Mustafa Khammash

ORCID

Publication Activity (10 Years)

Years Active: 1992-2023
Publications (10 Years): 44

Top Venues

CoRR

CDC

PLoS Comput. Biol.

IEEE Trans. Autom. Control.

Publications

Corentin Briat, Mustafa Khammash
Noise in Biomolecular Systems: Modeling, Analysis, and Control Implications. Annu. Rev. Control. Robotics Auton. Syst. 6 (2023)
Zhou Fang, Ankit Gupta, Mustafa Khammash
Convergence of Regularized Particle Filters for Stochastic Reaction Networks. SIAM J. Numer. Anal. 61 (2) (2023)
Corentin Briat, Mustafa Khammash
Noise in Biomolecular Systems: Modeling, Analysis, and Control Implications. CoRR (2022)
Corentin Briat, Mustafa Khammash
Continuous-Time and Sampled-Data Optimal Control of Linear Stochastic Reaction Networks. CDC (2022)
Zhou Fang, Ankit Gupta, Mustafa Khammash
Stochastic filtering for multiscale stochastic reaction networks based on hybrid approximations. J. Comput. Phys. 467 (2022)
Ankit Gupta, Mustafa Khammash
Padé SSA: A frequency domain method for estimating the dynamics of stochastic reaction networks. CDC (2022)
Corentin Briat, Mustafa Khammash
On the Innocuousness of Deterministic p-type Antithetic Integral Controllers Arising in Integral Rein Control. CoRR (2022)
Corentin Briat, Mustafa Khammash
Continuous and Sampled-Data H∞ Control of Linear Stochastic Reaction Networks. CDC (2022)
Maurice Filo, Sant Kumar, Stanislav Anastassov, Mustafa Khammash
Exploiting the Nonlinear Structure of the Antithetic Integral Controller to Enhance Dynamic Performance. CDC (2022)
Ankit Gupta, Christoph Schwab, Mustafa Khammash
DeepCME: A deep learning framework for computing solution statistics of the chemical master equation. PLoS Comput. Biol. 17 (12) (2021)
Fangzhou Xiao, Mustafa Khammash, John C. Doyle
Stability and Control of Biomolecular Circuits through Structure. ACC (2021)
Corentin Briat, Mustafa Khammash
Ergodicity, Output-Controllability, and Antithetic Integral Control of Uncertain Stochastic Reaction Networks. IEEE Trans. Autom. Control. 66 (5) (2021)
Corentin Briat, Mustafa Khammash
In-Silico Proportional-Integral Moment Control of Stochastic Gene Expression. IEEE Trans. Autom. Control. 66 (7) (2021)
Corentin Briat, Christoph Zechner, Mustafa Khammash
Design of a synthetic integral feedback circuit: dynamic analysis and DNA implementation. CoRR (2021)
Corentin Briat, Mustafa Khammash
Optimal and $H_\infty$ Control of Stochastic Reaction Networks. CoRR (2021)
Zhou Fang, Ankit Gupta, Mustafa Khammash
Stochastic filters based on hybrid approximations of multiscale stochastic reaction networks. CDC (2020)
Corentin Briat, Mustafa Khammash
Ergodicity, Output-Controllability, and Antithetic Integral Control of Uncertain Stochastic Reaction Networks. CoRR (2020)
Corentin Briat, Mustafa Khammash
Ergodicity Analysis and Antithetic Integral Control of a Class of Stochastic Reaction Networks with Delays. SIAM J. Appl. Dyn. Syst. 19 (3) (2020)
Milad Siami, Nader Motee, Gentian Buzi, Bassam Bamieh, Mustafa Khammash, John C. Doyle
Fundamental Limits and Tradeoffs in Autocatalytic Pathways. IEEE Trans. Autom. Control. 65 (2) (2020)
Jan Mikelson, Mustafa Khammash
Likelihood-free nested sampling for parameter inference of biochemical reaction networks. PLoS Comput. Biol. 16 (10) (2020)
Maurice Filo, Mustafa Khammash
Optimal Parameter Tuning of Feedback Controllers with Application to Biomolecular Antithetic Integral Control. CDC (2019)
Ankit Gupta, Mustafa Khammash
An antithetic integral rein controller for bio-molecular networks. CDC (2019)
Ankit Gupta, Mustafa Khammash, Guido Sanguinetti
Bayesian Parameter Estimation for Stochastic Reaction Networks from Steady-State Observations. CMSB (2019)
Daniele Cappelletti, Ankit Gupta, Mustafa Khammash
A linear constrained integral feedback for a class of reaction systems with absolute concentration robustness. CDC (2019)
Ankit Gupta, Patrik Dürrenberger, Mustafa Khammash
