Publications

Published Papers

Marceau West, R., Lu, W., Rotroff, D. M., Kuenemann, M., Chang, S.M., Wu, M.P., Wagner, M.J., Buse, J.B., Motsinger-Reif, A., Fourches, D., Tzeng J.Y. (2018)
Identifying individual risk rare variants using protein structure-guided local tests.
PLOS Computational Biology, provisionally accepted. [Sofrware]
Jeng, X.J., Zhang, T., Tzeng J.Y. (2018)
Adaptive false negative control under dependence with genomic applications.
Journal of the American Statistical Association, in press. NIHMSID:NIHMS988815
Yao, T.C., Chung, R.H., Lin, C.Y., Tsai, P.C., Chang, W.C., Yeh, K.W., Tsai, M.H., Liao, S.L., Hua, M.C., Lai, S.H., Chang, S.W., Yu, Y.W., Hsu, J.Y., Chang, S.C., Cheng, W.C., Hu, D., Hong, X., Burchard, E.G., Wang, X., Tzeng J.Y., Tsai, H.J., Huang, J.L. (2018)
Genetic loci determining total immunoglobulin E levels from birth through adulthood.
Allergy. Accepted. [Paper]
Wang, C., Tzeng J.Y.*, Wu, P.Z., Preisig, M., Hsiao, C.K.* (*: co-corresponding authors) (2018)
Re-examining dis/similarity-based tests for rare-variant association with case-control samples.
Genetics, 209:105-113. PMCID: PMC5937191 [Paper]
Davenport, C.A., Maity, A., Sullivan, P.F., Tzeng J.Y. (2018)
A powerful test for SNP effects on multivariate binary outcomes using kernel machine regression.
Luo, Y., Maity, A., Wu, M.C., Smith, C., Duan, Q., Li, Y., Tzeng J.Y. (2018)
On the substructure controls in rare variant analysis --- principal components or variance components?.
Genetic Epidemiology, 42:276-287. PMCID: PMC5851819 [Paper]
Maity, A., Zhao, J., Sullivan, P.F., Tzeng J.Y. (2018)
Inference on phenotype-specific effects of genes using multivariate kernel machine regression.
Genetic Epidemiology, 42:64-79. PMCID: PMC5768462. [Paper]
Green, A.J., Hoyo, C., Mattingly, C.J., Luo, Y., Tzeng J.Y., Murphy, S.K., Buchwalter, D.B., Planchart, A. (2018)
Cadmium Exposure Increases the Risk of Juvenile Obesity: A Human and Zebrafish Comparative Study.
International Journal of Obesity, 42:1285-1295 [Paper]
Kong, D., Maity, A., Hsu, F.C., Tzeng J.Y. (2018)
Rejoinder to "A note on testing and estimation in marker-set association study using semiparametric quantile regression kernel machine".
Biometrics, 74:767-768.. PMCID: PMC5932282 [Paper]
Chang, S.M., Chen, R.B., Tzeng J.Y. (2017)
Bayesian Variable Screenings for Binary Response Regressions in High-Dimensional and Sparse Settings.
Journal of Statistical Computation and Simulation, 87, 2708-2723. PMCID: PMC5653235 [Paper]
Lou, Y.*, McCullough, L.E.*, Tzeng J.Y.#, Darrah, T., Vengosh, A., Maguire, R.L., Maity, A., Murphy, S.K.,. Mendez, M.A., Hoyo, C#. (*: equal contribution; #: co-corresponding authors) (2017)
Maternal blood concentrations of cadmium, lead and arsenic, nutrients, and offspring birth weight.
BMC Public Health, 17:354. PMCID: PMC5402649 [Paper]
Jeng, X.J., Daye, Z.J., Lu, W., Tzeng J.Y. (2016)
Rare variants association analysis in large-scale sequencing studies at the single locus level.
PLoS Comoputational Biology, 12:e1004993. PMCID: PMC4927097 [Paper]
Kong, D., Maity, A., Hsu, F.C., Tzeng J.Y. (2016)
Testing and Estimation in Marker-Set Association Study Using Semiparametric Kernel Quantile Regression.
