Principal Investigator

Neda Bagheri, Ph. D.

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



Postdocs

Tyrone J. Yacoub, Ph. D.
email

Ty joined the lab in Fall 2015. He is interested in developing novel methods to analyze RNA-seq (gene expression) data in order to investigate the genetic causes of aging in mice. He is working closely with a group in Prof. Igal Szleifer's lab to develop a pipeline for translating raw RNA-seq data into meaningful insight.

Acknowledgements:        Hartwell Foundation Postdoctoral Fellowship

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
email

Sebastian joined the lab in late 2014 as a chemical engineering graduate student co-advised by Professors Amaral and Bagheri. His research interests span a wide variety of topics from sustainability to complex systems, and he is currently in the early stages of developing a social network analysis project.

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

Joshua I. Levy
email

Josh joined the lab in late 2016. He is a graduate student in the department of Engineering Science and Applied Mathematics and is co-advised by Professors Bagheri and Kath. He is interested in network inference problems related to circadian dynamics and immune system regulation.

Acknowledgements:        Cabell Fellowship

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 undertand the mechanisms by which these cells walk the fine line between protecting us and doing harm.

Acknowledgements:        Biotechnology Training Program Cluster Award

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

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

Albert Y. Xue, Ph. D. candidate
email

Large macromolecules that catalyze chemical reactions have yet to be fully understood, and enzyme characterization has remained limited due to lack of high-throughput methods. Recent advances can measure enzyme activity on high-throughput peptide arrays and provide comprehensive datasets. I am enabling greater control over enzyme characteristics and targets by applying machine learning tools to investigate and predict peptide-enzyme binding patterns.

Acknowledgements:        Biotechnology Training Program Cluster Award

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



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

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
Feinberg School of Medicine
Northwestern University

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

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

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