Research

Selected Publications

View full list at Google scholar

* denotes equal contribution

• A blended genome and exome sequencing method captures genetic variation in an unbiased, high-quality, and cost-effective manner
  Toni A Boltz*, Benjamin B. Chu*, Calwing Liao*, Julia M Sealock*, …, Benjamin M Neale, Daniel P Howrigan, Alicia R Martin. bioRxiv preprint (2024)

• Beyond guilty by association at scale: searching for causal variants on the basis of genome-wide summary statistics
  Zihuai He*, Benjamin B. Chu*, James Yang*, Jiaqi Gu*, Zhaomeng Chen, Linxi Liu, Tim Morrison, Michael Belloy, Xinran Qi, Nima Hejazi, Maya Mathur, Yann Le Guen, Hua Tang, Trevor Hastie, Iuliana Ionita-Iaza, Chiara Sabatti, Emmanuel Candes. bioRxiv preprint (2024)

• Second-order group knockoffs with applications to GWAS
  Benjamin B. Chu, Jiaqi Gu, Zhaomeng Chen, Tim Morrison, Emmanuel Candes, Zihuai He, Chiara Sabatti. accepted at Bioinformatics (2024)

• Multivariate Genome-wide Association Analysis with IHT
  Benjamin B. Chu, Seyoon Ko, Jin J. Zhou, Hua Zhou, Janet S. Sinsheimer, Kenneth Lange. Bioinformatics (2023)

• Optimized Replacement T4 and T4+ T3 Dosing in Male and Female Hypothyroid Patients With Different BMIs Using a Personalized Mechanistic Model of Thyroid Hormone Regulation Dynamics
  Mauricio Cruz-Loya*, Benjamin B. Chu*, Jacqueline Jonklaas, David F. Schneider, Joe DiStefano III. Frontiers in Endocrinology (2022)

• A Fast Data-Driven Method for Genotype Imputation, Phasing, and Local Ancestry Inference: MendelImpute.jl
  Benjamin B. Chu, Eric M Sobel, Rory Wasiolek, Janet S. Sinsheimer, Hua Zhou, Kenneth Lange. Bioinformatics (2021)

• Iterative Hard Thresholding in genome-wide association studies: Generalized Linear Models, Prior Weights, and Double Sparsity
  Benjamin B. Chu, Kevin L. Keys, Christopher A. German, Hua Zhou, Jin J. Zhou, Janet S. Sinsheimer, Kenneth Lange. GigaScience (2020)

Talks

• False discovery rate control for polygenic risk prediction. UCLA (online), Center for Admixed Population and Health Equity. (Slides)

• Scalable algorithms for genetic association studies, genotype imputation, and ancestry inference. 2021 University of Southern California (online), Biostatistics Seminar. (Slides)(Video)

• Scalable algorithms for GWAS, genotype imputation, and ancestry inference. 2020 University of Michigan (online), Biostatistics Seminar. (Slides)

• Julia Meets Mendel: Algorithms and Software for Modern Genomic Data Analysis. 2020 ASHG Workshop (home page)(ipynb)(html)(talk slides)

• OpenMendel Programming Workshop. 2020 Inaugural Lange Symposium, Los Angeles. (ipynb)(html)(binder)

• A multiple regression approach for GWAS and high dimensional inference. 2020 QCBio Luncheon, Los Angeles. (Slides)

• MendelIHT.jl: Generalized Linear Models for High Dimensional Genetics (GWAS) Data. 2019 JuliaCon, Baltimore. (Video)(Slides)