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portfolio
Portfolio item number 2
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publications
[Preprint] Bayesian model comparison for rare variant association studies of multiple phenotypes
Preprint posted on bioRxiv, 2018
Citation: C. DeBoever, M. Aguirre, Y. Tanigawa, C. C. A. Spencer, T. Poterba, M. J. Daly, M. Pirinen, M. A. Rivas, Bayesian model comparison for rare variant association studies of multiple phenotypes. bioRxiv, 257162 (2018). https://doi.org/10.1101/257162
Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus × yedoensis ‘Somei-yoshino’ across the Japanese archipelago
Published in Journal of Plant Research, 2018
Citation: T. Ohta, T. Kawashima, N. O. Shinozaki, A. Dobashi, S. Hiraoka, T. Hoshino, K. Kanno, T. Kataoka, S. Kawashima, M. Matsui, W. Nemoto, S. Nishijima, N. Suganuma, H. Suzuki, Y. Taguchi, Y. Takenaka, Y. Tanigawa, M. Tsuneyoshi, K. Yoshitake, Y. Sato, R. Yamashita, K. Arakawa, W. Iwasaki, Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus × yedoensis ‘Somei-yoshino’ across the Japanese archipelago. J Plant Res. 131, 709–717 (2018). https://doi.org/10.1007/s10265-018-1017-x
Medical relevance of protein-truncating variants across 337,205 individuals in the UK Biobank study
Published in Nature Communications, 2018
Using the UK Biobank population cohort, we investigated the genetic effects of Protein-truncating variants (PTVs) and the clinical impacts.
Citation: C. DeBoever, Y. Tanigawa, M. E. Lindholm, G. McInnes, A. Lavertu, E. Ingelsson, C. Chang, E. A. Ashley, C. D. Bustamante, M. J. Daly, M. A. Rivas, Medical relevance of protein-truncating variants across 337,205 individuals in the UK Biobank study. Nat Commun. 9, 1612 (2018). https://doi.org/10.1038/s41467-018-03910-9
SNPs2ChIP: Latent Factors of ChIP-seq to infer functions of non-coding SNPs
Published in Pacific Symposium on Biocomputing, 2018
We propose SNPs2ChIP, a method to infer biological functions of non-coding variants through unsupervised statistical learning methods applied to publicly-available epigenetic datasets.
Citation: S. Anand, L. Kalesinskas, C. Smail, Y. Tanigawa, SNPs2ChIP: Latent Factors of ChIP-seq to infer functions of non-coding SNPs. Pac Symp Biocomput. 2019, 24: 184-195 (WORLD SCIENTIFIC, 2018). https://doi.org/10.1142/9789813279827_0017
Global Biobank Engine: enabling genotype-phenotype browsing for biobank summary statistics
Published in Bioinformatics, 2018
Citation: G. McInnes, Y. Tanigawa, C. DeBoever, A. Lavertu, J. E. Olivieri, M. Aguirre, M. A. Rivas, Global Biobank Engine: enabling genotype-phenotype browsing for biobank summary statistics. Bioinformatics (2019). https://doi.org/10.1093/bioinformatics/bty999
Significant shared heritability underlies suicide attempt and clinically predicted probability of attempting suicide
Published in Molecular Psychiatry, 2019
Citation: D. M. Ruderfer, C. G. Walsh, M. W. Aguirre, Y. Tanigawa, J. D. Ribeiro, J. C. Franklin, M. A. Rivas, Significant shared heritability underlies suicide attempt and clinically predicted probability of attempting suicide. Mol Psychiatry. 1 (2019). https://doi.org/10.1038/s41380-018-0326-8
[Preprint] A Fast and Flexible Algorithm for Solving the Lasso in Large-scale and Ultrahigh-dimensional Problems
Preprint posted on bioRxiv, 2019
Citation: J. Qian, W. Du, Y. Tanigawa, M. Aguirre, R. Tibshirani, M. A. Rivas, T. Hastie, A Fast and Flexible Algorithm for Solving the Lasso in Large-scale and Ultrahigh-dimensional Problems. bioRxiv, 630079 (2019). https://doi.org/10.1101/630079
[Preprint] Genetics of 38 blood and urine biomarkers in the UK Biobank
Preprint posted on bioRxiv, 2019
Citation: N. Sinnott-Armstrong*, Y. Tanigawa*, D. Amar, N. J. Mars, M. Aguirre, G. R. Venkataraman, M. Wainberg, H. M. Ollila, J. P. Pirruccello, J. Qian, A. Shcherbina, FinnGen, F. Rodriguez, T. L. Assimes, V. Agarwala, R. Tibshirani, T. Hastie, S. Ripatti, J. K. Pritchard, M. J. Daly, M. A. Rivas, Genetics of 38 blood and urine biomarkers in the UK Biobank. bioRxiv, 660506 (2019). https://doi.org/10.1101/660506
[Preprint] Rare protein-altering variants in ANGPTL7 lower intraocular pressure and protect against glaucoma
Preprint posted on bioRxiv, 2019
Citation: Y. Tanigawa, M. Wainberg, J. Karjalainen, T. Kiiskinen, S. Lemmelä, J. A. Turunen, A. Palotie, FinnGen, M. J. Daly, M. A. Rivas, Rare protein-altering variants in ANGPTL7 lower intraocular pressure and protect against glaucoma. bioRxiv, 677443 (2019). https://doi.org/10.1101/677443
[Preprint] WhichTF is dominant in your open chromatin data?
