Principal Investigator

Prof. Neda Bagheri

Associate Professor of Biology
Associate 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
email | 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

Dr. Jason Y. Cain

email | github

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

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

Research Keywords	agent-based models \| machine learning \| angiogenesis
Acknowledgements	Northwestern University Data Science Fellowship Biotechnology Training Program Fellowship

Dr. Mugdha Sathe

Thesis: Understanding events leading up to CLIC/GEEC endocytic vesicle formation using BAR domains and actin machinery

Ph.D. Biology, National Center for Biological Sciences (TIFR), India

Research Keywords	galvanotaxis \| epithelial tissue \| wound healing
Collaborators	J. Theriot

Graduate Students

Po-Hao Chiu

email | github

Joined January 2022

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

Research Keywords	image processing \| wound-healing process \| agent-based models \| machine learning
Collaborators	Julie Theriot

Computation Lead

Jacob I. Evarts

Ph.D. candidate, Biology
email | github

Joined September 2021

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

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

Operations Lead

Sophia K. Jannetty

Ph.D. candidate, Biology
email | 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

Allison Li

email | github

Joined September 2023

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

Madeline (Maddy) Scott

email | github

Joined September 2023

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

Research Keywords	agent-based models \| emergent dynamics

Undergraduate Students

Zimo Zhu

email | github

Joined October 2022

B.S. Molecular, Cellular, & Developmental Biology, University of Washington (expected June 2024)

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. 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

Data Scientist at Citrine Informatics

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 Scientist at TenSixteen Bio

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

Aaron D. Oppenheimer

January 2013 — June 2015

Laboratory manager at Francis W. Parker School

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

Isabelle Chen

September 2020 — December 2023

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