Publications
Journal articles
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P. W. Sheppard, M. Rathinam, and M. Khammash.
SPSens: A software package for stochastic parameter sensitivity analysis of stochastic biochemical reaction networks.
Accepted for publication in Bioinformatics. [DOI]
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P. W. Sheppard, M. Rathinam, and M. Khammash.
A pathwise derivative approach to the computation of parameter sensitivities in discrete stochastic chemical systems.
Journal of Chemical Physics, 136(3), 034115, 2012. [DOI]
[PDF*]
Copyright 2012 American Institute of Physics.
This article appeared in Journal of Chemical Physics and may be found at this link.
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P. W. Sheppard, X. Sun, J. F. Emery, R. G. Giffard, and M. Khammash.
Quantitative characterization and analysis of the dynamic NF-κB response in microglia.
BMC Bioinformatics, 12: 276, 2011. [DOI]
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M. Rathinam, P. W. Sheppard, and M. Khammash.
Efficient computation of parameter sensitivities of discrete stochastic chemical reaction networks.
Journal of Chemical Physics, 132(3), 034103, 2010 [DOI]
[PDF*]
Copyright 2010 American Institute of Physics.
This article appeared in Journal of Chemical Physics and may be found at this link.
*These articles may be downloaded for personal use only.
Any other use requires prior permission of the author and the American Institute of Physics.
Conference posters
- Efficient parametric sensitivity analysis in stochastic biochemical reaction networks. ICSB, Edinburgh, Scotland, (2010).
- Using mathematical modeling to explore mechanisms for modulating inflammation signaling in glial cells, ICSB, Edinburgh, Scotland (2010).
- Computational modeling of the Regulation the Inflammatory Signaling Pathway in Microglia. The International Conference on Systems Biology, 2009, Stanford, CA, September 1, 2009. [abstract]
- Low variability estimators for sensitivity analysis of stochastic biochemical networks. 3rd q-bio Conference on Cellular Information Processing, Santa Fe, NM, August 8, 2009. [abstract]
- Computational modeling of stress response pathways in glial cells. Neuroscience 2008, Washington D.C., November 15-19, 2008.
- Modeling and analysis of the cellular response to ischemia: a systems biology approach. 2008 IGERT Project Meeting, Washington, DC. [abstract]
- A Computational Model of Apoptosis and Inflammation Signaling in Microglia. The 2007 International Conference on Systems Biology, Long Beach, CA, September 2007. [abstract]
Class projects