopharmacology. 2017 Feb; 2016 Aug 17. PMID: 27531626
• Hong F, Mohammad Rachidi S, Lundgren D, Han D, Huang X, Zhao H, Kimura Y, Hirano H, Ohara O, Udono H, Meng S, Liu B, Li Z: Mapping the Interactome of a Major Mammalian Endoplasmic Reticulum Heat Shock Protein 90. PLoS One. 2017; 2017 Jan 5. PMID: 28056051
• Wang Q, Polimanti R, Kranzler HR, Farrer LA, Zhao H, Gelernter J: Genetic factor common to schizophrenia and HIV infection is associated with risky sexual behavior: antagonistic vs. synergistic pleiotropic SNPs enriched for distinctly different biological functions. Hum Genet. 2017 Jan; 2016 Oct 17. PMID: 27752767
• Lin Z, Yang C, Zhu Y, Duchi J, Fu Y, Wang Y, Jiang B, Zamanighomi M, Xu X, Li M, Sestan N, Zhao H, Wong WH: Simultaneous dimension reduction and adjustment for confounding variation. Proc Natl Acad Sci U S A. 2016 Dec 20; 2016 Dec 7. PMID: 27930330
• Liu Y, Zhao H: Predicting synergistic effects between compounds through their structural similarity and effects on transcriptomes. Bioinformatics. 2016 Dec 15; 2016 Aug 18. PMID: 27540269
• Hu Y, Zhao H: CCor: A whole genome network-based similarity measure between two genes. Biometrics. 2016 Dec; 2016 Mar 8. PMID: 26953524
• Zhu R, Zhao Q, Zhao H, Ma S: Integrating multidimensional omics data for cancer outcome. Biostatistics. 2016 Oct; 2016 Mar 14. PMID: 26980320
• Chuang LS, Villaverde N, Hui KY, Mortha A, Rahman A, Levine AP, Haritunians T, Evelyn Ng SM, Zhang W, Hsu NY, Facey JA, Luong T, Fernandez-Hernandez H, Li D, Rivas M, Schiff ER, Gusev A, Schumm LP, Bowen BM, Sharma Y, Ning K, Remark R, Gnjatic S, Legnani P, George J, Sands BE, Stempak JM, Datta LW, Lipka S, Katz S, Cheifetz AS, Barzilai N, Pontikos N, Abraham C, Dubinsky MJ, Targan S, Taylor K, Rotter JI, Scherl EJ, Desnick RJ, Abreu MT, Zhao H, Atzmon G, Pe'er I, Kugathasan S, Hakonarson H, McCauley JL, Lencz T, Darvasi A, Plagnol V, Silverberg MS, Muise AM, Brant SR, Daly MJ, Segal AW, Duerr RH, Merad M, McGovern DP, Peter I, Cho JH: A Frameshift in CSF2RB Predominant Among Ashkenazi Jews Increases Risk for Crohn's Disease and Reduces Monocyte Signaling via GM-CSF. Gastroenterology. 2016 Oct; 2016 Jul 1. PMID: 27377463
• Dong K, Zhao H, Tong T, Wan X: NBLDA: negative binomial linear discriminant analysis for RNA-Seq data. BMC Bioinformatics. 2016 Sep 13; 2016 Sep 13. PMID: 27623864
• Timberlake AT, Choi J, Zaidi S, Lu Q, Nelson-Williams C, Brooks ED, Bilguvar K, Tikhonova I, Mane S, Yang JF, Sawh-Martinez R, Persing S, Zellner EG, Loring E, Chuang C, Galm A, Hashim PW, Steinbacher DM, DiLuna ML, Duncan CC, Pelphrey KA, Zhao H, Persing JA, Lifton RP: Two locus inheritance of non-syndromic midline craniosynostosis via rare SMAD6 and common BMP2 alleles. Elife. 2016 Sep 8; 2016 Sep 8. PMID: 27606499
• Lee KY, Li B, Zhao H: On an additive partial correlation operator and nonparametric estimation of graphical models. Biometrika. 2016 Sep; 2016 Aug 24. PMID: 29422689
• Polimanti R, Yang BZ, Zhao H, Gelernter J: Evidence of Polygenic Adaptation in the Systems Genetics of Anthropometric Traits. PLoS One. 2016; 2016 Aug 18. PMID: 27537407
• Zhang X, Justice AC, Hu Y, Wang Z, Zhao H, Wang G, Johnson EO, Emu B, Sutton RE, Krystal JH, Xu K: Epigenome-wide differential DNA methylation between HIV-infected and uninfected individuals. Epigenetics. 2016 Aug 12; 2016 Aug 12. PMID: 27672717
• Liu J, Yang C, Shi X, Li C, Huang J, Zhao H, Ma S: Analyzing Association Mapping in Pedigree-Based GWAS Using a Penalized Multitrait Mixed Model. Genet Epidemiol. 2016 Jul; 2016 Jun 1. PMID: 27247027
• Li N, Subrahmanyan L, Smith E, Yu X, Zaidi S, Choi M, Mane S, Nelson-Williams C, Behjati M, Kazemi M, Hashemi M, Fathzadeh M, Narayanan A, Tian L, Montazeri F, Mani M, Begleiter ML, Coon BG, Lynch HT, Olson EN, Zhao H, Ruland J, Lifton RP, Mani A: Mutations in the Histone Modifier PRDM6 Are Associated with Isolated Nonsyndromic Patent Ductus Arteriosus. Am J Hum Genet. 2016 Jun 2; 2016 May 12. PMID: 27181681
• Chen M, Gao C, Zhao H: Posterior Contraction Rates of the Phylogenetic Indian Buffet Processes. Bayesian Anal. 2016 Jun; 2015 Jun 5. PMID: 27087886
• Wang T, Chen M, Zhao H: Estimating DNA methylation levels by joint modeling of multiple methylation profiles from microarray data. Biometrics. 2016 Jun; 2015 Oct 4. PMID: 26433612
• Sherva R, Wang Q, Kranzler H, Zhao H, Koesterer R, Herman A, Farrer LA, Gelernter J: Genome-wide Association Study of Cannabis Dependence Severity, Novel Risk Variants, and Shared Genetic Risks. JAMA Psychiatry. 2016 May 1. PMID: 27028160
• Xie Z, Zhang D, Chung D, Tang Z, Huang H, Dai L, Qi S, Li J, Colak G, Chen Y, Xia C, Peng C, Ruan H, Kirkey M, Wang D, Jensen LM, Kwon OK, Lee S, Pletcher SD, Tan M, Lombard DB, White KP, Zhao H, Li J, Roeder RG, Yang X, Zhao Y: Metabolic Regulation of Gene Expression by Histone Lysine β-Hydroxybutyrylation. Mol Cell. 2016 Apr 21. PMID: 27105115
• Lu Q, Powles RL, Wang Q, He BJ, Zhao H: 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 Genet. 2016 Apr; 2016 Apr 8. PMID: 27058395
• Ryslik GA, Cheng Y, Modis Y, Zhao H: Leveraging protein quaternary structure to identify oncogenic driver mutations. BMC Bioinformatics. 2016 Mar 22; 2016 Mar 22. PMID: 27001666
• Yan X, Chu JH, Gomez J, Koenigs M, Holm C, He X, Perez MF, Zhao H, Mane S, Martinez FD, Ober C, Nicolae DL, Barnes KC, London SJ, Gilliland F, Weiss ST, Raby BA, Cohn L, Chupp GL: Noninvasive Analysis of the Sputum Transcriptome Discriminates Clinical Phenotypes of Asthma. Ann Am Thorac Soc. 2016 Mar. PMID: 27027945
• Chen M, Lin H, Zhao H: CHANGE POINT ANALYSIS OF HISTONE MODIFICATIONS REVEALS EPIGENETIC BLOCKS LINKING TO PHYSICAL DOMAINS. Ann Appl Stat. 2016 Mar; 2016 Mar 25. PMID: 27231496
• Chen M, Ren Z, Zhao H, Zhou H: Asymptotically Normal and Efficient Estimation of Covariate-Adjusted Gaussian Graphical Model. J Am Stat Assoc. 2016 Mar; 2016 May 5. PMID: 27499564
• Lu Q, Yao X, Hu Y, Zhao H: GenoWAP: GWAS signal prioritization through integrated analysis of genomic functional annotation. Bioinformatics. 2016 Feb 15; 2015 Oct 25. PMID: 26504140
• Huang X, Stern DF, Zhao H: Transcriptional Profiles from Paired Normal Samples Offer Complementary Information on Cancer Patient Survival--Evidence from TCGA Pan-Cancer Data. Sci Rep. 2016 Feb 3; 2016 Feb 3. PMID: 26837275
• Fragoso CA, Heffelfinger C, Zhao H, Dellaporta SL: Imputing Genotypes in Biallelic Populations from Low-Coverage Sequence Data. Genetics. 2016 Feb; 2015 Dec 29. PMID: 26715670
• Wang F, Xu H, Zhao H, Gelernter J, Zhang H: DNA co-methylation modules in postmortem prefrontal cortex tissues of European Australians with alcohol use disorders. Sci Rep. 2016 Jan 14; 2016 Jan 14. PMID: 26763658
