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

• Assistant Professor (non-PI), Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo (Yukinori Okada lab), Tokyo, Japan. 2023-current

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.†, 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

• 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
• 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
• Dean’s Award of MD Researcher Training Program, Faculty of Medicine, The University of Tokyo, 2017/10