Author

D. M. Chudakov

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· 19

Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 16 Organism:human· 15 Approach:statistical model· 11 Assay:scRNA-seq· 9 Research Focus:clustering· 7 Research Focus:differential expression· 7 Approach:deep learning· 6 Assay:CITE-seq· 5

Frequent Co-Authors

I. Z. Mamedov· 7 shared Y. B. Lebedev· 7 shared A. A. Minervina· 5 shared M. Shugay· 5 shared M. V. Pogorelyy· 5 shared T. Mora· 5 shared A. Franke· 4 shared A. M. Walczak· 4 shared

Activity by Year

2017-2024 · peak 5/yr

Co-Author Collaboration Network

10 top collaborators · 41 mutual co-author links

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7 shared papersImmunology

I. Z. Mamedov

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19 papers

Recent·Most cited

Splicing-aware resolution of scRNA-Seq data

D. K. Lukyanov, E. S. Egorov, V. V. Kriukova, K. Ladell, D. Price, A. Franke, D. M. Chudakov

The paper introduces SANSARA, a method for splicing-aware scRNA-Seq analysis, revealing splicing heterogeneity in T cell subsets and interactions between transcription factors.

bioRxiv · Mar 25, 2024 · PreprintImmunology

Robust detection of SARS-CoV-2 exposure in population using T-cell repertoire profiling

E. K. Vlasova, A. I. Nekrasova, A. Y. Komkov, M. Izraelson, E. A. Snigir, S. I. Mitrofanov, V. S. Yudin, V. V. Makarov, A. A. Kesnikov, D. Korneeva, A. Pivnyuk, P. V. Shelyakin, I. Z. Mamedov, D. V. Rebrikov, D. M. Chudakov, , M. A. Shugay

The paper develops a classifier for detecting SARS-CoV-2 exposure using T-cell repertoire profiling and machine learning, achieving high accuracy across different protocols.

bioRxiv · Nov 8, 2023 · PreprintImmunology

Repertoire-based mapping and time-tracking of helper T cell subsets in scRNA-Seq

D. K. Lukyanov, V. V. Kriukova, K. Ladell, I. A. Shagina, D. B. Staroverov, B. Minasian, A. S. Fedosova, P. Shelyakin, O. N. Suchalko, A. Komkov, K. A. Blagodatskikh, K. L. Miners, O. V. Britanova, A. Franke, D. A. Price, D. M. Chudakov

This paper introduces TCR-Track, a method to map and track helper T cell subsets in scRNA-Seq data, revealing their clonal relationships and functional programs over time.

bioRxiv · Oct 24, 2023Immunology

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

Non-canonical D1-D2 recombination produces two types of rearrangements and represents a conservative hidden stage of T-cell receptor beta chain generation

A. O. Smirnova, A. M. Miroshnichenkova, L. D. Belyaeva, I. V. Kelmanson, Y. B. Lebedev, I. Z. Mamedov, D. M. Chudakov, A. Y. Komkov

The paper identifies non-canonical D1-D2 recombination in T-cell receptor beta chain generation, revealing two types of rearrangements and their role in memory T-cell function.

bioRxiv · Apr 21, 2023 · PreprintImmunology

Systematic evaluation of intratumoral and peripheral BCR repertoires in three cancers

S. V. Krasik, E. A. Bryushkova, G. V. Sharonov, D. S. Myalik, E. V. Shurganova, D. V. Komarov, I. A. Shagina, P. S. Shpudeiko, M. A. Turchaninova, M. T. Vakhitova, I. V. Samoylenko, D. T. Marinov, L. V. Demidov, V. E. Zagainov, D. M. Chudakov, E. O. Serebrovskaya

This study evaluates BCR repertoires in tumors, draining lymph nodes, and blood of cancer patients, revealing differences in clonotype expansion, hypermutation, and CDR-H3 properties.

bioRxiv · Apr 16, 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

Pinpointing the tumor-specific T-cells via TCR clusters

M. Goncharov, E. A. Bryushkova, N. I. Sharayev, V. D. Skatova, A. M. Baryshnikova, G. V. Sharonov, I. V. Samoylenko, L. V. Demidov, D. M. Chudakov, E. O. Serebrovskaya

This paper demonstrates using TCR repertoires homology cluster analysis to identify tumor-reactive T cells and improve TIL culturing and enrichment.

bioRxiv · Jan 30, 2022Immunology

Inhibitory IL-10-producing CD4+ T cells develop in a T-bet-dependent manner and facilitate cytomegalovirus persistence via coexpression of arginase-1

