Mikhail Shugay

11 papers Journal 11
YearRankTypeTitle / Venue / Authors
2025 J jnl
Neighborhood enrichment for the identification of antigen-specific T-cell receptors.
Briefings Bioinform.
Kseniia R. Lupyr, Pavel V. Shelyakin, Konstantin A. Sobyanin, Ruslan A. Martynov, Vladimir S. Popov, Sevastyan O. Rabdano, Olga S. Nikitina, Yurii G. Yanushevich, Ilya A Kofiadi, Dmitry B. Staroverov, Mikhail Shugay, Dmitriy M. Chudakov, Olga V. Britanova
2024 J jnl
Structure-based prediction of T cell receptor recognition of unseen epitopes using TCRen.
Nat. Comput. Sci.
Vadim K. Karnaukhov, Dmitrii S. Shcherbinin, Anton O. Chugunov, Dmitriy M. Chudakov, Roman G. Efremov, Ivan V. Zvyagin, Mikhail Shugay
2020 J jnl
Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences.
Bioinform.
Erand Smakaj, Lmar Babrak, Mats Ohlin, Mikhail Shugay, Bryan S. Briney, Deniz Tosoni, Christopher Galli, Vendi Grobelsek, Igor D'Angelo, Branden J. Olson, Sai T. Reddy, Victor Greiff, Johannes Trück, Susanna Marquez, William D. Lees, Enkelejda Miho
2020 J jnl
Comprehensive analysis of structural and sequencing data reveals almost unconstrained chain pairing in TCRαβ complex.
PLoS Comput. Biol.
Dmitrii S. Shcherbinin, Vlad A. Belousov, Mikhail Shugay
2020 J jnl
VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium.
Nucleic Acids Res.
Dmitry V. Bagaev, Renske M. A. Vroomans, Jerome Samir, Ulrik Stervbo, Cristina Rius, Garry Dolton, Alexander Greenshields-Watson, Meriem Attaf, Evgeny S. Egorov, Ivan V. Zvyagin, Nina Babel, David K. Cole, Andrew J. Godkin, Andrew K. Sewell, Can Kesmir, Dmitry M. Chudakov, Fabio Luciani, Mikhail Shugay
2018 J jnl
VDJdb: a curated database of T-cell receptor sequences with known antigen specificity.
Nucleic Acids Res.
Mikhail Shugay, Dmitriy V. Bagaev, Ivan V. Zvyagin, Renske M. A. Vroomans, Jeremy Chase Crawford, Garry Dolton, Ekaterina Komech, Anastasiya L. Sycheva, Anna E. Koneva, 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 Kesmir, Paul G. Thomas, David A. Price, Andrew K. Sewell, Dmitry M. Chudakov
2017 J jnl
MAGERI: Computational pipeline for molecular-barcoded targeted resequencing.
PLoS Comput. Biol.
Mikhail Shugay, Andrew R. Zaretsky, Dmitriy A. Shagin, Irina A. Shagina, Ivan A. Volchenkov, Andrew A. Shelenkov, Mikhail Y. Lebedin, Dmitriy V. Bagaev, Sergey A. Lukyanov, Dmitry M. Chudakov
2015 J jnl
VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires.
PLoS Comput. Biol.
Mikhail Shugay, Dmitriy V. Bagaev, Maria A. Turchaninova, Dmitriy A. Bolotin, Olga V. Britanova, Ekaterina V. Putintseva, Mikhail V. Pogorelyy, Vadim I. Nazarov, Ivan V. Zvyagin, Vitalina I. Kirgizova, Kirill I. Kirgizov, Elena V. Skorobogatova, Dmitry M. Chudakov
2015 J jnl
tcR: an R package for T cell receptor repertoire advanced data analysis.
BMC Bioinform.
Vadim Nazarov, Mikhail Pogorelyy, Ekaterina Komech, Ivan Zvyagin, Dmitry Bolotin, Mikhail Shugay, Dmitry Chudakov, Yuri B. Lebedev, Ilgar Z. Mamedov
2013 J jnl
Oncofuse: a computational framework for the prediction of the oncogenic potential of gene fusions.
Bioinform.
Mikhail Shugay, Iñigo Ortiz de Mendíbil, José L. Vizmanos, Francisco J. Novo
2012 J jnl
Genomic Hallmarks of Genes Involved in Chromosomal Translocations in Hematological Cancer.
PLoS Comput. Biol.
Mikhail Shugay, Iñigo Ortiz de Mendíbil, José L. Vizmanos, Francisco J. Novo