2025

1   Constrained Evolutionary Funnels Shape Viral Immune Escape
 Marian Huot, Dianzhuo Wang, Eugene Shakhnovich, Rémi Monasson, Simona Cocco
2025 - BioRxiv
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2   An independent coding scheme for idiothetic distance in the hippocampus
 Mathilde Nordlund, Nicolas Levernier, Massimiliano Trippa, Romain Bourboulou, Geoffrey Marti, Rémi Monasson, Hervé Rouault, Jérôme Epsztein, Julie Koenig-Gambini
2025 - Current Biology
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3   Strong, but not Weak, Noise Correlations are Beneficial for Population Coding
 Gabriel Mahuas, Thomas Buffet, Olivier Marre, Ulisse Ferrari, Thierry Mora
2025 - PRX Life
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4   Divergent B-cell repertoire remodelling by mRNA, DNA and live attenuated vaccines in fish
 Dean Porter, Catherine Collins, Andrea Mazzolini, Luc Jouneau, Vanessa Mhanna, Céline Coiffier, Mathilde Peruzzi, Yan Jaszczyszyn, Encarnita Mariotti-Ferrandiz, François Huetz, Bertrand Collet, Thierry Mora, Aleksandra Walczak, Bernard Verrier, Pierre Boudinot
2025 - NPJ vaccines
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5   Speed Vascular Patterns in the Spatial Navigation System
 Felipe Cybis Pereira, Sebastian Castedo, Samuel Le Meur-Diebolt, Nathalie Ialy-Radio, Soumee Bhattacharya, Jeremy Ferrier, Bruno Félix Osmanski, Simona Cocco, Remi Monasson, Sophie Pezet, Mickaël Tanter
2025 - Cell Reports
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6   Optimizing Information Transmission in Neural Induction Constrains Cell Surface Contacts of Ascidian Embryos
 Rossana Bettoni, Geneviève Dupont, Aleksandra M Walczak, Sophie de Buyl
2025 - PRX Life
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7   Generative Modeling of RNA Sequence Families with Restricted Boltzmann Machines
 Jorge Fernandez-De-Cossio-Diaz
2025 -
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8   Inferring Resource Competition in Microbial Communities from Time Series
 Xiaowen Chen, Kyle Crocker, Seppe Kuehn, Aleksandra Walczak, Thierry Mora
2025 - PRX Life
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9   Learning evolutionary parameters from genealogies using allelic trees
 Antoine Aragon, Amaury Lambert, Thierry Mora, Aleksandra M Walczak
2025 - Genetics
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10   Deciphering the Code of Viral-Host Adaptation Through Maximum-Entropy Nucleotide Bias Models
 Andrea Di Gioacchino, Ivan Lecce, Benjamin Greenbaum, Rémi Monasson, Simona Cocco
2025 - Molecular Biology and Evolution
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11   How Host Mobility Patterns Shape Antigenic Escape During Viral-Immune Coevolution
 Natalie Blot, Caelan Brooks, Daniel Swartz, Eslam Abdelaleem, Martin Garic, Andrea Iglesias-Ramas, Michael Pasek, Thierry Mora, Aleksandra Walczak
2025 - PRX Life
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12   Learning with artificial and natural neural networks: trade-offs in energy consumption and representations
 Simona Cocco, Rémi Monasson
2025 - Europhysics News
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13   Continuous replenishment of the dysfunctional CD8 T cell axis is associated with response to chemoimmunotherapy in advanced breast cancer
 Christina Metoikidou, Vadim Karnaukhov, Bram Boeckx, Eleonora Timperi, Pierre-Emmanuel Bonté, Ling Wang, Marion Espenel, Benoit Albaud, Delphine Loirat, Xiaoxiao Wang, Christos Sotiriou, Philippe Aftimos, Kevin Punie, Hans Wildiers, Viktorija Labroska, Ming-Wei Wang, Joshua Waterfall, Martine Piccart-Gebhart, Thierry Mora, Aleksandra Walczak, Olivier Lantz, Laurence Buisseret, Diether Lambrechts, Sebastian Amigorena, Emanuela Romano
2025 - Cell Reports Medicine
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14   Learning predictive signatures of HLA type from T-cell repertoires
 María Ruiz Ortega, Mikhail Pogorelyy, Anastasia Minervina, Paul Thomas, Thierry Mora, Aleksandra Walczak
