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I am a postdoctoral fellow at Brigham and Women’s Hospital / Harvard Medical School / Broad Institute. Currently, I am working on the single-cell QTL analysis and CRISPR-base-editing at Brigham and Women’s Hospital (PI: Dr. Soumya Raychaudhuri). I got a degree of M.D. from the University of Tokyo and Ph.D. from Osaka University.

During my time as a medical student, I conducted research on the thymic selection of T cells and autoimmunity (PI: Dr. Hiroshi Takayanagi), engaging in both wet and dry experiments (Tomofuji Y et al. Nat. Immunol. 2020).

Following two years of clinical training, I started Ph.D. training under Dr. Yukinori Okada at Osaka University, focusing on bioinformatics research related to the gut microbiome and human genetics (Tomofuji Y et al. Ann. Rheum. Dis. 2021/2022, Tomofuji Y et al. Cell Genom. 2022, Tomofuji Y et al. Nat. Microbiol. 2023, Tomofuji Y et al. Cell Rep. in Press). After I got a Ph.D. from Osaka University, I moved to the University of Tokyo (Yukinori Okada’s lab) as an assistant professor and started to work with single-cell omics technology. Specifically, I developed a new method to refine the understanding of the basic biological phenomena such as X chromosome inactivation (Tomofuji Y et al. Cell Genomics 2024).

I always love to uncover the hidden treasures in omics data through the development of new methods.

Research interests

• My research employs CRISPR genome editing to define the function of GWAS variants. I am particularly interested in the application of single-base editing tools (e.g., base and prime editors) for the high-resolution functional mapping of disease-associated alleles.

• Integrative analysis of the single-cell omics data and genome data for immune cells. In addition to the conventional functional genomics approaches such as pseudobulk eQTL mapping, I am specifically interested in the development of new methods to uncover hidden biology in the omics data.
  • Evaluation of the escape from X chromosome inactivation (Tomofuji Y et al. Cell Genom. 2024; co-correspondence; Github URL)
• Analysis of the gut microbiome using metagenome shotgun sequencing. I am specifically interested in autoimmune diseases, Japanese-specific gut microbes, and integrative analysis with human genome data.
  • Gut microbiome analysis of the SLE patients (Tomofuji Y et al. Ann. Rheum. Dis. 2021)
  • Gut virome analysis of the RA/SLE/MS patients (Tomofuji Y et al. Ann. Rheum. Dis. 2022)
  • Catalogue of the microbes in the Japanese gut (Tomofuji Y et al. Cell Genom. 2022; co-correspondence)
  • Evaluation of the human genome in the metagenome shotgun sequencing data (Tomofuji Y et al. Nat. Microbiol. 2023)
  • Integrative analysis of the gut microbiome, human genome, and plasma metabolites (Tomofuji Y et al. Cell Rep. in Press; co-correspondence)

Contact

I’d be so happy if you contact me upon an interest in our work! If you do not get a reply within two days, please do not hesitate to follow up.

• E-mail (Broad Institute): ytomofuj[at]broadinstitute.org
• E-mail (The University of Tokyo): ytomofuji[at]m.u-tokyo.ac.jp