Anne-Florence Raphaëlle Bitbol

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Despite the structural and functional information contained in the statistical coupling between pairs of residues in a protein, coevolution associated with function is often obscured by artifactual signals such as genetic drift, which shapes a protein's ph ...

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 acid usage at contacting sites. Because homologous proteins share a common ance ...

Owing 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. In the weak mutation regime, while the mean steady-state fitness increases ...

MOTIVATION: Identifying interacting partners from two sets of protein sequences has important applications in computational biology. Interacting partners share similarities across species due to their common evolutionary history, and feature correlations i ...

We investigate the evolutionary rescue of a microbial population in a gradually deteriorating environment, through a combination of analytical calculations and stochastic simulations. We consider a population destined for extinction in the absence of mutan ...

Motivation Protein language models are enabling advances in elucidating the sequence-to-function mapping, and have important applications in protein design. Models based on multiple sequence alignments efficiently capture the evolutionary information in ho ...

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-ranged. Here, we study the geometry of two parallel dielectric cylinders. W ...

In nature, most microbial populations have complex spatial structures that can affect their evolution. Evolutionary graph theory predicts that some spatial structures modelled by placing individuals on the nodes of a graph affect the probability that a mut ...

Inferring protein-protein interactions from sequences is an important task in computational biology. Recent methods based on Direct Coupling Analysis (DCA) or Mutual Information (MI) allow to find interaction partners among paralogs of two protein families ...

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 with fixed size. We propose a simple and tractable model which bridges the Wr ...

The evolution of antimicrobial resistance can be strongly affected by variations of antimicrobial concentration. Here, we study the impact of periodic alternations of absence and presence of antimicrobial on resistance evolution in a microbial population, ...

The identification of cell borders ('segmentation') in microscopy images constitutes a bottleneck for large-scale experiments. For the model organism Saccharomyces cerevisiae, current segmentation methods face challenges when cells bud, crowd, or exhibit i ...

Computational models starting from large ensembles of evolutionarily related protein sequences capture a representation of protein families and learn constraints associated to protein structure and function. They thus open the possibility for generating no ...

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 collective correlations in their amino-acid usage, and they are associated to ...

Protein language models are significantly advancing the modeling of sequence-function relationships. However, most of them are not directly informed of homology and evolutionary relationships between protein sequences. Here, we propose a method to make the ...

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 protein language models trained on multiple sequence alignments (MSAs), such ...

The bacterial type VI secretion system (T6SS) is a widespread, kin-discriminatory weapon capable of shaping microbial communities. Due to the system’s dependency on contact, cellular interactions can lead to either competition or kin protection. Cell-to-ce ...

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 fixation probabilities. We introduce a model for structured populations on ...

Identifying protein-protein interactions is crucial for a systems-level understanding of the cell. Recently, algorithms based on inverse statistical physics, e.g., direct coupling analysis (DCA), have allowed to use evolutionarily related sequences to addr ...

Bacterial populations often have complex spatial structures, which can impact their evolution. Here, we study how spatial structure affects the evolution of antibiotic resistance in a bacterial population. We consider a minimal model of spatially structure ...

Anne-Florence Raphaëlle Bitbol

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Extracting phylogenetic dimensions of coevolution reveals hidden functional signals

Impact of phylogeny on structural contact inference from protein sequence data

Impact of population size on early adaptation in rugged fitness landscapes

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

Adapt or Perish: Evolutionary Rescue in a Gradually Deteriorating Environment

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

Universal Casimir attraction between filaments at the cell scale

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

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

Bridging Wright–Fisher and Moran models

Resist or perish: Fate of a microbial population subjected to a periodic presence of antimicrobial

A convolutional neural network segments yeast microscopy images with high accuracy

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

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

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

Pairing interacting protein sequences using masked language modeling

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

Toward a Universal Model for Spatially Structured Populations

Statistical physics of interacting proteins: Impact of dataset size and quality assessed in synthetic sequences

Spatial structure facilitates evolutionary rescue by drug resistance