2023

1   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
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2   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
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3   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
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4   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
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5   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
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6   Dynamical Information Synergy in Biochemical Signaling Networks
 Lauritz Hahn, Walczak Aleksandra, Thierry Mora
Physical Review Letters
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7   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
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8   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
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9   Transition paths in Potts-like energy landscapes: General properties and application to protein sequence models
 Eugenio Mauri, Simona Cocco, Rémi Monasson
Physical Review E
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10   Small-correlation expansion to quantify information in noisy sensory systems
 Gabriel Mahuas, Olivier Marre, Thierry Mora, Ulisse Ferrari
Physical Review E
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11   Quantitative Theory of Viral-Immune Coevolution May Be within Reach
 Thierry Mora, Aleksandra Walczak
PRX Life
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12   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
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13   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
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14   Towards a quantitative theory of tolerance
 Thierry Mora, Aleksandra Walczak
Trends in Immunology
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15   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
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16   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
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17   Emergence of time persistence in an interpretable data-driven neural network model
 Sebastien Wolf, Guillaume Le Goc, Simona Cocco, Georges Debrégeas, Rémi Monasson
eLife
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18   Mutational Paths with Sequence-Based Models of Proteins: From Sampling to Mean-Field Characterization
 Eugenio Mauri, Simona Cocco, Rémi Monasson
Physical Review Letters
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19   Collective response to local perturbations: how to evade threats without losing coherence
 Emanuele Loffredo, Davide Venturelli, Irene Giardina
Physical Biology
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20   Disentangling Representations in Restricted Boltzmann Machines without Adversaries
 Jorge Fernandez-De-Cossio-Diaz, Simona Cocco, Rémi Monasson
Physical Review X
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21   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
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22   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
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23   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
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24   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
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25   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
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26   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
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27   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
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28   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
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29   Generalized Glauber dynamics for inference in biology
 Xiaowen Chen, Maciej Winiarski, Alicja Puscian, Ewelina Knapska, Aleksandra M. Walczak, Thierry Mora
Physical Review X
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Publications
2023

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