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Synthetic DNA spike-ins (SDSIs) enable sample tracking and detection of inter-sample contamination in SARS-CoV-2 sequencing workflows.
Lagerborg KA, Normandin E, Bauer MR, Adams G, Figueroa K, Loreth C, Gladden-Young A, Shaw BM, Pearlman LR, Berenzy D, Dewey HB, Kales S, Dobbins ST, Shenoy ES, Hooper D, Pierce VM, Zachary KC, Park DJ, MacInnis BL, Tewhey R, Lemieux JE, Sabeti PC, Reilly SK, Siddle KJ. Lagerborg KA, et al. Among authors: siddle kj. 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.
Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018.
Siddle KJ, Eromon P, Barnes KG, Mehta S, Oguzie JU, Odia I, Schaffner SF, Winnicki SM, Shah RR, Qu J, Wohl S, Brehio P, Iruolagbe C, Aiyepada J, Uyigue E, Akhilomen P, Okonofua G, Ye S, Kayode T, Ajogbasile F, Uwanibe J, Gaye A, Momoh M, Chak B, Kotliar D, Carter A, Gladden-Young A, Freije CA, Omoregie O, Osiemi B, Muoebonam EB, Airende M, Enigbe R, Ebo B, Nosamiefan I, Oluniyi P, Nekoui M, Ogbaini-Emovon E, Garry RF, Andersen KG, Park DJ, Yozwiak NL, Akpede G, Ihekweazu C, Tomori O, Okogbenin S, Folarin OA, Okokhere PO, MacInnis BL, Sabeti PC, Happi CT. Siddle KJ, et al. N Engl J Med. 2018 Nov 1;379(18):1745-1753. doi: 10.1056/NEJMoa1804498. Epub 2018 Oct 17. N Engl J Med. 2018. PMID: 30332564 Free PMC article.
Capturing sequence diversity in metagenomes with comprehensive and scalable probe design.
Metsky HC, Siddle KJ, Gladden-Young A, Qu J, Yang DK, Brehio P, Goldfarb A, Piantadosi A, Wohl S, Carter A, Lin AE, Barnes KG, Tully DC, Corleis B, Hennigan S, Barbosa-Lima G, Vieira YR, Paul LM, Tan AL, Garcia KF, Parham LA, Odia I, Eromon P, Folarin OA, Goba A; Viral Hemorrhagic Fever Consortium; Simon-Lorière E, Hensley L, Balmaseda A, Harris E, Kwon DS, Allen TM, Runstadler JA, Smole S, Bozza FA, Souza TML, Isern S, Michael SF, Lorenzana I, Gehrke L, Bosch I, Ebel G, Grant DS, Happi CT, Park DJ, Gnirke A, Sabeti PC, Matranga CB. Metsky HC, et al. Among authors: siddle kj. Nat Biotechnol. 2019 Feb;37(2):160-168. doi: 10.1038/s41587-018-0006-x. Epub 2019 Feb 4. Nat Biotechnol. 2019. PMID: 30718881 Free PMC article.
Combining genomics and epidemiology to track mumps virus transmission in the United States.
Wohl S, Metsky HC, Schaffner SF, Piantadosi A, Burns M, Lewnard JA, Chak B, Krasilnikova LA, Siddle KJ, Matranga CB, Bankamp B, Hennigan S, Sabina B, Byrne EH, McNall RJ, Shah RR, Qu J, Park DJ, Gharib S, Fitzgerald S, Barreira P, Fleming S, Lett S, Rota PA, Madoff LC, Yozwiak NL, MacInnis BL, Smole S, Grad YH, Sabeti PC. Wohl S, et al. Among authors: siddle kj. PLoS Biol. 2020 Feb 11;18(2):e3000611. doi: 10.1371/journal.pbio.3000611. eCollection 2020 Feb. PLoS Biol. 2020. PMID: 32045407 Free PMC article.
Real-time Metagenomic Analysis of Undiagnosed Fever Cases Unveils a Yellow Fever Outbreak in Edo State, Nigeria.
Ajogbasile FV, Oguzie JU, Oluniyi PE, Eromon PE, Uwanibe JN, Mehta SB, Siddle KJ, Odia I, Winnicki SM, Akpede N, Akpede G, Okogbenin S, Ogbaini-Emovon E, MacInnis BL, Folarin OA, Modjarrad K, Schaffner SF, Tomori O, Ihekweazu C, Sabeti PC, Happi CT. Ajogbasile FV, et al. Among authors: siddle kj. Sci Rep. 2020 Feb 21;10(1):3180. doi: 10.1038/s41598-020-59880-w. Sci Rep. 2020. PMID: 32081931 Free PMC article.
Amplicon deep sequencing of kelch13 in Plasmodium falciparum isolates from Senegal.
Gaye A, Sy M, Ndiaye T, Siddle KJ, Park DJ, Deme AB, Mbaye A, Dieye B, Ndiaye YD, Neafsey DE, Early A, Farrell T, Yade MS, Diallo MA, Diongue K, Bei A, Ndiaye IM, Volkman SK, Badiane AS, Ndiaye D. Gaye A, et al. Among authors: siddle kj. Malar J. 2020 Mar 30;19(1):134. doi: 10.1186/s12936-020-03193-w. Malar J. 2020. PMID: 32228566 Free PMC article.
Lassa Virus Genetics.
Klitting R, Mehta SB, Oguzie JU, Oluniyi PE, Pauthner MG, Siddle KJ, Andersen KG, Happi CT, Sabeti PC. Klitting R, et al. Among authors: siddle kj. Curr Top Microbiol Immunol. 2023;440:23-65. doi: 10.1007/82_2020_212. Curr Top Microbiol Immunol. 2023. PMID: 32418034
70 results