2020

1   Online characterization of the retinal network
 Baptiste Lefebvre
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2   Population variability in the generation and thymic selection of T-cell repertoires
 Zachary Sethna, Giulio Isacchini, Thomas Dupic, Thierry Mora, Aleksandra Walczak, Yuval Elhanati
PLoS Computational Biology
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3   A self-consistent probabilistic formulation for inference of interactions
 Jorge Fernandez-De-Cossio, Jorge Fernandez-De-Cossio-Diaz, Yasser Perera-Negrin
Scientific Reports
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4   Modélisation et inférence Bayésienne pour la maturation d'affinité des anticorps
 Marco Molari
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5   Low-dimensional continuous attractors in recurrent neural networks : from statistical physics to computational neuroscience
 Aldo Battista
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6   Learning the heterogeneous hypermutation landscape of immunoglobulins from high-throughput repertoire data
 Natanael Spisak, Aleksandra Walczak, Thierry Mora
Nucleic Acids Research
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7   SOS: online probability estimation and generation of T-and B-cell receptors
 Giulio Isacchini, Carlos Olivares, Armita Nourmohammad, Aleksandra Walczak, Thierry Mora
Bioinformatics
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8   A mechanism for hunchback promoters to readout morphogenetic positional information in less than a minute
 Jonathan Desponds, Massimo Vergassola, Aleksandra Walczak
eLife
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9   Unsupervised Inference of Protein Fitness Landscape from Deep Mutational Scan
 Jorge Fernandez-De-Cossio-Diaz, Guido Uguzzoni, Andrea Pagnani
Molecular Biology and Evolution
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10   Blind deconvolution for spike inference from fluorescence recordings
 Jérôme Tubiana, Sébastien Wolf, Thomas Panier, Georges Debregeas
Journal of Neuroscience Methods
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11   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
Science
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12   Building General Langevin Models from Discrete Datasets
 Federica Ferretti, Victor Chardès, Thierry Mora, Aleksandra Walczak, Irene Giardina
Physical Review X
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13   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
eLife
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14   Generative models of T-cell receptor sequences
 Giulio Isacchini, Zachary Sethna, Yuval Elhanati, Armita Nourmohammad, Aleksandra Walczak, Thierry Mora
Physical Review E
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15   Spectrum of multispace Euclidean random matrices
 Aldo Battista, Remi Monasson
Physical Review E
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16   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
Journal of Physics A: Mathematical and Theoretical
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17   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
eLife
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18   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
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19   Capacity-Resolution Trade-Off in the Optimal Learning of Multiple Low-Dimensional Manifolds by Attractor Neural Networks
 Aldo Battista, Rémi Monasson
Physical Review Letters
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20   Inference of compressed Potts graphical models
 Francesca Rizzato, Alice Coucke, Eleonora de Leonardis, J. P. P. Barton, Jérôme Tubiana, Remi Monasson, Simona Cocco
Physical Review E
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21   From behavior to circuit modeling of light-seeking navigation in zebrafish larvae
 Sophia Karpenko, Sebastien Wolf, Julie Lafaye, Guillaume Le Goc, Thomas Panier, Volker Bormuth, R. Candelier, Georges Debrégeas
eLife
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22   Constraints and limitations on decoding positional information: the Bicoid case-study
 Huy Tran, Walczak Aleksandra, Nathalie Dostatni
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23   Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies
 Christoph Kreer, Henning Gruell, Thierry Mora, Aleksandra Walczak, Florian Klein
Vaccines
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24   Inferring the immune response from repertoire sequencing
 Maximilian Puelma Touzel, Aleksandra M Walczak, Thierry Mora
PLoS Computational Biology
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25   Quantitative Immunology for Physicists
 Grégoire Altan-Bonnet, Thierry Mora, Aleksandra M. Walczak
Physics Reports
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26   Gaussian closure scheme for evolving genomes: application to double-peak fitness landscape with short-range epistasis
 Eugenio Mauri, Simona Cocco, Rémi Monasson
EPL - Europhysics Letters
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26
Publications
2020

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