2022

51   Optimal regularizations for data generation with probabilistic graphical models
 A Fanthomme, F Rizzato, S Cocco, R Monasson
Journal of Statistical Mechanics: Theory and Experiment
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52   Mutual information maximization for amortized likelihood inference from sampled trajectories: MINIMALIST
 Giulio Isacchini, Natanael Spisak, Armita Nourmohammad, Thierry Mora, Aleksandra Walczak
Physical Review E
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53   Synthetic reconstruction of the hunchback promoter specifies the role of Bicoid, Zelda and Hunchback in the dynamics of its transcription
 Gonçalo Fernandes, Huy Tran, Maxime Andrieu, Youssoupha Diaw, Carmina Perez Romero, Cécile Fradin, Mathieu Coppey, Aleksandra Walczak, Nathalie Dostatni
eLife
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54   Renormalization group approach to connect discrete- and continuous-time descriptions of Gaussian processes
 Federica Ferretti, Victor Chardès, Thierry Mora, Aleksandra Walczak, Irene Giardina
Physical Review E
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55   Biophysical Modeling of Dopaminergic Denervation Landscapes in the Striatum Reveals New Therapeutic Strategy
 Mathias Heltberg, Hussein N Awada, Alessandra Lucchetti, Mogens H Jensen, Jakob K Dreyer, Rune N Rasmussen
eNeuro
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56   Affinity maturation for an optimal balance between long-term immune coverage and short-term resource constraints
 Victor Chardès, Massimo Vergassola, Aleksandra Walczak, Thierry Mora
Proceedings of the National Academy of Sciences of the United States of America
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57   Displacement and dissociation of oligonucleotides during DNA hairpin closure under strain
 Fangyuan Ding, Simona Cocco, Saurabh Raj, Maria Manosas, Thao Thi Thu Nguyen, Michelle M Spiering, David Bensimon, Jean-François Allemand, V. Croquette
Nucleic Acids Research
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2021

58   sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs
 Andrea Di Gioacchino, Rachel Legendre, Yannis Rahou, Valérie Najburg, Pierre Charneau, Benjamin Greenbaum, Frédéric Tangy, Sylvie van Der Werf, Simona Cocco, Anastassia Komarova
RNA
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59   AMaLa: Analysis of Directed Evolution Experiments via Annealed Mutational Approximated Landscape
 Luca Sesta, Guido Uguzzoni, Jorge Fernandez-De-Cossio-Diaz, Andrea Pagnani
International Journal of Molecular Sciences
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60   Binding affinity landscapes constrain the evolution of broadly neutralizing anti-influenza antibodies
 Angela Phillips, Katherine Lawrence, Alief Moulana, Thomas Dupic, Jeffrey Chang, Milo Johnson, Ivana Cvijovic, Thierry Mora, Aleksandra Walczak, Michael Desai
eLife
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61   Barriers and Dynamical Paths in Alternating Gibbs Sampling of Restricted Boltzmann Machines
 Clément Roussel, Simona Cocco, Rémi Monasson
Physical Review E
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62   Probing T-cell response by sequence-based probabilistic modeling
 Barbara Bravi, Vinod P Balachandran, Benjamin D Greenbaum, Aleksandra M Walczak, Thierry Mora, Rémi Monasson, Simona Cocco
PLoS Computational Biology
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63   Antigenic waves of virus–immune coevolution
 Jacopo Marchi, Michael Lässig, Aleksandra M Walczak, Thierry Mora
Proceedings of the National Academy of Sciences of the United States of America
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64   Emergent Statistical Laws in Single-Cell Transcriptomic Data
 Silvia Lazzardi, Filippo Valle, Andrea Mazzolini, Antonio Scialdone, Michele Caselle, Matteo Osella
Physical Review E
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65   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
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66   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 S Dewitt, Giulio Isacchini, Garrick K Yip, Wilson W Ng, Owen Tak-Yin Tsang, Meng Yuan, Hejun Liu, Ian A Wilson, J.S. Malik S Malik Peiris, Nicholas C Wu, Armita Nourmohammad, Chris Ka Pun Mok
Cell Reports
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67   Deep generative selection models of T and B cell receptor repertoires with soNNia
 Giulio Isacchini, Aleksandra M Walczak, Thierry Mora, Armita Nourmohammad
Proceedings of the National Academy of Sciences of the United States of America
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68   Optimal prediction with resource constraints using the information bottleneck
 Vedant Sachdeva, Thierry Mora, Aleksandra Walczak, Stephanie Palmer
PLoS Computational Biology
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69   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
Biotechnology and Bioengineering
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70   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
Cell Systems
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71   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
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72   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
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73   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
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74   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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75   Survival probability and size of lineages in antibody affinity maturation
 Marco Molari, Rémi Monasson, Simona Cocco
Physical Review E
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76   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
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2020

77   Online characterization of the retinal network
 Baptiste Lefebvre
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78   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
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79   A self-consistent probabilistic formulation for inference of interactions
 Jorge Fernandez-De-Cossio, Jorge Fernandez-De-Cossio-Diaz, Yasser Perera-Negrin
Scientific Reports
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80   Modélisation et inférence Bayésienne pour la maturation d'affinité des anticorps
 Marco Molari
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81   Low-dimensional continuous attractors in recurrent neural networks : from statistical physics to computational neuroscience
 Aldo Battista
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82   Learning the heterogeneous hypermutation landscape of immunoglobulins from high-throughput repertoire data
 Natanael Spisak, Aleksandra Walczak, Thierry Mora
Nucleic Acids Research
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83   SOS: online probability estimation and generation of T-and B-cell receptors
 Giulio Isacchini, Carlos Olivares, Armita Nourmohammad, Aleksandra Walczak, Thierry Mora
Bioinformatics
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84   A mechanism for hunchback promoters to readout morphogenetic positional information in less than a minute
 Jonathan Desponds, Massimo Vergassola, Aleksandra Walczak
eLife
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85   Unsupervised Inference of Protein Fitness Landscape from Deep Mutational Scan
 Jorge Fernandez-De-Cossio-Diaz, Guido Uguzzoni, Andrea Pagnani
Molecular Biology and Evolution
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86   Blind deconvolution for spike inference from fluorescence recordings
 Jérôme Tubiana, Sébastien Wolf, Thomas Panier, Georges Debregeas
Journal of Neuroscience Methods
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87   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
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88   Building General Langevin Models from Discrete Datasets
 Federica Ferretti, Victor Chardès, Thierry Mora, Aleksandra Walczak, Irene Giardina
Physical Review X
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89   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
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90   Generative models of T-cell receptor sequences
 Giulio Isacchini, Zachary Sethna, Yuval Elhanati, Armita Nourmohammad, Aleksandra Walczak, Thierry Mora
Physical Review E
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91   Spectrum of multispace Euclidean random matrices
 Aldo Battista, Remi Monasson
Physical Review E
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92   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
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93   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
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94   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
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95   Capacity-Resolution Trade-Off in the Optimal Learning of Multiple Low-Dimensional Manifolds by Attractor Neural Networks
 Aldo Battista, Rémi Monasson
Physical Review Letters
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96   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
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97   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
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98   Constraints and limitations on decoding positional information: the Bicoid case-study
 Huy Tran, Walczak Aleksandra, Nathalie Dostatni
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99   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
Advances in Neural Information Processing Systems
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100   Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies
 Christoph Kreer, Henning Gruell, Thierry Mora, Aleksandra Walczak, Florian Klein
Vaccines
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123
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