Statistical physics of immune-viral co-evolution

Publications

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

Author(s): Giulio Isacchini; Valentin Quiniou; Hélène Vantomme; Paul Stys; Encarnita Mariotti-Ferandiz; David Klatzmann; Aleksandra M. Walczak; Thierry Mora; Armita Nourmohammad
Published in: 2023
Publisher: arxiv
DOI: 10.48550/arxiv.2307.14376

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

Author(s): Francesco Camaglia; Ilya Nemenman; Thierry Mora; Aleksandra M. Walczak
Published in: 2023
Publisher: arxiv
DOI: 10.48550/arxiv.2307.04201

Generalized Glauber dynamics for inference in biology

Author(s): Xiaowen Chen; Maciej Winiarski; Alicja Puscian; Ewelina Knapska; Aleksandra M. Walczak; Thierry Mora
Published in: 2022
Publisher: arxiv
DOI: 10.48550/arxiv.2208.03483

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

Author(s): Xiaowen Chen; Maciej Winiarski; Alicja Puścian; Ewelina Knapska; Thierry Mora; Aleksandra M. Walczak
Published in: 2023
Publisher: bioarxiv
DOI: 10.1101/2023.07.26.550619

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

Author(s): Natanael Spisak; Thomas Dupic; Thierry Mora; Aleksandra M. Walczak
Published in: arxiv, Issue 1, 2022
Publisher: arxiv
DOI: 10.1101/2022.12.22.521661

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

Author(s): Francesco Camaglia, Arie Ryvkin, Erez Greenstein, Shlomit Reich-Zeliger, Benny Chain, Thierry Mora, Aleksandra M. Walczak, Nir Friedman
Published in: elife, 2023, ISSN 2050-084X
Publisher: 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

Author(s): Maria Ruiz Ortega, Natanael Spisak, Thierry Mora, Aleksandra M. Walczak
Published in: PloS Genetics, 2023, ISSN 1553-7390
Publisher: Public Library of Science
DOI: 10.1371/journal.pgen.1010652

Generative models of T-cell receptor sequences

Author(s): Giulio Isacchini, Zachary Sethna, Yuval Elhanati, Armita Nourmohammad, Aleksandra M. Walczak, Thierry Mora
Published in: Physical Review E, Issue 101/6, 2020, ISSN 2470-0045
Publisher: APS
DOI: 10.1103/physreve.101.062414

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

Author(s): Cosimo Lupo, Natanael Spisak, Aleksandra M. Walczak, Thierry Mora
Published in: PLoS CB, 2022, ISSN 1553-734X
Publisher: Public Library of Science

Quantitative Theory of Viral-Immune Coevolution May Be within Reach

Author(s): Thierry Mora; Aleksandra M. Walczak
Published in: PRXLife, 2023, ISSN 2835-8279
Publisher: 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

Author(s): Barbara Bravi, Jérôme Tubiana, Simona Cocco, Rémi Monasson, Thierry Mora, Aleksandra M. Walczak
Published in: Cell Systems, 2020, ISSN 2405-4712
Publisher: Elsevier
DOI: 10.1016/j.cels.2020.11.005

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

Author(s): Giulio Isacchini, Natanael Spisak, Armita Nourmohammad, Thierry Mora, Aleksandra M. Walczak
Published in: Physical Review E, 2022, ISSN 2470-0053
Publisher: American Physical Society

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

Author(s): 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
Published in: Nature Communications, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-42906-y

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

Author(s): 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
Published in: elife, 2021, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.71393

Immune fingerprinting through repertoire similarity

Author(s): Thomas Dupic, Meriem Bensouda Koraichi, Anastasia A. Minervina, Mikhail V. Pogorelyy, Thierry Mora, Aleksandra M. Walczak
Published in: PLOS Genetics, Issue 17/1, 2021, Page(s) e1009301, ISSN 1553-7404
Publisher: PloS
DOI: 10.1371/journal.pgen.1009301

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

Author(s): Faustine Ginoux; Xiaowen Chen; Martin Carbo-Tano; Thierry Mora; Aleksandra M Walczak; Claire Wyart
Published in: elife, Issue 6, 2023, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.81279

Probing T-cell response by sequence-based probabilistic modeling

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

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

Author(s): Giulio Isacchini, Aleksandra M Walczak, Thierry Mora, Armita Nourmohammad
Published in: PNAS, 2021, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2023141118

