Principal Investigator

Prof. Neda Bagheri

nbagheri [at] uw [dot] edu | abbreviated cv

Professor of Biology
Professor of Chemical Engineering
Washington Research Foundation Distinguished Investigator
University of Washington

Adjunct Professor of Chemical & Biological Engineering
Northwestern University

Mailing Address
University of Washington, Life Sciences Building
W Stevens Way NE
Seattle, WA 98195

Adjunct Assistant Scientific Director

Dr. Jessica S. Yu

Scientist at Allen Institute for Cell Science
jesyu [at] uw [dot] edu | github

Thesis: Multi-scale, multi-class agent-based models of biological systems

Ph.D. Chemical and Biological Engineering, Northwestern University

Acknowledgements	The Alumnae of Northwestern University NSF Graduate Research Fellowship

Graduate Students

Operations Lead

Po-Hao Chiu

Ph.D. candidate, Chemical Engineering
pohaoc2 [at] uw [dot] edu | github

Joined January 2022

B.S. Chemical Engineering, National Taiwan University
M.S. Chemical Engineering, University of Washington

Research Keywords	emergent dynamics \| bayesian inference \| machine learning \| image processing

Computation Lead

Jacob I. Evarts

Ph.D. candidate, Biology
jevarts [at] uw [dot] edu | github

Joined September 2021

B.S. Computer and Information Science, University of Oregon

Research Keywords	emergent properties \| representation learning \| information theory
Acknowledgements	NSF Graduate Research Fellowship

Sophia K. Jannetty

Ph.D. candidate, Biology
jannetty [at] uw [dot] edu | github

Joined September 2020

B.A. Biology, Williams College
Post Baccalaureate Computer Science Certificate, Tufts University

Research Keywords	agent-based models \| lateral root development \| emergent dynamics \| organogenesis
Acknowledgements	Washington NASA Space Grant
Collaborators	J. Nemhauser \| C. Cabernard

Allison W. Li

Ph.D. candidate, Biology
allli [at] uw [dot] edu | github

Joined September 2023

B.S. Biochemistry, University of Washington
B.S. Computer Science, Data Science, University of Washington

Research Keywords	agent-based models \| machine learning
Collaborators	M. B. Elowitz \| M. G. Shapiro

Krista Phommatha

krisphom [at] uw [dot] edu | github

Joined November 2024

B.S. Chemical Engineering, University of Colorado Boulder

Research Keywords	agent-based models

Community Lead

Madeline (Maddy) Scott

Ph.D. candidate, Biology
mts321 [at] uw [dot] edu | github

Joined September 2023

B.S. Mathematics, Johns Hopkins University
B.S. Natural Science, Johns Hopkins University

Research Keywords	agent-based models \| emergent dynamics
Collaborators	B. Kerr

Undergraduate Students

Alice Fu

afu5 [at] uw [dot] edu | github

Joined May 2025

B.S. Computer Science, University of Washington (expected June 2027)

Navya Jain

najain [at] uw [dot] edu | github

Joined May 2025

Intended B.S. Applied Mathematics and Biochemistry, University of Washington (expected June 2028)

Danielle Vahdat

dhv [at] uw [dot] edu | github

Joined January 2024

B.S. Molecular, Cellular, & Developmental Biology, University of Washington (expected June 2026)

High School Students

Patrick Feng

patrickfengsr [at] gmail [dot] com | github

Joined June 2025

Alumni

Graduate Students

Dr. Kate E. Dray

September 2017 — December 2022

Computational Biologist at Asimov

Thesis: A systematic workflow for model development enables rigorous exploration of synthetic biological systems

Ph.D. Chemical & Biological Engineering, Northwestern University

Acknowledgements	NSF Graduate Research Fellowship Biotechnology Training Program Cluster Award

Dr. Alexis N. Prybutok

September 2016 — June 2022

Assistant Teaching Professor in the Department of Chemical Engineering at the University of Washington

Thesis: Enabling exploration of CAR T-cell design and integration of social justice context into chemical engineering courses

Ph.D. Chemical & Biological Engineering, Northwestern University

Acknowledgements	NSF Graduate Research Fellowship

Dr. Narasimhan Balakrishnan

September 2015 — February 2022

Senior Consultant at Guidehouse

Thesis: Modeling, analysis, and control of heterogeneous multicellular oscillators