• Goffredo M, Caprio S, Feldstein AE, D'Adamo E, Shaw MM, Pierpont B, Savoye M, Zhao H, Bale AE, Santoro N: Role of TM6SF2 rs58542926 in the pathogenesis of nonalcoholic pediatric fatty liver disease: A multiethnic study. Hepatology. 2016 Jan; 2015 Nov 16. PMID: 26457389
• Harvey PD, Aslan M, Du M, Zhao H, Siever LJ, Pulver A, Gaziano JM, Concato J: Factor structure of cognition and functional capacity in two studies of schizophrenia and bipolar disorder: Implications for genomic studies. Neuropsychology. 2016 Jan. PMID: 26710094
• Lu Q, Jin C, Sun J, Bowler R, Kechris K, Kaminski N, Zhao H: Post-GWAS Prioritization Through Data Integration Provides Novel Insights on Chronic Obstructive Pulmonary Disease. Stat Biosci. 2016; 2016 Jun 13. PMID: 27812370
• Li G, Zhao H: M(3)-S: a genotype calling method incorporating information from samples with known genotypes. BMC Bioinformatics. 2015 Dec 3; 2015 Dec 3. PMID: 26634345
• Wang Q, Yang C, Gelernter J, Zhao H: Pervasive pleiotropy between psychiatric disorders and immune disorders revealed by integrative analysis of multiple GWAS. Hum Genet. 2015 Nov; 2015 Sep 4. PMID: 26340901
• Fang H, Huang C, Zhao H, Deng M: CCLasso: correlation inference for compositional data through Lasso. Bioinformatics. 2015 Oct 1; 2015 Jun 4. PMID: 26048598
• Pang H, Kim I, Zhao H: Random Effects Model for Multiple Pathway Analysis with Applications to Type II Diabetes Microarray Data. Stat Biosci. 2015 Oct 1; 2014 Jan 30. PMID: 26640601
• Xu K, Kranzler HR, Sherva R, Sartor CE, Almasy L, Koesterer R, Zhao H, Farrer LA, Gelernter J: Genomewide Association Study for Maximum Number of Alcoholic Drinks in European Americans and African Americans. Alcohol Clin Exp Res. 2015 Jul; 2015 Jun 3. PMID: 26036284
• Yang C, Li C, Wang Q, Chung D, Zhao H: Implications of pleiotropy: challenges and opportunities for mining Big Data in biomedicine. Front Genet. 2015; 2015 Jun 30. PMID: 26175753
• Lu Q, Hu Y, Sun J, Cheng Y, Cheung KH, Zhao H: A statistical framework to predict functional non-coding regions in the human genome through integrated analysis of annotation data. Sci Rep. 2015 May 27; 2015 May 27. PMID: 26015273
• Xie Y, Jin Y, Merenick BL, Ding M, Fetalvero KM, Wagner RJ, Mai A, Gleim S, Tucker DF, Birnbaum MJ, Ballif BA, Luciano AK, Sessa WC, Rzucidlo EM, Powell RJ, Hou L, Zhao H, Hwa J, Yu J, Martin KA: Phosphorylation of GATA-6 is required for vascular smooth muscle cell differentiation after mTORC1 inhibition. Sci Signal. 2015 May 12; 2015 May 12. PMID: 25969542
• Zheng C, Dalla Man C, Cobelli C, Groop L, Zhao H, Bale AE, Shaw M, Duran E, Pierpont B, Caprio S, Santoro N: A common variant in the MTNR1b gene is associated with increased risk of impaired fasting glucose (IFG) in youth with obesity. Obesity (Silver Spring). 2015 May. PMID: 25919927
• Stefani G, Chen X, Zhao H, Slack FJ: A novel mechanism of LIN-28 regulation of let-7 microRNA expression revealed by in vivo HITS-CLIP in C. elegans. RNA. 2015 May; 2015 Mar 24. PMID: 25805859
• Zuo L, Zhang CK, Sayward FG, Cheung KH, Wang K, Krystal JH, Zhao H, Luo X: Gene-based and pathway-based genome-wide association study of alcohol dependence. Shanghai Arch Psychiatry. 2015 Apr 25. PMID: 26120261
• Wang Q, Lu Q, Zhao H: A review of study designs and statistical methods for genomic epidemiology studies using next generation sequencing. Front Genet. 2015; 2015 Apr 20. PMID: 25941534
• Tadeu AM, Lin S, Hou L, Chung L, Zhong M, Zhao H, Horsley V: Transcriptional profiling of ectoderm specification to keratinocyte fate in human embryonic stem cells. PLoS One. 2015; 2015 Apr 7. PMID: 25849374
• Qi X, Luo R, Carroll RJ, Zhao H: Sparse Regression by Projection and Sparse Discriminant Analysis. J Comput Graph Stat. 2015 Apr 1. PMID: 26345204
• Lam W, Jiang Z, Guan F, Huang X, Hu R, Wang J, Bussom S, Liu SH, Zhao H, Yen Y, Cheng YC: PHY906(KD018), an adjuvant based on a 1800-year-old Chinese medicine, enhanced the anti-tumor activity of Sorafenib by changing the tumor microenvironment. Sci Rep. 2015 Mar 30; 2015 Mar 30. PMID: 25819872
• Lin Z, Sanders SJ, Li M, Sestan N, State MW, Zhao H: A MARKOV RANDOM FIELD-BASED APPROACH TO CHARACTERIZING HUMAN BRAIN DEVELOPMENT USING SPATIAL-TEMPORAL TRANSCRIPTOME DATA. Ann Appl Stat. 2015 Mar. PMID: 26877824
• Gelernter J, Kranzler HR, Sherva R, Almasy L, Herman AI, Koesterer R, Zhao H, Farrer LA: Genome-wide association study of nicotine dependence in American populations: identification of novel risk loci in both African-Americans and European-Americans. Biol Psychiatry. 2015 Mar 1; 2014 Sep 16. PMID: 25555482
• Li D, Zhao H, Kranzler HR, Li MD, Jensen KP, Zayats T, Farrer LA, Gelernter J: Genome-wide association study of copy number variations (CNVs) with opioid dependence. Neuropsychopharmacology. 2015 Mar; 2014 Sep 27. PMID: 25345593
• Evans BR, Gloria-Soria A, Hou L, McBride C, Bonizzoni M, Zhao H, Powell JR: A Multipurpose, High-Throughput Single-Nucleotide Polymorphism Chip for the Dengue and Yellow Fever Mosquito, Aedes aegypti. G3 (Bethesda). 2015 Feb 26; 2015 Feb 26. PMID: 25721127
• Sun J, Zhao H: The application of sparse estimation of covariance matrix to quadratic discriminant analysis. BMC Bioinformatics. 2015 Feb 18; 2015 Feb 18. PMID: 25886892
• Foxman EF, Storer JA, Fitzgerald ME, Wasik BR, Hou L, Zhao H, Turner PE, Pyle AM, Iwasaki A: Temperature-dependent innate defense against the common cold virus limits viral replication at warm temperature in mouse airway cells. Proc Natl Acad Sci U S A. 2015 Jan 20; 2015 Jan 5. PMID: 25561542
• Polimanti R, Yang C, Zhao H, Gelernter J: Dissecting ancestry genomic background in substance dependence genome-wide association studies. Pharmacogenomics. 2015; 2015 Aug 12. PMID: 26267224
• Pang H, Zhao H: Stratified pathway analysis to identify gene sets associated with oral contraceptive use and breast cancer. Cancer Inform. 2014; 2014 Dec 9. PMID: 25574128
• Heffelfinger C, Fragoso CA, Moreno MA, Overton JD, Mottinger JP, Zhao H, Tohme J, Dellaporta SL: Flexible and scalable genotyping-by-sequencing strategies for population studies. BMC Genomics. 2014 Nov 18; 2014 Nov 18. PMID: 25406744
• Sun N, Zhao H: Putting things in order. Proc Natl Acad Sci U S A. 2014 Nov 18; 2014 Nov 7. PMID: 25380598
• Chung D, Yang C, Li C, Gelernter J, Zhao H: GPA: a statistical approach to prioritizing GWAS results by integrating pleiotropy and annotation. PLoS Genet. 2014 Nov; 2014 Nov 13. PMID: 25393678
