Environment heterogeneity creates fast amplifiers of natural selection in graph-structured populations

C. Fruet; A. L. M. Alexandre; A. Abbara; C. Loverdo; A-F. Bitbol 

Environment heterogeneity creates fast amplifiers of natural selection in graph-structured populations

C. Fruet; A. Alexandre; A. Abbara; C. Loverdo; A. F. Bitbol 

ECCB 2026: the 25th European Conference on Computational Biology

N. Beerenwinkel; A-F. Bitbol; N. Gonzalez Gaarslev; S. Guye 

Systematic analysis of CDR contacts and sequence constraints between T cell receptor αβ chains

M. Milighetti; Y. Nagano; J. Henderson; U. Hershberg; A. Mayer et al. 

Competition against the intestinal microbiota selects for pathoadaptive traits in ESBL E. coli

P. K. Jangir; L. F. Lemos Rocha; M. Molari; N. Wenner; C. Fruet et al. 

Predicting host-pathogen interactions using a proteome-scale language model

C. Malbranke; C. Fruet; A-F. Bitbol 

ProteomeLM: A proteome-scale language model enables accurate and rapid prediction of protein–protein interactions and gene essentiality across taxa

C. Malbranke; G. P. Zalaffi; A-F. Bitbol 

Out-of-Equilibrium Selection Pressure Enhances Inference from Protein Sequence Data

N. Dietler; C. Malbranke; A. F. Bitbol 

Promotion of cooperation in deme-structured populations with growth-merging dynamics

D. Ribière; A. Abbara; A-F. Bitbol 

Rubisco is slow across the tree of life

B. de Pins; C. Malbranke; J. Jabłońska; A. Shmuel; I. Sharon et al. 

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

D. Sgarbossa; A-F. Bitbol 

ProteomeLM: A proteome-scale language model allowing fast prediction of protein-protein interactions and gene essentiality across taxa

C. A. Malbranke; G. P. Zalaffi; A-F. Bitbol 

What Shapes the Lives of the Gut’s Microbial Inhabitants

A-F. Bitbol 

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

D. Sgarbossa; C. Malbranke; A-F. Bitbol 

Out-of-equilibrium selection pressure enhances inference from protein sequence data

N. Dietler; C. A. Malbranke; A-F. Bitbol 

Spatial structure facilitates evolutionary rescue by drug resistance

C. Fruet; E. L. Müller; C. Loverdo; A. F. Bitbol 

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

A-F. Bitbol 

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

A-F. Bitbol 

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

R. Servajean; A. L. M. Alexandre; A-F. Bitbol 

Bridging Wright–Fisher and Moran models

A. Alexandre; A. Abbara; C. Fruet; C. Loverdo; A. F. Bitbol 

Revealing and exploiting coevolution through protein language models

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

U. Lupo; D. Sgarbossa; M. Milighetti; A-F. Bitbol 

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

A. Abbara; L. Pagani; C. García-Pareja; A. F. Bitbol 

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

N. Dietler; A. Abbara; S. Choudhury; A. F. Bitbol 

Pairing interacting protein sequences using masked language modeling

U. Lupo; D. Sgarbossa; A. F. Bitbol 

Evolution of cooperation in deme-structured populations on graphs

A. Moawad; A. Abbara; A-F. Bitbol 

Optimization and historical contingency in protein sequences

A-F. Bitbol 

Impact of phylogeny on inference from protein sequences: from models to natural data

Impact of spatial structure and finite size on the evolution and ecology of asexual microbial populations

Universal Casimir attraction between filaments at the cell scale

B. Spreng; H. Berthoumieux; A. Lambrecht; A-F. Bitbol; P. Maia Neto et al. 

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

S. B. Otto; R. M. Servajean; A. Lemopoulos; A-F. Bitbol; M. Blokesch 

Frequent asymmetric migrations suppress natural selection in spatially structured populations

A. Abbara; A-F. Bitbol 

Impact of population size on early adaptation in rugged fitness landscapes

R. Servajean; A-F. Bitbol 

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

C. Gandarilla-Perez; S. Pinilla; A-F. Bitbol; M. Weigt 

Impact of phylogeny on structural contact inference from protein sequence data

N. Dietler; U. Lupo; A-F. Bitbol 

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

D. Sgarbossa; U. Lupo; A-F. Bitbol 

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

S. B. Otto; R. M. Servajean; A. Lemopoulos; A-F. Bitbol; M. Blokesch 

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

U. Lupo; D. Sgarbossa; A-F. Bitbol 

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

A. Gerardos; N. Dietler; A-F. Bitbol 

Extracting phylogenetic dimensions of coevolution reveals hidden functional signals

A. Colavin; E. Atolia; A-F. Bitbol; K. C. Huang 

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

D. Labavić; C. Loverdo; A-F. Bitbol 

Toward a Universal Model for Spatially Structured Populations

L. Marrec; I. Lamberti; A-F. Bitbol 

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

P. Ortet; S. Fochesato; A-F. Bitbol; D. E. Whitworth; D. Lalaouna et al. 

A convolutional neural network segments yeast microscopy images with high accuracy

