Optimization and historical contingency in living systems: a biophysical approach

Información del proyecto

OptimHist

Identificador del acuerdo de subvención: 851173

DOI

10.3030/851173

Proyecto cerrado

Fecha de la firma de la CE 13 Noviembre 2019

Fecha de inicio 1 Marzo 2020

Fecha de finalización 28 Febrero 2026

Financiado con arreglo a

• EXCELLENT SCIENCE - European Research Council (ERC)

Coste total

€ 1 498 214,00

Aportación de la UE

€ 1 498 214,00

Coordinado por

ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE
Switzerland

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Publicaciones

Peer reviewed articles (25)

Pairing interacting protein sequences using masked language modeling

Autores: Umberto Lupo, Damiano Sgarbossa, Anne-Florence Bitbol
Publicado en: Proceedings of the National Academy of Sciences, 2024, ISSN 0027-8424
Editor: National Academy of Sciences
DOI: 10.1101/2023.08.14.553209

Frequent asymmetric migrations suppress natural selection in spatially structured populations

Autores: Alia Abbara, Anne-Florence Bitbol
Publicado en: PNAS Nexus, 2024, ISSN 2752-6542
Editor: 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

Autores: Colavin, Alexandre; Atolia, Esha; Bitbol, Anne-Florence; Huang, Kerwyn Casey
Publicado en: Scientific Reports, Edición 20452322, 2022, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-021-04260-1

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

Autores: Umberto Lupo, Damiano Sgarbossa, Martina Milighetti, Anne-Florence Bitbol
Publicado en: Bioinformatics, Edición 41, 2024, ISSN 1367-4811
Editor: 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

Autores: Simon B. Otto, Richard Servajean, Alexandre Lemopoulos, Anne-Florence Bitbol, Melanie Blokesch
Publicado en: Current Biology, 2023, ISSN 0960-9822
Editor: Cell Press
DOI: 10.1101/2023.10.25.564063

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

Autores: Umberto Lupo, Damiano Sgarbossa, Anne-Florence Bitbol
Publicado en: Nature Communications, Edición 20411723, 2022, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-022-34032-y

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

Autores: Nicola Dietler, Cyril Malbranke, Anne-Florence Bitbol
Publicado en: Physical Review Letters, Edición 136, 2026, ISSN 0031-9007
Editor: American Physical Society
DOI: 10.1103/1ht9-njrr

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

Autores: Darka Labavić, Claude Loverdo, Anne-Florence Bitbol
Publicado en: Proceedings of the National Academy of Sciences of the USA, 2022, ISSN 0027-8424
Editor: National Academy of Sciences
DOI: 10.1073/pnas.2108671119

Spatial structure facilitates evolutionary rescue by drug resistance

Autores: Cecilia Fruet, Ella Linxia Müller, Claude Loverdo, Anne-Florence Bitbol
Publicado en: PLOS Computational Biology, Edición 21, 2025, Página(s) e1012861, ISSN 1553-7358
Editor: Public Library of Science (PLoS)
DOI: 10.1371/journal.pcbi.1012861

Bridging Wright–Fisher and Moran models

Autores: Arthur Alexandre, Alia Abbara, Cecilia Fruet, Claude Loverdo, Anne-Florence Bitbol
Publicado en: Journal of Theoretical Biology, Edición 599, 2025, Página(s) 112030, ISSN 0022-5193
Editor: Academic Press
DOI: 10.1016/j.jtbi.2024.112030

Impact of phylogeny on structural contact inference from protein sequence data

Autores: Nicola Dietler; Umberto Lupo; Anne-Florence Bitbol
Publicado en: Journal of the Royal Society Interface, 2023, ISSN 1742-5689
Editor: The Royal Society
DOI: 10.1098/rsif.2022.0707

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

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

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

Autores: Damiano Sgarbossa; Umberto Lupo; Anne-Florence Bitbol
Publicado en: eLife, 2023, ISSN 2050-084X
Editor: eLife Sciences Publications
DOI: 10.7554/elife.79854

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

Autores: Damiano Sgarbossa, Cyril Malbranke, Anne-Florence Bitbol
Publicado en: Bioinformatics, Edición 41, 2025, ISSN 1367-4811
Editor: Oxford University Press (OUP)
DOI: 10.1093/bioinformatics/btaf348

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

Autores: Alia Abbara, Lisa Pagani, Celia García-Pareja, Anne-Florence Bitbol
Publicado en: PLOS Computational Biology, 2024, ISSN 1553-734X
Editor: Public Library of Science
DOI: 10.1101/2024.02.06.579097

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

Autores: Cecilia Fruet, Arthur Alexandre, Alia Abbara, Claude Loverdo, Anne-Florence Bitbol
Publicado en: Nature Communications, 2026, Página(s) in press, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1101/2025.07.31.667961

Evolution of cooperation in deme-structured populations on graphs

Autores: Alix Moawad, Alia Abbara, Anne-Florence Bitbol
Publicado en: Physical Review E, 2023, ISSN 2470-0045
Editor: American Physical Society
DOI: 10.1101/2023.09.18.558261

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

Autores: Nicola Dietler, Alia Abbara, Subham Choudhury, Anne-Florence Bitbol
Publicado en: PLOS Computational Biology, Edición 20, 2024, Página(s) e1012091, ISSN 1553-7358
Editor: Public Library of Science
DOI: 10.1371/journal.pcbi.1012091

Impact of population size on early adaptation in rugged fitness landscapes

Autores: Richard Servajean, Anne-Florence Bitbol
Publicado en: Philosphical Transactions of the Royal Society B: Biological Sciences, 2023, ISSN 0962-8436
Editor: Royal Society of London
DOI: 10.1098/rstb.2022.0045

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

Autores: Damiano Sgarbossa, Anne-Florence Bitbol
Publicado en: PRX Life, Edición 3, 2025, ISSN 2835-8279
Editor: 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

Autores: Cyril Malbranke, Gionata Paolo Zalaffi, Anne-Florence Bitbol
Publicado en: Proceedings of the National Academy of Sciences, 2026, Página(s) in press, ISSN 1091-6490
Editor: National Academy of Sciences
DOI: 10.1101/2025.08.01.668221

Toward a Universal Model for Spatially Structured Populations

Autores: Loïc Marrec; Irene Lamberti; Anne-Florence Bitbol; Anne-Florence Bitbol; Anne-Florence Bitbol
Publicado en: Physical Review Letters, 2021, ISSN 0031-9007
Editor: American Physical Society
DOI: 10.1103/physrevlett.127.218102

Rubisco is slow across the tree of life

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

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

Autores: Andonis Gerardos; Nicola Dietler; Anne-Florence Bitbol
Publicado en: PLOS Computational Biology, Edición 1553734X, 2022, ISSN 1553-734X
Editor: 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

Autores: Richard Servajean, Arthur Alexandre, Anne-Florence Bitbol
Publicado en: Evolution, 2026, ISSN 1558-5646
Editor: Oxford Academic
DOI: 10.1101/2024.09.23.614481