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Cybergenetics: Theory and Design Tools for Biomolecular Control Systems

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Publications

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
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
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
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
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
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
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
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
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
DOI: 10.1038/s41467-018-05882-2

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
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
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
DOI: 10.1109/CDC40024.2019.9030209