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  1. Article

    Open Access

    EGenBio: A Data Management System for Evolutionary Genomics and Biodiversity

    Evolutionary genomics requires management and filtering of large numbers of diverse genomic sequences for accurate analysis and inference on evolutionary processes of genomic and functional change. We developed E

    Laila A Nahum, Matthew T Reynolds, Zhengyuan O Wang, Jeremiah J Faith… in BMC Bioinformatics (2006)

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  2. Article

    Open Access

    Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context

    Lightweight genome viewer (lwgv) is a web-based tool for visualization of sequence annotations in their chromosomal context. It performs most of the functions of larger genome browsers, while relying on standa...

    Jeremiah J Faith, Andrew J Olson, Timothy S Gardner… in BMC Bioinformatics (2007)

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  3. No Access

    Article

    Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

    A systematic evaluation of parameters that affect short amplicons sequenced on Illumina platforms provides guidelines for how to eliminate erroneous reads and improve data interpretation.

    Nicholas A Bokulich, Sathish Subramanian, Jeremiah J Faith, Dirk Gevers… in Nature Methods (2013)

  4. No Access

    Article

    Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation

    Similar bacterial species and strains in metagenomes are resolved and linked to the plasmids that they harbor using DNA methylation analysis.

    John Beaulaurier, Shijia Zhu, Gintaras Deikus, Ilaria Mogno… in Nature Biotechnology (2018)