• Beech RD, Leffert JJ, Lin A, Hong KA, Hansen J, Umlauf S, Mane S, Zhao H, Sinha R: Stress-related alcohol consumption in heavy drinkers correlates with expression of miR-10a, miR-21, and components of the TAR-RNA-binding protein-associated complex. Alcohol Clin Exp Res. 2014 Nov. PMID: 25421511
• Zhang H, Wang F, Xu H, Liu Y, Liu J, Zhao H, Gelernter J: Differentially co-expressed genes in postmortem prefrontal cortex of individuals with alcohol use disorders: influence on alcohol metabolism-related pathways. Hum Genet. 2014 Nov; 2014 Jul 30. PMID: 25073604
• Hou L, Ma T, Zhao H: Incorporating functional annotation information in prioritizing disease associated SNPs from genome wide association studies. Sci China Life Sci. 2014 Nov; 2014 Oct 17. PMID: 25326070
• Della-Morte D, Wang L, Beecham A, Blanton SH, Zhao H, Sacco RL, Rundek T, Dong C: Novel genetic variants modify the effect of smoking on carotid plaque burden in Hispanics. J Neurol Sci. 2014 Sep 15; 2014 Jun 14. PMID: 24954085
• Xie P, Kranzler HR, Krystal JH, Farrer LA, Zhao H, Gelernter J: Deep resequencing of 17 glutamate system genes identifies rare variants in DISC1 and GRIN2B affecting risk of opioid dependence. Addict Biol. 2014 Sep; 2013 Jul 16. PMID: 23855403
• Zhang H, Wang F, Kranzler HR, Yang C, Xu H, Wang Z, Zhao H, Gelernter J: Identification of methylation quantitative trait loci (mQTLs) influencing promoter DNA methylation of alcohol dependence risk genes. Hum Genet. 2014 Sep; 2014 Jun 3. PMID: 24889829
• Li B, Chun H, Zhao H: On an Additive Semigraphoid Model for Statistical Networks With Application to Pathway Analysis. J Am Stat Assoc. 2014 Sep. PMID: 26401064
• Ryslik GA, Cheng Y, Cheung KH, Bjornson RD, Zelterman D, Modis Y, Zhao H: A spatial simulation approach to account for protein structure when identifying non-random somatic mutations. BMC Bioinformatics. 2014 Jul 3; 2014 Jul 3. PMID: 24990767
• Gelernter J, Kranzler HR, Sherva R, Koesterer R, Almasy L, Zhao H, Farrer LA: Genome-wide association study of opioid dependence: multiple associations mapped to calcium and potassium pathways. Biol Psychiatry. 2014 Jul 1; 2013 Oct 19. PMID: 24143882
• Yang C, Li C, Chen M, Chen X, Hou L, Zhao H: A penalized linear mixed model for genomic prediction using pedigree structures. BMC Proc. 2014; 2014 Jun 17. PMID: 25519399
• Li C, Yang C, Chen M, Chen X, Hou L, Zhao H: Adjustment of familial relatedness in association test for rare variants. BMC Proc. 2014; 2014 Jun 17. PMID: 25519384
• Chen M, Yang C, Li C, Hou L, Chen X, Zhao H: Admixture mapping analysis in the context of GWAS with GAW18 data. BMC Proc. 2014; 2014 Jun 17. PMID: 25519317
• Chung LM, Colangelo CM, Zhao H: Data Pre-Processing for Label-Free Multiple Reaction Monitoring (MRM) Experiments. Biology (Basel). 2014 Jun 5; 2014 Jun 5. PMID: 24905083
• Nish SA, Schenten D, Wunderlich FT, Pope SD, Gao Y, Hoshi N, Yu S, Yan X, Lee HK, Pasman L, Brodsky I, Yordy B, Zhao H, Brüning J, Medzhitov R: T cell-intrinsic role of IL-6 signaling in primary and memory responses. Elife. 2014 May 19; 2014 May 19. PMID: 24842874
• Hou L, Chen M, Zhang CK, Cho J, Zhao H: Guilt by rewiring: gene prioritization through network rewiring in genome wide association studies. Hum Mol Genet. 2014 May 15; 2013 Dec 30. PMID: 24381306
• Zhu R, Zhao H, Ma S: Identifying gene-environment and gene-gene interactions using a progressive penalization approach. Genet Epidemiol. 2014 May; 2014 Apr 10. PMID: 24723356
• Li C, Yang C, Gelernter J, Zhao H: Improving genetic risk prediction by leveraging pleiotropy. Hum Genet. 2014 May; 2013 Dec 13. PMID: 24337655
• Yang C, Li C, Kranzler HR, Farrer LA, Zhao H, Gelernter J: Exploring the genetic architecture of alcohol dependence in African-Americans via analysis of a genomewide set of common variants. Hum Genet. 2014 May; 2013 Dec 3. PMID: 24297757
• Gupta AR, Pirruccello M, Cheng F, Kang HJ, Fernandez TV, Baskin JM, Choi M, Liu L, Ercan-Sencicek AG, Murdoch JD, Klei L, Neale BM, Franjic D, Daly MJ, Lifton RP, De Camilli P, Zhao H, Sestan N, State MW: Rare deleterious mutations of the gene EFR3A in autism spectrum disorders. Mol Autism. 2014; 2014 Apr 29. PMID: 24860643
• Ryslik GA, Cheng Y, Cheung KH, Modis Y, Zhao H: A graph theoretic approach to utilizing protein structure to identify non-random somatic mutations. BMC Bioinformatics. 2014 Mar 26; 2014 Mar 26. PMID: 24669769
• Li D, Sulovari A, Cheng C, Zhao H, Kranzler HR, Gelernter J: Association of gamma-aminobutyric acid A receptor α2 gene (GABRA2) with alcohol use disorder. Neuropsychopharmacology. 2014 Mar; 2013 Oct 18. PMID: 24136292
• Brown JE, Evans BR, Zheng W, Obas V, Barrera-Martinez L, Egizi A, Zhao H, Caccone A, Powell JR: Human impacts have shaped historical and recent evolution in Aedes aegypti, the dengue and yellow fever mosquito. Evolution. 2014 Feb; 2013 Oct 23. PMID: 24111703
• Assis DN, Leng L, Du X, Zhang CK, Grieb G, Merk M, Garcia AB, McCrann C, Chapiro J, Meinhardt A, Mizue Y, Nikolic-Paterson DJ, Bernhagen J, Kaplan MM, Zhao H, Boyer JL, Bucala R: The role of macrophage migration inhibitory factor in autoimmune liver disease. Hepatology. 2014 Feb; 2013 Dec 20. PMID: 23913513
• Schenten D, Nish SA, Yu S, Yan X, Lee HK, Brodsky I, Pasman L, Yordy B, Wunderlich FT, Brüning JC, Zhao H, Medzhitov R: Signaling through the adaptor molecule MyD88 in CD4+ T cells is required to overcome suppression by regulatory T cells. Immunity. 2014 Jan 16. PMID: 24439266
• Xu F, Li L, Schulz VP, Gallagher PG, Xiang B, Zhao H, Li P: Cytogenomic mapping and bioinformatic mining reveal interacting brain expressed genes for intellectual disability. Mol Cytogenet. 2014 Jan 10; 2014 Jan 10. PMID: 24410907
• Wang L, Rundek T, Beecham A, Hudson B, Blanton SH, Zhao H, Sacco RL, Dong C: Genome-wide interaction study identifies RCBTB1 as a modifier for smoking effect on carotid intima-media thickness. Arterioscler Thromb Vasc Biol. 2014 Jan; 2013 Nov 7. PMID: 24202307
• Kim M, Chen X, Chin LJ, Paranjape T, Speed WC, Kidd KK, Zhao H, Weidhaas JB, Slack FJ: Extensive sequence variation in the 3' untranslated region of the KRAS gene in lung and ovarian cancer cases. Cell Cycle. 2014; 2014 Feb 3. PMID: 24552817
• Chun H, Chen M, Li B, Zhao H: Joint conditional Gaussian graphical models with multiple sources of genomic data. Front Genet. 2013; 2013 Dec 17. PMID: 24381584
• Hou L, Zhao H: A review of post-GWAS prioritization approaches. Front Genet. 2013 Dec 9; 2013 Dec 9. PMID: 24367376
• Han S, Yang BZ, Kranzler HR, Liu X, Zhao H, Farrer LA, Boerwinkle E, Potash JB, Gelernter J: Integrating GWASs and human protein interaction networks identifies a gene subnetwork underlying alcohol dependence. Am J Hum Genet. 2013 Dec 5; 2013 Nov 21. PMID: 24268660
