Laboratory of immunosequencing methods

The team works on development of molecular tools for the basic and biomedical studies, mainly in the filed of immunity and autoimmunity. The current focus of interest is the role of clonal T cell populations in the onset and development of autoimmune diseases, DNA technologies for the quantitative analysis of individual TCR and antibody repertoires in health and disease.

All publications (show selected)


Dmitriy Chudakov

Study of the role of tumor-infiltrating B-lymphocytes

- For the first time, the association of the isotype composition of antibodies and B-cell receptors in the tumor environment and the prognosis of patient survival associated with the presence of certain driver mutations is shown.

- The role of tumor-infiltrating B-lymphocytes was first systemically characterized through the prism of the analysis of repertoires of antibodies and B-cell receptors.

Joint work with Privolzhsky Research Medical University.



1) Isaeva OI, Sharonov GV, Serebrovskaya EO, Turchaninova MA, Zaretsky AR, Shugay M, Chudakov DM (2019). Intratumoral immunoglobulin isotypes predict survival in lung adenocarcinoma subtypes. J Immunother Cancer 7 (1), 279

2) Sharonov GV, Serebrovskaya EO, Yuzhakova DV, Britanova OV, Chudakov DM (2020). B cells, plasma cells and antibody repertoires in the tumour microenvironment. Nature Rev. Immunology, in press.


A new approach to the functional analysis of sequencing data for T-lymphocyte repertoires

In collaboration with Group of Immunosequencing Algorithms,  Laboratory of comparative and functional genomics

In order to extract clinically relevant information from large high-throughput sequencing of TCR repertoires we create a new statistical approach - Antigen-specific Lymphocyte Identification by Clustering of Expanded sequences (ALICE) /fig a/. We applied our algorithm to distinguish naïve from the effector memory cells in available TCR beta repertoires /fig b/, to identify reactive T-cell clones in mixed lymphocyte reaction (MLR) assay /fig c, d/, to fractionate TCR repertoires of patients with autoimmune disease or ones being under cancer immunotherapy, or subject to an acute viral infection. In summary, implementation of ALICE facilitate the identification of TCR variants associated with diseases and conditions, which can be used for diagnostics and rational vaccine design.

Photoswitchable red fluorescent proteins for nanoscopy of live cells

In collaboration with Laboratory of genetically encoded molecular tools

We developed new reversibly photoswitchable red fluorescent proteins based on FusionRed. These proteins, rsFusionRed1, 2 and 3, can be switched OFF and ON and by orange and green light, respectively. This photoswitching behavior allows to avoid illumination by phototoxic violet and blue light, which is commonly used for other photoswitchable proteins. Due to high brightness, high photostability, rapid photoswitching and low phototoxic excitation wavelengths rsFusionReds represent excellent tags for nanoscale imaging of living cells.


  1. Pennacchietti F, Serebrovskaya EO, Faro AR, Shemyakina II, Bozhanova NG, Kotlobay AA, Gurskaya NG, Bodén A, Dreier J, Chudakov DM, Lukyanov KA, Verkhusha VV, Mishin AS, Testa I (2018). Fast reversibly photoswitching red fluorescent proteins for live-cell RESOLFT nanoscopy. Nat Methods 15 (8), 601–604

Achievements 2017

Investigation of T-cell receptors and antibody repertoires in health and disease