Here is a list of my published and preprinted works. For a more reliably updated source, please refer to my Google Scholar profile.
Published in PLoS ONE, 2024
Merle Behr, Karl Kumbier, Aldo Cordova-Palomera, Matthew Aguirre, Omer Ronen, Chengzhong Ye, Euan Ashley, Atul J Butte, Rima Arnaout, Ben Brown, James Priest, Bin Yu, "Learning epistatic polygenic phenotypes with Boolean interactions." PLoS ONE, 2024. https://doi.org/10.1371/journal.pone.0298906
Published in bioRxiv, 2023
Marianne K DeGorter, Pagé C Goddard, Emre Karakoc, Soumya Kundu, Stephanie M Yan, Daniel Nachun, Nathan Abell, Matthew Aguirre, Tommy Carstensen, Ziwei Chen, Matthew Durrant, Vikranth R Dwaracherla, Karen Feng, Michael J Gloudemans, Naiomi Hunter, Mohana PS Moorthy, Cristina Pomilla, Kameron B Rodrigues, Courtney J Smith, Kevin S Smith, Rachel A Ungar, Brunilda Balliu, Jacques Fellay, Paul Flicek, Paul J McLaren, Brenna Henn, Rajiv C McCoy, Lauren Sugden, Anshul Kundaje, Manjinder S Sandhu, Deepti Gurdasani, Stephen B Montgomery, "Transcriptomics and chromatin accessibility in multiple African population samples." bioRxiv, 2023. https://doi.org/10.1101%2F2023.11.04.564839
Published in Circulation: Genomic and Precision Medicine, 2023
Mengyao Yu, Matthew Aguirre, Meiwen Jia, Ketrin Gjoni, Aldo Cordova-Palomera, Chad Munger, Dulguun Amgalan, X Rosa Ma, Alexandre Pereira, Catherine Tcheandjieu, Christine Seidman, Jonathan Seidman, Martin Tristani-Firouzi, Wendy Chung, Elizabeth Goldmuntz, Deepak Srivastava, Ruth JF Loos, Nathalie Chami, Heather Cordell, Martina Dreßen, Bertram Mueller-Myhsok, Harald Lahm, Markus Krane, Katherine S Pollard, Jesse M Engreitz, Sarah A Gagliano Taliun, Bruce D Gelb, James R Priest, "Oligogenic Architecture of Rare Noncoding Variants Distinguishes 4 Congenital Heart Disease Phenotypes" Circulation: Genomic and Precision Medicine, 2023. https://www.ahajournals.org/doi/abs/10.1161/CIRCGEN.122.003968
Published in Circulation: Genomic and Precision Medicine, 2023
Mengyao Yu, Andrew R Harper, Matthew Aguirre, Maureen Pittman, Catherine Tcheandjieu, Dulguun Amgalan, Christopher Grace, Anuj Goel, Martin Farrall, Ke Xiao, Jesse Engreitz, Katherine S Pollard, Hugh Watkins, James R Priest, "Genetic Determinants of the Interventricular Septum Are Linked to Ventricular Septal Defects and Hypertrophic Cardiomyopathy" Circulation: Genomic and Precision Medicine, 2023. https://www.ahajournals.org/doi/abs/10.1161/CIRCGEN.122.003708
Published in The American Journal of Human Genetics, 2022
Craig Smail, Nicole Ferraro, Qin Hui, Matthew Durrant, Matthew Aguirre, Yosuke Tanigawa, Marissa Keever-Keigher, Abhiram Rao, Johanne Justesen, Xin Li, Michael Gloudemans, Themistocles Assimes, Charles Kooperberg, Alexander Reiner, Jie Huang, Christopher O'Donnell, Yan Sun, Manuel Rivas, Stephen Montgomery, "Integration of rare expression outlier-associated variants improves polygenic risk prediction." The American Journal of Human Genetics, 2022. https://www.sciencedirect.com/science/article/pii/S000292972200163X
Published in The American Journal of Human Genetics, 2021
Guhan Venkataraman, Christopher DeBoever, Yosuke Tanigawa, Matthew Aguirre, Alexander Ioannidis, Hakhamanesh Mostafavi, Chris Spencer, Timothy Poterba, Carlos Bustamante, Mark Daly, Matti Pirinen, Manuel Rivas, "Bayesian model comparison for rare-variant association studies." The American Journal of Human Genetics, 2021. https://www.sciencedirect.com/science/article/pii/S0002929721004171
Published in medRxiv, 2021
Mengyao Yu, Andrew Harper, Matthew Aguirre, Maurren Pittman, Dulguun Amgalan, Christopher Grace, Anuj Goel, Martin Farrall, Ke Xiao, Jesse Engreitz, et. al., "Genetic determinants of interventricular septal anatomy and the risk of ventricular septal defects and hypertrophic cardiomyopathy." medRxiv, 2021. https://doi.org/10.1101/2021.04.19.21255650