• Chen M, Gunel M, Zhao H: SomatiCA: identifying, characterizing and quantifying somatic copy number aberrations from cancer genome sequencing data. PLoS One. 2013; 2013 Nov 12. PMID: 24265680
• Xie P, Kranzler HR, Yang C, Zhao H, Farrer LA, Gelernter J: Genome-wide association study identifies new susceptibility loci for posttraumatic stress disorder. Biol Psychiatry. 2013 Nov 1; 2013 May 28. PMID: 23726511
• Zhang S, Zhao H: Normalized modularity optimization method for community identification with degree adjustment. Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Nov; 2013 Nov 4. PMID: 24329313
• Gao Y, Nish SA, Jiang R, Hou L, Licona-Limón P, Weinstein JS, Zhao H, Medzhitov R: Control of T helper 2 responses by transcription factor IRF4-dependent dendritic cells. Immunity. 2013 Oct 17; 2013 Sep 26. PMID: 24076050
• Chen X, Slack FJ, Zhao H: Joint analysis of expression profiles from multiple cancers improves the identification of microRNA-gene interactions. Bioinformatics. 2013 Sep 1; 2013 Jun 14. PMID: 23772050
• Qian F, Chung L, Zheng W, Bruno V, Alexander RP, Wang Z, Wang X, Kurscheid S, Zhao H, Fikrig E, Gerstein M, Snyder M, Montgomery RR: Identification of genes critical for resistance to infection by West Nile virus using RNA-Seq analysis. Viruses. 2013 Jul 8; 2013 Jul 8. PMID: 23881275
• Saxe JP, Chen M, Zhao H, Lin H: Tdrkh is essential for spermatogenesis and participates in primary piRNA biogenesis in the germline. EMBO J. 2013 Jul 3; 2013 May 28. PMID: 23714778
• Zhang CK, Hewett J, Hemming J, Grant T, Zhao H, Abraham C, Oikonomou I, Kanakia M, Cho JH, Proctor DD: The influence of depression on quality of life in patients with inflammatory bowel disease. Inflamm Bowel Dis. 2013 Jul. PMID: 23669400
• Ma H, Zhao H: Drug target inference through pathway analysis of genomics data. Adv Drug Deliv Rev. 2013 Jun 30; 2013 Jan 28. PMID: 23369829
• Zhang H, Wang F, Kranzler HR, Zhao H, Gelernter J: Profiling of childhood adversity-associated DNA methylation changes in alcoholic patients and healthy controls. PLoS One. 2013; 2013 Jun 14. PMID: 23799031
• Ryslik GA, Cheng Y, Cheung KH, Modis Y, Zhao H: Utilizing protein structure to identify non-random somatic mutations. BMC Bioinformatics. 2013 Jun 13; 2013 Jun 13. PMID: 23758891
• Zaidi S, Choi M, Wakimoto H, Ma L, Jiang J, Overton JD, Romano-Adesman A, Bjornson RD, Breitbart RE, Brown KK, Carriero NJ, Cheung YH, Deanfield J, DePalma S, Fakhro KA, Glessner J, Hakonarson H, Italia MJ, Kaltman JR, Kaski J, Kim R, Kline JK, Lee T, Leipzig J, Lopez A, Mane SM, Mitchell LE, Newburger JW, Parfenov M, Pe'er I, Porter G, Roberts AE, Sachidanandam R, Sanders SJ, Seiden HS, State MW, Subramanian S, Tikhonova IR, Wang W, Warburton D, White PS, Williams IA, Zhao H, Seidman JG, Brueckner M, Chung WK, Gelb BD, Goldmuntz E, Seidman CE, Lifton RP: De novo mutations in histone-modifying genes in congenital heart disease. Nature. 2013 Jun 13; 2013 May 12. PMID: 23665959
• Ferguson J, Wheeler W, Fu Y, Prokunina-Olsson L, Zhao H, Sampson J: Statistical tests for detecting associations with groups of genetic variants: generalization, evaluation, and implementation. Eur J Hum Genet. 2013 Jun; 2012 Oct 24. PMID: 23092956
• Yang C, Wang L, Zhang S, Zhao H: Accounting for non-genetic factors by low-rank representation and sparse regression for eQTL mapping. Bioinformatics. 2013 Apr 15; 2013 Feb 17. PMID: 23419377
• Chung LM, Ferguson JP, Zheng W, Qian F, Bruno V, Montgomery RR, Zhao H: Differential expression analysis for paired RNA-Seq data. BMC Bioinformatics. 2013 Mar 27; 2013 Mar 27. PMID: 23530607
• Zheng W, Zhao H: Studying the evolution of transcription factor binding events using multi-species ChIP-Seq data. Stat Appl Genet Mol Biol. 2013 Mar 26; 2013 Mar 26. PMID: 23446869
• Qian F, Bolen CR, Jing C, Wang X, Zheng W, Zhao H, Fikrig E, Bruce RD, Kleinstein SH, Montgomery RR: Impaired toll-like receptor 3-mediated immune responses from macrophages of patients chronically infected with hepatitis C virus. Clin Vaccine Immunol. 2013 Feb; 2012 Dec 5. PMID: 23220997
• Zhang H, Herman AI, Kranzler HR, Anton RF, Zhao H, Zheng W, Gelernter J: Array-based profiling of DNA methylation changes associated with alcohol dependence. Alcohol Clin Exp Res. 2013 Jan; 2012 Aug 24. PMID: 22924764
• Ferguson JP, Cho JH, Yang C, Zhao H: Empirical Bayes correction for the Winner's Curse in genetic association studies. Genet Epidemiol. 2013 Jan; 2012 Sep 25. PMID: 23012258
• Ma H, Zhao H: FacPad: Bayesian sparse factor modeling for the inference of pathways responsive to drug treatment. Bioinformatics. 2012 Oct 15; 2012 Aug 24. PMID: 22923307
• Ge X, Ren Y, Bartulos O, Lee MY, Yue Z, Kim KY, Li W, Amos PJ, Bozkulak EC, Iyer A, Zheng W, Zhao H, Martin KA, Kotton DN, Tellides G, Park IH, Yue L, Qyang Y: Modeling supravalvular aortic stenosis syndrome with human induced pluripotent stem cells. Circulation. 2012 Oct 2; 2012 Aug 22. PMID: 22914687
• Lowthert L, Leffert J, Lin A, Umlauf S, Maloney K, Muralidharan A, Lorberg B, Mane S, Zhao H, Sinha R, Bhagwagar Z, Beech R: Increased ratio of anti-apoptotic to pro-apoptotic Bcl2 gene-family members in lithium-responders one month after treatment initiation. Biol Mood Anxiety Disord. 2012 Sep 12; 2012 Sep 12. PMID: 22967286
• Beech RD, Qu J, Leffert JJ, Lin A, Hong KA, Hansen J, Umlauf S, Mane S, Zhao H, Sinha R: Altered expression of cytokine signaling pathway genes in peripheral blood cells of alcohol dependent subjects: preliminary findings. Alcohol Clin Exp Res. 2012 Sep; 2012 Apr 4. PMID: 22471388
• Chen X, Listman JB, Slack FJ, Gelernter J, Zhao H: Biases and errors on allele frequency estimation and disease association tests of next-generation sequencing of pooled samples. Genet Epidemiol. 2012 Sep; 2012 Jun 6. PMID: 22674656
• Li D, Zhao H, Gelernter J: Further clarification of the contribution of the ADH1C gene to vulnerability of alcoholism and selected liver diseases. Hum Genet. 2012 Aug; 2012 Apr 5. PMID: 22476623
• Ma H, Zhao H: iFad: an integrative factor analysis model for drug-pathway association inference. Bioinformatics. 2012 Jul 15; 2012 May 10. PMID: 22581178
• Li D, Zhao H, Gelernter J: Strong protective effect of the aldehyde dehydrogenase gene (ALDH2) 504lys (*2) allele against alcoholism and alcohol-induced medical diseases in Asians. Hum Genet. 2012 May; 2011 Nov 20. PMID: 22102315
• Li D, Zhao H, Kranzler HR, Oslin D, Anton RF, Farrer LA, Gelernter J: Association of COL25A1 with comorbid antisocial personality disorder and substance dependence. Biol Psychiatry. 2012 Apr 15; 2012 Jan 31. PMID: 22297151
