Control Engineering of Biological Systems for Reliable Synthetic Biology Applications

Informacje na temat projektu

COSY-BIO

Identyfikator umowy o grant: 766840

DOI

10.3030/766840

Projekt został zamknięty

Data podpisania przez KE 24 Sierpnia 2017

Data rozpoczęcia 1 Października 2017

Data zakończenia 31 Marca 2021

Finansowanie w ramach

• EXCELLENT SCIENCE - Future and Emerging Technologies (FET)

Koszt całkowity

€ 2 996 856,25

Wkład UE

€ 2 975 345,00

Koordynowany przez

FONDAZIONE TELETHON ETS
Italy

CORDIS oferuje możliwość skorzystania z odnośników do publicznie dostępnych publikacji i rezultatów projektów realizowanych w ramach programów ramowych HORYZONT.

Odnośniki do rezultatów i publikacji związanych z poszczególnymi projektami 7PR, a także odnośniki do niektórych konkretnych kategorii wyników, takich jak zbiory danych i oprogramowanie, są dynamicznie pobierane z systemu OpenAIRE .

Rezultaty

Other (4)

Website and intranet portal

Website and intranet portal put online

Official Logo of COSY-BIO
Software tool suite
Software tool for model identification

Open Research Data Pilot (3)

Data Management plan
Final Dissemination and exploitation report
Detailed Dissemination and Exploitation plan

Demonstrators, pilots, prototypes (2)

Constructing and testing of reporters of the cell cycle
Optimal Experimental Design and BioModel Identification platform

Documents, reports (5)

Financial/Scientific report RP2
Comparison of model identification strategies
Modelling circuit/chassis interactions in high load conditions
Report of completed communication activity
Report on robust and adaptive control

Publikacje

Peer reviewed articles (28)

Self-adaptive biosystems through tunable genetic parts and circuits

Autorzy: Vittorio Bartoli, Mario di Bernardo, Thomas E. Gorochowski
Opublikowane w: Current Opinion in Systems Biology, Numer 24, 2020, Strona(/y) 78-85, ISSN 2452-3100
Wydawca: Elsevier
DOI: 10.1016/j.coisb.2020.10.006

Automatic synchronisation of the cell cycle in budding yeast through closed-loop feedback control

Autorzy: Giansimone Perrino, Sara Napolitano, Francesca Galdi, Antonella La Regina, Davide Fiore, Teresa Giuliano, Mario di Bernardo, Diego di Bernardo
Opublikowane w: Nature Communications, Numer 12/1, 2021, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-021-22689-w

ChipSeg: An Automatic Tool to Segment Bacterial and Mammalian Cells Cultured in Microfluidic Devices

Autorzy: 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
Opublikowane w: ACS Omega, Numer 6/4, 2021, Strona(/y) 2473-2476, ISSN 2470-1343
Wydawca: ACS Omega
DOI: 10.1021/acsomega.0c03906

In Vivo Feedback Control of an Antithetic Molecular-Titration Motif in Escherichia coli Using Microfluidics

Autorzy: Barbara Shannon, Criseida G. Zamora-Chimal, Lorena Postiglione, Davide Salzano, Claire S. Grierson, Lucia Marucci, Nigel J. Savery, Mario di Bernardo
Opublikowane w: ACS Synthetic Biology, Numer 9/10, 2020, Strona(/y) 2617-2624, ISSN 2161-5063
Wydawca: American Chemical Society
DOI: 10.1021/acssynbio.0c00105

Furthering genome design using models and algorithms

Autorzy: Joshua Rees-Garbutt, Jake Rightmyer, Jonathan R. Karr, Claire Grierson, Lucia Marucci
Opublikowane w: Current Opinion in Systems Biology, Numer 24, 2020, Strona(/y) 120-126, ISSN 2452-3100
Wydawca: Elsevier Ltd
DOI: 10.1016/j.coisb.2020.10.007

Analysis and Control of Genetic Toggle Switches Subject to Periodic Multi-Input Stimulation

Autorzy: Davide Fiore, Agostino Guarino, Mario di Bernardo
Opublikowane w: IEEE Control Systems Letters, Numer 3/2, 2019, Strona(/y) 278-283, ISSN 2475-1456
Wydawca: IEEE
DOI: 10.1109/lcsys.2018.2868925

Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology

Autorzy: 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
Opublikowane w: Frontiers in Bioengineering and Biotechnology, Numer 8, 2020, ISSN 2296-4185
Wydawca: Frontiers
DOI: 10.3389/fbioe.2020.00942

A universal biomolecular integral feedback controller for robust perfect adaptation

Autorzy: Stephanie K. Aoki, Gabriele Lillacci, Ankit Gupta, Armin Baumschlager, David Schweingruber, Mustafa Khammash
Opublikowane w: Nature, Numer 570/7762, 2019, Strona(/y) 533-537, ISSN 0028-0836
Wydawca: Nature Publishing Group
DOI: 10.1038/s41586-019-1321-1

