tcR: an R package for T cell receptor repertoire advanced data analysis. - Vadim Nazarov; Mikhail Pogorelyy; Ekaterina Komech; Ivan Zvyagin; Dmitry Bolotin; Mikhail Shugay; Dmitry Chudakov; Yuri B. Lebedev; Ilgar Z. Mamedov (BMC Bioinform., 2015)

VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires. - 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; et al. (PLoS Comput. Biol., 2015)

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 Komech; Anastasiya L. Sycheva; Anna E. Koneva; Evgeniy S. Egorov; Alexey V. Eliseev; Ewald van Dyk; et al. (Nucleic Acids Res., 2018)

VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium. - 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; et al. (Nucleic Acids Res., 2020)

Structure-based prediction of T cell receptor recognition of unseen epitopes using TCRen. - Vadim K. Karnaukhov; Dmitrii S. Shcherbinin; Anton O. Chugunov; Dmitriy M. Chudakov; Roman G. Efremov; Ivan V. Zvyagin; Mikhail Shugay (Nat. Comput. Sci., 2024)