Publications

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Genetic Predisposition to Disease
"Genome-wide association study identifies five new schizophrenia loci." Nat Genet 43, no. 10 (2011): 969-76.
Owzar, Kouros, Zhiguo Li, Nancy Cox, and Sin-Ho Jung. "Power and sample size calculations for SNP association studies with censored time-to-event outcomes." Genet Epidemiol 36, no. 6 (2012): 538-48.
Pang, Herbert, Michael Hauser, and Stéphane Minvielle. "Pathway-based identification of SNPs predictive of survival." Eur J Hum Genet 19, no. 6 (2011): 704-9.
R Baldwin, Michael, Kouros Owzar, Hitoshi Zembutsu, Aparna Chhibber, Michiaki Kubo, Chen Jiang, Dorothy Watson, Rachel J. Eclov, Joel Mefford, Howard L. McLeod et al. "A genome-wide association study identifies novel loci for paclitaxel-induced sensory peripheral neuropathy in CALGB 40101." Clin Cancer Res 18, no. 18 (2012): 5099-109.
Tzeng, Jung-Ying, Patrik K. E. Magnusson, Patrick F. Sullivan, and Jin P. Szatkiewicz. "A New Method for Detecting Associations with Rare Copy-Number Variants." PLoS Genet 11, no. 10 (2015): e1005403.
Knickmeyer, Rebecca C., Jiaping Wang, Hongtu Zhu, Xiujuan Geng, Sandra Woolson, Robert M. Hamer, Thomas Konneker, Weili Lin, Martin Styner, and John H. Gilmore. "Common variants in psychiatric risk genes predict brain structure at birth." Cereb Cortex 24, no. 5 (2014): 1230-46.
Chen, Yong, Haitao Chu, Sheng Luo, Lei Nie, and Sining Chen. "Bayesian analysis on meta-analysis of case-control studies accounting for within-study correlation." Stat Methods Med Res 24, no. 6 (2015): 836-55.
Wang, Zhi, Arnab Maity, Yiwen Luo, Megan L. Neely, and Jung-Ying Tzeng. "Complete effect-profile assessment in association studies with multiple genetic and multiple environmental factors." Genet Epidemiol 39, no. 2 (2015): 122-33.
West, Rachel Marceau, Wenbin Lu, Daniel M. Rotroff, Melaine A. Kuenemann, Sheng-Mao Chang, Michael C. Wu, Michael J. Wagner, John B. Buse, Alison A. Motsinger-Reif, Denis Fourches et al. "Identifying individual risk rare variants using protein structure guided local tests (POINT)." PLoS Comput Biol 15, no. 2 (2019): e1006722.
Jeng, Xinge Jessie, Zhongyin John Daye, Wenbin Lu, and Jung-Ying Tzeng. "Rare Variants Association Analysis in Large-Scale Sequencing Studies at the Single Locus Level." PLoS Comput Biol 12, no. 6 (2016): e1004993.
Brucker, Amanda, Wenbin Lu, Rachel Marceau West, Qi-You Yu, Chuhsing Kate Hsiao, Tzu-Hung Hsiao, Ching-Heng Lin, Patrik K. E. Magnusson, Patrick F. Sullivan, Jin P. Szatkiewicz et al. "Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis." PLoS Comput Biol 16, no. 5 (2020): e1007797.
Genetic Variation
Hu, Yi-Juan, Sonja I. Berndt, Stefan Gustafsson, Andrea Ganna, Joel Hirschhorn, Kari E. North, Erik Ingelsson, and Dan-Yu Lin. "Meta-analysis of gene-level associations for rare variants based on single-variant statistics." Am J Hum Genet 93, no. 2 (2013): 236-48.
Wang, Charlotte, Jung-Ying Tzeng, Pei-Zhen Wu, Martin Preisig, and Chuhsing Kate Hsiao. "Reexamining Dis/Similarity-Based Tests for Rare-Variant Association with Case-Control Samples." Genetics 209, no. 1 (2018): 105-113.
