Publications by authors named "Dmitry M Chudakov"

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Splicing-aware scRNA-Seq resolution reveals execution-ready programs in effector Tregs.
Daniil K Lukyanov, Evgeniy S Egorov, Valeriia V Kriukova, Denis Syrko, Victor V Kotliar, Dmitry M Chudakov

PLoS Comput Biol· November 2025

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Comprehensive analysis of αβT-cell receptor repertoires reveals signatures of thymic selection.
Daniil V Luppov, Elizaveta K Vlasova, Dmitry M Chudakov, Mikhail Shugay

Front Immunol· October 2025

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Repertoire-based mapping and time-tracking of T helper cell subsets in scRNA-Seq.
Daniil K Lukyanov, Valeriia V Kriukova, Kristin Ladell, Irina A Shagina, Dmitry B Staroverov, Dmitry M Chudakov

Front Immunol· April 2025

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Clonal structure and the specificity of vaccine-induced T cell response to SARS-CoV-2 Spike protein.
Saveliy A Sheetikov, Alexandra A Khmelevskaya, Ksenia V Zornikova, Ivan V Zvyagin, Alina S Shomuradova, Dmitry M Chudakov

Front Immunol· April 2024

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Targeted depletion of TRBV9 T cells as immunotherapy in a patient with ankylosing spondylitis.
Olga V Britanova, Kseniia R Lupyr, Dmitry B Staroverov, Irina A Shagina, Alexey A Aleksandrov, Dmitry M Chudakov

Nat Med· November 2023

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Comment on 'rigorous benchmarking of T cell receptor repertoire profiling methods for cancer RNA sequencing'.
Alexey N Davydov, Dmitry A Bolotin, Stanislav V Poslavsky, Dmitry M Chudakov

Brief Bioinform· September 2023

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HLA variants have different preferences to present proteins with specific molecular functions which are complemented in frequent haplotypes.
Vadim Karnaukhov, Wayne Paes, Isaac B Woodhouse, Thomas Partridge, Annalisa Nicastri, Dmitry M Chudakov

Front Immunol· January 2023

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Tocilizumab, netakimab, and baricitinib in patients with mild-to-moderate COVID-19: An observational study.
Ekaterina A Bryushkova, Valeria D Skatova, Zinaida Y Mutovina, Alena I Zagrebneva, Daria S Fomina, Dmitry M Chudakov

PLoS One· August 2022

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Deciphering Repertoire of B16 Melanoma Reactive TCRs by Immunization, In Vitro Restimulation and Sequencing of IFNγ-Secreting T Cells.
Anna V Izosimova, Diana V Yuzhakova, Valeria D Skatova, Lilia N Volchkova, Elena V Zagainova, Dmitry M Chudakov

Int J Mol Sci· September 2021

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HLA binding of self-peptides is biased towards proteins with specific molecular functions.
Vadim Karnaukhov, Wayne Paes, Isaac B Woodhouse, Thomas Partridge, Annalisa Nicastri, Dmitry M Chudakov

bioRxiv· February 2021

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Two independent routes of post-translational chemistry in fluorescent protein FusionRed.
Liya Muslinkina, Vladimir Z Pletnev, Nadya V Pletneva, Dmitry A Ruchkin, Danila V Kolesov, Dmitry M Chudakov

Int J Biol Macromol· July 2020

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γδ T-cell Receptors Derived from Breast Cancer-Infiltrating T Lymphocytes Mediate Antitumor Reactivity.
Anke Janssen, Jose Villacorta Hidalgo, Dennis X Beringer, Sanne van Dooremalen, Febilla Fernando, Dmitry M Chudakov

Cancer Immunol Res· April 2020

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An overview of immunoinformatics approaches and databases linking T cell receptor repertoires to their antigen specificity.
Ivan V Zvyagin, Vasily O Tsvetkov, Dmitry M Chudakov, Mikhail Shugay

Immunogenetics· February 2020

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Fast reversibly photoswitching red fluorescent proteins for live-cell RESOLFT nanoscopy.
Francesca Pennacchietti, Ekaterina O Serebrovskaya, Aline R Faro, Irina I Shemyakina, Nina G Bozhanova, Dmitry M Chudakov

Nat Methods· August 2018

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Exploring the pre-immune landscape of antigen-specific T cells.
Mikhail V Pogorelyy, Alla D Fedorova, James E McLaren, Kristin Ladell, Dmitri V Bagaev, Dmitry M Chudakov

Genome Med· August 2018

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Insertion of the voltage-sensitive domain into circularly permuted red fluorescent protein as a design for genetically encoded voltage sensor.
Liubov A Kost, Evgeny S Nikitin, Violetta O Ivanova, Uhna Sung, Ekaterina V Putintseva, Dmitry M Chudakov

PLoS One· October 2017

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Local fitness landscape of the green fluorescent protein.
Karen S Sarkisyan, Dmitry A Bolotin, Margarita V Meer, Dinara R Usmanova, Alexander S Mishin, Dmitry M Chudakov

Nature· May 2016

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tcR: an R package for T cell receptor repertoire advanced data analysis.
Vadim I Nazarov, Mikhail V Pogorelyy, Ekaterina A Komech, Ivan V Zvyagin, Dmitry A Bolotin, Dmitry M Chudakov

BMC Bioinformatics· May 2015

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Structure of the red fluorescent protein from a lancelet (Branchiostoma lanceolatum): a novel GYG chromophore covalently bound to a nearby tyrosine.
Vladimir Z Pletnev, Nadya V Pletneva, Konstantin A Lukyanov, Ekaterina A Souslova, Arkady F Fradkov, Dmitry M Chudakov

Acta Crystallogr D Biol Crystallogr· September 2013

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Yellow fluorescent protein phiYFPv (Phialidium): structure and structure-based mutagenesis.
Nadya V Pletneva, Vladimir Z Pletnev, Ekaterina Souslova, Dmitry M Chudakov, Sergey Lukyanov

Acta Crystallogr D Biol Crystallogr· June 2013

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Structural basis for bathochromic shift of fluorescence in far-red fluorescent proteins eqFP650 and eqFP670.
Sergei Pletnev, Nadya V Pletneva, Ekaterina A Souslova, Dmitry M Chudakov, Sergey Lukyanov

Acta Crystallogr D Biol Crystallogr· September 2012

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Circular permutation of red fluorescent proteins.
Bo Shui, Qi Wang, Frank Lee, Laura J Byrnes, Dmitry M Chudakov

PLoS One· September 2011

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Visualizing compound transgenic zebrafish in development: a tale of green fluorescent protein and KillerRed.
Vladimir Korzh, Cathleen Teh, Igor Kondrychyn, Dmitry M Chudakov, Sergey Lukyanov

Zebrafish· March 2011

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Optogenetic in vivo cell manipulation in KillerRed-expressing zebrafish transgenics.
Cathleen Teh, Dmitry M Chudakov, Kar-Lai Poon, Ilgar Z Mamedov, Jun-Yan Sek

BMC Dev Biol· November 2010

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Targeting cancer cells by using an antireceptor antibody-photosensitizer fusion protein.
Ekaterina O Serebrovskaya, Eveline F Edelweiss, Oleg A Stremovskiy, Konstantin A Lukyanov, Dmitry M Chudakov

Proc Natl Acad Sci U S A· June 2009

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