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Yosuke Tanigawa is a Postdoctoral Associate at MIT Computational Biology Lab (PI: Dr. Manolis Kellis).

Yosuke works at the intersection of statistical genetics and computational biology. Specifically, he develops computational and statistical methods to dissect disease heterogeneity and apply them in systematic analyses of large-scale phenotypic, genetic, epigenomic, functional genomic, and single-cell genomic datasets.

Before joining MIT, 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.

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., Ann. Appl. Stat. 16(3), 1891-1918 (2022).
• 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, PLOS Comput Biol 18(8), e1010378 (2022).

Upcoming presentations

• 2022/11/16: Yosuke will participate panel discussion at the Genetics and Genomics Digital Forum hosted by the American Society of Human Genetics.
• 2022/11/12-16: Yosuke will present at Neuroscience 2022 (Society for Neuroscience Annual meeting) at San Diego, CA, USA.
• 2022/11/7-11: Yosuke will present at 14th ISCB Conference on Regulatory & Systems Genomics with DREAM Challenges 2022 at Las Vegas, NV, USA.
• 2022/10/25-29: Yosuke will present at the American Society of Human Genetics Annual meeting 2022 at Los Angeles, CA, USA.
  • 2022/10/27 10:45 am - 11:00 am at Conv Ctr/Room 515/West
  • Title: “Single-cell Transcriptional Hallmarks and Individual Subtyping for Alzheimer’s Disease across 427 subjects”
  • My talk is a part of “The methylome and transcriptome of complex traits” platform session.

News

• 2022/10/4: New Publication “Single-cell dissection of the obesity-exercise axis in adipose-muscle tissues implies a critical role for mesenchymal stem cells”. Congrats, Jackie, Maria, Pasquale, and the team!
• 2022/8/30: New Publication “WhichTF is dominant in your open chromatin data?”. We develop an ontology-guided approach to ranking tissue-/cell-type-specific transcription factors (TFs) from chromatin accessibility data. This paper describes the last chapter of my Ph.D. thesis and I am so happy to see this out.
• 2022/8/30: New Publication “Deconvoluting complex correlates of COVID19 severity with a multi-omic pandemic tracking strategy”. Congrats, Vicki, Alex and the team!
• 2022/7/19: New Publication. “Large-scale multivariate sparse regression with applications to UK Biobank.” Congrats, Junyang and the team!
• 2022/7/11: Yosuke presented “Single-cell transcriptional hallmarks and patient subtyping for Alzheimer’s disease” at ROS/MAP meeting 2022 at Rush University Medical Center, Chicago, IL.
• 2022/6/7: Yosuke presented a poster titled, “Single-cell transcriptional hallmarks of Alzheimer’s disease across 427 individuals” at the Broad Institute Poster Day 2022.
• 2022/6/2: New Publication. “Integration of rare expression outlier-associated variants improves polygenic risk prediction.” Congrats, Craig and the team!
• 2022/5/10-14: Yosuke presented a poster titled, “Single-cell transcriptional hallmarks of Alzheimer’s disease across 427 individuals” at Biology of the Genomes conference at Cold Spring Harbor Laboratory.
• 2022/3/24: New Publication “Significant sparse polygenic risk scores across 813 traits in UK Biobank”. We performed a systematic assessment of the predictive performance of polygenic risk score (PRS) models across >1,500 traits in UK Biobank and report 813 PRS models with significant predictive performance.
• 2022/03/02: Yosuke presented polygenic score analyses at University of Osaka, Japan.
• 2022/01/28: Yosuke presented at Journal Club meeting at Debora Marks’s lab.
• 2022/01/27: Updated manuscript. We posted updated manuscript, titled Significant Sparse Polygenic Risk Scores across 813 traits in UK Biobank on medRxiv.
• 2022.01.01: Happy New Year!
• cf. News Archive

Blog posts

I write blog posts mostly on computing tips, including:

• GWAS and genetic analyses with PLINK2 and pgenlibr
• Notes on Apache Columnar format
• Working with very small values in R
• Commonly used commands in high performance cluster computing with Slurm workload manager

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).