Ph.D. Chemical & Biological Engineering, Northwestern University

Acknowledgements	Biotechnology Training Program Cluster Award

Dr. Joshua I. Levy

September 2016 — June 2021

Postdoctoral Fellow at Scripps Research

Thesis: Fundamentals of thermosensory navigation in Drosophila

Ph.D. Engineering Sciences & Applied Mathematics, Northwestern University

Acknowledgements	Cabell Fellowship

Slava S. Fazio (formerly Butkovich)

September 2017 — June 2021

Data Scientist at U.S. Department of Veterans Affairs

M.S. Chemical & Biological Engineering, Northwestern University

Acknowledgements	Cabell Fellowship Biotechnology Training Program Fellowship

Dr. Joseph J. Muldoon

June 2014 — September 2020

Postdoc at UCSF (Eyquem lab and Roybal lab)

Thesis: Model-driven elucidation of synthetic and immune signaling mechanisms

Ph.D. Biological Sciences, Northwestern University

Acknowledgements	Biotechnology Training Program Cluster Award

Dr. Sebastian M. Bernasek

September 2014 — June 2019

Senior Machine Learning Engineer at Albert Invent

Thesis: Quantitative analysis of cell fate decisions

Ph.D. Chemical & Biological Engineering, Northwestern University

Dr. Jia J. Wu

June 2013 — December 2018

Investigator II at Novartis Institutes for Biomedical Research

Thesis: Data-driven strategies for optimization of human megakaryocyte differentiation

Ph.D. Biological Sciences, Northwestern University

Acknowledgements	Biotechnology Training Program Cluster Award National Science Foundation GK-12 Fellowship Ruth Kirchstein National Research Service Award

Dr. Justin D. Finkle

June 2013 — November 2018

Senior Bioinformatics and Computational Biology Scientist at Precede Biosciences

Thesis: Regulatory insights from gene expression dynamics

Ph.D. Biological Sciences, Northwestern University

Acknowledgements	Biotechnology Training Program Fellowship Nicholson Fellowship

Dr. Albert Y. Xue

September 2012 — August 2018

Lead Data Scientist at Caterpillar Inc.

Thesis: Finding the needle in the haystack: Applying data science to address biological questions

Ph.D. Chemical & Biological Engineering, Northwestern University

Acknowledgements	Biotechnology Training Program Cluster Award NICO Data Science Research Support

M. Kasim Fassia

January 2013 — June 2016

Interventional Radiologist at New York Presbyterian and Weill Cornell Medical Center

M.S. Biomedical Engineering, Northwestern University

August (formerly Aaron) D. Oppenheimer

January 2013 — June 2015

STEM Educator

M.S. Chemical & Biological Engineering, Northwestern University

Acknowledgements	National Science Foundation GK-12 Fellowship

Postdocs

Dr. Jason Y. Cain

September 2017 — July 2025

Computational Biology Scientist at Envisagenics

Thesis: Unpacking the role of complexity in multi-class models of the tumor microenvironment

M.S. Chemical & Biological Engineering, Northwestern University
Ph.D. Chemical Engineering, University of Washington

Acknowledgements	Northwestern University Data Science Fellowship Biotechnology Training Program Fellowship

Dr. Tyrone J. Yacoub

September 2015 — September 2017

Bioinformatics scientist at CB Therapeutics

Ph.D. Chemical & Biological Engineering, Northwestern University

Acknowledgements	Hartwell Foundation Postdoctoral Fellowship

Dr. Mark F. Ciaccio

September 2012 — June 2015

Senior biology data scientist at AbbVie

Ph.D. Cellular and Molecular Physiology, University of Chicago

Acknowledgements	Hartwell Foundation Postdoctoral Fellowship Northwestern University Physical Science-Oncology Center

Undergraduate Students

Zimo Zhu

October 2022 — June 2024

Graduate student at Cornell University

B.S. Molecular, Cellular, & Developmental Biology, University of Washington

Isabelle Chen

September 2020 — December 2023

Graduate Student at Rockefeller University

B.S. Integrated Engineering Studies, Northwestern University

Michael Y. Li

November 2020 — March 2023

B.S. Computer Science, University of Washington

Antonio Hazboun

January 2019 — August 2021

B.S. Chemical & Biological Engineering, Northwestern University

Eduardo Muñoz

June 2018 — August 2018

Student at University of California Irvine

Weipeng Zhang

July 2017 — June 2018

Grad student at Georgetown University

B.S. Chemical & Biological Engineering, Northwestern University

Maureen Ferries

September 2012 — March 2013

Process automation engineer at Dow AgroSciences

B.S. Chemical & Biological Engineering, Northwestern University