Optimization and historical contingency in living systems: a biophysical approach

Informazioni relative al progetto

OptimHist

ID dell’accordo di sovvenzione: 851173

DOI

10.3030/851173

Progetto chiuso

Data della firma CE 13 Novembre 2019

Data di avvio 1 Marzo 2020

Data di completamento 28 Febbraio 2026

Finanziato da

• EXCELLENT SCIENCE - European Research Council (ERC)

Costo totale

€ 1 498 214,00

Contributo UE

€ 1 498 214,00

Coordinato da

ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE
Switzerland

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Pubblicazioni

Peer reviewed articles (25)

Pairing interacting protein sequences using masked language modeling

Autori: Umberto Lupo, Damiano Sgarbossa, Anne-Florence Bitbol
Pubblicato in: Proceedings of the National Academy of Sciences, 2024, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1101/2023.08.14.553209

Frequent asymmetric migrations suppress natural selection in spatially structured populations

Autori: Alia Abbara, Anne-Florence Bitbol
Pubblicato in: PNAS Nexus, 2024, ISSN 2752-6542
Editore: 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

Autori: Colavin, Alexandre; Atolia, Esha; Bitbol, Anne-Florence; Huang, Kerwyn Casey
Pubblicato in: Scientific Reports, Numero 20452322, 2022, ISSN 2045-2322
Editore: Nature Publishing Group
DOI: 10.1038/s41598-021-04260-1

DiffPaSS—high-performance differentiable pairing of protein sequences using soft scores

Autori: Umberto Lupo, Damiano Sgarbossa, Martina Milighetti, Anne-Florence Bitbol
Pubblicato in: Bioinformatics, Numero 41, 2024, ISSN 1367-4811
Editore: Oxford University Press (OUP)
DOI: 10.1093/bioinformatics/btae738

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

Autori: Simon B. Otto, Richard Servajean, Alexandre Lemopoulos, Anne-Florence Bitbol, Melanie Blokesch
Pubblicato in: Current Biology, 2023, ISSN 0960-9822
Editore: Cell Press
DOI: 10.1101/2023.10.25.564063

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

Autori: Umberto Lupo, Damiano Sgarbossa, Anne-Florence Bitbol
Pubblicato in: Nature Communications, Numero 20411723, 2022, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-022-34032-y

Out-of-Equilibrium Selection Pressure Enhances Inference from Protein Sequence Data

Autori: Nicola Dietler, Cyril Malbranke, Anne-Florence Bitbol
Pubblicato in: Physical Review Letters, Numero 136, 2026, ISSN 0031-9007
Editore: American Physical Society
DOI: 10.1103/1ht9-njrr

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

Autori: Darka Labavić, Claude Loverdo, Anne-Florence Bitbol
Pubblicato in: Proceedings of the National Academy of Sciences of the USA, 2022, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.2108671119

Spatial structure facilitates evolutionary rescue by drug resistance

Autori: Cecilia Fruet, Ella Linxia Müller, Claude Loverdo, Anne-Florence Bitbol
Pubblicato in: PLOS Computational Biology, Numero 21, 2025, Pagina/e e1012861, ISSN 1553-7358
Editore: Public Library of Science (PLoS)
DOI: 10.1371/journal.pcbi.1012861

Bridging Wright–Fisher and Moran models

Autori: Arthur Alexandre, Alia Abbara, Cecilia Fruet, Claude Loverdo, Anne-Florence Bitbol
Pubblicato in: Journal of Theoretical Biology, Numero 599, 2025, Pagina/e 112030, ISSN 0022-5193
Editore: Academic Press
DOI: 10.1016/j.jtbi.2024.112030

Impact of phylogeny on structural contact inference from protein sequence data

Autori: Nicola Dietler; Umberto Lupo; Anne-Florence Bitbol
Pubblicato in: Journal of the Royal Society Interface, 2023, ISSN 1742-5689
Editore: The Royal Society
DOI: 10.1098/rsif.2022.0707

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

Autori: C.A. Gandarilla-Pérez, S. Pinilla, A.-F. Bitbol and M. Weigt
Pubblicato in: PLOS Computational Biology, 2023, ISSN 1553-734X
Editore: Public Library of Science
DOI: 10.1371/journal.pcbi.1011010