Quantification of loading effects in interconnections of stochastic reaction networks. ECC (2019)
Corentin Briat, Mustafa Khammash
In-Silico Proportional-Integral Moment Control of Stochastic Reaction Networks with Applications to Gene Expression (with Dimerization). CoRR (2018)
Ankit Gupta, Muruhan Rathinam, Mustafa Khammash
Estimation of Parameter Sensitivities for Stochastic Reaction Networks Using Tau-Leap Simulations. SIAM J. Numer. Anal. 56 (2) (2018)
Corentin Briat, Mustafa Khammash
Ergodicity analysis and antithetic integral control of a class of stochastic reaction networks with delays. CoRR (2018)
Ankit Gupta, Mustafa Khammash
Computational Identification of Irreducible State-Spaces for Stochastic Reaction Networks. SIAM J. Appl. Dyn. Syst. 17 (2) (2018)
Corentin Briat, Ankit Gupta, Mustafa Khammash
Variance reduction in stochastic gene expression under integral feedback control. CDC (2018)
Milad Siami, Nader Motee, Gentian Buzi, Bassam Bamieh, Mustafa Khammash, John C. Doyle
Fundamental Limits and Tradeoffs in Autocatalytic Pathways. CoRR (2017)
Corentin Briat, Mustafa Khammash
Simple interval observers for linear impulsive systems with applications to sampled-data and switched systems. CoRR (2017)
Corentin Briat, Mustafa Khammash
Stability analysis of LPV systems with piecewise differentiable parameters. CoRR (2017)
Irena Kuzmanovska, Andreas Milias-Argeitis, Jan Mikelson, Christoph Zechner, Mustafa Khammash
Parameter inference for stochastic single-cell dynamics from lineage tree data. BMC Syst. Biol. 11 (1) (2017)
Ankit Gupta, Mustafa Khammash
Finding the steady-state solution of the chemical master equation. CCTA (2017)
Harrison Steel, Gabriele Lillacci, Mustafa Khammash, Antonis Papachristodoulou
Challenges at the interface of control engineering and synthetic biology. CDC (2017)
Corentin Briat, Mustafa Khammash
Robust and structural ergodicity analysis of stochastic biomolecular networks involving synthetic antithetic integral controllers. CoRR (2017)
Corentin Briat, Ankit Gupta, Mustafa Khammash
Variance reduction for antithetic integral control of stochastic reaction networks. CoRR (2017)
Gentian Buzi, Mustafa Khammash
Implementation Considerations, Not Topological Differences, Are the Main Determinants of Noise Suppression Properties in Feedback and Incoherent Feedforward Circuits. PLoS Comput. Biol. 12 (6) (2016)
Christoph Zechner, Mustafa Khammash
Approximate filtering distributions for characterizing input-output behavior of biochemical networks. ECC (2016)
Corentin Briat, Mustafa Khammash
Robust ergodicity and tracking in antithetic integral control of stochastic biochemical reaction networks. CoRR (2016)
Corentin Briat, Mustafa Khammash
Robust ergodicity and tracking in antithetic integral control of stochastic biochemical reaction networks. CDC (2016)
Christoph Zechner, Mustafa Khammash
A molecular implementation of the least mean squares estimator. CDC (2016)
Corentin Briat, Mustafa Khammash
Interval peak-to-peak observers for continuous- and discrete-time systems with persistent inputs and delays. Autom. 74 (2016)
Andreas Milias-Argeitis, Mustafa Khammash
Adaptive Model Predictive Control of an optogenetic system. CDC (2015)
Corentin Briat, Mustafa Khammash
Sign properties of Metzler matrices with applications. CoRR (2015)
Gentian Buzi, Mustafa Khammash
Detection of loading effects in bacterial stress response using biochemical stochasticity. CDC (2014)
Lorenzo Fagiano, Khanh Huynh, Bassam Bamieh, Mustafa Khammash
On Sensor Fusion for Airborne Wind Energy Systems. IEEE Trans. Control. Syst. Technol. 22 (3) (2014)
Lorenzo Fagiano, Aldo U. Zgraggen, Manfred Morari, Mustafa Khammash
Automatic Crosswind Flight of Tethered Wings for Airborne Wind Energy: Modeling, Control Design, and Experimental Results. IEEE Trans. Control. Syst. Technol. 22 (4) (2014)
Ankit Gupta, Corentin Briat, Mustafa Khammash
