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Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy

mSystems
2022-04-26 | Journal article
Contributors: Qiyun Zhu; Shi Huang; Antonio Gonzalez; Imran McGrath; Daniel McDonald; Niina Haiminen; George Armstrong; Yoshiki Vázquez-Baeza; Julian Yu; Justin Kuczynski et al.
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Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases

mSystems
2022-04-26 | Journal article
Contributors: George Armstrong; Cameron Martino; Justin Morris; Behnam Khaleghi; Jaeyoung Kang; Jeff DeReus; Qiyun Zhu; Daniel Roush; Daniel McDonald; Antonio Gonazlez et al.
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Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes

Genome Research
2021-11-03 | Journal article
Contributors: George Armstrong; Kalen Cantrell; Shi Huang; Daniel McDonald; Niina Haiminen; Anna Paola Carrieri; Qiyun Zhu; Antonio Gonzalez; Imran McGrath; Kristen L. Beck et al.
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Context-aware dimensionality reduction deconvolutes gut microbial community dynamics

Nature Biotechnology
2021-02-31 | Journal article
Contributors: Cameron Martino; Liat Shenhav; Clarisse A. Marotz; George Armstrong; Daniel McDonald; Yoshiki Vázquez-Baeza; James T. Morton; Lingjing Jiang; Maria Gloria Dominguez-Bello; Austin D. Swafford et al.
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