Publications

All COSY-BIO Publications are Open Access in ZENODO

Journal Articles

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Title of the

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DOI

Tools for engineering coordinated system behaviour in synthetic microbial consortia Nicolas Kylilis, Zoltan A. Tuza, Guy-Bart Stan, Karen M. Polizzi Nature Communications 10.1038/s41467-018-05046-2
An Optogenetic Platform for Real-Time, Single-Cell Interrogation of Stochastic Transcriptional Regulation Marc Rullan, Dirk Benzinger, Gregor W. Schmidt, Andreas Milias-Argeitis, Mustafa Khammash Molecular Cell 10.1016/j.molcel.2018.04.012
Synthetic control systems for high performance gene expression in mammalian cells Gabriele Lillacci, Yaakov Benenson, Mustafa Khammash Nucleic Acids Research 10.1093/nar/gky795
On-Line Optimal Input Design Increases the Efficiency and Accuracy of the Modelling of an Inducible Synthetic Promoter Lucia Bandiera, Zhaozheng Hou, Varun Kothamachu, Eva Balsa-Canto, Peter Swain, Filippo Menolascina Processes 10.3390/pr6090148
The Exit Time Finite State Projection Scheme: Bounding Exit Distributions and Occupation Measures of Continuous-Time Markov Chains Juan Kuntz, Philipp Thomas, Guy-Bart Stan, Mauricio Barahona SIAM Journal on Scientific Computing 10.1137/18m1168261
Multicellular Feedback Control of a Genetic Toggle-Switch in Microbial Consortia Davide Fiore, Davide Salzano, Enric Cristobal-Coppulo, Josep M. Olm, Mario di Bernardo IEEE Control Systems Letters 10.1109/lcsys.2020.3000954
A low-cost, open-source Turbidostat design for in-vivo control experiments in Synthetic Biology Agostino Guarino, Barbara Shannon, Lucia Marucci, Claire Grierson, Nigel Savery, Mario di Bernardo IFAC-PapersOnLine 10.1016/j.ifacol.2019.12.265
Balancing Cell Populations Endowed with a Synthetic Toggle Switch via Adaptive Pulsatile Feedback Control Agostino Guarino, Davide Fiore, Davide Salzano, Mario di Bernardo ACS Synthetic Biology 10.1021/acssynbio.9b00464
Furthering genome design using models and algorithms Joshua Rees-Garbutt, Jake Rightmyer, Jonathan R. Karr, Claire Grierson, Lucia Marucci Current Opinion in Systems Biology 10.1016/j.coisb.2020.10.007
Synchronisation of yeast cell cycle through quorum sensing coupling Giansimone Perrino, Diego di Bernardo IFAC-PapersOnLine 10.1016/j.ifacol.2020.12.1143
Regulation of Gene Expression and Signaling Pathway Activity in Mammalian Cells by Automated Microfluidics Feedback Control Lorena Postiglione, Sara Napolitano, Elisa Pedone, Daniel L. Rocca, Francesco Aulicino, Marco Santorelli, Barbara Tumaini, Lucia Marucci, Diego di Bernardo ACS Synthetic Biology 10.1021/acssynbio.8b00235
Face coverings and respiratory tract droplet dispersion Lucia Bandiera, Geethanjali Pavar, Gabriele Pisetta, Shuji Otomo, Enzo Mangano, Jonathan R. Seckl, Paul Digard, Emanuela Molinari, Filippo Menolascina, Ignazio Maria Viola Royal Society Open Science 10.1098/rsos.201663
A universal biomolecular integral feedback controller for robust perfect adaptation Stephanie K. Aoki, Gabriele Lillacci, Ankit Gupta, Armin Baumschlager, David Schweingruber, Mustafa Khammash Nature 10.1038/s41586-019-1321-1
Analysis and Control of Genetic Toggle Switches Subject to Periodic Multi-Input Stimulation Davide Fiore, Agostino Guarino, Mario di Bernardo IEEE Control Systems Letters 10.1109/lcsys.2018.2868925
Tunable genetic devices through simultaneous control of transcription and translation Vittorio Bartoli, Grace A. Meaker, Mario di Bernardo, Thomas E. Gorochowski Nature Communications 10.1038/s41467-020-15653-7
Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology Lucia Marucci, Matteo Barberis, Jonathan Karr, Oliver Ray, Paul R. Race, Miguel de Souza Andrade, Claire Grierson, Stefan Andreas Hoffmann, Sophie Landon, Elibio Rech, Joshua Rees-Garbutt, Richard Seabrook, William Shaw, Christopher Woods Frontiers in Bioengineering and Biotechnology 10.3389/fbioe.2020.00942
Autonomous and Assisted Control for Synthetic Microbiology Alvaro Banderas, Matthias Le Bec, Céline Cordier, Pascal Hersen International Journal of Molecular Sciences 10.3390/ijms21239223
ChipSeg: An Automatic Tool to Segment Bacterial and Mammalian Cells Cultured in Microfluidic Devices Irene de Cesare, Criseida G. Zamora-Chimal, Lorena Postiglione, Mahmoud Khazim, Elisa Pedone, Barbara Shannon, Gianfranco Fiore, Giansimone Perrino, Sara Napolitano, Diego di Bernardo, Nigel J. Savery, Claire Grierson, Mario di Bernardo, Lucia Marucci ACS Omega 10.1021/acsomega.0c03906
In Vivo Feedback Control of an Antithetic Molecular-Titration Motif in Escherichia coli Using Microfluidics Barbara Shannon, Criseida G. Zamora-Chimal, Lorena Postiglione, Davide Salzano, Claire S. Grierson, Lucia Marucci, Nigel J. Savery, Mario di Bernardo ACS Synthetic Biology 10.1021/acssynbio.0c00105
Characterization and mitigation of gene expression burden in mammalian cells Timothy Frei, Federica Cella, Fabiana Tedeschi, Joaquín Gutiérrez, Guy-Bart Stan, Mustafa Khammash, Velia Siciliano Nature Communications 10.1038/s41467-020-18392-x
Quantitative Characterization of α-Synuclein Aggregation in Living Cells through Automated Microfluidics Feedback Control Giansimone Perrino, Cathal Wilson, Marco Santorelli, Diego di Bernardo Cell Reports 10.1016/j.celrep.2019.03.081
Approximations of Countably Infinite Linear Programs over Bounded Measure Spaces Juan Kuntz, Philipp Thomas, Guy-Bart Stan, Mauricio Barahona SIAM Journal on Optimization 10.1137/19m1268847
A network model of Italy shows that intermittent regional strategies can alleviate the COVID-19 epidemic Fabio Della Rossa, Davide Salzano, Anna Di Meglio, Francesco De Lellis, Marco Coraggio, Carmela Calabrese, Agostino Guarino, Ricardo Cardona-Rivera, Pietro De Lellis, Davide Liuzza, Francesco Lo Iudice, Giovanni Russo, Mario di Bernardo Nature Communications 10.1038/s41467-020-18827-5
Automatic synchronisation of the cell cycle in budding yeast through closed-loop feedback control Giansimone Perrino, Sara Napolitano, Francesca Galdi, Antonella La Regina, Davide Fiore, Teresa Giuliano, Mario di Bernardo, Diego di Bernardo Nature Communications 10.1038/s41467-021-22689-w
Cheetah: A Computational Toolkit for Cybergenetic Control Elisa Pedone, Irene de Cesare, Criseida G. Zamora-Chimal, David Haener, Lorena Postiglione, Antonella La Regina, Barbara Shannon, Nigel J. Savery, Claire S. Grierson, Mario di Bernardo, Thomas E. Gorochowski, Lucia Marucci ACS Synthetic Biology 10.1021/acssynbio.0c00463
Self-adaptive biosystems through tunable genetic parts and circuits Vittorio Bartoli, Mario di Bernardo, Thomas E. Gorochowski Current Opinion in Systems Biology 10.1016/j.coisb.2020.10.006
Stationary Distributions of Continuous-Time Markov Chains: A Review of Theory and Truncation-Based Approximations Juan Kuntz, Philipp Thomas, Guy-Bart Stan, Mauricio Barahona SIAM Review 10.1137/19m1289625
A finite state projection method for steady-state sensitivity analysis of stochastic reaction networks Patrik Dürrenberger, Ankit Gupta, Mustafa Khammash The Journal of Chemical Physics 10.1063/1.5085271

 

 Other Publications 

 