N. Dietler; M. Minder; V. Gligorovski; A. M. Economou; D. A. H. L. Joly et al. 

Adapt or Perish: Evolutionary Rescue in a Gradually Deteriorating Environment

L. Marrec; A-F. Bitbol 

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

L. Marrec; A-F. Bitbol 

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

C. A. Gandarilla-Pérez; P. Mergny; M. Weigt; A-F. Bitbol 

Spatiotemporal pattern formation in E. coli biofilms explained by a simple physical energy balance

P. Thomen; J. D. P. Valentin; A-F. Bitbol; N. Henry 

Phylogenetic correlations can suffice to infer protein partners from sequences

G. Marmier; M. Weigt; A-F. Bitbol 

Antibody‐mediated crosslinking of gut bacteria hinders the spread of antibiotic resistance

F. Bansept; L. Marrec; A-F. Bitbol; C. Loverdo 

Revealing evolutionary constraints on proteins through sequence analysis

S-W. Wang; A-F. Bitbol; N. S. Wingreen 

Inferring interaction partners from protein sequences using mutual information

A-F. Bitbol 

Quantifying the impact of a periodic presence of antimicrobial on resistance evolution in a homogeneous microbial population of fixed size

L. Marrec; A-F. Bitbol 

pH sensing by lipids in membranes: The fundamentals of pH-driven migration, polarization and deformations of lipid bilayer assemblies

M. I. Angelova; A-F. Bitbol; M. Seigneuret; G. Staneva; A. Kodama et al. 

Membrane-Mediated Interactions

P. Bassereau; P. Sens; A-F. Bitbol; D. Constantin; J-B. Fournier 

Bacterial biofilm under flow: First a physical struggle to stay, then a matter of breathing

P. Thomen; J. Robert; A. Monmeyran; A-F. Bitbol; C. Douarche et al. 

Inferring interaction partners from protein sequences

A-F. Bitbol; R. S. Dwyer; L. J. Colwell; N. S. Wingreen 

Characterizing the Statistical Properties of Protein Surfaces

J. H. Bak; A-F. Bitbol; W. Bialek 

Fundamental Constraints on the Abundances of Chemotaxis Proteins

A-F. Bitbol; N. Wingreen 

Fundamental Constraints on the Abundances of Chemotaxis Proteins

A-F. Bitbol; N. S. Wingreen 

Direct Monolayer Packing Imbalance and Phospholipid Flip-Flop: Two Mechanisms of Local Bilayer Deformation. Application to Mitochondrial Cristae of Wild-Type and Cardiolipin-Deficient Mutant

N. Khalifat; M. Rahimi; A-F. Bitbol; M. Seigneuret; J-B. Fournier et al. 

Quantifying the Role of Population Subdivision in Evolution on Rugged Fitness Landscapes

A-F. Bitbol; D. J. Schwab 

Interplay of Packing and Flip-flop in Local Bilayer Deformation. How Phosphatidylglycerol Could Rescue Mitochondrial Function in a Cardiolipin-deficient Yeast Mutant

N. Khalifat; M. Rahimi; A-F. Bitbol; M. Seigneuret; J-B. Fournier et al. 

Large-scale filament formation inhibits the activity of CTP synthetase

R. M. Barry; A-F. Bitbol; A. Lorestani; E. J. Charles; C. H. Habrian et al. 

Elasticity of Lipid Bilayer Membranes at the Nanoscale: The Need for New Terms

A-F. Bitbol; D. Constantin; J-B. Fournier 

Membrane properties revealed by spatiotemporal response to a local inhomogeneity

A-F. Bitbol; J-B. Fournier 

Pairwise summation approximation for Casimir potentials and its limitations

A-F. Bitbol; A. Canaguier-Durand; A. Lambrecht; S. Reynaud 

Bilayer Elasticity at the Nanoscale: The Need for New Terms

A-F. Bitbol; D. Constantin; J-B. Fournier 

Lipid Membrane Deformation in Response to a Local pH Modification

A-F. Bitbol; N. Puff; Y. Sakuma; M. Imai; J-B. Fournier et al. 

Fluctuations of the Casimir-like force between two inclusions in a biological membrane

A-F. Bitbol; J-B. Fournier 

Lipid membrane deformation in response to a local pH modification: theory and experiments

A-F. Bitbol; N. Puff; Y. Sakuma; M. Imai; J-B. Fournier et al. 

Universal amplitudes of the Casimir-like interactions between four types of rods in fluid membranes

A-F. Bitbol; K. Sin Ronia; J-B. Fournier 

Dynamical membrane curvature instability controlled by intermonolayer friction

A-F. Bitbol; J-B. Fournier; M. I. Angelova; N. Puff 

Forces exerted by a correlated fluid on embedded inclusions

A-F. Bitbol; J-B. Fournier 

Membrane stress tensor in the presence of lipid density and composition inhomogeneities

A-F. Bitbol; L. Peliti; J. -B. Fournier 

Fluctuations of the Casimir-like force between two membrane inclusions

A-F. Bitbol; P. G. Dommersnes; J-B. Fournier 

Scaling and dynamics of washboard roads

A-F. Bitbol; N. Taberlet; S. W. Morris; J. N. McElwaine