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

Anne-Florence Bitbol EPFL, Institute of Bioengineering, Lausanne, Switzerland https://orcid.org/0000-0003-1020-494X https://www.wikidata.org/entity/Q37383974

Umberto Lupo Damiano Sgarbossa Martina Milighetti Anne-Florence Bitbol DiffPaSS - high-performance differentiable pairing of protein sequences using soft scores. 2025 41 Bioinform. 1 https://doi.org/10.1093/bioinformatics/btae738 db/journals/bioinformatics/bioinformatics41.html#LupoSMB25

Damiano Sgarbossa Cyril Malbranke Anne-Florence Bitbol ProtMamba: a homology-aware but alignment-free protein state space model. 2025 41 Bioinform. 6 https://doi.org/10.1093/bioinformatics/btaf348 db/journals/bioinformatics/bioinformatics41.html#SgarbossaMB25

Cecilia Fruet Ella Linxia Müller Claude Loverdo Anne-Florence Bitbol Spatial structure facilitates evolutionary rescue by drug resistance. 1012861 2025 21 PLoS Comput. Biol. 4 https://doi.org/10.1371/journal.pcbi.1012861 db/journals/ploscb/ploscb21.html#FruetMLB25 streams/journals/ploscb

Nicola Dietler Alia Abbara Subham Choudhury Anne-Florence Bitbol Impact of phylogeny on the inference of functional sectors from protein sequence data. 1012091 2024 20 PLoS Comput. Biol. 9 https://doi.org/10.1371/journal.pcbi.1012091 db/journals/ploscb/ploscb20.html#DietlerACB24 streams/journals/ploscb

Alia Abbara Lisa Pagani Celia García-Pareja Anne-Florence Bitbol Mutant fate in spatially structured populations on graphs: Connecting models to experiments. 1012424 2024 20 PLoS Comput. Biol. 9 https://doi.org/10.1371/journal.pcbi.1012424 db/journals/ploscb/ploscb20.html#AbbaraPGB24 streams/journals/ploscb

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 Gail Weiss Sepideh Mamooler Zeming Chen 0001 Simin Fan Silin Gao Mete Ismayilzada Debjit Paul Alexandre Schöpfer Andrej Janchevski Anja Tiede Clarence Linden Emanuele Troiani Francesco Salvi Freya Behrens Giacomo Orsi Giovanni Piccioli Hadrien Sevel Louis Coulon Manuela Pineros-Rodriguez Marin Bonnassies Pierre Hellich Puck van Gerwen Sankalp Gambhir Solal Pirelli Thomas Blanchard Timothée Callens Toni Abi Aoun Yannick Calvino Alonso Yuri Cho Alberto Silvio Chiappa Antonio Sclocchi Étienne Bruno Florian Hofhammer Gabriel Pescia Geovani Rizk Leello Dadi Lucas Stoffl Manoel Horta Ribeiro Matthieu Bovel Yueyang Pan Aleksandra Radenovic Alexandre Alahi Alexander Mathis Anne-Florence Bitbol Boi Faltings Cécile Hébert Devis Tuia François Maréchal George Candea Giuseppe Carleo Jean-Cédric Chappelier Nicolas Flammarion Jean-Marie Fürbringer Jean-Philippe Pellet Karl Aberer Lenka Zdeborová Marcel Salathé Martin Jaggi Martin Rajman Mathias Payer Matthieu Wyart Michael Gastpar Michele Ceriotti Ola Svensson Olivier Lévêque Paolo Ienne Rachid Guerraoui Robert West 0001 Sanidhya Kashyap Valerio Piazza Viesturs Simanis Viktor Kuncak Volkan Cevher Philippe Schwaller Sacha Friedli Patrick Jermann Tanja Käser Antoine Bosselut Could ChatGPT get an Engineering Degree? Evaluating Higher Education Vulnerability to AI Assistants. 2024 abs/2408.11841 CoRR https://doi.org/10.48550/arXiv.2408.11841 db/journals/corr/corr2408.html#abs-2408-11841 streams/journals/corr

Anne-Florence Bitbol Jennifer Listgarten Tomás Pluskal Anton Bushuiev Roman Bushuiev Machine Learning for Protein-Protein and Protein-Ligand Interactions (Dagstuhl Seminar 24451). 1-15 2024 14 Dagstuhl Reports 11 https://doi.org/10.4230/DagRep.14.11.1 db/journals/dagstuhl-reports/dagstuhl-reports14.html#BitbolLPBB24

Carlos A. Gandarilla-Pérez Sergio Pinilla Anne-Florence Bitbol Martin Weigt Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins. 2023 March 19 PLoS Comput. Biol. 3 https://doi.org/10.1371/journal.pcbi.1011010 db/journals/ploscb/ploscb19.html#GandarillaPerezPBW23

Umberto Lupo Damiano Sgarbossa Anne-Florence Bitbol Pairing interacting protein sequences using masked language modeling. 2023 abs/2308.07136 CoRR https://doi.org/10.48550/arXiv.2308.07136 db/journals/corr/corr2308.html#abs-2308-07136