Luo, Yiwen, Arnab Maity, Michael C. Wu, Chris Smith, Qing Duan, Yun Li, and Jung-Ying Tzeng. "On the substructure controls in rare variant analysis: Principal components or variance components?" Genet Epidemiol 42, no. 3 (2018): 276-287.
Brucker, Amanda, Wenbin Lu, Rachel Marceau West, Qi-You Yu, Chuhsing Kate Hsiao, Tzu-Hung Hsiao, Ching-Heng Lin, Patrik K. E. Magnusson, Patrick F. Sullivan, Jin P. Szatkiewicz et al. "Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis." PLoS Comput Biol 16, no. 5 (2020): e1007797.
West, Rachel Marceau, Wenbin Lu, Daniel M. Rotroff, Melaine A. Kuenemann, Sheng-Mao Chang, Michael C. Wu, Michael J. Wagner, John B. Buse, Alison A. Motsinger-Reif, Denis Fourches et al. "Identifying individual risk rare variants using protein structure guided local tests (POINT)." PLoS Comput Biol 15, no. 2 (2019): e1006722.
Marceau, Rachel, Wenbin Lu, Shannon Holloway, Michèle M. Sale, Bradford B. Worrall, Stephen R. Williams, Fang-Chi Hsu, and Jung-Ying Tzeng. "A Fast Multiple-Kernel Method With Applications to Detect Gene-Environment Interaction." Genet Epidemiol 39, no. 6 (2015): 456-68.
Hu, Y J., and D Y. Lin. "Analysis of untyped SNPs: maximum likelihood and imputation methods." Genet Epidemiol 34, no. 8 (2010): 803-15.
Tang, Zheng-Zheng, Paul Bunn, Ran Tao, Zhouwen Liu, and Dan-Yu Lin. "PreMeta: a tool to facilitate meta-analysis of rare-variant associations." BMC Genomics 18, no. 1 (2017): 160.
Tang, Zheng-Zheng, and Dan-Yu Lin. "MASS: meta-analysis of score statistics for sequencing studies." Bioinformatics 29, no. 14 (2013): 1803-5.
Knickmeyer, Rebecca C., Jiaping Wang, Hongtu Zhu, Xiujuan Geng, Sandra Woolson, Robert M. Hamer, Thomas Konneker, Weili Lin, Martin Styner, and John H. Gilmore. "Common variants in psychiatric risk genes predict brain structure at birth." Cereb Cortex 24, no. 5 (2014): 1230-46.
Acharya, Chaitanya R., Janice M. McCarthy, Kouros Owzar, and Andrew S. Allen. "Exploiting expression patterns across multiple tissues to map expression quantitative trait loci." BMC Bioinformatics 17 (2016): 257.
Tang, Zheng-Zheng, and Dan-Yu Lin. "Meta-analysis for Discovering Rare-Variant Associations: Statistical Methods and Software Programs." Am J Hum Genet 97, no. 1 (2015): 35-53.
He, Qianchuan, Christy L. Avery, and Dan-Yu Lin. "A general framework for association tests with multivariate traits in large-scale genomics studies." Genet Epidemiol 37, no. 8 (2013): 759-67.
Genome, Human
Brucker, Amanda, Wenbin Lu, Rachel Marceau West, Qi-You Yu, Chuhsing Kate Hsiao, Tzu-Hung Hsiao, Ching-Heng Lin, Patrik K. E. Magnusson, Patrick F. Sullivan, Jin P. Szatkiewicz et al. "Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis." PLoS Comput Biol 16, no. 5 (2020): e1007797.
"Genome-wide association study identifies five new schizophrenia loci." Nat Genet 43, no. 10 (2011): 969-76.
Hu, Y J., and D Y. Lin. "Analysis of untyped SNPs: maximum likelihood and imputation methods." Genet Epidemiol 34, no. 8 (2010): 803-15.
Yazdani, Azam, Akram Yazdani, Sarah H. Elsea, Daniel J. Schaid, Michael R. Kosorok, Gita Dangol, and Ahmad Samiei. "Genome analysis and pleiotropy assessment using causal networks with loss of function mutation and metabolomics." BMC Genomics 20, no. 1 (2019): 395.
