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Yosuke Tanigawa is a Ph.D. candidate in Biomedical Informatics program at Stanford University. His research interests are in various topics in population genomics, specifically focusing on analysis of large-scale datasets.

He is currently working 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 analysis of population biobanks.
  • N. Sinnott-Armstrong*, Y. Tanigawa*, et al., in press.
  • 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 analysis of transcription factors.
  • Y. Tanigawa*, E. S. Dyer*, G. Bejerano, bioRxiv, 730200 (2019).

News

• 2020/12/5: Yosuke (virtually) presented at Japanese San Francisco Bay Area Seminar regarding his project, titled “Genetics of 35 blood and urine biomarkers in the UK Biobank”.
• 2020/11/18-12/2: Yosuke (virtually) presented a poster at Japanese Society of Human Genetics annual meeting 2020 regarding his project, titled “Sparse polygenic risk scores in hundreds of diseases elucidate their biological basis”.
• 2020/11/16-19: Yosuke (virtually) presented a poster at the RECOMB/ISCB Conference on Regulatory and Systems Genomics with DREAM Challenge regarding his project, titled “WhichTF is open in your open chromatin data?”.
• 2020/10/27: New Manuscript. “A global atlas of genetic associations of 220 deep phenotypes”. In this project co-led by Saori and Masa, we dissected latent DeGAs components of multi-ethnic association summary statistics characterized from both European (UK Biobank and FinnGen) and East Asian (Biobank Japan) populations. We annotated each component by pathway and cell-type enrichment as well as projection of metabolomic and biomarker summary statistics. We demonstrate how can we use such trans-ethnic annotated latent components to classify diseases based on their genetic basis.
• 2020/10/26-30: Yosuke (virtually) presents a poster at American Society of Human Genetics annual meeting 2020.
• 2020/10/23: New Publication. “A fast and scalable framework for large-scale and ultrahigh-dimensional sparse regression with application to the UK Biobank”. In this project led by Junyang Qian, we developed BASIL, a novel algorithm to fit large-scale L1 penalized (Lasso) regression model using an iterative procedure, and implemented R snpnet package specially designed for genetic data. We demonstrate the ability of this approach in an application to UK Biobank dataset. Yosuke contributed to the validation of the method in UK Biobank as well as the development of the software. Congratulations, Junyang!! Link to the full text.
• 2020/9/29: New Publication. “Fast Lasso method for large-scale and ultrahigh-dimensional Cox model with applications to UK Biobank”. In this study led by Ruilin Li, we propose an extension of BASIL/snpnet alrogirhm to fit L1 penalized Cox proportional hazards model using a large-scale dataset from a genotyped cohort. We present its application to 300+ time-to-event traits in UK Biobank. Congratulations, Ruilin!! Link to the full text.
• 2020/9/1: New Publication. “Sex-specific genetic effects across biomarkers”. In this study led by Emily Flynn, we discovered a surprising sex-specificity in the genetics of testosterone. Yosuke performed polygenic risk score (PRS) analysis and demonstrated that PRS models trained for each sex show improvements in predictive accuracy. Congratulations, Emily!! Link to the full text (via Read Cube).
• 2020/9/1: Yosuke had an oral presentation at Informatics in Biology, Medicine, and Pharmacology virtual conference (annual meeting of Japanese Society of Bioinformatics). Presentation slides are available here.
  • 2020/9/3 Update: My talk received the Best Oral Presentation Award! Thank you for organizers and the folks attended to my talk.
• 2020/8/29: New Manuscript. We have a new manuscript for a pharmacogenetic project led by Greg McInnes and Adam Lavertu: “LPA and APOE are associated with statin selection in the UK Biobank”.
• 2020/8/27: 日本バイオインフォマティクス学会のニュースレターに留学体験談を寄稿しました。(Yosuke wrote a short commentary on his experience in the graduate school for a news letter in Japanese Society fo Bioinformatics.)
• 2020/8/4: Yosuke performed several science outreach talks to Japanese high schoolers.
• 2020/7/17: Our use of generalist repository for scientific data sharing was featured by NIH’s Office of Data Science Strategy (ODSS).
• 2020/5/5: New Publication. “Rare protein-altering variants in ANGPTL7 lower intraocular pressure and protect against glaucoma” was published in PLOS Genetics.
  • 2020/6/8 Update: This paper was highlighted as Editors’ Choice in Science!
  • 2020/7/14 Update: We made the supplementary data associated with this publication via figshare. They recently wrote a case study. Thank you very much for providing this awesome platform!
• 2020/6/25: Yosuke’s semi-annually report (in Japanese) to the Funai Foundation is posted on their website. He wrote a short commentary on the recent publication as well as the increasingly important role of scientific communication in the context of the COVID-19.
• 2020/6/25: New Manuscripts. We have several preprints from the Rivas lab. Yosuke is very excited to be part of those projects.
  • “Pervasive additive and non-additive effects within the HLA region contribute to disease risk in the UK Biobank”
  • “Large-Scale Sparse Regression for Multiple Responses with Applications to UK Biobank”
  • “Fast Sparse-Group Lasso Method for Multi-response Cox Model with Applications to UK Biobank”
• 2020/4/12: COVID-19 host genetics に関する研究と題した研究紹介記事を書きました。Yosuke also wrote a brief summary of this COVID-19 related research activities in Japanese.
• 2020/4/12: 日本語のプロフィールページを開設しました。(He created a Japanese version of the landing page.)
• 2020/4/9: New Publication. “Assessing Digital Phenotyping to Enhance Genetic Studies of Human Diseases” led by Dr. Christopher DeBoever was published in the American Journal of Human Genetics. Yosuke contributed as the 2nd author. We have a share link that allows people to download the full text pdf file before June 26, 2020. Congratulations, Chris!!
• 2020/4/6: Yosuke migrated his website from his previous website.
• 2020/3/27: Our preprint on COVID-19 host genetic analysis was mentioned in a news article in Science.
• 2020/3/24: New Manuscript. Yosuke and Dr. Manuel Rivas posted a manuscript, titled “Initial Review and Analysis of COVID-19 Host Genetics and Associated Phenotypes”.
• 2020/3/17: New Resource. Yosuke and his colleagues in the Rivas Lab investigates the genetic basis of COVID-19 susceptibility and severity, as a part of COVID-19 Host Genetics Initiative. We released GitHub repository for COVID-19 Host Genetics analysis.

Contact

Email is the best contact to reach out to me. If you don’t get reply within 2 days, please don’t hesitate to follow-up. Thank you very much for interested in my work.

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