Building biological computers from bacterial populations

Project Information

SynBioBrain

Grant agreement ID: 770835

DOI

10.3030/770835

Project closed

EC signature date 23 April 2018

Start date 1 May 2018

End date 31 October 2024

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 998 025,00

EU contribution

€ 1 998 025,00

Coordinated by

UNIVERSITY COLLEGE LONDON
United Kingdom

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

Non-peer reviewed articles (2)

Single strain control of microbial consortia

Author(s): Fedorec AJ, Karkaria BD, Sulu M, Barnes CP
Published in: Nature Communications, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1101/2019.12.23.887331

SynBioBrain: building biological computers from bacterial

Author(s): Neythen J Treloar, Ke Yan Wen, Alex JH Fedorec, Chris P Barnes
Published in: The Project Repository Journal, Issue 11, 2021, Page(s) 32-35, ISSN 2632-4067
Publisher: European Dissemination Media Agency Limited
DOI: 10.54050/prj1117751

Peer reviewed articles (12)

From Microbial Communities to Distributed Computing Systems

Author(s): Behzad D. Karkaria, Neythen J. Treloar, Chris P. Barnes, Alex J. H. Fedorec
Published in: Frontiers in Bioengineering and Biotechnology, Issue 8, 2020, ISSN 2296-4185
Publisher: Frontiers Media S.A.
DOI: 10.3389/fbioe.2020.00834

FlopR: An Open Source Software Package for Calibration and Normalization of Plate Reader and Flow Cytometry Data

Author(s): Alex J. H. Fedorec, Clare M. Robinson, Ke Yan Wen, Chris P. Barnes
Published in: ACS Synthetic Biology, Issue 9/9, 2020, Page(s) 2258-2266, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.0c00296

Toward Engineering Biosystems With Emergent Collective Functions

Author(s): Thomas E. Gorochowski, Sabine Hauert, Jan-Ulrich Kreft, Lucia Marucci, Namid R. Stillman, T.-Y. Dora Tang, Lucia Bandiera, Vittorio Bartoli, Daniel O. R. Dixon, Alex J. H. Fedorec, Harold Fellermann, Alexander G. Fletcher, Tim Foster, Luca Giuggioli, Antoni Matyjaszkiewicz, Scott McCormick, Sandra Montes Olivas, Jonathan Naylor, Ana Rubio Denniss, Daniel Ward
Published in: Frontiers in Bioengineering and Biotechnology, Issue 8, 2020, ISSN 2296-4185
Publisher: Frontiers Media SA
DOI: 10.3389/fbioe.2020.00705

Emergent digital bio-computation through spatial diffusion and engineered bacteria

Author(s): Alex J. H. Fedorec, Neythen J. Treloar, Ke Yan Wen, Linda Dekker, Qing Hsuan Ong, Gabija Jurkeviciute, Enbo Lyu, Jack W. Rutter, Kathleen J. Y. Zhang, Luca Rosa, Alexey Zaikin, Chris P. Barnes
Published in: Nature Communications, Issue 15, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-49264-3

Deep Reinforcement Learning for Optimal Experimental Design in Biology

Author(s): Neythen J. Treloar, Nathan Braniff, Brian Ingalls, Chris P. Barnes
Published in: PLOS Computational Biology, 2024, ISSN 1553-7358
Publisher: PLOS
DOI: 10.1101/2022.05.09.491138

Chaos in synthetic microbial communities

Author(s): Behzad D. Karkaria, Angelika Manhart, Alex J. H. Fedorec, Chris P. Barnes
Published in: PLOS Computational Biology, Issue 18, 2023, Page(s) e1010548, ISSN 1553-7358
Publisher: Public Library of Science (PLoS)
DOI: 10.1371/journal.pcbi.1010548

Towards an Aspect-Oriented Design and Modelling Framework for Synthetic Biology

Author(s): Philipp Boeing, Miriam Leon, Darren Nesbeth, Anthony Finkelstein, Chris Barnes
Published in: Processes, Issue 6/9, 2018, Page(s) 167, ISSN 2227-9717
Publisher: MDPI AG
DOI: 10.3390/pr6090167

Automated design of synthetic microbial communities

Author(s): Behzad D. Karkaria, Alex J. H. Fedorec, Chris P. Barnes
Published in: Nature Communications, Issue 12, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-20756-2

Automated design of gene circuits with optimal mushroom-bifurcation behavior

Author(s): Irene Otero-Muras, Ruben Perez-Carrasco, Julio R. Banga, Chris P. Barnes
Published in: iScience, Issue 26, 2025, Page(s) 106836, ISSN 2589-0042
Publisher: Cell Press
DOI: 10.1016/j.isci.2023.106836

Detecting Changes in the Caenorhabditis elegans Intestinal Environment Using an Engineered Bacterial Biosensor.

Author(s): Rutter, Jack W.; Ozdemir, Tanel; Galimov, Evgeniy R.; Quintaneiro, Leonor M.; Rosa, Luca; Thomas, Geraint M.; Cabreiro, Filipe; Barnes, Chris P.
Published in: ACS Synthetic Biology, Issue 1, 2019, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.9b00166

Engineered acetoacetate-inducible whole-cell biosensors based on the AtoSC two-component system

Author(s): Jack W. Rutter, Linda Dekker, Alex J. H. Fedorec, David T. Gonzales, Ke Yan Wen, Lewis E. S. Tanner, Emma Donovan, Tanel Ozdemir, Geraint Thomas, Chris P. Barnes
Published in: Biotechnology and Bioengineering, 2024, ISSN 1097-0290
Publisher: Wiley Periodicals LLC (United States)
DOI: 10.1101/035972

Deep reinforcement learning for the control of microbial co-cultures in bioreactors

Author(s): Neythen J. Treloar, Alex J. H. Fedorec, Brian Ingalls, Chris P. Barnes
Published in: PLOS Computational Biology, Issue 16/4, 2020, Page(s) e1007783, ISSN 1553-7358
Publisher: PLOS
DOI: 10.1371/journal.pcbi.1007783