Principal Investigator

Neda Bagheri, Ph. D.

Assistant Professor of Chemical and Biological Engineering
McCormick School of Engineering and Applied Science
Northwestern University




Graduate Students

Narasimhan Balakrishnan
email

Models for circadian rhythms are well explored in the context of single cell behavior. How do populations of heterogeneous cells with an internal oscillating gene regulatory network behave when coupled? We are investigating the effect of heterogeneity and coupling on the robustness of this system to external (light based) perturbations using a combination of theoretical and computational methods.

Acknowledgements:        Biotechnology Training Program Cluster Award

Sebastian M. Bernasek, Ph. D. candidate
email

An organism’s health depends on countless cellular decisions governing processes such as growth, division, death, and differentiation throughout time and space. These decisions are controlled by systems of biochemical reactions called regulatory networks, and their misregulation results in developmental defects, cancer, and disease. I combine elements of control theory, chemical kinetics, and stochastic simulation to computationally interrogate how the accuracy of cellular decisions depends upon a delicate balance between the structure of regulatory networks and the rate at which cells grow.

Collaborators:                  L. A. N. Amaral
                                        R. W. Carthew

Justin D. Finkle, Ph. D. candidate
email

The complex, dynamic, and context-dependent behavior of biology hampers the development of control strategies for living systems. Correct identification of biological regulatory systems yields the unique ability to rapidly design personalized, targeted therapeutics. My research focuses on creating computational methods to accurately infer intracellular signaling networks from high-throughput, time series data. I employ these methods to elucidate the regulatory role of Sprouty, a known tumor suppressor, and determine novel targets for cancer therapeutics.

Acknowledgements:        Biotechnology Training Program Fellowship
Collaborators:                  J. D. Licht

Joshua I. Levy, Ph. D. candidate
email

The circadian clock is a ubiquitous and strongly conserved gene regulatory motif present in most higher organisms. At its core it is a network of genes with oscillating expression of RNA and protein, providing a cellular timekeeping mechanism that has long been known to lead to periodic rest:activity patterns. We now know that clocks exist in many different tissues, each regulated by a combination of environmental factors (e.g., light, temperature, feeding) as well as by the outputs of surrounding cells and tissues. In my research, I use the fruit fly as a model to study the interplay between the central circadian clock and peripheral clocks in metabolic tissues. Synchrony of the central and peripheral clocks is essential to the fitness of the fly, yet different entraining factors in each tissue can lead to clock misalignment and unwanted metabolic changes. I seek to understand the underlying conditions and system dynamics during these periods of discordance and their impact on metabolic function.

Acknowledgements:        Cabell Fellowship
Collaborators:                  W. L. Kath
                                        R. Allada

Joseph J. Muldoon, Ph. D. candidate
email

Our body’s innate immune system is a tightrope walker, charged with the task of eliminating threats without overreacting or backfiring on us. This careful balancing act takes place across a range of health and disease processes. Among the key players are macrophages--equipped with an exquisite toolkit for monitoring their surroundings and a repertoire of secreted molecules to influence other cells. I use systems approaches to integrate experimental data with dynamical models to understand the mechanisms by which these cells walk the fine line between protecting us and doing harm.

Acknowledgements:        Biotechnology Training Program Cluster Award
Collaborators:                  J. N. Leonard

Alexis N. Prybutok
email

Alex Prybutok joined the lab in late 2016 as a Chemical and Biological Engineering graduate student co-advised by Dr. Neda Bagheri and Dr. Josh Leonard. She is interested in immunology, cellular responses to disease, and how cells function as a population.

Acknowledgements:        NSF Graduate Research Fellowship

Collaborators:                  J. N. Leonard

Jia J. Wu, Ph. D. candidate
email

How do cells adopt different cell fates during developmental processes? How is it that, as cells adopt these fates, they lose their ability to give rise to other cell types? Recent high-throughput experiments have described the architecture of the transcriptional regulatory networks responsible for hematopoiesis. My research focuses on delineating the transcriptional programs that regulate blood cell differentiation and the subsequent effects on downstream genes.

Acknowledgements:        Biotechnology Training Program Cluster Award
                                        National Science Foundation GK-12 Fellowship
                                        Ruth Kirchstein National Research Service Award
Collaborators:                 B. M. Miller
                                        L. D. Shea

Albert Y. Xue, Ph. D. candidate
email

Structure-activity relationships are an active area of study across multiple fields. Enzyme, nanoparticle, and peptide structure-activity relationships have remained limited due to lack of high-throughput methods. However, recent advances have allowed for high-throughput experimentation arrays to provide comprehensive datasets. I apply machine learning and cutting edge data visualization tools to understand and make predictions from these new datasets.

