Statistical physics of immune-viral co-evolution

Pubblicazioni

Variability in the local and global composition of human T-cell receptor repertoires during thymic development across cell types and individuals

Autori: Giulio Isacchini; Valentin Quiniou; Hélène Vantomme; Paul Stys; Encarnita Mariotti-Ferandiz; David Klatzmann; Aleksandra M. Walczak; Thierry Mora; Armita Nourmohammad
Pubblicato in: 2023
Editore: arxiv
DOI: 10.48550/arxiv.2307.14376

Bayesian estimation of the Kullback-Leibler divergence for categorical sytems using mixtures of Dirichlet priors

Autori: Francesco Camaglia; Ilya Nemenman; Thierry Mora; Aleksandra M. Walczak
Pubblicato in: 2023
Editore: arxiv
DOI: 10.48550/arxiv.2307.04201

Generalized Glauber dynamics for inference in biology

Autori: Xiaowen Chen; Maciej Winiarski; Alicja Puscian; Ewelina Knapska; Aleksandra M. Walczak; Thierry Mora
Pubblicato in: 2022
Editore: arxiv
DOI: 10.48550/arxiv.2208.03483

Modelling collective behavior in groups of mice housed under semi-naturalistic conditions

Autori: Xiaowen Chen; Maciej Winiarski; Alicja Puścian; Ewelina Knapska; Thierry Mora; Aleksandra M. Walczak
Pubblicato in: 2023
Editore: bioarxiv
DOI: 10.1101/2023.07.26.550619

Combining mutation and recombination statistics to infer clonal families in antibody repertoires

Autori: Natanael Spisak; Thomas Dupic; Thierry Mora; Aleksandra M. Walczak
Pubblicato in: arxiv, Numero 1, 2022
Editore: arxiv
DOI: 10.1101/2022.12.22.521661

Population based selection shapes the T cell receptor repertoire during thymic development

Autori: Francesco Camaglia, Arie Ryvkin, Erez Greenstein, Shlomit Reich-Zeliger, Benny Chain, Thierry Mora, Aleksandra M. Walczak, Nir Friedman
Pubblicato in: elife, 2023, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/elife.81622

Modeling and predicting the overlap of B- and T-cell receptor repertoires in healthy and SARS-CoV-2 infected individuals

Autori: Maria Ruiz Ortega, Natanael Spisak, Thierry Mora, Aleksandra M. Walczak
Pubblicato in: PloS Genetics, 2023, ISSN 1553-7390
Editore: Public Library of Science
DOI: 10.1371/journal.pgen.1010652

Generative models of T-cell receptor sequences

Autori: Giulio Isacchini, Zachary Sethna, Yuval Elhanati, Armita Nourmohammad, Aleksandra M. Walczak, Thierry Mora
Pubblicato in: Physical Review E, Numero 101/6, 2020, ISSN 2470-0045
Editore: APS
DOI: 10.1103/physreve.101.062414

Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies

Autori: Cosimo Lupo, Natanael Spisak, Aleksandra M. Walczak, Thierry Mora
Pubblicato in: PLoS CB, 2022, ISSN 1553-734X
Editore: Public Library of Science

Quantitative Theory of Viral-Immune Coevolution May Be within Reach

Autori: Thierry Mora; Aleksandra M. Walczak
Pubblicato in: PRXLife, 2023, ISSN 2835-8279
Editore: APS
DOI: 10.1103/prxlife.1.011001

RBM-MHC: A Semi-Supervised Machine-Learning Method for Sample-Specific Prediction of Antigen Presentation by HLA-I Alleles

Autori: Barbara Bravi, Jérôme Tubiana, Simona Cocco, Rémi Monasson, Thierry Mora, Aleksandra M. Walczak
Pubblicato in: Cell Systems, 2020, ISSN 2405-4712
Editore: Elsevier
DOI: 10.1016/j.cels.2020.11.005