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

Author(s): Mathias L. Heltberg, Judith Miné-Hattab, Angela Taddei, Aleksandra M. Walczak, Thierry Mora
Published in: elife, 2021, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.69181

Evolutionary stability of antigenically escaping viruses

Author(s): Victor Chardès; Andrea Mazzolini; Thierry Mora; Aleksandra M. Walczak
Published in: PNAS, 2023, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.230771212

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

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

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

Author(s): Andrea Mazzolini; Thierry Mora; Aleksandra M. Walczak
Published in: Philosophical Transactions of the Royal Society B: Biological Sciences, Issue 1, 2023, ISSN 0962-8436
Publisher: 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

Author(s): 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
Published in: Proceedings of the National Academy of Sciences, Issue 115/50, 2018, Page(s) 12704-12709, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1809642115

Method for identification of condition-associated public antigen receptor sequences

Author(s): Mikhail V Pogorelyy, Anastasia A Minervina, Dmitriy M Chudakov, Ilgar Z Mamedov, Yuri B Lebedev, Thierry Mora, Aleksandra M Walczak
Published in: eLife, Issue 7, 2018, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.33050

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

Author(s): Armita Nourmohammad, Jakub Otwinowski, Marta Łuksza, Thierry Mora, Aleksandra M Walczak
Published in: Molecular Biology and Evolution, Issue 36/10, 2019, Page(s) 2184-2194, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msz143

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

Author(s): 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
Published in: Frontiers in Immunology, Issue 9, 2018, ISSN 1664-3224
Publisher: Frontiers
DOI: 10.3389/fimmu.2018.02115

Genesis of the αβ T-cell receptor

Author(s): Thomas Dupic, Quentin Marcou, Aleksandra M. Walczak, Thierry Mora
Published in: PLOS Computational Biology, Issue 15/3, 2019, Page(s) e1006874, ISSN 1553-7358
Publisher: PLos
DOI: 10.1371/journal.pcbi.1006874

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

Author(s): Yuval Elhanati, Zachary Sethna, Curtis G. Callan, Thierry Mora, Aleksandra M. Walczak
Published in: Immunological Reviews, Issue 284/1, 2018, Page(s) 167-179, ISSN 0105-2896
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/imr.12665

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

Author(s): Serena Bradde, Thierry Mora, Aleksandra M. Walczak
Published in: Philosophical Transactions of the Royal Society B: Biological Sciences, Issue 374/1772, 2019, Page(s) 20180095, ISSN 0962-8436
Publisher: Royal Society of London
DOI: 10.1098/rstb.2018.0095

Evidence for Shaping of Light Chain Repertoire by Structural Selection

Author(s): Adar Toledano, Yuval Elhanati, Jennifer I. C. Benichou, Aleksandra M. Walczak, Thierry Mora, Yoram Louzoun
Published in: Frontiers in Immunology, Issue 9, 2018, ISSN 1664-3224
Publisher: Frontiers
DOI: 10.3389/fimmu.2018.01307

Size and structure of the sequence space of repeat proteins

Author(s): Jacopo Marchi, Ezequiel A. Galpern, Rocio Espada, Diego U. Ferreiro, Aleksandra M. Walczak, Thierry Mora
Published in: PLOS Computational Biology, Issue 15/8, 2019, Page(s) e1007282, ISSN 1553-7358
Publisher: PloS
DOI: 10.1371/journal.pcbi.1007282

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

Author(s): Mikhail V. Pogorelyy, Anastasia A. Minervina, Mikhail Shugay, Dmitriy M. Chudakov, Yuri B. Lebedev, Thierry Mora, Aleksandra M. Walczak
Published in: PLOS Biology, Issue 17/6, 2019, Page(s) e3000314, ISSN 1545-7885
Publisher: PLoS
DOI: 10.1371/journal.pbio.3000314

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

Author(s): Zachary Sethna, Yuval Elhanati, Curtis G Callan, Aleksandra M Walczak, Thierry Mora
Published in: Bioinformatics, Issue 35/17, 2019, Page(s) 2974-2981, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btz035

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

Author(s): Jacopo Marchi, Michael Lässig, Thierry Mora, Aleksandra M. Walczak
Published in: Pathogens, Issue 8/3, 2019, Page(s) 115, ISSN 2076-0817
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/pathogens8030115