2025 - PLoS Computational Biology
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15   Profiling of HIV-1 elite neutralizer cohort reveals a CD4bs bnAb for HIV-1 prevention and therapy
 Lutz Gieselmann, Andrew Delaitsch, Malena Rohde, Henning Gruell, Christoph Kreer, Meryem Seda Ercanoglu, Harry Gristick, Philipp Schommers, Elvin Ahmadov, Caelan Radford, Andrea Mazzolini, Lily Zhang, Anthony West, Johanna Worczinski, Anna Momot, Maren Reichwein, Jacqueline Knüfer, Ricarda Stumpf, Nonhlanhla Mkhize, Haajira Kaldine, Sinethemba Bhebhe, Sharvari Deshpande, Federico Giovannoni, Erin Stefanutti, Fabio Benigni, Colin Havenar-Daughton, Davide Corti, Arne Kroidl, Anurag Adhikari, Aubin Nanfack, Georgia Ambada, Ralf Duerr, Lucas Maganga, Wiston William, Nyanda Ntinginya, Timo Wolf, Christof Geldmacher, Michael Hoelscher, Clara Lehmann, Penny Moore, Thierry Mora, Aleksandra Walczak, Peter Gilbert, Nicole Doria-Rose, Yunda Huang, Jesse Bloom, Michael Seaman, Pamela Bjorkman, Florian Klein
2025 - Nature Immunology
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16   Designing molecular RNA switches with Restricted Boltzmann machines
 Jorge Fernandez-De-Cossio-Diaz, Pierre Hardouin, Francois-Xavier Lyonnet Du Moutier, Andrea Di Gioacchino, Bertrand Marchand, Yann Ponty, Bruno Sargueil, Rémi Monasson, Simona Cocco
2025 - Nature Communications
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2024

17   Lessons learned from the IMMREP23 TCR-epitope prediction challenge
 Morten Nielsen, Anne Eugster, Mathias Fynbo Jensen, Manisha Goel, Andreas Tiffeau-Mayer, Aurelien Pelissier, Sebastiaan Valkiers, María Rodríguez Martínez, Barthélémy Meynard-Piganeeau, Victor Greiff, Thierry Mora, Aleksandra M Walczak, Giancarlo Croce, Dana L Moreno, David Gfeller, Pieter Meysman, Justin Barton
2024 - ImmunoInformatics
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18   Task learning through stimulation-induced plasticity in neural networks
 Francesco Borra, Simona Cocco, Rémi Monasson
2024 - PRX Life
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19   Linking Brain and Behavior States in Zebrafish Larvae Locomotion using Hidden Markov Models
 Mattéo Dommanget-Kott, Jorge Fernandez-De-Cossio-Diaz, Monica Coraggioso, Volker Bormuth, Rémi Monasson, Georges Debrégeas, Simona Cocco
2024 - BioRxiv
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20   Continuous Quasi-Attractors dissolve with too much – or too little – variability
 Francesca Schönsberg, Rémi Monasson, Alessandro Treves
2024 - PNAS Nexus
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21   Replica method for computational problems with randomness: principles and illustrations
 J Steinberg, U Adomaitytė, A Fachechi, P Mergny, D Barbier, R Monasson
2024 - Journal of Statistical Mechanics: Theory and Experiment
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22   Inference and design of antibody specificity: From experiments to models and back
 Jorge Fernandez-De-Cossio-Diaz, Guido Uguzzoni, Kévin Ricard, Francesca Anselmi, Clément Nizak, Andrea Pagnani, Olivier Rivoire
2024 - PLoS Computational Biology
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23   Combining mutation and recombination statistics to infer clonal families in antibody repertoires
 Natanael Spisak, Gabriel Athènes, Thomas Dupic, Thierry Mora, Aleksandra Walczak
2024 - eLife
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24   A brief tutorial on information theory
 Tarek Tohme, William Bialek
2024 - SciPost Physics Lecture Notes
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25   Searching for long timescales without fine tuning
 Xiaowen Chen, William Bialek
2024 - Physical Review E
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26   Preschool-age children maintain a distinct memory CD4 + T cell and memory B cell response after SARS-CoV-2 infection
