Clinical Systems Biology

General Content

Clinical Systems Biology Team

Research Leadership and Staff

  • Gordon Broderick, Ph.D.

    Gordon Broderick, Ph.D.

    Director and Principal Investigator, Clinical Systems Biology – Research Associate Professor, Dept. of Biomedical Engineering, Rochester Institute of TechnologyAdjunct Professor, Thomas H. Gosnell School of Life Sciences (GSoLS), Rochester Institute of TechnologyAdjunct Professor, Dept. of Psychology and Neuroscience, Nova Southeastern UniversityAdjunct Associate Professor, Dept. of Medicine, University of AlbertaAn engineer by training, Gordon Broderick, Ph.D., holds a doctorate in chemical engineering from the University of Montreal as well as a master's in chemical engineering and an undergraduate in mechanical engineering, both from McGill University.He completed post-doctoral training at McGill’s School of Computer Science in cancer genomics and a research fellowship in computational biochemistry at the University of Alberta, where he led a high-performance computing effort in modeling the molecular dynamics of intracellular life. Building on this study of complex emergent behavior in biology, Dr. Broderick’s current research efforts focus primarily on the emerging field of computational immunology and on how an integrated systems perspective might improve our understanding of immune dysfunction and autoimmunity in complex multi-system illness.This work is funded under a number of grants from the U.S. Department of Defense (CDMRP), the National Institutes of Health (NIH) and the U.S. Department of Veterans Affairs.A member of the editorial board for the new journal Systems Biomedicine (Taylor & Francis), Dr. Broderick also contributes as an associate editor to the journal BMC Systems Biology.Dr. Broderick recently moved his research from the University of Alberta and Nova Southeastern University to join the research community at RGH in developing new initiatives in the area of translational and computational medicine. The new Center will bring together a truly cross-disciplinary mix of investigators from the computational, clinical and basic life sciences with the goal of developing immune and hormone-based therapies for complex illnesses that are both safe and effective.

    Link to ReasearchGate
  • Sol Efroni, Ph.D

    Sol Efroni, Ph.D

    Associate Director, Clinical Systems Biology (Visiting Scientist) – Dr. Efroni is a distinguished Visiting Scientist; he is an Associate Professor at The Mina & Everard Goodman Faculty of Life Sciences, Bar Ilan University, Israel.He received his PhD from the Weizmann Institute and completed his post-doctoral work at the National Cancer Institute at the National Institutes of Health in Maryland. He returned to Israel to Bar Ilan University, where he now heads the Systems BioMedicine LabDr. Efroni has contributed significantly to the field of systems biomedicine, having designed and implemented an approach now known as Reactive Animation that facilitates the visual, computer legible and intuitive simulation of complex multi-agent systems through reactive technology of reactive animation. RA allows the experimenter to intervene mid-simulation, suggest new hypotheses for cellular and molecular interactions, apply them to the simulation and observe their resulting outcomes online. He has pioneered the use of these techniques to the modeling of cellular pathway logic, in particular in understanding various cancers. He has published extensively in Cell and Nature, and maintains ongoing research partnerships with colleagues at Harvard, MIT and the NIH.MORE

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  • Cole Lyman, B.S.

    Cole Lyman., Chief Programmer, Team Leader, Computation – Cole Lyman is a graduate of Brigham Young University (BYU) with a B.Sc. in Computer Science where he specialized in bioinformatics and computational biology. He is currently completing his M.Sc. in Computer Science, also at BYU, where under the direction of Dr. Mark Clement he extended network theoretical aspects of Colored de Bruijn Graphs, developing novel applications to whole genome alignment, phylogenetic tree reconstruction, and genome wide association maps. Experienced in analyzing vast amounts of genomic data, he is well-versed in the design of distributed algorithms and will oversee the CCSB’s high-performance computing with alliance partner RIT, as well as new computing resources at the University of Buffalo’s Center for Computational Research (CCR). Leveraging his knowledge of these platforms he will focus on the development of robust and highly efficient code supporting the identification and simulation of complex biological regulatory networks such that code design is optimally suited for these large-scale computing resources. 

  •  Matt Morris, Ph. D.