• Zhang CK, Stein PB, Liu J, Wang Z, Yang R, Cho JH, Gregersen PK, Aerts JM, Zhao H, Pastores GM, Mistry PK: Genome-wide association study of N370S homozygous Gaucher disease reveals the candidacy of CLN8 gene as a genetic modifier contributing to extreme phenotypic variation. Am J Hematol. 2012 Apr; 2012 Mar 3. PMID: 22388998
• Morino K, Petersen KF, Sono S, Choi CS, Samuel VT, Lin A, Gallo A, Zhao H, Kashiwagi A, Goldberg IJ, Wang H, Eckel RH, Maegawa H, Shulman GI: Regulation of mitochondrial biogenesis by lipoprotein lipase in muscle of insulin-resistant offspring of parents with type 2 diabetes. Diabetes. 2012 Apr; 2012 Feb 24. PMID: 22368174
• Chen D, Zheng W, Lin A, Uyhazi K, Zhao H, Lin H: Pumilio 1 suppresses multiple activators of p53 to safeguard spermatogenesis. Curr Biol. 2012 Mar 6; 2012 Feb 16. PMID: 22342750
• Santoro N, Zhang CK, Zhao H, Pakstis AJ, Kim G, Kursawe R, Dykas DJ, Bale AE, Giannini C, Pierpont B, Shaw MM, Groop L, Caprio S: Variant in the glucokinase regulatory protein (GCKR) gene is associated with fatty liver in obese children and adolescents. Hepatology. 2012 Mar; 2011 Dec 18. PMID: 22105854
• Ferguson JP, Cho JH, Zhao H: A new approach for the joint analysis of multiple ChIP-seq libraries with application to histone modification. Stat Appl Genet Mol Biol. 2012 Feb 10; 2012 Feb 10. PMID: 22499701
• Li G, Gelernter J, Kranzler HR, Zhao H: M(3): an improved SNP calling algorithm for Illumina BeadArray data. Bioinformatics. 2012 Feb 1; 2011 Dec 8. PMID: 22155947
• Li B, Chuns H, Zhao H: Sparse Estimation of Conditional Graphical Models With Application to Gene Networks. J Am Stat Assoc. 2012 Jan 1. PMID: 24574574
• Zuo L, Gelernter J, Zhang CK, Zhao H, Lu L, Kranzler HR, Malison RT, Li CS, Wang F, Zhang XY, Deng HW, Krystal JH, Zhang F, Luo X: Genome-wide association study of alcohol dependence implicates KIAA0040 on chromosome 1q. Neuropsychopharmacology. 2012 Jan; 2011 Sep 28. PMID: 21956439
• Zhang W, Ferguson J, Ng SM, Hui K, Goh G, Lin A, Esplugues E, Flavell RA, Abraham C, Zhao H, Cho JH: Effector CD4+ T cell expression signatures and immune-mediated disease associated genes. PLoS One. 2012; 2012 Jun 8. PMID: 22715389
• Li G, Ferguson J, Zheng W, Lee JS, Zhang X, Li L, Kang J, Yan X, Zhao H: Large-scale risk prediction applied to Genetic Analysis Workshop 17 mini-exome sequence data. BMC Proc. 2011 Nov 29; 2011 Nov 29. PMID: 22373389
• Yan X, Li L, Lee JS, Zheng W, Ferguson J, Zhao H: Detecting functional rare variants by collapsing and incorporating functional annotation in Genetic Analysis Workshop 17 mini-exome data. BMC Proc. 2011 Nov 29; 2011 Nov 29. PMID: 22373324
• Li L, Zheng W, Lee JS, Zhang X, Ferguson J, Yan X, Zhao H: Collapsing-based and kernel-based single-gene analyses applied to Genetic Analysis Workshop 17 mini-exome data. BMC Proc. 2011; 2011 Nov 29. PMID: 22373309
• Kang J, Zheng W, Li L, Lee JS, Yan X, Zhao H: Use of Bayesian networks to dissect the complexity of genetic disease: application to the Genetic Analysis Workshop 17 simulated data. BMC Proc. 2011 Nov 29; 2011 Nov 29. PMID: 22373110
• Kato M, Chen X, Inukai S, Zhao H, Slack FJ: Age-associated changes in expression of small, noncoding RNAs, including microRNAs, in C. elegans. RNA. 2011 Oct; 2011 Aug 2. PMID: 21810936
• Xie P, Kranzler HR, Krauthammer M, Cosgrove KP, Oslin D, Anton RF, Farrer LA, Picciotto MR, Krystal JH, Zhao H, Gelernter J: Rare nonsynonymous variants in alpha-4 nicotinic acetylcholine receptor gene protect against nicotine dependence. Biol Psychiatry. 2011 Sep 15; 2011 Jun 17. PMID: 21683344
• Li D, Zhao H, Gelernter J: Strong association of the alcohol dehydrogenase 1B gene (ADH1B) with alcohol dependence and alcohol-induced medical diseases. Biol Psychiatry. 2011 Sep 15; 2011 Apr 17. PMID: 21497796
• Chun H, Ballard DH, Cho J, Zhao H: Identification of association between disease and multiple markers via sparse partial least-squares regression. Genet Epidemiol. 2011 Sep; 2011 Jun 15. PMID: 21678491
• Zheng W, Chung LM, Zhao H: Bias detection and correction in RNA-Sequencing data. BMC Bioinformatics. 2011 Jul 19; 2011 Jul 19. PMID: 21771300
• Kang J, Kugathasan S, Georges M, Zhao H, Cho JH, NIDDK IBD Genetics Consortium.: Improved risk prediction for Crohn's disease with a multi-locus approach. Hum Mol Genet. 2011 Jun 15; 2011 Mar 22. PMID: 21427131
• Qian F, Wang X, Zhang L, Lin A, Zhao H, Fikrig E, Montgomery RR: Impaired interferon signaling in dendritic cells from older donors infected in vitro with West Nile virus. J Infect Dis. 2011 May 15; 2011 Mar 11. PMID: 21398396
• Ma H, Schadt EE, Kaplan LM, Zhao H: COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method. Bioinformatics. 2011 May 1; 2011 Mar 16. PMID: 21414987
• Lee JS, Choi M, Yan X, Lifton RP, Zhao H: On optimal pooling designs to identify rare variants through massive resequencing. Genet Epidemiol. 2011 Apr; 2011 Jan 19. PMID: 21254222
• Qi X, Zhao H: Some theoretical properties of Silverman's method for Smoothed functional principal component analysis. J Multivar Anal. 2011 Apr 1. PMID: 21516205
• Chang X, Liu F, Wang X, Lin A, Zhao H, Su B: The kinases MEKK2 and MEKK3 regulate transforming growth factor-β-mediated helper T cell differentiation. Immunity. 2011 Feb 25; 2011 Feb 17. PMID: 21333552
• Luo R, Zhao H: BAYESIAN HIERARCHICAL MODELING FOR SIGNALING PATHWAY INFERENCE FROM SINGLE CELL INTERVENTIONAL DATA. Ann Appl Stat. 2011. PMID: 22162986
• Zheng W, Gianoulis TA, Karczewski KJ, Zhao H, Snyder M: Regulatory variation within and between species. Annu Rev Genomics Hum Genet. 2011. PMID: 21721942
• Zuo L, Zhang CK, Wang F, Li CS, Zhao H, Lu L, Zhang XY, Lu L, Zhang H, Zhang F, Krystal JH, Luo X: A novel, functional and replicable risk gene region for alcohol dependence identified by genome-wide association study. PLoS One. 2011; 2011 Nov 7. PMID: 22096494
• Berger C, Hoffmann K, Vasquez JG, Mane S, Lewis J, Filler R, Lin A, Zhao H, Durazzo T, Baird A, Lin W, Foss F, Christensen I, Girardi M, Tigelaar R, Edelson R: Rapid generation of maturationally synchronized human dendritic cells: contribution to the clinical efficacy of extracorporeal photochemotherapy. Blood. 2010 Dec 2; 2010 Aug 18. PMID: 20720185
• Huang S, Tong T, Zhao H: Bias-corrected diagonal discriminant rules for high-dimensional classification. Biometrics. 2010 Dec. PMID: 20222939
• Beech RD, Lowthert L, Leffert JJ, Mason PN, Taylor MM, Umlauf S, Lin A, Lee JY, Maloney K, Muralidharan A, Lorberg B, Zhao H, Newton SS, Mane S, Epperson CN, Sinha R, Blumberg H, Bhagwagar Z: Increased peripheral blood expression of electron transport chain genes in bipolar depression. Bipolar Disord. 2010 Dec. PMID: 21176028
