The paper introduces efficient storage and regression methods for whole genome sequencing studies, reducing computational costs and enabling broader access to genetic research.

Bioinformatics · Feb 5, 2025Peer-reviewedGenetics

Fast Numerical Optimization for Genome Sequencing Data in Population Biobanks

Ruilin Li, Christopher C. Chang, Yosuke Tanigawa, Balasubramanian Narasimhan, Trevor J. Hastie, Robert John Tibshirani, Manuel A. Rivas

The paper develops efficient solvers for large-scale regularized regressions on genetic data, reducing memory usage and improving computational speed.

Bioinformatics · Jun 16, 2021Peer-reviewedBioinformatics

A Fast and Scalable Framework for Large-scale and Ultrahigh-dimensional Sparse Regression with Application to the UK Biobank

Junyang Qian, Yosuke Tanigawa, Wenfei Du, Matthew Aguirre, Christopher C. Chang, Robert John Tibshirani, Manuel A. Rivas, Trevor J. Hastie

This paper introduces a scalable framework for sparse regression on large-scale data, demonstrating improved prediction performance on UK Biobank traits using the BASIL method and snpnet package.

PLoS Genetics · Oct 23, 2020Peer-reviewedBioinformatics

Survival Analysis on Rare Events Using Group-Regularized Multi-Response Cox Regression

Ruilin Li, Christopher C. Chang, Johanne Marie Justesen, Yosuke Tanigawa, Junyang Qian, Trevor J. Hastie, Manuel A. Rivas, Robert John Tibshirani

The paper introduces a group-regularized Cox regression method for survival analysis of rare events using common responses, showing improved prediction performance on UK Biobank data.

Biostatistics · Aug 20, 2020Peer-reviewedBioinformatics

Components of genetic associations across 2,138 phenotypes in the UK Biobank highlight novel adipocyte biology

Yosuke Tanigawa, Jiehan Li, Johanne Marie Justesen, Heiko Horn, Matthew Aguirre, Christopher DeBoever, Christopher C. Chang, Balasubramanian Narasimhan, Kasper Lage, Trevor J. Hastie, Chong Yon Park, Gill Bejerano, Erik Ingelsson, Manuel A. Rivas

The paper uses DeGAs to identify genetic components across 2,138 phenotypes in the UK Biobank, revealing novel adipocyte biology through variant and gene contributions to obesity-related traits.

Nature Communications · Sep 6, 2019Peer-reviewedGenetics

Medical relevance of protein-truncating variants across 337,208 individuals in the UK Biobank study

Christopher DeBoever, Yosuke Tanigawa, Maléne E. Lindholm, Gregory McInnes, Adam Lavertu, Erik Ingelsson, Christopher C. Chang, Euan Angus Ashley, Carlos D. Bustamante, Mark J. Daly, Manuel A. Rivas

The paper assesses the medical relevance of protein-truncating variants across 337,208 UK Biobank individuals, identifying 27 associations with 135 phenotypes and highlighting pleiotropic effects.

Nature Communications · Apr 18, 2018Peer-reviewedGenetics

No major flaws in "Identification of individuals by trait prediction using whole-genome sequencing data"

Christoph Lippert, Riccardo Sabatini, M. Cyrus Maher, Eun Yong Kang, Seunghak Lee, Okan Arıkan, Alena S. Harley, Axel Bernal, Peter Garst, Victor P. Lavrenko, Kenneth Yocum, Theodore M. Wong, Mingfu Zhu, Wen-Yun Yang, Christopher C. Chang, , J. Craig Venter

The paper addresses criticisms of a previous study on identifying individuals from whole-genome sequencing data by demonstrating the limitations of Erlich's simulation and highlighting the algorithm's use of multiple trait-based predictive models.

bioRxiv · Oct 19, 2017 · PreprintGenomics