A Scalable Computational Framework for Establishing Long-Term Behavior of Stochastic Reaction Networks. PLoS Comput. Biol. 10 (6) (2014)
Andreas Milias-Argeitis, Mustafa Khammash
Optimization-based Lyapunov function construction for continuous-time Markov chains with affine transition rates. CDC (2014)
Patrick W. Sheppard, Xiaoyun Sun, Mustafa Khammash, Rona G. Giffard
Overexpression of Heat Shock Protein 72 Attenuates NF-κB Activation Using a Combination of Regulatory Mechanisms in Microglia. PLoS Comput. Biol. 10 (2) (2014)
Corentin Briat, Ankit Gupta, Mustafa Khammash
Generic low-copy integral feedback for robust in-vivo adaptation. CoRR (2014)
Vladimir A. Kazeev, Mustafa Khammash, Michael Nip, Christoph Schwab
Direct Solution of the Chemical Master Equation Using Quantized Tensor Trains. PLoS Comput. Biol. 10 (3) (2014)
Lorenzo Fagiano, Aldo U. Zgraggen, Mustafa Khammash, Manfred Morari
On control of tethered wings for airborne wind energy. ACC (2013)
Lorenzo Fagiano, Aldo U. Zgraggen, Mustafa Khammash, Manfred Morari
Automatic control of tethered wings for airborne wind energy: Design and experimental results. ECC (2013)
Gabriele Lillacci, Mustafa Khammash
The signal within the noise: efficient inference of stochastic gene regulation models using fluorescence histograms and stochastic simulations. Bioinform. 29 (18) (2013)
Lorenzo Fagiano, Aldo U. Zgraggen, Manfred Morari, Mustafa Khammash
Automatic crosswind flight of tethered wings for airborne wind energy: modeling, control design and experimental results CoRR (2013)
Corentin Briat, Mustafa Khammash
Integral population control of a quadratic dimerization process. CoRR (2013)
Corentin Briat, Mustafa Khammash
Integral population control of a quadratic dimerization process. CDC (2013)
Michael Nip, João Pedro Hespanha, Mustafa Khammash
Direct numerical solution of algebraic Lyapunov equations for large-scale systems using Quantized Tensor Trains. CDC (2013)
Patrick W. Sheppard, Muruhan Rathinam, Mustafa Khammash
SPSens: a software package for stochastic parameter sensitivity analysis of biochemical reaction networks. Bioinform. 29 (1) (2013)
Ankit Gupta, Mustafa Khammash
Unbiased Estimation of Parameter Sensitivities for Stochastic Chemical Reaction Networks. SIAM J. Sci. Comput. 35 (6) (2013)
Michael J. Lawson, Brian Drawert, Mustafa Khammash, Linda R. Petzold, Tau-Mu Yi
Spatial Stochastic Dynamics Enable Robust Cell Polarization. PLoS Comput. Biol. 9 (7) (2013)
Lorenzo Fagiano, Khanh Huynh, Bassam Bamieh, Mustafa Khammash
Sensor fusion for tethered wings in airborne wind energy. ACC (2013)
Uwe Helmke, Knut Hüper, Mustafa Khammash
Global identifiability of a simple linear model for gene expression analysis. CDC (2013)
Corentin Briat, Ankit Gupta, Mustafa Khammash
A scalable computational framework for establishing long-term behavior of stochastic reaction networks CoRR (2013)
Lorenzo Fagiano, Mustafa Khammash
Nonlinear stochastic model predictive control via regularized polynomial chaos expansions. CDC (2012)
Lorenzo Fagiano, Khanh Huynh, Bassam Bamieh, Mustafa Khammash
On sensor fusion for airborne wind energy systems CoRR (2012)
Gabriele Lillacci, Mustafa Khammash
Measurement noise distribution as a metric for parameter estimation in dynamical systems. CDC (2012)
Michael Nip, João P. Hespanha, Mustafa Khammash
A spectral methods-based solution of the Chemical Master Equation for gene regulatory networks. CDC (2012)
Corentin Briat, Mustafa Khammash
Computer control of gene expression: Robust setpoint tracking of protein mean and variance using integral feedback CoRR (2012)
Lorenzo Fagiano, Mustafa Khammash
Simulation of stochastic systems via polynomial chaos expansions and convex optimization CoRR (2012)
Nader Motee, Bassam Bamieh, Mustafa Khammash
Stability analysis of quasi-polynomial dynamical systems with applications to biological network models. Autom. 48 (11) (2012)
Corentin Briat, Mustafa Khammash
