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Ivan V. Zvyagin
Researcher at Russian National Research Medical University
Publications - 41
Citations - 2453
Ivan V. Zvyagin is an academic researcher from Russian National Research Medical University. The author has contributed to research in topics: T-cell receptor & Immune system. The author has an hindex of 17, co-authored 28 publications receiving 1795 citations. Previous affiliations of Ivan V. Zvyagin include Central European Institute of Technology & Russian Academy of Sciences.
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Journal ArticleDOI
VDJtools: Unifying post-analysis of T cell receptor repertoires
Mikhail Shugay,Dmitriy V. Bagaev,Maria A. Turchaninova,Dmitriy A. Bolotin,Olga V. Britanova,Olga V. Britanova,Ekaterina V. Putintseva,Ekaterina V. Putintseva,Mikhail V. Pogorelyy,Vadim I. Nazarov,Ivan V. Zvyagin,Ivan V. Zvyagin,Vitalina I. Kirgizova,Kirill Kirgizov,E V Skorobogatova,Dmitriy M. Chudakov,Dmitriy M. Chudakov +16 more
TL;DR: VDJtools is reported, a complementary software suite that solves a wide range of T cell receptor (TCR) repertoires post-analysis tasks, provides a detailed tabular output and publication-ready graphics, and is built on top of a flexible API.
Journal ArticleDOI
VDJdb: a curated database of T-cell receptor sequences with known antigen specificity
Mikhail Shugay,Dmitriy V. Bagaev,Ivan V. Zvyagin,Renske M. A. Vroomans,Jeremy Chase Crawford,Garry Dolton,Ekaterina A Komech,Anastasiya L Sycheva,Anna E. Koneva,Evgeniy S. Egorov,Evgeniy S. Egorov,Alexey V. Eliseev,Ewald Van Dyk,Pradyot Dash,Meriem Attaf,Cristina Rius,Kristin Ladell,James E. McLaren,Katherine K. Matthews,E. Bridie Clemens,Daniel C. Douek,Fabio Luciani,Debbie van Baarle,Katherine Kedzierska,Can Keşmir,Paul G. Thomas,David Price,David Price,Andrew K. Sewell,Dmitriy M. Chudakov +29 more
TL;DR: VDJdb is a database that stores and aggregates the results of published T-cell specificity assays and provides a universal platform that couples antigen specificities with TCR sequences, enabling a concatenated view of antigen-specific TCR sequence motifs.
Journal ArticleDOI
VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium
Dmitry V. Bagaev,Renske M. A. Vroomans,Jerome Samir,Jerome Samir,Ulrik Stervbo,Ulrik Stervbo,Cristina Rius,Garry Dolton,Alexander Greenshields-Watson,Meriem Attaf,Evgeny S. Egorov,Ivan V. Zvyagin,Nina Babel,Nina Babel,David K. Cole,Andrew James Godkin,Andrew K. Sewell,Can Keşmir,Dmitriy M. Chudakov,Fabio Luciani,Fabio Luciani,Mikhail Shugay +21 more
TL;DR: An update of the VDJdb database with a substantial increase in the number of T-cell receptor (TCR) sequences and their cognate antigens and a reduced set of high-quality TCR motifs that can be used for both training TCR specificity predictors and matching against TCRs of interest are reported.
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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,Mikhail Shugay,Dmitry M. Chudakov,Yury B. Lebedev,Ilgar Z. Mamedov +8 more
TL;DR: stcR is a new R package, representing a platform for the advanced analysis of T cell receptor repertoires after primary TR sequences extraction from raw sequencing reads, which includes diversity measures, shared T cell receptors sequences identification, gene usage statistics computation and other widely used methods.
Journal ArticleDOI
Next generation sequencing for tcr repertoire profiling: platform-specific features and correction algorithms
Dmitry A. Bolotin,Ilgar Z. Mamedov,Olga V. Britanova,Ivan V. Zvyagin,Dmitriy A. Shagin,Svetlana V. Ustyugova,Maria A. Turchaninova,Sergey Lukyanov,Yury B. Lebedev,Dmitriy M. Chudakov +9 more
TL;DR: It is demonstrated that advanced correction allows the removal of the majority of artificial TCR diversity with concomitant rescue of most of the sequencing information, and this correction enhances the accuracy of clonotype identification and quantification as well as overall TCR Diversity measurements.