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Synthetic DNA spike-ins (SDSIs) enable sample tracking and detection of inter-sample contamination in SARS-CoV-2 sequencing workflows.
Nat Microbiol. 2022 Jan;7(1):108-119. doi: 10.1038/s41564-021-01019-2. Epub 2021 Dec 14.
Nat Microbiol. 2022.
PMID: 34907347
Free PMC article.
SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs.
Weingarten-Gabbay S, Klaeger S, Sarkizova S, Pearlman LR, Chen DY, Bauer MR, Taylor HB, Conway HL, Tomkins-Tinch CH, Finkel Y, Nachshon A, Gentili M, Rivera KD, Keskin DB, Rice CM, Clauser KR, Hacohen N, Carr SA, Abelin JG, Saeed M, Sabeti PC.
Weingarten-Gabbay S, et al. Among authors: pearlman lr.
bioRxiv [Preprint]. 2020 Oct 26:2020.10.02.324145. doi: 10.1101/2020.10.02.324145.
bioRxiv. 2020.
PMID: 33024965
Free PMC article.
Preprint.
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Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs.
Weingarten-Gabbay S, Klaeger S, Sarkizova S, Pearlman LR, Chen DY, Gallagher KME, Bauer MR, Taylor HB, Dunn WA, Tarr C, Sidney J, Rachimi S, Conway HL, Katsis K, Wang Y, Leistritz-Edwards D, Durkin MR, Tomkins-Tinch CH, Finkel Y, Nachshon A, Gentili M, Rivera KD, Carulli IP, Chea VA, Chandrashekar A, Bozkus CC, Carrington M; MGH COVID-19 Collection & Processing Team; Bhardwaj N, Barouch DH, Sette A, Maus MV, Rice CM, Clauser KR, Keskin DB, Pregibon DC, Hacohen N, Carr SA, Abelin JG, Saeed M, Sabeti PC.
Weingarten-Gabbay S, et al. Among authors: pearlman lr.
Cell. 2021 Jul 22;184(15):3962-3980.e17. doi: 10.1016/j.cell.2021.05.046. Epub 2021 Jun 3.
Cell. 2021.
PMID: 34171305
Free PMC article.
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Multimodal surveillance of SARS-CoV-2 at a university enables development of a robust outbreak response framework.
Petros BA, Paull JS, Tomkins-Tinch CH, Loftness BC, DeRuff KC, Nair P, Gionet GL, Benz A, Brock-Fisher T, Hughes M, Yurkovetskiy L, Mulaudzi S, Leenerman E, Nyalile T, Moreno GK, Specht I, Sani K, Adams G, Babet SV, Baron E, Blank JT, Boehm C, Botti-Lodovico Y, Brown J, Buisker AR, Burcham T, Chylek L, Cronan P, Dauphin A, Desreumaux V, Doss M, Flynn B, Gladden-Young A, Glennon O, Harmon HD, Hook TV, Kary A, King C, Loreth C, Marrs L, McQuade KJ, Milton TT, Mulford JM, Oba K, Pearlman L, Schifferli M, Schmidt MJ, Tandus GM, Tyler A, Vodzak ME, Krohn Bevill K, Colubri A, MacInnis BL, Ozsoy AZ, Parrie E, Sholtes K, Siddle KJ, Fry B, Luban J, Park DJ, Marshall J, Bronson A, Schaffner SF, Sabeti PC.
Petros BA, et al.
Med. 2022 Dec 9;3(12):883-900.e13. doi: 10.1016/j.medj.2022.09.003. Epub 2022 Sep 19.
Med. 2022.
PMID: 36198312
Free PMC article.
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HLA-I immunopeptidome profiling of human cells infected with high-containment enveloped viruses.
Weingarten-Gabbay S, Pearlman LR, Chen DY, Klaeger S, Taylor HB, Welch NL, Keskin DB, Carr SA, Abelin JG, Saeed M, Sabeti PC.
Weingarten-Gabbay S, et al. Among authors: pearlman lr.
STAR Protoc. 2022 Dec 16;3(4):101910. doi: 10.1016/j.xpro.2022.101910. Epub 2022 Dec 8.
STAR Protoc. 2022.
PMID: 36595954
Free PMC article.
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The HLA-II immunopeptidome of SARS-CoV-2.
Weingarten-Gabbay S, Chen DY, Sarkizova S, Taylor HB, Gentili M, Hernandez GM, Pearlman LR, Bauer MR, Rice CM, Clauser KR, Hacohen N, Carr SA, Abelin JG, Saeed M, Sabeti PC.
Weingarten-Gabbay S, et al. Among authors: pearlman lr.
Cell Rep. 2024 Jan 23;43(1):113596. doi: 10.1016/j.celrep.2023.113596. Epub 2023 Dec 20.
Cell Rep. 2024.
PMID: 38117652
Free PMC article.
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The HLA-II immunopeptidome of SARS-CoV-2.
Weingarten-Gabbay S, Chen DY, Sarkizova S, Taylor HB, Gentili M, Pearlman LR, Bauer MR, Rice CM, Clauser KR, Hacohen N, Carr SA, Abelin JG, Saeed M, Sabeti PC.
Weingarten-Gabbay S, et al. Among authors: pearlman lr.
bioRxiv [Preprint]. 2023 Jun 1:2023.05.26.542482. doi: 10.1101/2023.05.26.542482.
bioRxiv. 2023.
PMID: 37398281
Free PMC article.
Updated.
Preprint.
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Stimulation of Replication Template-Switching by DNA-Protein Crosslinks.
Laranjo LT, Klaric JA, Pearlman LR, Lovett ST.
Laranjo LT, et al. Among authors: pearlman lr.
Genes (Basel). 2018 Dec 27;10(1):14. doi: 10.3390/genes10010014.
Genes (Basel). 2018.
PMID: 30591691
Free PMC article.
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