•Statistical physics

Statistical physics and inference for biology

Publications

Statistical physics and inference for biology

101 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

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

103 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

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

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

106 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

107 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

108 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-

109 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

110 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

111 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

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

113 Constraints and limitations on the transcriptional response downstream of the Bicoid morphogen gradient
Huy Tran, Aleksandra Walczak, Nathalie Dostatni
2020 -

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 - Advances in Neural Information Processing Systems
-PROCEEDINGS-

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

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

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

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

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

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

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

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

123 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

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

125 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

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

127 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

128 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

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

130 Adaptation of olfactory receptor abundances for efficient coding
Tiberiu Teşileanu, Simona Cocco, Remi Monasson, Vijay Balasubramanian
2019 - eLife

131 Learning protein constitutive motifs from sequence data
Jérôme Tubiana, Simona Cocco, Remi Monasson
2019 - eLife

132 The imaginary Toda field theory
Thomas Dupic, Benoît Estienne, Yacine Ikhlef
2019 - Journal of Physics A: Mathematical and Theoretical

133 Multi-Lineage Evolution in Viral Populations Driven by Host Immune Systems
Jacopo Marchi, Michael Lässig, Thierry Mora, Aleksandra M. Walczak
2019 - Pathogens

134 Three-point functions in the fully packed loop model on the honeycomb lattice
Thomas Dupic, Benoît Estienne, Yacine Ikhlef
2019 - Journal of Physics A: Mathematical and Theoretical

135 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

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

137 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
2019 - PLoS Biology

138 Epistasis in a Fitness Landscape Defined by Antibody-Antigen Binding Free Energy
Rhys Adams, Justin Kinney, Aleksandra M Walczak, Thierry Mora
2019 - Cell Systems

139 Cost and benefits of clustered regularly interspaced short palindromic repeats spacer acquisition
Serena Bradde, Thierry Mora, Aleksandra M Walczak
2019 - Philosophical Transactions of the Royal Society B: Biological Sciences

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139

Publications

7

Years

Statistical physics