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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: zhu q. mSystems. 2021 Mar 16;6(2):e01216-20. doi: 10.1128/mSystems.01216-20. mSystems. 2021. PMID: 33727399 Free PMC article.
A communal catalogue reveals Earth's multiscale microbial diversity.
Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vázquez-Baeza Y, González A, Morton JT, Mirarab S, Zech Xu Z, Jiang L, Haroon MF, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK, Gilbert JA, Knight R; Earth Microbiome Project Consortium. Thompson LR, et al. Among authors: zhu q. Nature. 2017 Nov 23;551(7681):457-463. doi: 10.1038/nature24621. Epub 2017 Nov 1. Nature. 2017. PMID: 29088705 Free PMC article.
Creating a 3D microbial and chemical snapshot of a human habitat.
Kapono CA, Morton JT, Bouslimani A, Melnik AV, Orlinsky K, Knaan TL, Garg N, Vázquez-Baeza Y, Protsyuk I, Janssen S, Zhu Q, Alexandrov T, Smarr L, Knight R, Dorrestein PC. Kapono CA, et al. Among authors: zhu q. Sci Rep. 2018 Feb 27;8(1):3669. doi: 10.1038/s41598-018-21541-4. Sci Rep. 2018. PMID: 29487294 Free PMC article.
KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples.
Minich JJ, Zhu Q, Janssen S, Hendrickson R, Amir A, Vetter R, Hyde J, Doty MM, Stillwell K, Benardini J, Kim JH, Allen EE, Venkateswaran K, Knight R. Minich JJ, et al. Among authors: zhu q. mSystems. 2018 Mar 13;3(3):e00218-17. doi: 10.1128/mSystems.00218-17. eCollection 2018 May-Jun. mSystems. 2018. PMID: 29577086 Free PMC article.
Best practices for analysing microbiomes.
Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, Gonzalez A, Kosciolek T, McCall LI, McDonald D, Melnik AV, Morton JT, Navas J, Quinn RA, Sanders JG, Swafford AD, Thompson LR, Tripathi A, Xu ZZ, Zaneveld JR, Zhu Q, Caporaso JG, Dorrestein PC. Knight R, et al. Among authors: zhu q. Nat Rev Microbiol. 2018 Jul;16(7):410-422. doi: 10.1038/s41579-018-0029-9. Nat Rev Microbiol. 2018. PMID: 29795328 Review.
Methods for phylogenetic analysis of microbiome data.
Washburne AD, Morton JT, Sanders J, McDonald D, Zhu Q, Oliverio AM, Knight R. Washburne AD, et al. Among authors: zhu q. Nat Microbiol. 2018 Jun;3(6):652-661. doi: 10.1038/s41564-018-0156-0. Epub 2018 May 24. Nat Microbiol. 2018. PMID: 29795540 Review.
American Gut: an Open Platform for Citizen Science Microbiome Research.
McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q; American Gut Consortium; Knight R. McDonald D, et al. Among authors: zhu q. mSystems. 2018 May 15;3(3):e00031-18. doi: 10.1128/mSystems.00031-18. eCollection 2018 May-Jun. mSystems. 2018. PMID: 29795809 Free PMC article.
Are microbiome studies ready for hypothesis-driven research?
Tripathi A, Marotz C, Gonzalez A, Vázquez-Baeza Y, Song SJ, Bouslimani A, McDonald D, Zhu Q, Sanders JG, Smarr L, Dorrestein PC, Knight R. Tripathi A, et al. Among authors: zhu q. Curr Opin Microbiol. 2018 Aug;44:61-69. doi: 10.1016/j.mib.2018.07.002. Epub 2018 Jul 27. Curr Opin Microbiol. 2018. PMID: 30059804 Free PMC article. Review.
Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient.
Fang X, Monk JM, Nurk S, Akseshina M, Zhu Q, Gemmell C, Gianetto-Hill C, Leung N, Szubin R, Sanders J, Beck PL, Li W, Sandborn WJ, Gray-Owen SD, Knight R, Allen-Vercoe E, Palsson BO, Smarr L. Fang X, et al. Among authors: zhu q. Front Microbiol. 2018 Oct 30;9:2559. doi: 10.3389/fmicb.2018.02559. eCollection 2018. Front Microbiol. 2018. PMID: 30425690 Free PMC article.
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