•Axe Physique statistique

Physique Statistique et Inférence pour la Biologie

Publications

Physique Statistique et Inférence pour la Biologie

101 In‐silico media optimization for continuous cultures using genome scale metabolic networks: The case of CHO‐K1
Bárbara Pérez-Fernández, Jorge Fernandez-De-Cossio-Diaz, Tammy Boggiano, Kalet León, Roberto Mulet
2021 - Biotechnology and Bioengineering

102 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
2021 - Cell Systems

103 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
2021 - eLife

104 Chapter 22. Connections to Statistical Physics
Fabrizio Altarelli, Rémi Monasson, Guilhem Semerjian, Francesco Zamponi
2021 -

105 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
2021 - Science Immunology

106 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
2021 - eLife

107 Gaussian Closure Scheme in the Quasi--Linkage Equilibrium Regime of Evolving Genome Populations
Eugenio Mauri, Simona Cocco, Rémi Monasson
2021 - EPL - Europhysics Letters

108 Survival probability and size of lineages in antibody affinity maturation
Marco Molari, Rémi Monasson, Simona Cocco
2021 - Physical Review E

109 Parameters and determinants of responses to selection in antibody libraries
Steven Schulz, Sébastien Boyer, Matteo Smerlak, Simona Cocco, Rémi Monasson, Clément Nizak, Olivier Rivoire
2021 - PLoS Computational Biology

110 Immune fingerprinting through repertoire similarity
Thomas Dupic, Meriem Bensouda Koraichi, Anastasia Minervina, Mikhail Pogorelyy, Thierry Mora, Aleksandra Walczak
2021 - PLoS Genetics

111 Online characterization of the retinal network
Baptiste Lefebvre
2020 - -THESE-

112 Population variability in the generation and thymic selection of T-cell repertoires
Zachary Sethna, Giulio Isacchini, Thomas Dupic, Thierry Mora, Aleksandra Walczak, Yuval Elhanati
2020 - PLoS Computational Biology

113 A self-consistent probabilistic formulation for inference of interactions
Jorge Fernandez-De-Cossio, Jorge Fernandez-De-Cossio-Diaz, Yasser Perera-Negrin
2020 - Scientific Reports

114 A new inference approach for training shallow and deep generalized linear models of noisy interacting neurons
Gabriel Mahuas, Giulio Isacchini, Olivier Marre, Ulisse Ferrari, Thierry Mora
2020 -

115 Modélisation et inférence Bayésienne pour la maturation d'affinité des anticorps
Marco Molari
2020 - -THESE-

116 Low-dimensional continuous attractors in recurrent neural networks : from statistical physics to computational neuroscience
Aldo Battista
2020 - -THESE-

117 Learning the heterogeneous hypermutation landscape of immunoglobulins from high-throughput repertoire data
Natanael Spisak, Aleksandra Walczak, Thierry Mora
2020 - Nucleic Acids Research

118 SOS: online probability estimation and generation of T-and B-cell receptors
Giulio Isacchini, Carlos Olivares, Armita Nourmohammad, Aleksandra Walczak, Thierry Mora
2020 - Bioinformatics

119 A mechanism for hunchback promoters to readout morphogenetic positional information in less than a minute
Jonathan Desponds, Massimo Vergassola, Aleksandra Walczak
2020 - eLife

120 Unsupervised Inference of Protein Fitness Landscape from Deep Mutational Scan
Jorge Fernandez-De-Cossio-Diaz, Guido Uguzzoni, Andrea Pagnani
2020 - Molecular Biology and Evolution

121 Blind deconvolution for spike inference from fluorescence recordings
Jérôme Tubiana, Sébastien Wolf, Thomas Panier, Georges Debregeas
2020 - Journal of Neuroscience Methods

122 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
2020 - Science

123 Building General Langevin Models from Discrete Datasets
Federica Ferretti, Victor Chardès, Thierry Mora, Aleksandra Walczak, Irene Giardina
2020 - Physical Review X

