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, Dissemination, & Alliances
Allen Institute for Cell Science

Adjunct Associate Professor of Chemical & Biological Engineering
Northwestern University

Mailing Address
University of Washington, Life Sciences Building 561
W Stevens Way NE
Seattle, WA 98195

Assistant Scientific Director

Dr. Jessica S. Yu

Consultant at Allen Institute for Cell Science
email | github

Ph.D. Chemical and Biological Engineering, Northwestern University
Thesis: Multi-scale, multi-class agent-based models of biological systems

Postdocs

Dr. Mugdha Sathe

Ph.D. Biology, National Center for Biological Sciences (TIFR), India
Thesis: Understanding events leading up to CLIC/GEEC endocytic vesicle formation using BAR domains and actin machinery

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

Graduate Students

Computation Lead

Jason Y. Cain

Ph.D. candidate, Chemical Engineering
email | github

B.S. Chemical Engineering, Northeastern University
M.S. Chemical & Biological Engineering, Northwestern University
Joined September 2017

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

Po-Hao Chiu

email | github

B.S. Chemical Engineering, National Taiwan University
Joined January 2022

Research Keywords	image processing \| agent-based models \| machine learning

Kate E. Dray

Ph.D. candidate, Chemical & Biological Engineering
email | github

B.S. Chemical Engineering, University of Kentucky
Joined September 2017

Research Keywords	ordinary differential equations \| mammalian synthetic biology \| gene expression dynamics \| parameter identifiability analysis
Acknowledgements	NSF Graduate Research Fellowship Biotechnology Training Program Cluster Award
Collaborators	J. N. Leonard

Jacob I. Evarts

email | github

B.S. Computer and Information Science, University of Oregon
Joined September 2021

Research Keywords	emergent properties \| complex adaptive systems

Operations Lead

Sophia K. Jannetty

Ph.D. candidate, Biology
email | github

B.A. Biology, Williams College
Post Baccalaureate Computer Science Certificate, Tufts University
Joined September 2020

Research Keywords	agent-based models \| lateral root development \| emergent dynamics \| organogenesis
Collaborators	J. Nemhauser

Undergraduate Students

Isabelle Chen

Joined September 2020

Collaborators	J. N. Leonard

Michael Li

email | github

Joined November 2020

Alumni

Graduate Students

Dr. Narasimhan Balakrishnan

September 2015 — February 2022

Ph.D. Chemical & Biological Engineering, Northwestern University
Thesis: Modeling, analysis, and control of heterogeneous multicellular oscillators

Acknowledgements	Biotechnology Training Program Cluster Award

Dr. Sebastian M. Bernasek

September 2014 — June 2019

Ph.D. Chemical & Biological Engineering, Northwestern University
Thesis: Quantitative analysis of cell fate decisions

Slava S. Butkovich

September 2017 — June 2021

M.S. Chemical & Biological Engineering, Northwestern University

Acknowledgements	Cabell Fellowship Biotechnology Training Program Fellowship

M. Kasim Fassia

January 2013 — June 2016

Medical student at Michigan State University

M.S. Biomedical Engineering, Northwestern University

Dr. Justin D. Finkle

June 2013 — November 2018

Bioinformatics Scientist at Tempus

Ph.D. Biological Sciences, Northwestern University
Thesis: Regulatory insights from gene expression dynamics

Acknowledgements	Biotechnology Training Program Fellowship Nicholson Fellowship

Dr. Joshua I. Levy

September 2016 — June 2021

Postdoctoral Fellow at Scripps Research

Ph.D. Engineering Sciences & Applied Mathematics, Northwestern University
Thesis: Fundamentals of thermosensory navigation in Drosophila

Acknowledgements	Cabell Fellowship

Dr. Joseph J. Muldoon

June 2014 — September 2020

Postdoc at UCSF (Eyquem lab and Roybal lab)

Ph.D. Biological Sciences, Northwestern University
Thesis: Model-driven elucidation of synthetic and immune signaling mechanisms

Acknowledgements	Biotechnology Training Program Cluster Award

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

Dr. Alexis N. Prybutok

September 2016 — June 2022

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

Ph.D. Chemical & Biological Engineering, Northwestern University
Thesis: Enabling exploration of CAR T-cell design and integration of social justice context into chemical engineering courses

Acknowledgements	NSF Graduate Research Fellowship

Dr. Jia J. Wu

June 2013 — December 2018

Computational Biologist at Novartis

Ph.D. Biological Sciences, Northwestern University
Thesis: Data-driven strategies for optimization of human megakaryocyte differentiation

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

Dr. Albert Y. Xue

September 2012 — August 2018

Data Scientist at Uptake

Ph.D. Chemical & Biological Engineering, Northwestern University
Thesis: Finding the needle in the haystack: Applying data science to address biological questions

Acknowledgements	Biotechnology Training Program Cluster Award NICO Data Science Research Support

Postdocs

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

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

Undergraduate Students

Maureen Ferries

September 2012 — March 2013

Process automation engineer at Dow AgroSciences

B.S. Chemical & Biological Engineering, Northwestern University

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