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‎accessing-ancient-metagenomic-data.html‎

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<meta name="author" content="James A. Fellows Yates">
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<title>16&nbsp; Accessing Ancient Metagenomic Data – Introduction to Ancient Metagenomics</title>
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<h2 data-number="16.9" class="anchored" data-anchor-id="references"><span class="header-section-number">16.9</span> References</h2>
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<div id="ref-Anagnostou2015-mz" class="csl-entry" role="listitem">
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Anagnostou, Paolo, Marco Capocasa, Nicola Milia, Emanuele Sanna, Cinzia Battaggia, Daniela Luzi, and Giovanni Destro Bisol. 2015. <span>“When Data Sharing Gets Close to 100%: What Human Paleogenetics Can Teach the Open Science Movement.”</span> <em>PloS One</em> 10 (3): e0121409. <a href="https://doi.org/10.1371/journal.pone.0121409">https://doi.org/10.1371/journal.pone.0121409</a>.
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Anagnostou, Paolo, Marco Capocasa, Nicola Milia, et al. 2015. <span>“When Data Sharing Gets Close to 100%: What Human Paleogenetics Can Teach the Open Science Movement.”</span> <em>PloS One</em> 10 (3): e0121409. <a href="https://doi.org/10.1371/journal.pone.0121409">https://doi.org/10.1371/journal.pone.0121409</a>.
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Borry, Maxime, Adrian Forsythe, Aida Andrades Valtueña, Alexander Hübner, Anan Ibrahim, Andrea Quagliariello, Anna E White, et al. 2024. <span>“Facilitating Accessible, Rapid, and Appropriate Processing of Ancient Metagenomic Data with <span>AMDirT</span>.”</span> <em>F1000Research</em> 12 (926): 926. <a href="https://doi.org/10.12688/f1000research.134798.2">https://doi.org/10.12688/f1000research.134798.2</a>.
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Borry, Maxime, Adrian Forsythe, Aida Andrades Valtueña, et al. 2024. <span>“Facilitating Accessible, Rapid, and Appropriate Processing of Ancient Metagenomic Data with <span>AMDirT</span>.”</span> <em>F1000Research</em> 12 (926): 926. <a href="https://doi.org/10.12688/f1000research.134798.2">https://doi.org/10.12688/f1000research.134798.2</a>.
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<div id="ref-Fellows_Yates2021-rp" class="csl-entry" role="listitem">
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Fellows Yates, James A, Aida Andrades Valtueña, Åshild J Vågene, Becky Cribdon, Irina M Velsko, Maxime Borry, Miriam J Bravo-Lopez, et al. 2021. <span>“Community-Curated and Standardised Metadata of Published Ancient Metagenomic Samples with <span>AncientMetagenomeDir</span>.”</span> <em>Scientific Data</em> 8 (1): 31. <a href="https://doi.org/10.1038/s41597-021-00816-y">https://doi.org/10.1038/s41597-021-00816-y</a>.
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Fellows Yates, James A, Aida Andrades Valtueña, Åshild J Vågene, et al. 2021. <span>“Community-Curated and Standardised Metadata of Published Ancient Metagenomic Samples with <span>AncientMetagenomeDir</span>.”</span> <em>Scientific Data</em> 8 (1): 31. <a href="https://doi.org/10.1038/s41597-021-00816-y">https://doi.org/10.1038/s41597-021-00816-y</a>.
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Fellows Yates, James A, Thiseas C Lamnidis, Maxime Borry, Aida Andrades Valtueña, Zandra Fagernäs, Stephen Clayton, Maxime U Garcia, Judith Neukamm, and Alexander Peltzer. 2021. <span>“Reproducible, Portable, and Efficient Ancient Genome Reconstruction with Nf-Core/Eager.”</span> <em>PeerJ</em> 9 (March): e10947. <a href="https://doi.org/10.7717/peerj.10947">https://doi.org/10.7717/peerj.10947</a>.
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Fellows Yates, James A, Thiseas C Lamnidis, Maxime Borry, et al. 2021. <span>“Reproducible, Portable, and Efficient Ancient Genome Reconstruction with Nf-Core/Eager.”</span> <em>PeerJ</em> 9 (March): e10947. <a href="https://doi.org/10.7717/peerj.10947">https://doi.org/10.7717/peerj.10947</a>.
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Maixner, Frank, Mohamed S Sarhan, Kun D Huang, et al. 2021. <span>“Hallstatt Miners Consumed Blue Cheese and Beer During the Iron Age and Retained a Non-Westernized Gut Microbiome Until the Baroque Period.”</span> <em>Current Biology: CB</em>, ahead of print, October. <a href="https://doi.org/10.1016/j.cub.2021.09.031">https://doi.org/10.1016/j.cub.2021.09.031</a>.
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Mühlemann, Barbara, Lasse Vinner, Ashot Margaryan, et al. 2020. <span>“Diverse Variola Virus (Smallpox) Strains Were Widespread in Northern Europe in the Viking Age.”</span> <em>Science</em> 369 (6502). <a href="https://doi.org/10.1126/science.aaw8977">https://doi.org/10.1126/science.aaw8977</a>.
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Schubert, Mikkel, Luca Ermini, Clio Der Sarkissian, Hákon Jónsson, Aurélien Ginolhac, Robert Schaefer, Michael D Martin, et al. 2014. <span>“Characterization of Ancient and Modern Genomes by <span>SNP</span> Detection and Phylogenomic and Metagenomic Analysis Using <span>PALEOMIX</span>.”</span> <em>Nature Protocols</em> 9 (5): 1056–82. <a href="https://doi.org/10.1038/nprot.2014.063">https://doi.org/10.1038/nprot.2014.063</a>.
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Wilkinson, Mark D, Michel Dumontier, I Jsbrand Jan Aalbersberg, Gabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, et al. 2016. <span>“The <span>FAIR</span> Guiding Principles for Scientific Data Management and Stewardship.”</span> <em>Scientific Data</em> 3 (March): 160018. <a href="https://doi.org/10.1038/sdata.2016.18">https://doi.org/10.1038/sdata.2016.18</a>.
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