Publications

Here is a list of my published and preprinted works. For a more reliably updated source, please refer to my Google Scholar profile.

Oligogenic Architecture of Rare Noncoding Variants Distinguishes 4 Congenital Heart Disease Phenotypes

Published in Circulation: Genomic and Precision Medicine, 2023

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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

Genetic Determinants of the Interventricular Septum Are Linked to Ventricular Septal Defects and Hypertrophic Cardiomyopathy

Published in Circulation: Genomic and Precision Medicine, 2023

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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

Integration of rare expression outlier-associated variants improves polygenic risk prediction

Published in The American Journal of Human Genetics, 2022

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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

Bayesian model comparison for rare-variant association studies

Published in The American Journal of Human Genetics, 2021

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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

Genetic determinants of interventricular septal anatomy and the risk of ventricular septal defects and hypertrophic cardiomyopathy

Published in medRxiv, 2021

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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

Polygenic risk modeling with latent trait-related genetic components

Published in European Journal of Human Genetics, 2021

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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

Genetics of 35 blood and urine biomarkers in the UK Biobank

Published in Nature Genetics, 2021

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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

Learning epistatic polygenic phenotypes with Boolean interactions

Published in bioRxiv, 2020

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Merle Behr, Karl Kumbier, Aldo Cordova-Palomera, Matthew Aguirre, Euan Ashley, Atul Butte, Rima Arnaout, James Brown, James Preist, Bin Yu, "Learning epistatic polygenic phenotypes with Boolean interactions." bioRxiv, 2020. https://doi.org/10.1101/2020.11.24.396846

A phenome-wide association study of 26 mendelian genes reveals phenotypic expressivity of common and rare variants within the general population

Published in PLoS genetics, 2020

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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

A deep learning classifier for local ancestry inference

Published in arXiv preprint arXiv:2011.02081, 2020

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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

A fast and scalable framework for large-scale and ultrahigh-dimensional sparse regression with application to the UK Biobank

Published in PLoS genetics, 2020

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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

Assessing Digital Phenotyping to Enhance Genetic Studies of Human Diseases

Published in The American Journal of Human Genetics, 2020

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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

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

Published in Nature Communications, 2019

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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

Phenome-wide Burden of Copy-Number Variation in the UK Biobank

Published in The American Journal of Human Genetics, 2019

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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

Significant shared heritability underlies suicide attempt and clinically predicted probability of attempting suicide

Published in Molecular psychiatry, 2019

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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

Global Biobank Engine: enabling genotype-phenotype browsing for biobank summary statistics

Published in Bioinformatics, 2018

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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

Landscape of X chromosome inactivation across human tissues

Published in Nature, 2017

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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