Anne-Florence Raphaëlle Bitbol

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Publications associées (31)

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Pairing interacting protein sequences using masked language modeling

Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa, Umberto Lupo

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 ...

National Academy of Sciences2024

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

Melanie Blokesch, Anne-Florence Raphaëlle Bitbol, Alexandre Lemopoulos, Richard Marie Servajean, Simon Bernhard Otto

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 ...

2024

Toward a Universal Model for Spatially Structured Populations

Anne-Florence Raphaëlle Bitbol, Irene Lamberti

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 ...

AMER PHYSICAL SOC2021

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

Pierre Mergny, Anne-Florence Raphaëlle Bitbol

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 ...

2020

Spatial structure facilitates evolutionary rescue by drug resistance

Ella Linxia Müller, Anne-Florence Raphaëlle Bitbol, Cecilia Fruet

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 ...

2025

eLife Assessment: A differentiable Gillespie algorithm for simulating chemical kinetics, parameter estimation, and designing synthetic biological circuits

Anne-Florence Raphaëlle Bitbol

eLife Sciences Publications, Ltd2025

Impact of complex spatial population structure on early and long-term adaptation in rugged fitness landscapes

Anne-Florence Raphaëlle Bitbol, Richard Marie Servajean, Arthur Louis Mayeul Alexandre

We study how rugged fitness landscapes are explored by spatially structured populations with demes on the nodes of a graph, connected by migrations. In the weak mutation and rare migration regime, we find that, in most landscapes, migration asymmetries ass ...

Oxford University Press (OUP)2025

Evolution of cooperation in deme-structured populations on graphs

Anne-Florence Raphaëlle Bitbol, Alia Abbara

Understanding how cooperation can evolve in populations despite its cost to individual cooperators is an important challenge. Models of spatially structured populations with one individual per node of a graph have shown that cooperation, modeled via the pr ...

Amer Physical Soc2024

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa, Umberto Lupo

Self-supervised neural language models with attention have recently been applied to biological sequence data, advancing structure, function and mutational effect prediction. Some protein language models, including MSA Transformer and AlphaFold's EvoFormer, ...

Nature Portfolio2022

eLife Assessment: Exploring the repository of de novo-designed bifunctional antimicrobial peptides through deep learning

Anne-Florence Raphaëlle Bitbol

eLife Sciences Publications, Ltd2025

What Shapes the Lives of the Gut’s Microbial Inhabitants

Anne-Florence Raphaëlle Bitbol

American Physical Society (APS)2025