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Page 1
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: haiminen n. mSystems. 2022 Apr 26;7(2):e0016722. doi: 10.1128/msystems.00167-22. Epub 2022 Apr 4. mSystems. 2022. PMID: 35369727 Free PMC article.
Human Skin, Oral, and Gut Microbiomes Predict Chronological Age.
Huang S, Haiminen N, Carrieri AP, Hu R, Jiang L, Parida L, Russell B, Allaband C, Zarrinpar A, Vázquez-Baeza Y, Belda-Ferre P, Zhou H, Kim HC, Swafford AD, Knight R, Xu ZZ. Huang S, et al. Among authors: haiminen n. mSystems. 2020 Feb 11;5(1):e00630-19. doi: 10.1128/mSystems.00630-19. mSystems. 2020. PMID: 32047061 Free PMC article.
Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity.
Martino C, Kellman BP, Sandoval DR, Clausen TM, Marotz CA, Song SJ, Wandro S, Zaramela LS, Salido Benítez RA, Zhu Q, Armingol E, Vázquez-Baeza Y, McDonald D, Sorrentino JT, Taylor B, Belda-Ferre P, Liang C, Zhang Y, Schifanella L, Klatt NR, Havulinna AS, Jousilahti P, Huang S, Haiminen N, Parida L, Kim HC, Swafford AD, Zengler K, Cheng S, Inouye M, Niiranen T, Jain M, Salomaa V, Esko JD, Lewis NE, Knight R. Martino C, et al. Among authors: haiminen n. bioRxiv [Preprint]. 2020 Aug 18:2020.08.17.238444. doi: 10.1101/2020.08.17.238444. bioRxiv. 2020. PMID: 32839779 Free PMC article. 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. Among authors: haiminen n. medRxiv [Preprint]. 2020 Nov 22:2020.11.19.20234229. doi: 10.1101/2020.11.19.20234229. medRxiv. 2020. Update in: Microbiome. 2021 Jun 8;9(1):132. doi: 10.1186/s40168-021-01083-0 PMID: 33236030 Free PMC article. Updated. Preprint.
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: haiminen n. mSystems. 2021 Mar 16;6(2):e01216-20. doi: 10.1128/mSystems.01216-20. mSystems. 2021. PMID: 33727399 Free PMC article.
Challenges in benchmarking metagenomic profilers.
Sun Z, Huang S, Zhang M, Zhu Q, Haiminen N, Carrieri AP, Vázquez-Baeza Y, Parida L, Kim HC, Knight R, Liu YY. Sun Z, et al. Among authors: haiminen n. Nat Methods. 2021 Jun;18(6):618-626. doi: 10.1038/s41592-021-01141-3. Epub 2021 May 13. Nat Methods. 2021. PMID: 33986544 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: haiminen n. 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: haiminen n. 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: haiminen n. 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.
43 results