• Mistry PK, Liu J, Yang M, Nottoli T, McGrath J, Jain D, Zhang K, Keutzer J, Chuang WL, Mehal WZ, Zhao H, Lin A, Mane S, Liu X, Peng YZ, Li JH, Agrawal M, Zhu LL, Blair HC, Robinson LJ, Iqbal J, Sun L, Zaidi M: Glucocerebrosidase gene-deficient mouse recapitulates Gaucher disease displaying cellular and molecular dysregulation beyond the macrophage. Proc Natl Acad Sci U S A. 2010 Nov 9; 2010 Oct 20. PMID: 20962279
• Santoro N, Kursawe R, D'Adamo E, Dykas DJ, Zhang CK, Bale AE, Calí AM, Narayan D, Shaw MM, Pierpont B, Savoye M, Lartaud D, Eldrich S, Cushman SW, Zhao H, Shulman GI, Caprio S: A common variant in the patatin-like phospholipase 3 gene (PNPLA3) is associated with fatty liver disease in obese children and adolescents. Hepatology. 2010 Oct. PMID: 20803499
• Dávalos A, Fernández-Hernando C, Sowa G, Derakhshan B, Lin MI, Lee JY, Zhao H, Luo R, Colangelo C, Sessa WC: Quantitative proteomics of caveolin-1-regulated proteins: characterization of polymerase i and transcript release factor/CAVIN-1 IN endothelial cells. Mol Cell Proteomics. 2010 Oct; 2010 Jun 28. PMID: 20585024
• Hu JX, Zhao H, Zhou HH: False Discovery Rate Control With Groups. J Am Stat Assoc. 2010 Sep 1. PMID: 21931466
• Zheng W, Zhao H, Mancera E, Steinmetz LM, Snyder M: Genetic analysis of variation in transcription factor binding in yeast. Nature. 2010 Apr 22; 2010 Mar 17. PMID: 20237471
• Ballard DH, Cho J, Zhao H: Comparisons of multi-marker association methods to detect association between a candidate region and disease. Genet Epidemiol. 2010 Apr. PMID: 19810024
• Kang J, Cho J, Zhao H: Practical issues in building risk-predicting models for complex diseases. J Biopharm Stat. 2010 Mar. PMID: 20309766
• Mustavich LF, Miller P, Kidd KK, Zhao H: Using a pharmacokinetic model to relate an individual's susceptibility to alcohol dependence to genotypes. Hum Hered. 2010; 2010 Aug 12. PMID: 20714161
• Ballard DH, Aporntewan C, Lee JY, Lee JS, Wu Z, Zhao H: A pathway analysis applied to Genetic Analysis Workshop 16 genome-wide rheumatoid arthritis data. BMC Proc. 2009 Dec 15; 2009 Dec 15. PMID: 20018088
• Wu Z, Aporntewan C, Ballard DH, Lee JY, Lee JS, Zhao H: Two-stage joint selection method to identify candidate markers from genome-wide association studies. BMC Proc. 2009 Dec 15; 2009 Dec 15. PMID: 20018019
• Aporntewan C, Ballard DH, Lee JY, Lee JS, Wu Z, Zhao H: Gene hunting of the Genetic Analysis Workshop 16 rheumatoid arthritis data using rough set theory. BMC Proc. 2009 Dec 15; 2009 Dec 15. PMID: 20017992
• Sun N, Zhao H: Reconstructing transcriptional regulatory networks through genomics data. Stat Methods Med Res. 2009 Dec. PMID: 20048387
• Luo R, Colangelo CM, Sessa WC, Zhao H: Bayesian Analysis of iTRAQ Data with Nonrandom Missingness: Identification of Differentially Expressed Proteins. Stat Biosci. 2009 Nov. PMID: 21927625
• Wu Z, Zhao H: Statistical power of model selection strategies for genome-wide association studies. PLoS Genet. 2009 Jul; 2009 Jul 31. PMID: 19649321
• Sampson JN, Zhao H: Genotyping and inflated type I error rate in genome-wide association case/control studies. BMC Bioinformatics. 2009 Feb 23; 2009 Feb 23. PMID: 19236714
• Jiao Y, Tausta SL, Gandotra N, Sun N, Liu T, Clay NK, Ceserani T, Chen M, Ma L, Holford M, Zhang HY, Zhao H, Deng XW, Nelson T: A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies. Nat Genet. 2009 Feb; 2009 Jan 4. PMID: 19122662
• Datta D, Zhao H: Effect of false positive and false negative rates on inference of binding target conservation across different conditions and species from ChIP-chip data. BMC Bioinformatics. 2009 Jan 19; 2009 Jan 19. PMID: 19152696
• Holford ME, Rajeevan H, Zhao H, Kidd KK, Cheung KH: Semantic Web-based integration of cancer pathways and allele frequency data. Cancer Inform. 2009 Jan 15; 2009 Jan 15. PMID: 19458791
• Sampson J, Zhao H: Identifying individuals in a complex mixture of DNA with unknown ancestry. Stat Appl Genet Mol Biol. 2009; 2009 Sep 9. PMID: 19799556
• Budel S, Padukkavidana T, Liu BP, Feng Z, Hu F, Johnson S, Lauren J, Park JH, McGee AW, Liao J, Stillman A, Kim JE, Yang BZ, Sodi S, Gelernter J, Zhao H, Hisama F, Arnsten AF, Strittmatter SM: Genetic variants of Nogo-66 receptor with possible association to schizophrenia block myelin inhibition of axon growth. J Neurosci. 2008 Dec 3. PMID: 19052207
• Yang BZ, Kranzler HR, Zhao H, Gruen JR, Luo X, Gelernter J: Haplotypic variants in DRD2, ANKK1, TTC12, and NCAM1 are associated with comorbid alcohol and drug dependence. Alcohol Clin Exp Res. 2008 Dec; 2008 Sep 30. PMID: 18828801
• Xiang B, Li A, Valentin D, Nowak NJ, Zhao H, Li P: Analytical and clinical validity of whole-genome oligonucleotide array comparative genomic hybridization for pediatric patients with mental retardation and developmental delay. Am J Med Genet A. 2008 Aug 1. PMID: 18627053
• Ji W, Foo JN, O'Roak BJ, Zhao H, Larson MG, Simon DB, Newton-Cheh C, State MW, Levy D, Lifton RP: Rare independent mutations in renal salt handling genes contribute to blood pressure variation. Nat Genet. 2008 May; 2008 Apr 6. PMID: 18391953
• Datta D, Zhao H: Statistical methods to infer cooperative binding among transcription factors in Saccharomyces cerevisiae. Bioinformatics. 2008 Feb 15; 2007 Nov 7. PMID: 17989095
• Pang H, Zhao H: Building pathway clusters from Random Forests classification using class votes. BMC Bioinformatics. 2008 Feb 6; 2008 Feb 6. PMID: 18254968
• Yang BZ, Kranzler HR, Zhao H, Gruen JR, Luo X, Gelernter J: Association of haplotypic variants in DRD2, ANKK1, TTC12 and NCAM1 to alcohol dependence in independent case control and family samples. Hum Mol Genet. 2007 Dec 1; 2007 Aug 30. PMID: 17761687
• Dinu V, Zhao H, Miller PL: Integrating domain knowledge with statistical and data mining methods for high-density genomic SNP disease association analysis. J Biomed Inform. 2007 Dec; 2007 Jun 10. PMID: 17625973
• Kim I, Liu Y, Zhao H: Bayesian methods for predicting interacting protein pairs using domain information. Biometrics. 2007 Sep. PMID: 17825014
• Dinu V, Miller PL, Zhao H: Evidence for association between multiple complement pathway genes and AMD. Genet Epidemiol. 2007 Apr. PMID: 17266113
• Lee J, He K, Stolc V, Lee H, Figueroa P, Gao Y, Tongprasit W, Zhao H, Lee I, Deng XW: Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development. Plant Cell. 2007 Mar; 2007 Mar 2. PMID: 17337630
• Huang S, Ballard D, Zhao H: The role of heritability in mapping expression quantitative trait loci. BMC Proc. 2007; 2007 Dec 18. PMID: 18466589
