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Page 1
Diversity in immunogenomics: the value and the challenge.
Peng K, Safonova Y, Shugay M, Popejoy AB, Rodriguez OL, Breden F, Brodin P, Burkhardt AM, Bustamante C, Cao-Lormeau VM, Corcoran MM, Duffy D, Fuentes-Guajardo M, Fujita R, Greiff V, Jönsson VD, Liu X, Quintana-Murci L, Rossetti M, Xie J, Yaari G, Zhang W, Abedalthagafi MS, Adekoya KO, Ahmed RA, Chang WC, Gray C, Nakamura Y, Lees WD, Khatri P, Alachkar H, Scheepers C, Watson CT, Karlsson Hedestam GB, Mangul S. Peng K, et al. Among authors: shugay m. Nat Methods. 2021 Jun;18(6):588-591. doi: 10.1038/s41592-021-01169-5. Nat Methods. 2021. PMID: 34002093 Free PMC article.
Towards error-free profiling of immune repertoires.
Shugay M, Britanova OV, Merzlyak EM, Turchaninova MA, Mamedov IZ, Tuganbaev TR, Bolotin DA, Staroverov DB, Putintseva EV, Plevova K, Linnemann C, Shagin D, Pospisilova S, Lukyanov S, Schumacher TN, Chudakov DM. Shugay M, et al. Nat Methods. 2014 Jun;11(6):653-5. doi: 10.1038/nmeth.2960. Epub 2014 May 4. Nat Methods. 2014. PMID: 24793455
MiXCR: software for comprehensive adaptive immunity profiling.
Bolotin DA, Poslavsky S, Mitrophanov I, Shugay M, Mamedov IZ, Putintseva EV, Chudakov DM. Bolotin DA, et al. Among authors: shugay m. Nat Methods. 2015 May;12(5):380-1. doi: 10.1038/nmeth.3364. Nat Methods. 2015. PMID: 25924071 No abstract available.
A mechanism for expansion of regulatory T-cell repertoire and its role in self-tolerance.
Feng Y, van der Veeken J, Shugay M, Putintseva EV, Osmanbeyoglu HU, Dikiy S, Hoyos BE, Moltedo B, Hemmers S, Treuting P, Leslie CS, Chudakov DM, Rudensky AY. Feng Y, et al. Among authors: shugay m. Nature. 2015 Dec 3;528(7580):132-136. doi: 10.1038/nature16141. Epub 2015 Nov 25. Nature. 2015. PMID: 26605529 Free PMC article.
Antigen receptor repertoire profiling from RNA-seq data.
Bolotin DA, Poslavsky S, Davydov AN, Frenkel FE, Fanchi L, Zolotareva OI, Hemmers S, Putintseva EV, Obraztsova AS, Shugay M, Ataullakhanov RI, Rudensky AY, Schumacher TN, Chudakov DM. Bolotin DA, et al. Among authors: shugay m. Nat Biotechnol. 2017 Oct 11;35(10):908-911. doi: 10.1038/nbt.3979. Nat Biotechnol. 2017. PMID: 29020005 Free PMC article. No abstract available.
Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences.
Smakaj E, Babrak L, Ohlin M, Shugay M, Briney B, Tosoni D, Galli C, Grobelsek V, D'Angelo I, Olson B, Reddy S, Greiff V, Trück J, Marquez S, Lees W, Miho E. Smakaj E, et al. Among authors: shugay m. Bioinformatics. 2020 Mar 1;36(6):1731-1739. doi: 10.1093/bioinformatics/btz845. Bioinformatics. 2020. PMID: 31873728 Free PMC article.
Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases.
Barennes P, Quiniou V, Shugay M, Egorov ES, Davydov AN, Chudakov DM, Uddin I, Ismail M, Oakes T, Chain B, Eugster A, Kashofer K, Rainer PP, Darko S, Ransier A, Douek DC, Klatzmann D, Mariotti-Ferrandiz E. Barennes P, et al. Among authors: shugay m. Nat Biotechnol. 2021 Feb;39(2):236-245. doi: 10.1038/s41587-020-0656-3. Epub 2020 Sep 7. Nat Biotechnol. 2021. PMID: 32895550 Free article.
Ancestral diversity is limited in published T cell receptor sequencing studies.
Huang YN, Peng K, Popejoy AB, Hu J, Nowicki TS, Gold SM, Quintana-Murci L, Fuentes-Guajardo M, Shugay M, Greiff V, Burkhardt AM, Alachkar H, Mangul S. Huang YN, et al. Among authors: shugay m. Immunity. 2021 Oct 12;54(10):2177-2179. doi: 10.1016/j.immuni.2021.09.015. Immunity. 2021. PMID: 34644550 Free article. No abstract available.
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: shugay m. Nat Methods. 2022 Sep;19(9):1017-1019. doi: 10.1038/s41592-022-01578-0. Nat Methods. 2022. PMID: 35970936 No abstract available.
66 results