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STRUGGLE SIGNED

Statistical physics of immune-viral co-evolution

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EC-Contrib. €

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Project "STRUGGLE" data sheet

The following table provides information about the project.

Coordinator
CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS 

Organization address
address: RUE MICHEL ANGE 3
city: PARIS
postcode: 75794
website: www.cnrs.fr

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country France [FR]
 Project website https://www.phys.ens.fr/
 Total cost 1˙909˙750 €
 EC max contribution 1˙909˙750 € (100%)
 Programme 1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
 Code Call ERC-2016-COG
 Funding Scheme ERC-COG
 Starting year 2017
 Duration (year-month-day) from 2017-11-01   to  2022-10-31

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS FR (PARIS) coordinator 1˙909˙750.00

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 Project objective

The immune system within each individual host destroys viruses, which manage to escape immunity on the global scale. Recent experiments show population-level responses of both immune repertoires and viruses, and a history dependence of their functional phenotypes. This constrained long-term co-evolution of immune receptor and viral populations is a stochastic many-body problem occurring at many scales, in which the response emerges based on the past states of both the repertoire and viral populations. STRUGGLE infers the details of viral-immune receptor interactions from functional datasets to obtain a predictive statistical model of co-evolution between immune repertoires and viruses.

STRUGGLE covers the many scales of immune-virus interactions: from the molecular level, analyzing high-throughput mutational screens of libraries of antibodies binding a given antigen, through the population-level response of immune repertoires, analyzing next-generation sequencing of vaccine-stimulated whole repertoires, to the population level, modeling the long term co-evolution of both repertoires and viruses.

STRUGGLE combines a statistical data analysis approach with cross-scale many-body physics to: - build a molecular model for antigen-receptor binding; - learn statistical models for repertoire-level response to viral antigen stimulation; - validate dynamical models of interactions between antigen and immune receptors; - theoretically evaluate the predictive power of the immune system and viruses; - and predict virus strains and immune responses based on past infections.

The outcomes of STRUGGLE include the quantitative characterization of the human T-cell response to flu vaccines, with implications for vaccination strategies, and the trout B-cell response to life-threatening rhabdoviruses, which aids vaccine design for fish, with wide use in agriculture. The statistical properties of the co-evolutionary process are needed for informed development of immunotherapies.

 Publications

year authors and title journal last update
List of publications.
2019 Serena Bradde, Thierry Mora, Aleksandra M. Walczak
Cost and benefits of clustered regularly interspaced short palindromic repeats spacer acquisition
published pages: 20180095, ISSN: 0962-8436, DOI: 10.1098/rstb.2018.0095
Philosophical Transactions of the Royal Society B: Biological Sciences 374/1772 2019-05-27
2018 Yuval Elhanati, Zachary Sethna, Curtis G. Callan, Thierry Mora, Aleksandra M. Walczak
Predicting the spectrum of TCR repertoire sharing with a data-driven model of recombination
published pages: 167-179, ISSN: 0105-2896, DOI: 10.1111/imr.12665
Immunological Reviews 284/1 2019-05-27
2018 Pogorelyy, Mikhail V; Minervina, Anastasia A; Chudakov, Dmitriy M; Mamedov, Ilgar Z; Lebedev, Yuri B; Mora, Thierry; Walczak, Aleksandra M
Method for identification of condition-associated public antigen receptor sequences
published pages: , ISSN: 2050-084X, DOI: 10.1101/195057
eLife 3 2019-04-12
2018 Yuval Elhanati, Zachary Sethna, Curtis G. Callan, Thierry Mora, Aleksandra M. Walczak
Predicting the spectrum of TCR repertoire sharing with a data-driven model of recombination
published pages: 167-179, ISSN: 0105-2896, DOI: 10.1111/imr.12665
Immunological Reviews 284/1 2019-04-13
2018 Pogorelyy, Mikhail V; Minervina, Anastasia A; Shugay, Mikhail; Chudakov, Dmitriy M; Lebedev, Yuri B; Mora, Thierry; Walczak, Aleksandra M
Detecting T-cell receptors involved in immune responses from single repertoire snapshots
published pages: , ISSN: , DOI:
1 2019-04-13
2018 Armita Nourmohammad, Jakub Otwinowski, Marta Luksza, Thierry Mora, Aleksandra M Walczak
Clonal competition in B-cell repertoires during chronic HIV-1 infection
published pages: , ISSN: , DOI: 10.1101/271130
2019-04-13
2019 Andreas Mayer,Vijay Balasubramanian, Aleksandra M. Walczak*, Thierry Mora*
How a well-adapting immune system remembers
published pages: , ISSN: 1091-6490, DOI: 10.1101/347856
PNAS 2019-04-13
2019 Thomas Dupic, Quentin Marcou, Aleksandra M. Walczak, Thierry Mora
Genesis of the αβ T-cell receptor
published pages: e1006874, ISSN: 1553-7358, DOI: 10.1371/journal.pcbi.1006874
PLOS Computational Biology 15/3 2019-04-13
2018 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
Precise tracking of vaccine-responding T cell clones reveals convergent and personalized response in identical twins
published pages: 12704-12709, ISSN: 0027-8424, DOI: 10.1073/pnas.1809642115
Proceedings of the National Academy of Sciences 115/50 2019-04-12
2019 Serena Bradde, Thierry Mora, Aleksandra M. Walczak
Cost and benefits of clustered regularly interspaced short palindromic repeats spacer acquisition
published pages: 20180095, ISSN: 0962-8436, DOI: 10.1098/rstb.2018.0095
Philosophical Transactions of the Royal Society B: Biological Sciences 374/1772 2019-04-12

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