Publications

Antigenic waves of virus–immune coevolution

Marchi J., Lässig M., Walczak A.M., Mora T., PNAS 118 (27) e2103398118, 6. July 2021https://doi.org/10.1073/pnas.2103398118

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, https://doi.org/10.1073/pnas.2023141118

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, https://doi.org/10.7554/eLife.63502

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, https://doi.org/10.1093/nar/gkaa825

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, https://doi.org/10.1093/bioinformatics/btaa574

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, https://doi.org/10.1103/PhysRevE.101.062414

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, https://doi.org/10.7554/eLife.53704

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, https://doi.org/10.3390/vaccines8010013

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, https://doi.org/10.3390/pathogens8030115

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,               https://doi.org/10.7554/eLife.33050

High-throughput immune repertoire analysis with IGoR

Marcou Q., Mora T., Walczak A.M., Nature Communications Volume 9:561, 8. February 2018, https://doi.org/10.1038/s41467-018-02832-w