Education

• 1998-2003: BS Computer Science, BS Mathematics, University of Evansville, USA
• 2007-2010: Ph.D. course Biochemo-informatics, Kyoto University, Japan
• 2010-2010: Postdoctoral researcher, Kyoto University, Career Path Promotion Unit for Young Life Scientists, Laboratory of Theoretical Chemistry and Biophysics for Molecules
• 2010-2014: Postdoctoral researcher, Kyoto University, Graduate School of Pharmaceutical Sciences, Department of Systems Bioscience for Drug Discovery

Professional Experience

• 2003: Internship, Diagnostic Radiology, National Institutes of Health, USA
• 2014-2015: Assistant Professor, Kyoto University, Graduate School of Medicine, Department of Clinical System Onco-Informatics
• 2014-2016: Adjoint researcher, Foundation for Biomedical Research and Innovation (FBRI), Institute of Biomedical Research and Innovation Laboratory, Drug Research and Development Division, Simulation Drug Discovery Group
• 2015-2016: Senior Lecturer, Kyoto University, Graduate School of Medicine, Center for Medical Education
• 2016-2020: Junior Associate Professor, Kyoto University, Graduate School of Medicine; Unit Leader, Kyoto University, Life Science Informatics Research Unit, Laboratory for Molecular Biosciences, Graduate School of Medicine
• 2020~: Adjunct Associate Professor at CCII; Principal Scientist, Boehringer Ingelheim (Germany)

Research Focus

 I divide my research time into pursuit of the following topics:

• Active/adaptive machine learning for drug discovery
• Scientific data visualization methods with focus on active learning
• Clinical and biomedical informatics
• Large-scale software architecture design

Honors & Awards

• 2013 & 2017: University of Bonn (Germany), Department of Life Science Informatics, Bonn-Aachen International Center for Information Technology;  Life Science Informatics Retreat 2013, Chemoinformatics Summer School 2017, Invited Guest Lecturer and Researcher
• 2017: “Landmark paper” award for a publication in Future Medicinal Chemistry 2017  (article URL: https://dx.doi.org/10.4155/fmc-2016-0197)
• 2018: “Most downloaded paper” award for publication in Molecular Informatics 2018  (article URL: https://dx.doi.org/10.1002/minf.201700127)
• 2018: US National Toxicology Program, Predictive Models for Acute Oral Systemic Toxicity prediction challenge, selected presentation (total submissions: 123)
• 2019: University of Bonn Returning Scholars and Research Alumni Program, Selected Returning Scholar
• 2021: “Most downloaded paper” award for a publication in Molecular Informatics 2021 (article URL: https://doi.org/10.1002/minf.202100113 )

Selected Publications

Shiro Takamatsu, Junzo Hamanishi, J.B. Brown, Ken Yamaguchi, Koji Yamanoi, Kosuke Murakami, Osamu Gotoh, Seiichi Mori, Masaki Mandai, Noriomi Matsumura. Mutation burden-orthogonal tumor genomic subtypes delineate responses to immune checkpoint therapy (BMJ), Journal for ImmunoTherapy of Cancer (2022). DOI: doi.org/10.1136/jitc-2022-004831

Shiro Takamatsu, J.B. Brown, Ken Yamaguchi, Junzo Hamanishi, Koji Yamanoi, Hisamitsu Takaya, Tomoko Kaneyasu, Seiichi Mori, Masaki Mandai, Noriomi Matsumura. The utility of homologous recombination deficiency biomarkers across cancer types. (Amer Soc Clin Oncol) JCO Precision Oncology, 6:e2200085 (2022). DOI: 10.1200/PO.22.00085 

Yuki Makino, Yuki Kamiyama, J.B. Brown, Takashi Kobayashi. Comprehensive genomics in androgen receptor-dependent castration-resistant prostate cancer identifies an adaptation pathway mediated by opioid receptor kappa 1. (Nature) Communications Biology, 5(1):718 (2022). DOI: 10.1038/s42003-022-03227-w

Ryusuke Murakami, Junzo Hamanishi, J.B. Brown, Kaoru Abiko, Koji Yamanoi, Mana Taki, Yuko Hosoe, Ken Yamaguchi, Tsukasa Baba, Noriomi Matsumura, Ikuo Konishi, Masaki Mandai. Combination of gene set signatures correlates with response to nivolumab in platinum-resistant ovarian cancer. Scientific Reports, 11(1):11427 (2021). DOI: 10.1038/s41598-021-91012-w

A Yokoyama, S Ogawa, J.B. Brown, et al. Age-related remodelling of oesophageal epithelia by mutated common cancer drivers, Nature, 565(7739):312-317 (2019). DOI: 10.1038/s41586-018-0811-x