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Cybergenetics: Theory and Design Tools for Biomolecular Control Systems

Publications

DeepCME: A deep learning framework for computing solution statistics of the chemical master equation.

Author(s): Ankit Gupta; Christoph Schwab; Mustafa Khammash
Published in: PLoS Computational Biology, 3, 2021, ISSN 1553-734X
Publisher: Public Library of Science
DOI: 10.1371/journal.pcbi.1009623

Adaptive Circuits in Synthetic Biology

Author(s): T. Frei; Mustafa Khammash
Published in: Current Opinion in Systems Biology, 28, 2, 2021, ISSN 2452-3100
Publisher: Elsevier
DOI: 10.1016/j.coisb.2021.100399

Exploiting natural chemical photosensitivity of anhydrotetracycline and tetracycline for dynamic and setpoint chemo-optogenetic control

Author(s): Armin Baumschlager, Marc Rullan, Mustafa Khammash
Published in: Nature Communications, 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-17677-5

Ergodicity Analysis and Antithetic Integral Control of a Class of Stochastic Reaction Networks with Delays

Author(s): Corentin Briat, Mustafa Khammash
Published in: SIAM Journal on Applied Dynamical Systems, 2020, ISSN 1536-0040
Publisher: Society of Industrial and Applied Mathematics
DOI: 10.1137/19m1286219

A genetic mammalian proportional-integral feedback control circuit for robust and precise gene regulation

Author(s): Timothy Frei; Ching-Hsiang Chang; Maurice Filo; Asterios Arampatzis; Mustafa Khammash
Published in: Proceedings of the National Academy of Sciences, 2022, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2122132119

Synthetic Biological Approaches for Optogenetics and Tools for Transcriptional Light-Control in Bacteria.

Author(s): Armin Baumschlager; Mustafa Khammash
Published in: Advanced Biology, 8, 2021, ISSN 2701-0198
Publisher: Wiley-VCH
DOI: 10.3929/ethz-b-000469608

Ergodicity, Output-Controllability, and Antithetic Integral Control of Uncertain Stochastic Reaction Networks

Author(s): Corentin Briat; Mustafa Khammash
Published in: IEEE Transactions on Automatic Control, 66 (5), 7, 2020, ISSN 0018-9286
Publisher: Institute of Electrical and Electronics Engineers
DOI: 10.1109/tac.2020.3005188

A Hierarchy of Biomolecular Proportional-Integral-Derivative Feedback Controllers for Robust Perfect Adaptation and Dynamic Performance

Author(s): Maurice Filo; Sant Kumar; Mustafa Khammash
Published in: Nature Communications, 2, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1101/2021.03.21.436342

Synthetic control systems for high performance gene expression in mammalian cells

Author(s): Gabriele Lillacci, Yaakov Benenson, Mustafa Khammash
Published in: Nucleic Acids Research, 46/18, 2018, Page(s) 9855-9863, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gky795

Antithetic proportional-integral feedback for reduced variance and improved control performance of stochastic reaction networks

Author(s): Corentin Briat, Ankit Gupta, Mustafa Khammash
Published in: Journal of The Royal Society Interface, 15/143, 2018, Page(s) 20180079, ISSN 1742-5689
Publisher: The Royal Society
DOI: 10.1098/rsif.2018.0079

An Optogenetic Platform for Real-Time, Single-Cell Interrogation of Stochastic Transcriptional Regulation

Author(s): Marc Rullan, Dirk Benzinger, Gregor W. Schmidt, Andreas Milias-Argeitis, Mustafa Khammash
Published in: Molecular Cell, 70/4, 2018, Page(s) 745-756.e6, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2018.04.012

Sensitivity Analysis for Multiscale Stochastic Reaction Networks Using Hybrid Approximations

Author(s): Ankit Gupta, Mustafa Khammash
Published in: Bulletin of Mathematical Biology, 2019, ISSN 0092-8240
Publisher: Academic Press
DOI: 10.1007/s11538-018-0521-4

A universal biomolecular integral feedback controller for robust perfect adaptation

Author(s): Stephanie K. Aoki, Gabriele Lillacci, Ankit Gupta, Armin Baumschlager, David Schweingruber, Mustafa Khammash
Published in: Nature, 570/7762, 2019, Page(s) 533-537, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-019-1321-1

The probability distribution of the reconstructed phylogenetic tree with occurrence data

Author(s): Ankit Gupta, Marc Manceau, Timothy Vaughan, Mustafa Khammash, Tanja Stadler
Published in: Journal of Theoretical Biology, 488, 2020, Page(s) 110115, ISSN 0022-5193
Publisher: Academic Press
DOI: 10.1016/j.jtbi.2019.110115

