Quantifying the Role of Population Subdivision in Evolution on Rugged Fitness Landscapes. - Anne-Florence Bitbol; David J. Schwab (PLoS Comput. Biol., 2014)

Inferring interaction partners from protein sequences using mutual information. - Anne-Florence Bitbol (PLoS Comput. Biol., 2018)

Phylogenetic correlations can suffice to infer protein partners from sequences. - Guillaume Marmier; Martin Weigt; Anne-Florence Bitbol (PLoS Comput. Biol., 2019)

Revealing evolutionary constraints on proteins through sequence analysis. - Shou-Wen Wang; Anne-Florence Bitbol; Ned S. Wingreen (PLoS Comput. Biol., 2019)

Resist or perish: Fate of a microbial population subjected to a periodic presence of antimicrobial. - Loïc Marrec; Anne-Florence Bitbol (PLoS Comput. Biol., 2020)

Protein language models trained on multiple sequence alignments learn phylogenetic relationships. - Umberto Lupo; Damiano Sgarbossa; Anne-Florence Bitbol (CoRR, 2022)

Generative power of a protein language model trained on multiple sequence alignments. - Damiano Sgarbossa; Umberto Lupo; Anne-Florence Bitbol (CoRR, 2022)

Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences. - Andonis Gerardos; Nicola Dietler; Anne-Florence Bitbol (PLoS Comput. Biol., 2022)

Pairing interacting protein sequences using masked language modeling. - Umberto Lupo; Damiano Sgarbossa; Anne-Florence Bitbol (CoRR, 2023)

Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins. - Carlos A. Gandarilla-Pérez; Sergio Pinilla; Anne-Florence Bitbol; Martin Weigt (PLoS Comput. Biol., 2023)

Could ChatGPT get an Engineering Degree? Evaluating Higher Education Vulnerability to AI Assistants. - Beatriz Borges; Negar Foroutan; Deniz Bayazit; Anna Sotnikova; Syrielle Montariol; Tanya Nazaretzky; Mohammadreza Banaei; Alireza Sakhaeirad; Philippe Servant; Seyed Parsa Neshaei; Jibril Frej; Angelika Romanou; et al. (CoRR, 2024)

Machine Learning for Protein-Protein and Protein-Ligand Interactions (Dagstuhl Seminar 24451). - Anne-Florence Bitbol; Jennifer Listgarten; Tomás Pluskal; Anton Bushuiev; Roman Bushuiev (Dagstuhl Reports, 2024)

Mutant fate in spatially structured populations on graphs: Connecting models to experiments. - Alia Abbara; Lisa Pagani; Celia García-Pareja; Anne-Florence Bitbol (PLoS Comput. Biol., 2024)

Impact of phylogeny on the inference of functional sectors from protein sequence data. - Nicola Dietler; Alia Abbara; Subham Choudhury; Anne-Florence Bitbol (PLoS Comput. Biol., 2024)

Spatial structure facilitates evolutionary rescue by drug resistance. - Cecilia Fruet; Ella Linxia Müller; Claude Loverdo; Anne-Florence Bitbol (PLoS Comput. Biol., 2025)