Papers

Mixed Model with Correction for Case-Control Ascertainment Increases Association Power
Tristan Hayeck, Noah A Zaitlen, Po-Ru Loh, Bjarni J Vilhjalmsson, Samuela Pollack, Alexander Gusev, Jian Yang, Guo-Bo Chen, Michael E Goddard, Peter M Visscher, Nick Patterson, and Alkes L Price
bioRxiv, 2014

Efficient Bayesian mixed model analysis increases association power in large cohorts
Po-Ru Loh, George Tucker, Brendan K Bulik-Sullivan, Bjarni J Vilhjalmsson, Hilary K Finucane, Rany M Salem, Daniel I Chasman, Paul M Ridker, Benjamin M Neale, Bonnie Berger, Nick Patterson, and Alkes L Price
Nature Genetics, in press; see also the BOLT-LMM software page

LD Score Regression Distinguishes Confounding from Polygenicity in Genome-Wide Association Studies
Brendan Bulik-Sullivan, Po-Ru Loh, Hilary Finucane, Stephan Ripke, Jian Yang, Schizophrenia Working Group Psychiatric Genomics Consortium, Nick Patterson, Mark J Daly, Alkes L Price, and Benjamin M Neale
Nature Genetics, in press

Genomic Prediction and Genome Wide Association in Humans with Whole Genome Sequence Data
Alkes L Price and  Po-Ru Loh
Proceedings of the 10th World Congress of Genetics Applied to Livestock Production (WCGALP), 2014

Reconstructing Austronesian population history in Island Southeast Asia
Mark Lipson, Po-Ru Loh, Nick Patterson, Priya Moorjani, Ying-Chin Ko, Mark Stoneking, Bonnie Berger, and David Reich
Nature Communications, 2014
Featured in Nature 8/21/14 News & Views article by Jared Diamond

Ancient west Eurasian ancestry in southern and eastern Africa
Joseph K. Pickrell, Nick Patterson, Po-Ru Loh, Mark Lipson, Bonnie Berger, Mark Stoneking, Brigitte Pakendorf, and David Reich
PNAS, 2014

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach
Pablo Meyer, Thomas Cokelaer, Deepak Chandran, Kyung Hyuk Kim, Po-Ru Loh, George Tucker, Mark Lipson, Bonnie Berger, Clemens Kreutz, Andreas Raue, Bernhard Steiert, Jens Timmer, Erhan Bilal, DREAM 6&7 Parameter Estimation consortium, Herbert M Sauro, Gustavo Stolovitzky, and Julio Saez-Rodriguez
BMC Systems Biology, 2014

A sampling framework for incorporating quantitative mass spectrometry data in protein interaction analysis
George Tucker, Po-Ru Loh, and Bonnie Berger
BMC Bioinformatics, 2013

Genetic Evidence for Recent Population Mixture in India
Priya Moorjani, Kumarasamy Thangaraj, Nick Patterson, Mark Lipson, Po-Ru Loh, Periyasamy Govindaraj, Bonnie Berger, David Reich, and Lalji Singh
American Journal of Human Genetics, 2013

Efficient moment-based inference of admixture parameters and sources of gene flow
Mark Lipson, Po-Ru Loh, Alex Levin, David Reich, Nick Patterson, and Bonnie Berger
Molecular Biology and Evolution, 2013; see also the MixMapper software page

Inferring Admixture Histories of Human Populations Using Linkage Disequilibrium
Po-Ru Loh, Mark Lipson, Nick Patterson, Priya Moorjani, Joseph K Pickrell, David Reich, and Bonnie Berger
Genetics, 2013; see also the ALDER software page
Featured as the cover article of the April 2013 issue of Genetics

Reconstructing Roma history from genome-wide data
Priya Moorjani, Nick Patterson, Po-Ru Loh, Mark Lipson, Péter Kisfali, Bela I Melegh, Michael Bonin, Ľudevít Kádaši, Olaf Rieß, Bonnie Berger, David Reich, and Béla Melegh
PLoS ONE, 2013

Prize-based contests can provide solutions to computational biology problems
Karim R Lakhani, Kevin J Boudreau, Po-Ru Loh, Lars Backstrom, Carliss Baldwin, Eric Lonstein, Mike Lydon, Alan MacCormack, Ramy A Arnaout, and Eva C Guinan
Nature Biotechnology, 2013
Featured in Harvard Medical School News 2/7/13, Boston Globe 2/11/13

The genetic prehistory of southern Africa
Pickrell JK, Patterson N, Barbieri C, Berthold F, Gerlach L, Guldemann T, Kure B, Mpoloka SW, Nakagawa H, Naumann C, Lipson M, Loh PR, Lachance J, Mountain J, Bustamante C, Berger B, Tishkoff S, Henn B, Stoneking M, Reich D, and Pakendorf B
Nature Communications, 2012

Compressive Genomics
Po-Ru Loh, Michael Baym, and Bonnie Berger
Nature Biotechnology, 2012
Featured in the MIT Spotlight (home page) 7/12/12

Assessing Statistical Significance in Causal Graphs
Leonid Chindelevitch, Po-Ru Loh, Ahmed Enayetallah, Bonnie Berger, and Daniel Ziemek
BMC Bioinformatics, 2012

Phenotype prediction using regularized regression on genetic data in the DREAM5 Systems Genetics B Challenge
Po-Ru Loh, George Tucker, and Bonnie Berger
PLoS ONE, 2011

Building quantitative prediction models for tissue residue of two explosives compounds in earthworms from microarray gene expression data
Ping Gong, Po-Ru Loh, Natalie D. Barker, George Tucker, Nan Wang, Chenhua Zhang, B. Lynn Escalon, Bonnie Berger, and Edward J. Perkins
Environmental Science & Technology, 2011

Assessment of chemical mixtures and ground water effects on Daphnia magna transcriptomics
Natalia Garcia-Reyero, B. Lynn Escalon, Po-Ru Loh, Jennifer G. Laird, Alan J. Kennedy, Bonnie Berger, and Edward J. Perkins
Environmental Science & Technology, 2011

Making Polygons by Simple Folds and One Straight Cut
Erik Demaine, Martin Demaine, Andrea Hawksley, Hiro Ito, Po-Ru Loh, Shelly Manber, and Omari Stephens
Proceedings of the 2010 China-Japan Joint Conference on Computational Geometry, Graphs, and Applications (CGGA 2010), 2011

Fundamental relation between phase and group velocity, and application to the failure of perfectly matched layers in backward-wave structures
Po-Ru Loh, Ardavan F. Oskooi, Mihai Ibanescu, Maksim Skorobogatiy, and Steven G. Johnson
Physical Review E, 2009

Stepping to Infinity Along Gaussian Primes
Po-Ru Loh
American Mathematical Monthly, 2007

p-adic and Combinatorial Properties of Modular Form Coefficients
Po-Ru Loh and Robert Rhoades
International Journal of Number Theory, 2006