PhD Candidate, Systems Biology
T32 Trainee in Sleep, Circadian, and Respiratory Neurobiology
Harvard Medical School/Brigham and Women’s Hospital
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.
M.S. Chemical Engineering, UC Santa Barbara, 2015
B.S. Chemical Engineering, Tufts University, 2013
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.
johnhabel (at) g (dot) harvard (dot) edu
V Carmona-Alcocer, JH Abel, TC Sun, LR Petzold, FJ Doyle III, CL Simms, ED Herzog. “Ontogeny of circadian rhythms and synchrony in the suprachiasmatic nucleus,” Journal of Neuroscience, 2017. doi:10.1523/JNEUROSCI.2006-17.2017
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
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
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
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
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]
S. Jung, J.H. Abel, Starger, H. Yi, Biomacromolecules, 2016. DOI: 10.1021/acs.biomac.6b00582.
E. Kang, S. Jung, J.H. Abel, A. Pine, H. Yi, Langmuir, 32(21): 5394-402, 2016. doi: 10.1021/acs.langmuir.5b04653
- Mapping the circuit of our internal clock
Harvard SEAS: “Research sheds light the neural structure that controls our sleep, eating habits, hormones and more.” See within for press from our most recent study of the circadian clock. Harvard SEAS: here UCSB Current: here This has been featured elsewhere, including: ExtremeTech The Daily Mail
- ExtremeTech: Scientists nail down the network topology of the circadian clock
- ScienceDaily: Researchers reveal, to single-cell resolution, the network of circadian neurons
While the overall effects of circadian activities have been studied, relatively little is understood about the structure of the network of brain cells as they communicate to control the synchronization process. In a paper that appears in the Proceedings of the National Academy of Sciences, UC Santa Barbara [and Harvard!] researchers and collaborators infer the […]