 Benoît Manfroi, Bui Thi Cuc, Aurélien Sokal, Alexis Vandenberghe, Sarah Temmam, Mikaël Attia, Mohamed El Behi, Francesco Camaglia, Ngan Thu Nguyen, Jelka Pohar, Layale Salem-Wehbe, Valentine Pottez-Jouatte, Sibyline Borzakian, Narcisse Elenga, Caroline Galeotti, Guillaume Morelle, Camille de Truchis de Lays, Michaela Semeraro, Anne-Sophie Romain, Mélodie Aubart, Naim Ouldali, Florence Mahuteau-Betzer, Claire Beauvineau, Elsa Amouyal, Romain Berthaud, Célia Crétolle, Marc Duval Arnould, Albert Faye, Mathie Lorrot, Grégoire Benoist, Nelly Briand, Marie Courbebaisse, Roland Martin, Peter van Endert, Jean-Sébastien Hulot, Anne Blanchard, Eric Tartour, Maria Leite-De-Moraes, Guillaume Lezmi, Mickael Ménager, Marine Luka, Claude-Agnès Reynaud, Jean-Claude Weill, Laetitia Languille, Marc Michel, Pascal Chappert, Thierry Mora, Aleksandra Walczak, Marc Eloit, Petra Bacher, Alexander Scheffold, Matthieu Mahévas, Isabelle Sermet-Gaudelus, Simon Fillatreau
2024 - Science Translational Medicine
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27   Computational detection of antigen-specific B cell receptors following immunization
 Maria Francesca Abbate, Thomas Dupic, Emmanuelle Vigne, Melody Shahsavarian, Aleksandra Walczak, Thierry Mora
2024 - Proceedings of the National Academy of Sciences of the United States of America
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28   Unlearning regularization for Boltzmann machines
 Enrico Ventura, Simona Cocco, Rémi Monasson, Francesco Zamponi
2024 - Machine Learning: Science and Technology
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29   Accelerated Sampling with Stacked Restricted Boltzmann Machines
 Jorge Fernandez-De-Cossio-Diaz, Clément Roussel, Simona Cocco, Rémi Monasson
2024 -
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30   Innate-like T cell subset commitment in the murine thymus is independent of TCR characteristics and occurs during proliferation
 Vadim K. Karnaukhov, Anne‐laure Le Gac, Linda Bilonda Mutala, Aurelie Darbois, Laetitia Perrin, Francois Legoux, Walczak Aleksandra, Thierry Mora, Olivier Lantz
2024 - Proceedings of the National Academy of Sciences of the United States of America
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31   Local and Global Variability in Developing Human T-Cell Repertoires
 Giulio Isacchini, Valentin Quiniou, Pierre Barennes, Vanessa Mhanna, Hélène Vantomme, Paul Stys, Encarnita Mariotti-Ferrandiz, David Klatzmann, Aleksandra Walczak, Thierry Mora, Armita Nourmohammad
2024 - PRX Life
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32   Inference of annealed protein fitness landscapes with AnnealDCA
 Luca Sesta, Andrea Pagnani, Jorge Fernandez-De-Cossio-Diaz, Guido Uguzzoni
2024 - PLoS Computational Biology
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33   Unsupervised modeling of mutational landscapes of adeno-associated viruses viability
 Matteo de Leonardis, Jorge Fernandez-De-Cossio-Diaz, Guido Uguzzoni, Andrea Pagnani
2024 - BMC Bioinformatics
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34   Functional effects of mutations in proteins can be predicted and interpreted by guided selection of sequence covariation information
 Simona Cocco, Lorenzo Posani, Rémi Monasson
2024 - Proceedings of the National Academy of Sciences of the United States of America
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2023

35   A statistical mechanics framework for Bayesian deep neural networks beyond the infinite-width limit
 R. Pacelli, S. Ariosto, M. Pastore, F. Ginelli, M. Gherardi, P. Rotondo
2023 - Nature Machine Intelligence
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36   Probabilities of developing HIV-1 bNAb sequence features in uninfected and chronically infected individuals
 Christoph Kreer, Cosimo Lupo, Meryem Ercanoglu, Lutz Gieselmann, Natanael Spisak, Jan Grossbach, Maike Schlotz, Philipp Schommers, Henning Gruell, Leona Dold, Andreas Beyer, Armita Nourmohammad, Thierry Mora, Aleksandra Walczak, Florian Klein
2023 - Nature Communications