• Lee TS, Mane S, Eid T, Zhao H, Lin A, Guan Z, Kim JH, Schweitzer J, King-Stevens D, Weber P, Spencer SS, Spencer DD, de Lanerolle NC: Gene expression in temporal lobe epilepsy is consistent with increased release of glutamate by astrocytes. Mol Med. 2007 Jan-Feb. PMID: 17515952
• Wu SP, Leng L, Feng Z, Liu N, Zhao H, McDonald C, Lee A, Arnett FC, Gregersen PK, Mayes MD, Bucala R: Macrophage migration inhibitory factor promoter polymorphisms and the clinical expression of scleroderma. Arthritis Rheum. 2006 Nov. PMID: 17075815
• Zhang SS, Xu X, Liu MG, Zhao H, Soares MB, Barnstable CJ, Fu XY: A biphasic pattern of gene expression during mouse retina development. BMC Dev Biol. 2006 Oct 17; 2006 Oct 17. PMID: 17044933
• Pang H, Lin A, Holford M, Enerson BE, Lu B, Lawton MP, Floyd E, Zhao H: Pathway analysis using random forests classification and regression. Bioinformatics. 2006 Aug 15; 2006 Jun 29. PMID: 16809386
• Tsubouchi T, Zhao H, Roeder GS: The meiosis-specific zip4 protein regulates crossover distribution by promoting synaptonemal complex formation together with zip2. Dev Cell. 2006 Jun. PMID: 16740482
• Sun N, Carroll RJ, Zhao H: Bayesian error analysis model for reconstructing transcriptional regulatory networks. Proc Natl Acad Sci U S A. 2006 May 23; 2006 May 15. PMID: 16702552
• Gelernter J, Panhuysen C, Wilcox M, Hesselbrock V, Rounsaville B, Poling J, Weiss R, Sonne S, Zhao H, Farrer L, Kranzler HR: Genomewide linkage scan for opioid dependence and related traits. Am J Hum Genet. 2006 May; 2006 Mar 16. PMID: 16642432
• You X, Pan M, Gao W, Shiah HS, Tao J, Zhang D, Koumpouras F, Wang S, Zhao H, Madri JA, Baker D, Cheng YC, Yin Z: Effects of a novel tylophorine analog on collagen-induced arthritis through inhibition of the innate immune response. Arthritis Rheum. 2006 Mar. PMID: 16508970
• Yu W, Wu B, Lin N, Stone K, Williams K, Zhao H: Detecting and aligning peaks in mass spectrometry data with applications to MALDI. Comput Biol Chem. 2006 Feb; 2005 Nov 17. PMID: 16298163
• Yu W, Wu B, Liu J, Li X, Stone K, Williams KR, Zhao H: MALDI-MS data analysis for disease biomarker discovery. Methods Mol Biol. 2006. PMID: 16785651
• Enerson BE, Lin A, Lu B, Zhao H, Lawton MP, Floyd E: Acute drug-induced vascular injury in beagle dogs: pathology and correlating genomic expression. Toxicol Pathol. 2006. PMID: 16507541
• Huang S, Wang S, Liu N, Chen L, Oh C, Zhao H: Whole-genome association analysis to identify markers associated with recombination rates using single-nucleotide polymorphisms and microsatellites. BMC Genet. 2005 Dec 30; 2005 Dec 30. PMID: 16451663
• Liu N, Chen L, Wang S, Oh C, Zhao H: Comparison of single-nucleotide polymorphisms and microsatellites in inference of population structure. BMC Genet. 2005 Dec 30; 2005 Dec 30. PMID: 16451635
• Chen L, Liu N, Wang S, Oh C, Carriero NJ, Zhao H: Whole-genome association studies on alcoholism comparing different phenotypes using single-nucleotide polymorphisms and microsatellites. BMC Genet. 2005 Dec 30; 2005 Dec 30. PMID: 16451589
• Oh C, Wang S, Liu N, Chen L, Zhao H: A Bayesian genome screening of maximum number of drinks as an alcoholism phenotype with the new Haseman-Elston method. BMC Genet. 2005 Dec 30; 2005 Dec 30. PMID: 16451573
• Chen L, Zhao H: Negative correlation between compositional symmetries and local recombination rates. Bioinformatics. 2005 Nov 1; 2005 Aug 30. PMID: 16131519
• Huang T, Wu B, Lizardi P, Zhao H: Detection of DNA copy number alterations using penalized least squares regression. Bioinformatics. 2005 Oct 15; 2005 Aug 30. PMID: 16131523
• Yang BZ, Zhao H, Kranzler HR, Gelernter J: Characterization of a likelihood based method and effects of markers informativeness in evaluation of admixture and population group assignment. BMC Genet. 2005 Oct 14; 2005 Oct 14. PMID: 16225681
• Ma L, Chen C, Liu X, Jiao Y, Su N, Li L, Wang X, Cao M, Sun N, Zhang X, Bao J, Li J, Pedersen S, Bolund L, Zhao H, Yuan L, Wong GK, Wang J, Deng XW, Wang J: A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. Genome Res. 2005 Sep. PMID: 16140994
• Liu Y, Liu N, Zhao H: Inferring protein-protein interactions through high-throughput interaction data from diverse organisms. Bioinformatics. 2005 Aug 1; 2005 May 19. PMID: 15905281
• Zou G, Zhao H: Family-based association tests for different family structures using pooled DNA. Ann Hum Genet. 2005 Jul. PMID: 15996171
• Gulcicek EE, Colangelo CM, McMurray W, Stone K, Williams K, Wu T, Zhao H, Spratt H, Kurosky A, Wu B: Proteomics and the analysis of proteomic data: an overview of current protein-profiling technologies. Curr Protoc Bioinformatics. 2005 Jul. PMID: 18428746
• Jiao Y, Jia P, Wang X, Su N, Yu S, Zhang D, Ma L, Feng Q, Jin Z, Li L, Xue Y, Cheng Z, Zhao H, Han B, Deng XW: A tiling microarray expression analysis of rice chromosome 4 suggests a chromosome-level regulation of transcription. Plant Cell. 2005 Jun; 2005 Apr 29. PMID: 15863518
• Mor G, Visintin I, Lai Y, Zhao H, Schwartz P, Rutherford T, Yue L, Bray-Ward P, Ward DC: Serum protein markers for early detection of ovarian cancer. Proc Natl Acad Sci U S A. 2005 May 24; 2005 May 12. PMID: 15890779
• Yang BZ, Zhao H, Kranzler HR, Gelernter J: Practical population group assignment with selected informative markers: characteristics and properties of Bayesian clustering via STRUCTURE. Genet Epidemiol. 2005 May. PMID: 15782414
• Ma L, Sun N, Liu X, Jiao Y, Zhao H, Deng XW: Organ-specific expression of Arabidopsis genome during development. Plant Physiol. 2005 May. PMID: 15888681
• Holford M, Li N, Nadkarni P, Zhao H: VitaPad: visualization tools for the analysis of pathway data. Bioinformatics. 2005 Apr 15; 2004 Nov 25. PMID: 15564306
• Chen L, Zhao H: Gene expression analysis reveals that histone deacetylation sites may serve as partitions of chromatin gene expression domains. BMC Genomics. 2005 Mar 23; 2005 Mar 23. PMID: 15788094
• Zhang SS, Xu X, Li J, Liu MG, Zhao H, Soares MB, Barnstable CJ, Fu XY: Comprehensive in silico functional specification of mouse retina transcripts. BMC Genomics. 2005 Mar 18; 2005 Mar 18. PMID: 15777472
• Carriero N, Osier MV, Cheung KH, Miller PL, Gerstein M, Zhao H, Wu B, Rifkin S, Chang J, Zhang H, White K, Williams K, Schultz M: A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studies. J Am Med Inform Assoc. 2005 Jan-Feb; 2004 Oct 18. PMID: 15492032
• Liu N, Sawyer SL, Mukherjee N, Pakstis AJ, Kidd JR, Kidd KK, Brookes AJ, Zhao H: Haplotype block structures show significant variation among populations. Genet Epidemiol. 2004 Dec. PMID: 15389924
• Lai Y, Wu B, Chen L, Zhao H: A statistical method for identifying differential gene-gene co-expression patterns. Bioinformatics. 2004 Nov 22; 2004 Jul 1. PMID: 15231528
