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We solve computational challenges in biomedical research that require statistical or algorithmic innovations. Much of our work is aimed at unlocking the full power of biobank-scale genetic data sets now becoming available (e.g., N=500,000 UK Biobank). To this end, we develop high-performance open...

Phenotype prediction using regularized regression on genetic data in the DREAM5 Systems Genetics B Challenge

Publication: Journal Article

Loh, Po-Ru, George Tucker, and Bonnie Berger. 2011. “Phenotype Prediction Using Regularized Regression on Genetic Data in the DREAM5 Systems Genetics B Challenge”. PLoS One 6 (12): e29095.

Building quantitative prediction models for tissue residue of two explosives compounds in earthworms from microarray gene expression data

Publication: Journal Article

Gong, Ping, Po-Ru Loh, Natalie Barker, George Tucker, Nan Wang, Chenhua Zhang, Lynn Escalon, Bonnie Berger, and Edward Perkins. 2012. “Building Quantitative Prediction Models for Tissue Residue of Two Explosives Compounds in Earthworms from Microarray Gene Expression Data”. Environ Sci Technol 46 (1): 19-26.

Prize-based contests can provide solutions to computational biology problems

Publication: Journal Article

Lakhani, Karim, Kevin Boudreau, Po-Ru Loh, Lars Backstrom, Carliss Baldwin, Eric Lonstein, Mike Lydon, Alan MacCormack, Ramy Arnaout, and Eva Guinan. 2013. “Prize-Based Contests Can Provide Solutions to Computational Biology Problems”. Nat Biotechnol 31 (2): 108-11.

Reconstructing Austronesian population history in Island Southeast Asia

Publication: Journal Article

Lipson, Mark, Po-Ru Loh, Nick Patterson, Priya Moorjani, Ying-Chin Ko, Mark Stoneking, Bonnie Berger, and David Reich. 2014. “Reconstructing Austronesian Population History in Island Southeast Asia”. Nat Commun 5: 4689.

Mixed-model association for biobank-scale datasets

Publication: Journal Article

Loh, Po-Ru, Gleb Kichaev, Steven Gazal, Armin Schoech, and Alkes Price. 2018. “Mixed-Model Association for Biobank-Scale Datasets”. Nat Genet 50 (7): 906-8.

Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk

Publication: Journal Article

Reshef, YA, Hilary Finucane, David Kelley, Alexander Gusev, Dylan Kotliar, Jacob Ulirsch, Farhad Hormozdiari, et al. 2018. “Detecting Genome-Wide Directional Effects of Transcription Factor Binding on Polygenic Disease Risk”. Nat Genet 50 (10): 1483-93.

Maternal and fetal genetic effects on birth weight and their relevance to cardio-metabolic risk factors

Publication: Journal Article

Warrington, Nicole, Robin Beaumont, Momoko Horikoshi, Felix Day, Øyvind Helgeland, Charles Laurin, Jonas Bacelis, et al. 2019. “Maternal and Fetal Genetic Effects on Birth Weight and Their Relevance to Cardio-Metabolic Risk Factors”. Nat Genet 51 (5): 804-14.

Protein-coding repeat polymorphisms strongly shape diverse human phenotypes

Publication: Journal Article

Mukamel, Ronen E, Robert Handsaker, Maxwell Sherman, Alison Barton, Yiming Zheng, Steven McCarroll, and Po-Ru Loh. 2021. “Protein-Coding Repeat Polymorphisms Strongly Shape Diverse Human Phenotypes”. Science 373 (6562): 1499-1505.

Estimating the effective sample size in association studies of quantitative traits

Publication: Journal Article

Ziyatdinov, Andrey, Jihye Kim, Dmitry Prokopenko, Florian Privé, Fabien Laporte, Po-Ru Loh, Peter Kraft, and Hugues Aschard. 2021. “Estimating the Effective Sample Size in Association Studies of Quantitative Traits”. G3 11 (6): jkab057.