News

• 2023/10/12 I moved my HP to https://ytomofuji.github.io!

• 2023/5/19 Our personal information reconstruction from human reads in metagenome sequencing data paper is now published in Nature Microbiology!

• 2022/12/1 Our gut microbial genome databases (JMAG and JVD) is now published in Cell Genomics!

• 2021/12/9 Our gut virome analysis for the autoimmune diseases is now published in Annals of the Rheumatic Diseases!

• 2021/8/23 Our SLE gut-metagenome analysis paper is now online in Annals of the Rheumatic Diseases!

• 2021/8/23 HP was started

If you are interested in our JMAG and JVD, 

please check the paper (https://doi.org/10.1016/j.xgen.2022.100219) 

and visit my github (https://github.com/ytomofuji/JMAG_JVD).

Research interests

Statistical genetics/Gut microbiome/Metagenome/Immunology/Rheumatology/Population genetics/Multi-omics analysis/ GWAS/Metabolome ...

Education

• 2020/4 – PhD candidate, The Degree of Doctor of philosophy (Medicine), Graduate school of Osaka University, Department of statistical genetics

• 2012/4 – 2018/3 University of Tokyo（B.S.[Medicine], M.D.）

• 2012/3 Graduate from Senior High School at Komaba, University of Tsukuba

Job

• 2019/4 - 2020/3 University of Tokyo Hospital (Resident)

• 2018/4 - 2019/3 Yokohama Rosai Hospital (Resident)

Research

• 2021/12- RIKEN Center for Integrative Medical Sciences, Laboratory for Systems Genetics, Trainee

• 2021/10 -  Osaka University, Institute for Open and Transdisciplinary Research Initiatives（Concurrent young investigator）

• 2020/3 -  Graduate school of Osaka University, Department of statistical genetics（Ph.D. trainee, Supervisor: Prof. Yukinori Okada）

• 2013/10 - 2018/3 Department of immunology, University of Tokyo, Faculty of medicine (M.D. researcher training program, Supervisor: Prof. Hiroshi Takayanagi）

Publications

Tomofuji, Y., Sonehara, K., Kishikawa, T. et al. Reconstruction of the personal information from human genome reads in gut metagenome sequencing data. Nat Microbiol 8, 1079–1094 (2023). https://doi.org/10.1038/s41564-023-01381-3

Edahiro R, Shirai Y, ... Tomofuji, Y., et al, (2023) Single-cell analyses and host genetics highlight the role of innate immune cells in COVID-19 severity. Nat Genet 55:753–767. https://doi.org/10.1038/s41588-023-01375-1

Tomofuji, Y., Suzuki, K., Kishikawa, T. et al. Identification of serum metabolome signatures associated with retinal and renal complications of type 2 diabetes. Commun Med 3, 5 (2023). https://doi.org/10.1038/s43856-022-00231-3

Tomofuji Y, Kishikawa T, Maeda Y, Ogawa K, Otake-Kasamoto Y, Kawabata S, et al. Prokaryotic and viral genomes recovered from 787 Japanese gut metagenomes revealed microbial features linked to diets, populations, and diseases. Cell Genomics [Internet]. 2022 Dec 14;2(12). Available from: https://doi.org/10.1016/j.xgen.2022.100219

Itotagawa E, Tomofuji Y, Kato Y, et al. SLE stratification based on BAFF and IFN-I bioactivity for biologics and implications of BAFF produced by glomeruli in lupus nephritis. Rheumatology [Internet]. 2022 Sep 12;keac528. Available from: https://doi.org/10.1093/rheumatology/keac528

Yan M, Komatsu N, Muro R, Huynh NC-N, Tomofuji Y, Okada Y, et al. ETS1 governs pathological tissue-remodeling programs in disease-associated fibroblasts. Nat Immunol [Internet]. 2022;23(9):1330–41. Available from: https://doi.org/10.1038/s41590-022-01285-0

Tomofuji Y, Kishikawa T, Maeda Y, et al Whole gut virome analysis of 476 Japanese revealed a link between phage and autoimmune disease. Ann. Rheum. Dis. Published Online First: 08 December 2021. doi: 10.1136/annrheumdis-2021-221267

Tomofuji Y, Maeda Y, Oguro-Igashira E, et al. Metagenome-wide association study revealed disease-specific landscape of the gut microbiome of systemic lupus erythematosus in Japanese. Ann. Rheum. Dis. 2021;80:1575-1583.

