I am a postdoctoral researcher studying complex systems in the Complex Adaptive Systems & Computational Intelligence (CASCI) laboratory at Binghamton University. I have a math and physics background, and a focus on applications to systems biomedicine and computational social science.
Current work: complex systems science, network dynamics and control theory, systems biology and biomedicine
Previous work: galaxy modeling, airglow physics, differential geometry and Lie theory
I have a math and physics background, and a focus on applications to systems biology. My work is about studying how feedback loops underlie multistability in network models of complex systems, especially as applied to biomedical systems. Much of my work is about studying how feedback loops underlie multistability in network models of complex systems, and biomolecular systems in particular. I work on generalizing Boolean techniques to ODEs by considering how positive feedback loops in networks give rise to trap sets in phase space. I’ve used this framework to study attractor control of ODE models in various contexts, including the cell cycle regulation, pattern formation during embriogenesis, and immune cell signaling. I have studied attractor control of ODE models in cell cycle regulation, pattern formation during embriogenesis, and immune cell signaling. I am also interested in studying Boolean networks; I am the lead developer of the Python library pystablemotifs, which enables fast attractor identification and control in Boolean networks, and I have done work on the order-to-chaos transition in random Boolean networks. Recently, I have also been developing methods to sparsify multi-layer networks while taking into account multiple data sources. I am applying these methods to various problems in computational social science, health, and biomedical complexity.
Highlights: Understanding the biomolecular decisions that cells make
“Parity and time-reversal elucidate both decision-making in empirical models and attractor scaling in critical Boolean networks”
JC Rozum, JGT Zañudo, X Gan, D Deritei and R Albert
Science Advances 7 (29), eabf8124,2021
I led the development of the open-source Python library pystablemotifs, which provides one of the world’s fastest algorithms for attractor identification and control in Boolean networks. This library uses parity and time reversal provide new insights into the key regulatory circuits that underpin the biochemical “decisions” that cells make. We used this tool to identify the attractor repertoires of networks 80 times larger than ever before considered and thereby resolved a 50-year-old open problem about how stochasticity affects a cell’s diversity of phenotypes. This was the first time that stochastic genome-scale biomolecular models were analyzed in such detail. The results of our analysis showed that the behaviors of traditional random models of gene regulation are highly sensitive to stochasticity, suggesting biological selection pressures that are not accounted for in the canonical model.
See the relevant paper here, and a popular press summary here.
Highlights: Characterizing robust behaviors in cells
“Identifying (un) controllable dynamical behavior in complex networks”
JC Rozum and R Albert
PLoS Computational Biology 14 (12), 2018
I developed a formalism that allows one to identify positive feedback loops in ODE models that function in a manner analogous to the stable motifs of discrete models. I used this formalism to analyze the biomolecular decisions that lead to the formation of embryonic segments in the fly (Drosophila melanogaster) and to uncover a self-reinforcing feedback loop in the biomolecular circuitry that governs the response of T-cells to external signals. In both cases, I showed how my methods identify manipulations of the system that can disrupt observed phenotypes and manipulations that cannot. Apart from their utility in basic science research, observations of this nature have important potential applications in the development of pharmaceuticals because they can narrow the (often very expensive) search for potential drug targets.
See the relevant paper here.
Postdoctoral Researcher 2022-Present, Binghamton University (SUNY) Dept. of Systems Science and Industrial Engineering
I am a current member of the Complex Adaptive Systems & Computational Intelligence (CASCI) laboratory lead by Professor Luis Rocha. I work on developing new tools and algorithms for analyzing complex networks in a variety of domains, including social media, biomedical data, and systems biology.
Graduate Research Assistant 2016–2022, Pennsylvania State University Dept. of Physics
Developing new network control approaches that generalize methods for discrete dynamics to continuous ODE network models in collaboration with Professor Réka Albert. Apply network control theory to biological network models to better understand decision mechanisms in cellular systems, identify potential drug targets, and predict results of biological experiments.
Graduate Research Assistant 2014-2016, Utah State University Dept. of Mathematics
Classification of homogeneous space-times according to their symmetries as part of Master’s Thesis advised by Professor Ian Anderson and Professor Charles Torre. Devised a new coordinate-free classification scheme for Lie algebras of a certain type relevant to homogeneous solutions to the Einstein equations and implemented the classification using the DifferentialGeometry package of the computer algebra system Maple.
Undergraduate Researcher, 2011-2014, Utah State University Dept. of Electrical Engineering
Data validation for the SABER (Sounding of the Atmosphere using Broadband Emission Radiometry) satellite instrument in collaboration with Professor Gene Ware and Professor Doran Baker. Analyzed SABER data, and maintained the USU copy of the database. Focused on perceived bifurcation of hydroxyl airglow layer in the mesosphere.
Undergraduate Research Fellow, 2010-2014, Utah State University Dept. of Physics
Examining bias in galaxy catalogs due to galaxy geometry in collaboration with Professor Shane Larson as part of USU’s Undergraduate Research Fellowship. Wrote computer simulations of galaxy surface brightness. Performed statistical analyses of galaxy catalogs to search for possible indications of observation bias.
