Publications by 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