Cybergenetics: Theory and Design Tools for Biomolecular Control Systems

Project Information

CyberGenetics

Grant agreement ID: 743269

DOI

10.3030/743269

Project closed

EC signature date 19 June 2017

Start date 1 August 2017

End date 31 December 2022

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 2 499 887,00

EU contribution

€ 2 499 887,00

Coordinated by

EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH
Switzerland

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (31)

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, Issue 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, Issue 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, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-17677-5

Implementation of a Novel Optogenetic Tool in Mammalian Cells Based on a Split T7 RNA Polymerase

Author(s): Sara Dionisi; Karol Piera; Armin Baumschlager; Mustafa Khammash
Published in: ACS Synthetic Biology, 2022, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.2c00067

The dynamics of stochastic mono-molecular reaction systems in stochastic environments

Author(s): Daniele Cappelletti; Abhishek Pal Majumder; Carsten Wiuf
Published in: Stochastic Processes and their Applications, 137, Issue 4, 2021, ISSN 0304-4149
Publisher: Elsevier BV
DOI: 10.3929/ethz-b-000479434

Universal structural requirements for maximal robust perfect adaptation in biomolecular networks

Author(s): Ankit Gupta; Mustafa Khammash
Published in: Proceedings of the National Academies of Sciences, USA, Issue 5, 2022, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1101/2022.02.01.478605

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, Issue 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), Issue 7, 2020, ISSN 0018-9286
Publisher: Institute of Electrical and Electronics Engineers
DOI: 10.1109/tac.2020.3005188

Frequency Spectra and the Color of Cellular Noise

Author(s): Ankit Gupta; Mustafa Khammash
Published in: Nature Communications, Issue 5, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.3929/ethz-b-000561007

Dynamic cybergenetic control of bacterial co-culture composition via optogenetic feedback

Author(s): Joaquin Gutierrez Mena; Sant Kumar; Mustafa Khammash
Published in: Nature Communications, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-32392-z

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, Issue 2, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1101/2021.03.21.436342

Synthetic gene networks recapitulate dynamic signal decoding and differential gene expression

Author(s): Dirk Benzinger; Serguei Ovinnikov; Mustafa Khammash
Published in: Cell Systems, 2022, ISSN 2405-4712
Publisher: Cell Press
DOI: 10.1016/j.cels.2022.02.004

Synthetic control systems for high performance gene expression in mammalian cells

Author(s): Gabriele Lillacci, Yaakov Benenson, Mustafa Khammash
Published in: Nucleic Acids Research, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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), Issue 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, Issue 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, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-18392-x

Cybergenetics: Theory and Applications of Genetic Control Systems

Author(s): Mustafa H. Khammash
Published in: Proceedings of the IEEE, 110 (5), Issue 6, 2022, ISSN 0018-9219
Publisher: Institute of Electrical and Electronics Engineers
DOI: 10.1109/jproc.2022.3170599

Perfect adaptation in biology.

Author(s): Mustafa Khammash
Published in: Cell Systems, 12 (6), Issue 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, Issue 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), Issue 12, 2021, ISSN 1552-4450
Publisher: Nature Publishing Group
DOI: 10.1038/s41589-021-00787-6

Conference proceedings (5)

Continuous and Sampled-Data H∞ Control of Linear Stochastic Reaction Networks

Author(s): Corentin Briat, Mustafa Khammash
Published in: Proceedings of the 2022 Conference on Decision and Control, 2022
Publisher: IEEE
DOI: 10.1109/cdc51059.2022.9992946

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

Continuous-Time and Sampled-Data Optimal Control of Linear Stochastic Reaction Networks

Author(s): Corentin Briat, Mustafa Khammash
Published in: Proceedings of the 2022 Conference on Decision and Control, 2022
Publisher: IEEE
DOI: 10.1109/cdc51059.2022.9993017

Intellectual Property Rights

Patent (1)

EXPRESSION SYSTEM AND METHOD FOR CONTROLLING A NETWORK IN A CELL AND CELL COMPRISING THE EXPRESSION SYSTEM

Application/Publication number: 20 21081158
Date: 2021-11-09
Applicant(s): EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH