Breitwieser FP - Search Results

1

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. Among authors: breitwieser fp. 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.

2

Centrifuge: rapid and sensitive classification of metagenomic sequences.

Kim D, Song L, Breitwieser FP, Salzberg SL. Kim D, et al. Among authors: breitwieser fp. Genome Res. 2016 Dec;26(12):1721-1729. doi: 10.1101/gr.210641.116. Epub 2016 Oct 17. Genome Res. 2016. PMID: 27852649 Free PMC article.

3

Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification.

Breitwieser FP, Salzberg SL. Breitwieser FP, et al. Bioinformatics. 2020 Feb 15;36(4):1303-1304. doi: 10.1093/bioinformatics/btz715. Bioinformatics. 2020. PMID: 31553437 Free PMC article.

4

KrakenUniq: confident and fast metagenomics classification using unique k-mer counts.

Breitwieser FP, Baker DN, Salzberg SL. Breitwieser FP, et al. Genome Biol. 2018 Nov 16;19(1):198. doi: 10.1186/s13059-018-1568-0. Genome Biol. 2018. PMID: 30445993 Free PMC article.

5

Re-analysis of metagenomic sequences from acute flaccid myelitis patients reveals alternatives to enterovirus D68 infection.

Breitwieser FP, Pardo CA, Salzberg SL. Breitwieser FP, et al. F1000Res. 2015 Jul 2;4:180. doi: 10.12688/f1000research.6743.2. eCollection 2015. F1000Res. 2015. PMID: 26309730 Free PMC article.

6

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: breitwieser fp. 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.

7

Human contamination in bacterial genomes has created thousands of spurious proteins.

Breitwieser FP, Pertea M, Zimin AV, Salzberg SL. Breitwieser FP, et al. Genome Res. 2019 Jun;29(6):954-960. doi: 10.1101/gr.245373.118. Epub 2019 May 7. Genome Res. 2019. PMID: 31064768 Free PMC article.

8

Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system.

Salzberg SL, Breitwieser FP, Kumar A, Hao H, Burger P, Rodriguez FJ, Lim M, Quiñones-Hinojosa A, Gallia GL, Tornheim JA, Melia MT, Sears CL, Pardo CA. Salzberg SL, et al. Among authors: breitwieser fp. Neurol Neuroimmunol Neuroinflamm. 2016 Jun 13;3(4):e251. doi: 10.1212/NXI.0000000000000251. eCollection 2016 Aug. Neurol Neuroimmunol Neuroinflamm. 2016. PMID: 27340685 Free PMC article.

9

Development and Optimization of Metagenomic Next-Generation Sequencing Methods for Cerebrospinal Fluid Diagnostics.

Simner PJ, Miller HB, Breitwieser FP, Pinilla Monsalve G, Pardo CA, Salzberg SL, Sears CL, Thomas DL, Eberhart CG, Carroll KC. Simner PJ, et al. Among authors: breitwieser fp. J Clin Microbiol. 2018 Aug 27;56(9):e00472-18. doi: 10.1128/JCM.00472-18. Print 2018 Sep. J Clin Microbiol. 2018. PMID: 29976594 Free PMC article.

10

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

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

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