Multicellular Feedback Control of a Genetic Toggle-Switch in Microbial Consortia

Autorzy: Davide Fiore, Davide Salzano, Enric Cristobal-Coppulo, Josep M. Olm, Mario di Bernardo
Opublikowane w: IEEE Control Systems Letters, Numer 5/1, 2021, Strona(/y) 151-156, ISSN 2475-1456
Wydawca: IEEE
DOI: 10.1109/lcsys.2020.3000954

Approximations of Countably Infinite Linear Programs over Bounded Measure Spaces

Autorzy: Juan Kuntz, Philipp Thomas, Guy-Bart Stan, Mauricio Barahona
Opublikowane w: SIAM Journal on Optimization, Numer 31/1, 2021, Strona(/y) 604-625, ISSN 1052-6234
Wydawca: Society for Industrial and Applied Mathematics
DOI: 10.1137/19m1268847

The Exit Time Finite State Projection Scheme: Bounding Exit Distributions and Occupation Measures of Continuous-Time Markov Chains

Autorzy: Juan Kuntz, Philipp Thomas, Guy-Bart Stan, Mauricio Barahona
Opublikowane w: SIAM Journal on Scientific Computing, Numer 41/2, 2019, Strona(/y) A748-A769, ISSN 1064-8275
Wydawca: Society for Industrial and Applied Mathematics
DOI: 10.1137/18m1168261

Cheetah: A Computational Toolkit for Cybergenetic Control

Autorzy: 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
Opublikowane w: ACS Synthetic Biology, Numer 10/5, 2021, Strona(/y) 979-989, ISSN 2161-5063
Wydawca: American Chemical Society
DOI: 10.1021/acssynbio.0c00463

Stationary Distributions of Continuous-Time Markov Chains: A Review of Theory and Truncation-Based Approximations

Autorzy: Juan Kuntz, Philipp Thomas, Guy-Bart Stan, Mauricio Barahona
Opublikowane w: SIAM Review, Numer 63/1, 2021, Strona(/y) 3-64, ISSN 0036-1445
Wydawca: Society for Industrial and Applied Mathematics
DOI: 10.1137/19m1289625

A network model of Italy shows that intermittent regional strategies can alleviate the COVID-19 epidemic

Autorzy: 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
Opublikowane w: Nature Communications, Numer 11/1, 2020, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-020-18827-5

Face coverings and respiratory tract droplet dispersion

Autorzy: Lucia Bandiera, Geethanjali Pavar, Gabriele Pisetta, Shuji Otomo, Enzo Mangano, Jonathan R. Seckl, Paul Digard, Emanuela Molinari, Filippo Menolascina, Ignazio Maria Viola
Opublikowane w: Royal Society Open Science, Numer 7/12, 2020, Strona(/y) 201663, ISSN 2054-5703
Wydawca: Royal Society Publishing
DOI: 10.1098/rsos.201663

Tools for engineering coordinated system behaviour in synthetic microbial consortia

Autorzy: Nicolas Kylilis, Zoltan A. Tuza, Guy-Bart Stan, Karen M. Polizzi
Opublikowane w: Nature Communications, Numer 9/1, 2018, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-018-05046-2

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

Autorzy: Marc Rullan, Dirk Benzinger, Gregor W. Schmidt, Andreas Milias-Argeitis, Mustafa Khammash
Opublikowane w: Molecular Cell, Numer 70/4, 2018, Strona(/y) 745-756.e6, ISSN 1097-2765
Wydawca: Cell Press
DOI: 10.1016/j.molcel.2018.04.012

On-Line Optimal Input Design Increases the Efficiency and Accuracy of the Modelling of an Inducible Synthetic Promoter

Autorzy: Lucia Bandiera, Zhaozheng Hou, Varun Kothamachu, Eva Balsa-Canto, Peter Swain, Filippo Menolascina
Opublikowane w: Processes, Numer 6/9, 2018, Strona(/y) 148, ISSN 2227-9717
Wydawca: MDPI AG
DOI: 10.3390/pr6090148

Synthetic control systems for high performance gene expression in mammalian cells

Autorzy: Gabriele Lillacci, Yaakov Benenson, Mustafa Khammash
Opublikowane w: Nucleic Acids Research, Numer 46/18, 2018, Strona(/y) 9855-9863, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gky795

Characterization and mitigation of gene expression burden in mammalian cells

Autorzy: Timothy Frei, Federica Cella, Fabiana Tedeschi, Joaquín Gutiérrez, Guy-Bart Stan, Mustafa Khammash, Velia Siciliano
Opublikowane w: Nature Communications, Numer 11/1, 2020, Strona(/y) 4641, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-020-18392-x