MINIMALIST: Mutual INformatIon Maximization for Amortized Likelihood Inference from Sampled Trajectories

Autori: Giulio Isacchini, Natanael Spisak, Armita Nourmohammad, Thierry Mora, Aleksandra M. Walczak
Pubblicato in: Physical Review E, 2022, ISSN 2470-0053
Editore: American Physical Society

Probabilities of developing HIV-1 bNAb sequence features in uninfected and chronically infected individuals

Autori: Christoph Kreer; Cosimo Lupo; Meryem S. Ercanoglu; Lutz Gieselmann; Natanael Spisak; Jan Grossbach; Maike Schlotz; Philipp Schommers; Henning Gruell; Leona Dold; Andreas Beyer; Armita Nourmohammad; Thierry Mora; Aleksandra M. Walczak; Florian Klein
Pubblicato in: Nature Communications, 2023, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-023-42906-y

Binding affinity landscapes constrain the evolution of broadly neutralizing anti-influenza antibodies

Autori: Angela M Phillips, Katherine R Lawrence, Alief Moulana, Thomas Dupic, Jeffrey Chang, Milo S Johnson, Ivana Cvijovic, Thierry Mora, Aleksandra M Walczak, Michael M Desai
Pubblicato in: elife, 2021, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/elife.71393

Immune fingerprinting through repertoire similarity

Autori: Thomas Dupic, Meriem Bensouda Koraichi, Anastasia A. Minervina, Mikhail V. Pogorelyy, Thierry Mora, Aleksandra M. Walczak
Pubblicato in: PLOS Genetics, Numero 17/1, 2021, Pagina/e e1009301, ISSN 1553-7404
Editore: PloS
DOI: 10.1371/journal.pgen.1009301

Granger causality analysis for calcium transients in neuronal networks, challenges and improvements

Autori: Faustine Ginoux; Xiaowen Chen; Martin Carbo-Tano; Thierry Mora; Aleksandra M Walczak; Claire Wyart
Pubblicato in: elife, Numero 6, 2023, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/elife.81279

Probing T-cell response by sequence-based probabilistic modeling

Autori: Barbara Bravi, Vinod P. Balachandran, Benjamin D. Greenbaum, Aleksandra M. Walczak, Thierry Mora, Rémi Monasson, Simona Cocco
Pubblicato in: PloS CB, 2021, ISSN 1553-734X
Editore: Public Library of Science
DOI: 10.1371/journal.pcbi.1009297

Deep generative selection models of T and B cell receptor repertoires with soNNia

Autori: Giulio Isacchini, Aleksandra M Walczak, Thierry Mora, Armita Nourmohammad
Pubblicato in: PNAS, 2021, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.2023141118

Physical observables to determine the nature of membrane-less cellular sub-compartments

Autori: Mathias L. Heltberg, Judith Miné-Hattab, Angela Taddei, Aleksandra M. Walczak, Thierry Mora
Pubblicato in: elife, 2021, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/elife.69181

Evolutionary stability of antigenically escaping viruses

Autori: Victor Chardès; Andrea Mazzolini; Thierry Mora; Aleksandra M. Walczak
Pubblicato in: PNAS, 2023, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.230771212

A transfer-learning approach to predict antigen immunogenicity and T-cell receptor specificity

Autori: Barbara Bravi; Andrea Di Gioacchino;Jorge Fernandez-de-Cossio-Diaz; Aleksandra M Walczak;Thierry Mora;Simona Cocco;Rémi Monasson
Pubblicato in: elife, 2023, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/elife.85126

Inspecting the interaction between human immunodeficiency virus and the immune system through genetic turnover

Autori: Andrea Mazzolini; Thierry Mora; Aleksandra M. Walczak
Pubblicato in: Philosophical Transactions of the Royal Society B: Biological Sciences, Numero 1, 2023, ISSN 0962-8436
Editore: Royal Society of London
DOI: 10.1098/rstb.2022.0056

