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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. mSystems. 2022 Apr 26;7(2):e0016722. doi: 10.1128/msystems.00167-22. Epub 2022 Apr 4. mSystems. 2022. PMID: 35369727 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.
Evaluating the Information Content of Shallow Shotgun Metagenomics.
Hillmann B, Al-Ghalith GA, Shields-Cutler RR, Zhu Q, Gohl DM, Beckman KB, Knight R, Knights D. Hillmann B, et al. Among authors: zhu q. mSystems. 2018 Nov 13;3(6):e00069-18. doi: 10.1128/mSystems.00069-18. eCollection 2018 Nov-Dec. mSystems. 2018. PMID: 30443602 Free PMC article.
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