Mikhail Shugay

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FOXP3+ regulatory T (Treg) cells are indispensable for immune homeostasis, but their study in humans is complicated by heterogeneity within Treg, the difficulty in purifying Tregs using surface marker expression (e.g. CD25) and the transient expression of FOXP3 by activated effector cells. Here, we report that expression of CD39 and CD45RO distinguishes(More)
VOLUME 35 NUMBER 10 OCTOBER 2017 NATURE BIOTECHNOLOGY 24. Schellenberger, J. et al. Nat. Protoc. 6, 1290–1307 (2011). 25. Guzmán, G.I. et al. Proc. Natl. Acad. Sci. USA 112, 929–934 (2015). 26. Chang, R.L., Xie, L., Bourne, P.E. & Palsson, B.O. BMC Syst. Biol. 7, 102 (2013). 27. Chung, H. et al. Curr. Opin. Biotechnol. 36, 73–84 (2015). 28. Notebaart, R.A.(More)
Unique molecular identifiers (UMIs) show outstanding performance in targeted high-throughput resequencing, being the most promising approach for the accurate identification of rare variants in complex DNA samples. This approach has application in multiple areas, including cancer diagnostics, thus demanding dedicated software and algorithms. Here we(More)
The diversity, architecture, and dynamics of the TCR repertoire largely determine our ability to effectively withstand infections and malignancies with minimal mistargeting of immune responses. In this study, we have employed deep TCRβ repertoire sequencing with normalization based on unique molecular identifiers to explore the long-term dynamics of T cell(More)
High-throughput sequencing analysis of hypermutating immunoglobulin (IG) repertoires remains a challenging task. Here we present a robust protocol for the full-length profiling of human and mouse IG repertoires. This protocol uses unique molecular identifiers (UMIs) introduced in the course of cDNA synthesis to control bottlenecks and to eliminate PCR and(More)
αβT-cell-depleted allogeneic hematopoietic cell transplantation holds promise for the safe and accessible therapy of both malignant and non-malignant blood disorders. Here we employed molecular barcoding normalized T-cell receptor (TCR) profiling to quantitatively track T-cell immune reconstitution after TCRαβ-/CD19-depleted transplantation in children. We(More)
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