2022
51 Nonequilibrium dynamics of adaptation in sensory systems
Daniele Conti, Thierry Mora
2022 - Physical Review E
Daniele Conti, Thierry Mora
2022 - Physical Review E
52 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
53 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
54 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
55 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
56 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
57 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
58 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
59 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
60 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
61 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
62 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
63 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
64 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
65 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
66 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
67 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
68 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
69 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
70 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
71 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
72 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
73 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
74 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
75 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
76 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
77 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
78 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
79 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
80 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
81 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
82 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
83 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
84 In‐silico media optimization for continuous cultures using genome scale metabolic networks: The case of CHO‐K1
Bárbara Pérez-Fernández, Jorge Fernandez-De-Cossio-Diaz, Tammy Boggiano, Kalet León, Roberto Mulet
2021 - Biotechnology and Bioengineering
Bárbara Pérez-Fernández, Jorge Fernandez-De-Cossio-Diaz, Tammy Boggiano, Kalet León, Roberto Mulet
2021 - Biotechnology and Bioengineering
85 RBM-MHC: A Semi-Supervised Machine-Learning Method for Sample-Specific Prediction of Antigen Presentation by HLA-I Alleles
Barbara Bravi, Jérôme Tubiana, Simona Cocco, Rémi Monasson, Thierry Mora, Aleksandra M Walczak
2021 - Cell Systems
Barbara Bravi, Jérôme Tubiana, Simona Cocco, Rémi Monasson, Thierry Mora, Aleksandra M Walczak
2021 - Cell Systems
86 Single molecule microscopy reveals key physical features of repair foci in living cells
Judith Miné-Hattab, Mathias Heltberg, Marie Villemeur, Chloé Guedj, Thierry Mora, Aleksandra Walczak, Maxime Dahan, Angela Taddei
2021 - eLife
Judith Miné-Hattab, Mathias Heltberg, Marie Villemeur, Chloé Guedj, Thierry Mora, Aleksandra Walczak, Maxime Dahan, Angela Taddei
2021 - eLife
87 Chapter 22. Connections to Statistical Physics
Fabrizio Altarelli, Rémi Monasson, Guilhem Semerjian, Francesco Zamponi
2021 -
Fabrizio Altarelli, Rémi Monasson, Guilhem Semerjian, Francesco Zamponi
2021 -
88 Contribution of resident and circulating precursors to tumor-infiltrating CD8 + T cell populations in lung cancer
Paul Gueguen, Christina Metoikidou, Thomas Dupic, Myriam Lawand, Christel Goudot, Sylvain Baulande, Sonia Lameiras, Olivier Lantz, Nicolas Girard, Agathe Seguin-Givelet, Marine Lefevre, Thierry Mora, Aleksandra Walczak, Joshua Waterfall, Sebastian Amigorena
2021 - Science Immunology
Paul Gueguen, Christina Metoikidou, Thomas Dupic, Myriam Lawand, Christel Goudot, Sylvain Baulande, Sonia Lameiras, Olivier Lantz, Nicolas Girard, Agathe Seguin-Givelet, Marine Lefevre, Thierry Mora, Aleksandra Walczak, Joshua Waterfall, Sebastian Amigorena
2021 - Science Immunology
89 Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T-cell memory formation after mild COVID-19 infection
Anastasia Minervina, Ekaterina Komech, Aleksei Titov, Meriem Bensouda Koraichi, Elisa Rosati, Ilgar Mamedov, Andre Franke, Grigory Efimov, Dmitriy Chudakov, Thierry Mora, Aleksandra Walczak, Yuri Lebedev, Mikhail Pogorelyy
2021 - eLife
Anastasia Minervina, Ekaterina Komech, Aleksei Titov, Meriem Bensouda Koraichi, Elisa Rosati, Ilgar Mamedov, Andre Franke, Grigory Efimov, Dmitriy Chudakov, Thierry Mora, Aleksandra Walczak, Yuri Lebedev, Mikhail Pogorelyy
2021 - eLife
90 Gaussian closure scheme for evolving genomes: application to double-peak fitness landscape with short-range epistasis
Eugenio Mauri, Simona Cocco, Rémi Monasson
2021 - EPL - Europhysics Letters
Eugenio Mauri, Simona Cocco, Rémi Monasson
2021 - EPL - Europhysics Letters
91 Survival probability and size of lineages in antibody affinity maturation
Marco Molari, Rémi Monasson, Simona Cocco
2021 - Physical Review E
Marco Molari, Rémi Monasson, Simona Cocco
2021 - Physical Review E
92 Parameters and determinants of responses to selection in antibody libraries
Steven Schulz, Sébastien Boyer, Matteo Smerlak, Simona Cocco, Rémi Monasson, Clément Nizak, Olivier Rivoire
2021 - PLoS Computational Biology
Steven Schulz, Sébastien Boyer, Matteo Smerlak, Simona Cocco, Rémi Monasson, Clément Nizak, Olivier Rivoire
2021 - PLoS Computational Biology
93 Immune fingerprinting through repertoire similarity
Thomas Dupic, Meriem Bensouda Koraichi, Anastasia Minervina, Mikhail Pogorelyy, Thierry Mora, Aleksandra Walczak
2021 - PLoS Genetics
Thomas Dupic, Meriem Bensouda Koraichi, Anastasia Minervina, Mikhail Pogorelyy, Thierry Mora, Aleksandra Walczak
2021 - PLoS Genetics
2020
94 Online characterization of the retinal network
Baptiste Lefebvre
2020 - -THESE-
Baptiste Lefebvre
2020 - -THESE-
95 Population variability in the generation and thymic selection of T-cell repertoires
Zachary Sethna, Giulio Isacchini, Thomas Dupic, Thierry Mora, Aleksandra Walczak, Yuval Elhanati
2020 - PLoS Computational Biology
Zachary Sethna, Giulio Isacchini, Thomas Dupic, Thierry Mora, Aleksandra Walczak, Yuval Elhanati
2020 - PLoS Computational Biology
96 A self-consistent probabilistic formulation for inference of interactions
Jorge Fernandez-De-Cossio, Jorge Fernandez-De-Cossio-Diaz, Yasser Perera-Negrin
2020 - Scientific Reports
Jorge Fernandez-De-Cossio, Jorge Fernandez-De-Cossio-Diaz, Yasser Perera-Negrin
2020 - Scientific Reports
97 Modélisation et inférence Bayésienne pour la maturation d'affinité des anticorps
Marco Molari
2020 - -THESE-
Marco Molari
2020 - -THESE-
98 Low-dimensional continuous attractors in recurrent neural networks : from statistical physics to computational neuroscience
Aldo Battista
2020 - -THESE-
Aldo Battista
2020 - -THESE-
99 Learning the heterogeneous hypermutation landscape of immunoglobulins from high-throughput repertoire data
Natanael Spisak, Aleksandra Walczak, Thierry Mora
2020 - Nucleic Acids Research
Natanael Spisak, Aleksandra Walczak, Thierry Mora
2020 - Nucleic Acids Research
100 SOS: online probability estimation and generation of T-and B-cell receptors
Giulio Isacchini, Carlos Olivares, Armita Nourmohammad, Aleksandra Walczak, Thierry Mora
2020 - Bioinformatics
Giulio Isacchini, Carlos Olivares, Armita Nourmohammad, Aleksandra Walczak, Thierry Mora
2020 - Bioinformatics
Documents récupérés de l'archive ouverte HAL 