Synchronisation of yeast cell cycle through quorum sensing coupling

Autorzy: Giansimone Perrino, Diego di Bernardo
Opublikowane w: IFAC-PapersOnLine, Numer 53/2, 2020, Strona(/y) 16779-16784, ISSN 2405-8963
Wydawca: Elsevier, IFAC Publisher
DOI: 10.1016/j.ifacol.2020.12.1143

Autonomous and Assisted Control for Synthetic Microbiology

Autorzy: Alvaro Banderas, Matthias Le Bec, Céline Cordier, Pascal Hersen
Opublikowane w: International Journal of Molecular Sciences, Numer 21/23, 2020, Strona(/y) 9223, ISSN 1422-0067
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms21239223

Regulation of Gene Expression and Signaling Pathway Activity in Mammalian Cells by Automated Microfluidics Feedback Control

Autorzy: Lorena Postiglione, Sara Napolitano, Elisa Pedone, Daniel L. Rocca, Francesco Aulicino, Marco Santorelli, Barbara Tumaini, Lucia Marucci, Diego di Bernardo
Opublikowane w: ACS Synthetic Biology, Numer 7/11, 2018, Strona(/y) 2558-2565, ISSN 2161-5063
Wydawca: American Chemical Society
DOI: 10.1021/acssynbio.8b00235

Quantitative Characterization of α-Synuclein Aggregation in Living Cells through Automated Microfluidics Feedback Control

Autorzy: Giansimone Perrino, Cathal Wilson, Marco Santorelli, Diego di Bernardo
Opublikowane w: Cell Reports, Numer 27/3, 2019, Strona(/y) 916-927.e5, ISSN 2211-1247
Wydawca: Cell Press
DOI: 10.1016/j.celrep.2019.03.081

Balancing Cell Populations Endowed with a Synthetic Toggle Switch via Adaptive Pulsatile Feedback Control

Autorzy: Agostino Guarino, Davide Fiore, Davide Salzano, Mario di Bernardo
Opublikowane w: ACS Synthetic Biology, Numer 9/4, 2020, Strona(/y) 793-803, ISSN 2161-5063
Wydawca: American Chemical Society
DOI: 10.1021/acssynbio.9b00464

A low-cost, open-source Turbidostat design for in-vivo control experiments in Synthetic Biology

Autorzy: Agostino Guarino, Barbara Shannon, Lucia Marucci, Claire Grierson, Nigel Savery, Mario di Bernardo
Opublikowane w: IFAC-PapersOnLine, Numer 52/26, 2019, Strona(/y) 244-248, ISSN 2405-8963
Wydawca: Elsevier Ltd
DOI: 10.1016/j.ifacol.2019.12.265

A finite state projection method for steady-state sensitivity analysis of stochastic reaction networks

Autorzy: Patrik Dürrenberger, Ankit Gupta, Mustafa Khammash
Opublikowane w: The Journal of Chemical Physics, Numer 150/13, 2019, Strona(/y) 134101, ISSN 0021-9606
Wydawca: American Institute of Physics
DOI: 10.1063/1.5085271

Tunable genetic devices through simultaneous control of transcription and translation

Autorzy: Vittorio Bartoli, Grace A. Meaker, Mario di Bernardo, Thomas E. Gorochowski
Opublikowane w: Nature Communications, Numer 11/1, 2020, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-020-15653-7

Conference proceedings (10)

Towards feedback control of the cell-cycle across a population of yeast cells

Autorzy: Giansimone Perrino, Davide Fiore, Sara Napolitano, Mario di Bernardo, Diego di Bernardo
Opublikowane w: 2019 18th European Control Conference (ECC), 2019, Strona(/y) 2644-2650, ISBN 978-3-907144-00-8
Wydawca: IEEE
DOI: 10.23919/ecc.2019.8796301

Cybergenetics: Theory and Methods for Genetic Control System

Autorzy: M. Khammash, M. Di Bernardo, D. Di Bernardo
Opublikowane w: 2019 IEEE 58th Conference on Decision and Control (CDC), 2019, Strona(/y) 916-926, ISBN 978-1-7281-1398-2
Wydawca: IEEE
DOI: 10.1109/cdc40024.2019.9030209

Optimal Parameter Tuning of Feedback Controllers with Application to Biomolecular Antithetic Integral Control

Autorzy: Maurice Filo, Mustafa Khammash
Opublikowane w: 2019 IEEE 58th Conference on Decision and Control (CDC), 2019, Strona(/y) 951-957, ISBN 978-1-7281-1398-2
Wydawca: IEEE
DOI: 10.1109/cdc40024.2019.9029430

Quantification of loading effects in interconnections of stochastic reaction networks

Autorzy: Ankit Gupta, Patrik Durrenberger, Mustafa Khammash
Opublikowane w: 2019 18th European Control Conference (ECC), 2019, Strona(/y) 2165-2170, ISBN 978-3-907144-00-8
Wydawca: IEEE
DOI: 10.23919/ecc.2019.8796155

Can optimal experimental design serve as a tool to characterize highly non-linear synthetic circuits?