Precise tracking of vaccine-responding T cell clones reveals convergent and personalized response in identical twins

Autori: Mikhail V. Pogorelyy, Anastasia A. Minervina, Maximilian Puelma Touzel, Anastasiia L. Sycheva, Ekaterina A. Komech, Elena I. Kovalenko, Galina G. Karganova, Evgeniy S. Egorov, Alexander Yu. Komkov, Dmitriy M. Chudakov, Ilgar Z. Mamedov, Thierry Mora, Aleksandra M. Walczak, Yuri B. Lebedev
Pubblicato in: Proceedings of the National Academy of Sciences, Numero 115/50, 2018, Pagina/e 12704-12709, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.1809642115

Method for identification of condition-associated public antigen receptor sequences

Autori: Mikhail V Pogorelyy, Anastasia A Minervina, Dmitriy M Chudakov, Ilgar Z Mamedov, Yuri B Lebedev, Thierry Mora, Aleksandra M Walczak
Pubblicato in: eLife, Numero 7, 2018, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/elife.33050

Fierce Selection and Interference in B-Cell Repertoire Response to Chronic HIV-1

Autori: Armita Nourmohammad, Jakub Otwinowski, Marta Łuksza, Thierry Mora, Aleksandra M Walczak
Pubblicato in: Molecular Biology and Evolution, Numero 36/10, 2019, Pagina/e 2184-2194, ISSN 0737-4038
Editore: Oxford University Press
DOI: 10.1093/molbev/msz143

Origin of Public Memory B Cell Clones in Fish After Antiviral Vaccination

Autori: Susana Magadan, Luc Jouneau, Maximilian Puelma Touzel, Simon Marillet, Wahiba Chara, Adrien Six, Edwige Quillet, Thierry Mora, Aleksandra M. Walczak, Frédéric Cazals, Oriol Sunyer, Simon Fillatreau, Pierre Boudinot
Pubblicato in: Frontiers in Immunology, Numero 9, 2018, ISSN 1664-3224
Editore: Frontiers
DOI: 10.3389/fimmu.2018.02115

Genesis of the αβ T-cell receptor

Autori: Thomas Dupic, Quentin Marcou, Aleksandra M. Walczak, Thierry Mora
Pubblicato in: PLOS Computational Biology, Numero 15/3, 2019, Pagina/e e1006874, ISSN 1553-7358
Editore: PLos
DOI: 10.1371/journal.pcbi.1006874

Predicting the spectrum of TCR repertoire sharing with a data-driven model of recombination

Autori: Yuval Elhanati, Zachary Sethna, Curtis G. Callan, Thierry Mora, Aleksandra M. Walczak
Pubblicato in: Immunological Reviews, Numero 284/1, 2018, Pagina/e 167-179, ISSN 0105-2896
Editore: Blackwell Publishing Inc.
DOI: 10.1111/imr.12665

Cost and benefits of clustered regularly interspaced short palindromic repeats spacer acquisition

Autori: Serena Bradde, Thierry Mora, Aleksandra M. Walczak
Pubblicato in: Philosophical Transactions of the Royal Society B: Biological Sciences, Numero 374/1772, 2019, Pagina/e 20180095, ISSN 0962-8436
Editore: Royal Society of London
DOI: 10.1098/rstb.2018.0095

Evidence for Shaping of Light Chain Repertoire by Structural Selection

Autori: Adar Toledano, Yuval Elhanati, Jennifer I. C. Benichou, Aleksandra M. Walczak, Thierry Mora, Yoram Louzoun
Pubblicato in: Frontiers in Immunology, Numero 9, 2018, ISSN 1664-3224
Editore: Frontiers
DOI: 10.3389/fimmu.2018.01307

