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
Sebastien Wolf, Guillaume Le Goc, Simona Cocco, Georges Debrégeas, Rémi Monasson
eLife
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
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
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
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
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
eLife
Gonçalo Fernandes, Huy Tran, Maxime Andrieu, Youssoupha Diaw, Carmina Perez Romero, Cécile Fradin, Mathieu Coppey, Aleksandra Walczak, Nathalie Dostatni
eLife
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
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
Victor Chardès, Massimo Vergassola, Aleksandra Walczak, Thierry Mora
Proceedings of the National Academy of Sciences of the United States of America
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
Andrea Di Gioacchino, Rachel Legendre, Yannis Rahou, Valérie Najburg, Pierre Charneau, Benjamin Greenbaum, Frédéric Tangy, Sylvie van Der Werf, Simona Cocco, Anastassia Komarova
RNA
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
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
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
eLife
Angela Phillips, Katherine Lawrence, Alief Moulana, Thomas Dupic, Jeffrey Chang, Milo Johnson, Ivana Cvijovic, Thierry Mora, Aleksandra Walczak, Michael Desai
eLife
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
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
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
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
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
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
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
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
Steven Schulz, Sébastien Boyer, Matteo Smerlak, Simona Cocco, Rémi Monasson, Clément Nizak, Olivier Rivoire
PLoS Computational Biology
2020
21 Online characterization of the retinal network
Baptiste Lefebvre
-THESE-
Baptiste Lefebvre
-THESE-
22 Modélisation et inférence Bayésienne pour la maturation d'affinité des anticorps
Marco Molari
-THESE-
Marco Molari
-THESE-
23 Low-dimensional continuous attractors in recurrent neural networks : from statistical physics to computational neuroscience
Aldo Battista
-THESE-
Aldo Battista
-THESE-
24 Learning the heterogeneous hypermutation landscape of immunoglobulins from high-throughput repertoire data
Natanael Spisak, Aleksandra Walczak, Thierry Mora
Nucleic Acids Research
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
Bioinformatics
Giulio Isacchini, Carlos Olivares, Armita Nourmohammad, Aleksandra Walczak, Thierry Mora
Bioinformatics
26 Blind deconvolution for spike inference from fluorescence recordings
Jérôme Tubiana, Sébastien Wolf, Thomas Panier, Georges Debregeas
Journal of Neuroscience Methods
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
eLife
Jonathan Desponds, Massimo Vergassola, Aleksandra Walczak
eLife
28 A mechanism for hunchback promoters to readout morphogenetic positional information in less than a minute
Jonathan Desponds, Massimo Vergassola, Aleksandra Walczak
eLife
Jonathan Desponds, Massimo Vergassola, Aleksandra Walczak
eLife
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
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
Science
30 Building General Langevin Models from Discrete Datasets
Federica Ferretti, Victor Chardès, Thierry Mora, Aleksandra Walczak, Irene Giardina
Physical Review X
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
eLife
Marco Molari, Klaus Eyer, Jean Baudry, Simona Cocco, Remi Monasson
eLife
32 Generative models of T-cell receptor sequences
Giulio Isacchini, Zachary Sethna, Yuval Elhanati, Armita Nourmohammad, Aleksandra Walczak, Thierry Mora
Physical Review E
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
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
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
eLife
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
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
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
eLife
Sophia Karpenko, Sebastien Wolf, Julie Lafaye, Guillaume Le Goc, Thomas Panier, Volker Bormuth, R. Candelier, Georges Debrégeas
eLife
38 Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies
Christoph Kreer, Henning Gruell, Thierry Mora, Aleksandra Walczak, Florian Klein
Vaccines
Christoph Kreer, Henning Gruell, Thierry Mora, Aleksandra Walczak, Florian Klein
Vaccines
39 Quantitative Immunology for Physicists
Grégoire Altan-Bonnet, Thierry Mora, Aleksandra M. Walczak
Physics Reports
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
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
Eugenio Mauri, Simona Cocco, Rémi Monasson
EPL - Europhysics Letters
2019
42 Dissipation in Non-Steady State Regulatory Circuits
Paulina Szymańska-Rożek, Dario Villamaina, Jacek Miȩkisz, Aleksandra Walczak
Entropy
Paulina Szymańska-Rożek, Dario Villamaina, Jacek Miȩkisz, Aleksandra Walczak
Entropy
43 Can Grid Cell Ensembles Represent Multiple Spaces?
Davide Spalla, Alexis Dubreuil, Sophie Rosay, Remi Monasson, Alessandro Treves
Neural Computation
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
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
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
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
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
Bioinformatics
Zachary Sethna, Yuval Elhanati, Curtis G Callan, Aleksandra M. Walczak, Thierry Mora
Bioinformatics
49 Physique statistique et apprentissage machine : une méthode et trois exemples
Remi Monasson
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
Jacopo Marchi, Ezequiel A Galpern, Rocío Espada, Diego U Ferreiro, Aleksandra M. Walczak, Thierry Mora
PLoS Computational Biology
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