Wang, Xuefeng, Mengjie Chen, Xiaoqing Yu, Natapol Pornputtapong, Hao Chen, Nancy R. Zhang, Scott R Powers, and Michael Krauthammer. "Global copy number profiling of cancer genomes." Bioinformatics 32, no. 6 (2016): 926-8.
Lin, Dan-Yu. "A simple and accurate method to determine genomewide significance for association tests in sequencing studies." Genet Epidemiol 43, no. 4 (2019): 365-372.
McLeod, Howard L.. "Cancer pharmacogenomics: early promise, but concerted effort needed." Science 339, no. 6127 (2013): 1563-6.
He, Qianchuan, Christy L. Avery, and Dan-Yu Lin. "A general framework for association tests with multivariate traits in large-scale genomics studies." Genet Epidemiol 37, no. 8 (2013): 759-67.
Zhang, Xiang, Shunping Huang, Wei Sun, and Wei Wang. "Rapid and robust resampling-based multiple-testing correction with application in a genome-wide expression quantitative trait loci study." Genetics 190, no. 4 (2012): 1511-20.
Soneson, Charlotte, Michael I. Love, Rob Patro, Shobbir Hussain, Dheeraj Malhotra, and Mark D. Robinson. "A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs." Life Sci Alliance 2, no. 1 (2019).
Zhang, Xiang, Shunping Huang, Fei Zou, and Wei Wang. "TEAM: efficient two-locus epistasis tests in human genome-wide association study." Bioinformatics 26, no. 12 (2010): i217-27.
Wang, Rujin, Dan-Yu Lin, and Yuchao Jiang. "SCOPE: A Normalization and Copy-Number Estimation Method for Single-Cell DNA Sequencing." Cell Syst 10, no. 5 (2020): 445-452.e6.
Genome-Wide Association Study
Wang, Zhi, Arnab Maity, Yiwen Luo, Megan L. Neely, and Jung-Ying Tzeng. "Complete effect-profile assessment in association studies with multiple genetic and multiple environmental factors." Genet Epidemiol 39, no. 2 (2015): 122-33.
Maity, Arnab, Patrick F. Sullivan, and Jun-Ying Tzeng. "Multivariate phenotype association analysis by marker-set kernel machine regression." Genet Epidemiol 36, no. 7 (2012): 686-95.
"Genome-wide association study identifies five new schizophrenia loci." Nat Genet 43, no. 10 (2011): 969-76.
He, Qianchuan, and Dan-Yu Lin. "A variable selection method for genome-wide association studies." Bioinformatics 27, no. 1 (2011): 1-8.
Tzeng, Jung-Ying, Patrik K. E. Magnusson, Patrick F. Sullivan, and Jin P. Szatkiewicz. "A New Method for Detecting Associations with Rare Copy-Number Variants." PLoS Genet 11, no. 10 (2015): e1005403.
Jusakul, Apinya, Ioana Cutcutache, Chern Han Yong, Jing Quan Lim, Mi Ni Huang, Nisha Padmanabhan, Vishwa Nellore, Sarinya Kongpetch, Alvin Wei Tian Ng, Ley Moy Ng et al. "Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma." Cancer Discov 7, no. 10 (2017): 1116-1135.
Chua, Katherina C., Chenling Xiong, Carol Ho, Taisei Mushiroda, Chen Jiang, Flora Mulkey, Dongbing Lai, Bryan P. Schneider, Sara R. Rashkin, John S. Witte et al. "Genomewide Meta-Analysis Validates a Role for S1PR1 in Microtubule Targeting Agent-Induced Sensory Peripheral Neuropathy." Clin Pharmacol Ther 108, no. 3 (2020): 625-634.
Brucker, Amanda, Wenbin Lu, Rachel Marceau West, Qi-You Yu, Chuhsing Kate Hsiao, Tzu-Hung Hsiao, Ching-Heng Lin, Patrik K. E. Magnusson, Patrick F. Sullivan, Jin P. Szatkiewicz et al. "Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis." PLoS Comput Biol 16, no. 5 (2020): e1007797.
