Softwares
Published:
Below is a (non-exhausive) list of softwares I am involved in, that I think are pretty cool. See my github page for more.
GhostKnockoffGWAS
Analyzing GWAS summary statistics data under the knockoff framework.
- In silico identification of putative causal genetic variants 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)
Knockoffs.jl
Julia implementation of the Knockoff filter
GitHub page, python wrapper, R wrapper
- Second-order group knockoffs with applications to GWAS Benjamin B. Chu, Jiaqi Gu, Zhaomeng Chen, Tim Morrison, Emmanuel Candes, Zihuai He, Chiara Sabatti
MendelIHT.jl
Iterative hard thresholding as a multiple regression model for GWAS
Multivariate Genome-wide Association Analysis with IHT Benjamin B. Chu, Seyoon Ko, Jin J. Zhou, Hua Zhou, Janet S. Sinsheimer, Kenneth Lange. Bioinformatics (2023)*
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)
MendelImpute.jl
Fast genotype imputation, phasing, and admixture estimation
- 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)
SnpArrays.jl
Julia utilities for handling binary PLINK files
VCFTools.jl
Julia utilities for handling VCF files
MendelKinship.jl
Julia utilities for computing theoretical/empirical kinship and other identity coefficients
Thyrosim.jl
Mechanistic model for thyroid hormone regulation
- 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)