2023
51 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
Sebastien Wolf, Guillaume Le Goc, Simona Cocco, Georges Debrégeas, Rémi Monasson
2023 - eLife
52 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
Tobias Kühn, Rémi Monasson
2023 - Physical Review E
53 Mutational Paths with Sequence-Based Models of Proteins: From Sampling to Mean-Field Characterization
Eugenio Mauri, Simona Cocco, Rémi Monasson
2023 - Physical Review Letters
Eugenio Mauri, Simona Cocco, Rémi Monasson
2023 - Physical Review Letters
54 Collective response to local perturbations: how to evade threats without losing coherence
Emanuele Loffredo, Davide Venturelli, Irene Giardina
2023 - Physical Biology
Emanuele Loffredo, Davide Venturelli, Irene Giardina
2023 - Physical Biology
55 Disentangling Representations in Restricted Boltzmann Machines without Adversaries
Jorge Fernandez-De-Cossio-Diaz, Simona Cocco, Rémi Monasson
2023 - Physical Review X
Jorge Fernandez-De-Cossio-Diaz, Simona Cocco, Rémi Monasson
2023 - Physical Review X
56 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
Xiaowen Chen, Faustine Ginoux, Martin Carbo-Tano, Thierry Mora, Aleksandra Walczak, Claire Wyart
2023 - eLife
57 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
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
58 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
María Ruiz Ortega, Natanael Spisak, Thierry Mora, Aleksandra Walczak
2023 - PLoS Genetics
59 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
Francesco Camaglia, Arie Ryvkin, Erez Greenstein, Shlomit Reich-Zeliger, Benny Chain, Thierry Mora, Aleksandra Walczak, Nir Friedman
2023 - eLife
60 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
Meriem Bensouda Koraichi, Silvia Ferri, Aleksandra Walczak, Thierry Mora
2023 - Proceedings of the National Academy of Sciences of the United States of America
61 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
Cyril Malbranke, William Rostain, Florence Depardieu, Simona Cocco, Rémi Monasson, David Bikard
2023 - PLoS Computational Biology
62 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
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
63 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
Lorenzo Posani, Francesca Rizzato, Rémi Monasson, Simona Cocco
2023 - PLoS Computational Biology
64 Generalized Glauber dynamics for inference in biology
Xiaowen Chen, Maciej Winiarski, Alicja Puscian, Ewelina Knapska, Aleksandra M. Walczak, Thierry Mora
2023 - Physical Review X
Xiaowen Chen, Maciej Winiarski, Alicja Puscian, Ewelina Knapska, Aleksandra M. Walczak, Thierry Mora
2023 - Physical Review X
2022
65 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
José Antonio Pereiro-Morejon, Jorge Fernandez-De-Cossio-Diaz, Roberto Mulet
2022 - iScience
66 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
Matías Goldin, Baptiste Lefebvre, Samuele Virgili, Mathieu Kim Pham van Cang, Alexander Ecker, Thierry Mora, Ulisse Ferrari, Olivier Marre
2022 - Nature Communications
67 Nonequilibrium dynamics of adaptation in sensory systems
Daniele Conti, Thierry Mora
2022 - Physical Review E
Daniele Conti, Thierry Mora
2022 - Physical Review E
68 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
Meriem Bensouda Koraichi, Maximilian Puelma Touzel, Andrea Mazzolini, Thierry Mora, Aleksandra Walczak
2022 - Journal of Physical Chemistry A
69 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
Andrea Di Gioacchino, Jonah Procyk, Marco Molari, John Schreck, Yu Zhou, Yan Liu, Rémi Monasson, Simona Cocco, Petr Šulc
2022 - PLoS Computational Biology
70 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
Victor Greiff, Eline Luning Prak, Tim O’donnell, Francesca Finotello, Sai Reddy, Walczak Aleksandra, Thierry Mora
2022 - Cell Systems
71 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
Federica Ferretti, Simon Grosse-Holz, Caroline Holmes, Jordan Shivers, Irene Giardina, Thierry Mora, Aleksandra Walczak
2022 - Physical Review E
72 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
Ruy Gómez-Ocádiz, Massimiliano Trippa, Chun-Lei Zhang, Lorenzo Posani, Simona Cocco, Rémi Monasson, Christoph Schmidt-Hieber
2022 - Nature Communications