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Chapter in a Book Minimal Genome Design Algorithms Using Whole-Cell Models Joshua Rees-Garbutt, Oliver Chalkley, Claire Grierson, Lucia Marucci Computational Methods in Synthetic Biology 10.1007/978-1-0716-0822-7_14
Other Tutorial of numerical continuation and bifurcation theory for systems and synthetic biology Mark Blyth, Ludovic Renson, Lucia Marucci arxiv 10.5281/zenodo.4835824
Other A Class of Simple Biomolecular Antithetic Proportional-Integral-Derivative Controllers Maurice Filo, Mustafa Khammash   10.1101/2021.03.21.436342;
Other Feedback control promotes synchronisation of the cell-cycle across a population of yeast cells Giansimone Perrino, Davide Fiore, Sara Napolitano, Francesca Galdi, Antonella La Regina, Mario di Bernardo, and Diego di Bernardo biorXiv 10.1101/590844
Other Exploring the Dynamics of Nonlinear Biochemical Systems using Control-Based Continuation Brandon Gomes, Irene de Cesare, Agostino Guarino, Mario di Bernardo, Ludovic Renson, Lucia Marucci   10.1101/695866
Other Self-adaptive Biosystems Through Tunable Genetic Parts and Circuits Vittorio Bartoli, Mario di Bernardo, Thomas E. Gorochowski   10.20944/preprints202007.0751.v2
Publication in Conference proceedings/Workshop Can optimal experimental design serve as a tool to characterize highly non-linear synthetic circuits? Maxim Kryukov, Arthur Carcano, Gregory Batt, Jakob Ruess 2019 18th European Control Conference (ECC) 10.23919/ecc.2019.8796209
Publication in Conference proceedings/Workshop Optimally designed vs intuition-driven inputs: the study case of promoter activity modelling L. Bandiera, V. Kothamachu, E. Balsa-Canto, P. S. Swain, F. Menolascina 2018 IEEE Conference on Decision and Control (CDC) 10.1109/cdc.2018.8618920
Publication in Conference proceedings/Workshop Optimal Parameter Tuning of Feedback Controllers with Application to Biomolecular Antithetic Integral Control Maurice Filo, Mustafa Khammash 2019 IEEE 58th Conference on Decision and Control (CDC) 10.1109/cdc40024.2019.9029430
Publication in Conference proceedings/Workshop In-silico feedback control of a MIMO synthetic Toggle Switch via Pulse-Width Modulation Agostino Guarino, Davide Fiore, Mario Di Bernardo 2019 18th European Control Conference (ECC) 10.23919/ecc.2019.8795642
Publication in Conference proceedings/Workshop Ratiometric control for differentiation of cell populations endowed with synthetic toggle switches Davide Salzano, Davide Fiore, Mario di Bernardo 2019 IEEE 58th Conference on Decision and Control (CDC) 10.1109/cdc40024.2019.9029592
Publication in Conference proceedings/Workshop Quantification of loading effects in interconnections of stochastic reaction networks Ankit Gupta, Patrik Durrenberger, Mustafa Khammash 2019 18th European Control Conference (ECC) 10.23919/ecc.2019.8796155
Publication in Conference proceedings/Workshop Cybergenetics: Theory and Methods for Genetic Control System M. Khammash, M. Di Bernardo, D. Di Bernardo 2019 IEEE 58th Conference on Decision and Control (CDC) 10.1109/cdc40024.2019.9030209
Publication in Conference proceedings/Workshop Towards feedback control of the cell-cycle across a population of yeast cells Giansimone Perrino, Davide Fiore, Sara Napolitano, Mario di Bernardo, Diego di Bernardo 2019 18th European Control Conference (ECC) 10.23919/ecc.2019.8796301
Publication in Conference proceedings/Workshop Optimal control of an artificial microbial differentiation system for protein bioproduction Elise Weill, Virgile Andreani, Chetan Aditya, Pierre Martinon, Jakob Ruess, Gregory Batt, Frederic Bonnans 2019 18th European Control Conference (ECC) 10.23919/ecc.2019.8795858
Publication in Conference proceedings/Workshop Characterization of Biologically Relevant Network Structures form Time-series Data Zoltan A. Tuza, Guy-Bart Stan 2018 IEEE Conference on Decision and Control (CDC) 10.1109/cdc.2018.8619360