Allison W. Li
About Me
I am a 3rd year PhD student at the University of Washington, advised by Dr. Neda Bagheri. I am broadly interested in building spatiotemporal models for designing living therapeutics, and using machine learning models to identify disease signals.
Before this, I also completed my BS in both computer science and biochemistry at the University of Washington. I previously worked at the Fred Hutch Cancer Center with Dr. Trevor Bedford on phylogenetic modeling of Norovirus, and at UW BioFAB (now the Institute of Protein Design) under Dr. Eric Klavins designing reproducible workflows and inventory tracking for automating benchwork protocols.
Highlighted Research Projects
Spatiotemporal modeling of inhibitory CAR T therapies in the tumor microenvironment
Identifying iCAR therapy successes and shortcomings in different spatial contexts, proposing and testing strategies to improve therapeutic outcomes.
Model prediction of SynNotch CAR T therapy successes and pitfalls
Designing predictive SynNotch CAR T agent, analyzing parameter sweeps, forecasting therapy performance in immunosuppressive environments.
Disentangling context-specific Alzheimer's Disease progression signatures through an explainable AI framework
Isolating Alzherimer's Disease specific signals from large, noisy, single cell transcriptomic datasets. Translating latent space patterns to interpretable pathways and specific genes.
Publications
An asterisk * denotes that the authors contributed equally to the work.
Conferences & Talks
- In silico modeling forecasts iCAR inefficacy in tumors and evaluates migration constraints on selectivity — Synthetic Biology, Engineering, Evolution & Design (SEED), June 2026 [Presentation]
- In silico modeling guides design of combinatorial antigen recognition in engineered CAR T therapies — Synthetic Biology Consortium Automation Symposium, March 2026 [Presentation]
- Multiscale Modeling Informs Synthetic CAR T Circuit Design for Cell Therapy — UW Biology Graduate Seminar, March 2026 [Presentation]
- Modeling multi-scale in silico dynamics of combinatorial recognition circuits in T cell therapies — Engineering Biology Research Symposium (EBRC), May 2024 [Presentation]
- Capturing Biological Signals in Alzheimer’s Single Cell Transcriptomic Data by Isolating Salient Variations — Machine Learning in Computational Biology (MLCB), September 2024 [Presentation]
- Phylogenetic Modeling Analysis of Norovirus Reveals Varying Genotype and Gene Adaptive Mutation Rates — Fred Hutch SURP Conference 2022, August 2022 [Presentation]
Awards & Honors
- 2026 — Washington Space Grant Fellowship, WA NASA Space Grant Consortium
- 2023 — Top Scholar Fellowship, University of Washington Department of Biology
- 2022 — Tapia Conference Scholarship, Paul G. Allen School of Computer Science
- 2021 — Burkhardt Family Scholarship, Paul G. Allen School of Computer Science
- 2020 — Phi Beta Kappa Honor Society Member, Phi Beta Kappa Honor Society
Media & Press
- From Models to Impact: Making the Case for your Research — Women in Machine Learning and Data Science (WiMLDS), March 2026
- New Resources for Norovirus — Nextstrain, January 2026
Teaching
- BIOL 200 – Introduction to Biology. UW Department of Biology
- CSE 331 – Software Design and Implementation. UW Paul G. Allen School of Computer Science and Engineering
- CSE142 – Computer Programming I. UW Paul G. Allen School of Computer Science and Engineering
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