Jung-Ying Tzeng

Wang, Y., Tzeng, J.-Y., Huang, Y., Maguire, R., Hoyo, C., & Allen, T. K. (2023). Duration of exposure to epidural anesthesia at delivery, DNA methylation in umbilical cord blood and their association with offspring asthma in Non-Hispanic Black women. ENVIRONMENTAL EPIGENETICS, 9(1). https://doi.org/10.1093/eep/dvac026

Clark, K., Fu, W., Liu, C.-L., Ho, P.-C., Wang, H., Lee, W.-P., … Tzeng, J.-Y. (2023). The prediction of Alzheimer's disease through multi-trait genetic modeling. FRONTIERS IN AGING NEUROSCIENCE, 15. https://doi.org/10.3389/fnagi.2023.1168638

Jeng, X. J., Hu, Y., Venkat, V., Lu, T.-P., & Tzeng, J.-Y. (2023). Transfer learning with false negative control improves polygenic risk prediction. PLOS GENETICS, 19(11). https://doi.org/10.1371/journal.pgen.1010597

Huang, C., Callahan, B. J., Wu, M. C., Holloway, S. T., Brochu, H., Lu, W., … Tzeng, J.-Y. (2022). Phylogeny-guided microbiome OTU-specific association test (POST). MICROBIOME, 10(1). https://doi.org/10.1186/s40168-022-01266-3

Yu, Q.-Y., Lu, T.-P., Hsiao, T.-H., Lin, C.-H., Wu, C.-Y., Tzeng, J.-Y., & Hsiao, C. K. (2021). An Integrative Co-localization (INCO) Analysis for SNV and CNV Genomic Features With an Application to Taiwan Biobank Data. FRONTIERS IN GENETICS, 12. https://doi.org/10.3389/fgene.2021.709555

Chang, S.-M., Yang, M., Lu, W., Huang, Y.-J., Huang, Y., Hung, H., … Tzeng, J.-Y. (2021). Gene-set integrative analysis of multi-omics data using tensor-based association test. BIOINFORMATICS, 37(16), 2259–2265. https://doi.org/10.1093/bioinformatics/btab125

Chi, J. T., Ipsen, I. C. F., Hsiao, T.-H., Lin, C.-H., Wang, L.-S., Lee, W.-P., … Tzeng, J.-Y. (2021). SEAGLE: A Scalable Exact Algorithm for Large-Scale Set-Based Gene-Environment Interaction Tests in Biobank Data. FRONTIERS IN GENETICS, 12. https://doi.org/10.3389/fgene.2021.710055

Brucker, A., Lu, W., West, R. M., Yu, Q.-Y., Hsiao, C. K., Hsiao, T.-H., … Tzeng, J.-Y. (2020). Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis. PLOS COMPUTATIONAL BIOLOGY, 16(5). https://doi.org/10.1371/journal.pcbi.1007797

Jeng, X. J., Rhyne, J., Zhang, T., & Tzeng, J.-Y. (2020). Effective SNP ranking improves the performance of eQTL mapping. GENETIC EPIDEMIOLOGY, 44(6), 611–619. https://doi.org/10.1002/gepi.22293

Rhyne, J., Jeng, X. J., Chi, E. C., & Tzeng, J.-Y. (2020). FastLORS: Joint modelling for expression quantitative trait loci mapping in R. STAT, 9(1). https://doi.org/10.1002/sta4.265

Martinez, K., Maity, A., Yolken, R. H., Sullivan, P. F., & Tzeng, J.-Y. (2020). Robust kernel association testing (RobKAT). GENETIC EPIDEMIOLOGY, 44(3), 272–282. https://doi.org/10.1002/gepi.22280

Huang, Y., Tzeng, J.-Y., Maguire, R., Hoyo, C., & Allen, T. (2020). The association between neuraxial anesthesia and the development of childhood asthma - a secondary analysis of the newborn epigenetics study cohort. CURRENT MEDICAL RESEARCH AND OPINION, 36(6), 1025–1032. https://doi.org/10.1080/03007995.2020.1747417

