Publications

The lab’s publications span disease heterogeneity, statistical genetics, computational genomics, and translational discovery. This page collects peer-reviewed papers and preprints, with keyword links to help you browse by topic.

Browse by keyword

UK Biobank

(19)

Sparse models

(10)

Polygenic scores

(8)

Phenotyping

(7)

Rare variants

(5)

Epigenomics

(5)

Latent components

(5)

Resources

(5)

Disease heterogeneity

(3)

Obesity

(3)

List of publications and preprints

Select papers are highlighted.

PRISM: ancestry-aware integration of tissue-specific genomic annotations enhances the transferability of polygenic scores
X Tian, T Fabiha, WF Li, KK Dey, M Kellis, Y Tanigawa. bioRxiv. 2025
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Single-cell multiregion epigenomic rewiring in Alzheimer’s disease progression and cognitive resilience
Z Liu, S Zhang, BT James, K Galani, RJ Mangan, SB Fass, C Liang, MM Wagle, CA Boix, Y Tanigawa, S Yun, Y Sung, X Xiong, N Sun, L Hou, M Wohlwend, M Qiu, X Han, L Xiong, E Preka, L Huang, WF Li, LL Ho, A Grayson, J Mantero, A Kozlenkov, H Mathys, T Chen, S Dracheva, DA Bennett, LH Tsai. Cell. 2025
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Hypometric genetics: Improved power in genetic discovery by incorporating quality control flags
Y Tanigawa, M Kellis. The American Journal of Human Genetics. 2024
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A polygenic score method boosted by non-additive models
R Ohta, Y Tanigawa, Y Suzuki, M Kellis, S Morishita. Nature Communications. 2024
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Power of inclusion: Enhancing polygenic prediction with admixed individuals
Y Tanigawa, M Kellis. The American Journal of Human Genetics. 2023
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Human microglial state dynamics in Alzheimer's disease progression
N Sun, MB Victor, YP Park, X Xiong, AN Scannail, N Leary, S Prosper, S Viswanathan, X Luna, CA Boix, BT James, Y Tanigawa, K Galani, H Mathys, X Jiang, AP Ng, DA Bennett, LH Tsai. Cell. 2023
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A second update on mapping the human genetic architecture of COVID-19
The COVID-19 Host Genetics Initiative. Nature. 2023
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Single-cell dissection of the obesity-exercise axis in adipose-muscle tissues implies a critical role for mesenchymal stem cells
J Yang, M Vamvini, P Nigro, LL Ho, K Galani, M Alvarez, Y Tanigawa, A Renfro, NP Carbone, M Laakso, LZ Agudelo, P Pajukanta, MF Hirshman, RJW Middelbeek, K Grove, L Goodyear, M Kellis. Cell Metab. 2022
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WhichTF is dominant in your open chromatin data?
Y Tanigawa, ES Dyer, G Bejerano. PLOS Comput Biol. 2022
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Deconvoluting complex correlates of COVID19 severity with a multi-omic pandemic tracking strategy
VN Parikh, AG Ioannidis, D Jimenez-Morales, JE Gorzynski, HND Jong, X Liu, J Roque, VP Cepeda-Espinoza, K Osoegawa, C Hughes, SC Sutton, N Youlton, R Joshi, D Amar, Y Tanigawa, D Russo, J Wong, JT Lauzon, J Edelson, DM Montserrat, Y Kwon, S Rubinacci, O Delaneau, L Cappello, J Kim, MJ Shoura, AN Raja, N Watson, N Hammond, E Spiteri, KC Mallempati, G Montero-Martin, J Christle, J Kim, A Kirillova, K Seo, Y Huang, C Zhao, S Moreno-Grau, S Hershman, KP Dalton, J Zhen, J Kamm, K Bhatt, A Isakova, M Morri, T Ranganath, CA Blish, AJ Rogers, K Nadeau, S Yang, A Blomkalns, R O’Hara, NF Neff, C DeBoever, S Szalma, MT Wheeler, C Gates, K Farh, GP Schroth, P Febbo, F deSouza, O Cornejo, M Fernandez-Vina, A Kistler, J Palacios, BA Pinsky, CD Bustamante, MA Rivas, EA Ashley. Nat Commun. 2022