Preprint posted on bioRxiv, 2019
Citation: Y. Tanigawa*, E. S. Dyer*, G. Bejerano, WhichTF is dominant in your open chromatin data? bioRxiv, 730200 (2019). https://doi.org/10.1101/730200
Components of genetic associations across 2,138 phenotypes in the UK Biobank highlight adipocyte biology
Published in Nature Communications, 2019
While many pleiotropic genetic loci have been identified, how they contribute to phenotypes across traits and diseases is unclear. Here, the authors propose decomposition of genetic associations (DeGAs), which uses singular value decomposition, to characterize the underlying latent structure of genetic associations of 2,138 phenotypes.
Citation: Y. Tanigawa*, J. Li*, J. M. Justesen, H. Horn, M. Aguirre, C. DeBoever, C. Chang, B. Narasimhan, K. Lage, T. Hastie, C. Y. Park, G. Bejerano, E. Ingelsson, M. A. Rivas, Components of genetic associations across 2,138 phenotypes in the UK Biobank highlight adipocyte biology. Nat Commun. 10, 1–14 (2019). https://doi.org/10.1038/s41467-019-11953-9
[Preprint] Reported CCR5-∆32 deviation from Hardy-Weinberg equilibrium is explained by poor genotyping of rs62625034
Preprint posted on bioRxiv, 2019
Citation: Y. Tanigawa, M. A. Rivas, Reported CCR5-∆32 deviation from Hardy-Weinberg equilibrium is explained by poor genotyping of rs62625034. bioRxiv, 791517 (2019). https://doi.org/10.1101/791517
[Preprint] Polygenic risk modeling with latent trait-related genetic components
Preprint posted on bioRxiv, 2019
Citation: M. Aguirre, Y. Tanigawa, G. Venkataraman, R. J. Tibshirani, T. Hastie, M. A. Rivas, Polygenic risk modeling with latent trait-related genetic components. bioRxiv, 808675 (2019). https://doi.org/10.1101/808675
[Preprint] Sex-specific genetic effects across biomarkers
Preprint posted on bioRxiv, 2019
Citation: E. Flynn, Y. Tanigawa, F. Rodriguez, R. B. Altman, N. Sinnott-Armstrong, M. A. Rivas, Sex-specific genetic effects across biomarkers. bioRxiv, 837021 (2019). https://doi.org/10.1101/837021
[Preprint] Medical relevance of common protein-altering variants in GPCR genes across 337,205 individuals in the UK Biobank study
Preprint posted on bioRxiv, 2019
Citation: C. DeBoever, A. J. Venkatakrishnan, J. M. Paggi, F. M. Heydenreich, S.-A. Laurin, M. Masureel, Y. Tanigawa, G. Venkataraman, M. Bouvier, R. Dror, M. A. Rivas, Medical relevance of common protein-altering variants in GPCR genes across 337,205 individuals in the UK Biobank study. bioRxiv, 2019.12.13.876250 (2019). https://doi.org/10.1101/2019.12.13.876250
[Preprint] Fast Lasso method for Large-scale and Ultrahigh-dimensional Cox Model with applications to UK Biobank
Preprint posted on bioRxiv, 2020
Citation: R. Li, C. Chang, J. M. Justesen, Y. Tanigawa, J. Qian, T. Hastie, M. A. Rivas, R. J. Tibshirani, Fast Lasso method for Large-scale and Ultrahigh-dimensional Cox Model with applications to UK Biobank. bioRxiv, 2020.01.20.913194 (2020). https://doi.org/10.1101/2020.01.20.913194
[Preprint] Initial Review and Analysis of COVID-19 Host Genetics and Associated Phenotypes
Preprint posted on Preprints.org, 2020
Citation: Y. Tanigawa, M. Rivas, Initial Review and Analysis of COVID-19 Host Genetics and Associated Phenotypes (2020). https://doi.org/10.20944/preprints202003.0356.v1
[Preprint] Cardiac imaging of aortic valve area from 26,142 UK Biobank participants reveal novel genetic associations and shared genetic comorbidity with multiple disease phenotypes
Preprint posted on medRxiv, 2020
