Location
NCRC, Building 520, Room 3328
1600 Huron Parkway
Ann Arbor, MI 48109
Phone
(734) 764-1566
Primary Website
Research Interests
- Fighting drug resistance using AI: We are developing mechanistic AI tools (e.g. INDIGO, MAGENTA, CARAMEL) to design drug combinations with enhanced potency and reduced potential for developing resistance. We also study pathogen metabolism and pathogen-immune interactions to discover new synergistic antibiotics against M. tuberculosis, S. aureus and other pathogens.
- Systems biology methods for simulating metabolic regulation: Our lab is developing new modeling tools to simulate the activity of thousands of metabolic reactions in a human or microbial cell, providing a unique systems perspective on metabolic regulation. We have applied the methods that we developed (e.g. PROM, DFA, GEMINI, RECON8D, and ASTRIX) to understand microbial, stem-cell, cancer, and brain metabolism using omics datasets.
Research Areas:
Biomedical Computation and Modeling, Cancer, Drug Delivery and Therapeutics, Tissue Engineering and Biomaterials, Tissue Engineering and Regenerative Medicine
Teaching
- AI in BME (BME 487): This course introduces students to AI and machine-learning algorithms and their applications in BME. The course is open to both graduate and undergraduate students. Learn more at the course website: https://systemsbiologylab.org/ai-bme-syllabus
Publications
- A structural machine learning approach for rapid prediction of thermodynamically destabilizing tyrosine phosphorylations. Cell Reports Methods 2025.
- Inferring Metabolic Objectives and Tradeoffs in Single Cells During Embryogenesis, Cell Systems, 2025.
- A flux-based machine learning model to simulate the impact of pathogen metabolic heterogeneity on drug interactions. PNAS Nexus, 2022.
- Genome-scale network model of metabolism and histone acetylation reveals metabolic dependencies of histone deacetylase inhibitors, Genome Biology, 2019
- Transcriptomic signatures predict regulators of drug synergy and clinical regimen efficacy against Tuberculosis, mBio, 2019
- Comprehensive mapping of pluripotent stem cell metabolism using dynamic genome-scale network modeling, Cell Reports, 2017
- Granzyme B disrupts central metabolism and protein synthesis in bacteria to promote an immune cell death program, Cell, 2017
Recent News Articles:
- Unlocking Cellular Objectives Through Machine Learning
- Multimodal AI to guide personalized treatments for TB
- Deep learning AI discovers surprising new antibiotics
- Closest look yet at killer T-cell activity could yield new approach to tackling antibiotic resistance
- A ‘decathlon’ for antibiotics puts them through more realistic testing