Advancing Evidence-Based Cancer Treatment
with AI and Data Science

From Multi-omics Big Data to Clinical Application — Building Verifiable New Therapeutic Strategies

Our Mission

Cancer treatment is rapidly entering a new era driven by data and artificial intelligence. Our team is dedicated to Translational Data Science, Cancer Multi-omics, and AI-Driven Drug Discovery.

We are a cross-disciplinary team that integrates data collection, analysis, and biological experimentation. We investigate how AI can tangibly influence cancer treatment decision-making and the new drug development process, addressing core challenges in biomedical research.

Photo of Dr. Hsuan-Yu Chen

Dr. Hsuan-Yu Chen

  • Research Fellow, Institute of Statistical Science, Academia Sinica
  • Joint Appointment Professor, National Taiwan University / National Chung Hsing University / Kaohsiung Medical University
  • President, Taiwan Society for Precision Health and Toxicogenomics
  • Member, US-Taiwan Cancer Moonshot International Research Team
Translational Data Science Cancer Multi-omics AI-driven Precision Medicine

Core Research Areas

01. Data Science & Precision Medicine

Integrating high-dimensional multi-omics data (genomics, transcriptomics, proteomics) with large-scale clinical data.

  • Building explainable and applicable disease risk prediction models.
  • Developing treatment response prediction models.
  • Translating research findings into clinical studies and applications.

02. Generative AI & Drug Design

Developing molecular design methods centered on Generative AI to build a verifiable "Intelligent Agent Platform for Molecular Design."

  • Dry–Wet Loop: A "Prediction-Validation-Feedback" framework combining cell experiments, animal models, and mass spectrometry.
  • Establishing a scalable AI drug design workflow.
  • Challenging cancer targets that are difficult to address with traditional methods.

Team & Environment

We are a multidisciplinary research team comprising clinicians, statisticians, computer scientists/engineers, and biologists.

3 Postdoctoral Fellows
7 Ph.D. Students
7 Research Assistants

Selected Publications

Ya-Hsuan Chang, Tzu-Chan Hong, Kuen-Tyng Lin,…,Hsuan-Yu Chen*, Sung-Liang Yu, Ming-Shiang Wu, Yu-Ju Chen, Integrative proteogenomics maps multifactorial aetiology, progression and therapeutic vulnerabilities in gastric cancer, Gut, doi: 10.1136/gutjnl-2025-337247 (IF: 26.2; Ranking: 4/148, 2.7%) Corresponding author
Shankha Satpathy, Natalie M. Clark, Yi-Ju Chen,…,Hsuan-Yu Chen*, Alexey I. Nesvizhskii, Steven A. Carr, D. R. Mani, Marcin P. Cieslik, Yu-Ju Chen, Michael A. Gillette, 2025, Integrative Analysis of Lung Adenocarcinoma Across Diverse Ethnicities and Exposures, Cancer Cell, 43: 1731-1757 (IF: 44.5; Ranking: 5/326, 1.5%) Corresponding author
Shih-Pin Chen, Ya-Hsuan Chang, Yen-Feng Wang, Hsuan-Yu Chen*, Shuu-Jiun Wang, 2025, Composite microRNA-genetic risk score model links to migraine and implicates its pathogenesis, Brain, 148: 2178-2188 (IF: 11.7; Ranking: 5/285, 1.8%) Corresponding author
Yi-Ju Chen, Theodoros I. Roumeliotis, Ya-Hsuan Chang,…,Hsuan-Yu Chen*, Pan-Chyr Yang, Yu-Ju Chen, 2020, Proteogenomics of Non-smoking Lung Cancer in East Asia Delineates Molecular Signatures of Pathogenesis and Progression, Cell, 182, 226-244. (IF: 42.5; Ranking: 2/320, 0.6%) Corresponding author
Poyin Huang, Yuan-Han Yang, Ya-Hsuan Chang, Shu-Ling Chang, Mei-Chuan Chou, Chiou-Lian Lai, Ching-Kuan Liu, Hsuan-Yu Chen*, 2020, Association of early-onset Alzheimers disease with germline-generated high affinity self-antigen load, Translational Psychiatry, 10, 146. (IF: 6.2; Ranking: 21/288, 7.3%) Corresponding author
Chen HY, Yu SL, Ho BC,…,Chang GC, Yang PC, Li KC, 2015, R331W Missense Mutation of Oncogene YAP1 Is a Germline Risk Allele for Lung Adenocarcinoma With Medical Actionability., Journal of Clinical Oncology, 33, 2303-2310. (IF: 41.9; Ranking: 6/326, 1.8%)
Chen HY, Yu SL, Chen CH, Chang GC, Chen CY, Yuan A, Cheng CL, Wang CH, Terng HJ, Kao SF, Chan WK, Li HN, Liu CC, Singh S, Chen WJ, Chen JJ, Yang PC, 2007, A five-gene signature and clinical outcome in non-small-cell lung cancer., New England Journal of Medicine, 356, 11-20. (IF: 78.5; Ranking: 2/332, 0.6%)
Full Publication List (Web of Science)