Published in European Journal of Human Genetics, 2021
Matthew Aguirre, Yosuke Tanigawa, Guhan Venkataraman, Rob Tibshirani, Trevor Hastie, Manuel Rivas, "Polygenic risk modeling with latent trait-related genetic components." European Journal of Human Genetics, 2021. https://doi.org/10.1038/s41431-021-00813-0
Published in Nature Genetics, 2021
Nasa Sinnott-Armstrong, Yosuke Tanigawa, David Amar, Nina Mars, Christian Benner, Matthew Aguirre, Guhan Venkataraman, Michael Wainberg, Hanna Ollila, Tuomo Kiiskinen, et. al., "Genetics of 35 blood and urine biomarkers in the UK Biobank." Nature Genetics, 2021. https://doi.org/10.1038/s41588-020-00757-z
Published in PLoS genetics, 2020
Catherine Tcheandjieu, Matthew Aguirre, Stefan Gustafsson, Priyanka Saha, Praneetha Potiny, Melissa Haendel, Erik Ingelsson, Manuel Rivas, James Priest, "A phenome-wide association study of 26 mendelian genes reveals phenotypic expressivity of common and rare variants within the general population." PLoS genetics, 2020. https://doi.org/10.1371/journal.pgen.1008802
Published in arXiv preprint arXiv:2011.02081, 2020
Matthew Aguirre, Jan Sokol, Guhan Venkataraman, Alexander Ioannidis, "A deep learning classifier for local ancestry inference." arXiv preprint arXiv:2011.02081, 2020. https://arxiv.org/abs/2011.02081
Published in PLoS genetics, 2020
Junyang Qian, Yosuke Tanigawa, Wenfei Du, Matthew Aguirre, Chris Chang, Robert Tibshirani, Manuel Rivas, Trevor Hastie, "A fast and scalable framework for large-scale and ultrahigh-dimensional sparse regression with application to the UK Biobank." PLoS genetics, 2020. https://doi.org/10.1371/journal.pgen.1009141
Published in The American Journal of Human Genetics, 2020
Christopher DeBoever, Yosuke Tanigawa, Matthew Aguirre, Greg McInnes, Adam Lavertu, Manuel Rivas, "Assessing Digital Phenotyping to Enhance Genetic Studies of Human Diseases." The American Journal of Human Genetics, 2020. https://www.sciencedirect.com/science/article/pii/S0002929720300835
Published in Nature Communications, 2019
Yosuke Tanigawa, Jiehan Li, Johanne Justesen, Heiko Horn, Matthew Aguirre, Christopher DeBoever, Chris Chang, Balasubramanian Narasimhan, Kasper Lage, Trevor Hastie, et. al., "Components of genetic associations across 2,138 phenotypes in the UK Biobank highlight adipocyte biology." Nature Communications, 2019. https://doi.org/10.1038/s41467-019-11953-9
Published in The American Journal of Human Genetics, 2019
Matthew Aguirre, Manuel Rivas, James Priest, "Phenome-wide Burden of Copy-Number Variation in the UK Biobank." The American Journal of Human Genetics, 2019. https://www.sciencedirect.com/science/article/pii/S0002929719302642
Published in Molecular psychiatry, 2019
Douglas Ruderfer, Colin Walsh, Matthew Aguirre, Yosuke Tanigawa, Jessica Ribeiro, Joseph Franklin, Manuel Rivas, "Significant shared heritability underlies suicide attempt and clinically predicted probability of attempting suicide." Molecular psychiatry, 2019. https://doi.org/10.1038/s41380-018-0326-8
Published in Bioinformatics, 2018
Gregory McInnes, Yosuke Tanigawa, Chris DeBoever, Adam Lavertu, Julia Olivieri, Matthew Aguirre, Manuel Rivas, "Global Biobank Engine: enabling genotype-phenotype browsing for biobank summary statistics." Bioinformatics, 2018. https://doi.org/10.1093/bioinformatics/bty999
Published in Nature, 2017
Taru Tukiainen, Alexandra-Chloe Villani, Angela Yen, Manuel Rivas, Jamie Marshall, Rahul Satija, Matt Aguirre, Laura Gauthier, Mark Fleharty, Andrew Kirby, et. al., "Landscape of X chromosome inactivation across human tissues." Nature, 2017. https://doi.org/10.1038/nature24265