Optimization and historical contingency in living systems: a biophysical approach

Pubblicazioni

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

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

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, Numero 00278424, 2022, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.2108671119

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

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

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, Numero 00319007, 2021, ISSN 0031-9007
Editore: American Physical Society
DOI: 10.1103/physrevlett.127.218102

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

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