73 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
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
74 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
Cosimo Lupo, Natanael Spisak, Aleksandra M Walczak, Thierry Mora
2022 - PLoS Computational Biology
75 Heat flux in chains of nonlocally coupled harmonic oscillators: Mean-field limit
Lucianno Defaveri, Carlos Olivares, Celia Anteneodo
2022 - Physical Review E
Lucianno Defaveri, Carlos Olivares, Celia Anteneodo
2022 - Physical Review E
76 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
A Fanthomme, F Rizzato, S. Cocco, R Monasson
2022 - Journal of Statistical Mechanics: Theory and Experiment
77 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
Gonçalo Fernandes, Huy Tran, Maxime Andrieu, Youssoupha Diaw, Carmina Perez Romero, Cécile Fradin, Mathieu Coppey, Aleksandra Walczak, Nathalie Dostatni
2022 - eLife
78 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
Mathias Heltberg, Hussein N Awada, Alessandra Lucchetti, Mogens H Jensen, Jakob K Dreyer, Rune N Rasmussen
2022 - eNeuro
79 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
Victor Chardès, Massimo Vergassola, Aleksandra Walczak, Thierry Mora
2022 - Proceedings of the National Academy of Sciences of the United States of America
80 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
Walther Akemann, Sébastien Wolf, Vincent Villette, Benjamin Mathieu, Astou Tangara, Jozsua Fodor, Cathie Ventalon, Jean-François Léger, Stéphane Dieudonné, Laurent Bourdieu
2022 - Nature Methods
81 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
Federica Ferretti, Victor Chardès, Thierry Mora, Aleksandra Walczak, Irene Giardina
2022 - Physical Review E
82 Gell-Mann–Low Criticality in Neural Networks
Lorenzo Tiberi, Jonas Stapmanns, Tobias Kühn, Thomas Luu, David Dahmen, Moritz Helias
2022 - Physical Review Letters
Lorenzo Tiberi, Jonas Stapmanns, Tobias Kühn, Thomas Luu, David Dahmen, Moritz Helias
2022 - Physical Review Letters
83 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
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
84 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
Giulio Isacchini, Natanael Spisak, Armita Nourmohammad, Thierry Mora, Aleksandra Walczak
2022 - Physical Review E
85 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
Ezequiel Galpern, Jacopo Marchi, Thierry Mora, Aleksandra Walczak, Diego Ferreiro
2022 - Proceedings of the National Academy of Sciences of the United States of America
2021
86 sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs
Andrea Di Gioacchino, Rachel Legendre, Yannis Rahou, Valérie Najburg, Pierre Charneau, Benjamin Greenbaum, Frédéric Tangy, Sylvie van Der Werf, Simona Cocco, Anastassia Komarova
2021 - RNA
Andrea Di Gioacchino, Rachel Legendre, Yannis Rahou, Valérie Najburg, Pierre Charneau, Benjamin Greenbaum, Frédéric Tangy, Sylvie van Der Werf, Simona Cocco, Anastassia Komarova
2021 - RNA
87 AMaLa: Analysis of Directed Evolution Experiments via Annealed Mutational Approximated Landscape
Luca Sesta, Guido Uguzzoni, Jorge Fernandez-De-Cossio-Diaz, Andrea Pagnani
2021 - International Journal of Molecular Sciences
Luca Sesta, Guido Uguzzoni, Jorge Fernandez-De-Cossio-Diaz, Andrea Pagnani
2021 - International Journal of Molecular Sciences
88 Large-Deviation Approach to Random Recurrent Neuronal Networks: Parameter Inference and Fluctuation-Induced Transitions
Alexander van Meegen, Tobias Kühn, Moritz Helias
2021 - Physical Review Letters
Alexander van Meegen, Tobias Kühn, Moritz Helias
2021 - Physical Review Letters
89 Barriers and Dynamical Paths in Alternating Gibbs Sampling of Restricted Boltzmann Machines
Clément Roussel, Simona Cocco, Rémi Monasson
2021 - Physical Review E
Clément Roussel, Simona Cocco, Rémi Monasson
2021 - Physical Review E
90 Binding affinity landscapes constrain the evolution of broadly neutralizing anti-influenza antibodies
Angela Phillips, Katherine Lawrence, Alief Moulana, Thomas Dupic, Jeffrey Chang, Milo Johnson, Ivana Cvijovic, Thierry Mora, Aleksandra Walczak, Michael Desai
2021 - eLife
Angela Phillips, Katherine Lawrence, Alief Moulana, Thomas Dupic, Jeffrey Chang, Milo Johnson, Ivana Cvijovic, Thierry Mora, Aleksandra Walczak, Michael Desai
