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VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium.
Bagaev DV, Vroomans RMA, Samir J, Stervbo U, Rius C, Dolton G, Greenshields-Watson A, Attaf M, Egorov ES, Zvyagin IV, Babel N, Cole DK, Godkin AJ, Sewell AK, Kesmir C, Chudakov DM, Luciani F, Shugay M. Bagaev DV, et al. Among authors: luciani f. Nucleic Acids Res. 2020 Jan 8;48(D1):D1057-D1062. doi: 10.1093/nar/gkz874. Nucleic Acids Res. 2020. PMID: 31588507 Free PMC article.
VDJdb: a curated database of T-cell receptor sequences with known antigen specificity.
Shugay M, Bagaev DV, Zvyagin IV, Vroomans RM, Crawford JC, Dolton G, Komech EA, Sycheva AL, Koneva AE, Egorov ES, Eliseev AV, Van Dyk E, Dash P, Attaf M, Rius C, Ladell K, McLaren JE, Matthews KK, Clemens EB, Douek DC, Luciani F, van Baarle D, Kedzierska K, Kesmir C, Thomas PG, Price DA, Sewell AK, Chudakov DM. Shugay M, et al. Among authors: luciani f. Nucleic Acids Res. 2018 Jan 4;46(D1):D419-D427. doi: 10.1093/nar/gkx760. Nucleic Acids Res. 2018. PMID: 28977646 Free PMC article.
B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle.
Rizzetto S, Koppstein DNP, Samir J, Singh M, Reed JH, Cai CH, Lloyd AR, Eltahla AA, Goodnow CC, Luciani F. Rizzetto S, et al. Among authors: luciani f. Bioinformatics. 2018 Aug 15;34(16):2846-2847. doi: 10.1093/bioinformatics/bty203. Bioinformatics. 2018. PMID: 29659703
Single-Cell Transcriptome Analysis of T Cells.
Van Der Byl W, Rizzetto S, Samir J, Cai C, Eltahla AA, Luciani F. Van Der Byl W, et al. Among authors: luciani f. Methods Mol Biol. 2019;2048:155-205. doi: 10.1007/978-1-4939-9728-2_16. Methods Mol Biol. 2019. PMID: 31396939
VDJdb in the pandemic era: a compendium of T cell receptors specific for SARS-CoV-2.
Goncharov M, Bagaev D, Shcherbinin D, Zvyagin I, Bolotin D, Thomas PG, Minervina AA, Pogorelyy MV, Ladell K, McLaren JE, Price DA, Nguyen THO, Rowntree LC, Clemens EB, Kedzierska K, Dolton G, Rius CR, Sewell A, Samir J, Luciani F, Zornikova KV, Khmelevskaya AA, Sheetikov SA, Efimov GA, Chudakov D, Shugay M. Goncharov M, et al. Among authors: luciani f. Nat Methods. 2022 Sep;19(9):1017-1019. doi: 10.1038/s41592-022-01578-0. Nat Methods. 2022. PMID: 35970936 No abstract available.
213 results