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Yosuke Tanigawa is a Postdoctoral Associate at MIT Computational Biology Lab (PI: Dr. Manolis Kellis). His research interests are in various topics in population genomics, specifically focusing on the analysis of large-scale datasets.

He completed his doctoral training at Stanford University (Ph.D. in Biomedical Informatics), where he worked with Dr. Manuel Rivas and Dr. Gill Bejerano.

Please check CV, Publications, and/or Google Scholar profile for list of publications and pre-prints. Please also check Resources page for datasets, analysis and visualization scripts, and web applications from our research activities (mainly from the Rivas lab and the Bejerano lab).

Research interests

• Application of statistical genetics for human disease genetic studies. I am specifically interested in the analysis of population biobanks.
  • N. Sinnott-Armstrong*, Y. Tanigawa*, et al., Nature Genetics. (2021).
  • Y. Tanigawa, et al., PLOS Genetics. 16, e1008682 (2020).
  • G. McInnes, Y. Tanigawa, et al., Bioinformatics 35(14), 2495-2497 (2019).
• Statistical and computational method development for large-scale datasets in the context of human genomic studies.
  • Y. Tanigawa*, J. Li*, et al., Nat Commun. 10, 4064 (2019).
  • J. Qian, Y. Tanigawa, et al., PLOS Genetics. 16, e1009141 (2020).
  • J. Qian, Y. Tanigawa, et al., bioRxiv, 2020.05.30.125252 (2020).
• Functional analysis of non-coding regions in the human genome. I am specifically interested in the analysis of transcription factors.
  • Y. Tanigawa*, E. S. Dyer*, G. Bejerano, bioRxiv, 730200 (2019).

News

• 2021/11/26: Updated manuscript. We posted pdated manuscript, titled Significant Sparse Polygenic Risk Scores across 813 traits in UK Biobank on medRxiv.
• 2021/11/24: New Publication. “Bayesian model comparison for rare-variant association studies Author links open overlay panel.” (Link to the full text). Congratulations, Guhan and the team!
• 2021/11/23: New Manuscript. “Single-cell dissection of obesity-exercise axis in adipose-muscle tissues .” Congratulations, Jackie (Jiekun), Maria, Pasquale, and the team!
• 2021/10/18-22: Yosuke presented a poster on his recent manuscript, “Significant Sparse Polygenic Risk Scores across 428 traits in UK Biobank” at American Society of Human Genetics annual meeting 2021 (virtual).
• 2021/9/30: New Publication “A cross-population atlas of genetic associations for 220 human phenotypes” (full-text link). In this project co-led by Saori and Masa, we defined 220 disease end points in Biobank Japan and performed GWAS meta-analysis with the corresponding phenotypes in European populations in the UK and Finland. We dissected latent DeGAs components of multi-ethnic association summary statistics. This paper was highlighted in the cover of the journal. Huge congratulations to Saori, Masa, and the team!
• 2021/9/21: New Publication “APOC3 genetic variation, serum triglycerides, and risk of coronary artery disease in Asian Indians, Europeans, and other ethnic groups.” We examined the causal relationship between the genetically increased triglycerides and the risk of coronary artery diseases in Asian Indians.
• 2021/9/7: New Manuscript. “Significant Sparse Polygenic Risk Scores across 428 traits in UK Biobank.” We performed a systematic assessment of the predictive performance of PRS models across >1,600 traits in UK Biobank and report 428 PRS models with significant predictive performance.
• 2021/8/5: New Manuscript. Our preprint describing Multiple Rare-Variants and Phenotypes Mixture Model (MRPMM), an application of Bayesian Mixture Model for the analysis of rare-variants is now posted on bioRxiv. Congratulations, Guhan!
• 2021/7/24: Updated manuscript. Our latest version of the preprint describing the MRP model, a Bayesian model comparison-based approach for rare-variant association studies, is now posted on bioRxiv. In this update, we describe the latest results from the exome-sequencing analysis of ~200,000 individuals from UK Biobank. Congratulations, Guhan!
• 2021/7/8: New Publication. The COVID19 Host Genetics Initiative’s flaghip paper is published. I am one of the 2,000+ co-authors of this paper. Congrats for everbody involved.
• 2021/7/1: Hello, Boston/Cambridge! Yosuke started his postdoc appointment at MIT computational biology lab (PI: Prof. Manolis Kellis).
• 2021/6/19: New Publication. Our paper describing snpnet-v2 and sparse-snpnet is now published! Congratulations, Ruilin!
  • “Fast Numerical Optimization for Genome Sequencing Data in Population Biobanks” (full-text link)
• 2021/6/13: Commencement day at Stanford. Yosuke received Ph.D. He is grateful for all the support and help he received.
• 2021/5/13: Yosuke will present (WhichTF) at Stanford Cardiovasular Institute’s Research Roundtable (Zoom seminar).
• 2021/5/11-14: Yosuke will present a poster on “Significant Sparse Polygenic Risk Scores in 428 traits in UK Biobank” at the Biology of Genomes virtual meeting (#poster-324 channel on the conference slack).
• 2021/5/3: Yosuke passed his Ph.D. defense! Thank you very much for everyone who supported me along the way.
• 2021/4/23: New Publication (review article 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). GWAS、polygenic risk score、高次元データセットでの penalized regression (Lasso など) に関する人類統計遺伝学の解析手法について執筆しました。
• 2021/4/21: Yosuke gave an invited lecture on Japanese Education.
• 2021/1/18: New Publication. “Genetics of 35 blood and urine biomarkers in the UK Biobank”. In this project co-led by Nasa Sinnott-Armstrong, myself, and Dr. Manuel A. Rivas, we performed large-scale characterization of the genetic basis of biomarkers and cataloged their influence on diseases. We developed the ‘multi-PRS’ method and demonstrated its improved ability of disease prediction. Please check out highlights and the full-text link.
  • 2021/1/29 Update: Our paper is featured as Research highlights in Nature Reviews Nephrology
  • 2021/2/25 Update: Our paper is recommended in Faculty Opinions
• 2021/2/16: New Manuscript. We have a new preprint led by Ruilin Li describing a new version of the R snpnet package and its application to the exome sequencing data in UK Biobank: “Fast Numerical Optimization for Genome Sequencing Data in Population Biobanks”.
• 2021/2/9: New Publications. We have two papers from the Rivas lab. Yosuke contributed to each of them as the second author and is very excited to see them published! Congratulations, Matt and Ruilin!
  • “Survival Analysis on Rare Events Using Group-Regularized Multi-Response Cox Regression”
  • “Polygenic risk modeling with latent trait-related genetic components” (full-text link via ReadCube)
• News Archive:
  • News in 2020

Contact

Email is the best contact to reach out to me. If you do not get a reply within two days, please do not hesitate to follow-up. Thank you very much for your interest in our work.

• Email: yosuke <dot> tanigawa [at] alumni <dot> stanford <dot> edu
• Social media accounts can be found on the left (for PC) or “Follow” button on the top (for smartphone).