Mustafa Khammash

132 papers C 15Journal 64Unranked 51

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Filtered Finite State Projection Method for the Analysis and Estimation of Stochastic Biochemical Reaction Networks. SIAM J. Appl. Dyn. Syst. Elena D'ambrosio, Zhou Fang, Ankit Gupta, Sant Kumar, Mustafa Khammash
2026	J	`jnl`	GenAI-Net: A Generative AI Framework for Automated Biomolecular Network Design. CoRR Maurice Filo, Nicolò Rossi, Zhou Fang, Mustafa Khammash
2026	J	`jnl`	Unbiased Estimation of Second-Order Parameter Sensitivities for Stochastic Reaction Networks. SIAM J. Sci. Comput. Quentin Badolle, Ankit Gupta, Mustafa Khammash
2025	—	`conf`	Bang-Bang Optimal Light Control for Maximum Protein Production in Yeast CDC Walid Djema, Térence Bayen, Mustafa Khammash
2025	—	`conf`	Control with Practical Guarantees of Stationary Variance in Stochastic Chemical Reaction Networks. CDC Armin Mohammadie Zand, Ankit Gupta, Mustafa Khammash
2025	J	`jnl`	Interpretable Neural Approximation of Stochastic Reaction Dynamics with Guaranteed Reliability. CoRR Quentin Badolle, Arthur Theuer, Zhou Fang, Ankit Gupta, Mustafa Khammash
2025	—	`conf`	Realizing Reduced and Sparse Biochemical Reaction Networks from Dynamics. CDC Maurice Filo, Mustafa Khammash
2025	J	`jnl`	Realizing Reduced and Sparse Biochemical Reaction Networks from Dynamics. CoRR Maurice Filo, Mustafa Khammash
2024	J	`jnl`	Cascaded Antithetic Integral Feedback for Enhanced Stability and Performance. IEEE Control. Syst. Lett. Armin Mohammadie Zand, Ankit Gupta, Mustafa Khammash
2024	—	`conf`	Effective filtering approach for joint parameter-state estimation in SDEs via Rao-Blackwellization and modularization. CDC Zhou Fang, Ankit Gupta, Mustafa Khammash
2024	—	`conf`	SynthEvo: A Gradient-Guided Evolutionary Approach for Synthetic Circuit Design. CDC Nicolò Rossi, Ankit Gupta, Mustafa Khammash
2023	J	`jnl`	Convergence of Regularized Particle Filters for Stochastic Reaction Networks. SIAM J. Numer. Anal. Zhou Fang, Ankit Gupta, Mustafa Khammash
2023	J	`jnl`	Noise in Biomolecular Systems: Modeling, Analysis, and Control Implications. Annu. Rev. Control. Robotics Auton. Syst. Corentin Briat, Mustafa Khammash
2022	—	`conf`	Continuous and Sampled-Data H∞ Control of Linear Stochastic Reaction Networks. CDC Corentin Briat, Mustafa Khammash
2022	—	`conf`	Continuous-Time and Sampled-Data Optimal Control of Linear Stochastic Reaction Networks. CDC Corentin Briat, Mustafa Khammash
2022	—	`conf`	Exploiting the Nonlinear Structure of the Antithetic Integral Controller to Enhance Dynamic Performance. CDC Maurice Filo, Sant Kumar, Stanislav Anastassov, Mustafa Khammash
2022	J	`jnl`	Noise in Biomolecular Systems: Modeling, Analysis, and Control Implications. CoRR Corentin Briat, Mustafa Khammash
2022	J	`jnl`	On the Innocuousness of Deterministic p-type Antithetic Integral Controllers Arising in Integral Rein Control. CoRR Corentin Briat, Mustafa Khammash
2022	—	`conf`	Padé SSA: A frequency domain method for estimating the dynamics of stochastic reaction networks. CDC Ankit Gupta, Mustafa Khammash
2022	J	`jnl`	Stochastic filtering for multiscale stochastic reaction networks based on hybrid approximations. J. Comput. Phys. Zhou Fang, Ankit Gupta, Mustafa Khammash
2021	J	`jnl`	DeepCME: A deep learning framework for computing solution statistics of the chemical master equation. PLoS Comput. Biol. Ankit Gupta, Christoph Schwab, Mustafa Khammash
