Shuto Hayashi - My portal

Profile Information

Affiliation: Associate Professor, Department of Computational and Systems Biology, Medical Research Institute, Tokyo Medical and Dental University

Degree: 博士（情報理工学）(Mar, 2019, 東京大学)

Contact information: s-haya.csbtmd.ac.jp
Researcher number: 30902332
ORCID ID: https://orcid.org/0000-0002-1623-0738
J-GLOBAL ID: 202101014211741613
researchmap Member ID: R000016382

External link: http://www.shimamlab.info/

Research Interests

Research Areas

Research History

Apr, 2023 - Present

Associate Professor, Department of Computational and Systems Biology, Medical Research Institute, Tokyo Medical and Dental University
Jan, 2023 - Apr, 2023

Project Associate Professor, Department of Computational and Systems Biology, Medical Research Institute, Tokyo Medical and Dental University
Apr, 2021 - Dec, 2022

Designated Associate Professor, Division of Systems Biology, Graduate School of Medicine, Nagoya University
Apr, 2019 - Mar, 2021

Research Associate, Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo

Education

Apr, 2016 - Mar, 2019

Department of Computer Science Doctoral Course, The Graduate School of Information Science and Technology, The University of Tokyo
Apr, 2014 - Mar, 2016

Department of Computer Science Master Course, The Graduate School of Information Science and Technology, The University of Tokyo
Apr, 2010 - Mar, 2014

Department of Information Science, Faculty of Science, The University of Tokyo

Papers

Single-cell colocalization analysis using a deep generative model

Yasuhiro Kojima, Shinji Mii, Shuto Hayashi, Haruka Hirose, Masato Ishikawa, Masashi Akiyama, Atsushi Enomoto, Teppei Shimamura

Cell Systems, 15(2) 180-192.e7, Feb, 2024 Peer-reviewed
Subclonal accumulation of immune escape mechanisms in microsatellite instability-high colorectal cancers

Yuta Kobayashi, Atsushi Niida, Satoshi Nagayama, Koichi Saeki, Hiroshi Haeno, Kazuki K. Takahashi, Shuto Hayashi, Yuki Ozato, Hideyuki Saito, Takanori Hasegawa …

British Journal of Cancer, 129(7) 1105-1118, Aug 18, 2023 Peer-reviewed
Topological data analysis of protein structure and inter/intra- molecular interaction changes attributable to amino acid mutations

Jun Koseki, Shuto Hayashi, Yasuhiro Kojima, Haruka Hirose, Teppei Shimamura

Computational and Structural Biotechnology Journal, 21 2950-2959, May 9, 2023 Peer-reviewedLead author
Spatial and single-cell transcriptomics decipher the cellular environment containing HLA-G+ cancer cells and SPP1+ macrophages in colorectal cancer.

Yuki Ozato, Yasuhiro Kojima, Yuta Kobayashi, Yuuichi Hisamatsu, Takeo Toshima, Yusuke Yonemura, Takaaki Masuda, Kouichi Kagawa, Yasuhiro Goto, Mitsuaki Utou …

Cell Reports, 42(1) 111929-111929, Jan 17, 2023 Peer-reviewed
Bayesian statistical method for detecting structural and topological diversity in polymorphic proteins.

Shuto Hayashi, Jun Koseki, Teppei Shimamura

Computational and Structural Biotechnology Journal, 20 6519-6525, Nov 21, 2022 Peer-reviewedInvitedLead authorCorresponding author
Nucleic Acid-triggered Tumoral Immunity Propagates pH-selective Therapeutic Antibodies through Tumor-driven Epitope Spreading.

Genta Furuya, Hiroto Katoh, Shinichiro Atsumi, Itaru Hashimoto, Daisuke Komura, Ryo Hatanaka, Shogo Senga, Shuto Hayashi, Shoji Akita, Hirofumi Matsumura …

Cancer Science, 114(1) 321-338, Sep 22, 2022 Peer-reviewed
Immunogenomic pan-cancer landscape reveals immune escape mechanisms and immunoediting histories

Shinichi Mizuno, Rui Yamaguchi, Takanori Hasegawa, Shuto Hayashi, Masashi Fujita, Fan Zhang, Youngil Koh, Su Yeon Lee, Sung Soo Yoon, Eigo Shimizu …

Scientific Reports, 11(1) 15713-15713, Aug 3, 2021 Peer-reviewedLead author
Neoantimon: A multifunctional R package for identification of tumor-specific neoantigens

