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Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission.
Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, McHardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Schiabor Barrett KM, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Sha… See abstract for full author list ➔ Karthikeyan S, et al. Among authors: belda ferre p. Nature. 2022 Sep;609(7925):101-108. doi: 10.1038/s41586-022-05049-6. Epub 2022 Jul 7. Nature. 2022. PMID: 35798029 Free PMC article.
Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea.
Zhu Q, Mai U, Pfeiffer W, Janssen S, Asnicar F, Sanders JG, Belda-Ferre P, Al-Ghalith GA, Kopylova E, McDonald D, Kosciolek T, Yin JB, Huang S, Salam N, Jiao JY, Wu Z, Xu ZZ, Cantrell K, Yang Y, Sayyari E, Rabiee M, Morton JT, Podell S, Knights D, Li WJ, Huttenhower C, Segata N, Smarr L, Mirarab S, Knight R. Zhu Q, et al. Nat Commun. 2019 Dec 2;10(1):5477. doi: 10.1038/s41467-019-13443-4. Nat Commun. 2019. PMID: 31792218 Free PMC article.
The Microbiome and Its Potential for Pharmacology.
Chavira A, Belda-Ferre P, Kosciolek T, Ali F, Dorrestein PC, Knight R. Chavira A, et al. Handb Exp Pharmacol. 2019;260:301-326. doi: 10.1007/164_2019_317. Handb Exp Pharmacol. 2019. PMID: 31820171 Review.
Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment.
Minich JJ, Ali F, Marotz C, Belda-Ferre P, Chiang L, Shaffer JP, Carpenter CS, McDonald D, Gilbert JA, Allard SM, Allen EE, Knight R, Sweeney DA, Swafford AD. Minich JJ, et al. medRxiv [Preprint]. 2020 Aug 13:2020.05.12.20073577. doi: 10.1101/2020.05.12.20073577. medRxiv. 2020. PMID: 32511552 Free PMC article. Updated. Preprint.
Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information.
Chen Z, Pham L, Wu TC, Mo G, Xia Y, Chang PL, Porter D, Phan T, Che H, Tran H, Bansal V, Shaffer J, Belda-Ferre P, Humphrey G, Knight R, Pevzner P, Pham S, Wang Y, Lei M. Chen Z, et al. Genome Res. 2020 Jun;30(6):898-909. doi: 10.1101/gr.260380.119. Epub 2020 Jun 15. Genome Res. 2020. PMID: 32540955 Free PMC article.
SARS-CoV-2 Screening Among Symptom-Free Healthcare Workers.
Demmer RT, Ulrich AK, Wiggen TD, Strickland A, Naumchik BM, Kulasingam S, Stovitz SD, Marotz C, Belda-Ferre P, Humphrey G, De Hoff P, Laurent L, Kline S, Knight R. Demmer RT, et al. medRxiv [Preprint]. 2020 Nov 14:2020.07.31.20166066. doi: 10.1101/2020.07.31.20166066. medRxiv. 2020. PMID: 32793921 Free PMC article. Updated. Preprint.
Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment.
Minich J, Ali F, Marotz C, Belda-Ferre P, Chiang L, Shaffer JP, Carpenter CS, McDonald D, Gilbert J, Allard SM, Allen EE, Knight R, Sweeney DA, Swafford AD. Minich J, et al. Res Sq [Preprint]. 2020 Dec 15:rs.3.rs-56028. doi: 10.21203/rs.3.rs-56028/v1. Res Sq. 2020. PMID: 32839765 Free PMC article. Updated. Preprint.
A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities.
Shaffer JP, Marotz C, Belda-Ferre P, Martino C, Wandro S, Estaki M, Salido RA, Carpenter CS, Zaramela LS, Minich JJ, Bryant M, Sanders K, Fraraccio S, Ackermann G, Humphrey G, Swafford AD, Miller-Montgomery S, Knight R. Shaffer JP, et al. bioRxiv [Preprint]. 2020 Nov 14:2020.11.13.370387. doi: 10.1101/2020.11.13.370387. bioRxiv. 2020. PMID: 33200135 Free PMC article. Updated. Preprint.
Microbial context predicts SARS-CoV-2 prevalence in patients and the hospital built environment.
Marotz C, Belda-Ferre P, Ali F, Das P, Huang S, Cantrell K, Jiang L, Martino C, Diner RE, Rahman G, McDonald D, Armstrong G, Kodera S, Donato S, Ecklu-Mensah G, Gottel N, Garcia MCS, Chiang LY, Salido RA, Shaffer JP, Bryant M, Sanders K, Humphrey G, Ackermann G, Haiminen N, Beck KL, Kim HC, Carrieri AP, Parida L, Vázquez-Baeza Y, Torriani FJ, Knight R, Gilbert JA, Sweeney DA, Allard SM. Marotz C, et al. medRxiv [Preprint]. 2020 Nov 22:2020.11.19.20234229. doi: 10.1101/2020.11.19.20234229. medRxiv. 2020. PMID: 33236030 Free PMC article. Updated. Preprint.
58 results