Publications

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Humans
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.
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.
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.
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.
Gao, Fei, Donglin Zeng, and Dan-Yu Lin. "Semiparametric estimation of the accelerated failure time model with partly interval-censored data." Biometrics 73, no. 4 (2017): 1161-1168.
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.
Gao, Fei, Donglin Zeng, and Dan-Yu Lin. "Semiparametric regression analysis of interval-censored data with informative dropout." Biometrics 74, no. 4 (2018): 1213-1222.
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.
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.
Lin, Dan-Yu, Ran Tao, William D. Kalsbeek, Donglin Zeng, Franklyn Gonzalez, Lindsay Fernández-Rhodes, Mariaelisa Graff, Gary G. Koch, Kari E. North, and Gerardo Heiss. "Genetic association analysis under complex survey sampling: the Hispanic Community Health Study/Study of Latinos." Am J Hum Genet 95, no. 6 (2014): 675-88.
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.
Tang, Zheng-Zheng, and Dan-Yu Lin. "Meta-analysis of sequencing studies with heterogeneous genetic associations." Genet Epidemiol 38, no. 5 (2014): 389-401.
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.
Little, Paul, Dan-Yu Lin, and Wei Sun. "Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time." Genome Med 11, no. 1 (2019): 37.
Lin, Dan-Yu, Donglin Zeng, and Zheng-Zheng Tang. "Quantitative trait analysis in sequencing studies under trait-dependent sampling." Proc Natl Acad Sci U S A 110, no. 30 (2013): 12247-52.
Tang, Zheng-Zheng, and Dan-Yu Lin. "MASS: meta-analysis of score statistics for sequencing studies." Bioinformatics 29, no. 14 (2013): 1803-5.
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.
Sun, Wei, Paul Bunn, Chong Jin, Paul Little, Vasyl Zhabotynsky, Charles M. Perou, David Neil Hayes, Mengjie Chen, and Dan-Yu Lin. "The association between copy number aberration, DNA methylation and gene expression in tumor samples." Nucleic Acids Res 46, no. 6 (2018): 3009-3018.
Hispanic or Latino
Lin, Dan-Yu, Ran Tao, William D. Kalsbeek, Donglin Zeng, Franklyn Gonzalez, Lindsay Fernández-Rhodes, Mariaelisa Graff, Gary G. Koch, Kari E. North, and Gerardo Heiss. "Genetic association analysis under complex survey sampling: the Hispanic Community Health Study/Study of Latinos." Am J Hum Genet 95, no. 6 (2014): 675-88.
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.
High-Throughput Nucleotide Sequencing
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.
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.
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.
Health Surveys
Lin, Dan-Yu, Ran Tao, William D. Kalsbeek, Donglin Zeng, Franklyn Gonzalez, Lindsay Fernández-Rhodes, Mariaelisa Graff, Gary G. Koch, Kari E. North, and Gerardo Heiss. "Genetic association analysis under complex survey sampling: the Hispanic Community Health Study/Study of Latinos." Am J Hum Genet 95, no. 6 (2014): 675-88.
Health Status Disparities
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.
Health Equity
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.
Glioma
Sun, Wei, Paul Bunn, Chong Jin, Paul Little, Vasyl Zhabotynsky, Charles M. Perou, David Neil Hayes, Mengjie Chen, and Dan-Yu Lin. "The association between copy number aberration, DNA methylation and gene expression in tumor samples." Nucleic Acids Res 46, no. 6 (2018): 3009-3018.
Glioblastoma
Sun, Wei, Paul Bunn, Chong Jin, Paul Little, Vasyl Zhabotynsky, Charles M. Perou, David Neil Hayes, Mengjie Chen, and Dan-Yu Lin. "The association between copy number aberration, DNA methylation and gene expression in tumor samples." Nucleic Acids Res 46, no. 6 (2018): 3009-3018.
Genotyping Techniques
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.
Genotype
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.