Computer control of gene expression: Robust setpoint tracking of protein mean and variance using integral feedback. CDC (2012)
Lorenzo Fagiano, Mustafa Khammash, Carlo Novara
On the guaranteed accuracy of Polynomial Chaos Expansions. CDC/ECC (2011)
Patrick W. Sheppard, Xiaoyun Sun, John F. Emery, Rona G. Giffard, Mustafa Khammash
Quantitative characterization and analysis of the dynamic NF-kappaB response in microglia. BMC Bioinform. 12 (2011)
Sandra H. Dandach, Mustafa Khammash
Stochastic strategies for survival: Bacterial competence in Bacillus Subtilis. ACC (2011)
Anahita Mirtabatabaei, Francesco Bullo, Mustafa Khammash
Flow cytometry based state aggregation of a stochastic model of protein expression. CDC/ECC (2011)
Gabriele Lillacci, Mustafa Khammash
Model selection in stochastic chemical reaction networks using flow cytometry data. CDC/ECC (2011)
Nader Motee, Bassam Bamieh, Mustafa Khammash
Model reduction of polynomial dynamical systems using differential algebra. CDC (2010)
Gabriele Lillacci, Mustafa Khammash
criteria. CDC (2010)
Hana El-Samad, Mustafa Khammash
Modelling and analysis of gene regulatory network using feedback control theory. Int. J. Syst. Sci. 41 (1) (2010)
Nader Motee, Fiona Chandra, Bassam Bamieh, Mustafa Khammash, John C. Doyle
Performance limitations in autocatalytic networks in biology. CDC (2010)
Gabriele Lillacci, Mustafa Khammash
Parameter Estimation and Model Selection in Computational Biology. PLoS Comput. Biol. 6 (3) (2010)
Sandra H. Dandach, Mustafa Khammash
Analysis of Stochastic Strategies in Bacterial Competence: A Master Equation Approach. PLoS Comput. Biol. 6 (11) (2010)
Nader Motee, Bassam Bamieh, Mustafa Khammash
Stability analysis of a class of biological network models. ACC (2010)
Keith B. Purvis, Karl Johan Åström, Mustafa Khammash
Estimation and Optimal Configurations for Localization Using Cooperative UAVs. IEEE Trans. Control. Syst. Technol. 16 (5) (2008)
Mustafa Khammash, Claire J. Tomlin, M. Vidyasagar
Guest Editorial - Special Issue on Systems Biology. IEEE Trans. Autom. Control. 53 (2008)
Brian Munsky, Mustafa Khammash
Using noise transmission properties to identify stochastic gene regulatory networks. CDC (2008)
Brian Munsky, Mustafa Khammash
Computation of switch time distributions in stochastic gene regulatory networks. ACC (2008)
Brian Munsky, Mustafa Khammash
The Finite State Projection Approach for the Analysis of Stochastic Noise in Gene Networks. IEEE Trans. Autom. Control. 53 (2008)
Brian Munsky, Mustafa Khammash
A multiple time interval finite state projection algorithm for the solution to the chemical master equation. J. Comput. Phys. 226 (1) (2007)
Pablo A. Iglesias, Mustafa Khammash, Brian Munsky, Eduardo D. Sontag, Domitilla Del Vecchio
Systems biology and control - A tutorial. CDC (2007)
Brian Munsky, Slaven Peles, Mustafa Khammash
Stochastic analysis of gene regulatory networks using finite state projections and singular perturbation. ACC (2007)
Keith B. Purvis, Karl Johan Åström, Mustafa Khammash
Online Control Strategies for Highly Coupled Cooperative UAVs. ACC (2007)
Hana El-Samad, Stephen Prajna, Antonis Papachristodoulou, John Doyle, Mustafa Khammash
Advanced Methods and Algorithms for Biological Networks Analysis. Proc. IEEE 94 (4) (2006)
Hana El-Samad, Mustafa Khammash
Coherence Resonance: A Mechanism for Noise Induced Stable Oscillations in Gene Regulatory Networks. CDC (2006)
Hiroyuki Kurata, Hana El-Samad, Rei Iwasaki, Hisao Ohtake, John C. Doyle, Irina Grigorova, Carol A. Gross, Mustafa Khammash
Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System. PLoS Comput. Biol. 2 (7) (2006)
Brian Munsky, Mustafa Khammash
A reduced model solution for the chemical master equation arising in stochastic analyses of biological networks. CDC (2006)

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Publication Activity (10 Years)

Top Topics

Top Venues

Mustafa Khammash