10 papers
Environment heterogeneity creates fast amplifiers of natural selection in graph-structured populations
Cecilia Fruet, Arthur Alexandre, Alia Abbara +2
Complex spatial structure, with partially isolated subpopulations, and environment heterogeneity, such as gradients in nutrients, oxygen, and drugs, both shape the evolution of nat…
Out-of-equilibrium selection pressure enhances inference from protein sequence data
Nicola Dietler, Cyril Malbranke, Anne-Florence Bitbol
Homologous proteins have similar three-dimensional structures and biological functions that shape their sequences. The resulting coevolution-driven correlations underlie methods fr…
Promotion of cooperation in deme-structured populations with growth-merging dynamics
Damien Ribière, Damien Ribière, Alia Abbara +1
The spatial structure of populations may promote the emergence and maintenance of cooperation. Cooperation in the prisoner's dilemma is favored under specific update rules in evolu…
Impact of complex spatial population structure on early and long-term adaptation in rugged fitness landscapes
Richard Servajean, Arthur Alexandre, Anne-Florence Bitbol
We investigate the exploration of rugged fitness landscapes by spatially structured populations with demes on the nodes of a graph, connected by migrations. In the rare migration r…
DiffPaSS -- High-performance differentiable pairing of protein sequences using soft scores
Umberto Lupo, Damiano Sgarbossa, Martina Milighetti +1
Identifying interacting partners from two sets of protein sequences has important applications in computational biology. Interacting partners share similarities across species due…
Impact of phylogeny on the inference of functional sectors from protein sequence data
Nicola Dietler, Alia Abbara, Subham Choudhury +1
Statistical analysis of multiple sequence alignments of homologous proteins has revealed groups of coevolving amino acids called sectors. These groups of amino-acid sites feature c…