Cybergenetics: Theory and Design Tools for Biomolecular Control Systems

Publicaciones

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

Autores: Ankit Gupta; Christoph Schwab; Mustafa Khammash
Publicado en: PLoS Computational Biology, Edición 3, 2021, ISSN 1553-734X
Editor: Public Library of Science
DOI: 10.1371/journal.pcbi.1009623

Adaptive Circuits in Synthetic Biology

Autores: T. Frei; Mustafa Khammash
Publicado en: Current Opinion in Systems Biology, 28, Edición 2, 2021, ISSN 2452-3100
Editor: Elsevier
DOI: 10.1016/j.coisb.2021.100399

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

Autores: Armin Baumschlager, Marc Rullan, Mustafa Khammash
Publicado en: Nature Communications, Edición 11/1, 2020, ISSN 2041-1723
Editor: 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

Autores: Sara Dionisi; Karol Piera; Armin Baumschlager; Mustafa Khammash
Publicado en: ACS Synthetic Biology, 2022, ISSN 2161-5063
Editor: American Chemical Society
DOI: 10.1021/acssynbio.2c00067

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

Autores: Daniele Cappelletti; Abhishek Pal Majumder; Carsten Wiuf
Publicado en: Stochastic Processes and their Applications, 137, Edición 4, 2021, ISSN 0304-4149
Editor: Elsevier BV
DOI: 10.3929/ethz-b-000479434

Universal structural requirements for maximal robust perfect adaptation in biomolecular networks

Autores: Ankit Gupta; Mustafa Khammash
Publicado en: Proceedings of the National Academies of Sciences, USA, Edición 5, 2022, ISSN 0027-8424
Editor: 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

Autores: Corentin Briat, Mustafa Khammash
Publicado en: SIAM Journal on Applied Dynamical Systems, 2020, ISSN 1536-0040
Editor: Society of Industrial and Applied Mathematics
DOI: 10.1137/19m1286219

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

Autores: Timothy Frei; Ching-Hsiang Chang; Maurice Filo; Asterios Arampatzis; Mustafa Khammash
Publicado en: Proceedings of the National Academy of Sciences, 2022, ISSN 0027-8424
Editor: National Academy of Sciences
DOI: 10.1073/pnas.2122132119

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

Autores: Armin Baumschlager; Mustafa Khammash
Publicado en: Advanced Biology, Edición 8, 2021, ISSN 2701-0198
Editor: Wiley-VCH
DOI: 10.3929/ethz-b-000469608

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

Autores: Corentin Briat; Mustafa Khammash
Publicado en: IEEE Transactions on Automatic Control, 66 (5), Edición 7, 2020, ISSN 0018-9286
Editor: Institute of Electrical and Electronics Engineers
DOI: 10.1109/tac.2020.3005188

Frequency Spectra and the Color of Cellular Noise

Autores: Ankit Gupta; Mustafa Khammash
Publicado en: Nature Communications, Edición 5, 2022, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.3929/ethz-b-000561007

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

Autores: Joaquin Gutierrez Mena; Sant Kumar; Mustafa Khammash
Publicado en: Nature Communications, 2022, ISSN 2041-1723
Editor: 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

Autores: Maurice Filo; Sant Kumar; Mustafa Khammash
Publicado en: Nature Communications, Edición 2, 2022, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1101/2021.03.21.436342

Synthetic gene networks recapitulate dynamic signal decoding and differential gene expression

Autores: Dirk Benzinger; Serguei Ovinnikov; Mustafa Khammash
Publicado en: Cell Systems, 2022, ISSN 2405-4712
Editor: Cell Press
DOI: 10.1016/j.cels.2022.02.004

Synthetic control systems for high performance gene expression in mammalian cells

Autores: Gabriele Lillacci, Yaakov Benenson, Mustafa Khammash
Publicado en: Nucleic Acids Research, Edición 46/18, 2018, Página(s) 9855-9863, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gky795

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

Autores: Corentin Briat, Ankit Gupta, Mustafa Khammash
Publicado en: Journal of The Royal Society Interface, Edición 15/143, 2018, Página(s) 20180079, ISSN 1742-5689
Editor: The Royal Society
DOI: 10.1098/rsif.2018.0079

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

Autores: Marc Rullan, Dirk Benzinger, Gregor W. Schmidt, Andreas Milias-Argeitis, Mustafa Khammash
Publicado en: Molecular Cell, Edición 70/4, 2018, Página(s) 745-756.e6, ISSN 1097-2765
Editor: Cell Press
DOI: 10.1016/j.molcel.2018.04.012

Sensitivity Analysis for Multiscale Stochastic Reaction Networks Using Hybrid Approximations

Autores: Ankit Gupta, Mustafa Khammash
Publicado en: Bulletin of Mathematical Biology, 2019, ISSN 0092-8240
Editor: Academic Press
DOI: 10.1007/s11538-018-0521-4

A universal biomolecular integral feedback controller for robust perfect adaptation

Autores: Stephanie K. Aoki, Gabriele Lillacci, Ankit Gupta, Armin Baumschlager, David Schweingruber, Mustafa Khammash
Publicado en: Nature, Edición 570/7762, 2019, Página(s) 533-537, ISSN 0028-0836
Editor: Nature Publishing Group
DOI: 10.1038/s41586-019-1321-1