Lin, Dan-Yu, Ran Tao, William D. Kalsbeek, Donglin Zeng, Franklyn Gonzalez, Lindsay Fernández-Rhodes, Mariaelisa Graff, Gary G. Koch, Kari E. North, and Gerardo Heiss. "Genetic association analysis under complex survey sampling: the Hispanic Community Health Study/Study of Latinos." Am J Hum Genet 95, no. 6 (2014): 675-88.
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.
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, 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.
Genomics
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, Donglin Zeng, and David Couper. "A general framework for integrative analysis of incomplete multiomics data." Genet Epidemiol 44, no. 7 (2020): 646-664.
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.
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.
Genome-Wide Association Study
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.
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.
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.
He, Qianchuan, and Dan-Yu Lin. "A variable selection method for genome-wide association studies." Bioinformatics 27, no. 1 (2011): 1-8.
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
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.
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. "A simple and accurate method to determine genomewide significance for association tests in sequencing studies." Genet Epidemiol 43, no. 4 (2019): 365-372.
Genetics, Medical
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.
Genetic Variation
Tang, Zheng-Zheng, and Dan-Yu Lin. "MASS: meta-analysis of score statistics for sequencing studies." Bioinformatics 29, no. 14 (2013): 1803-5.
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.
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.
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.
Genetic Loci
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.
Genetic Heterogeneity
Little, Paul, Dan-Yu Lin, and Wei Sun. "Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time." Genome Med 11, no. 1 (2019): 37.
Genetic Diseases, Inborn
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.
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.
Genetic Association Studies
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.
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.
Lin, Dan-Yu, Ran Tao, William D. Kalsbeek, Donglin Zeng, Franklyn Gonzalez, Lindsay Fernández-Rhodes, Mariaelisa Graff, Gary G. Koch, Kari E. North, and Gerardo Heiss. "Genetic association analysis under complex survey sampling: the Hispanic Community Health Study/Study of Latinos." Am J Hum Genet 95, no. 6 (2014): 675-88.
Tang, Zheng-Zheng, and Dan-Yu Lin. "Meta-analysis of sequencing studies with heterogeneous genetic associations." Genet Epidemiol 38, no. 5 (2014): 389-401.
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.
Gene Regulatory Networks
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.
Gene Frequency
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.
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.
Gene Expression Regulation, Neoplastic
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.
Sun, Wei, Paul Bunn, Chong Jin, Paul Little, Vasyl Zhabotynsky, Charles M. Perou, David Neil Hayes, Mengjie Chen, and Dan-Yu Lin. "The association between copy number aberration, DNA methylation and gene expression in tumor samples." Nucleic Acids Res 46, no. 6 (2018): 3009-3018.
Gene Expression Profiling
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.
Female
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.
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.
Sun, Wei, Paul Bunn, Chong Jin, Paul Little, Vasyl Zhabotynsky, Charles M. Perou, David Neil Hayes, Mengjie Chen, and Dan-Yu Lin. "The association between copy number aberration, DNA methylation and gene expression in tumor samples." Nucleic Acids Res 46, no. 6 (2018): 3009-3018.
Lin, Dan-Yu, Ran Tao, William D. Kalsbeek, Donglin Zeng, Franklyn Gonzalez, Lindsay Fernández-Rhodes, Mariaelisa Graff, Gary G. Koch, Kari E. North, and Gerardo Heiss. "Genetic association analysis under complex survey sampling: the Hispanic Community Health Study/Study of Latinos." Am J Hum Genet 95, no. 6 (2014): 675-88.
Family Health
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.
Exome
Lin, Dan-Yu, Donglin Zeng, and Zheng-Zheng Tang. "Quantitative trait analysis in sequencing studies under trait-dependent sampling." Proc Natl Acad Sci U S A 110, no. 30 (2013): 12247-52.
Tang, Zheng-Zheng, and Dan-Yu Lin. "Meta-analysis of sequencing studies with heterogeneous genetic associations." Genet Epidemiol 38, no. 5 (2014): 389-401.
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.
DNA, Neoplasm
Little, Paul, Dan-Yu Lin, and Wei Sun. "Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time." Genome Med 11, no. 1 (2019): 37.
DNA Mutational Analysis
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.
DNA Methylation
Sun, Wei, Paul Bunn, Chong Jin, Paul Little, Vasyl Zhabotynsky, Charles M. Perou, David Neil Hayes, Mengjie Chen, and Dan-Yu Lin. "The association between copy number aberration, DNA methylation and gene expression in tumor samples." Nucleic Acids Res 46, no. 6 (2018): 3009-3018.
DNA Copy Number Variations
Sun, Wei, Paul Bunn, Chong Jin, Paul Little, Vasyl Zhabotynsky, Charles M. Perou, David Neil Hayes, Mengjie Chen, and Dan-Yu Lin. "The association between copy number aberration, DNA methylation and gene expression in tumor samples." Nucleic Acids Res 46, no. 6 (2018): 3009-3018.
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.
Diabetes Mellitus, Type 1
Gao, Fei, Donglin Zeng, and Dan-Yu Lin. "Semiparametric regression analysis of interval-censored data with informative dropout." Biometrics 74, no. 4 (2018): 1213-1222.
Databases, Genetic
Sun, Wei, Paul Bunn, Chong Jin, Paul Little, Vasyl Zhabotynsky, Charles M. Perou, David Neil Hayes, Mengjie Chen, and Dan-Yu Lin. "The association between copy number aberration, DNA methylation and gene expression in tumor samples." Nucleic Acids Res 46, no. 6 (2018): 3009-3018.
Data Interpretation, Statistical
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.
Tang, Zheng-Zheng, and Dan-Yu Lin. "MASS: meta-analysis of score statistics for sequencing studies." Bioinformatics 29, no. 14 (2013): 1803-5.
Data Analysis
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.
Cross-Sectional Studies
Tang, Zheng-Zheng, and Dan-Yu Lin. "Meta-analysis of sequencing studies with heterogeneous genetic associations." Genet Epidemiol 38, no. 5 (2014): 389-401.
CpG Islands
Sun, Wei, Paul Bunn, Chong Jin, Paul Little, Vasyl Zhabotynsky, Charles M. Perou, David Neil Hayes, Mengjie Chen, and Dan-Yu Lin. "The association between copy number aberration, DNA methylation and gene expression in tumor samples." Nucleic Acids Res 46, no. 6 (2018): 3009-3018.
Computer Simulation
Lin, Dan-Yu, Ran Tao, William D. Kalsbeek, Donglin Zeng, Franklyn Gonzalez, Lindsay Fernández-Rhodes, Mariaelisa Graff, Gary G. Koch, Kari E. North, and Gerardo Heiss. "Genetic association analysis under complex survey sampling: the Hispanic Community Health Study/Study of Latinos." Am J Hum Genet 95, no. 6 (2014): 675-88.
Mao, Lu, Dan-Yu Lin, and Donglin Zeng. "Semiparametric regression analysis of interval-censored competing risks data." Biometrics 73, no. 3 (2017): 857-865.
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, 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.
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.
Gao, Fei, Donglin Zeng, and Dan-Yu Lin. "Semiparametric regression analysis of interval-censored data with informative dropout." Biometrics 74, no. 4 (2018): 1213-1222.
Gao, Fei, Donglin Zeng, and Dan-Yu Lin. "Semiparametric estimation of the accelerated failure time model with partly interval-censored data." Biometrics 73, no. 4 (2017): 1161-1168.
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.
He, Qianchuan, and Dan-Yu Lin. "A variable selection method for genome-wide association studies." Bioinformatics 27, no. 1 (2011): 1-8.
Computational Biology
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.
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.
Colonic Neoplasms
Sun, Wei, Paul Bunn, Chong Jin, Paul Little, Vasyl Zhabotynsky, Charles M. Perou, David Neil Hayes, Mengjie Chen, and Dan-Yu Lin. "The association between copy number aberration, DNA methylation and gene expression in tumor samples." Nucleic Acids Res 46, no. 6 (2018): 3009-3018.

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