Author

M. Shugay

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Immunology· 9

Signature Assays, Organisms & Methods

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Organism:human· 6 Research Focus:cell type annotation· 5 Approach:statistical model· 4 Approach:experimental assay· 3 Assay:scRNA-seq· 3 Research Focus:benchmarking· 2 Assay:CITE-seq· 2 Approach:deep learning· 2

Frequent Co-Authors

D. M. Chudakov· 5 shared D. B. Staroverov· 2 shared D. S. Shcherbinin· 2 shared I. V. Zvyagin· 2 shared M. V. Pogorelyy· 2 shared O. V. Britanova· 2 shared T. O. Nakonechnaya· 2 shared A. A. Minervina· 1 shared

Activity by Year

2018-2023 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 19 mutual co-author links

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5 shared papersImmunology

D. M. Chudakov

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9 papers

Recent·Most cited

Convergence, plasticity, and tissue residence of regulatory T cell response via TCR repertoire prism

T. O. Nakonechnaya, B. Moltedo, E. V. Putintseva, S. Leyn, D. A. Bolotin, O. V. Britanova, M. Shugay, D. M. Chudakov

This study investigates Treg cell responses to different antigenic challenges using TCR repertoire analysis, revealing challenge-specific and tissue-specific clonal expansions and plasticity.

bioRxiv · Jun 15, 2023Immunology

TCRen: predicting TCR recognition of unseen epitopes based on residue-level pairwise statistical potential

V. K. Karnaukhov, D. S. Shcherbinin, A. O. Chugunov, D. M. Chudakov, R. G. Efremov, I. V. Zvyagin, M. Shugay

TCRen predicts TCR recognition of unseen epitopes using residue-level pairwise statistical potential from TCR-peptide contacts in crystal structures.

bioRxiv · Feb 15, 2022 · PreprintImmunology

Memory persistence and differentiation into antibody-secreting cells accompanied by positive selection in longitudinal BCR repertoires

A. I. Mikelov, E. I. Alekseeva, E. A. Komech, D. B. Staroverov, M. A. Turchaninova, M. Shugay, D. M. Chudakov, G. A. Bazykin, I. V. Zvyagin

The paper analyzes longitudinal BCR repertoires to show clonal persistence and differentiation into ASCs with positive selection and affinity maturation.

bioRxiv · Dec 30, 2021Immunology

Evaluating performance of existing computational models in predicting CD8+ T cell pathogenic epitopes and cancer neoantigens

P. Buckley, R. Ma, C. H.-J. Lee, I. Woodhouse, J. Woo, V. O. Tsvetkov, D. S. Shcherbinin, M. Shugay, M. Rei, A. Simmons, H. Koohy

This study evaluates existing computational models for predicting CD8+ T cell epitopes and cancer neoantigens, finding poor performance for emerging viruses and cancer peptides.

bioRxiv · Dec 25, 2020Immunology

Human thymopoiesis produces polyspecific CD8+ alfa/beta T cells responding to multiple viral antigens

V. Quiniou, P. Barennes, V. Mhanna, P. Stys, H. Vantomme, Z. Zhou, F. Martina, N. Coatnoan, M. Barbie-Sastre, H. P. Pham, B. Clemenceau, H. Vie, M. Shugay, A. Six, B. Brandao, , D. Klatzmann

The paper shows human thymopoiesis produces CD8+ T cells with polyspecific TCRs that recognize multiple viral antigens, supporting broad antiviral immunity.

bioRxiv · Jul 27, 2020Immunology

sumrep: a summary statistic framework for immune receptor repertoire comparison and model validation

B. J. Olson, P. Moghimi, C. Schramm, A. Obraztsova, D. Ralph, J. A. Vander Heiden, M. Shugay, A. Shepherd, W. Lees, F. A. Matsen

sumrep is an R package for analyzing and comparing immune receptor repertoires, showing that recombination features are more discriminative than amino acid composition summaries and that generative models capture some but not all repertoire properties.

bioRxiv · Aug 6, 2019Immunology

A framework for annotation of antigen specificities in high-throughput T-cell repertoire sequencing studies

M. V. Pogorelyy, M. Shugay

The paper presents a framework to analyze T-cell receptor sequencing data, controlling for biases to identify antigen-specific TCRs using HLA restriction and known antigen-specific TCR databases.

bioRxiv · Jun 20, 2019Immunology

T cell immunity does not age in a long-lived rodent species

M. Izraelson, T. O. Nakonechnaya, A. N. Davydov, M. A. Dronina, D. A. Miskevich, I. Z. Mamedov, L. N. Barbashova, M. Shugay, D. Bolotin, D. B. Staroverov, E. Y. Kondratyuk, E. A. Bogdanova, S. Lukyanov, I. Shams, O. V. Britanova, D. M. Chudakov

This study compares T cell receptor diversity across species, finding that long-lived rodents maintain stable TCR diversity with age, unlike humans and mice.

bioRxiv · Sep 5, 2018Immunology

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

M. V. Pogorelyy, A. A. Minervina, M. Shugay, D. M. Chudakov, Y. B. Lebedev, T. Mora, A. M. Walczak

This paper introduces ALICE, a method to identify TCRs involved in immune responses from single RepSeq samples, showing its effectiveness across various disease conditions.

bioRxiv · Jul 23, 2018Immunology