2022
101 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
102 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
103 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
104 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
105 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
106 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
107 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
108 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
109 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
110 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
111 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
112 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
113 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
114 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
115 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
116 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
117 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
118 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
119 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
120 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
121 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
122 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
123 Chapter 22. Connections to Statistical Physics
Fabrizio Altarelli, Rémi Monasson, Guilhem Semerjian, Francesco Zamponi
2021 -
Fabrizio Altarelli, Rémi Monasson, Guilhem Semerjian, Francesco Zamponi
2021 -
124 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
125 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
126 Gaussian Closure Scheme in the Quasi--Linkage Equilibrium Regime of Evolving Genome Populations
Eugenio Mauri, Simona Cocco, Rémi Monasson
2021 - EPL - Europhysics Letters
Eugenio Mauri, Simona Cocco, Rémi Monasson
2021 - EPL - Europhysics Letters
127 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
128 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
129 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
131 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
132 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
133 A new inference approach for training shallow and deep generalized linear models of noisy interacting neurons
Gabriel Mahuas, Giulio Isacchini, Olivier Marre, Ulisse Ferrari, Thierry Mora
2020 -
Gabriel Mahuas, Giulio Isacchini, Olivier Marre, Ulisse Ferrari, Thierry Mora
2020 -
134 Modélisation et inférence Bayésienne pour la maturation d'affinité des anticorps
Marco Molari
2020 - -THESE-
Marco Molari
2020 - -THESE-
135 Low-dimensional continuous attractors in recurrent neural networks : from statistical physics to computational neuroscience
Aldo Battista
2020 - -THESE-
Aldo Battista
2020 - -THESE-
136 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
137 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
138 A mechanism for hunchback promoters to readout morphogenetic positional information in less than a minute
Jonathan Desponds, Massimo Vergassola, Aleksandra Walczak
2020 - eLife
Jonathan Desponds, Massimo Vergassola, Aleksandra Walczak
2020 - eLife
139 Unsupervised Inference of Protein Fitness Landscape from Deep Mutational Scan
Jorge Fernandez-De-Cossio-Diaz, Guido Uguzzoni, Andrea Pagnani
2020 - Molecular Biology and Evolution
Jorge Fernandez-De-Cossio-Diaz, Guido Uguzzoni, Andrea Pagnani
2020 - Molecular Biology and Evolution
140 Blind deconvolution for spike inference from fluorescence recordings
Jérôme Tubiana, Sébastien Wolf, Thomas Panier, Georges Debregeas
2020 - Journal of Neuroscience Methods
Jérôme Tubiana, Sébastien Wolf, Thomas Panier, Georges Debregeas
2020 - Journal of Neuroscience Methods
141 An evolution-based model for designing chorismate mutase enzymes
William P Russ, Matteo Figliuzzi, Christian Stocker, Pierre Barrat-Charlaix, Michael Socolich, Peter Kast, Donald Hilvert, Remi Monasson, Simona Cocco, Martin Weigt, Rama Ranganathan
2020 - Science
William P Russ, Matteo Figliuzzi, Christian Stocker, Pierre Barrat-Charlaix, Michael Socolich, Peter Kast, Donald Hilvert, Remi Monasson, Simona Cocco, Martin Weigt, Rama Ranganathan
2020 - Science
142 Building General Langevin Models from Discrete Datasets
Federica Ferretti, Victor Chardès, Thierry Mora, Aleksandra Walczak, Irene Giardina
2020 - Physical Review X
Federica Ferretti, Victor Chardès, Thierry Mora, Aleksandra Walczak, Irene Giardina
2020 - Physical Review X
143 Quantitative modeling of the effect of antigen dosage on B-cell affinity distributions in maturating germinal centers
Marco Molari, Klaus Eyer, Jean Baudry, Simona Cocco, Remi Monasson
2020 - eLife
Marco Molari, Klaus Eyer, Jean Baudry, Simona Cocco, Remi Monasson
2020 - eLife
144 Generative models of T-cell receptor sequences
Giulio Isacchini, Zachary Sethna, Yuval Elhanati, Armita Nourmohammad, Aleksandra Walczak, Thierry Mora
2020 - Physical Review E
Giulio Isacchini, Zachary Sethna, Yuval Elhanati, Armita Nourmohammad, Aleksandra Walczak, Thierry Mora
2020 - Physical Review E
145 Spectrum of multispace Euclidean random matrices
Aldo Battista, Remi Monasson
2020 - Physical Review E
Aldo Battista, Remi Monasson
2020 - Physical Review E
146 Place-cell' emergence and learning of invariant data with restricted Boltzmann machines: breaking and dynamical restoration of continuous symmetries in the weight space
Moshir Harsh, Jérôme Tubiana, Simona Cocco, Rémi Monasson
2020 - Journal of Physics A: Mathematical and Theoretical
Moshir Harsh, Jérôme Tubiana, Simona Cocco, Rémi Monasson
2020 - Journal of Physics A: Mathematical and Theoretical
147 Primary and secondary anti-viral response captured by the dynamics and phenotype of individual T cell clones
Anastasia Minervina, Mikhail Pogorelyy, Ekaterina Komech, Vadim Karnaukhov, Petra Bacher, Elisa Rosati, Andre Franke, Dmitriy Chudakov, Ilgar Mamedov, Yuri Lebedev, Thierry Mora, Aleksandra M Walczak
2020 - eLife
Anastasia Minervina, Mikhail Pogorelyy, Ekaterina Komech, Vadim Karnaukhov, Petra Bacher, Elisa Rosati, Andre Franke, Dmitriy Chudakov, Ilgar Mamedov, Yuri Lebedev, Thierry Mora, Aleksandra M Walczak
2020 - eLife
148 Rapport de conjoncture 2019 : CID 51 Modélisation mathématique, informatique et physique pour les sciences du vivant
Franck Picard, Myriam Ferro, Alice Cleynen, Marie Doumic, Xavier Duchemin, Guillaume Fertin, Jonathan Filee, Philippe Juin, Romain Koszul, Rafael Laboissiere, Dominique Lavenier, Thérèse Malliavin, Antonio Monari, Isabelle Nondier, Françoise Peyrin, Pierre Pouget, David Vallenet, Rufin Vanrullen, Stéphane Vezian, Aleksandra Walczak
2020 - -REPORT-
Franck Picard, Myriam Ferro, Alice Cleynen, Marie Doumic, Xavier Duchemin, Guillaume Fertin, Jonathan Filee, Philippe Juin, Romain Koszul, Rafael Laboissiere, Dominique Lavenier, Thérèse Malliavin, Antonio Monari, Isabelle Nondier, Françoise Peyrin, Pierre Pouget, David Vallenet, Rufin Vanrullen, Stéphane Vezian, Aleksandra Walczak
2020 - -REPORT-
149 Capacity-Resolution Trade-Off in the Optimal Learning of Multiple Low-Dimensional Manifolds by Attractor Neural Networks
Aldo Battista, Rémi Monasson
2020 - Physical Review Letters
Aldo Battista, Rémi Monasson
2020 - Physical Review Letters
150 Inference of compressed Potts graphical models
Francesca Rizzato, Alice Coucke, Eleonora de Leonardis, J. P. P. Barton, Jérôme Tubiana, Remi Monasson, Simona Cocco
2020 - Physical Review E
Francesca Rizzato, Alice Coucke, Eleonora de Leonardis, J. P. P. Barton, Jérôme Tubiana, Remi Monasson, Simona Cocco
2020 - Physical Review E
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