Takanori Hasegawa, Shuto Hayashi, Eigo Shimizu, Shinichi Mizuno, Atsushi Niida, Rui Yamaguchi, Satoru Miyano, Hidewaki Nakagawa, Seiya Imoto

Bioinformatics, 36(18) 4813-4816, Sep 15, 2020 Peer-reviewed
Classification of primary liver cancer with immunosuppression mechanisms and correlation with genomic alterations

Masashi Fujita, Rui Yamaguchi, Takanori Hasegawa, Shu Shimada, Koji Arihiro, Shuto Hayashi, Kazuhiro Maejima, Kaoru Nakano, Akihiro Fujimoto, Atsushi Ono …

EBioMedicine, 53 102659-102659, Feb 26, 2020 Peer-reviewed
Pan-cancer analysis of whole genomes

Peter J. Campbell, Gad Getz, Jan O. Korbel, Joshua M. Stuart, Jennifer L. Jennings, Lincoln D. Stein, Marc D. Perry, Hardeep K. Nahal-Bose, B. F. Francis Ouellette, Constance H. Li …

Nature, 578(7793) 82-93, Feb 5, 2020 Peer-reviewed
ALPHLARD-NT: Bayesian Method for Human Leukocyte Antigen Genotyping and Mutation Calling through Simultaneous Analysis of Normal and Tumor Whole-Genome Sequence Data

Shuto Hayashi, Takuya Moriyama, Rui Yamaguchi, Shinichi Mizuno, Mitsuhiro Komura, Satoru Miyano, Hidewaki Nakagawa, Seiya Imoto

Journal of Computational Biology, 26(9) 923-937, Sep 1, 2019 Peer-reviewedLead author
Quantifying immune-based counterselection of somatic mutations

Fan Yang, Dae Kyum Kim, Hidewaki Nakagawa, Shuto Hayashi, Seiya Imoto, Lincoln Stein, Frederick P. Roth

PLoS Genetics, 15(7) e1008227, Jul 25, 2019 Peer-reviewed
A Bayesian model integration for mutation calling through data partitioning

Takuya Moriyama, Seiya Imoto, Shuto Hayashi, Yuichi Shiraishi, Satoru Miyano, Rui Yamaguchi

Bioinformatics, 35(21) 4247-4254, Mar 29, 2019 Peer-reviewed
ALPHLARD: A Bayesian method for analyzing HLA genes from whole genome sequence data

Shuto Hayashi, Rui Yamaguchi, Shinichi Mizuno, Mitsuhiro Komura, Satoru Miyano, Hidewaki Nakagawa, Seiya Imoto

BMC Genomics, 19(1) 790-790, Nov 1, 2018 Peer-reviewedLead author
A temporal shift of the evolutionary principle shaping intratumor heterogeneity in colorectal cancer

Tomoko Saito, Atsushi Niida, Ryutaro Uchi, Hidenari Hirata, Hisateru Komatsu, Shotaro Sakimura, Shuto Hayashi, Sho Nambara, Yosuke Kuroda, Shuhei Ito …

Nature Communications, 9(1) 2884-2884, Jul 23, 2018 Peer-reviewed
An in silico automated pipeline to identify tumor specic neoantigens from whole genome and exome sequencing data

Takanori Hasegawa, Shuto Hayashi, Eigo Shimizu, Shinichi Mizuno, Rui Yamaguchi, Satoru Miyano, Hidewaki Nakagawa, Seiya Imoto

Proceeding of 12th International Symposium on Bioinformatics Research and Applications, 2016 Peer-reviewed

Misc.

Topological data analysis for protein structural changes caused by some mutations

小関準, 小嶋泰弘, 林周斗, 廣瀬遥香, NAM Hyunha, 島村徹平

分子科学討論会講演プログラム&要旨(Web), 15th, 2021
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Matthew H. Bailey, William U. Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Wen-Wei Liang, Amila Weerasinghe, Shantao Li, Yize Li, Sean Kelso, M …

Nature Communications, 11(1) 4748-4748, Sep 21, 2020 Peer-reviewed
Sex differences in oncogenic mutational processes

Constance H. Li, Stephenie D, Prokopec, Ren X. Sun, Fouad Yousif, Nathaniel Schmitz, PCAWG Tumour Subtypes Clinical Translation, Paul C. Boutros, PCAWG Consortium

Nature Communications, 11(1) 4330-4330, Aug 28, 2020 Peer-reviewed
凍結臨床試料を用いたシングルセルRNA-seq法の確立

