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EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets.
Cantrell K, Fedarko MW, Rahman G, McDonald D, Yang Y, Zaw T, Gonzalez A, Janssen S, Estaki M, Haiminen N, Beck KL, Zhu Q, Sayyari E, Morton JT, Armstrong G, Tripathi A, Gauglitz JM, Marotz C, Matteson NL, Martino C, Sanders JG, Carrieri AP, Song SJ, Swafford AD, Dorrestein PC, Andersen KG, Parida L, Kim HC, Vázquez-Baeza Y, Knight R. Cantrell K, et al. Among authors: beck kl. mSystems. 2021 Mar 16;6(2):e01216-20. doi: 10.1128/mSystems.01216-20. mSystems. 2021. PMID: 33727399 Free PMC article.
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. Among authors: beck kl. 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.
Monitoring the microbiome for food safety and quality using deep shotgun sequencing.
Beck KL, Haiminen N, Chambliss D, Edlund S, Kunitomi M, Huang BC, Kong N, Ganesan B, Baker R, Markwell P, Kawas B, Davis M, Prill RJ, Krishnareddy H, Seabolt E, Marlowe CH, Pierre S, Quintanar A, Parida L, Dubois G, Kaufman J, Weimer BC. Beck KL, et al. NPJ Sci Food. 2021 Feb 8;5(1):3. doi: 10.1038/s41538-020-00083-y. NPJ Sci Food. 2021. PMID: 33558514 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: beck kl. Microbiome. 2021 Jun 8;9(1):132. doi: 10.1186/s40168-021-01083-0. Microbiome. 2021. PMID: 34103074 Free PMC article.
Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes.
Armstrong G, Cantrell K, Huang S, McDonald D, Haiminen N, Carrieri AP, Zhu Q, Gonzalez A, McGrath I, Beck KL, Hakim D, Havulinna AS, Méric G, Niiranen T, Lahti L, Salomaa V, Jain M, Inouye M, Swafford AD, Kim HC, Parida L, Vázquez-Baeza Y, Knight R. Armstrong G, et al. Among authors: beck kl. Genome Res. 2021 Nov;31(11):2131-2137. doi: 10.1101/gr.275777.121. Epub 2021 Sep 3. Genome Res. 2021. PMID: 34479875 Free PMC article.
Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity.
Shaffer JP, Nothias LF, Thompson LR, Sanders JG, Salido RA, Couvillion SP, Brejnrod AD, Lejzerowicz F, Haiminen N, Huang S, Lutz HL, Zhu Q, Martino C, Morton JT, Karthikeyan S, Nothias-Esposito M, Dührkop K, Böcker S, Kim HW, Aksenov AA, Bittremieux W, Minich JJ, Marotz C, Bryant MM, Sanders K, Schwartz T, Humphrey G, Vásquez-Baeza Y, Tripathi A, Parida L, Carrieri AP, Beck KL, Das P, González A, McDonald D, Ladau J, Karst SM, Albertsen M, Ackermann G, DeReus J, Thomas T, Petras D, Shade A, Stegen J, Song SJ, Metz TO, Swafford AD, Dorrestein PC, Jansson JK, Gilbert JA, Knight R; Earth Microbiome Project 500 (EMP500) Consortium. Shaffer JP, et al. Among authors: beck kl. Nat Microbiol. 2022 Dec;7(12):2128-2150. doi: 10.1038/s41564-022-01266-x. Epub 2022 Nov 28. Nat Microbiol. 2022. PMID: 36443458 Free PMC article.
Food authentication from shotgun sequencing reads with an application on high protein powders.
Haiminen N, Edlund S, Chambliss D, Kunitomi M, Weimer BC, Ganesan B, Baker R, Markwell P, Davis M, Huang BC, Kong N, Prill RJ, Marlowe CH, Quintanar A, Pierre S, Dubois G, Kaufman JH, Parida L, Beck KL. Haiminen N, et al. Among authors: beck kl. NPJ Sci Food. 2019 Nov 19;3:24. doi: 10.1038/s41538-019-0056-6. eCollection 2019. NPJ Sci Food. 2019. PMID: 31754632 Free PMC article.
Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities.
Vangay P, Burgin J, Johnston A, Beck KL, Berrios DC, Blumberg K, Canon S, Chain P, Chandonia JM, Christianson D, Costes SV, Damerow J, Duncan WD, Dundore-Arias JP, Fagnan K, Galazka JM, Gibbons SM, Hays D, Hervey J, Hu B, Hurwitz BL, Jaiswal P, Joachimiak MP, Kinkel L, Ladau J, Martin SL, McCue LA, Miller K, Mouncey N, Mungall C, Pafilis E, Reddy TBK, Richardson L, Roux S, Schriml LM, Shaffer JP, Sundaramurthi JC, Thompson LR, Timme RE, Zheng J, Wood-Charlson EM, Eloe-Fadrosh EA. Vangay P, et al. Among authors: beck kl. mSystems. 2021 Feb 23;6(1):e01194-20. doi: 10.1128/mSystems.01194-20. mSystems. 2021. PMID: 33622857 Free PMC article.
Correction for Vangay et al., "Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities".
Vangay P, Burgin J, Johnston A, Beck KL, Berrios DC, Blumberg K, Canon S, Chain P, Chandonia JM, Christianson D, Costes SV, Damerow J, Duncan WD, Dundore-Arias JP, Fagnan K, Galazka JM, Gibbons SM, Hays D, Hervey J, Hu B, Hurwitz BL, Jaiswal P, Joachimiak MP, Kinkel L, Ladau J, Martin SL, McCue LA, Miller K, Mouncey N, Mungall C, Pafilis E, Reddy TBK, Richardson L, Roux S, Schriml LM, Shaffer JP, Sundaramurthi JC, Thompson LR, Timme RE, Zheng J, Wood-Charlson EM, Eloe-Fadrosh EA. Vangay P, et al. Among authors: beck kl. mSystems. 2021 May 4;6(3):e00273-21. doi: 10.1128/mSystems.00273-21. mSystems. 2021. PMID: 33947809 Free PMC article. No abstract available.
104 results