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Removing contaminants from databases of draft genomes.
Lu J, Salzberg SL. Lu J, et al. PLoS Comput Biol. 2018 Jun 25;14(6):e1006277. doi: 10.1371/journal.pcbi.1006277. eCollection 2018 Jun. PLoS Comput Biol. 2018. PMID: 29939994 Free PMC article.
Improved metagenomic analysis with Kraken 2.
Wood DE, Lu J, Langmead B. Wood DE, et al. Among authors: lu j. Genome Biol. 2019 Nov 28;20(1):257. doi: 10.1186/s13059-019-1891-0. Genome Biol. 2019. PMID: 31779668 Free PMC article.
Metagenome analysis using the Kraken software suite.
Lu J, Rincon N, Wood DE, Breitwieser FP, Pockrandt C, Langmead B, Salzberg SL, Steinegger M. Lu J, et al. Nat Protoc. 2022 Dec;17(12):2815-2839. doi: 10.1038/s41596-022-00738-y. Epub 2022 Sep 28. Nat Protoc. 2022. PMID: 36171387 Free PMC article. Review.
Major data analysis errors invalidate cancer microbiome findings.
Gihawi A, Ge Y, Lu J, Puiu D, Xu A, Cooper CS, Brewer DS, Pertea M, Salzberg SL. Gihawi A, et al. Among authors: lu j. mBio. 2023 Oct 31;14(5):e0160723. doi: 10.1128/mbio.01607-23. Epub 2023 Oct 9. mBio. 2023. PMID: 37811944 Free PMC article.
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