•Statistical physics

Statistical physics and inference for biology

Publications

Statistical physics and inference for biology

1 Online characterization of the retinal network
Baptiste Lefebvre
-THESE-

2 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

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

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

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

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

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

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

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

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

11 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

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

13 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

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

15 Spectrum of multispace Euclidean random matrices
Aldo Battista, Remi Monasson
Physical Review E

16 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

17 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

18 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-

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

20 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

21 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

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

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

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

26 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

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Publications

Statistical physics