•Statistical physics

Statistical physics and inference for biology

Publications

Statistical physics and inference for biology

1 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
ImmunoInformatics

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

3 A brief tutorial on information theory
Tarek Tohme, William Bialek
SciPost Physics Lecture Notes

4 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
Science Translational Medicine

5 Computational detection of antigen-specific B cell receptors following immunization
Maria Francesca Abbate, Thomas Dupic, Emmanuelle Vigne, Melody Shahsavarian, Aleksandra Walczak, Thierry Mora
Proceedings of the National Academy of Sciences of the United States of America

6 Functional effects of mutations in proteins can be predicted and interpreted by guided selection of sequence covariation information
Simona Cocco, Lorenzo Posani, Rémi Monasson
Proceedings of the National Academy of Sciences of the United States of America

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

8 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
Proceedings of the National Academy of Sciences of the United States of America

9 Unsupervised modeling of mutational landscapes of adeno-associated viruses viability
Matteo de Leonardis, Jorge Fernandez-De-Cossio-Diaz, Guido Uguzzoni, Andrea Pagnani
BMC Bioinformatics

10 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
Nature Machine Intelligence

11 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
Nature Communications

12 Evolutionary stability of antigenically escaping viruses
Victor Chardès, Andrea Mazzolini, Thierry Mora, Aleksandra Walczak
Proceedings of the National Academy of Sciences of the United States of America

13 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
Journal of Physics A: Mathematical and Theoretical

14 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
Data in Brief

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

16 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
eLife

17 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
Biochemical Engineering Journal

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

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

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

21 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
Proceedings of the National Academy of Sciences of the United States of America

22 Bayesian estimation of the Kullback-Leibler divergence for categorical sytems using mixtures of Dirichlet priors
Francesco Camaglia, Ilya Nemenman, Thierry Mora, Aleksandra Walczak
Physical Review E

23 Towards a quantitative theory of tolerance
Thierry Mora, Aleksandra Walczak
Trends in Immunology

24 Machine learning for evolutionary-based and physics-inspired protein design: Current and future synergies
Cyril Malbranke, David Bikard, Simona Cocco, Rémi Monasson, Jérôme Tubiana
Current Opinion in Structural Biology

25 Inspecting the interaction between human immunodeficiency virus and the immune system through genetic turnover
Andrea Mazzolini, Thierry Mora, Aleksandra Walczak
Philosophical Transactions of the Royal Society B: Biological Sciences

26 Emergence of time persistence in an interpretable data-driven neural network model
Sebastien Wolf, Guillaume Le Goc, Simona Cocco, Georges Debrégeas, Rémi Monasson
eLife

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

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

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

30 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
eLife

31 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
ImmunoInformatics

32 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
PLoS Genetics

33 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
eLife

34 Inferring the T cell repertoire dynamics of healthy individuals
Meriem Bensouda Koraichi, Silvia Ferri, Aleksandra Walczak, Thierry Mora
Proceedings of the National Academy of Sciences of the United States of America

35 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
PLoS Computational Biology

36 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
Nature Communications

37 Infer global, predict local: Quantity-relevance trade-off in protein fitness predictions from sequence data
Lorenzo Posani, Francesca Rizzato, Rémi Monasson, Simona Cocco
PLoS Computational Biology

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

39 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
iScience

40 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
Nature Communications

41 Nonequilibrium dynamics of adaptation in sensory systems
Daniele Conti, Thierry Mora
Physical Review E

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

43 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
PLoS Computational Biology

44 Signatures of irreversibility in microscopic models of flocking
Federica Ferretti, Simon Grosse-Holz, Caroline Holmes, Jordan Shivers, Irene Giardina, Thierry Mora, Aleksandra Walczak
Physical Review E

45 What are the current driving questions in immune repertoire research?
Victor Greiff, Eline Luning Prak, Tim O’donnell, Francesca Finotello, Sai Reddy, Walczak Aleksandra, Thierry Mora
Cell Systems

46 Evolution and folding of repeat proteins
Ezequiel Galpern, Jacopo Marchi, Thierry Mora, Aleksandra Walczak, Diego Ferreiro
Proceedings of the National Academy of Sciences of the United States of America

47 A synaptic signal for novelty processing in the hippocampus
Ruy Gómez-Ocádiz, Massimiliano Trippa, Chun-Lei Zhang, Lorenzo Posani, Simona Cocco, Rémi Monasson, Christoph Schmidt-Hieber
Nature Communications

48 Neoantigen quality predicts immunoediting in survivors of pancreatic cancer
Marta Łuksza, Zachary Sethna, Luis Rojas, Jayon Lihm, Barbara Bravi, Yuval Elhanati, Kevin Soares, Masataka Amisaki, Anton Dobrin, David Hoyos, Pablo Guasp, Abderezak Zebboudj, Rebecca Yu, Adrienne Kaya Chandra, Theresa Waters, Zagaa Odgerel, Joanne Leung, Rajya Kappagantula, Alvin Makohon-Moore, Amber Johns, Anthony Gill, Mathieu Gigoux, Jedd Wolchok, Taha Merghoub, Michel Sadelain, Erin Patterson, Remi Monasson, Thierry Mora, Aleksandra Walczak, Simona Cocco, Christine Iacobuzio-Donahue, Benjamin Greenbaum, Vinod Balachandran
Nature

49 Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies
Cosimo Lupo, Natanael Spisak, Aleksandra M Walczak, Thierry Mora
PLoS Computational Biology

50 Optimal regularizations for data generation with probabilistic graphical models
A Fanthomme, F Rizzato, S Cocco, R Monasson
Journal of Statistical Mechanics: Theory and Experiment

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120

Publications

6

Years

9

Statistical physics