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List of works by Dmitry M. Chudakov

A Crystallographic Study of Bright Far-Red Fluorescent Protein mKate Reveals pH-induced cis-trans Isomerization of the Chromophore

scientific article

A genetically encoded photosensitizer

scientific article published on 20 December 2005

A high-throughput assay for quantitative measurement of PCR errors

scientific article

A mechanism for expansion of regulatory T-cell repertoire and its role in self-tolerance

scientific article published on 25 November 2015

A monomeric red fluorescent protein with low cytotoxicity

scientific article published in January 2012

Adoptive Immunotherapy Based on Chain-Centric TCRs in Treatment of Infectious Diseases

scientific article published on 24 November 2020

Age-related decrease in TCR repertoire diversity measured with deep and normalized sequence profiling

scientific article published on 07 February 2014

An overview of immunoinformatics approaches and databases linking T cell receptor repertoires to their antigen specificity

scientific article published on 18 November 2019

Antigen receptor repertoire profiling from RNA-seq data.

scientific article published in October 2017

Astroglia are a possible cellular substrate of angiotensin(1-7) effects in the rostral ventrolateral medulla

scientific article

B cells, plasma cells and antibody repertoires in the tumour microenvironment

scientific article published on 27 January 2020

Bright far-red fluorescent protein for whole-body imaging

scientific article published on 26 August 2007

Bright monomeric red fluorescent protein with an extended fluorescence lifetime

scientific article published on 17 June 2007

CXCR3 Identifies Human Naive CD8+ T Cells with Enhanced Effector Differentiation Potential

scientific article published on 18 November 2019

Cell culture medium affects GFP photostability: a solution

scientific article published in December 2009

Chromophore environment provides clue to "kindling fluorescent protein" riddle

scientific article published on 19 December 2002

Chromophore-assisted light inactivation (CALI) using the phototoxic fluorescent protein KillerRed.

scientific article published in January 2006

Chromoproteins of the green fluorescent protein family: properties and applications

scientific article published in September 2008

Circular Permutation of Red Fluorescent Proteins

scientific article

Common pathway for the red chromophore formation in fluorescent proteins and chromoproteins

scientific article published on June 2004

Comparative analysis of murine T-cell receptor repertoires.

scientific article

Comparative study reveals better far-red fluorescent protein for whole body imaging

scientific article

Contribution of functional KIR3DL1 to ankylosing spondylitis.

scientific article published on 6 September 2010

Conversion of red fluorescent protein into a bright blue probe

scientific article published on October 2008

Crystallographic study of red fluorescent protein eqFP578 and its far-red variant Katushka reveals opposite pH-induced isomerization of chromophore

scientific article

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

scientific article published on 13 June 2019

Discovery and properties of GFP-like proteins from nonbioluminescent anthozoa

scientific article

Distinctive properties of identical twins' TCR repertoires revealed by high-throughput sequencing.

scientific article

Dynamics of Individual T Cell Repertoires: From Cord Blood to Centenarians

scientific article published on 13 May 2016

Experimental models of arthritis in which pathogenesis is dependent on TNF expression.

scientific article published on December 2014

Exploring the pre-immune landscape of antigen-specific T cells

scientific article published on 25 August 2018

Extracellular calcium depletion transiently elevates oxygen consumption in neurosecretory PC12 cells through activation of mitochondrial Na+/Ca2+ exchange

scientific article published on 13 June 2010

Far-red fluorescent proteins evolved from a blue chromoprotein from Actinia equina

scientific article published on December 2005

Far-red fluorescent tags for protein imaging in living tissues

scientific article

Fast and precise protein tracking using repeated reversible photoactivation

scientific article published on 2 August 2006

Fast reversibly photoswitching red fluorescent proteins for live-cell RESOLFT nanoscopy

scientific article published on 09 July 2018

First autologous hematopoietic SCT for ankylosing spondylitis: a case report and clues to understanding the therapy

scientific article published on 12 March 2012

Fluorescent proteins and their applications in imaging living cells and tissues

scientific article

Fluorescent proteins as a toolkit for in vivo imaging

scientific article

Fluorescent proteins as light-inducible photochemical partners

scientific article published on 30 July 2010

Functionally specialized human CD4<sup>+</sup> T cell subsets express physicochemically distinct TCRs

scientific article published on 08 December 2020

Genetically encoded intracellular sensors based on fluorescent proteins.