Quantitative immunology for physicists

Author(s): Grégoire Altan-Bonnet, Thierry Mora, Aleksandra M. Walczak
Published in: Physics Reports, Issue 849, 2020, Page(s) 1-83, ISSN 0370-1573
Publisher: 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

Author(s): 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
Published in: eLife, Issue 9, 2020, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.53704

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

Author(s): Christoph Kreer, Henning Gruell, Thierry Mora, Aleksandra M. Walczak, Florian Klein
Published in: Vaccines, Issue 8/1, 2020, Page(s) 13, ISSN 2076-393X
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/vaccines8010013

Inferring the immune response from repertoire sequencing

Author(s): Maximilian Puelma Touzel, Aleksandra M. Walczak, Thierry Mora
Published in: PLOS Computational Biology, Issue 16/4, 2020, Page(s) e1007873, ISSN 1553-7358
Publisher: PLoS
DOI: 10.1371/journal.pcbi.1007873

Building General Langevin Models from Discrete Datasets

Author(s): Federica Ferretti, Victor Chardès, Thierry Mora, Aleksandra M. Walczak, Irene Giardina
Published in: Physical Review X, Issue 10/3, 2020, ISSN 2160-3308
Publisher: American Physical Society
DOI: 10.1103/physrevx.10.031018

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

Author(s): Zachary Sethna, Giulio Isacchini, Thomas Dupic, Thierry Mora, Aleksandra M. Walczak, Yuval Elhanati
Published in: PLOS Computational Biology, Issue 16/12, 2020, Page(s) e1008394, ISSN 1553-7358
Publisher: PloS
DOI: 10.1371/journal.pcbi.1008394

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

Author(s): Giulio Isacchini, Carlos Olivares, Armita Nourmohammad, Aleksandra M Walczak, Thierry Mora
Published in: Bioinformatics, 2020, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa574

Optimal prediction with resource constraints using the information bottleneck

Author(s): Vedant Sachdeva, Thierry Mora, Aleksandra Walczak, Stephanie E. Palmer
Published in: PloS CB, 2021, ISSN 1553-734X
Publisher: Public Library of Science
DOI: 10.1371/journal.pcbi.1008743

Inferring the T-cells repertoire dynamics of healthy individuals

Author(s): Meriem Bensouda Koraichi, Silvia Ferri, Aleksandra M Walczak, Thierry Mora
Published in: PNAS, 2022, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2207516120

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

Author(s): Natanael Spisak, Aleksandra M Walczak, Thierry Mora
Published in: Nucleic Acids Research, Issue 48/19, 2020, Page(s) 10702-10712, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa825

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

Author(s): 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
Published in: Science Immunology, 2021, ISSN 2470-9468
Publisher: AAAS
DOI: 10.1126/sciimmunol.abd5778

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

Author(s): Federica Ferretti, Victor Chardes, Thierry Mora, Aleksandra M Walczak, Irene Giardina
Published in: Physical Review E, 2022, ISSN 2470-0045
Publisher: American Physical Society

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

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

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

Author(s): Victor Chardes, Massimo Vergassola, Aleksandra M. Walczak, Thierry Mora
Published in: PNAS, 2022, ISSN 0027-8424
Publisher: 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

Author(s): 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
Published in: eLife, Issue 10, 2021, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.63502

Towards a quantitative theory of tolerance

Author(s): Mora, Thierry; Walczak, Aleksandra M.
Published in: Trends in Immunology, Issue 1, 2023, ISSN 1471-4981
Publisher: Cell Press
DOI: 10.1016/j.it.2023.04.008

Antigenic waves of virus–immune coevolution

Author(s): Jacopo Marchi, Michael Lässig, Aleksandra M. Walczak, Thierry Mora
Published in: PNAS, 2021, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2103398118

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

Author(s): Meriem Bensouda Koraichi, Maximilian Puelma Touzel, Thierry Mora, Aleksandra M. Walczak
Published in: J. Phys. Chem. A, 2022, ISSN 1520-5215
Publisher: ACS
DOI: 10.1021/acs.jpca.2c05002

How many different clonotypes do immune repertoires contain?

Author(s): Thierry Mora, Aleksandra M. Walczak
Published in: Current Opinion in Systems Biology, Issue 18, 2019, Page(s) 104-110, ISSN 2452-3100
Publisher: Elsevier
DOI: 10.1016/j.coisb.2019.10.001

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