Biometrics, 72:364-71. NIHMSID: NIHMS735278 [Paper]
Hung, H., Lin, Y.T., Chen, P., Wang C.C., Huang, S.Y., Tzeng J.Y. (2016)
Detection of gene-gene interactions by multistage sparse and low-rank regression.
Biometrics, 72:85-94. NIHMSID: NIHMS697633 [paper]
Zhang, G., Huang, K.C., Xu, Z., Tzeng J.Y., Conneely, K.N., Guan, W., Kang, J., Li Y. (2016)
Across-platform imputation of DNA methylation levels incorporating non-local information using penalized functional regression.
Genetic Epidemiology, 40:333-40 [paper]
Tzeng J.Y., Magnusson, P.K.E., Sullivan, P.F., The Swedish Schizophrenia Consortium, Szatkiewicz, J. (2015)
A new method for detecting associations with rare copy-number variants.
PLoS Genetics, 11(10):e1005403, PMCID: PMC4592002 [Software] [Paper]
Marceau, R., Lu W. Sale, M.M., Bradford, B.M., Williams, S.R., Hsu, F.C., Tzeng J.Y. (2015)
A fast multiple-kernel method with applications to detect gene-environment interaction.
Genetic Epidemiology, 39:456-68. PMCID: PMC4544636 [paper] [fastKM Software]
Hu, Y., Tzeng J.Y., Perou, C.M., Sun W. (2015)
Proper use of allele-specific expression improves statistical power for cis-eQTL mapping with RNA-Seq data.
Journal of the American Statistical Association, 110, 962-974. PMCID: PMC4642818 [paper]
Zhao, G., Marceau, R., Zhang, Z., Tzeng J.Y. (2015)
Assessing Gene-Environment Interactions for Common and Rare Variants with Binary Traits Using Gene-Trait Similarity Regression.
Genetics, 199:695-710. [This is a highlighted paper in Genetics.] PMCID: PMC4349065 [Paper] [Software] [Data]
Wang, Z., Maity, A., Hsiao, C.K., Voora, V., Kaddurah-Daouk, R., Tzeng J.Y. (2015)
Module-based association analysis for omics data with network structure.
Plos One, 10(3):e0122309 PMCID: PMC4378989 [Paper]
Neely, M.L., Bondell, H.D., Tzeng J.Y. (2015)
A penalized likelihood approach for pharmacogenetic studies via understanding haplotype effect structures for gene and gene-drug interaction.
Biometrics, 71:529-37 PMCID: PMC4480191 [Paper]
Wang, Z., Maity, A., Luo, Y., Neely, M.L., Tzeng J.Y. (2015)
Complete effect-profile assessment in association studies with multiple genetic and environmental factors.
Genetic Epidemiology, 39:122-33. PMCID: PMC4314365 [Paper]
Tzeng J.Y.*, Lu, W.*, Hsu, F.C. [* Equal Contribution] (2014)
Gene-level pharmacogenetic analysis on survival outcomes by gene-trait similarity regression.
Annals of Applied Statistics, 8:1232-1255. PMCID: PMC4091797 [Paper]
Hu, J., Tzeng J.Y. (2014)
Integrative Gene Set Analysis of Multi-platform Data with Sample Heterogeneity.
Bioinformatics, 30:1501-7 [Paper]
Wang, X., Zhang, D., Tzeng J.Y. (2014)
Pathway-guided Identification of Gene-Gene Interaction.
Annals of Human Genetics, 78:478-491, PMCID: PMC4363308 [Paper]
Wang, X., Epstein, M.P., Tzeng J.Y. (2014)
Analysis of gene-gene interactions using gene-trait similarity regression.
Human Heredity, 78:17-26 PMCID: PMC4115296 [Paper]
Wright, F., Sullivan, P.F., Brooks, A.,...Tzeng J.Y.,...Penninx, B.W.J.H., Boomsma, D. (2014.)
Heritability and Genomics of Gene Expression in Peripheral Blood.
Nature Genetics, 46:430-7. [Paper]
Cross-Disorder Group of the Psychiatric Genomics Consortium (2013)
Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs.