Ph.D. in Physics from Pennsylvania State University, 2022
- Concentration: Network biophysics and dynamical systems
- Dissertation: Attractor identification and control of Boolean and ODE network models in Systems Biology
- Advisor: Professor Réka Albert
Master’s in Mathematics from Utah State University, 2016
- Concentration: Mathematical physics and differential geometry
- Thesis: Classification of Five-dimensional Lie Algebras with One-dimensional Subalgebras Acting as Subalgebras of the Lorentz Algebra
- Advisors: Professor Ian Anderson and Professor Charles Torre
Bachelor’s in Physics and Mathematics from Utah State University, 2014
- Magna Cum Laude
- Capstone project: Analyzing solutions to the Einstein equations using the Maple package DifferentialGeometry
Honors, Awards, and Society Memberships
- PSU ICDS Featured Researcher (link), 2021
- PSU Peter Eklund Memorial Lectureship Award Honorable Mention, 2019-2020
- PSU David Duncan Graduate Fellowship ($1650), 2019
- PSU Department of Physics David H. Rank Memorial Award ($1200), 2017
- PSU College of Science Roberts Scholarship Award ($2000), 2016
- USU Magna Cum Laude, 2014
- USU Physics Department Outstanding Senior, 2014
- Barry M. Goldwater Scholar ($7500), 2013
- Barry M. Goldwater Scholarship Honorable Mention, 2012
- USU A-Pin Award for Consecutive 4.0 Semesters, 2010-2014
- USU Undergraduate Research Fellow ($4000), 2010-2014
- USU Presidential Scholar (tuition & fees, approx. $40,000), 2010-2014
- Sigma Pi Sigma honor society member
- NetSci member
Teaching Assistant, Pennsylvania State University Department of Mathematics 2016-2017
Course: Introductory Classical Mechanics
Course Instructor, Utah State University 2015
Course: Advanced Calculus
Teaching Assistant, Utah State University Department of Mathematics 2015
Courses: Introductory College Algebra
Teaching Assistant, Utah State University Department of Physics 2013-2014
Courses: Introductory Physics I and II
Undergraduate Teaching Fellow, Utah State University 2011-2013
Courses: Classical Mechanics, Electromagnetism I and II
Programming expertise in Python, familiarity in C++, CUDA, Octave, R, Sage, others
Lead developer of pystablemotifs (Python) and cubewalkers (Python+CUDA) libraries
Expertise in network science and discrete dynamical modeling
Strong background in mathematics and algorithm development
Experience with high-performance computing and managing large datasets
JC Rozum and R Albert. Leveraging network structure in nonlinear control. npj Systems Biology and Applications 8, 36 (2022)
JC Rozum. Attractor identification and control of Boolean and ODE network models in Systems Biology. PhD Dissertation in Physics, Pennsylvania State University (2022)
JC Rozum, D Deritei, KH Park, JGT Zañudo, R Albert. pystablemotifs: Python library for attractor identification and control in Boolean networks. Bioinformatics 38 (5), btab825 (2021)
JC Rozum, JGT Zañudo, X Gan, D Deritei and R Albert. Parity and time-reversal elucidate both decision-making in empirical models and attractor scaling in critical Boolean networks. Science Advances 7 (29), eabf8124 (2021)
JC Rozum and R Albert. Controlling the cell cycle restriction switch across the information gradient. Advances in Complex Systems 22 (07n08), 1950020 (2020)
D Deritei, JC Rozum, E Ravasz Regan, R Albert. A feedback loop of conditionally stable circuits drives the cell cycle from checkpoint to checkpoint. Scientific Reports 9 16430 (2019)
JC Rozum and R Albert. Identifying (un) controllable dynamical behavior in complex networks. PLoS Computational Biology 14 (12) (2018)
JC Rozum and R Albert. Self-sustaining positive feedback loops in discrete and continuous systems. Journal of Theoretical Biology 459 35-44 (2018)
JC Rozum. Classification of Five-dimensional Lie Algebras with One-dimensional Subalgebras Acting as Subalgebras of the Lorentz Algebra. Master’s Thesis in Mathematics, Utah State University (2015)
J Price, JC Rozum, G Ware, and D Baker. Global Nightly OH and O2 Mesospheric Airglow: Examining a Decade of Measurements Using the NASA SABER Satellite Sensor. Journal of the Utah Academy of Sciences, Arts, and Letters, 91 (2014)
Selected Talks and Poster Presentations
JC Rozum, JGT Zañudo, X Gan, D Deritei and R Albert. Parity and time-reversal in Boolean networks. Poster presented at the Cold Spring Harbor Laboratory Cellular Dyanamics and Models meeting, May 19-21, 2021.
JC Rozum. Boolean Networks: discrete dynamical models of high-dimensional nonlinear systems. Invited talk given at the University of Pennsylvania Mathematical Biology Seminar, Apr. 6, 2021.
JC Rozum, JGT Zañudo, X Gan, and R Albert. Parity and time-reversal in Boolean networks. Talk given at the NetSci 2020 meeting, Rome, Italy (remote), Sep. 25, 2020
JC Rozum and R Albert. Control robust trap spaces with applications to biomolecular networks. Talk given at the NetSci 2019 meeting, Burlington, VT, May 29, 2019
JC Rozum and R Albert. Identifying (un)controllable dynamical behavior with applications to biomolecular networks. Invited talk given at Pennsylvania State University Theoretical biology seminar, State College, PA, Feb. 20, 2018
JC Rozum and SL Larson. Modeling spiral galaxy surface luminosity to explain non-uniform inclination distributions. Poster presented at AAS National Conference, Washington D.C., Jan. 5, 2014
JC Rozum, GA. Ware, DJ Baker, MG Mlynczak, J Russell. Multiple peaks in SABER mesospheric OH emission altitude profiles. Poster presented at AGU Fall Meeting, San Francisco, CA, Dec. 4, 2012