2021	J	`jnl`	Design of a synthetic integral feedback circuit: dynamic analysis and DNA implementation. CoRR Corentin Briat, Christoph Zechner, Mustafa Khammash
2021	J	`jnl`	Ergodicity, Output-Controllability, and Antithetic Integral Control of Uncertain Stochastic Reaction Networks. IEEE Trans. Autom. Control. Corentin Briat, Mustafa Khammash
2021	J	`jnl`	In-Silico Proportional-Integral Moment Control of Stochastic Gene Expression. IEEE Trans. Autom. Control. Corentin Briat, Mustafa Khammash
2021	C	`conf`	Stability and Control of Biomolecular Circuits through Structure. ACC Fangzhou Xiao, Mustafa Khammash, John C. Doyle
2020	J	`jnl`	Ergodicity Analysis and Antithetic Integral Control of a Class of Stochastic Reaction Networks with Delays. SIAM J. Appl. Dyn. Syst. Corentin Briat, Mustafa Khammash
2020	J	`jnl`	Ergodicity, Output-Controllability, and Antithetic Integral Control of Uncertain Stochastic Reaction Networks. CoRR Corentin Briat, Mustafa Khammash
2020	J	`jnl`	Fundamental Limits and Tradeoffs in Autocatalytic Pathways. IEEE Trans. Autom. Control. Milad Siami, Nader Motee, Gentian Buzi, Bassam Bamieh, Mustafa Khammash, John C. Doyle
2020	J	`jnl`	Likelihood-free nested sampling for parameter inference of biochemical reaction networks. PLoS Comput. Biol. Jan Mikelson, Mustafa Khammash
2020	—	`conf`	Stochastic filters based on hybrid approximations of multiscale stochastic reaction networks. CDC Zhou Fang, Ankit Gupta, Mustafa Khammash
2019	—	`conf`	A linear constrained integral feedback for a class of reaction systems with absolute concentration robustness. CDC Daniele Cappelletti, Ankit Gupta, Mustafa Khammash
2019	—	`conf`	An antithetic integral rein controller for bio-molecular networks. CDC Ankit Gupta, Mustafa Khammash
2019	—	`conf`	Bayesian Parameter Estimation for Stochastic Reaction Networks from Steady-State Observations. CMSB Ankit Gupta, Mustafa Khammash, Guido Sanguinetti
2019	—	`conf`	Cybergenetics: Theory and Methods for Genetic Control System. CDC Mustafa Khammash, Mario di Bernardo, Diego di Bernardo
2019	—	`conf`	Optimal Parameter Tuning of Feedback Controllers with Application to Biomolecular Antithetic Integral Control. CDC Maurice Filo, Mustafa Khammash
2019	—	`conf`	Quantification of loading effects in interconnections of stochastic reaction networks. ECC Ankit Gupta, Patrik Dürrenberger, Mustafa Khammash
2018	J	`jnl`	Computational Identification of Irreducible State-Spaces for Stochastic Reaction Networks. SIAM J. Appl. Dyn. Syst. Ankit Gupta, Mustafa Khammash
2018	J	`jnl`	Ergodicity analysis and antithetic integral control of a class of stochastic reaction networks with delays. CoRR Corentin Briat, Mustafa Khammash
2018	J	`jnl`	Estimation of Parameter Sensitivities for Stochastic Reaction Networks Using Tau-Leap Simulations. SIAM J. Numer. Anal. Ankit Gupta, Muruhan Rathinam, Mustafa Khammash
2018	J	`jnl`	In-Silico Proportional-Integral Moment Control of Stochastic Reaction Networks with Applications to Gene Expression (with Dimerization). CoRR Corentin Briat, Mustafa Khammash
2018	—	`conf`	Variance reduction in stochastic gene expression under integral feedback control. CDC Corentin Briat, Ankit Gupta, Mustafa Khammash
2017	—	`conf`	Challenges at the interface of control engineering and synthetic biology. CDC Harrison Steel, Gabriele Lillacci, Mustafa Khammash, Antonis Papachristodoulou
2017	—	`conf`	Finding the steady-state solution of the chemical master equation. CCTA Ankit Gupta, Mustafa Khammash
