2020

1   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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2   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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3   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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4   Building General Langevin Models from Discrete Datasets
 Federica Ferretti, Victor Chardès, Thierry Mora, Aleksandra Walczak, Irene Giardina
Physical Review X
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5   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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6   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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7   Spectrum of multispace Euclidean random matrices
 Aldo Battista, Remi Monasson
Physical Review E
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8   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 Walczak
eLife
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9   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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10   Inference of compressed Potts graphical models
 Francesca Rizzato, Alice Coucke, Eleonora de Leonardis, J. P. Barton, Jérôme Tubiana, Remi Monasson, Simona Cocco
Physical Review E
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11   Quantitative Immunology for Physicists
 Grégoire Altan-Bonnet, Thierry Mora, Aleksandra M. Walczak
Physics Reports
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12   Inferring the immune response from repertoire sequencing
 Maximilian Puelma Touzel, Aleksandra Walczak, Thierry Mora
PLoS Computational Biology
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13   Gaussian Closure Scheme in the Quasi--Linkage Equilibrium Regime of Evolving Genome Populations
 Eugenio Mauri, Simona Cocco, Rémi Monasson
EPL - Europhysics Letters
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14   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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2019

15   Dissipation in Non-Steady State Regulatory Circuits
 Paulina Szymańska-Rożek, Dario Villamaina, Jacek Miȩkisz, Aleksandra Walczak
Entropy
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16   How many different clonotypes do immune repertoires contain?
 Thierry Mora, Aleksandra Walczak
Current Opinion in Systems Biology
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17   Can Grid Cell Ensembles Represent Multiple Spaces?
 Davide Spalla, Alexis Dubreuil, Sophie Rosay, Remi Monasson, Alessandro Treves
Neural Computation
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18   Adaptive cluster expansion for Ising spin models
 Simona Cocco, Giancarlo Croce, Francesco Zamponi
European Physical Journal B: Condensed Matter and Complex Systems
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19   Fierce Selection and Interference in B-Cell Repertoire Response to Chronic HIV-1
 Armita Nourmohammad, Jakub Otwinowski, Marta Łuksza, Thierry Mora, Aleksandra Walczak
Molecular Biology and Evolution
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20   OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs
 Zachary Sethna, Yuval Elhanati, Curtis Callan, Aleksandra Walczak, Thierry Mora
Bioinformatics
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21   OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs
 Zachary Sethna, Yuval Elhanati, Curtis Callan, Aleksandra M. Walczak, Thierry Mora
Bioinformatics
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22   Physique statistique et apprentissage machine : une méthode et trois exemples
 Remi Monasson
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23   Size and structure of the sequence space of repeat proteins
 Jacopo Marchi, Ezequiel Galpern, Rocío Espada, Diego Ferreiro, Aleksandra M. Walczak, Thierry Mora
PLoS Computational Biology
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24   Learning Compositional Representations of Interacting Systems with Restricted Boltzmann Machines: Comparative Study of Lattice Proteins
 Jérôme Tubiana, Simona Cocco, Remi Monasson
Neural Computation
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25   How a well-adapting immune system remembers
 Andreas Mayer, Vijay Balasubramanian, Aleksandra M. Walczak, Thierry Mora
Proceedings of the National Academy of Sciences of the United States of America
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26   Learning protein constitutive motifs from sequence data
 Jérôme Tubiana, Simona Cocco, Remi Monasson
eLife
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27   Modeling the Correlated Activity of Neural Populations: A Review
 Christophe Gardella, Olivier Marre, Thierry Mora
Neural Computation
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28   Receptor crosstalk improves concentration sensing of multiple ligands
 Martín Carballo-Pacheco, Jonathan Desponds, Tatyana Gavrilchenko, Andreas Mayer, Roshan Prizak, Gautam Reddy, Ilya Nemenman, Thierry Mora
Physical Review E
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29   Multi-Lineage Evolution in Viral Populations Driven by Host Immune Systems
 Jacopo Marchi, Michael Lässig, Thierry Mora, Aleksandra M. Walczak
Pathogens
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30   Detecting T cell receptors involved in immune responses from single repertoire snapshots
 Mikhail Pogorelyy, Anastasia Minervina, Mikhail Shugay, Dmitriy Chudakov, Yuri Lebedev, Thierry Mora, Aleksandra Walczak
PLoS Biology
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31   Epistasis in a Fitness Landscape Defined by Antibody-Antigen Binding Free Energy
 Rhys Adams, Justin Kinney, Aleksandra Walczak, Thierry Mora
Cell Systems
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32   Genesis of the αβ T-cell receptor
 Thomas Dupic, Quentin Marcou, Aleksandra M. Walczak, Thierry Mora
PLoS Computational Biology
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33   Cost and benefits of clustered regularly interspaced short palindromic repeats spacer acquisition
 Serena Bradde, Thierry Mora, Aleksandra Walczak
Philosophical Transactions of the Royal Society B: Biological Sciences
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33
Publications
2
Years
2020
14
2019
19

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