Yao, T.-C., Chung, R.-H., Lin, C.-Y., Tsai, P.-C., Chang, W.-C., Yeh, K.-W., … Huang, J.-L. (2019, March). Genetic loci determining total immunoglobulin E levels from birth through adulthood. https://doi.org/10.1111/all.13654

West, R. M., Lu, W., Rotroff, D. M., Kuenemann, M. A., Chang, S.-M., Wu, M. C., … Tzeng, J.-Y. (2019). Identifying individual risk rare variants using protein structure guided local tests (POINT). PLOS COMPUTATIONAL BIOLOGY, 15(2). https://doi.org/10.1371/journal.pcbi.1006722

Chang, S.-M., Tsai, H.-J., Tzeng, J.-Y., Yeh, K.-W., Chen, L.-C., Lai, S.-H., … Yao, T.-C. (2019). Reference equations for spirometry in healthy Asian children aged 5 to 18 years in Taiwan. WORLD ALLERGY ORGANIZATION JOURNAL, 12(11). https://doi.org/10.1016/j.waojou.2019.100074

Szatkiewicz, J., Marceau, R., Yilmaz, Z., Bulik, C., Crowley, J., Mattheisen, M., … al. (2019). VARIANCE COMPONENT TEST FOR CROSS-DISORDER PATHWAY ANALYSIS. EUROPEAN NEUROPSYCHOPHARMACOLOGY, Vol. 29, pp. 1204–1205. https://doi.org/10.1016/j.euroneuro.2018.08.252

Green, A. J., Hoyo, C., Mattingly, C. J., Luo, Y., Tzeng, J.-Y., Murphy, S. K., … Planchart, A. (2018). Cadmium exposure increases the risk of juvenile obesity: a human and zebrafish comparative study. International Journal of Obesity, 42(7), 1285–1295. https://doi.org/10.1038/S41366-018-0036-Y

Jeng, X. J., Zhang, T., & Tzeng, J.-Y. (2018). Efficient Signal Inclusion With Genomic Applications. Journal of the American Statistical Association, 1–23. https://doi.org/10.1080/01621459.2018.1518236

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(1), 64–79. https://doi.org/10.1002/gepi.22096

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(3), 276–287. https://doi.org/10.1002/gepi.22102

Wang, C., Tzeng, J.-Y., Wu, P.-Z., Preisig, M., & Hsiao, C. K. (2018). Reexamining Dis/Similarity-Based Tests for Rare-Variant Association with Case-Control Samples. GENETICS, 209(1), 105–113. https://doi.org/10.1534/genetics.118.300769

Kong, D., Maity, A., Hsu, F.-C., & Tzeng, J.-Y. (2018, June). Rejoinder to "A note on testing and estimation in marker-set association study using semiparametric quantile regression kernel machine". https://doi.org/10.1111/biom.12786

Davenport, C. A., Maity, A., Sullivan, P. F., & Tzeng, J.-Y. (2017). A Powerful Test for SNP Effects on Multivariate Binary Outcomes Using Kernel Machine Regression. Statistics in Biosciences, 10(1), 117–138. https://doi.org/10.1007/S12561-017-9189-9

Szatkiewicz, J., Tzeng, J. Y., Magnusson, P., & Sullivan, P. (2017). A new method for detecting associations with rare copy-number variants. European Neuropsychopharmacology, 27, S165–166.

Chang, S.-M., Tzeng, J.-Y., & Chen, R.-B. (2017). Fast Bayesian variable screenings for binary response regressions with small sample size. JOURNAL OF STATISTICAL COMPUTATION AND SIMULATION, 87(14), 2708–2723. https://doi.org/10.1080/00949655.2017.1341887

Luo, Y. W., McCullough, L. E., Tzeng, J. Y., Darrah, T., Vengosh, A., Maguire, R. L., … Hoyo, C. (2017). Maternal blood cadmium, lead and arsenic levels, nutrient combinations, and offspring birthweight. BMC Public Health, 17.