Acknowledgements:        Biotechnology Training Program Cluster Award
                                        NICO Data Science Research Support

Collaborators:                  M. Mrksich
                                        C. A. Mirkin
                                        P. Gerami

Jessica S. Yu, Ph. D. candidate
email

Agent-based modeling presents a unique modeling platform and approach to biological questions. The models are a natural representation of cells and cell interactions but, given its high computational demand, are still relatively new to the field. My work aims to develop agent-based models of tumor growth to better characterize and understand the dynamics of cancer. Specifically, my work focuses on the emergent properties of the tumors that develop from cancer cells that follow different proposed explanations for tumor heterogeneity.

Acknowledgements:        The Alumnae of Northwestern University
                                        NSF Graduate Research Fellowship
Collaborators:                  K. E. J. Tyo



External Collaborators

Jon D. Licht
Professor of Medicine
Director, UF Health Cancer Center
Marshall E. Rinker Sr. Foundation and David B and Leighan R. Rinker Chair
University of Florida

Lonnie D. Shea
Professor and William and Valerie Hall Chair, Department of Biomedical Engineering; Professor of Chemical Engineering
University of Michigan

Anne E. Todgham
Professor of Animal Physiology
University of California, Davis

Lars Tomanek
Professor of Biological Sciences
California Polytechnic State University




Internal Collaborators

Ravi Allada
Edward C. Stuntz distinguished professor and chair of Neurobiology
Feinberg School of Medicine
Northwestern University

Luís A. N. Amaral
Professor of Chemical and Biological Engineering
McCormick School of Engineering and Applied Science
Northwestern University

G. R. Scott Budinger
Professor in Medicine-Pulmonary and Cell and Molecular Biology
Weinberg College of Arts and Sciences
Northwestern University

Richard W. Carthew
Owen L. Coon Professor, Molecular Biosciences
Weinberg College of Arts and Sciences
Northwestern University

Pedram Gerami
Professor of Dermatology, Pathology, and Pediatrics
Feinberg School of Medicine
Northwestern University

Bill M. Kath
Professor of Engineering Science and Applied Math
McCormick School of Engineering and Applied Science
Northwestern University

Joshua N. Leonard
Professor of Chemical and Biological Engineering
McCormick School of Engineering and Applied Science
Northwestern University

Julius B. Lucks
Professor of Chemical and Biological Engineering
McCormick School of Engineering and Applied Science
Northwestern University

Madhav Mani
Professor of Engineering Science and Applied Math
McCormick School of Engineering and Applied Science
Northwestern University

Bill M. Miller
Professor of Chemical and Biological Engineering
Director of Master of Biotechnology Program
McCormick School of Engineering and Applied Science
Northwestern University

Alexander Misharin
Professor in Medicine-Pulmonary
Feinberg School of Medicine
Northwestern University

Milan Mrksich
Henry Wade Rogers Professor of Biomedical Engineering, Chemistry and Cell and Molecular Biology
McCormick School of Engineering and Applied Science
Northwestern University

Eva E. Redei
David Lawrence Stein Research Professor of Psychiatric Diseases Affecting Children and Adolescents; Psychiatry and Behavioral Sciences and Physiology
Feinberg School of Medicine
Northwestern University

Igal G. Szleifer
Professor of Chemical and Biological Engineering; Christina Enroth-Cugell Professor of Biomedical Engineering
McCormick School of Engineering and Applied Science
Northwestern University

Jacob I. Sznajder
Professor in Medicine-Pulmonary
Feinberg School of Medicine
Northwestern University

Keith E. J. Tyo
Professor of Chemical and Biological Engineering
McCormick School of Engineering and Applied Science
Northwestern University




Alumni

Dr. Tyrone J. Yacoub
Postdoc in Chemical & Biological Engineering

Acknowledgements:        Hartwell Foundation Postdoctoral Fellowship

M. Kasim Fassia, medical student at Michigan State University
M.S. in Biomedical Engineering

Dr. Mark F. Ciaccio, senior biology data scientist at AbbVie Biopharmaceuticals
Postdoc in Chemical & Biological Engineering
Acknowledgements:        Northwestern University Physical Science-Oncology Center
                                     Hartwell Foundation Postdoctoral Fellowship

Aaron D. Oppenheimer
M.S. in Chemical & Biological Engineering
Acknowledgements:        National Science Foundation GK-12 Fellowship

Maureen Ferries, process automation engineer with Dow AgroSciences
B.S. in Chemical & Biological Engineering