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

Senior Advisor of Modeling
Allen Institute for Cell Science

Adjunct Associate 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

Postdocs and Visiting Scientists

Dr. Jason Y. Cain

Postdoctoral Scholar
jcain [at] uw [dot] edu | github

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

Graduate Students

Community 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

Operations Lead

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
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

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)

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. 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