2017	J	`jnl`	Fundamental Limits and Tradeoffs in Autocatalytic Pathways. CoRR Milad Siami, Nader Motee, Gentian Buzi, Bassam Bamieh, Mustafa Khammash, John C. Doyle
2017	J	`jnl`	Parameter inference for stochastic single-cell dynamics from lineage tree data. BMC Syst. Biol. Irena Kuzmanovska, Andreas Milias-Argeitis, Jan Mikelson, Christoph Zechner, Mustafa Khammash
2017	J	`jnl`	Robust and structural ergodicity analysis of stochastic biomolecular networks involving synthetic antithetic integral controllers. CoRR Corentin Briat, Mustafa Khammash
2017	J	`jnl`	Simple interval observers for linear impulsive systems with applications to sampled-data and switched systems. CoRR Corentin Briat, Mustafa Khammash
2017	J	`jnl`	Stability analysis of LPV systems with piecewise differentiable parameters. CoRR Corentin Briat, Mustafa Khammash
2017	J	`jnl`	Variance reduction for antithetic integral control of stochastic reaction networks. CoRR Corentin Briat, Ankit Gupta, Mustafa Khammash
2016	—	`conf`	A molecular implementation of the least mean squares estimator. CDC Christoph Zechner, Mustafa Khammash
2016	—	`conf`	Approximate filtering distributions for characterizing input-output behavior of biochemical networks. ECC Christoph Zechner, Mustafa Khammash
2016	J	`jnl`	Implementation Considerations, Not Topological Differences, Are the Main Determinants of Noise Suppression Properties in Feedback and Incoherent Feedforward Circuits. PLoS Comput. Biol. Gentian Buzi, Mustafa Khammash
2016	J	`jnl`	Interval peak-to-peak observers for continuous- and discrete-time systems with persistent inputs and delays. Autom. Corentin Briat, Mustafa Khammash
2016	—	`conf`	Robust ergodicity and tracking in antithetic integral control of stochastic biochemical reaction networks. CDC Corentin Briat, Mustafa Khammash
2016	J	`jnl`	Robust ergodicity and tracking in antithetic integral control of stochastic biochemical reaction networks. CoRR Corentin Briat, Mustafa Khammash
2015	—	`conf`	Adaptive Model Predictive Control of an optogenetic system. CDC Andreas Milias-Argeitis, Mustafa Khammash
2015	—	`ch.`	Identification and Control of Cell Populations. Encyclopedia of Systems and Control Mustafa Khammash, John Lygeros
2015	J	`jnl`	Sign properties of Metzler matrices with applications. CoRR Corentin Briat, Mustafa Khammash
2015	—	`ch.`	Stochastic Description of Biochemical Networks. Encyclopedia of Systems and Control João Pedro Hespanha, Mustafa Khammash
2014	J	`jnl`	A Scalable Computational Framework for Establishing Long-Term Behavior of Stochastic Reaction Networks. PLoS Comput. Biol. Ankit Gupta, Corentin Briat, Mustafa Khammash
2014	J	`jnl`	Automatic Crosswind Flight of Tethered Wings for Airborne Wind Energy: Modeling, Control Design, and Experimental Results. IEEE Trans. Control. Syst. Technol. Lorenzo Fagiano, Aldo U. Zgraggen, Manfred Morari, Mustafa Khammash
2014	—	`conf`	Detection of loading effects in bacterial stress response using biochemical stochasticity. CDC Gentian Buzi, Mustafa Khammash
2014	J	`jnl`	Direct Solution of the Chemical Master Equation Using Quantized Tensor Trains. PLoS Comput. Biol. Vladimir A. Kazeev, Mustafa Khammash, Michael Nip, Christoph Schwab
2014	J	`jnl`	Generic low-copy integral feedback for robust in-vivo adaptation. CoRR Corentin Briat, Ankit Gupta, Mustafa Khammash