Size and structure of the sequence space of repeat proteins

Autori: Jacopo Marchi, Ezequiel A. Galpern, Rocio Espada, Diego U. Ferreiro, Aleksandra M. Walczak, Thierry Mora
Pubblicato in: PLOS Computational Biology, Numero 15/8, 2019, Pagina/e e1007282, ISSN 1553-7358
Editore: PloS
DOI: 10.1371/journal.pcbi.1007282

Detecting T cell receptors involved in immune responses from single repertoire snapshots

Autori: Mikhail V. Pogorelyy, Anastasia A. Minervina, Mikhail Shugay, Dmitriy M. Chudakov, Yuri B. Lebedev, Thierry Mora, Aleksandra M. Walczak
Pubblicato in: PLOS Biology, Numero 17/6, 2019, Pagina/e e3000314, ISSN 1545-7885
Editore: PLoS
DOI: 10.1371/journal.pbio.3000314

OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs

Autori: Zachary Sethna, Yuval Elhanati, Curtis G Callan, Aleksandra M Walczak, Thierry Mora
Pubblicato in: Bioinformatics, Numero 35/17, 2019, Pagina/e 2974-2981, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btz035

Multi-Lineage Evolution in Viral Populations Driven by Host Immune Systems

Autori: Jacopo Marchi, Michael Lässig, Thierry Mora, Aleksandra M. Walczak
Pubblicato in: Pathogens, Numero 8/3, 2019, Pagina/e 115, ISSN 2076-0817
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/pathogens8030115

Quantitative immunology for physicists

Autori: Grégoire Altan-Bonnet, Thierry Mora, Aleksandra M. Walczak
Pubblicato in: Physics Reports, Numero 849, 2020, Pagina/e 1-83, ISSN 0370-1573
Editore: Elsevier BV
DOI: 10.1016/j.physrep.2020.01.001

Primary and secondary anti-viral response captured by the dynamics and phenotype of individual T cell clones

Autori: Anastasia A Minervina, Mikhail V Pogorelyy, Ekaterina A Komech, Vadim K Karnaukhov, Petra Bacher, Elisa Rosati, Andre Franke, Dmitriy M Chudakov, Ilgar Z Mamedov, Yuri B Lebedev, Thierry Mora, Aleksandra M Walczak
Pubblicato in: eLife, Numero 9, 2020, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/elife.53704

Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies

Autori: Christoph Kreer, Henning Gruell, Thierry Mora, Aleksandra M. Walczak, Florian Klein
Pubblicato in: Vaccines, Numero 8/1, 2020, Pagina/e 13, ISSN 2076-393X
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/vaccines8010013

Inferring the immune response from repertoire sequencing

Autori: Maximilian Puelma Touzel, Aleksandra M. Walczak, Thierry Mora
Pubblicato in: PLOS Computational Biology, Numero 16/4, 2020, Pagina/e e1007873, ISSN 1553-7358
Editore: PLoS
DOI: 10.1371/journal.pcbi.1007873

Building General Langevin Models from Discrete Datasets

Autori: Federica Ferretti, Victor Chardès, Thierry Mora, Aleksandra M. Walczak, Irene Giardina
Pubblicato in: Physical Review X, Numero 10/3, 2020, ISSN 2160-3308
Editore: American Physical Society
DOI: 10.1103/physrevx.10.031018

Population variability in the generation and selection of T-cell repertoires

Autori: Zachary Sethna, Giulio Isacchini, Thomas Dupic, Thierry Mora, Aleksandra M. Walczak, Yuval Elhanati
Pubblicato in: PLOS Computational Biology, Numero 16/12, 2020, Pagina/e e1008394, ISSN 1553-7358
Editore: PloS
DOI: 10.1371/journal.pcbi.1008394

SOS: online probability estimation and generation of T-and B-cell receptors

Autori: Giulio Isacchini, Carlos Olivares, Armita Nourmohammad, Aleksandra M Walczak, Thierry Mora
Pubblicato in: Bioinformatics, 2020, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btaa574