Nature Genetics. doi: 10.1038/ng.2711 [Paper]
Zhang, A.J., Tzeng J.Y., Chow, S.C. (2013)
Establishment of reference standards in biosimilar studies.
Generics and Biosimilars Initiative Journal. 2. NIHMSID: NIHMS554364 [Paper]
Zhang, A.J., Tzeng J.Y., Chow, S.C. (2013)
Statistical Considerations in Biosimilar Assessment Using Biosimilarity Index.
Journal of Bioequivalence and Bioavailability. 5: 209-214. NIHMSID: NIHMS555465 [Paper]
Major Depressive Disorder Working Group of the Psychiatric GWAS Consortium. (2013)
A mega-analysis of genome-wide association studies for major depressive disorder.
Mol Psychiatry. 18:497-511 [Paper]
Maity A., Sullivan P.F., Tzeng J.Y. (2012)
Multivariate Phenotype Association Analysis by Marker-Set Kernel Machine Regressions.
Genetic Epidemiology. 36:686-95 [Paper] [R code]
Pongpanich M., Neely M., Tzeng J.Y. (2012)
On the aggregation of multimarker information for marker-set and sequencing data analysis: genotype collapsing vs. similarity collapsing.
Frontiers in Statistical Genetics and Methodology. 2:110 [Paper]
Tzeng J.Y., Zhang D., Pongpanich M., Smith C., McCarthy M.I., Sale, M.M., Bradford B.W., Hsu, F.C., Thomas D.C., Sullivan P.F. (2011)
Detecting gene and gene-environment effects of common and uncommon variants on quantitative traits: A marker-set approach using gene-trait similarity regression.
The American Journal of Human Genetics. 89:277-88. [Paper] [Software Download and Documentation]
Sullivan P.; 96 Psychiatric Genetics Investigators. (2012)
Don't give up on GWAS.
Mol Psychiatry. 17:2-3. [Paper]
Lee M.H., Tzeng J.Y., Huang S.Y., Hsiao C.K. (2011)
Combining an evolution-guided clustering algorithm and haplotype-based likelihood ratio test in family-based association studies.
BMC Genetics. 12:48. [Paper]
Koehler M., Bondell H., Tzeng J.Y. (2010)
Evaluating Haplotype Effects in Case-Control Studies via Penalized-Likelihood Approaches: Prospective or Retrospective Analysis?.
Genetic Epidemiology. 34:892-911. [Paper] [R-Code]
Pongpanich M, Sullivan P.F., Tzeng J.Y. (2010)
A Quality Control Algorithmm for Filtering SNPs in Genomewide Association Studies.
Bioinformatics. 15:1731-7. [Paper] [Software Download and Documentation]
Tzeng J.Y.*, Lu W.*, Farmen M.W., Liu Y., Sullivan P.F. [* Equal Contribution] (2010)
Haplotype-based Pharmacogenetic Analysis for Longitudinal Quantitative Traits in the Presence of Dropout.
Journal of Biopharmaceutical Statistics (Special Issue of Statistical Genomics in Clinical Trials). 20:334-50. [Paper] [R-Code]
Tzeng J.Y., Bondell H. (2010)
A Comprehensive Approach to Haplotype Specific Analysis via Penalized Likelihood.
European Journal of Human Genetics. 18:95-103. [Paper] [Software Download and Documentation]
Liu Y., Li Y.J, Satten G., Allen A.S., Tzeng J.Y. (2009)
A Regression-Based Association Test Using Inferred Ancestral Haplotype Similarity.
Annals of Human Genetics. 73:520-526. [Paper]
Tzeng J.Y., Zhang D., Chang S.M., Thomas D.C., Davidian M. (2009)
Gene-Trait Similarity Regression for Multimarker-based Association Analysis.
