2025

1   Generative Modeling of RNA Sequence Families with Restricted Boltzmann Machines
 Jorge Fernandez-De-Cossio-Diaz
2025 -
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2   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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2024

3   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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4   Task learning through stimulation-induced plasticity in neural networks
 Francesco Borra, Simona Cocco, Rémi Monasson
2024 - PRX Life
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5   Continuous Quasi-Attractors dissolve with too much – or too little – variability
 Francesca Schönsberg, Rémi Monasson, Alessandro Treves
2024 - PNAS Nexus
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6   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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7   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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8   A brief tutorial on information theory
 Tarek Tohme, William Bialek
2024 - SciPost Physics Lecture Notes
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9   Searching for long timescales without fine tuning
 Xiaowen Chen, William Bialek
2024 - Physical Review E
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10   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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11   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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12   Unlearning regularization for Boltzmann machines
 Enrico Ventura, Simona Cocco, Rémi Monasson, Francesco Zamponi
2024 - Machine Learning: Science and Technology
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13   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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14   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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15   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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16   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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17   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

18   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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19   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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20   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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21   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, S Cocco, R Monasson
2023 - Journal of Physics A: Mathematical and Theoretical
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22   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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23   Dynamical Information Synergy in Biochemical Signaling Networks
 Lauritz Hahn, Walczak Aleksandra, Thierry Mora
2023 - Physical Review Letters
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24   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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25   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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26   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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27   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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28   Quantitative Theory of Viral-Immune Coevolution May Be within Reach
 Thierry Mora, Aleksandra Walczak
2023 - PRX Life
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29   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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30   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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31   Towards a quantitative theory of tolerance
 Thierry Mora, Aleksandra Walczak
2023 - Trends in Immunology
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32   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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33   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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34   Emergence of time persistence in an interpretable data-driven neural network model
 Sebastien Wolf, Guillaume Le Goc, Simona Cocco, Georges Debrégeas, Rémi Monasson
2023 - eLife
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35   Information content in continuous attractor neural networks is preserved in the presence of moderate disordered background connectivity
 Tobias Kühn, Rémi Monasson
2023 - Physical Review E
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36   Mutational Paths with Sequence-Based Models of Proteins: From Sampling to Mean-Field Characterization
 Eugenio Mauri, Simona Cocco, Rémi Monasson
2023 - Physical Review Letters
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37   Collective response to local perturbations: how to evade threats without losing coherence
 Emanuele Loffredo, Davide Venturelli, Irene Giardina
2023 - Physical Biology
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38   Disentangling Representations in Restricted Boltzmann Machines without Adversaries
 Jorge Fernandez-De-Cossio-Diaz, Simona Cocco, Rémi Monasson
2023 - Physical Review X
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39   Granger causality analysis for calcium transients in neuronal networks, challenges and improvements
 Xiaowen Chen, Faustine Ginoux, Martin Carbo-Tano, Thierry Mora, Aleksandra Walczak, Claire Wyart
2023 - eLife
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40   Benchmarking solutions to the T-cell receptor epitope prediction problem: IMMREP22 workshop report
 Pieter Meysman, Justin Barton, Barbara Bravi, Liel Cohen-Lavi, Vadim Karnaukhov, Elias Lilleskov, Alessandro Montemurro, Morten Nielsen, Thierry Mora, Paul Pereira, Anna Postovskaya, María Rodríguez Martínez, Jorge Fernandez-De-Cossio-Diaz, Alexandra Vujkovic, Aleksandra Walczak, Anna Weber, Rose Yin, Anne Eugster, Virag Sharma
2023 - ImmunoInformatics
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41   Modeling and predicting the overlap of B- and T-cell receptor repertoires in healthy and SARS-CoV-2 infected individuals
 María Ruiz Ortega, Natanael Spisak, Thierry Mora, Aleksandra Walczak
2023 - PLoS Genetics
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42   Quantifying changes in the T cell receptor repertoire during thymic development
 Francesco Camaglia, Arie Ryvkin, Erez Greenstein, Shlomit Reich-Zeliger, Benny Chain, Thierry Mora, Aleksandra Walczak, Nir Friedman
2023 - eLife
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43   Inferring the T cell repertoire dynamics of healthy individuals
 Meriem Bensouda Koraichi, Silvia Ferri, Aleksandra Walczak, Thierry Mora
2023 - Proceedings of the National Academy of Sciences of the United States of America
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44   DRAG in situ barcoding reveals an increased number of HSPCs contributing to myelopoiesis with age
 Jos Urbanus, Jason Cosgrove, Joost Beltman, Yuval Elhanati, Rafael Moral, Cecile Conrad, Jeroen van Heijst, Emilie Tubeuf, Arno Velds, Lianne Kok, Candice Merle, Jens Magnusson, Léa Guyonnet, Jonas Frisén, Silvia Fre, Aleksandra Walczak, Thierry Mora, Heinz Jacobs, Ton Schumacher, Leïla Perié
2023 - Nature Communications
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45   Computational design of novel Cas9 PAM-interacting domains using evolution-based modelling and structural quality assessment
 Cyril Malbranke, William Rostain, Florence Depardieu, Simona Cocco, Rémi Monasson, David Bikard
2023 - PLoS Computational Biology
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46   Infer global, predict local: Quantity-relevance trade-off in protein fitness predictions from sequence data
 Lorenzo Posani, Francesca Rizzato, Rémi Monasson, Simona Cocco
2023 - PLoS Computational Biology
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47   Generalized Glauber dynamics for inference in biology
 Xiaowen Chen, Maciej Winiarski, Alicja Puscian, Ewelina Knapska, Aleksandra M. Walczak, Thierry Mora
2023 - Physical Review X
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2022

48   Inference of metabolic fluxes in nutrient-limited continuous cultures: A Maximum Entropy approach with the minimum information
 José Antonio Pereiro-Morejon, Jorge Fernandez-De-Cossio-Diaz, Roberto Mulet
2022 - iScience
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49   Context-dependent selectivity to natural images in the retina
 Matías Goldin, Baptiste Lefebvre, Samuele Virgili, Mathieu Kim Pham van Cang, Alexander Ecker, Thierry Mora, Ulisse Ferrari, Olivier Marre
2022 - Nature Communications
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50   Nonequilibrium dynamics of adaptation in sensory systems
 Daniele Conti, Thierry Mora
2022 - Physical Review E
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141
Publications
7
Années
2025
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2024
15
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30
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21
2021
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2019
22

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