Hu, Yi-Juan, Sonja I. Berndt, Stefan Gustafsson, Andrea Ganna, Joel Hirschhorn, Kari E. North, Erik Ingelsson, and Dan-Yu Lin. "Meta-analysis of gene-level associations for rare variants based on single-variant statistics." Am J Hum Genet 93, no. 2 (2013): 236-48.
Lee, Mei-Hsien, Jung-Ying Tzeng, Su-Yun Huang, and Chuhsing Kate Hsiao. "Combining an evolution-guided clustering algorithm and haplotype-based LRT in family association studies." BMC Genet 12 (2011): 48.
Lin, D Y., and D Zeng. "Meta-analysis of genome-wide association studies: no efficiency gain in using individual participant data." Genet Epidemiol 34, no. 1 (2010): 60-6.
X Jeng, Jessie, Jacob Rhyne, Teng Zhang, and Jung-Ying Tzeng. "Effective SNP ranking improves the performance of eQTL mapping." Genet Epidemiol 44, no. 6 (2020): 611-619.
Pang, Herbert, and Sin-Ho Jung. "Sample size considerations of prediction-validation methods in high-dimensional data for survival outcomes." Genet Epidemiol 37, no. 3 (2013): 276-82.
He, Qianchuan, Hao Helen Zhang, Christy L. Avery, and D Y. Lin. "Sparse meta-analysis with high-dimensional data." Biostatistics 17, no. 2 (2016): 205-20.
Bhattacharya, Arjun, Montserrat García-Closas, Andrew F. Olshan, Charles M. Perou, Melissa A. Troester, and Michael I. Love. "A framework for transcriptome-wide association studies in breast cancer in diverse study populations." Genome Biol 21, no. 1 (2020): 42.
R Baldwin, Michael, Kouros Owzar, Hitoshi Zembutsu, Aparna Chhibber, Michiaki Kubo, Chen Jiang, Dorothy Watson, Rachel J. Eclov, Joel Mefford, Howard L. McLeod et al. "A genome-wide association study identifies novel loci for paclitaxel-induced sensory peripheral neuropathy in CALGB 40101." Clin Cancer Res 18, no. 18 (2012): 5099-109.
Li, Zhiguo, Jiaxing Lin, Alexander B. Sibley, Tracy Truong, Katherina C. Chua, Yu Jiang, Janice McCarthy, Deanna L. Kroetz, Andrew Allen, and Kouros Owzar. "Efficient estimation of grouped survival models." BMC Bioinformatics 20, no. 1 (2019): 269.
Lin, Jiaxing, Alexander Sibley, Ivo Shterev, Andrew Nixon, Federico Innocenti, Cliburn Chan, and Kouros Owzar. "fastJT: An R package for robust and efficient feature selection for machine learning and genome-wide association studies." BMC Bioinformatics 20, no. 1 (2019): 333.
Owzar, Kouros, Zhiguo Li, Nancy Cox, and Sin-Ho Jung. "Power and sample size calculations for SNP association studies with censored time-to-event outcomes." Genet Epidemiol 36, no. 6 (2012): 538-48.
Wojcik, Genevieve L., Mariaelisa Graff, Katherine K. Nishimura, Ran Tao, Jeffrey Haessler, Christopher R. Gignoux, Heather M. Highland, Yesha M. Patel, Elena P. Sorokin, Christy L. Avery et al. "Genetic analyses of diverse populations improves discovery for complex traits." Nature 570, no. 7762 (2019): 514-518.
Kim, Jinseog, Insuk Sohn, Dae-Soon Son, Dong Hwan Kim, Taejin Ahn, and Sin-Ho Jung. "Prediction of a time-to-event trait using genome wide SNP data." BMC Bioinformatics 14 (2013): 58.
Zhang, Xiang, Shunping Huang, Fei Zou, and Wei Wang. "TEAM: efficient two-locus epistasis tests in human genome-wide association study." Bioinformatics 26, no. 12 (2010): i217-27.
Mitha, Faheem, Herodotos Herodotou, Nedyalko Borisov, Chen Jiang, Josh Yoder, and Kouros Owzar. "SNPpy--database management for SNP data from genome wide association studies." PLoS One 6, no. 10 (2011): e24982.