Autorzy: Maxim Kryukov, Arthur Carcano, Gregory Batt, Jakob Ruess
Opublikowane w: 2019 18th European Control Conference (ECC), 2019, Strona(/y) 1176-1181, ISBN 978-3-907144-00-8
Wydawca: IEEE
DOI: 10.23919/ecc.2019.8796209

Ratiometric control for differentiation of cell populations endowed with synthetic toggle switches

Autorzy: Davide Salzano, Davide Fiore, Mario di Bernardo
Opublikowane w: 2019 IEEE 58th Conference on Decision and Control (CDC), 2019, Strona(/y) 927-932, ISBN 978-1-7281-1398-2
Wydawca: IEEE
DOI: 10.1109/cdc40024.2019.9029592

Optimal control of an artificial microbial differentiation system for protein bioproduction

Autorzy: Elise Weill, Virgile Andreani, Chetan Aditya, Pierre Martinon, Jakob Ruess, Gregory Batt, Frederic Bonnans
Opublikowane w: 2019 18th European Control Conference (ECC), 2019, Strona(/y) 2663-2668, ISBN 978-3-907144-00-8
Wydawca: IEEE
DOI: 10.23919/ecc.2019.8795858

In-silico feedback control of a MIMO synthetic Toggle Switch via Pulse-Width Modulation

Autorzy: Agostino Guarino, Davide Fiore, Mario Di Bernardo
Opublikowane w: 2019 18th European Control Conference (ECC), 2019, Strona(/y) 680-685, ISBN 978-3-907144-00-8
Wydawca: IEEE
DOI: 10.23919/ecc.2019.8795642

Optimally designed vs intuition-driven inputs: the study case of promoter activity modelling

Autorzy: L. Bandiera, V. Kothamachu, E. Balsa-Canto, P. S. Swain, F. Menolascina
Opublikowane w: 2018 IEEE Conference on Decision and Control (CDC), 2018, Strona(/y) 1880-1885, ISBN 978-1-5386-1395-5
Wydawca: IEEE
DOI: 10.1109/cdc.2018.8618920

Characterization of Biologically Relevant Network Structures form Time-series Data

Autorzy: Zoltan A. Tuza, Guy-Bart Stan
Opublikowane w: 2018 IEEE Conference on Decision and Control (CDC), 2018, Strona(/y) 1089-1095, ISBN 978-1-5386-1395-5
Wydawca: IEEE
DOI: 10.1109/cdc.2018.8619360

Other (5)

Exploring the Dynamics of Nonlinear Biochemical Systems using Control-Based Continuation

Autorzy: Brandon Gomes, Irene de Cesare, Agostino Guarino, Mario di Bernardo, Ludovic Renson, Lucia Marucci
Opublikowane w: 2019
Wydawca: biorxiv
DOI: 10.1101/695866

A Class of Simple Biomolecular Antithetic Proportional-Integral-Derivative Controllers

Autorzy: Maurice Filo, Mustafa Khammash
Opublikowane w: 2021
Wydawca: biorxiv
DOI: 10.1101/2021.03.21.436342;

Tutorial of numerical continuation and bifurcation theory for systems and synthetic biology

Autorzy: Mark Blyth, Ludovic Renson, Lucia Marucci
Opublikowane w: arxiv, 2020
Wydawca: arxiv
DOI: 10.5281/zenodo.4835824

Feedback control promotes synchronisation of the cell-cycle across a population of yeast cells

Autorzy: Giansimone Perrino, Davide Fiore, Sara Napolitano, Francesca Galdi, Antonella La Regina, Mario di Bernardo, and Diego di Bernardo
Opublikowane w: biorXiv, 2019
Wydawca: biorXiv
DOI: 10.1101/590844

Self-adaptive Biosystems Through Tunable Genetic Parts and Circuits

Autorzy: Vittorio Bartoli, Mario di Bernardo, Thomas E. Gorochowski
Opublikowane w: 2020
Wydawca: Preprints
DOI: 10.20944/preprints202007.0751.v2

Book chapters (1)

Minimal Genome Design Algorithms Using Whole-Cell Models

Autorzy: Joshua Rees-Garbutt, Oliver Chalkley, Claire Grierson, Lucia Marucci
Opublikowane w: Computational Methods in Synthetic Biology, Numer 2189, 2021, Strona(/y) 183-198, ISBN 978-1-0716-0821-0
Wydawca: Springer US
DOI: 10.1007/978-1-0716-0822-7_14