2014	J	`jnl`	On Sensor Fusion for Airborne Wind Energy Systems. IEEE Trans. Control. Syst. Technol. Lorenzo Fagiano, Khanh Huynh, Bassam Bamieh, Mustafa Khammash
2014	—	`conf`	Optimization-based Lyapunov function construction for continuous-time Markov chains with affine transition rates. CDC Andreas Milias-Argeitis, Mustafa Khammash
2014	J	`jnl`	Overexpression of Heat Shock Protein 72 Attenuates NF-κB Activation Using a Combination of Regulatory Mechanisms in Microglia. PLoS Comput. Biol. Patrick W. Sheppard, Xiaoyun Sun, Mustafa Khammash, Rona G. Giffard
2013	J	`jnl`	A scalable computational framework for establishing long-term behavior of stochastic reaction networks CoRR Corentin Briat, Ankit Gupta, Mustafa Khammash
2013	—	`conf`	Automatic control of tethered wings for airborne wind energy: Design and experimental results. ECC Lorenzo Fagiano, Aldo U. Zgraggen, Mustafa Khammash, Manfred Morari
2013	J	`jnl`	Automatic crosswind flight of tethered wings for airborne wind energy: modeling, control design and experimental results CoRR Lorenzo Fagiano, Aldo U. Zgraggen, Manfred Morari, Mustafa Khammash
2013	—	`conf`	Direct numerical solution of algebraic Lyapunov equations for large-scale systems using Quantized Tensor Trains. CDC Michael Nip, João Pedro Hespanha, Mustafa Khammash
2013	—	`conf`	Global identifiability of a simple linear model for gene expression analysis. CDC Uwe Helmke, Knut Hüper, Mustafa Khammash
2013	—	`conf`	Integral population control of a quadratic dimerization process. CDC Corentin Briat, Mustafa Khammash
2013	J	`jnl`	Integral population control of a quadratic dimerization process. CoRR Corentin Briat, Mustafa Khammash
2013	C	`conf`	On control of tethered wings for airborne wind energy. ACC Lorenzo Fagiano, Aldo U. Zgraggen, Mustafa Khammash, Manfred Morari
2013	J	`jnl`	SPSens: a software package for stochastic parameter sensitivity analysis of biochemical reaction networks. Bioinform. Patrick W. Sheppard, Muruhan Rathinam, Mustafa Khammash
2013	C	`conf`	Sensor fusion for tethered wings in airborne wind energy. ACC Lorenzo Fagiano, Khanh Huynh, Bassam Bamieh, Mustafa Khammash
2013	J	`jnl`	Spatial Stochastic Dynamics Enable Robust Cell Polarization. PLoS Comput. Biol. Michael J. Lawson, Brian Drawert, Mustafa Khammash, Linda R. Petzold, Tau-Mu Yi
2013	J	`jnl`	The signal within the noise: efficient inference of stochastic gene regulation models using fluorescence histograms and stochastic simulations. Bioinform. Gabriele Lillacci, Mustafa Khammash
2013	J	`jnl`	Unbiased Estimation of Parameter Sensitivities for Stochastic Chemical Reaction Networks. SIAM J. Sci. Comput. Ankit Gupta, Mustafa Khammash
2012	—	`conf`	A spectral methods-based solution of the Chemical Master Equation for gene regulatory networks. CDC Michael Nip, João P. Hespanha, Mustafa Khammash
2012	J	`jnl`	Computer control of gene expression: Robust setpoint tracking of protein mean and variance using integral feedback CoRR Corentin Briat, Mustafa Khammash
2012	—	`conf`	Computer control of gene expression: Robust setpoint tracking of protein mean and variance using integral feedback. CDC Corentin Briat, Mustafa Khammash
2012	—	`conf`	Measurement noise distribution as a metric for parameter estimation in dynamical systems. CDC Gabriele Lillacci, Mustafa Khammash
2012	—	`conf`	Nonlinear stochastic model predictive control via regularized polynomial chaos expansions. CDC Lorenzo Fagiano, Mustafa Khammash
2012	J	`jnl`	On sensor fusion for airborne wind energy systems CoRR Lorenzo Fagiano, Khanh Huynh, Bassam Bamieh, Mustafa Khammash