Optimal prediction with resource constraints using the information bottleneck

Autori: Vedant Sachdeva, Thierry Mora, Aleksandra Walczak, Stephanie E. Palmer
Pubblicato in: PloS CB, 2021, ISSN 1553-734X
Editore: Public Library of Science
DOI: 10.1371/journal.pcbi.1008743

Inferring the T-cells repertoire dynamics of healthy individuals

Autori: Meriem Bensouda Koraichi, Silvia Ferri, Aleksandra M Walczak, Thierry Mora
Pubblicato in: PNAS, 2022, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.2207516120

Learning the heterogeneous hypermutation landscape of immunoglobulins from high-throughput repertoire data

Autori: Natanael Spisak, Aleksandra M Walczak, Thierry Mora
Pubblicato in: Nucleic Acids Research, Numero 48/19, 2020, Pagina/e 10702-10712, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkaa825

Contribution of resident and circulating precursors to tumor-infiltrating CD8+ T cell populations in lung cancer

Autori: 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 M. Walczak, Joshua J Waterfall, Sebastian Amigorena
Pubblicato in: Science Immunology, 2021, ISSN 2470-9468
Editore: AAAS
DOI: 10.1126/sciimmunol.abd5778

A Renormalization Group Approach to Connect Discrete- and Continuous-Time Descriptions of Gaussian Processes

Autori: Federica Ferretti, Victor Chardes, Thierry Mora, Aleksandra M Walczak, Irene Giardina
Pubblicato in: Physical Review E, 2022, ISSN 2470-0045
Editore: American Physical Society

Single molecule microscopy reveals key physical features of repair foci in living cells

Autori: Judith Miné-Hattab, Mathias Heltberg, Marie Villemeur, Chloé Guedj, Thierry Mora, Aleksandra M. Walczak, Maxime Dahan, Angela Taddei
Pubblicato in: elife, 2020, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/elife.60577

Affinity maturation for an optimal balance between long-term immune coverage and short-term resource constraints

Autori: Victor Chardes, Massimo Vergassola, Aleksandra M. Walczak, Thierry Mora
Pubblicato in: PNAS, 2022, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.2113512119

Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T-cell memory formation after mild COVID-19 infection

Autori: Anastasia A Minervina, Ekaterina A Komech, Aleksei Titov, Meriem Bensouda Koraichi, Elisa Rosati, Ilgar Z Mamedov, Andre Franke, Grigory A Efimov, Dmitriy M Chudakov, Thierry Mora, Aleksandra M Walczak, Yuri B Lebedev, Mikhail V Pogorelyy
Pubblicato in: eLife, Numero 10, 2021, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/elife.63502

Towards a quantitative theory of tolerance

Autori: Mora, Thierry; Walczak, Aleksandra M.
Pubblicato in: Trends in Immunology, Numero 1, 2023, ISSN 1471-4981
Editore: Cell Press
DOI: 10.1016/j.it.2023.04.008

Antigenic waves of virus–immune coevolution

Autori: Jacopo Marchi, Michael Lässig, Aleksandra M. Walczak, Thierry Mora
Pubblicato in: PNAS, 2021, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.2103398118

NoisET: Noise learning and Expansion detection of T-cell receptors with Python

Autori: Meriem Bensouda Koraichi, Maximilian Puelma Touzel, Thierry Mora, Aleksandra M. Walczak
Pubblicato in: J. Phys. Chem. A, 2022, ISSN 1520-5215
Editore: ACS
DOI: 10.1021/acs.jpca.2c05002

How many different clonotypes do immune repertoires contain?

Autori: Thierry Mora, Aleksandra M. Walczak
Pubblicato in: Current Opinion in Systems Biology, Numero 18, 2019, Pagina/e 104-110, ISSN 2452-3100
Editore: Elsevier
DOI: 10.1016/j.coisb.2019.10.001

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