Jung-Ying Tzeng

Copy Number Variation and Haplotype Analysis of 17q21.31 Reveals Increased Risk Associated with Progressive Supranuclear Palsy and Gene Expression Changes in Neuronal Cells

Wang, H., Chang, T. S., Dombroski, B. A., Cheng, P. L., Si, Y. Q., Tucci, A., … Lee, W. P. (2025, March 8). Movement Disorders, Vol. 3.

Hi-C informed kernel association test: integrating 3-dimensional genome structure into variant-set association for whole-genome sequencing data

Huang, Y., Basu, R., Lu, W., Holloway, S. T., Li, Y., & Tzeng, J.-Y. (2025, October 30).

NIAGADS: A data repository for Alzheimer's disease and related dementia genomics

Kuzma, A., Valladares, O., Greenfest‐Allen, E., Nicaretta, H., Kirsch, M., Ren, Y., … Wang, L. S. (2025, June 1). Alzheimer s & Dementia, Vol. 21.

Structural variation detection and association analysis of whole‐genome‐sequence data from 16,543 Alzheimer's disease sequencing project subjects

Wang, H., Dombroski, B. A., Cheng, P. L., Tucci, A., Si, Y. Q., Farrell, J. J., … Lee, W. P. (2025, June 1). Alzheimer s & Dementia, Vol. 21.

Structural Variation Detection and Association Analysis of Whole-Genome-Sequence Data from 16,905 Alzheimer’s Diseases Sequencing Project Subjects

The prediction of Alzheimer’s disease through multi-trait genetic modeling

Clark, K., Fu, W., Liu, C.-L., Ho, P.-C., Wang, H., Lee, W.-P., … Tzeng, J.-Y. (2023, July 27). Frontiers in Aging Neuroscience, Vol. 15.

Transfer Learning with False Negative Control Improves Polygenic Risk Prediction

Jeng, X. J., Hu, Y., & Tzeng, J.-Y. (2023, January 3).

Transfer learning with false negative control improves polygenic risk prediction

PLOS Genetics, 19(11), e1010597.

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

Wang, Y., Tzeng, J.-Y., Huang, Y., Maguire, R., Hoyo, C., & Allen, T. K. (2022, December 13). Current Zoology, Vol. 9.

Phylogeny-guided microbiome OTU-specific association test (POST)

Huang, C., Callahan, B. J., Wu, M. C., Holloway, S. T., Brochu, H., Lu, W., … Tzeng, J.-Y. (2022, June 7). Microbiome, Vol. 6.

An Integrative Co-localization (INCO) Analysis for SNV and CNV Genomic Features With an Application to Taiwan Biobank Data

Yu, Q.-Y., Lu, T.-P., Hsiao, T.-H., Lin, C.-H., Wu, C.-Y., Tzeng, J.-Y., & Hsiao, C. K. (2021, September 8). Frontiers in Genetics, Vol. 12.

Gene-set integrative analysis of multi-omics data using tensor-based association test

Chang, S.-M., Yang, M., Lu, W., Huang, Y.-J., Huang, Y., Hung, H., … Tzeng, J.-Y. (2021, February 24). (A. Valencia, Ed.). Bioinformatics, Vol. 37, pp. 2259–2265.

Phylogeny-Guided Microbiome OTU-Specific Association Test (POST)

Huang, C., Callahan, B. J., Wu, M. C., Holloway, S. T., Brochu, H., Lu, W., … Tzeng, J.-Y. (2021, November 1).

SEAGLE: A Scalable Exact Algorithm for Large-Scale Set-Based Gene-Environment Interaction Tests in Biobank Data

Chi, J. T., Ipsen, I. C. F., Hsiao, T.-H., Lin, C.-H., Wang, L.-S., Lee, W.-P., … Tzeng, J.-Y. (2021, November 2). Frontiers in Genetics, Vol. 11.

Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis

Brucker, A., Lu, W., West, R. M., Yu, Q.-Y., Hsiao, C. K., Hsiao, T.-H., … Tzeng, J.-Y. (2020, May 4). (J. Ma, Ed.). PLoS Computational Biology, Vol. 16, p. e1007797.

