174 citations · 1.2k across the 47 of their papers we have counts for
48 papers
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, Alia Abbara, Anne-Florence Bitbol
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…
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…
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…
Spatial structure facilitates evolutionary rescue by drug resistance
Cecilia Fruet, Ella Linxia Müller, Claude Loverdo +1
Bacterial populations often have complex spatial structures, which can impact their evolution. Here, we study how spatial structure affects the evolution of antibiotic resistance i…
Could ChatGPT get an Engineering Degree? Evaluating Higher Education Vulnerability to AI Assistants
Beatriz Borges, Negar Foroutan, Deniz Bayazit +87
AI assistants are being increasingly used by students enrolled in higher education institutions. While these tools provide opportunities for improved teaching and education, they a…
Bridging Wright-Fisher and Moran models
Arthur Alexandre, Alia Abbara, Cecilia Fruet +2
The Wright-Fisher model and the Moran model are both widely used in population genetics. They describe the time evolution of the frequency of an allele in a well-mixed population w…
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…
Mutant fate in spatially structured populations on graphs: connecting models to experiments
Alia Abbara, Lisa Pagani, Celia García-Pareja +1
In nature, most microbial populations have complex spatial structures that can affect their evolution. Evolutionary graph theory predicts that some spatial structures modelled by p…
Evolution of cooperation in deme-structured populations on graphs
Alix Moawad, Alia Abbara, Anne-Florence Bitbol
Understanding how cooperation can evolve in populations despite its cost to individual cooperators is an important challenge. Models of spatially structured populations with one in…
Pairing interacting protein sequences using masked language modeling
Umberto Lupo, Damiano Sgarbossa, Anne-Florence Bitbol
Predicting which proteins interact together from amino-acid sequences is an important task. We develop a method to pair interacting protein sequences which leverages the power of p…
Universal Casimir attraction between filaments at the cell scale
Benjamin Spreng, Hélène Berthoumieux, Astrid Lambrecht +3
The electromagnetic Casimir interaction between dielectric objects immersed in salted water includes a universal contribution that is not screened by the solvent and therefore long…
Frequent asymmetric migrations suppress natural selection in spatially structured populations
Alia Abbara, Anne-Florence Bitbol
Natural microbial populations often have complex spatial structures. This can impact their evolution, in particular the ability of mutants to take over. While mutant fixation proba…
A universal attractive interaction between filaments at the cell scale
Anne-Florence Bitbol, Hélène Berthoumieux, Benjamin Spreng +2
Actin filaments and microtubules both often form bundles of parallel filaments within cells. Here, we shed light on a universal attractive interaction between two such parallel fil…
Impact of phylogeny on structural contact inference from protein sequence data
Nicola Dietler, Umberto Lupo, Anne-Florence Bitbol
Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino-aci…
Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins
Carlos A. Gandarilla-Perez, Sergio Pinilla, Anne-Florence Bitbol +1
Predicting protein-protein interactions from sequences is an important goal of computational biology. Various sources of information can be used to this end. Starting from the sequ…
Impact of population size on early adaptation in rugged fitness landscapes
Richard Servajean, Anne-Florence Bitbol
Due to stochastic fluctuations arising from finite population size, known as genetic drift, the ability of a population to explore a rugged fitness landscape depends on its size. I…
Generative power of a protein language model trained on multiple sequence alignments
Damiano Sgarbossa, Umberto Lupo, Anne-Florence Bitbol
Computational models starting from large ensembles of evolutionarily related protein sequences capture a representation of protein families and learn constraints associated to prot…
Protein language models trained on multiple sequence alignments learn phylogenetic relationships
Umberto Lupo, Damiano Sgarbossa, Anne-Florence Bitbol
Self-supervised neural language models with attention have recently been applied to biological sequence data, advancing structure, function and mutational effect prediction. Some p…
Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences
Andonis Gerardos, Nicola Dietler, Anne-Florence Bitbol
Inferring protein-protein interactions from sequences is an important task in computational biology. Recent methods based on Direct Coupling Analysis (DCA) or Mutual Information (M…
Hydrodynamic flow and concentration gradients in the gut enhance neutral bacterial diversity
Darka Labavić, Claude Loverdo, Anne-Florence Bitbol
The gut microbiota features important genetic diversity, and the specific spatial features of the gut may shape evolution within this environment. We investigate the fixation proba…
Toward a universal model for spatially structured populations
Loïc Marrec, Irene Lamberti, Anne-Florence Bitbol
A key question in evolution is how likely a mutant is to take over. This depends on natural selection and on stochastic fluctuations. Population spatial structure can impact mutant…
Adapt or perish: Evolutionary rescue in a gradually deteriorating environment
Loïc Marrec, Anne-Florence Bitbol
We investigate the evolutionary rescue of a microbial population in a gradually deteriorating environment, through a combination of analytical calculations and stochastic simulatio…