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11 changes: 9 additions & 2 deletions index.html
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Expand Up @@ -21,6 +21,7 @@ <h2 class="project-tagline">Database-Integrated Genome Screening</h2>
<a href="./website/user-guide/user-guide.html" class="btn">Manual</a>
<a href="https://github.com/giffordlabcvr/DIGS-tool/zipball/master" class="btn">Download</a>
<a target="_blank" href="https://github.com/giffordlabcvr/DIGS-tool" class="btn">GitHub</a>
<a href="./website/user-guide/publications.html" class="btn">Publications</a>
<a target="_blank" href="https://twitter.com/DigsTool" class="btn">Twitter</a>

</section>
Expand All @@ -41,15 +42,21 @@ <h3>

<strong>Systematic, sequence similarity search-based genome screening</strong> is a powerful
approach for identifying and characterising genome features in silico.
This approach extends the basic <strong><a target="_blank" href="https://blast.ncbi.nlm.nih.gov/">sequence similarity search</a></strong> by:
<ol>
<li> Performing multiple searches systematically, involving various <strong>query sequences</strong> and/or <strong>target databases</strong>.</li>
<li> Classifying “<strong>hits</strong>” (matching sequences) via comparison to a <strong>reference sequence library</strong> curated by the investigator.</li>
</ol>

</p>


<p>

<strong>Database-integrated genome-screening (DIGS)</strong> is a form of systematic genome screening
in which a sequence similarity search-based screening pipeline is linked to a <strong>relational database management
system (RDBMS)</strong>. This provides a robust foundation for implementing large-scale, automated screens,
and allows screening output to be investigated via database-querying.
system</strong>. This provides a robust foundation for implementing large-scale, automated screens, and
enables a 'database querying' approach to investigating screening output.
</p>

<p>
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1 change: 1 addition & 0 deletions website/user-guide/explore.html
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Expand Up @@ -29,6 +29,7 @@ <h2 class="project-tagline">Database-Integrated Genome Screening</h2>

<a href="https://github.com/giffordlabcvr/DIGS-tool/zipball/master" class="btn">Download</a>
<a target="_blank" href="https://github.com/giffordlabcvr/DIGS-tool" class="btn">GitHub</a>
<a href="./publications.html" class="btn">Publications</a>
<a target="_blank" href="https://twitter.com/DigsTool" class="btn">Twitter</a>

</section>
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240 changes: 240 additions & 0 deletions website/user-guide/publications.html
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<!DOCTYPE html>
<html lang="en-us">

<head>


<meta charset="UTF-8">
<title>DIGS Tool: Publications</title>
<meta name="viewport" content="width=device-width, initial-scale=1">
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</head>

<body>

<section class="page-header">



<h1 class="project-name">The DIGS Tool</h1>
<h2 class="project-tagline">Database-Integrated Genome Screening</h2>


<a href="../../index.html" class="btn">Home</a>
<a href="./explore.html" class="btn">Background</a>
<a href="./user-guide.html" class="btn">Manual</a>

<a href="https://github.com/giffordlabcvr/DIGS-tool/zipball/master" class="btn">Download</a>
<a target="_blank" href="https://github.com/giffordlabcvr/DIGS-tool" class="btn">GitHub</a>
<a target="_blank" href="https://twitter.com/DigsTool" class="btn">Twitter</a>

</section>

<section class="main-content">


<h3>
<a id="Publications" class="anchor" href="#Publications" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>Main DIGS Tool Publication</strong>
</h3>
<hr>


Blanco-Melo D, Campbell MA, Zhu H, Dennis TPW, Modha S, Lytras S, Hughes J, Gatseva A, and Gifford RJ
<b>(2024)</b>
<br>
A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus fossil record.
<br>
<i>Genome Biology</i>
<a href="https://doi.org/10.1186/s13059-024-03258-y" target="_blank">[view]</a>
<br>
<br>



<h3>
<a id="Publications" class="anchor" href="#Publications" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>Publications Utilising the DIGS Tool</strong>
</h3>
<hr>

<p>


Campbell M, Loncar S, Gifford RJ, Kotin R, and RJ Gifford
<b>(2022)</b>
<br>
Comparative analysis reveals the long-term co-evolutionary history of parvoviruses and vertebrates.
<br>
<i>Plos Biology</i>
<a href="https://doi.org/10.1371/journal.pbio.3001867" target="_blank">[view]</a>
<br>
<br>


Bamford CGG, de Souza WM, Parry R and RJ Gifford
<b>(2022)</b>
<br>
Comparative analysis of genome-encoded viral sequences reveals the evolutionary history of the <i>Flaviviridae</i>.
<br>
<i>Virus Evolution</i>
<a href="https://doi.org/10.1093/ve/veac085" target="_blank">[view]</a>
<br>
<br>