    Team Leader, Bio-modeling – Dr. Morris is a research scientist with expertise in immunology, molecular biology, and computer science. At Virginia Tech, he studied intracellular signaling dynamics governing the innate immune response to bacterial endotoxin. At RGH, he has focused on mucosal immunology in children, including adaptive responses in the tonsils and adenoids and neutrophil responses in the nasopharynx. In the Clinical Systems Biology group, he applies an interdisciplinary skill set that spans applied computation, cellular and molecular biology to construct executable network models of living systems. He is currently active in developing comprehensive network models of signal transduction pathways as they apply to neurotoxic exposure, in collaboration with colleagues at the CDC NIOSH, as well as overseeing new initiatives in modeling cell-cell signaling mechanisms at various levels of biology ranging from molecular to organ systems as they apply to cancer biology, vaccine immunology and endocrine-immune disorders.

  • Jonathan Tory Toole

    Jonathan Tory Toole, M.S.

    Team Leader, Behavioral Systems (Visiting Scientist) – Jonathan Tory Toole is originally from Georgia where he completed bachelors’ degrees in psychology and religion at the University of Georgia. He also holds Master’s degree in General Psychology from New York University (NYU), where he studied fear memory reconsolidation and pain processing. He is currently completing his Ph.D. in Clinical Psychology at Nova Southeastern University’s (NSU) College of Psychology and continues his work with the Broderick group in computational psychoneuroimmunology (PNI). Over the past 3 years he has brought his extensive background in clinical psychology to the team and become a key contributor to the integration of symptom severity constructs into multilevel models that bridge the molecular and cellular realms with symptom burden. He has used these models to study the characteristic network biology and bio-behavioral dynamics of complex chronic illnesses such as Gulf War illness (GWI) and Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), bringing a new perspective to understanding the molecular underpinnings of symptomatology and developing more effective treatment approaches.

Students

  • Spencer Richman, B.S.

    Spencer Richman (B.S. / M.S. Bioinformatics, Senior, RIT). Spencer is completing a dual B.S. and M.S. degree in Bioinformatics at the Rochester Institute of Technology. His work focuses on the integration of pharmacological databases with drug target information derived from computational models of biological signaling at the intracellular and cellular levels as they apply to various complex chronic immune and endocrine disorders. Bringing to bear information about drug availability, contraindications and off-target effects through advanced applications of natural language processing, Spencer is developing novel criteria and methods to assess the accessibility of predicted treatment targets to drug repurposing strategies and their actionability in a clinical setting.

  • Kimberly Dautel

    Kimberly Dautel, B.S.

    (PhD, Mathematical Modeling, 2nd year, RIT). Kim is completing her PhD in Mathematical Modeling at Rochester Institute of Technology. She will be studying numerical approaches for capturing the complex kinetics of broad families of interacting cellular and molecular markers and their in vivo response to challenge. Her objective is to assess various functional forms for these kinetics and refine a mathematically rigorous means of representing these large sets of coupled differential equations as network structures that may be compared across illness states. Applied to surveys of immune signaling under infectious or physiological challenge, changes in the topological properties of such networks will help advance our understanding of the biological mechanisms that underlie complex chronic immune disorders like COPD, ME/CFS and Gulf War Illness.

Collaborators

  • Joel Zysman, Center for Computational Science (CCS) – U Miami
  • Dr. Patrick McGowan – U Toronto (Canada)
  • Drs. Jim O’Callaghan / Diane Miller - CDC NIOSH - Neurotoxicology group
  • Dr. Dane Cook – U Wisconsin Madison
  • Dr. Ross Tsuyuki – U Alberta (Canada)
  • Dr. Eileen Shinn – MD Anderson Cancer Center
  • Drs. Sanjay Sethi, Peter Elkin, SUNY at Buffalo
  • Dr. Darrell Whitley, Colorado State University
  • Drs. Nancy Klimas, Mary Ann Fletcher, Mariana Morris, Miami VA Medical Center
  • Drs. Travis Craddock, Barry Nierenberg, College of Psychology, Nova Southeastern University

Partners/Funders

  • Center for Computational Science - University of Miami
  • Congressionally Directed Medical Research Projects (CDMRP) - Dept. of Defense
  • Department of Veterans Affairs
  • National Institutes of Health

Alumni

  • 2018-2019 Jeselle Clark (BSc/ MSc, Bioinformatics, Rochester Institute of Technology, 2019), Research Intern/ MSc candidate, "Simulating Pathway-Based Steady States to Prevent Epithelial-Mesenchymal Transition in Ovarian Cancer"

  • 2017-2018 Katherine Cooney (B.Sc., Biotechnology, Rochester Institute of Technology, 2018) Research intern, “A Regulatory Logic Map of Endocrine-immune Control in Female Physiology".

