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Real-time, portable genome sequencing for Ebola surveillance.
Quick J, Loman NJ, Duraffour S, Simpson JT, Severi E, Cowley L, Bore JA, Koundouno R, Dudas G, Mikhail A, Ouédraogo N, Afrough B, Bah A, Baum JH, Becker-Ziaja B, Boettcher JP, Cabeza-Cabrerizo M, Camino-Sanchez A, Carter LL, Doerrbecker J, Enkirch T, Dorival IGG, Hetzelt N, Hinzmann J, Holm T, Kafetzopoulou LE, Koropogui M, Kosgey A, Kuisma E, Logue CH, Mazzarelli A, Meisel S, Mertens M, Michel J, Ngabo D, Nitzsche K, Pallash E, Patrono LV, Portmann J, Repits JG, Rickett NY, Sachse A, Singethan K, Vitoriano I, Yemanaberhan RL, Zekeng EG, Trina R, Bello A, Sall AA, Faye O, Faye O, Magassouba N, Williams CV, Amburgey V, Winona L, Davis E, Gerlach J, Washington F, Monteil V, Jourdain M, Bererd M, Camara A, Somlare H, Camara A, Gerard M, Bado G, Baillet B, Delaune D, Nebie KY, Diarra A, Savane Y, Pallawo RB, Gutierrez GJ, Milhano N, Roger I, Williams CJ, Yattara F, Lewandowski K, Taylor J, Rachwal P, Turner D, Pollakis G, Hiscox JA, Matthews DA, O'Shea MK, Johnston AM, Wilson D, Hutley E, Smit E, Di Caro A, Woelfel R, Stoecker K, Fleischmann E, Gabriel M, Weller SA, Koivogui L, Diallo B, Keita S, Rambaut A, Formenty P, Gunther S, Carroll MW. Quick J, et al. Among authors: simpson jt. Nature. 2016 Feb 11;530(7589):228-232. doi: 10.1038/nature16996. Epub 2016 Feb 3. Nature. 2016. PMID: 26840485 Free PMC article.
Establishment and cryptic transmission of Zika virus in Brazil and the Americas.
Faria NR, Quick J, Claro IM, Thézé J, de Jesus JG, Giovanetti M, Kraemer MUG, Hill SC, Black A, da Costa AC, Franco LC, Silva SP, Wu CH, Raghwani J, Cauchemez S, du Plessis L, Verotti MP, de Oliveira WK, Carmo EH, Coelho GE, Santelli ACFS, Vinhal LC, Henriques CM, Simpson JT, Loose M, Andersen KG, Grubaugh ND, Somasekar S, Chiu CY, Muñoz-Medina JE, Gonzalez-Bonilla CR, Arias CF, Lewis-Ximenez LL, Baylis SA, Chieppe AO, Aguiar SF, Fernandes CA, Lemos PS, Nascimento BLS, Monteiro HAO, Siqueira IC, de Queiroz MG, de Souza TR, Bezerra JF, Lemos MR, Pereira GF, Loudal D, Moura LC, Dhalia R, França RF, Magalhães T, Marques ET Jr, Jaenisch T, Wallau GL, de Lima MC, Nascimento V, de Cerqueira EM, de Lima MM, Mascarenhas DL, Neto JPM, Levin AS, Tozetto-Mendoza TR, Fonseca SN, Mendes-Correa MC, Milagres FP, Segurado A, Holmes EC, Rambaut A, Bedford T, Nunes MRT, Sabino EC, Alcantara LCJ, Loman NJ, Pybus OG. Faria NR, et al. Among authors: simpson jt. Nature. 2017 Jun 15;546(7658):406-410. doi: 10.1038/nature22401. Epub 2017 May 24. Nature. 2017. PMID: 28538727 Free PMC article.
Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples.
Quick J, Grubaugh ND, Pullan ST, Claro IM, Smith AD, Gangavarapu K, Oliveira G, Robles-Sikisaka R, Rogers TF, Beutler NA, Burton DR, Lewis-Ximenez LL, de Jesus JG, Giovanetti M, Hill SC, Black A, Bedford T, Carroll MW, Nunes M, Alcantara LC Jr, Sabino EC, Baylis SA, Faria NR, Loose M, Simpson JT, Pybus OG, Andersen KG, Loman NJ. Quick J, et al. Among authors: simpson jt. Nat Protoc. 2017 Jun;12(6):1261-1276. doi: 10.1038/nprot.2017.066. Epub 2017 May 24. Nat Protoc. 2017. PMID: 28538739 Free PMC article.
Shotgun metagenomics, from sampling to analysis.
Quince C, Walker AW, Simpson JT, Loman NJ, Segata N. Quince C, et al. Among authors: simpson jt. Nat Biotechnol. 2017 Sep 12;35(9):833-844. doi: 10.1038/nbt.3935. Nat Biotechnol. 2017. PMID: 28898207 Review.
Nanopore sequencing and assembly of a human genome with ultra-long reads.
Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, Tyson JR, Beggs AD, Dilthey AT, Fiddes IT, Malla S, Marriott H, Nieto T, O'Grady J, Olsen HE, Pedersen BS, Rhie A, Richardson H, Quinlan AR, Snutch TP, Tee L, Paten B, Phillippy AM, Simpson JT, Loman NJ, Loose M. Jain M, et al. Among authors: simpson jt. Nat Biotechnol. 2018 Apr;36(4):338-345. doi: 10.1038/nbt.4060. Epub 2018 Jan 29. Nat Biotechnol. 2018. PMID: 29431738 Free PMC article.
Nanopore native RNA sequencing of a human poly(A) transcriptome.
Workman RE, Tang AD, Tang PS, Jain M, Tyson JR, Razaghi R, Zuzarte PC, Gilpatrick T, Payne A, Quick J, Sadowski N, Holmes N, de Jesus JG, Jones KL, Soulette CM, Snutch TP, Loman N, Paten B, Loose M, Simpson JT, Olsen HE, Brooks AN, Akeson M, Timp W. Workman RE, et al. Among authors: simpson jt. Nat Methods. 2019 Dec;16(12):1297-1305. doi: 10.1038/s41592-019-0617-2. Epub 2019 Nov 18. Nat Methods. 2019. PMID: 31740818 Free PMC article.
Author Correction: Nanopore native RNA sequencing of a human poly(A) transcriptome.
Workman RE, Tang AD, Tang PS, Jain M, Tyson JR, Razaghi R, Zuzarte PC, Gilpatrick T, Payne A, Quick J, Sadowski N, Holmes N, de Jesus JG, Jones KL, Soulette CM, Snutch TP, Loman N, Paten B, Loose M, Simpson JT, Olsen HE, Brooks AN, Akeson M, Timp W. Workman RE, et al. Among authors: simpson jt. Nat Methods. 2020 Jan;17(1):114. doi: 10.1038/s41592-019-0697-z. Nat Methods. 2020. PMID: 31819268 Free PMC article.
151 results