Searching journal content for articles similar to Naccache et al. 24 (7): 1180.

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  1. Method: Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid
    • Steve Miller,
    • Samia N. Naccache,
    • Erik Samayoa,
    • Kevin Messacar,
    • Shaun Arevalo,
    • Scot Federman,
    • Doug Stryke,
    • Elizabeth Pham,
    • Becky Fung,
    • William J. Bolosky,
    • Danielle Ingebrigtsen,
    • Walter Lorizio,
    • Sandra M. Paff,
    • John A. Leake,
    • Rick Pesano,
    • Roberta DeBiasi,
    • Samuel Dominguez,
    • and Charles Y. Chiu
    Genome Res. May 2019 29: 831-842; Published in Advance April 16, 2019, doi:10.1101/gr.238170.118
    ...to 20 million sequences per library (Fig. 1A,B). Raw mNGS sequence data were analyzed using SURPI+, a bioinformatics analysis pipeline for pathogen identification (Naccache et al. 2014) that was modified for clinical use. Specifically, the modified pipeline incorporated filtering algorithms...
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  2. Method: A virome-wide clonal integration analysis platform for discovering cancer viral etiology
    • Xun Chen,
    • Jason Kost,
    • Arvis Sulovari,
    • Nathalie Wong,
    • Winnie S. Liang,
    • Jian Cao,
    • and Dawei Li
    Genome Res. May 2019 29: 819-830; Published in Advance March 14, 2019, doi:10.1101/gr.242529.118
    ...oncoviruses.ResultsVIcaller: a novel bioinformatics tool for virome-wide integration callingTo implement our strategy, we developed a novel bioinformatics platform, Viral Integration caller (VIcaller), for detecting virome-wide viral sequences, integration events, and fusion transcripts from HTS data...
  3. Resource: Using populations of human and microbial genomes for organism detection in metagenomes
    • Sasha K. Ames,
    • Shea N. Gardner,
    • Jose Manuel Marti,
    • Tom R. Slezak,
    • Maya B. Gokhale,
    • and Jonathan E. Allen
    Genome Res. July 2015 25: 1056-1067; Published in Advance April 29, 2015, doi:10.1101/gr.184879.114
    .... This can be particularly challenging when trying to uncover a poorly characterized etiologic agent thatmay or may not be recoverable from a diagnostic next-generation sequencing run (Yozwiak et al. 2012;Wilson et al. 2014). Ideally each sequencer read should be examined and its relationship relative to all...
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