2021 - eLife
91 Probing T-cell response by sequence-based probabilistic modeling
Barbara Bravi, Vinod P Balachandran, Benjamin D Greenbaum, Aleksandra M Walczak, Thierry Mora, Rémi Monasson, Simona Cocco
2021 - PLoS Computational Biology
Barbara Bravi, Vinod P Balachandran, Benjamin D Greenbaum, Aleksandra M Walczak, Thierry Mora, Rémi Monasson, Simona Cocco
2021 - PLoS Computational Biology
92 Inferring epistasis from genomic data with comparable mutation and outcrossing rate
Hong-Li Zeng, Eugenio Mauri, Vito Dichio, Simona Cocco, Rémi Monasson, Erik Aurell
2021 - Journal of Statistical Mechanics: Theory and Experiment
Hong-Li Zeng, Eugenio Mauri, Vito Dichio, Simona Cocco, Rémi Monasson, Erik Aurell
2021 - Journal of Statistical Mechanics: Theory and Experiment
93 Antigenic waves of virus–immune coevolution
Jacopo Marchi, Michael Lässig, Aleksandra M Walczak, Thierry Mora
2021 - Proceedings of the National Academy of Sciences of the United States of America
Jacopo Marchi, Michael Lässig, Aleksandra M Walczak, Thierry Mora
2021 - Proceedings of the National Academy of Sciences of the United States of America
94 Emergent Statistical Laws in Single-Cell Transcriptomic Data
Silvia Lazzardi, Filippo Valle, Andrea Mazzolini, Antonio Scialdone, Michele Caselle, Matteo Osella
2021 - Physical Review E
Silvia Lazzardi, Filippo Valle, Andrea Mazzolini, Antonio Scialdone, Michele Caselle, Matteo Osella
2021 - Physical Review E
95 Transient Chaotic Dimensionality Expansion by Recurrent Networks
Christian Keup, Tobias Kühn, David Dahmen, Moritz Helias
2021 - Physical Review X
Christian Keup, Tobias Kühn, David Dahmen, Moritz Helias
2021 - Physical Review X
96 The heterogeneous landscape and early evolution of pathogen-associated CpG dinucleotides in SARS-CoV-2
Andrea Di Gioacchino, Petr Sulc, Anastassia V Komarova, Benjamin D Greenbaum, Remi Monasson, Simona Cocco
2021 - Molecular Biology and Evolution
Andrea Di Gioacchino, Petr Sulc, Anastassia V Komarova, Benjamin D Greenbaum, Remi Monasson, Simona Cocco
2021 - Molecular Biology and Evolution
97 Roadmap on biology in time varying environments
Arvind Murugan, Kabir Husain, Michael Rust, Chelsea Hepler, Joseph Bass, Julian Pietsch, Peter Swain, Siddhartha Jena, Jared Toettcher, Arup Chakraborty, Kayla Sprenger, T Mora, A Walczak, Olivier Rivoire, Shenshen Wang, Kevin Wood, Antun Skanata, Edo Kussell, Rama Ranganathan, Hong-Yan Shih, Nigel Goldenfeld
2021 - Physical Biology
Arvind Murugan, Kabir Husain, Michael Rust, Chelsea Hepler, Joseph Bass, Julian Pietsch, Peter Swain, Siddhartha Jena, Jared Toettcher, Arup Chakraborty, Kayla Sprenger, T Mora, A Walczak, Olivier Rivoire, Shenshen Wang, Kevin Wood, Antun Skanata, Edo Kussell, Rama Ranganathan, Hong-Yan Shih, Nigel Goldenfeld
2021 - Physical Biology
98 Dynamics of B cell repertoires and emergence of cross-reactive responses in patients with different severities of COVID-19
Zachary Montague, Huibin Lv, Jakub Otwinowski, William S Dewitt, Giulio Isacchini, Garrick K Yip, Wilson W Ng, Owen Tak-Yin Tsang, Meng Yuan, Hejun Liu, Ian A Wilson, J.S. Malik S Malik Peiris, Nicholas C Wu, Armita Nourmohammad, Chris Ka Pun Mok
2021 - Cell Reports
Zachary Montague, Huibin Lv, Jakub Otwinowski, William S Dewitt, Giulio Isacchini, Garrick K Yip, Wilson W Ng, Owen Tak-Yin Tsang, Meng Yuan, Hejun Liu, Ian A Wilson, J.S. Malik S Malik Peiris, Nicholas C Wu, Armita Nourmohammad, Chris Ka Pun Mok
2021 - Cell Reports
99 Deep generative selection models of T and B cell receptor repertoires with soNNia
Giulio Isacchini, Aleksandra M Walczak, Thierry Mora, Armita Nourmohammad
2021 - Proceedings of the National Academy of Sciences of the United States of America
Giulio Isacchini, Aleksandra M Walczak, Thierry Mora, Armita Nourmohammad
2021 - Proceedings of the National Academy of Sciences of the United States of America
100 Optimal prediction with resource constraints using the information bottleneck
Vedant Sachdeva, Thierry Mora, Aleksandra Walczak, Stephanie Palmer
2021 - PLoS Computational Biology
Vedant Sachdeva, Thierry Mora, Aleksandra Walczak, Stephanie Palmer
2021 - PLoS Computational Biology
Documents récupérés de l'archive ouverte HAL 