scientific article published on July 2007

Genetically encoded photoimmunosensitizer

scientific article published in January 2011

Green fluorescent proteins are light-induced electron donors

scientific article published on July 2009

HRES-1/Rab4 promotes the formation of LC3(+) autophagosomes and the accumulation of mitochondria during autophagy

scientific article published on 3 January 2014

HRES-1/Rab4-mediated depletion of Drp1 impairs mitochondrial homeostasis and represents a target for treatment in SLE.

scientific article

Hetero-oligomeric tagging diminishes non-specific aggregation of target proteins fused with Anthozoa fluorescent proteins.

scientific article published in April 2003

High-quality full-length immunoglobulin profiling with unique molecular barcoding.

scientific article

High-throughput identification of antigen-specific TCRs by TCR gene capture

scientific article

Huge Overlap of Individual TCR Beta Repertoires.

scientific article published on 25 December 2013

Human Miltons associate with mitochondria and induce microtubule-dependent remodeling of mitochondrial networks

article

Identification of the amino acid residues responsible for the reversible photoconversion of the monomeric red fluorescent protein TagRFP protein

scientific article published in March 2010

In vivo imaging of ligand receptor binding with Gaussia luciferase complementation

scientific article published on 4 December 2011

Individual characterization of stably expanded T cell clones in ankylosing spondylitis patients.

scientific article

Innovation: Photoactivatable fluorescent proteins.

scientific article

Insertion of the voltage-sensitive domain into circularly permuted red fluorescent protein as a design for genetically encoded voltage sensor.

scientific article published on September 2017

Interconversion of Anthozoa GFP-like fluorescent and non-fluorescent proteins by mutagenesis

scientific article

Intratumoral immunoglobulin isotypes predict survival in lung adenocarcinoma subtypes

scientific article published on 29 October 2019

Kindling fluorescent protein from Anemonia sulcata: dark-state structure at 1.38 A resolution

scientific article published in April 2005

Kindling fluorescent proteins for precise in vivo photolabeling

scientific article published on 13 January 2003

Light-induced blockage of cell division with a chromatin-targeted phototoxic fluorescent protein

scientific article published in April 2011

Local fitness landscape of the green fluorescent protein

scientific article published on 11 May 2016

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

scientific article published on 05 January 2021

MAGERI: Computational pipeline for molecular-barcoded targeted resequencing.

scientific article

MHC-II alleles shape the CDR3 repertoires of conventional and regulatory naïve CD4+ T cells

scientific article published on 01 June 2020

Method for identification of condition-associated public antigen receptor sequences. ⬇️

scientific article published on 13 March 2018

MiTCR: software for T-cell receptor sequencing data analysis.

scientific article

MiXCR: software for comprehensive adaptive immunity profiling.

scientific article published in May 2015

Molecular Mechanism of a Green-Shifted, pH-Dependent Red Fluorescent Protein mKate Variant

scientific article

Mother and child T cell receptor repertoires: deep profiling study.

scientific article published on 25 December 2013

Near-infrared fluorescent proteins

scientific article published on 5 September 2010

New class of blue animal pigments based on Frizzled and Kringle protein domains

scientific article

Next generation sequencing for TCR repertoire profiling: platform-specific features and correction algorithms.

scientific article

Optogenetic experimentation on astrocytes ⬇️

scientific article published on November 1, 2010

Optogenetic in vivo cell manipulation in KillerRed-expressing zebrafish transgenics

scientific article

Pairing of T-cell receptor chains via emulsion PCR.

scientific article

Persisting fetal clonotypes influence the structure and overlap of adult human T cell receptor repertoires

scientific article

Photoswitchable cyan fluorescent protein as a FRET donor

scientific article published in March 2006

Photoswitchable cyan fluorescent protein for protein tracking

scientific article published on 24 October 2004

Practical and reliable FRET/FLIM pair of fluorescent proteins

scientific article

Preparing unbiased T-cell receptor and antibody cDNA libraries for the deep next generation sequencing profiling.

