Journal Publications

Main content

Most recent

A. Gupta, B. Hepp and M. Khammash. "Noise induces the population entrainment of incoherent uncoupled intracellular oscillators," Cell Systems, In press.  

A. Milias-Argeitis, M. Rullan, S. Aoki, P. Buchmann, and M. Khammash. "Automated optogenetic feedback control for precise and robust regulation of gene expression and cell growth," Nature Communications, 2016. doi:10.1038/ncomms12546  Article

C. Briat, C. Zechner, and M. Khammash. "Design of a Synthetic Integral Feedback Circuit: Dynamic Analysis and DNA Implementation,"  ACS Synthetic Bioliogy, 2016. doi:10.1021/acssynbio.6b00014  Article    

Publications by year

Publications earlier than 2012

2016

Interval peak-to-peak observers for continuous- and discrete-time systems with persistent inputs and delays.
Corentin Briat, and Mustafa Khammash
Automatica, (2016) Kidlington: Elsevier.
Noise Induces the Population-Level Entrainment of Incoherent, Uncoupled Intracellular Oscillators.
Ankit Gupta, Benjamin Hepp, and Mustafa Khammash
Cell Systems, (2016) Cambridge, MA: Cell Press.
Design of a Synthetic Integral Feedback Circuit: Dynamic Analysis and DNA Implementation.
Corentin Briat, Christoph Zechner, and Mustafa Khammash
ACS Synthetic Biology, (2016) Washington, DC: American Chemical Society.
Molecular circuits for dynamic noise filtering.
Christoph Zechner, Georg Seelig, Marc Rullan, and Mustafa H. Khammash
Proceedings of the National Academy of Sciences of the United States of America, (2016) Washington, DC: National Academy of Sciences.
Digital quantification of proteins and mRNA in single mammalian cells.
Cem Albayrak, Christian A. Jordi, Christoph Zechner, Jing Lin, Colette A. Bichsel, Mustafa Khammash, and Savaş Tay
Molecular Cell, (2016) Cambridge, MA: Cell Press.
Antithetic Integral Feedback Ensures Robust Perfect Adaptation in Noisy Bimolecular Networks.
Corentin Briat, Ankit K. Gupta, and Mustafa H. Khammash
Cell Systems, (2016) Cambridge, MA: Cell Press.
Implementation Considerations, Not Topological Differences, Are the Main Determinants of Noise Suppression Properties in Feedback and Incoherent Feedforward Circuits.
Gentian Buzi, and Mustafa Khammash
PLOS Computational Biology, (2016) Lawrence: Public Library of Science.
An engineering viewpoint on biological robustness.
Mustafa Khammash
BMC Biology, (2016) Heidelberg: BioMed Central.
Automated optogenetic feedback control for precise and robust regulation of gene expression and cell growth.
Andreas Milias-Argeitis, Marc Rullan, Stephanie K. Aoki, Peter Buchmann, and Mustafa Khammash
Nature Communications, (2016) London: Nature Publishing Group.

2015

Stochastic focusing coupled with negative feedback enables robust regulation in biochemical reaction networks.
Andreas Milias-Argeitis, Stefan Engblom, Pavol Bauer, and Mustafa Khammash
Journal of the Royal Society Interface, (2015) London: Royal Society.
Iterative experiment design guides the characterization of a light-inducible gene expression circuit.
Jakob Ruess, Francesca Parise, Andreas Milias-Argeitis, Mustafa Khammash, and John Lygeros
Proceedings of the National Academy of Sciences of the United States of America, (2015) Washington, D.C.: National Academy of Sciences.
Cell lineage branching as a strategy for proliferative control.
Gentian Buzi, Arthur D. Lander, and Mustafa Khammash
BMC Biology, (2015) London: BioMed Central.
Adaptive Hybrid Simulations for Multiscale Stochastic Reaction Networks.
Benjamin Hepp, Ankit Gupta, and Mustafa Khammash
The Journal of Chemical Physics, (2015) Melville, NY: American Institute of Physics.
Stochastic Description of Biochemical Networks.
Joao Hespanha, and Mustafa Khammash
In Encyclopedia of systems and control, edited by John Baillieul and Tariq Samad, 1328-1333. (2015) London: Springer London.
Identification and control of cell populations.
Mustafa Khammash, and John Lygeros
Edited by John Baillieul and Tariq Samad, 547-552. (2015) London: Springer.

2014

Equilibrium distributions of simple biochemical reaction systems for time-scale separation in stochastic reaction networks.
Bence Mélykúti, João P. Hespanha, and Mustafa Khammash
Interface : journal of the Royal Society, (2014) London: Royal Society.
Automatic crosswind flight of tethered wings for airborne wind energy. Modeling, control design and experimental results.
Lorenzo Fagiano, Aldo U. Zgraggen, Mustafa Khammash, and Manfred Morari
IEEE transactions on control systems technology, (2014) New York, NY: IEEE.
A Scalable Computational Framework for Establishing Long-Term Behavior of Stochastic Reaction Networks.
Ankit Gupta, Corentin Briat, and Mustafa Khammash
PLoS computational biology, (2014) San Francisco, CA: Public Library of Science.
Direct solution of the chemical master equation using quantized tensor trains.
Vladimir Kazeev, Mustafa Khammash, Michael Nip, and Christoph Schwab
PLoS computational biology, (2014) San Francisco, CA: Public Library of Science.
Overexpression of Heat Shock Protein 72 Attenuates NF-kappa B Activation Using a Combination of Regulatory Mechanisms in Microglia.
Patrick W. Sheppard, Xiaoyun Sun, Mustafa Khammash, and Rona G. Giffard
PLoS computational biology, (2014) San Francisco, Calif.: Public Library of Science.
On Sensor Fusion for Airborne Wind Energy Systems.
Lorenzo Fagiano, Khanh Huynh, Bassam Bamieh, and Mustafa Khammash
IEEE Transactions on Control Systems Technology, (2014) New York, NY: IEEE.
An efficient and unbiased method for sensitivity analysis of stochastic reaction networks.
Ankit Gupta, and Mustafa Khammash
Interface : journal of the Royal Society, (2014) London: Royal Society.
Sensitivity analysis for stochastic chemical reaction networks with multiple time-scales.
Ankit Gupta, and Mustafa Khammash
Electronic journal of probability : EJP, (2014) Bethesda, MD: Institute of Mathematical Statistics.
Fast variance reduction for steady-state simulation and sensitivity analysis of stochastic chemical systems using shadow functions.
Andreas Milias-Argeitis, John Lygeros, and Mustafa Khammash
The journal of chemical physics, (2014) Melville, NY: American Institute of Physics.

