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, Department of Genetics and Rheumatology, Brigham and Women’s Hospital (Soumya Raychaudhuri lab), Boston, USA. 2025-current
Assistant Professor (non-PI), Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo (Yukinori Okada lab), Tokyo, Japan. 2023-2025
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.
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
- Young Scientist Award of the Japanese Society of Immunology, 2025/12
- ASHG 2025 Trainee Research Excellence Awards, semifinalist, 2025/10
- Young Scientist Award of the Japan College of Rheumatology, 2024/4
- Osaka University Faculty of Medicine, Yamamura Award and Outstanding PhD Student Award, 2024/3
- Japan College of Rheumatology 2023 ICW Excellent Abstract Award, 2023/4
- The 14th International Workshop on Advanced Genomics, Poster Award, 2023/10
- Japan College of Rheumatology 2023 ICW Excellent Abstract Award, 2023/4
- JSPS Ikushi Prize, 2023/3 (URL[https://www.jsps.go.jp/english/e-ikushi-prize/])
- The 7th Annual Meeting of the Japanese Society of Osteoimmunology, Best Presentation Award, 2022/6
- Japan College of Rheumatology 2022 ICW Excellent Abstract Award, 2022/4
- Dean’s Award of MD Researcher Training Program, Faculty of Medicine, The University of Tokyo, 2017/10
Grant/fellowship
- JSPS KAKENHI Grant-in-Aid for Early-Career Scientists, 2025–2027
- JSPS, Postdoctoral Fellowship for Research Abroad, 2025–2027
- Astellas Foundation for Research on Metabolic Disorders, Research Fellowship for Study Abroad, 2024–2025
- Osaka University, Institute for Open and Transdisciplinary Research Initiatives, Junior Researcher Joint Projects, Project Leader, 2021/12 (Grant)
- Takeda Science Foundation Scholarship, 2020/4 - 2023/9