  • 2012-2018 Mark Rice (B.Sc.), Chief Programmer, Broderick Lab, distinguished contributor to multiple DOD, VA and NIH initiatives in veteran's and women's health and key designer of the logic network paradigm and executable biology initiative. 

  • 2012-2017 Saurabh Vashishtha (M.S.), Ph.D. candidate, Broderick Lab, Dept. of Medicine, University of Alberta Graduate student research assistant “Dynamic Network Models of Response to Challenge in Complex Endocrine-immune illnesses”

  • 2014 Samuel Thomas (B.S., Behavioral Neuroscience, Nova Southeastern University, 2015) Research intern “A Biobehavioral Study of the Effects of Psychological Stress on the Sleep Patterns of Female College Students"

  • 2013-2015 Jeanna Harvey (B.A. Distinction, M.D., University of Miami, 2015). Research intern. “Mechanisms of Immune-endocrine Interaction in Episodic Exacerbation of Chronic Fatigue Syndrome”

  • 2014, 2016 Shane Hills (B.S. Physics, Queen’s University, 2012) Research intern “Mapping Neurological Response to Exercise Challenge in Gulf War Illness”

  • 2013 Lundy McKibbin (B.S. Distinction, M.D. student, class of 2016) Research intern “A study of the effects of PTSD co-morbidity on immune signature in Gulf War Illness”

  • 2013 Simar Singh (M.S. Distinction, Stanford University)Graduate research assistant “A study of neuro-inflammatory mechanisms in Gulf War Illness”

  • 2013 Alanna Bowie (B.S. Distinction, M.D. student, class of 2016). Research intern.“Prognostic Clinical Markers for Early Detection Chronic Sequela from Infectious Mononucleosis”

  • 2013 Melissa Hwang (B.S. Distinction, M.D. student, class of 2016). Research intern. “Mechanisms of Immune-endocrine Interaction in Episodic Exacerbation of Chronic Fatigue Syndrome”

  • 2012-2013 T. Craddock, Ph.D. (Ph.D., 2011). Research fellow. “Integrated Control and Multi-stability of the Fight or Flight Axis”

  • 2012 AnneLiese Smylie (B.S. Honours, M.D., 2015). Research intern.“A Cytokine-based Screening Test for Gulf War Illness”

  • 2012 Henrique Fernandes (B.Eng. Distinction, M.D., 2015). Research intern.“Identifying Common Molecular Traits and Emergent Patient Sub-groups in Chronic Fatigue Syndrome”

  • 2011- Jeanna Harvey (B.S., M.D. University of Miami, 2015). Research intern.“Exercise Induced Immune Gene Expression in Gulf War Illness”

  • 2010-2011 Scott De Graff (B.S., M.D., 2012). Research intern.“Models for Cardiovascular Dysregulation in Chronic Fatigue Syndrome”

  • 2009 Christina Yang (M.S., M.D., 2011). Research intern.“A Study of Cognitive Deficits in Patients with Chronic Fatigue Syndrome”

  • 2009 Andrea Kreitz (B.S., M.D., 2011). Research intern.“Emergent Patterns of Cytokine Expression in Chronic Fatigue Syndrome and Gulf War Illness”

  • 2008-2009 Michael Gallagher (M.D. student, class of 2010). Research intern.“Immune Biomarkers in Gulf War Syndrome” 

  • 2007-2010 J Fuite, Ph.D. (Ph.D., 2008). Research fellow."Network Theoretical Study of Neuro-immune Deficiency in Chronic Fatigue and Gulf War Illness"

  • 2007 Ann Aspler (M.S.) (M.D., 2010). Research intern. “Evidence of Altered Neuroendocrine-immune Function in a Population-based Study of Chronic Fatigue Syndrome”

  • 2007 Carly Bolshin (B.S.) (M.D., 2010). Research intern.“Evidence of Altered Neuroendocrine-immune Function in a Population-based Study of Chronic Fatigue Syndrome”