2013

The signal within the noise. Efficient inference of stochastic gene regulation models using fluorescence histograms and stochastic simulations.
Gabriele Lillacci, and Mustafa Khammash
Bioinformatics, (2013) Oxford: Oxford University Press.
Systematic Identification of Signal-Activated Stochastic Gene Regulation.
Gregor Neuert, Brian Munsky, Rui Zhen Tan, Leonid Teytelman, Mustafa Khammash, and Alexander van Oudenaarden
Science, (2013) Cambridge, MA: Science.
Unbiased Estimation of Parameter Sensitivities for Stochastic Chemical Reaction Networks.
Ankit Gupta, and Mustafa Khammash
SIAM journal on scientific computing, (2013) Philadelphia, PA: SIAM.
Spatial Stochastic Dynamics Enable Robust Cell Polarization.
M. J. Lawson, B. Drawert, M. Khammash, L. Petzold, and T. M. Yi
PLoS computational biology, (2013) San Francisco, CA, USA: Public Library.
SPSens: a software package for stochastic parameter sensitivity analysis of biochemical reaction networks.
Patrick W. Sheppard, Muruhan Rathinam, and Mustafa Khammash
Bioinformatics, (2013) Oxford, England: Oxford University Press.

2012

Stability analysis of quasi-polynomial dynamical systems with applications to biological network models.
Nader Motee, Bassam Bamieh, and Mustafa Khammash
Automatica, (2012) Kidlington: Elsevier.
Simulation of stochastic systems via polynomial chaos expansions and convex optimization.
Lorenzo Fagiano, and Mustafa Khammash
Physical Review E, (2012) Ridge, NY: American Physical Society.
Dynamical optimization using reduced order models. A method to guarantee performance.
Jan Hasenauer, Martin Löhning, Mustafa Khammash, and Frank Allgöwer
Journal of process control, (2012) Oxford: Elsevier.
A distribution matching method for parameter estimation and model selection in computational biology.
Gabriele Lillacci, and Mustafa Khammash
International journal of robust and nonlinear control, (2012) Chichester: Wiley-Blackwell.
A pathwise derivative approach to the computation of parameter sensitivities in discrete stochastic chemical systems.
Patrick W. Sheppard, Muruhan Rathinam, and Mustafa Khammash
Journal of Chemical Physics, (2012) Melville, NY: American Institute of Physics.

2011

S.H. Dandach and M. Khammash, "Analysis of Stochastic Strategies in bacterial competence: a master equation approach,'' PLoS Computational Biology, 6(11), 2011. (doi:10.1371/journal.pcbi.1000985)

C. Pahlajani, P. Atzberger, and M. Khammash, "Stochastic Reduction Method for Biological Chemical Kinetics Using Time-Scale Separation,'' Journal of Theoretical Biology, Vol. 272, Issue 1, pp. 96-112, 2011. (doi:http://dx.doi.org/10.1016/j.jtbi.2010.11.023)

A. Milias-Argeitis, S. Summers, J. Stewart-Ornstein, I. Zuleta, D. Pincus, H. El-Samad, M. Khammash, and J. Lygeros. "In silico feedback for in vivo regulation of a gene expression circuit," Nature Biotechnology, 2011. (doi:10.1038/nbt.2018)

P. Sheppard, X. Sun, J. Emery, R. Giffard, and M. Khammash, "Quantitative characterization and analysis of the dynamic NF-kappaB response in microglia", BMC Bioinformatics, 12:276, 2011. (doi:10.1186/1471-2105-12-276)

2010

Brian Munsky and Mustafa Khammash, "Identification of a Stochastic Model for the Genetic Toggle Switch," IET Systems Biology, 4, No. 6, 356-366, 2010. (doi:10.1049/iet-syb.2010.0013)

G. Lillacci and Mustafa Khammash, "Parameter Estimation and Model Selection in Computational Biology," PLos Computational Biology, 6(3), e1000696, 2010. (doi:10.1371/journal.pcbi.1000696)

B. Drawert, M. Lawson, L. Petzold, and Mustafa Khammash, "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. (doi:10.1063/1.3310809)

M. Rathinam, P. Sheppard, and M. Khammash, "Efficient Computation of Parameter Sensitivities of Discrete Stochastic Chemical Reaction Networks," Journal of Chemical Physics, Vol. 132, 034103, January 2010. (doi:10.1063/1.3280166)

H. El-Samad and M. Khammash, "Modelling and Analysis of Gene Regulatory Networks Using Feedback Control Theory," Int'l Journal of System Science, Vol. 14, pp. 17-33, 2010. (doi:10.1080/00207720903144545)

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)

 
 
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