Andonis Gerardos Nicola Dietler Anne-Florence Bitbol Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences. 2022 18 PLoS Comput. Biol. 5 https://doi.org/10.1371/journal.pcbi.1010147 https://www.wikidata.org/entity/Q113308523 db/journals/ploscb/ploscb18.html#GerardosDB22

Umberto Lupo Damiano Sgarbossa Anne-Florence Bitbol Protein language models trained on multiple sequence alignments learn phylogenetic relationships. 2022 abs/2203.15465 CoRR https://doi.org/10.48550/arXiv.2203.15465 db/journals/corr/corr2203.html#abs-2203-15465

Damiano Sgarbossa Umberto Lupo Anne-Florence Bitbol Generative power of a protein language model trained on multiple sequence alignments. 2022 abs/2204.07110 CoRR https://doi.org/10.48550/arXiv.2204.07110 db/journals/corr/corr2204.html#abs-2204-07110

Loïc Marrec Anne-Florence Bitbol Resist or perish: Fate of a microbial population subjected to a periodic presence of antimicrobial. 2020 16 PLoS Comput. Biol. 4 https://doi.org/10.1371/journal.pcbi.1007798 https://www.wikidata.org/entity/Q91806155 db/journals/ploscb/ploscb16.html#MarrecB20

Shou-Wen Wang Anne-Florence Bitbol Ned S. Wingreen Revealing evolutionary constraints on proteins through sequence analysis. 2019 15 PLoS Comput. Biol. 4 https://doi.org/10.1371/journal.pcbi.1007010 https://www.wikidata.org/entity/Q64095077 db/journals/ploscb/ploscb15.html#WangBW19

Guillaume Marmier Martin Weigt Anne-Florence Bitbol Phylogenetic correlations can suffice to infer protein partners from sequences. 2019 15 PLoS Comput. Biol. 10 https://doi.org/10.1371/journal.pcbi.1007179 https://www.wikidata.org/entity/Q90694220 db/journals/ploscb/ploscb15.html#MarmierWB19

Anne-Florence Bitbol Inferring interaction partners from protein sequences using mutual information. 2018 14 PLoS Comput. Biol. 11 https://doi.org/10.1371/journal.pcbi.1006401 https://www.wikidata.org/entity/Q59809275 db/journals/ploscb/ploscb14.html#Bitbol18

Anne-Florence Bitbol David J. Schwab Quantifying the Role of Population Subdivision in Evolution on Rugged Fitness Landscapes. 2014 10 PLoS Comput. Biol. 8 https://doi.org/10.1371/journal.pcbi.1003778 https://www.wikidata.org/entity/Q35224832 db/journals/ploscb/ploscb10.html#BitbolS14

Alia Abbara Karl Aberer Alexandre Alahi Yannick Calvino Alonso Toni Abi Aoun Mohammadreza Banaei Deniz Bayazit Freya Behrens Thomas Blanchard Marin Bonnassies Beatriz Borges Antoine Bosselut Matthieu Bovel Étienne Bruno Anton Bushuiev Roman Bushuiev Timothée Callens George Candea Giuseppe Carleo Michele Ceriotti Volkan Cevher Jean-Cédric Chappelier Zeming Chen 0001 Alberto Silvio Chiappa Yuri Cho Subham Choudhury Louis Coulon Leello Tadesse DadiLeello Dadi Nicola Dietler Negar Foroutan EghlidiNegar Foroutan Boi Faltings Simin Fan Nicolas Flammarion Jibril Frej Sacha Friedli Cecilia Fruet Jean-Marie Fürbringer Sankalp Gambhir Carlos A. Gandarilla-Pérez Silin Gao Celia García-Pareja Michael Gastpar Andonis Gerardos Puck van Gerwen Rachid Guerraoui Cécile Hébert Pierre Hellich Florian Hofhammer Paolo Ienne Mete Ismayilzada Martin Jaggi Andrej Janchevski Patrick Jermann Tanja Käser Sanidhya Kashyap Viktor Kuncak Olivier Lévêque Clarence Linden Jennifer Listgarten Claude Loverdo Umberto Lupo Cyril Malbranke Sepideh Mamooler François Maréchal Guillaume Marmier Loïc Marrec Alexander Mathis Martina Milighetti Syrielle Montariol Ella Linxia Müller Tanya Nazaretzky Seyed Parsa Neshaei Giacomo Orsi Lisa Pagani Yueyang Pan Debjit Paul Mathias Payer Jean-Philippe Pellet Gabriel Pescia Valerio Piazza Giovanni Piccioli Manuela Pineros-Rodriguez Sergio Pinilla Solal Pirelli Tomás Pluskal Aleksandra Radenovic Martin Rajman Manoel Horta Ribeiro Geovani Rizk Angelika Romanou Alireza Sakhaeirad Marcel Salathé Francesco Salvi Alexandre Schöpfer David J. Schwab Philippe Schwaller Antonio Sclocchi Philippe Servant Hadrien Sevel Damiano Sgarbossa Viesturs Simanis Anna Sotnikova Lucas Stoffl Ola Svensson Anja Tiede Emanuele Troiani Devis Tuia Shouwen WangShou-Wen Wang Martin Weigt Gail Weiss Robert West 0001 Ned S. Wingreen Matthieu Wyart Lenka Zdeborová