• Wilson FH, Hariri A, Farhi A, Zhao H, Petersen KF, Toka HR, Nelson-Williams C, Raja KM, Kashgarian M, Shulman GI, Scheinman SJ, Lifton RP: A cluster of metabolic defects caused by mutation in a mitochondrial tRNA. Science. 2004 Nov 12; 2004 Oct 21. PMID: 15498972
• Liu Y, Zhao H: A computational approach for ordering signal transduction pathway components from genomics and proteomics Data. BMC Bioinformatics. 2004 Oct 25; 2004 Oct 25. PMID: 15504238
• Hoek K, Rimm DL, Williams KR, Zhao H, Ariyan S, Lin A, Kluger HM, Berger AJ, Cheng E, Trombetta ES, Wu T, Niinobe M, Yoshikawa K, Hannigan GE, Halaban R: Expression profiling reveals novel pathways in the transformation of melanocytes to melanomas. Cancer Res. 2004 Aug 1. PMID: 15289333
• Marathe R, Guan Z, Anandalakshmi R, Zhao H, Dinesh-Kumar SP: Study of Arabidopsis thaliana resistome in response to cucumber mosaic virus infection using whole genome microarray. Plant Mol Biol. 2004 Jul. PMID: 15604696
• Zou G, Zhao H: The estimation of sibling genetic risk parameters revisited. Genet Epidemiol. 2004 May. PMID: 15095388
• Sun N, Zhao H: Genomic approaches in dissecting complex biological pathways. Pharmacogenomics. 2004 Mar. PMID: 15016608
• Gao Y, Li J, Strickland E, Hua S, Zhao H, Chen Z, Qu L, Deng XW: An arabidopsis promoter microarray and its initial usage in the identification of HY5 binding targets in vitro. Plant Mol Biol. 2004 Mar. PMID: 15356388
• Goh CS, Lan N, Douglas SM, Wu B, Echols N, Smith A, Milburn D, Montelione GT, Zhao H, Gerstein M: Mining the structural genomics pipeline: identification of protein properties that affect high-throughput experimental analysis. J Mol Biol. 2004 Feb 6. PMID: 14741208
• Xia Y, Yu H, Jansen R, Seringhaus M, Baxter S, Greenbaum D, Zhao H, Gerstein M: Analyzing cellular biochemistry in terms of molecular networks. Annu Rev Biochem. 2004. PMID: 15189167
• Zou G, Zhao H: The impacts of errors in individual genotyping and DNA pooling on association studies. Genet Epidemiol. 2004 Jan. PMID: 14691952
• Jiao Y, Yang H, Ma L, Sun N, Yu H, Liu T, Gao Y, Gu H, Chen Z, Wada M, Gerstein M, Zhao H, Qu LJ, Deng XW: A genome-wide analysis of blue-light regulation of Arabidopsis transcription factor gene expression during seedling development. Plant Physiol. 2003 Dec; 2003 Nov 6. PMID: 14605227
• Pan D, Sun N, Cheung KH, Guan Z, Ma L, Holford M, Deng X, Zhao H: PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis. BMC Bioinformatics. 2003 Nov 7; 2003 Nov 7. PMID: 14604444
• Wang S, Zhao H: Sample size needed to detect gene-gene interactions using association designs. Am J Epidemiol. 2003 Nov 1. PMID: 14585768
• Sun N, Ma L, Pan D, Zhao H, Deng XW: Evaluation of light regulatory potential of Calvin cycle steps based on large-scale gene expression profiling data. Plant Mol Biol. 2003 Nov. PMID: 15010613
• Zheng L, Wang S, Romans P, Zhao H, Luna C, Benedict MQ: Quantitative trait loci in Anopheles gambiae controlling the encapsulation response against Plasmodium cynomolgi Ceylon. BMC Genet. 2003 Oct 24; 2003 Oct 24. PMID: 14577840
• Wu B, Abbott T, Fishman D, McMurray W, Mor G, Stone K, Ward D, Williams K, Zhao H: Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data. Bioinformatics. 2003 Sep 1. PMID: 12967959
• Garcia-Rostan G, Zhao H, Camp RL, Pollan M, Herrero A, Pardo J, Wu R, Carcangiu ML, Costa J, Tallini G: ras mutations are associated with aggressive tumor phenotypes and poor prognosis in thyroid cancer. J Clin Oncol. 2003 Sep 1. PMID: 12947056
• Sun LV, Chen L, Greil F, Negre N, Li TR, Cavalli G, Zhao H, Van Steensel B, White KP: Protein-DNA interaction mapping using genomic tiling path microarrays in Drosophila. Proc Natl Acad Sci U S A. 2003 Aug 5; 2003 Jul 22. PMID: 12876199
• Luo X, Kranzler HR, Zhao H, Gelernter J: Haplotypes at the OPRM1 locus are associated with susceptibility to substance dependence in European-Americans. Am J Med Genet B Neuropsychiatr Genet. 2003 Jul 1. PMID: 12815747
• Zou G, Pan D, Zhao H: Genotyping error detection through tightly linked markers. Genetics. 2003 Jul. PMID: 12871922
• Wikonkal NM, Remenyik E, Knezevic D, Zhang W, Liu M, Zhao H, Berton TR, Johnson DG, Brash DE: Inactivating E2f1 reverts apoptosis resistance and cancer sensitivity in Trp53-deficient mice. Nat Cell Biol. 2003 Jul. PMID: 12833065
• Ma L, Zhao H, Deng XW: 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. 2003 Mar. PMID: 12538522
• Zhao H, Pfeiffer R, Gail MH: Haplotype analysis in population genetics and association studies. Pharmacogenomics. 2003 Mar. PMID: 12605551
• Wang S, Kidd KK, Zhao H: On the use of DNA pooling to estimate haplotype frequencies. Genet Epidemiol. 2003 Jan. PMID: 12508258
• Zhang S, Zhu X, Zhao H: On a semiparametric test to detect associations between quantitative traits and candidate genes using unrelated individuals. Genet Epidemiol. 2003 Jan. PMID: 12508255
• Zou G, Zhao H: Haplotype frequency estimation in the presence of genotyping errors. Hum Hered. 2003. PMID: 14614247
• Wang H, Ma L, Habashi J, Li J, Zhao H, Deng XW: Analysis of far-red light-regulated genome expression profiles of phytochrome A pathway mutants in Arabidopsis. Plant J. 2002 Dec. PMID: 12472688
• Mani A, Meraji SM, Houshyar R, Radhakrishnan J, Mani A, Ahangar M, Rezaie TM, Taghavinejad MA, Broumand B, Zhao H, Nelson-Williams C, Lifton RP: Finding genetic contributions to sporadic disease: a recessive locus at 12q24 commonly contributes to patent ductus arteriosus. Proc Natl Acad Sci U S A. 2002 Nov 12; 2002 Oct 30. PMID: 12409608
• Ma L, Gao Y, Qu L, Chen Z, Li J, Zhao H, Deng XW: Genomic evidence for COP1 as a repressor of light-regulated gene expression and development in Arabidopsis. Plant Cell. 2002 Oct. PMID: 12368493
• Wu G, Tian X, Nishimura S, Markowitz GS, D'Agati V, Park JH, Yao L, Li L, Geng L, Zhao H, Edelmann W, Somlo S: Trans-heterozygous Pkd1 and Pkd2 mutations modify expression of polycystic kidney disease. Hum Mol Genet. 2002 Aug 1. PMID: 12140187
• Zhang S, Zhao H: Linkage disequilibrium mapping with genotype data. Genet Epidemiol. 2002 Jan. PMID: 11754474
• Zhang S, Zhang K, Li J, Zhao H: On a family-based haplotype pattern mining method for linkage disequilibrium mapping. Pac Symp Biocomput. 2002. PMID: 11928467
• Cheung KH, White K, Hager J, Gerstein M, Reinke V, Nelson K, Masiar P, Srivastava R, Li Y, Li J, Zhao H, Li J, Allison DB, Snyder M, Miller P, Williams K: YMD: a microarray database for large-scale gene expression analysis. Proc AMIA Symp. 2002. PMID: 12463803

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