2021

51   Single molecule microscopy reveals key physical features of repair foci in living cells
 Judith Miné-Hattab, Mathias Heltberg, Marie Villemeur, Chloé Guedj, Thierry Mora, Aleksandra Walczak, Maxime Dahan, Angela Taddei
eLife
52   Flexible machine learning prediction of antigen presentation for rare and common HLA-I alleles
 Barbara Bravi, Jérôme Tubiana, Simona Cocco, Rémi Monasson, Thierry Mora, Aleksandra Walczak
Cell Systems
53   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
54   Contribution of resident and circulating precursors to tumor-infiltrating CD8 + T cell populations in non-small cell lung cancer patients
 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
55   Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T-cell memory formation after mild COVID-19 infection
 Anastasia Minervina, Ekaterina Komech, Aleksei Titov, Meriem Bensouda Koraichi, Elisa Rosati, Ilgar Mamedov, Andre Franke, Grigory Efimov, Dmitriy Chudakov, Thierry Mora, Aleksandra Walczak, Yuri Lebedev, Mikhail Pogorelyy
eLife
56   Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T cell memory formation after mild COVID-19 infection
 Anastasia Minervina, Ekaterina Komech, Aleksei Titov, Meriem Bensouda Koraichi, Elisa Rosati, Ilgar Mamedov, Andre Franke, Grigory Efimov, Dmitriy Chudakov, Thierry Mora, Aleksandra Walczak, Yuri Lebedev, Mikhail Pogorelyy
eLife
57   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

58   Online characterization of the retinal network
 Baptiste Lefebvre
-THESE-
59   Population variability in the generation and thymic selection of T-cell repertoires
 Zachary Sethna, Giulio Isacchini, Thomas Dupic, Thierry Mora, Aleksandra Walczak, Yuval Elhanati
PLoS Computational Biology
60   Modélisation et inférence Bayésienne pour la maturation d'affinité des anticorps
 Marco Molari
-THESE-
61   Low-dimensional continuous attractors in recurrent neural networks : from statistical physics to computational neuroscience
 Aldo Battista
-THESE-
62   Learning the heterogeneous hypermutation landscape of immunoglobulins from high-throughput repertoire data
 Natanael Spisak, Aleksandra Walczak, Thierry Mora
Nucleic Acids Research
63   SOS: online probability estimation and generation of T-and B-cell receptors
 Giulio Isacchini, Carlos Olivares, Armita Nourmohammad, Aleksandra Walczak, Thierry Mora
Bioinformatics
64   Blind deconvolution for spike inference from fluorescence recordings
 Jérôme Tubiana, Sébastien Wolf, Thomas Panier, Georges Debregeas
Journal of Neuroscience Methods
65   A mechanism for hunchback promoters to readout morphogenetic positional information in less than a minute
 Jonathan Desponds, Massimo Vergassola, Aleksandra M. Walczak
eLife
66   A mechanism for hunchback promoters to readout morphogenetic positional information in less than a minute
 Jonathan Desponds, Massimo Vergassola, Aleksandra Walczak
eLife
67   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
68   Building General Langevin Models from Discrete Datasets
 Federica Ferretti, Victor Chardès, Thierry Mora, Aleksandra Walczak, Irene Giardina
Physical Review X
69   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
70   Generative models of T-cell receptor sequences
 Giulio Isacchini, Zachary Sethna, Yuval Elhanati, Armita Nourmohammad, Aleksandra Walczak, Thierry Mora
Physical Review E
71   Spectrum of multispace Euclidean random matrices
 Aldo Battista, Remi Monasson
Physical Review E
72   Place-cell' emergence and learning of invariant data with restricted Boltzmann machines: breaking and dynamical restoration of continuous symmetries in the weight space
 Moshir Harsh, Jérôme Tubiana, Simona Cocco, Rémi Monasson
Journal of Physics A: Mathematical and Theoretical
73   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
74   Rapport de conjoncture 2019 : CID 51 Modélisation mathématique, informatique et physique pour les sciences du vivant
 Franck Picard, Myriam Ferro, Alice Cleynen, Marie Doumic, Xavier Duchemin, Guillaume Fertin, Jonathan Filee, Philippe Juin, Romain Koszul, Rafael Laboissiere, Dominique Lavenier, Thérèse Malliavin, Antonio Monari, Isabelle Nondier, Françoise Peyrin, Pierre Pouget, David Vallenet, Rufin Vanrullen, Stéphane Vezian, Aleksandra Walczak
-REPORT-
75   Capacity-Resolution Trade-Off in the Optimal Learning of Multiple Low-Dimensional Manifolds by Attractor Neural Networks
 Aldo Battista, Rémi Monasson
Physical Review Letters
76   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
77   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
78   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
79   Constraints and limitations on decoding positional information: the Bicoid case-study
 Huy Tran, Walczak Aleksandra, Nathalie Dostatni
80   Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies
 Christoph Kreer, Henning Gruell, Thierry Mora, Aleksandra Walczak, Florian Klein
Vaccines
81   Quantitative Immunology for Physicists
 Grégoire Altan-Bonnet, Thierry Mora, Aleksandra M. Walczak
Physics Reports
82   Inferring the immune response from repertoire sequencing
 Maximilian Puelma Touzel, Aleksandra M Walczak, Thierry Mora
PLoS Computational Biology