Sullivan P, de Geus E, Willeen G, James MR, Smit JH, Zandbelt T, Arolt V, Baune BT, Blackwood D, Cichon S, Coventry WL, DohkeM, Farmer A, Fava M, Gordon SD, He Q, Heath A, Heutink P, Holsboer F, Hoogendijk WJ, Hottenga JJ, Hu Y, Kohli M, Lin D, Lucae S, MacIntyre DJ, Maier W, McGhee KA, McGuffin P, Montgomery G, Muir WJ, Nolen W, Nothen MM, Perlis RH, Pirlo K, Posthuma D, Rietschel M, Rizzu P, Schosser A, Smit AB, Smoller JW, Tzeng J.Y., van Dyck R, Verhage M, G. ZF, Martin NG, Wray NR, Booma DI, Penninx B. (2009)
Genomewide Association for Major Depressive Disorder: a Possible Role for the Presynaptic Protein Piccolo.
Molecular Psychiatry 14:359-375. [Paper]
Psychiatric GWAS Consortium Coordinating Committee. (2009)
Genomewide Association Studies: History, Rationale, and Prospects for Psychiatric Disorders.
The American Journal of Psychiatry. 166:540-556. [Paper]
Jones M.L., Epstein M.P., Kao J.T., Allen A.S., SattenG.A., Tzeng J.Y. (2008)
Retrospective Haplotype Clustering Methods for Detecting Haplotypes Effects and Haplotype-Environment Interactions.
Institute of Statistics MimeoSeries No. 2611 [Paper]
Sullivan P.F., Lin D., Tzeng J.Y., van den OordE.J.C.G., Perkins D., Stroup T.S., Wagner M., Lee S., Wright F.A., Zou F., Liu W., Downing A.C., Lieberman J.A., Close S.L. (2008)
Genomewide association for schizophrenia in the CATIE study.
Molecular Psychiatry.13:570-84. [Paper]
Tzeng J.Y., Zhang D. (2007)
Haplotype-based association analysis via variance component score test.
The American Journal of Human Genetics. 81:927-938. [Paper] [Software Download and Documentation]
Tzeng J.Y., Wang C.H., Kao J.T., and Hsiao C.K. (2006)
Regression-based association analysis with clustered haplotypes using genotypes.
The American Journal of Human Genetics, 78:231-242. [Paper] [R-Code]
Tzeng J.Y. and Roeder K. (2006)
Comment on "Likelihood-based inference on haplotype effects in genetic association studies".
Journal of the American Statistical Association, 101:111-114.
Wen S.H, Tzeng J.Y., Kao J.T., and Hsiao C.K. (2006)
A two-stage design for multiple testing in large-scale association studies.
Journal of Human Genetics, 51:523-532. [Paper]
Tzeng J.Y. (2005)
Evolutionary-based Grouping of Haplotypes in Association Analysis.
Genetic Epidemiology, 28:220-231. [Paper]
Tzeng J.Y., Byerley W., Devlin B., Roeder K. and Wasserman L. (2003)
Outlier detection and false discoveryrates for whole-genome DNA matching.
Journal of the American Statistical Association, 98:236-246. [Paper]
Tzeng J.Y., Devlin B., Wasserman L. and Roeder K. (2003)
On the identification of disease mutations by the analysis of haplotype similarity and goodness-of-fit.
The American Journal of Human Genetics, 72:891-902. [Paper] [R-Code]
Hsiao C.K., Tzeng J.Y., and Wang C.H. (2000)
Comparing the performance of two indexes for spatial model selection: applications to two mortality data.
Statistics in Medicine, 19:1915-1930. [Paper]
Hsiao C.K., Chen C.J., Shih Y.-F., Lin LL.-K., Hung P.T., Yao C.L., Su T.C., Lin T.C., Tzeng J.Y., and Chen Y. (2000)
Design and statistical analysis for the myopia intervention trial in Taiwan.
In Lin, L.L.-K., Shih, Y.-F. and Hung, P.T. (Eds.), MyopiaUpdates II (pp. 161-164). Springer-Verlag, Tokyo.
Tzeng J.Y., Hsiao C.K. and Chen C.J. (1998)
Spatial model selection using Bayes factor and ratio of variabilities for asthma mortality data.
Chinese Journal of Public Health, 17:158-169.
Cheng Y.H. and Tzeng J.Y. (1997)
Chinese version of "Primer of Biostatistics (4th ed.) by Glantz, S.A.".
McGraw-Hill, Taipei