2012	J	`jnl`	Simulation of stochastic systems via polynomial chaos expansions and convex optimization CoRR Lorenzo Fagiano, Mustafa Khammash
2012	J	`jnl`	Stability analysis of quasi-polynomial dynamical systems with applications to biological network models. Autom. Nader Motee, Bassam Bamieh, Mustafa Khammash
2011	—	`conf`	Flow cytometry based state aggregation of a stochastic model of protein expression. CDC/ECC Anahita Mirtabatabaei, Francesco Bullo, Mustafa Khammash
2011	—	`conf`	Model selection in stochastic chemical reaction networks using flow cytometry data. CDC/ECC Gabriele Lillacci, Mustafa Khammash
2011	—	`conf`	On the guaranteed accuracy of Polynomial Chaos Expansions. CDC/ECC Lorenzo Fagiano, Mustafa Khammash, Carlo Novara
2011	J	`jnl`	Quantitative characterization and analysis of the dynamic NF-kappaB response in microglia. BMC Bioinform. Patrick W. Sheppard, Xiaoyun Sun, John F. Emery, Rona G. Giffard, Mustafa Khammash
2011	C	`conf`	Stochastic strategies for survival: Bacterial competence in Bacillus Subtilis. ACC Sandra H. Dandach, Mustafa Khammash
2010	J	`jnl`	Analysis of Stochastic Strategies in Bacterial Competence: A Master Equation Approach. PLoS Comput. Biol. Sandra H. Dandach, Mustafa Khammash
2010	—	`conf`	Model reduction of polynomial dynamical systems using differential algebra. CDC Nader Motee, Bassam Bamieh, Mustafa Khammash
2010	J	`jnl`	Modelling and analysis of gene regulatory network using feedback control theory. Int. J. Syst. Sci. Hana El-Samad, Mustafa Khammash
2010	J	`jnl`	Parameter Estimation and Model Selection in Computational Biology. PLoS Comput. Biol. Gabriele Lillacci, Mustafa Khammash
2010	—	`conf`	Parameter identification of biological networks using extended Kalman filtering and χ CDC Gabriele Lillacci, Mustafa Khammash
2010	—	`conf`	Performance limitations in autocatalytic networks in biology. CDC Nader Motee, Fiona Chandra, Bassam Bamieh, Mustafa Khammash, John C. Doyle
2010	C	`conf`	Stability analysis of a class of biological network models. ACC Nader Motee, Bassam Bamieh, Mustafa Khammash
2008	C	`conf`	Computation of switch time distributions in stochastic gene regulatory networks. ACC Brian Munsky, Mustafa Khammash
2008	J	`jnl`	Estimation and Optimal Configurations for Localization Using Cooperative UAVs. IEEE Trans. Control. Syst. Technol. Keith B. Purvis, Karl Johan Åström, Mustafa Khammash
2008	J	`jnl`	Guest Editorial - Special Issue on Systems Biology. IEEE Trans. Autom. Control. Mustafa Khammash, Claire J. Tomlin, M. Vidyasagar
2008	J	`jnl`	The Finite State Projection Approach for the Analysis of Stochastic Noise in Gene Networks. IEEE Trans. Autom. Control. Brian Munsky, Mustafa Khammash
2008	—	`conf`	Using noise transmission properties to identify stochastic gene regulatory networks. CDC Brian Munsky, Mustafa Khammash
2007	J	`jnl`	A multiple time interval finite state projection algorithm for the solution to the chemical master equation. J. Comput. Phys. Brian Munsky, Mustafa Khammash
2007	C	`conf`	Online Control Strategies for Highly Coupled Cooperative UAVs. ACC Keith B. Purvis, Karl Johan Åström, Mustafa Khammash
2007	C	`conf`	Stochastic analysis of gene regulatory networks using finite state projections and singular perturbation. ACC Brian Munsky, Slaven Peles, Mustafa Khammash
2007	—	`conf`	Systems biology and control - A tutorial. CDC Pablo A. Iglesias, Mustafa Khammash, Brian Munsky, Eduardo D. Sontag, Domitilla Del Vecchio