Zhang, G., Huang, K.-C., Xu, Z., Tzeng, J.-Y., Conneely, K. N., Guan, W., … Li, Y. (2016). Across-Platform Imputation of DNA Methylation Levels Incorporating Nonlocal Information Using Penalized Functional Regression. GENETIC EPIDEMIOLOGY, 40(4), 333–340. https://doi.org/10.1002/gepi.21969

Hung, H., Lin, Y.-T., Chen, P., Wang, C.-C., Huang, S.-Y., & Tzeng, J.-Y. (2016). Detection of Gene-Gene Interactions Using Multistage Sparse and Low-Rank Regression. BIOMETRICS, 72(1), 85–94. https://doi.org/10.1111/biom.12374

Jeng, X. J., Daye, Z. J., Lu, W. B., & Tzeng, J. Y. (2016). Rare variants association analysis in large-scale sequencing studies at the single locus level. PLoS Computational Biology, 12(6).

Kong, D., Maity, A., Hsu, F. C., Tzeng, J. Y., & Biometrics. (2016). Testing and estimation in marker-set association study using semiparametric quantile regression kernel machine. BIOMETRICS, 72(2), 364–371. https://doi.org/10.1111/biom.12438

Marceau, R., Lu, W., Holloway, S., Sale, M. M., Worrall, B. B., Williams, S. R., … Tzeng, J.-Y. (2015). A Fast Multiple-Kernel Method With Applications to Detect Gene-Environment Interaction. GENETIC EPIDEMIOLOGY, 39(6), 456–468. https://doi.org/10.1002/gepi.21909

Tzeng, J. Y., Magnusson, P. K. E., Sullivan, P. F., & Szatkiewicz, J. P. (2015). A new method for detecting associations with rare copy-number variants. PLoS Genetics, 11(10).

Neely, M. L., Bondell, H. D., & Tzeng, J.-Y. (2015). A penalized likelihood approach for investigating gene-drug interactions in pharmacogenetic studies. BIOMETRICS, 71(2), 529–537. https://doi.org/10.1111/biom.12259

Zhao, G. L., Marceau, R., Zhang, D. W., & Tzeng, J. Y. (2015). Assessing gene-environment interactions for common and rare variants with binary traits using gene-trait similarity regression. Genetics, 199(3), 695-.

Wang, Z., Maity, A., Luo, Y., Neely, M. L., & Tzeng, J.-Y. (2015). Complete Effect-Profile Assessment in Association Studies With Multiple Genetic and Multiple Environmental Factors. GENETIC EPIDEMIOLOGY, 39(2), 122–133. https://doi.org/10.1002/gepi.21877

Maier, R., Moser, G., Chen, G.-B., Ripke, S., Coryell, W., Potash, J. B., … Zöllner, S. (2015). Joint Analysis of Psychiatric Disorders Increases Accuracy of Risk Prediction for Schizophrenia, Bipolar Disorder, and Major Depressive Disorder. The American Journal of Human Genetics, 96(2), 283–294. https://doi.org/10.1016/J.AJHG.2014.12.006

Wang, Z., Maity, A., Hsiao, C. K., Voora, D., Kaddurah-Daouk, R., & Tzeng, J. Y. (2015). Module-based association analysis for omics data with network structure. PLoS One, 10(3).

Hu, Y.-J., Sun, W., Tzeng, J.-Y., & Perou, C. M. (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(511), 962–974. https://doi.org/10.1080/01621459.2015.1038449

Tzeng, J.-Y. (2015). Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways. Nature Neuroscience, 18(2), 199–209. https://doi.org/10.1038/NN.3922

O'Dushlaine, C., Rossin, L., Lee, P. H., Duncan, L., Parikshak, N. N., Newhouse, S., … Goddard, M. E. (2015). Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways. Nature Neuroscience, 18(2), 199–209.

