Yoshihiko Tomofuji (M.D., Ph.D.)

Yoshihiko Tomofuji (M.D., Ph.D.)

Assistant professor at the University of Tokyo. Investigating the Immune-related diseases through omics technologies (e.g. single-cell RNA/ATAC-seq, metagenome sequencing, GWAS, etc...).

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Pages

Posts

Future Blog Post

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Blog Post number 1

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portfolio

publications

Reconstruction of the personal information from human genome reads in gut metagenome sequencing data

Published in Nature Microbiology, 2023

It is known that a small amount of human DNA is contained in the stool samples. Using a statistical genetics approach, we asked how much personal information is contained in the human reads in the metagenome shotgun sequencing data. We demonstrated that human reads in the metagenome shotgun sequencing data were sufficient to identify an individual’s genetics sex, genetic ancestry, and matched genotype data. Study overview

Recommended citation: 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). https://doi.org/10.1038/s41564-023-01381-3

Quantification of the escape from X chromosome inactivation with the million cell-scale human single-cell omics datasets reveals heterogeneity of escape across cell types and tissues

Published in bioRxiv, 2023

One of the two X chromosomes of females is silenced through X chromosome inactivation (XCI) to compensate for the difference in the dosage between sexes. Among the X-linked genes, several genes escape from XCI, which could contribute to the differential gene expression between the sexes. However, the differences in the escape across cell types and tissues are still poorly characterized because no methods could directly evaluate the escape under a physiological condition at the cell-cluster resolution with versatile technology. Here, we developed a method, single-cell Level inactivated X chromosome mapping (scLinaX), which directly quantifies relative gene expression from the inactivated X chromosome with droplet-based single-cell RNA-sequencing (scRNA-seq) data. Study overview

Recommended citation: Yoshihiko Tomofuji†, Ryuya Edahiro, Yuya Shirai, Kian Hong Kock, Kyuto Sonehara, Qingbo S. Wang, Shinichi Namba, Jonathan Moody, Yoshinari Ando, Akari Suzuki, Tomohiro Yata, Kotaro Ogawa, Ho Namkoong, Quy Xiao Xuan Lin, Eliora Violain Buyamin, Le Min Tan, Radhika Sonthalia, Kyung Yeon Han, Hiromu Tanaka, Ho Lee, Asian Immune Diversity Atlas Network, Japan COVID-19 Task Force, The BioBank Japan Project, Tatsusada Okuno, Boxiang Liu, Koichi Matsuda, Koichi Fukunaga, Hideki Mochizuki, Woong-Yang Park, Kazuhiko Yamamoto, Chung-Chau Hon, Jay W. Shin, Shyam Prabhakar, Atsushi Kumanogoh, & Yukinori Okada†. Quantification of the escape from X chromosome inactivation with the million cell-scale human single-cell omics datasets reveals heterogeneity of escape across cell types and tissues. bioRxiv 2023.10.14.561800 (2023) doi:10.1101/2023.10.14.561800. https://www.biorxiv.org/content/10.1101/2023.10.14.561800v1

talks

teaching

Teaching experience 1

Undergraduate course, University 1, Department, 2014

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Teaching experience 2

Workshop, University 1, Department, 2015

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