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37   Evolutionary stability of antigenically escaping viruses
 Victor Chardès, Andrea Mazzolini, Thierry Mora, Aleksandra Walczak
2023 - Proceedings of the National Academy of Sciences of the United States of America
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38   Evolutionary dynamics of a lattice dimer: a toy model for stability vs. affinity trade-offs in proteins
 E Loffredo, E Vesconi, R Razban, O Peleg, E Shakhnovich, Simona Cocco, R Monasson
2023 - Journal of Physics A: Mathematical and Theoretical
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39   HEK293 producing the extracellular domain HER1: Full datasets of continuous fermentation process and metabolites analysis
 Lisandra Calzadilla, Erick Hernández, Julio Dustet, Jorge Fernandez-De-Cossio-Diaz, Kalet León, Matthias Pietzke, Alexei Vazquez, Roberto Mulet, Tammy Boggiano
2023 - Data in Brief
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40   Dynamical Information Synergy in Biochemical Signaling Networks
 Lauritz Hahn, Walczak Aleksandra, Thierry Mora
2023 - Physical Review Letters
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41   A transfer-learning approach to predict antigen immunogenicity and T-cell receptor specificity
 Barbara Bravi, Andrea Di Gioacchino, Jorge Fernandez-De-Cossio-Diaz, Aleksandra Walczak, Thierry Mora, Simona Cocco, Rémi Monasson
2023 - eLife
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42   Multiple steady states and metabolic switches in continuous cultures of HEK293: Experimental evidences and metabolomics
 Lisandra Calzadilla, Erick Hernández, Julio Dustet, Jorge Fernandez-De-Cossio-Diaz, Kalet León, Matthias Pietzke, Alexei Vazquez, Roberto Mulet, Tammy Boggiano
2023 - Biochemical Engineering Journal
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43   Transition paths in Potts-like energy landscapes: General properties and application to protein sequence models
 Eugenio Mauri, Simona Cocco, Rémi Monasson
2023 - Physical Review E
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44   Small-correlation expansion to quantify information in noisy sensory systems
 Gabriel Mahuas, Olivier Marre, Thierry Mora, Ulisse Ferrari
2023 - Physical Review E
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45   Quantitative Theory of Viral-Immune Coevolution May Be within Reach
 Thierry Mora, Aleksandra Walczak
2023 - PRX Life
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46   TULIP — a Transformer based Unsupervised Language model for Interacting Peptides and T-cell receptors that generalizes to unseen epitopes
 Barthelemy Meynard-Piganeau, Christoph Feinauer, Martin Weigt, Aleksandra Walczak, Thierry Mora
2023 - Proceedings of the National Academy of Sciences of the United States of America
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47   Bayesian estimation of the Kullback-Leibler divergence for categorical sytems using mixtures of Dirichlet priors
 Francesco Camaglia, Ilya Nemenman, Thierry Mora, Aleksandra Walczak
2023 - Physical Review E
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48   Towards a quantitative theory of tolerance
 Thierry Mora, Aleksandra Walczak
2023 - Trends in Immunology
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49   Machine learning for evolutionary-based and physics-inspired protein design: Current and future synergies
 Cyril Malbranke, David Bikard, Simona Cocco, Rémi Monasson, Jérôme Tubiana
2023 - Current Opinion in Structural Biology
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50   Inspecting the interaction between human immunodeficiency virus and the immune system through genetic turnover
 Andrea Mazzolini, Thierry Mora, Aleksandra Walczak
2023 - Philosophical Transactions of the Royal Society B: Biological Sciences
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158
Publications
7
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2024
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