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Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases.
Armstrong G, Martino C, Morris J, Khaleghi B, Kang J, DeReus J, Zhu Q, Roush D, McDonald D, Gonazlez A, Shaffer JP, Carpenter C, Estaki M, Wandro S, Eilert S, Akel A, Eno J, Curewitz K, Swafford AD, Moshiri N, Rosing T, Knight R. Armstrong G, et al. Among authors: shaffer jp. mSystems. 2022 Apr 26;7(2):e0137821. doi: 10.1128/msystems.01378-21. Epub 2022 Mar 16. mSystems. 2022. PMID: 35293792 Free PMC article.
Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity.
Kaplan RC, Wang Z, Usyk M, Sotres-Alvarez D, Daviglus ML, Schneiderman N, Talavera GA, Gellman MD, Thyagarajan B, Moon JY, Vázquez-Baeza Y, McDonald D, Williams-Nguyen JS, Wu MC, North KE, Shaffer J, Sollecito CC, Qi Q, Isasi CR, Wang T, Knight R, Burk RD. Kaplan RC, et al. Genome Biol. 2019 Nov 1;20(1):219. doi: 10.1186/s13059-019-1831-z. Genome Biol. 2019. PMID: 31672155 Free PMC article.
Author Correction: Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity.
Kaplan RC, Wang Z, Usyk M, Sotres-Alvarez D, Daviglus ML, Schneiderman N, Talavera GA, Gellman MD, Thyagarajan B, Moon JY, Vázquez-Baeza Y, McDonald D, Williams-Nguyen JS, Wu MC, North KE, Shaffer J, Sollecito CC, Qi Q, Isasi CR, Wang T, Knight R, Burk RD. Kaplan RC, et al. Genome Biol. 2020 Feb 25;21(1):50. doi: 10.1186/s13059-020-01970-z. Genome Biol. 2020. PMID: 32098632 Free PMC article.
Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome.
Taylor BC, Lejzerowicz F, Poirel M, Shaffer JP, Jiang L, Aksenov A, Litwin N, Humphrey G, Martino C, Miller-Montgomery S, Dorrestein PC, Veiga P, Song SJ, McDonald D, Derrien M, Knight R. Taylor BC, et al. Among authors: shaffer jp. mSystems. 2020 Mar 17;5(2):e00901-19. doi: 10.1128/mSystems.00901-19. mSystems. 2020. PMID: 32184365 Free PMC article.
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. Among authors: shaffer jp. 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.
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. Among authors: shaffer jp. 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.
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 J, Allard SM, Allen EE, Knight R, Sweeney DA, Swafford AD. Minich JJ, et al. Among authors: shaffer jp. Microbiome. 2021 Jan 22;9(1):25. doi: 10.1186/s40168-020-00960-4. Microbiome. 2021. PMID: 33482920 Free PMC article.
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. Biotechniques. 2021 Mar;70(3):149-159. doi: 10.2144/btn-2020-0153. Epub 2021 Jan 29. Biotechniques. 2021. PMID: 33512248 Free PMC article.
SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital 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, Salas Garcia MC, Chiang LY, Salido RA, Shaffer JP, Bryant MK, Sanders K, Humphrey G, Ackermann G, Haiminen N, Beck KL, Kim HC, Carrieri AP, Parida L, Vázquez-Baeza Y, Torriani FJ, Knight R, Gilbert J, Sweeney DA, Allard SM. Marotz C, et al. Among authors: shaffer jp. Microbiome. 2021 Jun 8;9(1):132. doi: 10.1186/s40168-021-01083-0. Microbiome. 2021. PMID: 34103074 Free PMC article.
71 results