Project B5

Co-evolution of viruses and immune repertoires across scales

Aleksandra Walczak, École normale supérieure | web | email

The project studies evolutionary correlations between immune repertoires and viral antigens. It establishes principled models of immune response and, in collaboration with projects B1 and B3, predicts the evolutionary likelihood of specific B-cell responses to HIV. Related models of viral dynamics under multi-host immune challenge are developed in collaboration with project B2 and will be applied to human influenza.

Predictability in Evolution

Collaborative Research Center 1310


Antigenic waves of virus–immune coevolution

Marchi J., Lässig M., Walczak A.M., Mora T., PNAS 118 (27) e2103398118, 6. July 2021

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

Isacchini G., Walczak A.M., Mora T., Nourmohammad A., PNAS 118 (14) e2023141118, 6. April 2021,

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

Minervina A.A., Komech E.A., Titov A., Koraichi M.B., Rosati E., Mamedov I.Z., Franke A., Efimov G.A., Chudakov D.M., Mora T., Walczak A.M., Lebedev Y.B., Pogorelyy M.V., eLife 2021;10:e63502, 5. January 2021,

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

Spisak N., Walczak A.M., Mora T., Nucleic Acids Research, Volume 48, Issue 19, Pages 10702–10712, 4 November 2020,

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

Isacchini G., Olivares C., Nourmohammad. A, Walczak A.M., Mora T., Bioinformatics, Volume 36, Issue 16, 4510–4512, 15. August 2020,

Generative models of T-cell receptor sequences

Isacchini G., Sethna Z., Elhanati Y., Nourmohammad A., Walczak A.M., Mora T., Phys. Rev. E 101, 062414, 15. June 2020,

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

Minervina A.A., Pogorelyy M.V, Komech E.A., Karnaukhov V.K., Bacher P. , Rosat E. , Franke A., Chudakov D.M., Mamedov I.Z., Lebedev Y.B., Mora T., Walczak A.M., eLife2020;9:e53704, 21. February 2020,

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

Kreer C., Gruell H., Mora T., Walczak A.M., Klein F., Vaccines 8(1) 13, 1. January 2020,

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

Nourmohammad A., Otwinowski J., Łuksza M., Mora T., Walczak A.M. , Molecular Biology and Evolution 36(10) 2184-2194, 29. July 2019,

Method for identification of condition-associated public antigen receptor sequences

Pogorelyy M.V., Minervina A.A., Chudakov D.M., Mamedov I.Z., Lebedev Y.B., Mora T., Walczak A.M., eLife 2018;7:e33050, 13. May 2018,     

High-throughput immune repertoire analysis with IGoR

Marcou Q., Mora T., Walczak A.M., Nature Communications Volume 9:561, 8. February 2018,