Hu, Y J., and D Y. Lin. "Analysis of untyped SNPs: maximum likelihood and imputation methods." Genet Epidemiol 34, no. 8 (2010): 803-15.
Acharya, Chaitanya R., Janice M. McCarthy, Kouros Owzar, and Andrew S. Allen. "Exploiting expression patterns across multiple tissues to map expression quantitative trait loci." BMC Bioinformatics 17 (2016): 257.
He, Qianchuan, Christy L. Avery, and Dan-Yu Lin. "A general framework for association tests with multivariate traits in large-scale genomics studies." Genet Epidemiol 37, no. 8 (2013): 759-67.
Lin, Dan-Yu, and Zheng-Zheng Tang. "A general framework for detecting disease associations with rare variants in sequencing studies." Am J Hum Genet 89, no. 3 (2011): 354-67.
Genomics
Brucker, Amanda, Wenbin Lu, Rachel Marceau West, Qi-You Yu, Chuhsing Kate Hsiao, Tzu-Hung Hsiao, Ching-Heng Lin, Patrik K. E. Magnusson, Patrick F. Sullivan, Jin P. Szatkiewicz et al. "Association test using Copy Number Profile Curves (CONCUR) enhances power in rare copy number variant analysis." PLoS Comput Biol 16, no. 5 (2020): e1007797.
Lin, Dan-Yu, Donglin Zeng, and David Couper. "A general framework for integrative analysis of incomplete multiomics data." Genet Epidemiol 44, no. 7 (2020): 646-664.
Pang, Herbert, Keita Ebisu, Emi Watanabe, Laura Y. Sue, and Tiejun Tong. "Analysing breast cancer microarrays from African Americans using shrinkage-based discriminant analysis." Hum Genomics 5, no. 1 (2010): 5-16.
He, Qianchuan, Hao Helen Zhang, Christy L. Avery, and D Y. Lin. "Sparse meta-analysis with high-dimensional data." Biostatistics 17, no. 2 (2016): 205-20.
Kim, Jinseog, Insuk Sohn, Dae-Soon Son, Dong Hwan Kim, Taejin Ahn, and Sin-Ho Jung. "Prediction of a time-to-event trait using genome wide SNP data." BMC Bioinformatics 14 (2013): 58.
He, Qianchuan, Christy L. Avery, and Dan-Yu Lin. "A general framework for association tests with multivariate traits in large-scale genomics studies." Genet Epidemiol 37, no. 8 (2013): 759-67.
Wang, Rujin, Dan-Yu Lin, and Yuchao Jiang. "SCOPE: A Normalization and Copy-Number Estimation Method for Single-Cell DNA Sequencing." Cell Syst 10, no. 5 (2020): 445-452.e6.
McCabe, Sean D., Dan-Yu Lin, and Michael I. Love. "Consistency and overfitting of multi-omics methods on experimental data." Brief Bioinform 21, no. 4 (2020): 1277-1284.
Kimes, Patrick K., Yufeng Liu, David Neil Hayes, and James Stephen Marron. "Statistical significance for hierarchical clustering." Biometrics 73, no. 3 (2017): 811-821.
Wang, WeiBo, Wei Wang, Wei Sun, James J. Crowley, and Jin P. Szatkiewicz. "Allele-specific copy-number discovery from whole-genome and whole-exome sequencing." Nucleic Acids Res 43, no. 14 (2015): e90.
Hu, Jun, and Jung-Ying Tzeng. "Integrative gene set analysis of multi-platform data with sample heterogeneity." Bioinformatics 30, no. 11 (2014): 1501-7.
Jeng, Xinge Jessie, Zhongyin John Daye, Wenbin Lu, and Jung-Ying Tzeng. "Rare Variants Association Analysis in Large-Scale Sequencing Studies at the Single Locus Level." PLoS Comput Biol 12, no. 6 (2016): e1004993.
Cruz-Garcia, Lourdes, Grainne O'Brien, Botond Sipos, Simon Mayes, Michael I. Love, Daniel J. Turner, and Christophe Badie. "Generation of a Transcriptional Radiation Exposure Signature in Human Blood Using Long-Read Nanopore Sequencing." Radiat Res 193, no. 2 (2020): 143-154.
