2023

1   Emergence of time persistence in an interpretable data-driven neural network model
 Sebastien Wolf, Guillaume Le Goc, Simona Cocco, Georges Debrégeas, Rémi Monasson
eLife
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2022

2   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
Cell Systems
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3   Evolution and folding of repeat proteins
 Ezequiel Galpern, Jacopo Marchi, Thierry Mora, Aleksandra Walczak, Diego Ferreiro
Proceedings of the National Academy of Sciences of the United States of America
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4   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
Nature Communications
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5   Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies
 Cosimo Lupo, Natanael Spisak, Aleksandra M Walczak, Thierry Mora
PLoS Computational Biology
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6   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
eLife
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7   Renormalization group approach to connect discrete- and continuous-time descriptions of Gaussian processes
 Federica Ferretti, Victor Chardès, Thierry Mora, Aleksandra Walczak, Irene Giardina
Physical Review E
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8   Affinity maturation for an optimal balance between long-term immune coverage and short-term resource constraints
 Victor Chardès, Massimo Vergassola, Aleksandra Walczak, Thierry Mora
Proceedings of the National Academy of Sciences of the United States of America
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2021

9   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
RNA
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10   AMaLa: Analysis of Directed Evolution Experiments via Annealed Mutational Approximated Landscape
 Luca Sesta, Guido Uguzzoni, Jorge Fernandez-De-Cossio-Diaz, Andrea Pagnani
International Journal of Molecular Sciences
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11   Barriers and Dynamical Paths in Alternating Gibbs Sampling of Restricted Boltzmann Machines
 Clément Roussel, Simona Cocco, Rémi Monasson
Physical Review E : Statistical, Nonlinear, and Soft Matter Physics
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12   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
PLoS Computational Biology
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13   Antigenic waves of virus–immune coevolution
 Jacopo Marchi, Michael Lässig, Aleksandra M Walczak, Thierry Mora
Proceedings of the National Academy of Sciences of the United States of America
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14   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
Molecular Biology and Evolution
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15   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
Cell Reports
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16   Deep generative selection models of T and B cell receptor repertoires with soNNia
 Giulio Isacchini, Aleksandra M Walczak, Thierry Mora, Armita Nourmohammad
Proceedings of the National Academy of Sciences of the United States of America
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17   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
Cell Systems
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18   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
Science Immunology
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19   Parameters and determinants of responses to selection in antibody libraries
 Steven Schulz, Sébastien Boyer, Matteo Smerlak, Simona Cocco, Rémi Monasson, Clément Nizak, Olivier Rivoire
PLoS Computational Biology
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2020

20   Online characterization of the retinal network
 Baptiste Lefebvre
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21   Modélisation et inférence Bayésienne pour la maturation d'affinité des anticorps
 Marco Molari
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22   Low-dimensional continuous attractors in recurrent neural networks : from statistical physics to computational neuroscience
 Aldo Battista
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23   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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24   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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25   Blind deconvolution for spike inference from fluorescence recordings
 Jérôme Tubiana, Sébastien Wolf, Thomas Panier, Georges Debregeas
Journal of Neuroscience Methods
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26   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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27   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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28   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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29   Building General Langevin Models from Discrete Datasets
 Federica Ferretti, Victor Chardès, Thierry Mora, Aleksandra Walczak, Irene Giardina
Physical Review X
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30   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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31   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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32   Spectrum of multispace Euclidean random matrices
 Aldo Battista, Remi Monasson
Physical Review E
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33   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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34   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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35   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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36   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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37   Inferring the immune response from repertoire sequencing
 Maximilian Puelma Touzel, Aleksandra M Walczak, Thierry Mora
PLoS Computational Biology
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38   Quantitative Immunology for Physicists
 Grégoire Altan-Bonnet, Thierry Mora, Aleksandra M. Walczak
Physics Reports
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39   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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2019

40   Dissipation in Non-Steady State Regulatory Circuits
 Paulina Szymańska-Rożek, Dario Villamaina, Jacek Miȩkisz, Aleksandra Walczak
Entropy
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41   Can Grid Cell Ensembles Represent Multiple Spaces?
 Davide Spalla, Alexis Dubreuil, Sophie Rosay, Remi Monasson, Alessandro Treves
Neural Computation
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42   How many different clonotypes do immune repertoires contain?
 Thierry Mora, Aleksandra Walczak
Current Opinion in Systems Biology
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43   Physical Limit to Concentration Sensing in a Changing Environment
 Thierry Mora, Ilya Nemenman
Physical Review Letters
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44   Adaptive cluster expansion for Ising spin models
 Simona Cocco, Giancarlo Croce, Francesco Zamponi
The European Physical Journal B: Condensed Matter and Complex Systems
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45   Fierce Selection and Interference in B-Cell Repertoire Response to Chronic HIV-1
 Armita Nourmohammad, Jakub Otwinowski, Marta Łuksza, Thierry Mora, Aleksandra M Walczak
Molecular Biology and Evolution
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46   OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs
 Zachary Sethna, Yuval Elhanati, Curtis G Callan, Aleksandra M. Walczak, Thierry Mora
Bioinformatics
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47   Physique statistique et apprentissage machine : une méthode et trois exemples
 Remi Monasson
HAL
48   Size and structure of the sequence space of repeat proteins
 Jacopo Marchi, Ezequiel A Galpern, Rocío Espada, Diego U Ferreiro, Aleksandra M. Walczak, Thierry Mora
PLoS Computational Biology
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49   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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50   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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58
Publications
5
Années

2023
1
2022
7
2020
20

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