Publications
Feature publications
A genetic mammalian proportional-integral feedback control circuit for robust and precise gene regulation
Timothy Frei, Ching-Hsiang Chang, Maurice Filo, Asterios Arampatzis, and Mustafa Khammash. Proceedings of the National Academy of Sciences (2022) (external page DOI: 10.1073/pnas.2122132119).
A Class of Simple Biomolecular Antithetic Proportional-Integral-Derivative Controllers
Maurice Filo and Mustafa Khammash. Nature Communications (in press). Currently found in external page bioRxiv.
Synthetic gene networks recapitulate dynamic signal decoding and differential gene expression
Dirk Benzinger, Serguei Ovinnikov, Mustafa Khammash. Cell Systems (2022).
external page DOI: 10.1016/j.cels.2022.02.004
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Publications by year
Publications earlier than 20122011
S.H. Dandach and M. Khammash, "external page Analysis of Stochastic Strategies in bacterial competence: a master equation approach,'' PLoS Computational Biology, 6(11), 2011.
C. Pahlajani, P. Atzberger, and M. Khammash, "external page Stochastic Reduction Method for Biological Chemical Kinetics Using Time-Scale Separation,'' Journal of Theoretical Biology, Vol. 272, Issue 1, pp. 96-112, 2011.
A. Milias-Argeitis, S. Summers, J. Stewart-Ornstein, I. Zuleta, D. Pincus, H. El-Samad, M. Khammash, and J. Lygeros. "external page In silico feedback for in vivo regulation of a gene expression circuit," Nature Biotechnology, 2011.
P. Sheppard, X. Sun, J. Emery, R. Giffard, and M. Khammash, "external page Quantitative characterization and analysis of the dynamic NF-kappaB response in microglia", BMC Bioinformatics, 12:276, 2011.
2010
Brian Munsky and Mustafa Khammash, "external page Identification of a Stochastic Model for the Genetic Toggle Switch," IET Systems Biology, 4, No. 6, 356-366, 2010.
G. Lillacci and Mustafa Khammash, "external page Parameter Estimation and Model Selection in Computational Biology," PLos Computational Biology, 6(3), e1000696, 2010.
B. Drawert, M. Lawson, L. Petzold, and Mustafa Khammash, "external page The Diffusive Finite State Projection Algorithm for Efficient Simulation of the Stochastic Reaction-Diffusion Master Equation," Journal of Chemical Physics, Vol. 132, No. 7, 074101, 2010.
M. Rathinam, P. Sheppard, and M. Khammash, "external page Efficient Computation of Parameter Sensitivities of Discrete Stochastic Chemical Reaction Networks," Journal of Chemical Physics, Vol. 132, 034103, January 2010.
H. El-Samad and M. Khammash, "external page Modelling and Analysis of Gene Regulatory Networks Using Feedback Control Theory," Int'l Journal of System Science, Vol. 14, pp. 17-33, 2010.
2009
B. Munsky, B. Trinh, and M. Khammash, "Listening to the Noise: Random Fluctuations Reveal Gene Network Parameters," Molecular Systems Biology, EMBO/Nature, Vol. 5, p. 318, 2009. (Leon Heller Postdoctoral Publication Prize in Theoretical Physics) (doi:10.1038/msb.2009.75)
2008
B. Munsky and M. Khammash, "Transient Analysis of Stochastic Switches and Trajectories with Applications to Gene Regulatory Networks," IET Systems Biology, Vol. 2, No. 5, pp. 323-333, 2008. (doi:10.1049/iet-syb:20070082)
M. Khammash, "Reverse Engineering: The Architecture of Biological Networks," Bio Techniques, Vol. 44, No. 3, pp. 323-329, March 2008. (doi:10.2144/000112772)
B. Munsky and M. Khammash, "The Finite State Projection Approach for the Analyses of Stochastic Noise in Gene Networks," IEEE Transactions on Automatic Control, and IEEE Transactions on Circuits and Systems I, Joint Special Issue on Systems Biology, Vol. 53, pp. 201-214, 2008.
K. Purvis, K. Astrom, and M. Khammash, "Estimation and Optimal Configuration for Localization Using Cooperative UAVs," IEEE Transactions on Control Systems Technology, Vol. 16, No. 5, pp. 947-958, 2008.
2007
B. Munsky and M. Khammash, "A Multiple Time Interval Finite State Projection Algorithm for the Solution to the Chemical Master Equation," Journal of Computational Physics, Vol. 226, No. 1, pp. 818-835, 2007.
