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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. mSystems. 2022 Apr 26;7(2):e0137821. doi: 10.1128/msystems.01378-21. Epub 2022 Mar 16. mSystems. 2022. PMID: 35293792 Free PMC article.
Context-aware dimensionality reduction deconvolutes gut microbial community dynamics.
Martino C, Shenhav L, Marotz CA, Armstrong G, McDonald D, Vázquez-Baeza Y, Morton JT, Jiang L, Dominguez-Bello MG, Swafford AD, Halperin E, Knight R. Martino C, et al. Among authors: armstrong g. Nat Biotechnol. 2021 Feb;39(2):165-168. doi: 10.1038/s41587-020-0660-7. Epub 2020 Aug 31. Nat Biotechnol. 2021. PMID: 32868914 Free PMC article.
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: armstrong g. mSystems. 2021 Mar 16;6(2):e01216-20. doi: 10.1128/mSystems.01216-20. mSystems. 2021. PMID: 33727399 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: armstrong g. 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. 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.
Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy.
Zhu Q, Huang S, Gonzalez A, McGrath I, McDonald D, Haiminen N, Armstrong G, Vázquez-Baeza Y, Yu J, Kuczynski J, Sepich-Poore GD, Swafford AD, Das P, Shaffer JP, Lejzerowicz F, Belda-Ferre P, Havulinna AS, Méric G, Niiranen T, Lahti L, Salomaa V, Kim HC, Jain M, Inouye M, Gilbert JA, Knight R. Zhu Q, et al. Among authors: armstrong g. mSystems. 2022 Apr 26;7(2):e0016722. doi: 10.1128/msystems.00167-22. Epub 2022 Apr 4. mSystems. 2022. PMID: 35369727 Free PMC article.
1,434 results