Publications de Anne-Florence Raphaëlle Bitbol

Publications associées (31)

Extracting phylogenetic dimensions of coevolution reveals hidden functional signals

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 ...

Nature Portfolio2022

Impact of phylogeny on structural contact inference from protein sequence data

Anne-Florence Raphaëlle Bitbol, Umberto Lupo, Nicola Dietler

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

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

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

Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa, Umberto Lupo

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 ...

Oxford University Press2024

Adapt or Perish: Evolutionary Rescue in a Gradually Deteriorating Environment

Anne-Florence Raphaëlle Bitbol

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 ...

2020

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

Cyril Antoine Malbranke, 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 Press2025

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

Hydrodynamic flow and concentration gradients in the gut enhance neutral bacterial diversity

Anne-Florence Raphaëlle 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 probability of neutral bacterial mutants within a minimal model of the gut that i ...

National Academy of Sciences2022

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

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

Lisa Pagani, Anne-Florence Raphaëlle Bitbol, Alia Abbara, Celia Garcia Pareja

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

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

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

Anne-Florence Raphaëlle Bitbol, Nicola Dietler

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 ...

Public Library Science2022

Bridging Wright–Fisher and Moran models

Anne-Florence Raphaëlle Bitbol, Alia Abbara, Arthur Louis Mayeul Alexandre, Cecilia Fruet

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

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

Anne-Florence Raphaëlle Bitbol

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, ...

2020

A convolutional neural network segments yeast microscopy images with high accuracy

Matthias Minder, Anne-Florence Raphaëlle Bitbol, Martin Weigert, Sahand Jamal Rahi, Mateusz Kozinski, Vojislav Gligorovski, Nicola Dietler, Chun Hei Michael Chan, Denis Alain Henri Lucien Joly, Ahmad Sadeghi, Augoustina Maria Economou

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 ...

Nature Research2020

Evolutionary history expands the range of signaling interactions in hybrid multikinase networks

Anne-Florence Raphaëlle Bitbol

Two-component systems (TCSs) are ubiquitous signaling pathways, typically comprising a sensory histidine kinase (HK) and a response regulator, which communicate via intermolecular kinase-to-receiver domain phosphotransfer. Hybrid HKs constitute non-canonic ...

NATURE RESEARCH2021

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

Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa, Umberto Lupo

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

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

Anne-Florence Raphaëlle Bitbol, Subham Choudhury, Alia Abbara, Nicola Dietler

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

Mitochondrial cristae modeled as an out-of-equilibrium membrane driven by a proton field

Anne-Florence Raphaëlle Bitbol

As the places where most of the fuel of the cell, namely, ATP, is synthesized, mitochondria are crucial organelles in eukaryotic cells. The shape of the invaginations of the mitochondria inner membrane, known as a crista, has been identified as a signature ...

2020

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