Wang, X., Epstein, M. P., & Tzeng, J.-Y. (2014). Analysis of Gene-Gene Interactions Using Gene-Trait Similarity Regression. HUMAN HEREDITY, 78(1), 17–26. https://doi.org/10.1159/000360161

Tzeng, J.-Y., Lu, W., & Hsu, F.-C. (2014). GENE-LEVEL PHARMACOGENETIC ANALYSIS ON SURVIVAL OUTCOMES USING GENE-TRAIT SIMILARITY REGRESSION. ANNALS OF APPLIED STATISTICS, 8(2), 1232–1255. https://doi.org/10.1214/14-aoas735

Wright, F. A., Sullivan, P. F., Brooks, A. I., Zou, F., Sun, W., Xia, K., … Boomsma, D. I. (2014). Heritability and genomics of gene expression in peripheral blood. Nature Genetics, 46(5), 430–437. https://doi.org/10.1038/NG.2951

Wright, F. A., Sullivan, P. F., Brooks, A. I., Zou, F., Sun, W., Xia, K., … Hottenga, J. J. (2014). Heritability and genomics of gene expression in peripheral blood. Nature Genetics, 46(5), 430–437.

Hu, J., & Tzeng, J.-Y. (2014). Integrative gene set analysis of multi-platform data with sample heterogeneity. BIOINFORMATICS, 30(11), 1501–1507. https://doi.org/10.1093/bioinformatics/btu060

Wang, X., Zhang, D., & Tzeng, J.-Y. (2014). Pathway-Guided Identification of Gene-Gene Interactions. ANNALS OF HUMAN GENETICS, 78(6), 478–491. https://doi.org/10.1111/ahg.12080

Sullivan, P. F., Daly, M. J., Ripke, S., Lewis, C. M., Lin, D. Y., Wray, N. R., … Hamilton, S. P. (2013). A mega-analysis of genome-wide association studies for major depressive disorder. Molecular Psychiatry, 18(4), 497–511.

Tzeng, J.-Y. (2013). Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs. Nature Genetics, 45(9), 984–994. https://doi.org/10.1038/NG.2711

Lee, S. H., Ripke, S., Neale, B. M., Faraone, S. V., Purcell, S. M., Perlis, R. H., … Anttila, V. (2013). Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs. Nature Genetics, 45(9), 984-.

Maity, A., Sullivan, P. E., & Tzeng, J.-Y. (2012). Multivariate Phenotype Association Analysis by Marker-Set Kernel Machine Regression. GENETIC EPIDEMIOLOGY, 36(7), 686–695. https://doi.org/10.1002/gepi.21663

Lee, M. H., Tzeng, J. Y., Huang, S. Y., & Hsiao, C. K. (2011). Combining an evolution-guided clustering algorithm and haplotype-based LRT in family association studies. BMC Genetics, 12.

Tzeng, J.-Y., Zhang, D., Pongpanich, M., Smith, C., McCarthy, M. I., Sale, M. M., … Sullivan, P. F. (2011). Studying Gene and Gene-Environment Effects of Uncommon and Common Variants on Continuous Traits: A Marker-Set Approach Using Gene-Trait Similarity Regression. AMERICAN JOURNAL OF HUMAN GENETICS, 89(2), 277–288. https://doi.org/10.1016/j.ajhg.2011.07.007

Pongpanich, M., Sullivan, P. F., & Tzeng, J.-Y. (2010). A quality control algorithm for filtering SNPs in genome-wide association studies. BIOINFORMATICS, 26(14), 1731–1737. https://doi.org/10.1093/bioinformatics/btq272

Koehler, M. L., Bondell, H. D., & Tzeng, J.-Y. (2010). Evaluating Haplotype Effects in Case-Control Studies via Penalized-Likelihood Approaches: Prospective or Retrospective Analysis? GENETIC EPIDEMIOLOGY, 34(8), 892–911. https://doi.org/10.1002/gepi.20545

