Lu J - Search Results

1

Novel metagenomics analysis of stony coral tissue loss disease.

Heinz JM, Lu J, Huebner LK, Salzberg SL, Sommer M, Rosales SM. Heinz JM, et al. Among authors: lu j. G3 (Bethesda). 2024 Aug 7;14(8):jkae137. doi: 10.1093/g3journal/jkae137. G3 (Bethesda). 2024. PMID: 38900914 Free PMC article.

2

A review of methods and databases for metagenomic classification and assembly.

Breitwieser FP, Lu J, Salzberg SL. Breitwieser FP, et al. Among authors: lu j. Brief Bioinform. 2019 Jul 19;20(4):1125-1136. doi: 10.1093/bib/bbx120. Brief Bioinform. 2019. PMID: 29028872 Free PMC article. Review.

3

Identifying Corneal Infections in Formalin-Fixed Specimens Using Next Generation Sequencing.

Li Z, Breitwieser FP, Lu J, Jun AS, Asnaghi L, Salzberg SL, Eberhart CG. Li Z, et al. Among authors: lu j. Invest Ophthalmol Vis Sci. 2018 Jan 1;59(1):280-288. doi: 10.1167/iovs.17-21617. Invest Ophthalmol Vis Sci. 2018. PMID: 29340642 Free PMC article.

4

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.

5

Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2.

Lu J, Salzberg SL. Lu J, et al. Microbiome. 2020 Aug 28;8(1):124. doi: 10.1186/s40168-020-00900-2. Microbiome. 2020. PMID: 32859275 Free PMC article.

6

SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes.

Lu J, Salzberg SL. Lu J, et al. PLoS Comput Biol. 2020 Dec 4;16(12):e1008439. doi: 10.1371/journal.pcbi.1008439. eCollection 2020 Dec. PLoS Comput Biol. 2020. PMID: 33275607 Free PMC article.

7

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.

8

Identification of microbial agents in tissue specimens of ocular and periocular sarcoidosis using a metagenomics approach.

Shifera AS, Pockrandt C, Rincon N, Ge Y, Lu J, Varabyou A, Jedlicka AE, Sun K, Scott AL, Eberhart C, Thorne JE, Salzberg SL. Shifera AS, et al. Among authors: lu j. F1000Res. 2021 Aug 17;10:820. doi: 10.12688/f1000research.55090.1. eCollection 2021. F1000Res. 2021. PMID: 36212901 Free PMC article.

9

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. bioRxiv [Preprint]. 2023 Jul 31:2023.07.28.550993. doi: 10.1101/2023.07.28.550993. bioRxiv. 2023. Update in: mBio. 2023 Oct 31;14(5):e0160723. doi: 10.1128/mbio.01607-23 PMID: 37577699 Free PMC article. Updated. Preprint.

10

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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