橋本至, 加藤洋人, 林周斗, 河村大輔, 大島貴, 利野靖, 益田宗孝, 石川俊平

日本衛生学雑誌, 75(Suppl.) S187-S187, Mar, 2020
ヒト胃癌環境における主要な抗体クローンとして同定された抗硫酸化グリコサミノグリカン抗体の解析

古谷弦太, 加藤洋人, 林周斗, 河村大輔, 石川俊平

日本衛生学雑誌, 75(Suppl.) S202-S202, Mar, 2020
Butler enables rapid cloud-based analysis of thousands of human genomes

Sergei Yakneen, Sebastian M. Waszak, PCAWG Technical Working Group, Michael Gertz, Jan O. Korbel, PCAWG Consortium

Nature Biotechnology, 38(3) 288-292, Feb 5, 2020 Peer-reviewed
Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

Bernardo Rodriguez-Martin, Eva G. Alvarez, Adrian Baez-Ortega, Jorge Zamora, Fran Supek, Jonas Demeulemeester, Martin Santamarina, Young Seok Ju, Javier Temes, Daniel Garcia-Souto …

Nature Genetics, 52(3) 306-319, Feb 5, 2020 Peer-reviewed
Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer

Kadir C. Akdemir, Victoria T. Le, Sahaana Chandran, Yilong Li, Roel G. Verhaak, Rameen Beroukhim, Peter J. Campbell, Lynda Chin, Jesse R. Dixon, P. Andrew Futreal …

Nature Genetics, 52(3) 294-305, Feb 5, 2020 Peer-reviewed
The landscape of viral associations in human cancers

Marc Zapatka, Ivan Borozan, Daniel S. Brewer, Murat Iskar, Adam Grundhoff, Malik Alawi, Nikita Desai, Holger Sültmann, Holger Moch, PCAWG Pathogens …

Nature Genetics, 52(3) 320-330, Feb 5, 2020 Peer-reviewed
Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Isidro Cortés-Ciriano, Jake June-Koo Lee, Ruibin Xi, Dhawal Jain, Youngsook L. Jung, Lixing Yang, Dmitry Gordenin, Leszek J. Klimczak, Cheng-Zhong Zhang, David S. Pellman …

Nature Genetics, 52(3) 331-341, Feb 5, 2020 Peer-reviewed
Comprehensive molecular characterization of mitochondrial genomes in human cancers

Yuan Yuan, Young Seok Ju, Youngwook Kim, Jun Li, Yumeng Wang, Christopher J. Yoon, Yang Yang, Inigo Martincorena, Chad J. Creighton, John N. Weinstein …

Nature Genetics, 52(3) 342-352, Feb 5, 2020 Peer-reviewed
The repertoire of mutational signatures in human cancer

Ludmil B. Alexandrov, Jaegil Kim, Nicholas J. Haradhvala, Mi Ni Huang, Alvin Wei Tian Ng, Yang Wu, Arnoud Boo, Kyle R. Covington, Dmitry A. Gordenin, Erik N. Bergstrom …

Nature, 578(7793) 94-101, Feb 5, 2020 Peer-reviewed
Patterns of somatic structural variation in human cancer genomes

Yilong Li, Nicola D. Roberts, Jeremiah A. Wala, Ofer Shapira, Steven E. Schumacher, Kiran Kumar, Ekta Khurana, Sebastian Waszak, Jan O. Korbel, James E. Haber …

Nature, 578(7793) 112-121, Feb 5, 2020 Peer-reviewed
The evolutionary history of 2,658 cancers

Moritz Gerstung, Clemency Jolly, Ignaty Leshchiner, Stefan C. Dentro, Santiago Gonzalez, Daniel Rosebrock, Thomas J. Mitchell, Yulia Rubanova, Pavana Anur, Kaixian Yu …

Nature, 578(7793) 122-128, Feb 5, 2020 Peer-reviewed
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah A. Wala, Ofer Shapira, Grace Tiao, Henrik Hornshøj, Julian M. Hess, Randi Istrup Juul, Ziao Lin …

Nature, 578(7793) 102-111, Feb 5, 2020 Peer-reviewed
Genomic basis for RNA alterations in cancer

Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah A. Wala, Ofer Shapira, Grace Tiao, Henrik Hornshøj, Julian M. Hess, Randi Istrup Juul, Ziao Lin …

Nature, 578(7793) 129-136, Feb 5, 2020 Peer-reviewed
Divergent mutational processes distinguish hypoxic and normoxic tumours