124 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
2020 - eLife

125 Generative models of T-cell receptor sequences
Giulio Isacchini, Zachary Sethna, Yuval Elhanati, Armita Nourmohammad, Aleksandra Walczak, Thierry Mora
2020 - Physical Review E

126 Spectrum of multispace Euclidean random matrices
Aldo Battista, Remi Monasson
2020 - Physical Review E

127 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
2020 - Journal of Physics A: Mathematical and Theoretical

128 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
2020 - eLife

129 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
2020 - -REPORT-

130 Capacity-Resolution Trade-Off in the Optimal Learning of Multiple Low-Dimensional Manifolds by Attractor Neural Networks
Aldo Battista, Rémi Monasson
2020 - Physical Review Letters

131 Inference of compressed Potts graphical models
Francesca Rizzato, Alice Coucke, Eleonora de Leonardis, J. P. P. Barton, Jérôme Tubiana, Remi Monasson, Simona Cocco
2020 - Physical Review E

132 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
2020 - eLife

133 Constraints and limitations on decoding positional information: the Bicoid case-study
Huy Tran, Walczak Aleksandra, Nathalie Dostatni
2020 -

134 Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies
Christoph Kreer, Henning Gruell, Thierry Mora, Aleksandra Walczak, Florian Klein
2020 - Vaccines

135 Quantitative Immunology for Physicists
Grégoire Altan-Bonnet, Thierry Mora, Aleksandra M. Walczak
2020 - Physics Reports

136 Inferring the immune response from repertoire sequencing
Maximilian Puelma Touzel, Aleksandra M Walczak, Thierry Mora
2020 - PLoS Computational Biology

137 Dissipation in Non-Steady State Regulatory Circuits
Paulina Szymańska-Rożek, Dario Villamaina, Jacek Miȩkisz, Aleksandra Walczak
2019 - Entropy

138 Can Grid Cell Ensembles Represent Multiple Spaces?
Davide Spalla, Alexis Dubreuil, Sophie Rosay, Remi Monasson, Alessandro Treves
2019 - Neural Computation

139 How many different clonotypes do immune repertoires contain?
Thierry Mora, Aleksandra Walczak
2019 - Current Opinion in Systems Biology

140 Physical Limit to Concentration Sensing in a Changing Environment
Thierry Mora, Ilya Nemenman
2019 - Physical Review Letters

141 Adaptive cluster expansion for Ising spin models
Simona Cocco, Giancarlo Croce, Francesco Zamponi
2019 - The European Physical Journal B: Condensed Matter and Complex Systems

142 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
2019 - Bioinformatics

143 Physique statistique et apprentissage machine : une méthode et trois exemples
Remi Monasson
2019 -

144 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
2019 - PLoS Computational Biology

145 Learning Compositional Representations of Interacting Systems with Restricted Boltzmann Machines: Comparative Study of Lattice Proteins
Jérôme Tubiana, Simona Cocco, Remi Monasson
2019 - Neural Computation

146 How a well-adapting immune system remembers
Andreas Mayer, Vijay Balasubramanian, Aleksandra M. Walczak, Thierry Mora
2019 - Proceedings of the National Academy of Sciences of the United States of America

147 Modeling the Correlated Activity of Neural Populations: A Review
Christophe Gardella, Olivier Marre, Thierry Mora
2019 - Neural Computation

148 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
2019 - Physical Review E

149 Genesis of the αβ T-cell receptor
Thomas Dupic, Quentin Marcou, Aleksandra M. Walczak, Thierry Mora
2019 - PLoS Computational Biology

150 Fierce Selection and Interference in B-Cell Repertoire Response to Chronic HIV-1
Armita Nourmohammad, Jakub Otwinowski, Marta Łuksza, Thierry Mora, Aleksandra M Walczak
2019 - Molecular Biology and Evolution

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158

Publications

7

Années

Statistical physics