The probability distribution of the reconstructed phylogenetic tree with occurrence data

Autores: Ankit Gupta, Marc Manceau, Timothy Vaughan, Mustafa Khammash, Tanja Stadler
Publicado en: Journal of Theoretical Biology, Edición 488, 2020, Página(s) 110115, ISSN 0022-5193
Editor: Academic Press
DOI: 10.1016/j.jtbi.2019.110115

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

Autores: Melinda Liu Perkins, Dirk Benzinger, Murat Arcak, Mustafa Khammash
Publicado en: Nature Communications, Edición 11/1, 2020, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-020-15166-3

Stochastic chemical reaction networks for robustly approximating arbitrary probability distributions

Autores: Daniele Cappelletti, Andrés Ortiz-Muñoz, David F. Anderson, Erik Winfree
Publicado en: Theoretical Computer Science, Edición 801, 2020, Página(s) 64-95, ISSN 0304-3975
Editor: Elsevier BV
DOI: 10.1016/j.tcs.2019.08.013

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

Autores: Dirk Benzinger, Mustafa Khammash
Publicado en: Nature Communications, Edición 9/1, 2018, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-018-05882-2

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

Autores: Corentin Briat; Mustafa Khammash
Publicado en: IEEE Transactions on Automatic Control, Edición 1, 2021, ISSN 0018-9286
Editor: Institute of Electrical and Electronics Engineers
DOI: 10.1109/tac.2020.3013851

Rapid prototyping and design of cybergenetic single-cell controllers.

Autores: Sant Kumar; Marc Rullan; Mustafa Khammash
Publicado en: Nature Communications, 12 (1), Edición 8, 2021, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-021-25754-6

Stochastically modeled weakly reversible reaction networks with a single linkage class

Autores: David F. Anderson; Daniele Cappelletti; Jinsu Kim
Publicado en: Journal of Applied Probability, Edición 1, 2020, ISSN 0021-9002
Editor: Applied Probability Trust
DOI: 10.1017/jpr.2020.28

Characterization and mitigation of gene expression burden in mammalian cells

Autores: Timothy Frei, Federica Cella, Fabiana Tedeschi, Joaquín Gutiérrez, Guy-Bart Stan, Mustafa Khammash, Velia Siciliano
Publicado en: Nature Communications, Edición 11/1, 2020, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-020-18392-x

Cybergenetics: Theory and Applications of Genetic Control Systems

Autores: Mustafa H. Khammash
Publicado en: Proceedings of the IEEE, 110 (5), Edición 6, 2022, ISSN 0018-9219
Editor: Institute of Electrical and Electronics Engineers
DOI: 10.1109/jproc.2022.3170599

Perfect adaptation in biology.

Autores: Mustafa Khammash
Publicado en: Cell Systems, 12 (6), Edición 1, 2021, ISSN 2405-4712
Editor: 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

Autores: Daniele Cappelletti; Ankit Gupta; Mustafa Khammash
Publicado en: Journal of the Royal Society Interface, Edición 1, 2020, ISSN 1742-5689
Editor: The Royal Society
DOI: 10.1101/830430

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

Autores: 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
Publicado en: Nature Chemical Biology, 17 (7), Edición 12, 2021, ISSN 1552-4450
Editor: Nature Publishing Group
DOI: 10.1038/s41589-021-00787-6

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

Autores: Corentin Briat, Mustafa Khammash
Publicado en: Proceedings of the 2022 Conference on Decision and Control, 2022
Editor: IEEE
DOI: 10.1109/cdc51059.2022.9992946

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

Autores: Daniele Cappelletti, Ankit Gupta, Mustafa Khammash
Publicado en: 2019 IEEE 58th Conference on Decision and Control (CDC), 2019, Página(s) 945-950, ISBN 978-1-7281-1398-2
Editor: IEEE
DOI: 10.1109/CDC40024.2019.9029246

Quantification of loading effects in interconnections of stochastic reaction networks

Autores: Ankit Gupta, Patrik Durrenberger, Mustafa Khammash
Publicado en: 2019 18th European Control Conference (ECC), 2019, Página(s) 2165-2170, ISBN 978-3-907144-00-8
Editor: IEEE
DOI: 10.23919/ecc.2019.8796155

Cybergenetics: Theory and Methods for Genetic Control System

Autores: M. Khammash, M. Di Bernardo, D. Di Bernardo
Publicado en: 2019 IEEE 58th Conference on Decision and Control (CDC), 2019, Página(s) 916-926, ISBN 978-1-7281-1398-2
Editor: IEEE
DOI: 10.1109/CDC40024.2019.9030209

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

Autores: Corentin Briat, Mustafa Khammash
Publicado en: Proceedings of the 2022 Conference on Decision and Control, 2022
Editor: IEEE
DOI: 10.1109/cdc51059.2022.9993017

Derechos de propiedad intelectual

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

Número de solicitud/publicación: 20 21081158
Fecha: 2021-11-09

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

Número de solicitud/publicación: 20 21081158
Fecha: 2021-11-09

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Publicaciones

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