Education

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

Professional Experience

• 2020~: Adjunct Associate Professor at CCII; Principal Scientist, Boehringer Ingelheim (Germany)
• 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
• 2015-2016: Senior Lecturer, Kyoto University, Graduate School of Medicine, Center for Medical Education
• 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
• 2014-2015: Assistant Professor, Kyoto University, Graduate School of Medicine, Department of Clinical System Onco-Informatics
• 2003: Internship, Diagnostic Radiology, National Institutes of Health, USA

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

• 2025: “Most Technological” Special Mention Award, Boehringer-Ingelheim AI Challenge 2025.
• 2021: “Most downloaded paper” award for a publication in Molecular Informatics 2021 (article URL: https://doi.org/10.1002/minf.202100113 )
• 2019: University of Bonn Returning Scholars and Research Alumni Program, Selected Returning Scholar
• 2018: US National Toxicology Program, Predictive Models for Acute Oral Systemic Toxicity prediction challenge, selected presentation (total submissions: 123)
• 2018: “Most downloaded paper” award for publication in Molecular Informatics 2018  (article URL: https://dx.doi.org/10.1002/minf.201700127)
• 2017: “Landmark paper” award for a publication in Future Medicinal Chemistry 2017  (article URL: https://dx.doi.org/10.4155/fmc-2016-0197)
• 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

Selected Publications

Fumihiko Kakizaki, Hiroyuki Miyoshi, Takehito Yamamoto, Tomonori Morimoto, Hiroyuki Matsubara, Shoichi Kitano, Tadayoshi Yamaura, Hisatsugu Maekawa, J B Brown, Tosiya Shun Sato, Kazutaka Obama, Yoshiharu Sakai, Kenji Kawada, Makoto Mark Taketo. Comprehensive Colorectal Cancer Stem Cell Transcriptomic Signatures That Can Predict Patient Prognostic Outcomes. Cancer Science (2025). DOI: 10.1111/cas.70235

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