Tomofuji Y, Takaba H, Suzuki HI, et al. Chd4 choreographs self antigen expression for central immune tolerance. Nat Immunol. 2020;21(August) 892-901.

Nitta T, Tsutsumi M, Nitta S, Muro R, Suzuki EC, Nakano K, Tomofuji Y, et al. Fibroblasts as a source of self-antigens for central immune tolerance. Nat Immunol. 2020;21(10):1172–80.

Tomofuji Y, Ishikawa Y, Hattori K, Fujiwara M, Kita Y. Successful treatment of refractory acute lupus haemophagocytic syndrome using rituximab: a case report. Mod Rheumatol Case Reports. 2020 Jul 2;4(2):222–8.

Nitta T, Kochi Y, Muro R, Tomofuji Y, et al. Human thymoproteasome variations influence CD8 T cell selection. Sci Immunol. 2017;2–11.

Takaba H, Morishita Y, Tomofuji Y, et al. Fezf2 Orchestrates a Thymic Program of Self-Antigen Expression for Immune Tolerance. Cell. 2015;163(4):975–87.

Presentation

Tomofuji Y, et al. "Leveraging the Japanese microbial genome database to identify rheumatic diseases-crAss-like phage associations". The 67th Annual General Assembly and Scientific Meeting of the Japan College of Rheumatology, Session ICW3-6, Hakata, Fukuoka, Japan, April, 2023 (oral presentation)

Tomofuji Y, et al. "Prokaryotic and viral genomes recovered from 787 Japanese gut metagenomes revealed microbial features associated with diets, populations, and diseases". The 67th Annual Meeting of the Japan Society of Human Genetics, Session OE5-4, Yokohama, Kanagawa, Japan, December, 2022 (oral presentation)

Tomofuji Y, et al. "Prokaryotic and viral genomes recovered from 787 Japanese gut metagenomes revealed microbial features associated with diets, populations, and diseases". American Society of Human Genetics 2022 Annual Meeting,  PB3108, October, 2022 (poster presentation)

Tomofuji Y, et al. "Analysis for the gut bacteriome and virome in autoimmune diseases". The 7th Annual  Meeting of the japanese Society of Osteoimmunology, ST-2, Nago, Okinawa, Japan, June, 2022 (poster & oral presentation)

Tomofuji Y, et al. "Metagenome-wide association studies revealed the altered gut bacteriome and virome in autoimmune diseases". The 66th Annual General Assembly and Scientific Meeting of the Japan College of Rheumatology, Session ICW21-6, Yokohama, Kanagawa, Japan, April, 2022 (oral presentation)

Tomofuji Y, et al. "A metagenome-wide association study revealed disease-specific landscape of the gut microbiome of systemic lupus erythematosus in Japanese". The 50th Annual Meeting of the Japanese Society for Immunology, 2-B-WS7-08-O/P, Nara, Nara, Japan, December, 2021 (oral and poster presentation)

Tomofuji Y, et al. "A metagenome-wide association study revealed disease-specific landscape of the gut microbiome of systemic lupus erythematosus in Japanese". The 8th JCR Basic Research Conference, P-35, online, November, 2021 (poster presentation)

Tomofuji Y, et al. "A Metagenome-wide Association Study Revealed Disease-specific Landscape of the Gut Microbiome of Systemic Lupus Erythematosus in Japanese". American College of Rheumatology Convergence 2021, 1496, online, November, 2021 (poster presentation)

Tomofuji Y, et al. "A metagenome-wide association study revealed disease-specific landscape of the gut microbiome of systemic lupus erythematosus in Japanese". American Society of Human Genetics 2021 Virtual Meeting, PrgmNr 2272, online, October, 2021 (poster presentation)

Tomofuji Y, et al. "A metagenome-wide association study revealed an alteration of the gut microbiome in systemic lupus erythematosus". The 66th Annual Meeting of the Japan Society of Human Genetics and the 28th Annual Meeting of the Japanese Society for Gene Diagnosis and Therapy – Joint Conference 2021, Session OE12-5, Yokohama, Kanagawa, Japan, October, 2021 (oral presentation)

Yoshihiko Tomofuji, Hiroyuki Takaba, Hiroshi Takayanagi. “Distinct Features of Fezf2-induced Promiscuous Gene Expression.” ThymOz 2018 an international conference on T lymphocytes, Session 11-8, Heron Island, Queensland, Australia, March, 2018 (oral presentation) 

Awards & Grant

・Japan College of Rheumatology 2023 ICW Excellent Abstract Award, 2023/4

・JSPS Ikushi Prize, 2023/3

・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 -

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