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  6. Yu-Chen Liu (James Liu)

Yu-Chen Liu (James Liu)

Affiliation

Department of Molecular Biosciences
E-mail: liu_y@rerf.or.jp

About

Dr. Liu specializes in bioinformatics, immunology, and single-cell multi-omics analysis. His research focuses on the development and application of computational approaches for next-generation sequencing (NGS) data analysis, including machine learning and deep learning methods for biological data interpretation. He has worked extensively with single-cell RNA sequencing, T-cell receptor (TCR) repertoire analysis, long-read sequencing, and spatial transcriptomics to investigate immune system dynamics and disease-associated biological mechanisms. During the COVID-19 pandemic, Dr. Liu participated in Japan’s COVID-19 Task Force, where he was involved in large-scale single-cell and immunological data analysis for infectious disease and immune response studies. Through this work, he accumulated extensive experience in immunology research based on single-cell multi-omics technologies. Currently at RERF, Dr. Liu is engaged in immunological and genomic analyses of atomic bomb survivor cohorts, particularly focusing on T-cell repertoire analysis, age-related hematopoietic alterations, and immune system changes associated with radiation exposure. He is also interested in integrating computational science, data-driven analysis, and quantitative approaches to better understand long-term biological changes using single-cell multi-omics data.

Education

2016
Ph.D. Program, Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Taiwan
2012
B.S. in Bioengineering: Bioinformatics, University of California San Diego (UCSD)

Experience

2025-
Associate Senior Scientist, Department of Molecular Biosciences, Radiation Effects Research Foundation
2023–2025
Project Assistant Professor, Immunology Frontier Research Center (IFReC), Osaka University
2020–2023
Project Researcher, Immunology Frontier Research Center (IFReC), Osaka University
2018–2020
KOTAI Biotechnologies Inc.
2017–2018
University of California San Diego (UCSD)
2016–2017
Institute of Bioinformatics and Systems Biology, National Chiao Tung University

Selected publications

Liu YC, Li JR, Sun CH, Andrews E, Chao RF, Lin FM, Weng SL, Hsu S Da, Huang CC, Cheng C, et al. CircNet: A database of circular RNAs derived from transcriptome sequencing data. Nucleic Acids Res (2016) 44:D209–D215. doi: 10.1093/nar/gkv940
Chu SY, Chou CH, Huang H Da, Yen MH, Hong HC, Chao PH, Wang YH, Chen PY, Nian SX, Chen YR, …, Liu YC, et al. Mechanical stretch induces hair regeneration through the alternative activation of macrophages. Nat Commun (2019) 10: doi: 10.1038/s41467-019-09402-8
Liu C, Liu YC, Huang H Da, Wang W. Biogenesis mechanisms of circular RNA can be categorized through feature extraction of a machine learning model. Bioinformatics (2019) 35:4867–4870. doi: 10.1093/bioinformatics/btz705
Namkoong H, Edahiro R, Takano T, Nishihara H, Shirai Y, Sonehara K, Tanaka H, Azekawa S, Mikami Y, Lee H…, Liu YC, et al. DOCK2 is involved in the host genetics and biology of severe COVID-19. Nature (2022) 609:754–760. doi: 10.1038/s41586-022-05163-5
Taniguchi S, Matsui T, Kimura K, Funaki S, Miyamoto Y, Uchida Y, Sudo T, Kikuta J, Hara T, Motooka D…, Liu YC, et al. In vivo induction of activin A-producing alveolar macrophages supports the progression of lung cell carcinoma. Nat Commun (2023) 14:143. doi: 10.1038/s41467-022-35701-8
Edahiro R, Shirai Y, Takeshima Y, Sakakibara S, Yamaguchi Y, Murakami T, Morita T, Kato Y, Liu Y-C, Motooka D, et al. Single-cell analyses and host genetics highlight the role of innate immune cells in COVID-19 severity. Nat Genet (2023) doi: 10.1038/s41588-023-01375-1
Shirai T, Nakai A, Ando E, Fujimoto J, Leach S, Arimori T, Higo D, van Eerden FJ, Tulyeu J, Liu YC, et al. Celastrol suppresses humoral immune responses and autoimmunity by targeting the COMMD3/8 complex. Sci Immunol (2023) 8: doi: 10.1126/sciimmunol.adc9324
Shimizu K, Kikuta J, Ohta Y, Uchida Y, Miyamoto Y, Morimoto A, Yari S, Sato T, Kamakura T, Oshima K…, Liu YC, et al. Single-cell transcriptomics of human cholesteatoma identifies an activin A-producing osteoclastogenic fibroblast subset inducing bone destruction. Nat Commun (2023) 14: doi: 10.1038/s41467-023-40094-3
Miyamoto Y, Kikuta J, Matsui T, Hasegawa T, Fujii K, Okuzaki D, Liu Y, Yoshioka T, Seno S, Motooka D, et al. Periportal macrophages protect against commensal-driven liver inflammation. Nature (2024) 629:901–909. doi: 10.1038/s41586-024-07372-6
Sakakibara S, Liu Y-C, Ishikawa M, Edahiro R, Shirai Y, Haruna S, El Hussien MA, Xu Z, Li S, Yamaguchi Y, et al. Clonal landscape of autoantibody-secreting plasmablasts in COVID-19 patients. Life Sci Alliance (2024) 7:e202402774. doi: 10.26508/lsa.202402774
Liu Y-C, Ishikawa M, Sakakibara S, Kadi M Al, Motooka D, Naito Y, Ito S, Imamura Y, Matsumoto H, Sugihara F, et al. Full-length nanopore sequencing of circular RNA landscape in peripheral blood cells following sequential BNT162b2 mRNA vaccination. Gene (2025) 933:148971. doi: 10.1016/j.gene.2024.148971

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