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

Autori: Damiano Sgarbossa; Umberto Lupo; Anne-Florence Bitbol
Pubblicato in: eLife, 2023, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/elife.79854

ProtMamba: a homology-aware but alignment-free protein state space model

Autori: Damiano Sgarbossa, Cyril Malbranke, Anne-Florence Bitbol
Pubblicato in: Bioinformatics, Numero 41, 2025, ISSN 1367-4811
Editore: Oxford University Press (OUP)
DOI: 10.1093/bioinformatics/btaf348

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

Autori: Alia Abbara, Lisa Pagani, Celia García-Pareja, Anne-Florence Bitbol
Pubblicato in: PLOS Computational Biology, 2024, ISSN 1553-734X
Editore: Public Library of Science
DOI: 10.1101/2024.02.06.579097

Environment heterogeneity creates fast amplifiers of natural selection in graph-structured populations

Autori: Cecilia Fruet, Arthur Alexandre, Alia Abbara, Claude Loverdo, Anne-Florence Bitbol
Pubblicato in: Nature Communications, 2026, Pagina/e in press, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1101/2025.07.31.667961

Evolution of cooperation in deme-structured populations on graphs

Autori: Alix Moawad, Alia Abbara, Anne-Florence Bitbol
Pubblicato in: Physical Review E, 2023, ISSN 2470-0045
Editore: American Physical Society
DOI: 10.1101/2023.09.18.558261

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

Autori: Nicola Dietler, Alia Abbara, Subham Choudhury, Anne-Florence Bitbol
Pubblicato in: PLOS Computational Biology, Numero 20, 2024, Pagina/e e1012091, ISSN 1553-7358
Editore: Public Library of Science
DOI: 10.1371/journal.pcbi.1012091

Impact of population size on early adaptation in rugged fitness landscapes

Autori: Richard Servajean, Anne-Florence Bitbol
Pubblicato in: Philosphical Transactions of the Royal Society B: Biological Sciences, 2023, ISSN 0962-8436
Editore: Royal Society of London
DOI: 10.1098/rstb.2022.0045

RAG-ESM: Improving Pretrained Protein Language Models via Sequence Retrieval

Autori: Damiano Sgarbossa, Anne-Florence Bitbol
Pubblicato in: PRX Life, Numero 3, 2025, ISSN 2835-8279
Editore: American Physical Society (APS)
DOI: 10.1103/db1b-hy16

ProteomeLM: A proteome-scale language model enables accurate and rapid prediction of protein-protein interactions and gene essentiality across taxa

Autori: Cyril Malbranke, Gionata Paolo Zalaffi, Anne-Florence Bitbol
Pubblicato in: Proceedings of the National Academy of Sciences, 2026, Pagina/e in press, ISSN 1091-6490
Editore: National Academy of Sciences
DOI: 10.1101/2025.08.01.668221

Toward a Universal Model for Spatially Structured Populations

Autori: Loïc Marrec; Irene Lamberti; Anne-Florence Bitbol; Anne-Florence Bitbol; Anne-Florence Bitbol
Pubblicato in: Physical Review Letters, 2021, ISSN 0031-9007
Editore: American Physical Society
DOI: 10.1103/physrevlett.127.218102

Rubisco is slow across the tree of life

Autori: Benoit de Pins, Cyril Malbranke, Jagoda Jabłońska, Assaf Shmuel, Itai Sharon, Anne-Florence Bitbol, Oliver Mueller-Cajar, Elad Noor, Ron Milo
Pubblicato in: Proceedings of the National Academy of Sciences, Numero 122, 2025, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.2501433122

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

Autori: Andonis Gerardos; Nicola Dietler; Anne-Florence Bitbol
Pubblicato in: PLOS Computational Biology, Numero 1553734X, 2022, ISSN 1553-734X
Editore: Public Library of Science
DOI: 10.1371/journal.pcbi.1010147

Impact of complex spatial population structure on early and long-term adaptation in rugged fitness landscapes

Autori: Richard Servajean, Arthur Alexandre, Anne-Florence Bitbol
Pubblicato in: Evolution, 2026, ISSN 1558-5646
Editore: Oxford Academic
DOI: 10.1101/2024.09.23.614481