CV

CV including full publications and presentations are available as PDF.

Education

• Osaka University, Osaka, Japan. 2020-2023
  • Ph.D. in Medicine
  • Dissertation: “Prokaryotic and viral genomes recovered from 787 Japanese gut metagenomes revealed microbial features linked to diets, populations, and diseases” (URL)
  • Mentor: Dr. Yukinori Okada
• The University of Tokyo, Tokyo, Japan. 2012-2018
  • Doctor of Medicine
  • MD Researcher Training Program (Mentor: Dr. Hiroshi Takayanagi)

Academic Appointments

• Postdoctoral fellow, Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA. 2024-current

• Assistant Professor, Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan. 2023-2024

Clinical Residencies

• The University of Tokyo Hospital, Tokyo, Japan. 2019-2020
• Yokohama Rosai Hospital, Yokohama, Japan. 2018-2019

Teaching experiences

• A practical course, Biochemistry, 2023-, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan

Selected Publications and Preprints

The ‘*’ and ‘†’ symbols indicate equal contribution and correspondence, respectively, in the following list.

• Yoshihiko Tomofuji, Mu, Z., Mire, H., Zhao, Y., Liu, C., Jayanthi, V., Sugiarto, N., Accelerating Medicines Partnership®: RA/SLE Network, Sparks, J. A. & Raychaudhuri, S.† Identifying the causal allele in the CD40 autoimmune locus enables discovery of context-specific trans-effects in B cells. bioRxiv 2026.07.29.741564 (2026) doi:10.64898/2026.07.29.741564. (Preprint)

• Tomofuji, Y.†, Edahiro, R., Sonehara, K., Shirai, Y., Kock, K. H., Wang, Q. S., Namba, S., Moody, J., Ando, Y., Suzuki, A., Yata, T., Ogawa, K., Naito, T., Namkoong, H., Lin, Q. X. X., Buyamin, E. V., Tan, L. M., Sonthalia, R., Han, K. Y., Tanaka, H., Lee, H., Asian Immune Diversity Atlas (AIDA) Network, Japan COVID-19 Task Force, The Biobank Japan Project, Okuno, T., Liu, B., Matsuda, K., Fukunaga, K., Mochizuki, H., Park, W.-Y., Yamamoto, K., Hon, C.-C., Shin, J. W., Prabhakar, S., Kumanogoh, A. & Okada, Y.† Quantification of escape from X chromosome inactivation with single-cell omics data reveals heterogeneity across cell types and tissues. Cell Genomics 4, 100625 (2024).

• Tomofuji, Y.†*, Kishikawa, T.*, Sonehara, K., Maeda, Y., Ogawa, K., Kawabata, S., Oguro-Igashira, E., Okuno, T., Nii, T., Kinoshita, M., Takagaki, M., Yamamoto, K., Arase, N., Yagita-Sakamaki, M., Hosokawa, A., Motooka, D., Matsumoto, Y., Matsuoka, H., Yoshimura, M., Ohshima, S., Nakamura, S., Fujimoto, M., Inohara, H., Kishima, H., Mochizuki, H., Takeda, K., Kumanogoh, A. & Okada, Y.† Analysis of gut microbiome, host genetics, and plasma metabolites reveals gut microbiome-host interactions in the Japanese population. Cell Reports 42, 113324 (2023).

• Tomofuji, Y.†, Sonehara, K., Kishikawa, T., Maeda, Y., Ogawa, K., Kawabata, S., Nii, T., Okuno, T., Oguro-Igashira, E., Kinoshita, M., Takagaki, M., Yamamoto, K., Kurakawa, T., Yagita-Sakamaki, M., Hosokawa, A., Motooka, D., Matsumoto, Y., Matsuoka, H., Yoshimura, M., Ohshima, S., Nakamura, S., Inohara, H., Kishima, H., Mochizuki, H., Takeda, K., Kumanogoh, A. & Okada, Y.† Reconstruction of the personal information from human genome reads in gut metagenome sequencing data. Nature Microbiology 8, 1079–1094 (2023).

• Tomofuji, Y.†, Kishikawa, T., Maeda, Y., Ogawa, K., Otake-Kasamoto, Y., Kawabata, S., Nii, T., Okuno, T., Oguro-Igashira, E., Kinoshita, M., Takagaki, M., Oyama, N., Todo, K., Yamamoto, K., Sonehara, K., Yagita, M., Hosokawa, A., Motooka, D., Matsumoto, Y., Matsuoka, H., Yoshimura, M., Ohshima, S., Shinzaki, S., Nakamura, S., Iijima, H., Inohara, H., Kishima, H., Takehara, T., Mochizuki, H., Takeda, K., Kumanogoh, A. & Okada, Y.† Prokaryotic and viral genomes recovered from 787 Japanese gut metagenomes revealed microbial features linked to diets, populations, and diseases. Cell Genomics 2, 100219 (2022).

• Tomofuji, Y., Kishikawa, T., Maeda, Y., Ogawa, K., Nii, T., Okuno, T., Oguro-Igashira, E., Kinoshita, M., Yamamoto, K., Sonehara, K., Yagita, M., Hosokawa, A., Motooka, D., Matsumoto, Y., Matsuoka, H., Yoshimura, M., Ohshima, S., Nakamura, S., Inohara, H., Mochizuki, H., Takeda, K., Kumanogoh, A. & Okada, Y. Whole gut virome analysis of 476 Japanese revealed a link between phage and autoimmune disease. Annals of the Rheumatic Diseases 81, 278–288 (2022).

• Tomofuji, Y.*, Maeda, Y.*, Oguro-Igashira, E.*, Kishikawa, T., Yamamoto, K., Sonehara, K., Motooka, D., Matsumoto, Y., Matsuoka, H., Yoshimura, M., Yagita, M., Nii, T., Ohshima, S., Nakamura, S., Inohara, H., Takeda, K., Kumanogoh, A. & Okada, Y. Metagenome-wide association study revealed disease-specific landscape of the gut microbiome of systemic lupus erythematosus in Japanese. Annals of the Rheumatic Diseases 80, 1575–1583 (2021).

• Tomofuji, Y.*, Takaba, H.*, Suzuki, H. I., Benlaribi, R., Martinez, C. D. P., Abe, Y., Morishita, Y., Okamura, T., Taguchi, A., Kodama, T. & Takayanagi, H. Chd4 choreographs self-antigen expression for central immune tolerance. Nature Immunology 21, 892–901 (2020).

Awards

• American Society of Human Genetics, Trainee Award, Semifinalist, 2025
• Japanese Society for Immunology Young Investigator Award, Japanese Society for Immunology, 2025
• Japan College of Rheumatology Encouragement Award, Japan College of Rheumatology, 2024
• Yamamura Award, Faculty of Medicine, Osaka University (Outstanding Doctoral Student Award, Graduate School of Medicine), 2024
• JSPS Ikushi Prize, 2023 (URL)
• Dean’s Award of MD Researcher Training Program, Faculty of Medicine, The University of Tokyo, 2017

Grant/fellowship

• JSPS Overseas Research Fellowships, 2025
• Grant-in-Aid for Early-Career Scientists (KAKENHI), JSPS, 2025
• Overseas Research Grant, Astellas Foundation for Research on Metabolic Disorders, 2024
• Osaka University, Institute for Open and Transdisciplinary Research Initiatives, Junior Researcher Joint Projects, Project Leader, 2021
• Takeda Science Foundation Scholarship, 2020