Publications

Physique Statistique et Inférence pour la Biologie

1 Theoretical limits for sensing through phase separation
Henry Alston, Mason Rouches, Arvind Murugan, Aleksandra Walczak, Thierry Mora
2026 - Proceedings of the National Academy of Sciences of the United States of America

DOI
PDF
HAL

2 A vascular code for speed in the spatial navigation system
Felipe Cybis Pereira, Sebastian H Castedo, Samuel Le Meur-Diebolt, Nathalie Ialy-Radio, Soumee Bhattacharya, Jeremy Ferrier, Bruno Félix Osmanski, Simona Cocco, Rémi Monasson, Sophie Pezet, Mickaël Tanter
2026 - Cell Reports

DOI
HAL

3 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
2026 - PLoS Computational Biology

DOI
HAL

4 Constrained Evolutionary Funnels Shape Viral Immune Escape
Marian Huot, Dianzhuo Wang, Eugene Shakhnovich, Rémi Monasson, Simona Cocco
2025 - BioRxiv

DOI
PDF
HAL

5 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

DOI
HAL

6 Strong, but not Weak, Noise Correlations are Beneficial for Population Coding
Gabriel Mahuas, Thomas Buffet, Olivier Marre, Ulisse Ferrari, Thierry Mora
2025 - PRX Life

DOI
PDF
HAL

7 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

DOI
PDF
HAL

8 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

DOI
PDF
HAL

9 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

DOI
HAL

10 Generative Modeling of RNA Sequence Families with Restricted Boltzmann Machines
Jorge Fernandez-De-Cossio-Diaz
2025 -

DOI
HAL

11 Inferring Resource Competition in Microbial Communities from Time Series
Xiaowen Chen, Kyle Crocker, Seppe Kuehn, Aleksandra Walczak, Thierry Mora
2025 - PRX Life

DOI
PDF
HAL

12 Learning evolutionary parameters from genealogies using allelic trees
Antoine Aragon, Amaury Lambert, Thierry Mora, Aleksandra M Walczak
2025 - Genetics

DOI
HAL

13 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

DOI
PDF
HAL

14 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

DOI
PDF
HAL

15 Learning with artificial and natural neural networks: trade-offs in energy consumption and representations
Simona Cocco, Rémi Monasson
2025 - Europhysics News
-ISSUE-

DOI
PDF
HAL

16 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

DOI
PDF
HAL

17 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

DOI
PDF
HAL

18 Repeats mimic pathogen-associated patterns across a vast evolutionary landscape
Petr Šulc, Andrea Di Gioacchino, Alexander Solovyov, Siyu Sun, Stephen Martis, Sajid A Marhon, Håvard T Lindholm, Raymond Chen, Amir Hosseini, Hua Jiang, Bao-Han Ly, Martin S Taylor, Parinaz Mehdipour, Omar Abdel-Wahab, Nicole Rusk, Nicolas Vabret, John Lacava, Daniel D de Carvalho, Rémi Monasson, Simona Cocco, Benjamin D Greenbaum
2025 - Cell Genomics

DOI
PDF
HAL

19 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

DOI
PDF
HAL

20 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

DOI
HAL

21 Energy-based generative models for monoclonal antibodies
Paul Pereira, Hervé Minoux, Aleksandra M Walczak, Thierry Mora
2025 - mAbs

DOI
PDF
HAL

22 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

DOI
HAL

23 Task learning through stimulation-induced plasticity in neural networks
Francesco Borra, Simona Cocco, Rémi Monasson
2024 - PRX Life

DOI
HAL

24 Continuous Quasi-Attractors dissolve with too much – or too little – variability
Francesca Schönsberg, Rémi Monasson, Alessandro Treves
2024 - PNAS Nexus

DOI
HAL

25 Replica method for computational problems with randomness: principles and illustrations
J Steinberg, U Adomaitytė, A Fachechi, P Mergny, D Barbier, Rémi Monasson
2024 - Journal of Statistical Mechanics: Theory and Experiment

DOI
PDF
HAL

26 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

DOI
PDF
HAL

27 Combining mutation and recombination statistics to infer clonal families in antibody repertoires
Natanael Spisak, Gabriel Athènes, Thomas Dupic, Thierry Mora, Aleksandra Walczak
2024 - eLife

DOI
PDF
HAL

28 A brief tutorial on information theory
Tarek Tohme, William Bialek
2024 - SciPost Physics Lecture Notes

DOI
HAL

29 Searching for long timescales without fine tuning
Xiaowen Chen, William Bialek
2024 - Physical Review E

DOI
PDF
HAL

30 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

DOI
HAL

31 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

DOI
PDF
HAL

32 Unlearning regularization for Boltzmann machines
Enrico Ventura, Simona Cocco, Rémi Monasson, Francesco Zamponi
2024 - Machine Learning: Science and Technology

DOI
PDF
HAL

33 Accelerated Sampling with Stacked Restricted Boltzmann Machines
Jorge Fernandez-De-Cossio-Diaz, Clément Roussel, Simona Cocco, Rémi Monasson
2024 -

HAL

34 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

DOI
PDF
HAL

35 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

DOI
PDF
HAL

36 Inference of annealed protein fitness landscapes with AnnealDCA
Luca Sesta, Andrea Pagnani, Jorge Fernandez-De-Cossio-Diaz, Guido Uguzzoni
2024 - PLoS Computational Biology

DOI
PDF
HAL

37 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

DOI
PDF
HAL

38 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

DOI
PDF
HAL

39 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

DOI
PDF
HAL

40 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

DOI
PDF
HAL

41 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

DOI
PDF
HAL

42 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, Rémi Monasson
2023 - Journal of Physics A: Mathematical and Theoretical

DOI
PDF
HAL

43 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

DOI
PDF
HAL

44 Dynamical Information Synergy in Biochemical Signaling Networks
Lauritz Hahn, Walczak Aleksandra, Thierry Mora
2023 - Physical Review Letters

DOI
PDF
HAL

45 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

DOI
PDF
HAL

46 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

DOI
HAL

47 Transition paths in Potts-like energy landscapes: General properties and application to protein sequence models
Eugenio Mauri, Simona Cocco, Remi Monasson
2023 - Physical Review E

DOI
PDF
HAL

48 Small-correlation expansion to quantify information in noisy sensory systems
Gabriel Mahuas, Olivier Marre, Thierry Mora, Ulisse Ferrari
2023 - Physical Review E

DOI
PDF
HAL

49 Quantitative Theory of Viral-Immune Coevolution May Be within Reach
Thierry Mora, Aleksandra Walczak
2023 - PRX Life

DOI
PDF
HAL

50 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

DOI
PDF
HAL