Anne-Florence Raphaëlle Bitbol

About
Privacy
Disclaimer

Graph Chatbot

Related publications (31)

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

Anne-Florence Raphaëlle Bitbol, Nicola Dietler, Andonis Samuel Rene Gerardos

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

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

Extracting phylogenetic dimensions of coevolution reveals hidden functional signals

Anne-Florence Raphaëlle Bitbol

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

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

Anne-Florence Raphaëlle Bitbol, Umberto Lupo, Damiano Sgarbossa

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

Toward a Universal Model for Spatially Structured Populations

Anne-Florence Raphaëlle 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 fixation probabilities. We introduce a model for structured populations on ...

AMER PHYSICAL SOC2021

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

Anne-Florence Raphaëlle Bitbol, Mohamed Barakat

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

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

A convolutional neural network segments yeast microscopy images with high accuracy

Anne-Florence Raphaëlle Bitbol, Sahand Jamal Rahi, Vojislav Gligorovski, Mateusz Kozinski, Martin Weigert, Nicola Dietler, Matthias Minder, Ahmad Sadeghi

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

Adapt or Perish: Evolutionary Rescue in a Gradually Deteriorating Environment

Anne-Florence Raphaëlle Bitbol, Loïc Marrec

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

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

Anne-Florence Raphaëlle Bitbol, Loïc Marrec

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

Page 3 of 4