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Large-scale multivariate sparse regression with applications to UK Biobank
J Qian, Y Tanigawa, R Li, R Tibshirani, MA Rivas, T Hastie. Ann. Appl. Stat. 2022
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Integration of rare expression outlier-associated variants improves polygenic risk prediction
C Smail, NM Ferraro, Q Hui, MG Durrant, M Aguirre, Y Tanigawa, MR Keever-Keigher, AS Rao, JM Justesen, X Li, MJ Gloudemans, TL Assimes, C Kooperberg, AP Reiner, J Huang, CJ O'Donnell, YV Sun, Million Veteran Program, MA Rivas, SB Montgomery. The American Journal of Human Genetics. 2022
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Significant Sparse Polygenic Risk Scores across 813 traits in UK Biobank
Y Tanigawa, J Qian, GR Venkataraman, JM Justesen, R Li, R Tibshirani, T Hastie, MA Rivas. PLOS Genetics. 2022
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Bayesian model comparison for rare-variant association studies of multiple phenotypes
GR Venkataraman, C DeBoever, Y Tanigawa, M Aguirre, AG Ioannidis, H Mostafavi, CCA Spencer, T Poterba, CD Bustamante, MJ Daly, M Pirinen, MA Rivas. Am J Hum Genet. 2021
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A cross-population atlas of genetic associations for 220 human phenotypes
S Sakaue, M Kanai, Y Tanigawa, J Karjalainen, M Kurki, S Koshiba, A Narita, T Konuma, K Yamamoto, M Akiyama, K Ishigaki, A Suzuki, K Suzuki, W Obara, K Yamaji, K Takahashi, S Asai, Y Takahashi, T Suzuki, N Shinozaki, H Yamaguchi, S Minami, S Murayama, K Yoshimori, S Nagayama, D Obata, M Higashiyama, A Masumoto, Y Koretsune, FinnGen, K Ito, C Terao, T Yamauchi, I Komuro, T Kadowaki, G Tamiya, M Yamamoto, Y Nakamura, M Kubo, Y Murakami, K Yamamoto, Y Kamatani, A Palotie, MA Rivas, MJ Daly, K Matsuda, Y Okada. Nature Genetics. 2021
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APOC3 genetic variation, serum triglycerides, and risk of coronary artery disease in Asian Indians, Europeans, and other ethnic groups
S Goyal, Y Tanigawa, W Zhang, J Chai, M Almeida, X Sim, M Lerner, J Chainakul, JG Ramiu, C Seraphin, B Apple, A Vaughan, J Muniu, J Peralta, DM Lehman, S Ralhan, GS Wander, JR Singh, NK Mehra, E Sidorov, MD Peyton, PR Blackett, JE Curran, ES Tai, Rv Dam, C Cheng, R Duggirala, J Blangero, JC Chambers, C Sabanayagam, JS Kooner, MA Rivas, CE Aston, D Sanghera, APOC3 genetic variation, s triglycerides. Lipids in Health and Disease. 2021
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Mapping the human genetic architecture of COVID-19
COVID-19 Host Genetics Initiative. Nature. 2021
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Fast Numerical Optimization for Genome Sequencing Data in Population Biobanks
R Li, C Chang, Y Tanigawa, B Narasimhan, T Hastie, R Tibshirani, MA Rivas. Bioinformatics. 2021
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[Review in Japanese] 複数の表現型を用いた人類遺伝統計学の大規模情報解析 (Large-scale human genetic statistical inference with multiple phenotypes)
Y Tanigawa. JSBi Bioinformatics Review. 2021
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Genetics of 35 blood and urine biomarkers in the UK Biobank
N Sinnott-Armstrong, Y Tanigawa, D Amar, N Mars, C Benner, M Aguirre, GR Venkataraman, M Wainberg, HM Ollila, T Kiiskinen, AS Havulinna, JP Pirruccello, J Qian, A Shcherbina, FinnGen, F Rodriguez, TL Assimes, V Agarwala, R Tibshirani, T Hastie, S Ripatti, JK Pritchard, MJ Daly, MA Rivas. Nature Genetics. 2021
Code Dataset PDF
Survival Analysis on Rare Events Using Group-Regularized Multi-Response Cox Regression
R Li, Y Tanigawa, JM Justesen, J Taylor, T Hastie, R Tibshirani, MA Rivas. Bioinformatics. 2021
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Polygenic risk modeling with latent trait-related genetic components
