2021

1   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
2   Probing T-cell response by sequence-based probabilistic modeling
 Barbara Bravi, Vinod Balachandran, Benjamin Greenbaum, Aleksandra Walczak, Thierry Mora, Rémi Monasson, Simona Cocco
PLoS Computational Biology
3   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
4   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 Dewitt, Giulio Isacchini, Garrick Yip, Wilson Ng, Owen Tak-Yin Tsang, Meng Yuan, Hejun Liu, Ian Wilson, J.S. Malik Peiris, Nicholas Wu, Armita Nourmohammad, Chris Mok
Cell Reports
5   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 Walczak
Cell Systems
6   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

2020

7   Online characterization of the retinal network
 Baptiste Lefebvre
-THESE-
8   Modélisation et inférence Bayésienne pour la maturation d'affinité des anticorps
 Marco Molari
-THESE-
9   Low-dimensional continuous attractors in recurrent neural networks : from statistical physics to computational neuroscience
 Aldo Battista
-THESE-
10   Learning the heterogeneous hypermutation landscape of immunoglobulins from high-throughput repertoire data
 Natanael Spisak, Aleksandra Walczak, Thierry Mora
Nucleic Acids Research
11   SOS: online probability estimation and generation of T-and B-cell receptors
 Giulio Isacchini, Carlos Olivares, Armita Nourmohammad, Aleksandra Walczak, Thierry Mora
Bioinformatics
12   A mechanism for hunchback promoters to readout morphogenetic positional information in less than a minute
 Jonathan Desponds, Massimo Vergassola, Aleksandra Walczak
eLife
13   A mechanism for hunchback promoters to readout morphogenetic positional information in less than a minute
 Jonathan Desponds, Massimo Vergassola, Aleksandra Walczak
eLife
14   An evolution-based model for designing chorismate mutase enzymes
 William Russ, Matteo Figliuzzi, Christian Stocker, Pierre Barrat-Charlaix, Michael Socolich, Peter Kast, Donald Hilvert, Remi Monasson, Simona Cocco, Martin Weigt, Rama Ranganathan
Science
15   Building General Langevin Models from Discrete Datasets
 Federica Ferretti, Victor Chardès, Thierry Mora, Aleksandra Walczak, Irene Giardina
Physical Review X
16   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
17   Generative models of T-cell receptor sequences
 Giulio Isacchini, Zachary Sethna, Yuval Elhanati, Armita Nourmohammad, Aleksandra Walczak, Thierry Mora
Physical Review E
18   Spectrum of multispace Euclidean random matrices
 Aldo Battista, Remi Monasson
Physical Review E
19   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
20   Capacity-Resolution Trade-Off in the Optimal Learning of Multiple Low-Dimensional Manifolds by Attractor Neural Networks
 Aldo Battista, Rémi Monasson
Physical Review Letters
21   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
22   Gaussian Closure Scheme in the Quasi--Linkage Equilibrium Regime of Evolving Genome Populations
 Eugenio Mauri, Simona Cocco, Rémi Monasson
EPL - Europhysics Letters
23   Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies
 Christoph Kreer, Henning Gruell, Thierry Mora, Aleksandra Walczak, Florian Klein
Vaccines
24   Quantitative Immunology for Physicists
 Grégoire Altan-Bonnet, Thierry Mora, Aleksandra M. Walczak
Physics Reports
25   Inferring the immune response from repertoire sequencing
 Maximilian Puelma Touzel, Aleksandra Walczak, Thierry Mora
PLoS Computational Biology

2019

26   How many different clonotypes do immune repertoires contain?
 Thierry Mora, Aleksandra Walczak
Current Opinion in Systems Biology
27   Can Grid Cell Ensembles Represent Multiple Spaces?
 Davide Spalla, Alexis Dubreuil, Sophie Rosay, Remi Monasson, Alessandro Treves
Neural Computation
28   Dissipation in Non-Steady State Regulatory Circuits
 Paulina Szymańska-Rożek, Dario Villamaina, Jacek Miȩkisz, Aleksandra Walczak
Entropy
29   Physical Limit to Concentration Sensing in a Changing Environment
 Thierry Mora, Ilya Nemenman
Physical Review Letters
30   Adaptive cluster expansion for Ising spin models
 Simona Cocco, Giancarlo Croce, Francesco Zamponi
European Physical Journal B: Condensed Matter and Complex Systems
31   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
32   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
33   Physique statistique et apprentissage machine : une méthode et trois exemples
 Remi Monasson
34   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
35   Learning Compositional Representations of Interacting Systems with Restricted Boltzmann Machines: Comparative Study of Lattice Proteins
 Jérôme Tubiana, Simona Cocco, Remi Monasson
Neural Computation
36   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
37   Learning protein constitutive motifs from sequence data
 Jérôme Tubiana, Simona Cocco, Remi Monasson
eLife
38   Modeling the Correlated Activity of Neural Populations: A Review
 Christophe Gardella, Olivier Marre, Thierry Mora
Neural Computation
39   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
40   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
41   Genesis of the αβ T-cell receptor
 Thomas Dupic, Quentin Marcou, Aleksandra M. Walczak, Thierry Mora
PLoS Computational Biology
42   Multi-Lineage Evolution in Viral Populations Driven by Host Immune Systems
 Jacopo Marchi, Michael Lässig, Thierry Mora, Aleksandra M. Walczak
Pathogens
43   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
44   Epistasis in a Fitness Landscape Defined by Antibody-Antigen Binding Free Energy
 Rhys Adams, Justin Kinney, Aleksandra Walczak, Thierry Mora
Cell Systems
44
Publications