2019

83   Dissipation in Non-Steady State Regulatory Circuits
 Paulina Szymańska-Rożek, Dario Villamaina, Jacek Miȩkisz, Aleksandra Walczak
Entropy
84   Can Grid Cell Ensembles Represent Multiple Spaces?
 Davide Spalla, Alexis Dubreuil, Sophie Rosay, Remi Monasson, Alessandro Treves
Neural Computation
85   How many different clonotypes do immune repertoires contain?
 Thierry Mora, Aleksandra Walczak
Current Opinion in Systems Biology
86   Adaptive cluster expansion for Ising spin models
 Simona Cocco, Giancarlo Croce, Francesco Zamponi
The European Physical Journal B: Condensed Matter and Complex Systems
87   Physical Limit to Concentration Sensing in a Changing Environment
 Thierry Mora, Ilya Nemenman
Physical Review Letters
88   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
89   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
90   Physique statistique et apprentissage machine : une méthode et trois exemples
 Remi Monasson
91   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
92   Learning Compositional Representations of Interacting Systems with Restricted Boltzmann Machines: Comparative Study of Lattice Proteins
 Jérôme Tubiana, Simona Cocco, Remi Monasson
Neural Computation
93   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
94   Learning protein constitutive motifs from sequence data
 Jérôme Tubiana, Simona Cocco, Remi Monasson
eLife
95   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
96   Modeling the Correlated Activity of Neural Populations: A Review
 Christophe Gardella, Olivier Marre, Thierry Mora
Neural Computation
97   Cost and benefits of clustered regularly interspaced short palindromic repeats spacer acquisition
 Serena Bradde, Thierry Mora, Aleksandra M Walczak
Philosophical Transactions of the Royal Society B: Biological Sciences
98   Multi-Lineage Evolution in Viral Populations Driven by Host Immune Systems
 Jacopo Marchi, Michael Lässig, Thierry Mora, Aleksandra M. Walczak
Pathogens
99   Genesis of the αβ T-cell receptor
 Thomas Dupic, Quentin Marcou, Aleksandra M. Walczak, Thierry Mora
PLoS Computational Biology
100   Detecting T cell receptors involved in immune responses from single repertoire snapshots
 Mikhail V Pogorelyy, Anastasia Minervina, Mikhail Shugay, Dmitriy Chudakov, Yuri Lebedev, Thierry Mora, Aleksandra M Walczak
PLoS Biology
101
Publications
5
Années