B. Munsky and M. Khammash, "Analysis of Noise Induced Stochastic Fluctuations in Gene Regulatory Networks," Journal of the Society of Instrument and Control Engineers (SICE), 2007.
2006
Slaven Peles, Brian Munsky and Mustafa Khammash, "Reduction and Solution of the Chemical Master Equation Using Time-Scale Separation and Finite State Projection," Journal of Chemical Physics, 125 (22), 503646, December 2006.
Brian Munsky and Mustafa Khammash, "The Finite State Projection Algorithm for the Solution of the Chemical Master Equation," Journal of Chemical Physics, Vol. 124, 044104, 2006.
H. Kurata, H. El-Samad, R. Iwasaki, H. Ohtake, J. C. Doyle, I. Grigorova, C. Gross, and M. Khammash, "Module-Based Analysis of Robustness, Tradeoffs in the Heat Shock Response System," PLoS Comuptational Biology, 2006.
Hana El-Samad, Stephen Prajna, Antonis Papachristodoulou, John Doyle, and Mustafa Khammash, "Advanced Methods and Algorithms for Biological Networks Analysis,” Proceedings of the IEEE, Vol. 94, No. 4, April 2006.
Hana El Samad, and Mustafa Khammash, "Regulated Degradation is a Mechanism for Suppressing Stochastic Fluctuations in Gene Regulatory Networks," Biophysical Journal, Vol. 90, pp. 3749-3761, 2006.
2005
H. El-Samad, H. Kurata, J. C. Doyle, C. Gross, and M. Khammash, "Surviving Heat Shock: Control Strategies for Robustness and Performance," Proceedings of the National Academy of Sciences (PNAS), Vol. 102, No. 8, pp. 2736-2741, 2005.
Hana El Samad, Mustafa Khammash, Linda Petzold, and Dan Gillespie, "Stochastic Modeling of Gene Regulatory Networks," International Journal of Robust Nonlinear Control, Vol. 15, pp691–711, 2005.
2004
M. Khammash and H. El Samad, "Systems Biology: From Physiology to Gene Regulation," IEEE Control Systems Magazine, Vol. 24, No. 4, pp. 62-76, 2004.
Xin Qi, Murti V. Salapaka, Petros G. Voulgaris, and M. Khammash, "Structured Optimal and Robust Control with Multiple Criteria: A Convex Solution,” Transactions on Automatic Control, 2004.
Wenzheng Qiu, Vijay Vittal, and Mustafa Khammash, “Decentralized Power System Stabilizer Design using Linear Parameter Varying Approach,” IEEE Transactions on Power Systems, 2004.
2003
M. Khammash, "l1 Robust Control," UNESCO Encyclopedia of Life Support Systems (EOLSS), edited by Heinz Unvehauen, developed under the auspices of the UNESCO, Eolss Publishers, Oxford, U.K. 2003.
P.O. Malaterre and M. Khammash, "l1 Controller Design for a High-Order 5-Pool Irrigation Canal System," ASME Journel of Dynamic Systems Measurement and Control, Vol. 125, No. 4, pp. 639-645, 2003.
C. Zhu, Mustafa Khammash, V. Vittal, and W. Qiu, “Robust Power System Stabilizer Design Using H-Infinity Loop Shaping Approach,” IEEE Transactions on Power Systems, Vol. 18, No. 2, pp. 810-818, 2003.
2002
H. El-Samad, J. Goff and Mustafa Khammash, "Calcium Homeostasis and Parturient Hypocalcemia: An Integral Feedback Perspective," Journal of Theoretical Biology, Vol. 17, No. 29, p. 214, 2002.
2001
M. Khammash and L. Zou, "Analysis of Steady-State Tracking Errors in Sampled-Data Systems with Uncertainty," Automatica, Vol. 37, No. 6, 2001. (doi)
M. Khammash, M. Salapaka, and T. Van Voorhis, "Robust Synthesis in l1: A Globally Optimal Solution," IEEE Transactions on Automatic Control, Vol. 46, No. 11, pp. 1744-1754, 2001.
