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


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
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
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
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
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
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
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


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
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
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
12   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
13   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
14   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
15   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
16   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
17   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
18   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
19   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
20   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


21   Online characterization of the retinal network
 Baptiste Lefebvre
22   Modélisation et inférence Bayésienne pour la maturation d'affinité des anticorps
 Marco Molari
23   Low-dimensional continuous attractors in recurrent neural networks : from statistical physics to computational neuroscience
 Aldo Battista
24   Learning the heterogeneous hypermutation landscape of immunoglobulins from high-throughput repertoire data
 Natanael Spisak, Aleksandra Walczak, Thierry Mora
Nucleic Acids Research
25   SOS: online probability estimation and generation of T-and B-cell receptors
 Giulio Isacchini, Carlos Olivares, Armita Nourmohammad, Aleksandra Walczak, Thierry Mora
26   Blind deconvolution for spike inference from fluorescence recordings
 Jérôme Tubiana, Sébastien Wolf, Thomas Panier, Georges Debregeas
Journal of Neuroscience Methods
27   A mechanism for hunchback promoters to readout morphogenetic positional information in less than a minute
 Jonathan Desponds, Massimo Vergassola, Aleksandra Walczak
28   A mechanism for hunchback promoters to readout morphogenetic positional information in less than a minute
 Jonathan Desponds, Massimo Vergassola, Aleksandra Walczak
29   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
30   Building General Langevin Models from Discrete Datasets
 Federica Ferretti, Victor Chardès, Thierry Mora, Aleksandra Walczak, Irene Giardina
Physical Review X
31   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
32   Generative models of T-cell receptor sequences
 Giulio Isacchini, Zachary Sethna, Yuval Elhanati, Armita Nourmohammad, Aleksandra Walczak, Thierry Mora
Physical Review E
33   Spectrum of multispace Euclidean random matrices
 Aldo Battista, Remi Monasson
Physical Review E
34   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
35   Capacity-Resolution Trade-Off in the Optimal Learning of Multiple Low-Dimensional Manifolds by Attractor Neural Networks
 Aldo Battista, Rémi Monasson
Physical Review Letters
36   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
37   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
38   Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies
 Christoph Kreer, Henning Gruell, Thierry Mora, Aleksandra Walczak, Florian Klein
39   Quantitative Immunology for Physicists
 Grégoire Altan-Bonnet, Thierry Mora, Aleksandra M. Walczak
Physics Reports
40   Inferring the immune response from repertoire sequencing
 Maximilian Puelma Touzel, Aleksandra M Walczak, Thierry Mora
PLoS Computational Biology
41   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


42   Dissipation in Non-Steady State Regulatory Circuits
 Paulina Szymańska-Rożek, Dario Villamaina, Jacek Miȩkisz, Aleksandra Walczak
43   Can Grid Cell Ensembles Represent Multiple Spaces?
 Davide Spalla, Alexis Dubreuil, Sophie Rosay, Remi Monasson, Alessandro Treves
Neural Computation
44   How many different clonotypes do immune repertoires contain?
 Thierry Mora, Aleksandra Walczak
Current Opinion in Systems Biology
45   Adaptive cluster expansion for Ising spin models
 Simona Cocco, Giancarlo Croce, Francesco Zamponi
The European Physical Journal B: Condensed Matter and Complex Systems
46   Physical Limit to Concentration Sensing in a Changing Environment
 Thierry Mora, Ilya Nemenman
Physical Review Letters
47   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
48   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
49   Physique statistique et apprentissage machine : une méthode et trois exemples
 Remi Monasson
50   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