Optimization and historical contingency in living systems: a biophysical approach

Project Information

OptimHist

Grant agreement ID: 851173

DOI 10.3030/851173

EC signature date 13 November 2019

Start date 1 March 2020

End date 28 February 2026

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost € 1 498 214,00

EU contribution € 1 498 214,00

Coordinated by

ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE
Switzerland

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

Peer reviewed articles (15)

Pairing interacting protein sequences using masked language modeling

Author(s): Umberto Lupo, Damiano Sgarbossa, Anne-Florence Bitbol
Published in: Proceedings of the National Academy of Sciences, 2024, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1101/2023.08.14.553209

Frequent asymmetric migrations suppress natural selection in spatially structured populations

Author(s): Alia Abbara, Anne-Florence Bitbol
Published in: PNAS Nexus, 2024, ISSN 2752-6542
Publisher: Oxford University Press on behalf of the National Academy of Sciences
DOI: 10.1101/2023.06.19.545559

Extracting phylogenetic dimensions of coevolution reveals hidden functional signals

Author(s): Colavin, Alexandre; Atolia, Esha; Bitbol, Anne-Florence; Huang, Kerwyn Casey
Published in: Scientific Reports, Issue 20452322, 2022, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-04260-1

Interactions between pili affect the outcome of bacterial competition driven by the type VI secretion system

Author(s): Simon B. Otto, Richard Servajean, Alexandre Lemopoulos, Anne-Florence Bitbol, Melanie Blokesch
Published in: Current Biology, 2023, ISSN 0960-9822
Publisher: Cell Press
DOI: 10.1101/2023.10.25.564063

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

Author(s): Umberto Lupo, Damiano Sgarbossa, Anne-Florence Bitbol
Published in: Nature Communications, Issue 20411723, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-34032-y

Hydrodynamic flow and concentration gradients in the gut enhance neutral bacterial diversity

Author(s): Darka Labavić, Claude Loverdo, Anne-Florence Bitbol
Published in: Proceedings of the National Academy of Sciences of the USA, Issue 00278424, 2022, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2108671119

Impact of phylogeny on structural contact inference from protein sequence data

Author(s): Nicola Dietler; Umberto Lupo; Anne-Florence Bitbol
Published in: Journal of the Royal Society Interface, 2023, ISSN 1742-5689
Publisher: The Royal Society
DOI: 10.1098/rsif.2022.0707

Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins

Author(s): C.A. Gandarilla-Pérez, S. Pinilla, A.-F. Bitbol and M. Weigt
Published in: PLOS Computational Biology, 2023, ISSN 1553-734X
Publisher: Public Library of Science
DOI: 10.1371/journal.pcbi.1011010

Generative power of a protein language model trained on multiple sequence alignments

Author(s): Damiano Sgarbossa; Umberto Lupo; Anne-Florence Bitbol
Published in: eLife, 2023, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.79854

Mutant fate in spatially structured populations on graphs: connecting models to experiments

Author(s): Alia Abbara, Lisa Pagani, Celia García-Pareja, Anne-Florence Bitbol
Published in: PLOS Computational Biology, 2024, ISSN 1553-734X
Publisher: Public Library of Science
DOI: 10.1101/2024.02.06.579097

Evolution of cooperation in deme-structured populations on graphs

Author(s): Alix Moawad, Alia Abbara, Anne-Florence Bitbol
Published in: Physical Review E, 2023, ISSN 2470-0045
Publisher: American Physical Society
DOI: 10.1101/2023.09.18.558261

Impact of phylogeny on the inference of functional sectors from protein sequence data

Author(s): Nicola Dietler, Alia Abbara, Subham Choudhury, Anne-Florence Bitbol
Published in: PLOS Computational Biology, Issue 20, 2024, Page(s) e1012091, ISSN 1553-7358
Publisher: Public Library of Science
DOI: 10.1371/journal.pcbi.1012091

Impact of population size on early adaptation in rugged fitness landscapes

Author(s): Richard Servajean, Anne-Florence Bitbol
Published in: Philosphical Transactions of the Royal Society B: Biological Sciences, 2023, ISSN 0962-8436
Publisher: Royal Society of London
DOI: 10.1098/rstb.2022.0045

Toward a Universal Model for Spatially Structured Populations

Author(s): Loïc Marrec; Irene Lamberti; Anne-Florence Bitbol; Anne-Florence Bitbol; Anne-Florence Bitbol
Published in: Physical Review Letters, Issue 00319007, 2021, ISSN 0031-9007
Publisher: American Physical Society
DOI: 10.1103/physrevlett.127.218102

Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences

Author(s): Andonis Gerardos; Nicola Dietler; Anne-Florence Bitbol
Published in: PLOS Computational Biology, Issue 1553734X, 2022, ISSN 1553-734X
Publisher: Public Library of Science
DOI: 10.1371/journal.pcbi.1010147