X. Yu, Mustafa Khammash, and V. Vittal, “Robust Damping Controller Synthesis for Static Var Compensators in Power Systems,” IEEE Transactions on Power Systems, Vol. 16, No. 3, pp. 456-462, 2001. (doi)
2000
M. Khammash, "A New Approach to the Solution of the l1 Control Problem: The Scaled-Q Method," IEEE Transactions on Automatic Control, Vol. 25, No. 2, pp. 180-187, 2000. (doi)
M. Djukanovic, M. Khammash, and V. Vittal, “Sensitivity-Based Structured Singular Value Approach to Stability Robustness of Power Systems,” IEEE Transactions on Power Systems, Vol. 15, No. 2, pp. 825-830, 2000. (doi)
1999
M. Salapaka, M. Khammash, and M. Dahleh, "Solution of MIMO H2/l1 without Zero Interpolation," Siam Journal of Optimization and Control, Vol. 37, No. 6, pp. 1865-1873, 1999.
M. Djukanovic, M.Khammash, and V. Vittal, “Sequential Synthesis of Structured Singular Value-Based Decentralized Controllers in Power Systems,” IEEE Transactions on Power Systems, Vol. 14, No. 2, pp. 635-641, 1999. (doi)
1998
M. Djukanovic, M. Khammash, and V. Vittal, "Application of the Structured Singular Value Theory for Robust Stability and Control Analysis in Multi-Machine Power Systems, Part II: Numerical Simulations and Results,” IEEE Transactions on Power Systems, Vol. 13, No. 4, pp. 1317-1322, 1998.
M. Djukanovic, M. Khammash, and V. Vittal, “Application of the Structured Singular Value Theory for Robust Stability and Control Analysis in Multi-Machine Power Systems, Part I: Framework Development,” IEEE Transactions on Power Systems, Vol.13, No.4, pp. 1311-1316, 1998.
1997
T. T. Georgiou, M. Khammash, and A. Megretski, "On a Large Gain Theorem," Systems and Control Letters, Vol. 32, No. 4, 1997. (doi)
M. Khammash, "Robust Performance: Unknown Disturbances and Fixed Known Inputs," IEEE Transactions on Automatic Control, Vol. 42, No. 12, pp. 1730-1734, 1997. (doi)
1996
M. Khammash, "Synthesis of Globally Optimal Controllers for Robust Performance with Unstructured Uncertainty," IEEE Transactions on Automatic Control, Vol. 41, No. 2, pp. 189-198, 1996. (doi)
1995
M. Khammash, "Robust Steady-State Tracking," IEEE Transactions on Automatic Control, Vol. 40, No. 11, pp. 1872-1880, 1995. (doi)
S. Venkataraman, M.Khammash, and V. Vittal, “Analysis and Synthesis of HVDC Controls for Robust Stability of Power Systems,” IEEE Transactions on Power Systems, Vol. 10, No. 4, pp. 1933-1938, 1995. (doi)
1994
M.Khammash, V. Vittal, and C. Pawloski, “Analysis of Control Performance for Stability Robustness of Power Systems,” Power Systems, Vol. 9, No. 4, pp. 1861-1867, 1994.
1993
M. A. Dahleh and M. Khammash, "Controller Design in the Presence of Uncertainty," Automatica, Vol. 29, pp. 37-56, 1993. (doi)
M. Khammash and J. B. Pearson, "Analysis and Design for Robust Performance with Structured Uncertainty," Systems and Control Letters, Vol 20, pp. 179-187, 1993. (doi)
M. Khammash, "Necessary and Sufficient Conditions for the Robustness of Time-Varying Systems with Applications to Sampled-Data Systems," IEEE Transactions on Automatic Control, Vol. 38, No. 1, pp. 49-57, 1993. (doi)
V. Vittal, M.Khammash, and C. Pawloski, “System Dynamic Performance: Robust Stabilization of Controls over a Range of Operating Conditions,” SADHANA Indian National Science Academy Proceedings in Engineering Sciences, Vol. 18, pp. 801-814, 1993. (doi)
1992
M. Khammash, "Time-Varying Control and the Robust Performance of Systems with Structured Norm-Bounded Perturbations," Automatica, Vol. 28, No. 4, pp. 819-821, 1992. (doi)
1991
M. Khammash and J. B. Pearson, "Performance Robustness of Discrete-Time Systems with Structured Uncertainty," IEEE Transactions on Automatic Control, Vol. 36, pp. 398-412, 1991. (doi)
1990
M. Khammash and J. B. Pearson, "Robust Disturbance Rejection in l1 Optimal Control Systems," Systems and Control Letters, Vol. 14, pp. 93-101. 1990. (doi)