Publications de Anne-Florence Raphaëlle Bitbol

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

eLife Sciences Publications, Ltd2025

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

eLife Sciences Publications, Ltd2025

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

Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa

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 ...

Oxford University Press (OUP)2025

Bridging Wright–Fisher and Moran models

Anne-Florence Raphaëlle Bitbol, Alia Abbara

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 ...

2025

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

Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa

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 ...

American Physical Society (APS)2025

Spatial structure facilitates evolutionary rescue by drug resistance

Anne-Florence Raphaëlle Bitbol

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

What Shapes the Lives of the Gut’s Microbial Inhabitants

Anne-Florence Raphaëlle Bitbol

American Physical Society (APS)2025

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

Anne-Florence Raphaëlle Bitbol, Richard Marie Servajean

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

Universal Casimir attraction between filaments at the cell scale

Anne-Florence Raphaëlle Bitbol

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 ...

Iop Publishing Ltd2024

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

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

Anne-Florence Raphaëlle Bitbol, Alia Abbara

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 ...

2024

Pairing interacting protein sequences using masked language modeling

Umberto Lupo, Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa

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, Simon Bernhard Otto, Richard Marie Servajean, Alexandre Lemopoulos

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

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

Umberto Lupo, Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa

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 ...

2024

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

Nicola Dietler, Anne-Florence Raphaëlle Bitbol, Alia Abbara

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 ...

2024

Frequent asymmetric migrations suppress natural selection in spatially structured populations

Anne-Florence Raphaëlle Bitbol, Alia Abbara

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 probabilities are known to be unaffected by sufficiently symmetric structures, ev ...

Oxford Univ Press2023

Impact of population size on early adaptation in rugged fitness landscapes

Anne-Florence Raphaëlle Bitbol, Richard Marie Servajean

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 ...

ROYAL SOC2023

Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins

Anne-Florence Raphaëlle Bitbol

Author summaryWhen two protein families interact, their sequences feature statistical dependencies. First, interacting proteins tend to share a common evolutionary history. Second, maintaining structure and interactions through the course of evolution yiel ...

PUBLIC LIBRARY SCIENCE2023

Impact of phylogeny on structural contact inference from protein sequence data

Nicola Dietler, Umberto Lupo, Anne-Florence Raphaëlle 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 acid usage at contacting sites. Because homologous proteins share a common ance ...

ROYAL SOC2023

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

Umberto Lupo, Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa

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 ...

eLIFE SCIENCES PUBL LTD2023