2006	—	`conf`	A reduced model solution for the chemical master equation arising in stochastic analyses of biological networks. CDC Brian Munsky, Mustafa Khammash
2006	J	`jnl`	Advanced Methods and Algorithms for Biological Networks Analysis. Proc. IEEE Hana El-Samad, Stephen Prajna, Antonis Papachristodoulou, John Doyle, Mustafa Khammash
2006	—	`conf`	Coherence Resonance: A Mechanism for Noise Induced Stable Oscillations in Gene Regulatory Networks. CDC Hana El-Samad, Mustafa Khammash
2006	J	`jnl`	Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System. PLoS Comput. Biol. Hiroyuki Kurata, Hana El-Samad, Rei Iwasaki, Hisao Ohtake, John C. Doyle, Irina Grigorova, Carol A. Gross, Mustafa Khammash
2005	C	`conf`	Estimating radar positions using cooperative unmanned air vehicle teams. ACC Keith B. Purvis, Karl Johan Åström, Mustafa Khammash
2005	C	`conf`	Repressilators and promotilators: loop dynamics in synthetic gene networks. ACC Hana El-Samad, Domitilla Del Vecchio, Mustafa Khammash
2005	—	`conf`	Stochastic Modeling and Analysis of Genetic Networks. CDC/ECC Mustafa Khammash, Hana El-Samad
2004	—	`conf`	Stochastic stability and its application to the analysis of gene regulatory networks. CDC Hana El-Samad, Mustafa Khammash
2004	J	`jnl`	Structured optimal and robust control with multiple criteria: a convex solution. IEEE Trans. Autom. Control. Xin Qi, Murti V. Salapaka, Petros G. Voulgaris, Mustafa Khammash
2003	—	`conf`	Model validation and robust stability analysis of the bacterial heat shock response using SOSTOOLS. CDC Hana El-Samad, Stephen Prajna, Antonis Papachristodoulou, Mustafa Khammash, John C. Doyle
2003	C	`conf`	Structured optimal control with applications to network flow coordination. ACC Xin Qi, Murti V. Salapaka, Petros G. Voulgaris, Mustafa Khammash
2002	C	`conf`	Robustness analysis of the heat shock response in E. coli. ACC Hana El-Samad, Mustafa Khammash, Hiroyuki Kurata, John Doyle
2001	—	`conf`	Comparison of different polynomial factorization approaches as an alternative to FIR approximation to solve the ℓ1 design problem. ECC Pierre-Olivier Malaterre, Mustafa Khammash
2001	—	`conf`	Feedback regulation of the heat shock response in E. coli. CDC Hiroyuki Kurata, Hana El-Samad, Tau-Mu Yi, Mustafa Khammash, John Doyle
2001	C	`conf`	Robust gain-scheduled aircraft longitudinal controller design using an H ACC Zhe Lin, Mustafa Khammash
2001	J	`jnl`	Robust synthesis in IEEE Trans. Autom. Control. Mustafa Khammash, Murti V. Salapaka, Timothy Van Voorhis
2000	J	`jnl`	A new approach to the solution of the l IEEE Trans. Autom. Control. Mustafa Khammash
2000	C	`conf`	Calcium Homeostasis: A Feedback Control Point of View. BIBE Hana El-Samad, Mustafa Khammash
2000	C	`conf`	Calcium homeostasis: a feedback control point of view. ACC Hana El-Samad, Mustafa Khammash, J. Goff
2000	—	`conf`	ℓ CDC Pierre-Olivier Malaterre, Mustafa Khammash
1998	—	`conf`	Multi-objective MIMO optimal control design without zero interpolation. Robustness in Identification and Control Murti V. Salapaka, Mustafa Khammash
1998	—	`conf`	Robustness synthesis in l 1: A globally optimal solution. Robustness in Identification and Control Mustafa Khammash, Murti V. Salapaka, Timothy Van Voorhis
1992	J	`jnl`	Time-varying control and the robust performance of systems with structured norm-bounded perturbations. Autom. Mustafa Khammash, Mohammed Dahleh