Wong, Kin Yau, Cheng Fan, Maki Tanioka, Joel S. Parker, Andrew B. Nobel, Donglin Zeng, Dan-Yu Lin, and Charles M. Perou. "I-Boost: an integrative boosting approach for predicting survival time with multiple genomics platforms." Genome Biol 20, no. 1 (2019): 52.
Zhang, Xiang, Shunping Huang, Fei Zou, and Wei Wang. "TEAM: efficient two-locus epistasis tests in human genome-wide association study." Bioinformatics 26, no. 12 (2010): i217-27.
Love, Michael I., Charlotte Soneson, Peter F. Hickey, Lisa K. Johnson, Tessa N Pierce, Lori Shepherd, Martin Morgan, and Rob Patro. "Tximeta: Reference sequence checksums for provenance identification in RNA-seq." PLoS Comput Biol 16, no. 2 (2020): e1007664.
Jiang, Yuchao, Rujin Wang, Eugene Urrutia, Ioannis N. Anastopoulos, Katherine L. Nathanson, and Nancy R. Zhang. "CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing." Genome Biol 19, no. 1 (2018): 202.
Urrutia, Eugene, Hao Chen, Zilu Zhou, Nancy R. Zhang, and Yuchao Jiang. "Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny." Bioinformatics 34, no. 12 (2018): 2126-2128.
Genotype
Hu, Y J., and D Y. Lin. "Analysis of untyped SNPs: maximum likelihood and imputation methods." Genet Epidemiol 34, no. 8 (2010): 803-15.
R Baldwin, Michael, Kouros Owzar, Hitoshi Zembutsu, Aparna Chhibber, Michiaki Kubo, Chen Jiang, Dorothy Watson, Rachel J. Eclov, Joel Mefford, Howard L. McLeod et al. "A genome-wide association study identifies novel loci for paclitaxel-induced sensory peripheral neuropathy in CALGB 40101." Clin Cancer Res 18, no. 18 (2012): 5099-109.
Lin, Dan-Yu. "A simple and accurate method to determine genomewide significance for association tests in sequencing studies." Genet Epidemiol 43, no. 4 (2019): 365-372.
Pang, Herbert, Michael Hauser, and Stéphane Minvielle. "Pathway-based identification of SNPs predictive of survival." Eur J Hum Genet 19, no. 6 (2011): 704-9.
Hu, Yi-Juan, Yun Li, Paul L. Auer, and Dan-Yu Lin. "Integrative analysis of sequencing and array genotype data for discovering disease associations with rare mutations." Proc Natl Acad Sci U S A 112, no. 4 (2015): 1019-24.
Hu, Y J., D Y. Lin, and D Zeng. "A general framework for studying genetic effects and gene-environment interactions with missing data." Biostatistics 11, no. 4 (2010): 583-98.
Zhang, Xiang, Shunping Huang, Wei Sun, and Wei Wang. "Rapid and robust resampling-based multiple-testing correction with application in a genome-wide expression quantitative trait loci study." Genetics 190, no. 4 (2012): 1511-20.
Wang, Xin, Daowen Zhang, and Jung-Ying Tzeng. "Pathway-guided identification of gene-gene interactions." Ann Hum Genet 78, no. 6 (2014): 478-91.
Appell, Malin L., Jonathan Berg, John Duley, William E. Evans, Martin A. Kennedy, Lynne Lennard, Tony Marinaki, Howard L. McLeod, Mary V. Relling, Elke Schaeffeler et al. "Nomenclature for alleles of the thiopurine methyltransferase gene." Pharmacogenet Genomics 23, no. 4 (2013): 242-8.
Knickmeyer, Rebecca C., Jiaping Wang, Hongtu Zhu, Xiujuan Geng, Sandra Woolson, Robert M. Hamer, Thomas Konneker, Weili Lin, Martin Styner, and John H. Gilmore. "Common variants in psychiatric risk genes predict brain structure at birth." Cereb Cortex 24, no. 5 (2014): 1230-46.

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