•Axe Physique statistique

Physique Statistique et Inférence pour la Biologie

Publications

Physique Statistique et Inférence pour la Biologie

51 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

52 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

53 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, Simona Cocco, Rémi Monasson
2023 - Journal of Physics A: Mathematical and Theoretical

54 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

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

56 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

57 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

58 Transition paths in Potts-like energy landscapes: General properties and application to protein sequence models
Eugenio Mauri, Simona Cocco, Remi Monasson
2023 - Physical Review E

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

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

61 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

62 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

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

64 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

65 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

66 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

67 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

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

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

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

71 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

72 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

73 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

74 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

75 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

76 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

77 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

78 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

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

80 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

81 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

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

83 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

84 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

85 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
2022 - Cell Systems

86 Signatures of irreversibility in microscopic models of flocking
Federica Ferretti, Simon Grosse-Holz, Caroline Holmes, Jordan Shivers, Irene Giardina, Thierry Mora, Aleksandra Walczak
2022 - Physical Review E

87 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
2022 - Nature Communications

88 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
2022 - Nature

89 Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies
Cosimo Lupo, Natanael Spisak, Aleksandra M Walczak, Thierry Mora
2022 - PLoS Computational Biology

90 Heat flux in chains of nonlocally coupled harmonic oscillators: Mean-field limit
Lucianno Defaveri, Carlos Olivares, Celia Anteneodo
2022 - Physical Review E

91 Optimal regularizations for data generation with probabilistic graphical models
A Fanthomme, F Rizzato, S. Cocco, R Monasson
2022 - Journal of Statistical Mechanics: Theory and Experiment

92 Synthetic reconstruction of the hunchback promoter specifies the role of Bicoid, Zelda and Hunchback in the dynamics of its transcription
Gonçalo Fernandes, Huy Tran, Maxime Andrieu, Youssoupha Diaw, Carmina Perez Romero, Cécile Fradin, Mathieu Coppey, Aleksandra Walczak, Nathalie Dostatni
2022 - eLife

93 Biophysical Modeling of Dopaminergic Denervation Landscapes in the Striatum Reveals New Therapeutic Strategy
Mathias Heltberg, Hussein N Awada, Alessandra Lucchetti, Mogens H Jensen, Jakob K Dreyer, Rune N Rasmussen
2022 - eNeuro

94 Renormalization group approach to connect discrete- and continuous-time descriptions of Gaussian processes
Federica Ferretti, Victor Chardès, Thierry Mora, Aleksandra Walczak, Irene Giardina
2022 - Physical Review E

95 Gell-Mann–Low Criticality in Neural Networks
Lorenzo Tiberi, Jonas Stapmanns, Tobias Kühn, Thomas Luu, David Dahmen, Moritz Helias
2022 - Physical Review Letters

96 Affinity maturation for an optimal balance between long-term immune coverage and short-term resource constraints
Victor Chardès, Massimo Vergassola, Aleksandra Walczak, Thierry Mora
2022 - Proceedings of the National Academy of Sciences of the United States of America

97 Fast optical recording of neuronal activity by three-dimensional custom-access serial holography
Walther Akemann, Sébastien Wolf, Vincent Villette, Benjamin Mathieu, Astou Tangara, Jozsua Fodor, Cathie Ventalon, Jean-François Léger, Stéphane Dieudonné, Laurent Bourdieu
2022 - Nature Methods

98 Displacement and dissociation of oligonucleotides during DNA hairpin closure under strain
Fangyuan Ding, Simona Cocco, Saurabh Raj, Maria Manosas, Thao Thi Thu Nguyen, Michelle M Spiering, David Bensimon, Jean-François Allemand, V. Croquette
2022 - Nucleic Acids Research

99 Mutual information maximization for amortized likelihood inference from sampled trajectories: MINIMALIST
Giulio Isacchini, Natanael Spisak, Armita Nourmohammad, Thierry Mora, Aleksandra Walczak
2022 - Physical Review E

100 Evolution and folding of repeat proteins
Ezequiel Galpern, Jacopo Marchi, Thierry Mora, Aleksandra Walczak, Diego Ferreiro
2022 - Proceedings of the National Academy of Sciences of the United States of America

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173

Publications

8

Années

Statistical physics