•Statistical physics

Statistical physics and inference for biology

Publications

Statistical physics and inference for biology

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

2 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

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

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

5 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

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

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

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

9 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

10 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

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

12 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

13 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

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

15 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

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

17 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

18 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

19 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

20 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

21 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

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

23 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

24 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

25 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

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

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

28 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

29 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

30 Towards a quantitative theory of tolerance
Thierry Mora, Aleksandra Walczak
2023 - Trends in Immunology

31 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

32 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

33 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

34 Mutational Paths with Sequence-Based Models of Proteins: From Sampling to Mean-Field Characterization
Eugenio Mauri, Simona Cocco, Rémi Monasson
2023 - Physical Review Letters

35 Collective response to local perturbations: how to evade threats without losing coherence
Emanuele Loffredo, Davide Venturelli, Irene Giardina
2023 - Physical Biology

36 Disentangling Representations in Restricted Boltzmann Machines without Adversaries
Jorge Fernandez-De-Cossio-Diaz, Simona Cocco, Rémi Monasson
2023 - Physical Review X

37 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

38 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

39 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

40 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

41 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

42 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

43 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

44 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

45 Generalized Glauber dynamics for inference in biology
Xiaowen Chen, Maciej Winiarski, Alicja Puscian, Ewelina Knapska, Aleksandra M. Walczak, Thierry Mora
2023 - Physical Review X

46 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

47 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

48 Nonequilibrium dynamics of adaptation in sensory systems
Daniele Conti, Thierry Mora
2022 - Physical Review E

49 NoisET: Noise learning and Expansion detection of T-cell receptors with Python
Meriem Bensouda Koraichi, Maximilian Puelma Touzel, Andrea Mazzolini, Thierry Mora, Aleksandra Walczak
2022 - Journal of Physical Chemistry A

50 Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection
Andrea Di Gioacchino, Jonah Procyk, Marco Molari, John Schreck, Yu Zhou, Yan Liu, Rémi Monasson, Simona Cocco, Petr Šulc
2022 - PLoS Computational Biology

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137

Publications

7

Years

Statistical physics