scientific article

Primary and secondary anti-viral response captured by the dynamics and phenotype of individual T cell clones

scientific article published on 21 February 2020

Quantitative profiling of immune repertoires for minor lymphocyte counts using unique molecular identifiers.

scientific article published on 08 May 2015

Quantitative tracking of T cell clones after haematopoietic stem cell transplantation.

scientific article

Reliability of immune receptor rearrangements as genetic markers for minimal residual disease monitoring.

scientific article published on 23 May 2016

Reply to "Evaluation of immune repertoire inference methods from RNA-seq data"

scientific article published on 01 November 2018

Sequencing rare T-cell populations

scientific article published on 18 November 2015

Single fluorescent protein-based Ca2+ sensors with increased dynamic range.

scientific article

Single high-dose treatment with glucosaminyl-muramyl dipeptide is ineffective in treating ankylosing spondylitis

scientific article published on 30 November 2010

Single-cell analysis of glandular T cell receptors in Sjögren's syndrome.

scientific article published on June 2016

Spectrally-resolved response properties of the three most advanced FRET based fluorescent protein voltage probes

scientific article

Structural basis for bathochromic shift of fluorescence in far-red fluorescent proteins eqFP650 and eqFP670

scientific article

Structural basis for the fast maturation of Arthropoda green fluorescent protein.

scientific article

Structure of the red fluorescent protein from a lancelet (Branchiostoma lanceolatum): a novel GYG chromophore covalently bound to a nearby tyrosine

scientific article

Substrate recognition of anthrax lethal factor examined by combinatorial and pre-steady-state kinetic approaches

scientific article

Substrate specificity of the anthrax lethal factor

scientific article published on 01 January 2008

T-cell tracking, safety, and effect of low-dose donor memory T-cell infusions after αβ T cell-depleted hematopoietic stem cell transplantation

scientific article published on 17 November 2020

TCR usage, gene expression and function of two distinct FOXP3(+)Treg subsets within CD4(+)CD25(hi) T cells identified by expression of CD39 and CD45RO.

scientific article published on 15 October 2015

Targeting cancer cells by using an antireceptor antibody-photosensitizer fusion protein

scientific article published on 20 May 2009

The Structure of Ca2+ Sensor Case16 Reveals the Mechanism of Reaction to Low Ca2+ Concentrations

scientific article

Three-dimensional structure of yellow fluorescent protein zYFP538 from Zoanthus sp. at the resolution 1.8 angstrom

scientific article

Towards error-free profiling of immune repertoires.

scientific article published on 04 May 2014

Tracking intracellular protein movements using photoswitchable fluorescent proteins PS-CFP2 and Dendra2.

scientific article

Two independent routes of post-translational chemistry in fluorescent protein FusionRed

scientific article published on 31 March 2020

Two subsets of stem-like CD8+ memory T cell progenitors with distinct fate commitments in humans

scientific article published on 12 October 2020

Use of green fluorescent protein (GFP) and its homologs for in vivo protein motility studies.

scientific article published on September 2003

Using photoactivatable fluorescent protein Dendra2 to track protein movement

scientific article

VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires.

scientific article published on 25 November 2015

VDJviz: a versatile browser for immunogenomics data.

scientific article

Visualizing compound transgenic zebrafish in development: a tale of green fluorescent protein and KillerRed

scientific article published on 24 February 2011

Wnt/β-Catenin Signaling Induces Integrin α4β1 in T Cells and Promotes a Progressive Neuroinflammatory Disease in Mice.

scientific article

Yellow fluorescent protein phiYFPv (Phialidium): structure and structure-based mutagenesis

scientific article

tcR: an R package for T cell receptor repertoire advanced data analysis.

scientific article

γδ T-cell Receptors Derived from Breast Cancer-Infiltrating T Lymphocytes Mediate Antitumor Reactivity

scientific article published on 04 February 2020

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