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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS 2nd, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson … See abstract for full author list ➔ Bolyen E, et al. Among authors: caporaso jg. Nat Biotechnol. 2019 Aug;37(8):852-857. doi: 10.1038/s41587-019-0209-9. Nat Biotechnol. 2019. PMID: 31341288 Free PMC article. No abstract available.
Pan-Enterovirus Characterization Reveals Cryptic Circulation of Clinically Relevant Subtypes in Arizona Wastewater.
Erickson DE, Simmons KM, Barrand ZA, Ridenour CL, Hawkinson PB, Lemke L, Sellner SP, Brock BN, Rivas AN, Sheridan K, Lemmer D, Yaglom HD, Porter WT, Belanger M, Torrey RM, Stills AJR, McCormack K, Black M, Holmes W, Rostain D, Mikus J, Sotelo K, Haq E, Neupane R, Weiss J, Johnson J, Collins C, Avalle S, White C, Howard BJ, Maltinsky SA, Whealy RN, Gordon NB, Sahl JW, Pearson T, Fofanov VY, Furstenau T, Driebe EM, Caporaso JG, Barber J, Terriquez J, Engelthaler DM, Hepp CM. Erickson DE, et al. Among authors: caporaso jg. medRxiv [Preprint]. 2024 Mar 20:2023.11.20.23297677. doi: 10.1101/2023.11.20.23297677. medRxiv. 2024. PMID: 38562876 Free PMC article. Preprint.
PyCogent: a toolkit for making sense from sequence.
Knight R, Maxwell P, Birmingham A, Carnes J, Caporaso JG, Easton BC, Eaton M, Hamady M, Lindsay H, Liu Z, Lozupone C, McDonald D, Robeson M, Sammut R, Smit S, Wakefield MJ, Widmann J, Wikman S, Wilson S, Ying H, Huttley GA. Knight R, et al. Among authors: caporaso jg. Genome Biol. 2007;8(8):R171. doi: 10.1186/gb-2007-8-8-r171. Genome Biol. 2007. PMID: 17708774 Free PMC article.
QIIME allows analysis of high-throughput community sequencing data.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. Caporaso JG, et al. Nat Methods. 2010 May;7(5):335-6. doi: 10.1038/nmeth.f.303. Epub 2010 Apr 11. Nat Methods. 2010. PMID: 20383131 Free PMC article. No abstract available.
Bacterial communities associated with the lichen symbiosis.
Bates ST, Cropsey GW, Caporaso JG, Knight R, Fierer N. Bates ST, et al. Among authors: caporaso jg. Appl Environ Microbiol. 2011 Feb;77(4):1309-14. doi: 10.1128/AEM.02257-10. Epub 2010 Dec 17. Appl Environ Microbiol. 2011. PMID: 21169444 Free PMC article.
126 results