•Axe Physique statistique

Physique Statistique et Inférence pour la Biologie

Publications

Physique Statistique et Inférence pour la Biologie

1 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

2 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

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

4 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

5 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

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

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

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

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

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

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

12 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

13 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

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

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

16 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

17 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

18 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

19 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

20 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

21 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

22 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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Publications

Statistical physics