Effective SNP ranking improves the performance of eQTL mapping

Jeng, X. J., Rhyne, J., Zhang, T., & Tzeng, J. Y. (2020, March 26). Genetic Epidemiology, Vol. 44, pp. 611–619.

FastLORS: Joint modelling for expression quantitative trait loci mapping in R

Rhyne, J., Jeng, X. J., Chi, E. C., & Tzeng, J. Y. (2020, January 1). Stat, Vol. 9.

Robust kernel association testing (RobKAT)

Martinez, K., Maity, A., Yolken, R. H., Sullivan, P. F., & Tzeng, J. Y. (2020, January 14). Genetic Epidemiology, Vol. 44, pp. 272–282.

The association between neuraxial anesthesia and the development of childhood asthma – a secondary analysis of the newborn epigenetics study cohort

Huang, Y., Tzeng, J.-Y., Maguire, R., Hoyo, C., & Allen, T. (2020, March 26). Current Medical Research and Opinion, Vol. 36, pp. 1025–1032.

Identifying individual risk rare variants using protein structure guided local tests (POINT)

West, R. M., Lu, W., Rotroff, D. M., Kuenemann, M. A., Chang, S.-M., Wu, M. C., … Tzeng, J.-Y. (2019, February 19). PLoS Computational Biology, Vol. 15.

Reference equations for spirometry in healthy Asian children aged 5 to 18 years in Taiwan

Chang, S.-M., Tsai, H.-J., Tzeng, J.-Y., Yeh, K.-W., Chen, L.-C., Lai, S.-H., … Yao, T.-C. (2019, October 28). World Allergy Organization Journal, Vol. 12.

SA30VARIANCE COMPONENT TEST FOR CROSS-DISORDER PATHWAY ANALYSIS

Szatkiewicz, J., Marceau, R., Yilmaz, Z., Bulik, C., Crowley, J., Mattheisen, M., … al. (2019, January 1). European Neuropsychopharmacology, Vol. 29, pp. 1204–1205.

Cadmium exposure increases the risk of juvenile obesity: a human and zebrafish comparative study

International Journal of Obesity, 42(7), 1285–1295.

Efficient Signal Inclusion With Genomic Applications

Journal of the American Statistical Association, 114(528), 1–23.

Genetic loci determining total immunoglobulin E levels from birth through adulthood

Yao, T. C., Chung, R. H., Lin, C. Y., Tsai, P. C., Chang, W. C., Yeh, K. W., … Huang, J. L. (2018, October 31). Allergy, Vol. 74, pp. 621–625.

Identifying individual risk rare variants using protein structure-guided local tests (POINT)

West, R. M., Lu, W., Rotroff, D. M., Kuenemann, M., Chang, S.-M., Wagner, M. J., … Tzeng, J.-Y. (2018, May 29).

Inference on phenotype‐specific effects of genes using multivariate kernel machine regression

Maity, A., Zhao, J., Sullivan, P. F., & Tzeng, J. Y. (2018, January 3). Genetic Epidemiology, Vol. 42, pp. 64–79.

Reexamining Dis/Similarity-Based Tests for Rare-Variant Association with Case-Control Samples

Wang, C., Tzeng, J.-Y., Wu, P.-Z., Preisig, M., & Hsiao, C. K. (2018, March 14). Genetics, Vol. 209, pp. 105–113.

A Powerful Test for SNP Effects on Multivariate Binary Outcomes Using Kernel Machine Regression

Statistics in Biosciences, 10(1), 117–138.

A new method for detecting associations with rare copy-number variants

European Neuropsychopharmacology, 27, S165–166.

Fast Bayesian variable screenings for binary response regressions with small sample size

Chang, S.-M., Tzeng, J.-Y., & Chen, R.-B. (2017, June 25). Journal of Statistical Computation and Simulation, Vol. 87, pp. 2708–2723.