Citation: 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, J. R. Priest, Cardiac imaging of aortic valve area from 26,142 UK Biobank participants reveal novel genetic associations and shared genetic comorbidity with multiple disease phenotypes. medRxiv, 2020.04.09.20060012 (2020). https://doi.org/10.1101/2020.04.09.20060012
Rare protein-altering variants in ANGPTL7 lower intraocular pressure and protect against glaucoma
Published in PLOS Genetics, 2020
Citation: Y. Tanigawa, M. Wainberg, J. Karjalainen, T. Kiiskinen, G. Venkataraman, S. Lemmelä, J. A. Turunen, R. R. Graham, A. S. Havulinna, M. Perola, A. Palotie, FinnGen, M. J. Daly, M. A. Rivas, Rare protein-altering variants in ANGPTL7 lower intraocular pressure and protect against glaucoma. PLOS Genetics. 16, e1008682 (2020). https://doi.org/10.1371/journal.pgen.1008682
Assessing Digital Phenotyping to Enhance Genetic Studies of Human Diseases
Published in The American Journal of Human Genetics, 2020
Citation: C. DeBoever, Y. Tanigawa, M. Aguirre, G. McInnes, A. Lavertu, M. A. Rivas, Assessing Digital Phenotyping to Enhance Genetic Studies of Human Diseases. The American Journal of Human Genetics. 106, 611-622 (2020). https://doi.org/10.1016/j.ajhg.2020.03.007
[Preprint] Pervasive additive and non-additive effects within the HLA region contribute to disease risk in the UK Biobank
Preprint posted on bioRxiv, 2020
Citation: G. R. Venkataraman, J. E. Olivieri, C. DeBoever, Y. Tanigawa, J. M. Justesen, M. A. Rivas, Pervasive additive and non-additive effects within the HLA region contribute to disease risk in the UK Biobank. bioRxiv, 2020.05.28.119669 (2020). https://doi.org/10.1101/2020.05.28.119669
[Preprint] Large-Scale Sparse Regression for Multiple Responses with Applications to UK Biobank
Preprint posted on bioRxiv, 2020
Citation: J. Qian, Y. Tanigawa, R. Li, R. Tibshirani, M. A. Rivas, T. Hastie, Large-Scale Sparse Regression for Multiple Responses with Applications to UK Biobank. bioRxiv, 2020.05.30.125252 (2020). https://doi.org/10.1101/2020.05.30.125252
talks
Invited lecture
Published:
I was one of the invited guest speakers at Statistical genetics summer school at Osaka University.
Genetic risk modeling based on L1-penalized regression
Published:
I gave a research-in-progress talk in our department seminar.
teaching
[TA] BIODS215: Topics in Biomedical Data Science, Large-scale inference
Graduate course, Stanford University, Department of Biomedical Data Science, 2018
I was a teaching assistant for a graduate-level class, BIODS215: Topics in Biomedical Data Science, Large-scale inference. I taught a section on “Data visualization”, hosted office hours, maintained the class website, and graded the assignments.
[TA] BIOMEDIN 210: Modeling Biomedical Systems: Ontology, Terminology, Problem Solving (CS 270)
Graduate course, Stanford University, Department of Biomedical Data Science, 2019
I was a teaching assistant for a graduate-level class, BIOMEDIN 210: Modeling Biomedical Systems: Ontology, Terminology, Problem Solving (CS 270).
[TA] BIODS215: Topics in Biomedical Data Science, Large-scale inference
Graduate course, Stanford University, Department of Biomedical Data Science, 2020
I was a teaching assistant for a graduate-level class, BIODS215: Topics in Biomedical Data Science, Large-scale inference. I taught a section on “Reproducible large-scale inference”, hosted office hours, maintained the class website, and graded the assignments.