Tzeng, J.-Y., Lu, W., Farmen, M. W., Liu, Y., & Sullivan, P. F. (2010). Haplotype-Based Pharmacogenetic Analysis for Longitudinal Quantitative Traits in the Presence of Dropout. JOURNAL OF BIOPHARMACEUTICAL STATISTICS, 20(2), 334–350. https://doi.org/10.1080/10543400903572787

Liu, Y., Li, Y.-J., Satten, G. A., Allen, A. S., & Tzeng, J.-Y. (2009). A Regression-based Association Test for Case-control Studies that Uses Inferred Ancestral Haplotype Similarity. ANNALS OF HUMAN GENETICS, 73, 520–526. https://doi.org/10.1111/j.1469-1809.2009.00536.x

Tzeng, J.-Y., & Bondell, H. D. (2009). A comprehensive approach to haplotype-specific analysis by penalized likelihood. European Journal of Human Genetics, 18(1), 95–103. https://doi.org/10.1038/ejhg.2009.118

Sullivan, P. F., Lin, D., Tzeng, J.-Y., van den Oord, E., Perkins, D., Stroup, T. S., … Close, S. L. (2009). Erratum: Genomewide association for schizophrenia in the CATIE study: results of stage 1. Molecular Psychiatry, 14(12), 1144–1144. https://doi.org/10.1038/mp.2008.74

Tzeng, J.-Y., Zhang, D., Chang, S.-M., Thomas, D. C., & Davidian, M. (2009). Gene-Trait Similarity Regression for Multimarker-Based Association Analysis. Biometrics, 65(3), 822–832. https://doi.org/10.1111/j.1541-0420.2008.01176.x

Sullivan, P. F., Geus, E. J. C., Willemsen, G., James, M. R., Smit, J. H., Zandbelt, T., … Heutink, P. (2009). [Review of Genome-wide association for major depressive disorder: A possible role for the presynaptic protein piccolo]. Molecular Psychiatry, 14(4), 359–375.

Sullivan, P. F., de Geus, E. J. C., Willemsen, G., James, M. R., Smit, J. H., Zandbelt, T., … Penninx, B. W. J. H. (2008). Genome-wide association for major depressive disorder: a possible role for the presynaptic protein piccolo. Molecular Psychiatry, 14(4), 359–375. https://doi.org/10.1038/mp.2008.125

Sullivan, P. F., Lin, D., Tzeng, J.-Y., van den Oord, E., Perkins, D., Stroup, T. S., … Close, S. L. (2008). Genomewide association for schizophrenia in the CATIE study: results of stage 1. Molecular Psychiatry, 13(6), 570–584. https://doi.org/10.1038/mp.2008.25

Tzeng, J.-Y., & Zhang, D. (2007). Haplotype-based association analysis via variance-components score test. AMERICAN JOURNAL OF HUMAN GENETICS, 81(5), 927–938. https://doi.org/10.1086/521558

Wen, S.-H., Tzeng, J.-Y., Kao, J.-T., & Hsiao, C. K. (2006). A two-stage design for multiple testing in large-scale association studies. JOURNAL OF HUMAN GENETICS, 51(6), 523–532. https://doi.org/10.1007/s10038-006-0393-6

Tzeng, J. Y., & Roeder, K. (2006). Likelihood-based inference on haplotype effects in genetic association studies - Comment. Journal of the American Statistical Association, 101(473), 111–114.

Tzeng, J. Y., Wang, C. H., Kao, J. T., & Hsiao, C. K. (2006). Regression-based association analysis with clustered haplotypes through use of genotypes. AMERICAN JOURNAL OF HUMAN GENETICS, 78(2), 231–242. https://doi.org/10.1086/500025

Tzeng, J. Y. (2005). Evolutionary-based grouping of haplotypes in association analysis. GENETIC EPIDEMIOLOGY, 28(3), 220–231. https://doi.org/10.1002/gepi.20063