M. Clement, K. Ladell, K. L. Miners, M. Marsden, L. Chapman, A. Cardus-Figueras, J. Scott, R. Andrews, S. Clare, V. V. Kriukova, K. R. Lupyr, O. V. Britanova, D. R. Withers, D. M. Chudakov, S. A. Jones, , I. Humphreys

The paper identifies IL-10-producing CD4+ T cells that develop via T-bet dependence and Arg1 coexpression, promoting cytomegalovirus persistence.

bioRxiv · Jan 25, 2022Immunology

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

The use of non-functional clonotypes as a natural calibrator for quantitative bias correction in adaptive immune receptor repertoire profiling

A. O. Smirnova, A. M. Miroshnichenkova, Y. V. Olshanskaya, M. A. Maschan, Y. B. Lebedev, D. M. Chudakov, I. Mamedov, A. Y. Komkov

The paper introduces a method to correct PCR bias in immune repertoire sequencing by using non-functional clonotypes as a calibrator, improving accuracy across different sequencing approaches.

bioRxiv · Mar 24, 2021Immunology

Accounting for B cell behaviour and sampling bias yields a superior predictor of anti-PD-L1 response in bladder cancer

I. A. Dyugay, D. K. Lukyanov, M. A. Turchaninova, A. R. Zaretsky, O. A. Khalmurzaev, V. B. Matveev, M. M. Shugay, P. V. Shelyakin, D. M. Chudakov

The paper develops a RNA-Seq-based predictor of anti-PD-L1 response in bladder cancer by integrating B, NK, and T cell components and accounting for sampling bias.

bioRxiv · Mar 4, 2021 · PreprintImmunology

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

A. A. Minervina, E. A. Komech, A. Titov, M. Bensouda Koraichi, E. Rosati, I. Z. Mamedov, A. Franke, G. A. Efimov, D. M. Chudakov, T. Mora, A. M. Walczak, Y. B. Lebedev, M. V. Pogorelyy

This study tracks T cell memory formation after mild COVID-19 infection using longitudinal TCR sequencing, showing clonal expansion and memory phenotype acquisition in infected individuals.

bioRxiv · May 18, 2020Immunology

Comprehensive analysis of antiviral adaptive immunity formation and reactivation down to single-cell level

A. A. Minervina, M. V. Pogorelyy, E. A. Komech, V. K. Karnauhov, P. Bacher, E. Rosati, A. Franke, D. M. Chudakov, I. Z. Mamedov, Y. B. Lebedev, T. Mora, A. M. Walczak

The paper tracks T-cell clone dynamics and TCR repertoire changes after primary and secondary yellow fever vaccination using single-cell RNAseq and TCRseq.

bioRxiv · Oct 25, 2019 · PreprintImmunology

CD4+ T follicular helper (Tfh) cells in human tonsil and blood are clonally convergent, but divergent from non-Tfh CD4+ cells

E. Brenna, A. N. Davydov, K. Ladell, J. E. McLaren, P. Bonaiuti, M. Metsger, S. C. Gilbert, T. Lambe, D. A. Price, S. L. Campion, D. M. Chudakov, P. Borrow, A. J. McMichael

The paper examines clonal relationships between Tfh cells in blood and tonsil, finding clonal convergence between peripheral and tonsillar Tfh cells but divergence from non-Tfh CD4+ cells.

bioRxiv · Aug 22, 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

Precise tracking of vaccine-responding T-cell clones reveals convergent and personalized response in identical twins

M. V. Pogorelyy, A. A. Minervina, M. Puelma Touzel, A. L. Sycheva, E. A. Komech, E. I. Kovalenko, G. G. Karganova, E. S. Egorov, A. Y. Komkov, D. M. Chudakov, I. Z. Mamedov, T. Mora, A. Walczak, Y. B. Lebedev

The paper develops a statistical framework to detect TCR clone changes in vaccinated twins and finds convergent yet personalized TCR responses.

bioRxiv · Apr 13, 2018Immunology

Method for identification of condition-associated public antigen receptor sequences

M. V. Pogorelyy, A. A. Minervina, D. M. Chudakov, I. Z. Mamedov, Y. B. Lebedev, T. Mora, A. M. Walczak

The paper develops a statistical framework to associate antigen receptor sequences with diseases using a small patient cohort, successfully identifying validated receptors for Cytomegalovirus and type 1 diabetes.

bioRxiv · Sep 28, 2017Immunology