Vinayak Bhandari, Constance H. Li, Robert G. Bristow, Paul C. Boutros, PCAWG Consortium

Nature Communications, 11(1) 7569-7569, Feb 5, 2020 Peer-reviewed
Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis

Joana Carlevaro-Fita, Andrés Lanzós, Lars Feuerbach, Chen Hong, David Mas-Ponte, Jakob Skou Pedersen, PCAWG Drivers Functional Interpretation Group, Rory Johnson, PCAWG Consortium

Communications Biology, 3(1) 1347-1347, Feb 5, 2020 Peer-reviewed
Inferring structural variant cancer cell fraction

Marek Cmero, Ke Yuan, Cheng Soon Ong, Jan Schröder, PCAWG Evolution Heterogeneity Working Group, Niall M. Corcoran, Tony Papenfuss, Christopher M. Hovens, Florian Markowetz, Geoff Macintyre …

Nature Communications, 11(1) 7568-7568, Feb 5, 2020 Peer-reviewed
A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns

Wei Jiao, Gurnit Atwal, Paz Polak, Rosa Karlic, Edwin Cuppen, PCAWG Tumor Subtypes Clinical Translation Working Group, Alexandra Danyi, Jeroen de Ridder, Carla van Herpen, Martijn P. Lolkema …

Nature Communications, 11(1) 7573-7573, Feb 5, 2020 Peer-reviewed

Books and Other Publications

Analyzing Antibody Repertoire Using Next-Generation Sequencing and Machine Learning.

Shuto Hayashi, Shumpei Ishikawa

Humana, Nov, 2022
論文図表を読む作法 : はじめて出会う実験&解析法も正しく解釈! : 生命科学・医学論文をスラスラ読むためのFigure事典

牛島, 俊和, 中山, 敬一

羊土社, Jul, 2022 (ISBN: 9784758122603)

Presentations

Deep learning-based approach for accelerating molecular dynamics simulation

Sep 7, 2023
Acceleration of molecular dynamics simulation using deep learning

Shuto Hayashi, Jun Koseki, Yasuhiro Kojima, Teppei Shimamura

The 31st Annual Intelligent Systems for Molecular Biology and the 22nd Annual European Conference on Computational Biology, Jul 24, 2023
Comprehensive analysis of structural diversity in human B cell repertoire

Mar 8, 2021
分子動力学を用いた抗体構造ランドスケープ解析

林周斗

第5回理論免疫学ワークショップ, Feb 13, 2021
ヒト抗体における網羅的構造多様性解析

林周斗

第9回生命医薬情報学連合大会, Sep 3, 2020
Whole genome sequence-based analysis of HLA genes with Bayesian statistical model

Shuto Hayashi, Rui Yamaguchi, Shinichi Mizuno, Mitsuhiro Komura, Satoru Miyano, Hidewaki Nakagawa, Seiya Imoto

17th International Workshop on Bioinformatics and Systems Biology, Jul 26, 2017
Statistical method for comprehensive analysis of HLA class I and II genes.

Shuto Hayashi, Rui Yamaguchi, Shinichi Mizuno, Mitsuhiro Komura, Satoru Miyano, Hidewaki Nakagawa, Seiya Imoto

16th International Workshop on Bioinformatics and Systems Biology, Aug 9, 2016
Bayesian Method for HLA Genotyping from Whole Genome Sequencing Data

Shuto Hayashi, Rui Yamaguchi, Shinichi Mizuno, Mitsuhiro Komura, Satoru Miyano, Hidewaki Nakagawa, Seiya Imoto

15th International Workshop on Bioinformatics and Systems Biology, Jul 21, 2015

Professional Memberships

Jul, 2023 - Present

日本バイオインフォマティクス学会
Jun, 2023 - Present

International Society for Computational Biology
May, 2020 - Dec, 2022

The Japanese Society for Hygiene

Research Projects

深層学習を用いた高速タンパク質構造サンプリング手法の開発

医学系研究助成, 公益財団法人武田科学振興財団, Jul, 2022 - Mar, 2027

林周斗
マウス発生休止胚において、再発生能の有無を予測する技術と付与する技術の創出

科学研究費助成事業, 挑戦的研究(萌芽), 日本学術振興会, Jun, 2023 - Mar, 2025

高岡勝吉, 林周斗
Development of a fast molecular dynamics simulation method using deep learning

Grants-in-Aid for Scientific Research, Grant-in-Aid for Early-Career Scientists, Japan Society for the Promotion of Science, Apr, 2022 - Mar, 2025