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Structure: Internal structure identifier : 1004930
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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 et al.
Cell Systems, 2021, 12 (2), pp.195-202.e9. ⟨10.1016/j.cels.2020.11.005⟩
Journal articles hal-03153691v1

A mechanism for hunchback promoters to readout morphogenetic positional information in less than a minute

Jonathan Desponds , Massimo Vergassola , Aleksandra Walczak
Journal articles hal-03277598v1
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Learning the heterogeneous hypermutation landscape of immunoglobulins from high-throughput repertoire data

Natanael Spisak , Aleksandra Walczak , Thierry Mora
Nucleic Acids Research, 2020, 48, pp.10702 - 10712. ⟨10.1093/nar/gkaa825⟩
Journal articles hal-02988489v1

Evolution and folding of repeat proteins

Ezequiel Galpern , Jacopo Marchi , Thierry Mora , Aleksandra Walczak , Diego Ferreiro et al.
Proceedings of the National Academy of Sciences of the United States of America, 2022, 119 (31), ⟨10.1073/pnas.2204131119⟩
Journal articles hal-03854601v1
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A synaptic signal for novelty processing in the hippocampus

Ruy Gómez-Ocádiz , Massimiliano Trippa , Chun-Lei Zhang , Lorenzo Posani , Simona Cocco et al.
Nature Communications, 2022, 13 (1), pp.4122. ⟨10.1038/s41467-022-31775-6⟩
Journal articles pasteur-03875609v1

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 et al.
Science Immunology, 2021, 6 (55), ⟨10.1126/sciimmunol.abd5778⟩
Journal articles hal-03877456v1
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Inference of compressed Potts graphical models

Francesca Rizzato , Alice Coucke , Eleonora de Leonardis , J. P. P. Barton , Jérôme Tubiana et al.
Physical Review E , 2020, 101 (1), pp.012309. ⟨10.1103/PhysRevE.101.012309⟩
Journal articles hal-02196442v2
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A mechanism for hunchback promoters to readout morphogenetic positional information in less than a minute

Jonathan Desponds , Massimo Vergassola , Aleksandra Walczak
Journal articles hal-02988492v1
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Survival probability and size of lineages in antibody affinity maturation

Marco Molari , Rémi Monasson , Simona Cocco
Preprints, Working Papers, ... hal-02974976v2
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Parameters and determinants of responses to selection in antibody libraries

Steven Schulz , Sébastien Boyer , Matteo Smerlak , Simona Cocco , Rémi Monasson et al.
PLoS Computational Biology, 2021, 17 (3), pp.e1008751. ⟨10.1371/journal.pcbi.1008751⟩
Journal articles hal-03190048v1
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Barriers and Dynamical Paths in Alternating Gibbs Sampling of Restricted Boltzmann Machines

Clément Roussel , Simona Cocco , Rémi Monasson
Physical Review E : Statistical, Nonlinear, and Soft Matter Physics, 2021, ⟨10.1103/PhysRevE.104.034109⟩
Journal articles hal-03284805v2
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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 et al.
eLife, 2022, 11, ⟨10.7554/elife.74509⟩
Journal articles hal-03666554v1
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Modélisation et inférence Bayésienne pour la maturation d'affinité des anticorps

Marco Molari
Physics [physics]. Université Paris sciences et lettres, 2020. English. ⟨NNT : 2020UPSLE017⟩
Theses tel-03267835v1
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Low-dimensional continuous attractors in recurrent neural networks : from statistical physics to computational neuroscience

Aldo Battista
Physics [physics]. Université Paris sciences et lettres, 2020. English. ⟨NNT : 2020UPSLE012⟩
Theses tel-03203294v1
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Mutational paths with sequence-based models of proteins: from sampling to mean-field characterisation

Eugenio Mauri , Simona Cocco , Rémi Monasson
Preprints, Working Papers, ... hal-03645394v4
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Capacity-Resolution Trade-Off in the Optimal Learning of Multiple Low-Dimensional Manifolds by Attractor Neural Networks

Aldo Battista , Rémi Monasson
Physical Review Letters, 2020, ⟨10.1103/PhysRevLett.124.048302⟩
Journal articles hal-02314069v2

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 et al.
Preprints, Working Papers, ... hal-03008612v1
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Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies

Christoph Kreer , Henning Gruell , Thierry Mora , Aleksandra Walczak , Florian Klein et al.
Vaccines, 2020, 8 (1), pp.13. ⟨10.3390/vaccines8010013⟩
Journal articles hal-02496965v1
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Probing T-cell response by sequence-based probabilistic modeling

Barbara Bravi , Vinod P Balachandran , Benjamin D Greenbaum , Aleksandra M Walczak , Thierry Mora et al.
PLoS Computational Biology, 2021, 17 (9), pp.e1009297. ⟨10.1371/journal.pcbi.1009297⟩
Journal articles hal-03351495v1
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sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs

Andrea Di Gioacchino , Rachel Legendre , Yannis Rahou , Valérie Najburg , Pierre Charneau et al.
RNA, 2021, 28 (3), pp.277-289. ⟨10.1261/rna.078969.121⟩
Journal articles pasteur-03591131v1
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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 et al.
Molecular Biology and Evolution, 2021, 38 (6), pp.2428-2445. ⟨10.1093/molbev/msab036⟩
Journal articles hal-02866680v1
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Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies

Cosimo Lupo , Natanael Spisak , Aleksandra M Walczak , Thierry Mora
PLoS Computational Biology, 2022, 18 (6), pp.e1010167. ⟨10.1371/journal.pcbi.1010167⟩
Journal articles hal-03854594v1
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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 et al.
Journal articles hal-02935710v1
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Blind deconvolution for spike inference from fluorescence recordings

Jérôme Tubiana , Sébastien Wolf , Thomas Panier , Georges Debregeas
Journal of Neuroscience Methods, 2020, 342, pp.108763. ⟨10.1016/j.jneumeth.2020.108763⟩
Journal articles hal-03064793v1

Renormalization group approach to connect discrete- and continuous-time descriptions of Gaussian processes

Federica Ferretti , Victor Chardès , Thierry Mora , Aleksandra Walczak , Irene Giardina et al.
Physical Review E , 2022, 105 (4), pp.044133. ⟨10.1103/PhysRevE.105.044133⟩
Journal articles hal-03854599v1
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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, 2021, 118 (27), pp.e2103398118. ⟨10.1073/pnas.2103398118⟩
Journal articles hal-03367761v1

What are the current driving questions in immune repertoire research?

Victor Greiff , Eline Luning Prak , Tim O’donnell , Francesca Finotello , Sai Reddy et al.
Cell Systems, 2022, 13 (9), pp.683-686. ⟨10.1016/j.cels.2022.08.006⟩
Journal articles hal-03854592v1
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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, 2021, 118 (14), pp.e2023141118. ⟨10.1101/2020.11.05.370346⟩
Journal articles hal-02991468v2
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Generative models of T-cell receptor sequences

Giulio Isacchini , Zachary Sethna , Yuval Elhanati , Armita Nourmohammad , Aleksandra Walczak et al.
Physical Review E , 2020, 101 (6), ⟨10.1103/PhysRevE.101.062414⟩
Journal articles hal-02988458v1
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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 et al.
Cell Reports, 2021, 35 (8), pp.109173. ⟨10.1016/j.celrep.2021.109173⟩
Journal articles hal-03264272v1