Cell-in-the-loop pattern formation with optogenetically emulated cell-to-cell signaling

Author(s): Melinda Liu Perkins, Dirk Benzinger, Murat Arcak, Mustafa Khammash
Published in: Nature Communications, 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-15166-3

Stochastic chemical reaction networks for robustly approximating arbitrary probability distributions

Author(s): Daniele Cappelletti, Andrés Ortiz-Muñoz, David F. Anderson, Erik Winfree
Published in: Theoretical Computer Science, 801, 2020, Page(s) 64-95, ISSN 0304-3975
Publisher: Elsevier BV
DOI: 10.1016/j.tcs.2019.08.013

Pulsatile inputs achieve tunable attenuation of gene expression variability and graded multi-gene regulation

Author(s): Dirk Benzinger, Mustafa Khammash
Published in: Nature Communications, 9/1, 2018, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-018-05882-2

In-Silico Proportional-Integral Moment Control of Stochastic Gene Expression

Author(s): Corentin Briat; Mustafa Khammash
Published in: IEEE Transactions on Automatic Control, 1, 2021, ISSN 0018-9286
Publisher: Institute of Electrical and Electronics Engineers
DOI: 10.1109/tac.2020.3013851

Rapid prototyping and design of cybergenetic single-cell controllers.

Author(s): Sant Kumar; Marc Rullan; Mustafa Khammash
Published in: Nature Communications, 12 (1), 8, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-25754-6

Stochastically modeled weakly reversible reaction networks with a single linkage class

Author(s): David F. Anderson; Daniele Cappelletti; Jinsu Kim
Published in: Journal of Applied Probability, 1, 2020, ISSN 0021-9002
Publisher: Applied Probability Trust
DOI: 10.1017/jpr.2020.28

Characterization and mitigation of gene expression burden in mammalian cells

Author(s): Timothy Frei, Federica Cella, Fabiana Tedeschi, Joaquín Gutiérrez, Guy-Bart Stan, Mustafa Khammash, Velia Siciliano
Published in: Nature Communications, 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-18392-x

Perfect adaptation in biology.

Author(s): Mustafa Khammash
Published in: Cell Systems, 12 (6), 1, 2021, ISSN 2405-4712
Publisher: Cell Press
DOI: 10.1016/j.cels.2021.05.020

A hidden integral structure endows Absolute Concentration Robust systems with resilience to dynamical concentration disturbances

Author(s): Daniele Cappelletti; Ankit Gupta; Mustafa Khammash
Published in: Journal of the Royal Society Interface, 1, 2020, ISSN 1742-5689
Publisher: The Royal Society
DOI: 10.1101/830430

Engineering AraC to make it responsive to light instead of arabinose.

Author(s): Edoardo Romano; Edoardo Romano; Armin Baumschlager; Emir Bora Akmeriç; Navaneethan Palanisamy; Navaneethan Palanisamy; Moustafa Houmani; Gregor W. Schmidt; Mehmet Ali Öztürk; Leonard Ernst; Mustafa Khammash; Barbara Di Ventura
Published in: Nature Chemical Biology, 17 (7), 12, 2021, ISSN 1552-4450
Publisher: Nature Publishing Group
DOI: 10.1038/s41589-021-00787-6

A linear constrained integral feedback for a class of reaction systems with absolute concentration robustness

Author(s): Daniele Cappelletti, Ankit Gupta, Mustafa Khammash
Published in: 2019 IEEE 58th Conference on Decision and Control (CDC), 2019, Page(s) 945-950, ISBN 978-1-7281-1398-2
Publisher: IEEE
DOI: 10.1109/CDC40024.2019.9029246

Quantification of loading effects in interconnections of stochastic reaction networks

Author(s): Ankit Gupta, Patrik Durrenberger, Mustafa Khammash
Published in: 2019 18th European Control Conference (ECC), 2019, Page(s) 2165-2170, ISBN 978-3-907144-00-8
Publisher: IEEE
DOI: 10.23919/ecc.2019.8796155

Cybergenetics: Theory and Methods for Genetic Control System

Author(s): M. Khammash, M. Di Bernardo, D. Di Bernardo
Published in: 2019 IEEE 58th Conference on Decision and Control (CDC), 2019, Page(s) 916-926, ISBN 978-1-7281-1398-2
Publisher: IEEE
DOI: 10.1109/CDC40024.2019.9030209