Maternal blood cadmium, lead and arsenic levels, nutrient combinations, and offspring birthweight

BMC Public Health, 17.

On the substructure controls in rare variant analysis: Principal components or variance components?

Luo, Y., Maity, A., Wu, M. C., Smith, C., Duan, Q., Li, Y., & Tzeng, J. Y. (2017, December 26). Genetic Epidemiology, Vol. 42, pp. 276–287.

Rejoinder to “A Note on Testing and Estimation in Marker-set Association Study Using Semiparametric Quantile Regression Kernel Machine”

Kong, D., Maity, A., Hsu, F.-C., & Tzeng, J.-Y. (2017, November 2). Rejoinder to “A Note on Testing and Estimation in Marker-set Association Study Using Semiparametric Quantile Regression Kernel Machine.” Biometrics, Vol. 74, pp. 767–768.

Across‐Platform Imputation of DNA Methylation Levels Incorporating Nonlocal Information Using Penalized Functional Regression

Zhang, G., Huang, K. C., Xu, Z., Tzeng, J. Y., Conneely, K. N., Guan, W., … Li, Y. (2016, April 7). Genetic Epidemiology, Vol. 40, pp. 333–340.

Rare variants association analysis in large-scale sequencing studies at the single locus level

PLoS Computational Biology, 12(6).

A Fast Multiple‐Kernel Method With Applications to Detect Gene‐Environment Interaction

Marceau, R., Lu, W., Holloway, S., Sale, M. M., Worrall, B. B., Williams, S. R., … Tzeng, J. Y. (2015, July 3). Genetic Epidemiology, Vol. 39, pp. 456–468.

A Penalized Likelihood Approach for Investigating Gene–Drug Interactions in Pharmacogenetic Studies

Neely, M. L., Bondell, H. D., & Tzeng, J.-Y. (2015, January 20). Biometrics, Vol. 71, pp. 529–537.

A new method for detecting associations with rare copy-number variants

PLoS Genetics, 11(10).

Assessing gene-environment interactions for common and rare variants with binary traits using gene-trait similarity regression

Genetics, 199(3), 695-.

Detection of Gene–Gene Interactions Using Multistage Sparse and Low-Rank Regression

Hung, H., Lin, Y.-T., Chen, P., Wang, C.-C., Huang, S.-Y., & Tzeng, J.-Y. (2015, August 19). Biometrics, Vol. 72, pp. 85–94.

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.

Module-based association analysis for omics data with network structure

PLoS One, 10(3).

Proper Use of Allele-Specific Expression Improves Statistical Power forcis-eQTL Mapping with RNA-Seq Data

Hu, Y.-J., Sun, W., Tzeng, J.-Y., & Perou, C. M. (2015, May 6). Journal of the American Statistical Association, Vol. 110, pp. 962–974.

Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways

Nature Neuroscience, 18(2), 199–209.

Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways

Nature Neuroscience, 18(2), 199–209.

Testing and Estimation in Marker-Set Association Study Using Semiparametric Quantile Regression Kernel Machine

Kong, D., Maity, A., Hsu, F. C., Tzeng, J. Y., & Biometrics. (2015, November 17). Biometrics, Vol. 72, pp. 364–371.

Analysis of Gene-Gene Interactions Using Gene-Trait Similarity Regression

Wang, X., Epstein, M. P., & Tzeng, J.-Y. (2014, January 1). Human Heredity, Vol. 78, pp. 17–26.

Complete Effect‐Profile Assessment in Association Studies With Multiple Genetic and Multiple Environmental Factors

Wang, Z., Maity, A., Luo, Y., Neely, M. L., & Tzeng, J. Y. (2014, December 23). Genetic Epidemiology, Vol. 39, pp. 122–133.

Gene-level pharmacogenetic analysis on survival outcomes using gene-trait similarity regression

Tzeng, J.-Y., Lu, W., & Hsu, F.-C. (2014, June 1). The Annals of Applied Statistics, Vol. 8, pp. 1232–1255.

