February 25, 2014 Read More →

John Abel

John Abel

PhD Candidate, Systems Biology
Harvard University

T32 Trainee in Sleep, Circadian, and Respiratory Neurobiology
Harvard Medical School/Brigham and Women’s Hospital

Research

The circadian oscillator is a biological control system designed to regulate gene expression in a 24-hour periodic environment. The gene regulatory network comprising the circadian oscillator may be modeled through systems of coupled chemical reactions. Mathematically, these reactions may be described as a set of coupled nonlinear ordinary differential equations. In systems with low molecular counts, such as at a cellular level, deterministic modeling does not capture the effects of intrinsic molecular noise. My work involves the use of ODE and stochastic models, and dynamical systems and control theory, to understand and manipulate the mammalian circadian oscillator.

Education

M.S. Chemical Engineering, UC Santa Barbara, 2015
B.S. Chemical Engineering, Tufts University, 2013

Software

GillesPy: a Python package for stochastic model building and simulation
GillesPy is a modeling toolkit for discrete stochastic simulations of biochemical systems authored by myself, Brian Drawert (UCSB), Andreas Hellander (Uppsala University), and Linda Petzold (UCSB). GillesPy uses the StochKit2 solvers including the optimized direct method and tau-leaping to perform stochastic simulations. See the link above for installation instructions and examples.

Contact

johnhabel (at) g (dot) harvard (dot) edu

Publications
GillesPy: a Python package for stochastic model building and simulation
J.H. Abel, B. Drawert, A. Hellander, and L.R. Petzold, “GillesPy: a Python package for stochastic model building and simulation,” IEEE Life Sciences Letters, 2017. doi: 10.1109/LLS.2017.2652448
A systems theoretic approach to analysis and control of mammalian circadian dynamics
J.H. Abel and F.J. Doyle III. “A systems theoretic approach to analysis and control of mammalian circadian dynamics.” Chemical Engineering Research and Design, 2016. doi:10.1016/j.cherd.2016.09.033
Functional network inference of the suprachiasmatic nucleus
J.H. Abel, K. Meeker, D. Granados-Fuentes, P.C. St. John, T.J. Wang, B.B. Bales, F.J. Doyle III, E.D. Herzog, L.R. Petzold. “Functional network inference of the suprachiasmatic nucleus.” Proceedings of the National Academy of Sciences of the United States of America, 113(16), 2016. doi:10.1073/pnas.1521178113
A Coupled Stochastic Model Explains Differences in Cry Knockout Behavior
J.H. Abel, L.A. Widmer, P.C. St. John, J. Stelling, and F.J. Doyle III, ” A Coupled Stochastic Model Explains Differences in Cry Knockout Behavior.” IEEE Life Sciences Letters, Jun 2015. doi:10.1109/LLS.2015.2439498
Amplitude metrics for cellular circadian bioluminescence reporters
P.C. St John, S.R. Taylor, J.H. Abel, F.J. Doyle III, “Amplitude metrics for cellular circadian bioluminescence reporters,” Biophysical Journal, vol. 107, no. 11, pp. 2712-22,Dec 2014. [DOI]
Porosity-Tuned Chitosan-Polyacrylamide Hydrogel Microspheres for Improved Protein Conjugation.
S. Jung, J.H. Abel, Starger, H. Yi, Biomacromolecules, 2016. DOI: 10.1021/acs.biomac.6b00582.
Shape-Encoded Chitosan-Polyacrylamide Hybrid Hydrogel Microparticles with Controlled Macroporous Structures via Replica Molding for Programmable Biomacromolecular Conjugation.
E. Kang, S. Jung, J.H. Abel, A. Pine, H. Yi, Langmuir, 32(21): 5394-402, 2016. doi: 10.1021/acs.langmuir.5b04653
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