M Aguirre, Y Tanigawa, GR Venkataraman, R Tibshirani, T Hastie, MA Rivas. European Journal of Human Genetics. 2021
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Cardiac Imaging of Aortic Valve Area From 34287 UK Biobank Participants Reveals Novel Genetic Associations and Shared Genetic Comorbidity With Multiple Disease Phenotypes
A Cordova-Palomera, C Tcheandjieu, J Fries, P Varma, V Chen, M Fiterau, K Xiao, H Tejeda, B Keavney, H Cordell, Y Tanigawa, G Venkataraman, M Rivas, C Re, E Ashley, JR Priest. Circ Genom Precis Med. 2020
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A fast and scalable framework for large-scale and ultrahigh-dimensional sparse regression with application to the UK Biobank
J Qian, Y Tanigawa, W Du, M Aguirre, C Chang, R Tibshirani, MA Rivas, T Hastie. PLOS Genetics. 2020
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Fast Lasso method for large-scale and ultrahigh-dimensional Cox model with applications to UK Biobank
R Li, C Chang, JM Justesen, Y Tanigawa, J Qiang, T Hastie, MA Rivas, R Tibshirani. Biostatistics. 2020
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Sex-specific genetic effects across biomarkers
E Flynn, Y Tanigawa, F Rodriguez, RB Altman, N Sinnott-Armstrong, MA Rivas. European Journal of Human Genetics. 2021
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Rare protein-altering variants in ANGPTL7 lower intraocular pressure and protect against glaucoma
Y Tanigawa, M Wainberg, J Karjalainen, T Kiiskinen, G Venkataraman, S Lemmel\"a, JA Turunen, RR Graham, AS Havulinna, M Perola, A Palotie, FinnGen, MJ Daly, MA Rivas. PLOS Genetics. 2020
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Assessing Digital Phenotyping to Enhance Genetic Studies of Human Diseases
C DeBoever, Y Tanigawa, M Aguirre, G McInnes, A Lavertu, MA Rivas. The American Journal of Human Genetics. 2020
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Components of genetic associations across 2,138 phenotypes in the UK Biobank highlight adipocyte biology
Y Tanigawa, J Li, JM Justesen, H Horn, M Aguirre, C DeBoever, C Chang, B Narasimhan, K Lage, T Hastie, CY Park, G Bejerano, E Ingelsson, MA Rivas. Nature Communications. 2019
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Significant shared heritability underlies suicide attempt and clinically predicted probability of attempting suicide
DM Ruderfer, CG Walsh, MW Aguirre, Y Tanigawa, JD Ribeiro, JC Franklin, MA Rivas. Molecular Psychiatry. 2020
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Global Biobank Engine: enabling genotype-phenotype browsing for biobank summary statistics
G McInnes, Y Tanigawa, C DeBoever, A Lavertu, JE Olivieri, M Aguirre, MA Rivas. Bioinformatics. 2019
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SNPs2ChIP: Latent Factors of ChIP-seq to infer functions of non-coding SNPs
S Anand, L Kalesinskas, C Smail, Y Tanigawa. Pacific Symposium on Biocomputing. 2018
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Medical relevance of protein-truncating variants across 337,205 individuals in the UK Biobank study
C DeBoever, Y Tanigawa, ME Lindholm, G McInnes, A Lavertu, E Ingelsson, C Chang, EA Ashley, CD Bustamante, MJ Daly, MA Rivas. Nature Communications. 2018
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Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus × yedoensis ‘Somei-yoshino’ across the Japanese archipelago
T Ohta, T Kawashima, NO Shinozaki, A Dobashi, S Hiraoka, T Hoshino, K Kanno, T Kataoka, S Kawashima, M Matsui, W Nemoto, S Nishijima, N Suganuma, H Suzuki, YH Taguchi, Y Takenaka, Y Tanigawa, M Tsuneyoshi, K Yoshitake, Y Sato, R Yamashita, K Arakawa, W Iwasaki. Journal of Plant Research. 2018
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