Heritability and genomics of gene expression in peripheral blood

Nature Genetics, 46(5), 430–437.

Heritability and genomics of gene expression in peripheral blood

Nature Genetics, 46(5), 430–437.

Integrative gene set analysis of multi-platform data with sample heterogeneity

Hu, J., & Tzeng, J.-Y. (2014, January 30). Bioinformatics, Vol. 30, pp. 1501–1507.

Pathway-Guided Identification of Gene-Gene Interactions

Wang, X., Zhang, D., & Tzeng, J.-Y. (2014, September 17). Annals of Human Genetics, Vol. 78, pp. 478–491.

A mega-analysis of genome-wide association studies for major depressive disorder

Molecular Psychiatry, 18(4), 497–511.

Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs

Nature Genetics, 45(9), 984–994.

Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs

Nature Genetics, 45(9), 984-.

Multivariate Phenotype Association Analysis by Marker‐Set Kernel Machine Regression

Maity, A., Sullivan, P. F., & Tzeng, J. (2012, August 16). Genetic Epidemiology, Vol. 36, p. 686–695.

On the Aggregation of Multimarker Information for Marker-Set and Sequencing Data Analysis: Genotype Collapsing vs. Similarity Collapsing

Pongpanich, M., Neely, M. L., & Tzeng, J.-Y. (2012, January 1). Frontiers in Genetics, Vol. 2.

Combining an Evolution-guided Clustering Algorithm and Haplotype-based LRT in Family Association Studies

Lee, M.-H., Tzeng, J.-Y., Huang, S.-Y., & Hsiao, C. K. (2011, May 19). BMC Genetics, Vol. 12, p. 48.

Combining an evolution-guided clustering algorithm and haplotype-based LRT in family association studies

BMC Genetics, 12.

Studying Gene and Gene-Environment Effects of Uncommon and Common Variants on Continuous Traits: A Marker-Set Approach Using Gene-Trait Similarity Regression

Tzeng, J.-Y., Zhang, D., Pongpanich, M., Smith, C., McCarthy, M. I., Sale, M. M., … Sullivan, P. F. (2011, August 1). The American Journal of Human Genetics, Vol. 89, pp. 277–288.

A quality control algorithm for filtering SNPs in genome-wide association studies

Pongpanich, M., Sullivan, P. F., & Tzeng, J.-Y. (2010, May 25). Bioinformatics, Vol. 26, pp. 1731–1737.

Evaluating haplotype effects in case‐control studies via penalized‐likelihood approaches: prospective or retrospective analysis?

Koehler, M. L., Bondell, H. D., & Tzeng, J. Y. (2010, November 22). Genetic Epidemiology, Vol. 34, pp. 892–911.

Haplotype-Based Pharmacogenetic Analysis for Longitudinal Quantitative Traits in the Presence of Dropout

Tzeng∗, J.-Y., Lu∗, W., Farmen, M. W., Liu, Y., & Sullivan, P. F. (2010, March 19). Journal of Biopharmaceutical Statistics, Vol. 20, pp. 334–350.

A Regression‐based Association Test for Case‐control Studies that Uses Inferred Ancestral Haplotype Similarity

Liu, Y., Li, Y. J., Satten, G. A., Allen, A. S., & Tzeng, J. Y. (2009, July 20). Annals of Human Genetics, Vol. 73, pp. 520–526.

A comprehensive approach to haplotype-specific analysis by penalized likelihood

European Journal of Human Genetics, 18(1), 95–103.

Erratum: Genomewide association for schizophrenia in the CATIE study: results of stage 1

Molecular Psychiatry, 14(12), 1144–1144.

Gene-Trait Similarity Regression for Multimarker-Based Association Analysis

Biometrics, 65(3), 822–832.

Genome-wide association for major depressive disorder: A possible role for the presynaptic protein piccolo

[Review of ]. Molecular Psychiatry, 14(4), 359–375.

Genome-wide association for major depressive disorder: a possible role for the presynaptic protein piccolo

Molecular Psychiatry, 14(4), 359–375.