Wickenhagen A, Sugrue E, Lytras S, Kuchi S, Noerenberg M, Turnbull ML, Loney C, Herder V, Allan J, Jarmson I, Cameron-Ruiz N, Varjak M, Pinto RM, Lee JY, Iselin L, Palmalux N, Stewart DG, Swingler S, Greenwood EJD, Crozier TWM, Gu Q, Davies EL, Clohisey S, Wang B, Trindade Maranhão Costa F, Freire Santana M, de Lima Ferreira LC, Murphy L, Fawkes A, Meynert A, Grimes G, Da Silva Filho JL, Marti M, Hughes J, Stanton RJ, Wang ECY, Ho A, Davis I, Jarrett RF, Castello A, Robertson DL, Semple MG, Openshaw PJM, Palmarini M, Lehner PJ, Baillie JK, Rihn SJ, and SJ Wilson
<b>(2021)</b>
<br>
A prenylated dsRNA sensor protects against severe COVID-19.
<br>
<i>Science</i>
<a href="http://dx.doi.org/10.1126/science.abj3624" target="_blank">[view]</a>
<br>
<br>

Lytras S, Arriagada G, and RJ Gifford
<b>(2021)</b>
<br>
Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes.
<br>
<i>Virus Evolution</i>
<a href="https://academic.oup.com/ve/advance-article/doi/10.1093/ve/veab012/6157734" target="_blank">[view]</a>
<br>
<br>

Hildebrandt E, Penzes J, Gifford RJ, Agbandje-Mckenna M, and R Kotin
<b>(2020)</b>
<br>
Evolution of dependoparvoviruses across geological timescales – implications for design of AAV-based gene therapy vectors.
<i>Virus Evolution</i>
<a href="https://academic.oup.com/ve/article/doi/10.1093/ve/veaa043/5842153">[view]</a>
<br>
<br>

Pénzes JJ, de Souza WM, Agbandje-Mckenna M, and RJ Gifford
<b>(2019)</b>
<br>
An ancient lineage of highly divergent parvoviruses infects both vertebrate and invertebrate hosts.
<br>
<i>Viruses</i>
<a href="https://www.mdpi.com/1999-4915/11/6/525" target="_blank">[view]</a>
<br>
<br>

Ito J, Gifford RJ, and Kei Sato
<b>(2019)</b>
<br>
Retroviruses drive the rapid evolution of mammalian APOBEC3 genes.
<br>
<i>PNAS</i>
<a href="https://www.pnas.org/content/early/2019/12/11/1914183116" target="_blank">[view]</a>
<br>
<br>

Shaw AE, Hughes J, Gu Q, Behdenna A, Singer J, Dennis T, Orton RJ, Varela M, Gifford RJ, Wilson SJ and M Palmarini
<b>(2017)</b>
<br>
Fundamental properties of the mammalian innate immune system revealed by multi-species comparison of type I interferon responses.
<br>
<i>Plos Biology</i>
<a href="http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2004086" target="_blank">[view]</a>
<br>
<br>

Hron T, Elleder D, and RJ Gifford
<b>(2019)</b>
<br>
Deltaretroviruses have circulated since at least the Paleogene and infected a broad range of mammalian species.
<br>
<i>Retrovirology</i>
<a href="https://retrovirology.biomedcentral.com/articles/10.1186/s12977-019-0495-9" target="_blank">[view]</a>
<br>
<br>

Pénzes JJ, Marsile-Medun S, Agbandje-McKenna M, and RJ Gifford
<b>(2018)</b>
<br>
Endogenous amdoparvovirus-related elements reveal insights into the biology and evolution of vertebrate parvoviruses.
<br>
<i>Virus Evolution</i>
<a href="https://academic.oup.com/ve/article/4/2/vey026/5179240" target="_blank">[view]</a>
<br>
<br>

Blanco Melo D, Gifford RJ, and P. Bieniasz
<b>(2018)</b>
<br>
Reconstruction of a replication-competent ancestral murine endogenous retrovirus-L.
<br>
<i>Retrovirology</i>
<a href="https://retrovirology.biomedcentral.com/articles/10.1186/s12977-018-0416-3" target="_blank">[view]</a>
<br>
<br>

Dennis TPW, Flynn PJ, de Souza WM, Singer JB, Moreau CS, Wilson SJ, and RJ Gifford
<b>(2018)</b>
<br>
Insights into circovirus host range from the genomic fossil record.
<br>
<i>Journal of Virology</i>
<a href="http://jvi.asm.org/content/92/16/e00145-18.full" target="_blank">[view]</a>
<br>
<br>

Dennis TPW, de Souza WM, Marsile-Medun S, Singer JB, Wilson SJ, and RJ Gifford
<b>(2018)</b>
<br>
The evolution, distribution and diversity of endogenous circoviral elements in vertebrate genomes.
<br>
<i>Virus Research</i>
<a href="https://www.sciencedirect.com/science/article/pii/S0168170217309048" target="_blank">[view]</a>
<br>
<br>


Blanco-Melo D, Gifford RJ, and PD Bieniasz
<b>(2017)</b>
<br>
Co-option of an endogenous retrovirus envelope for host defense in hominid ancestors.
<br>
<i>Elife</i>
<a href="https://elifesciences.org/articles/22519" target="_blank">[view]</a>
<br>
<br>


</p>










<footer class="site-footer">
<span class="site-footer-owner"><a href="https://github.com/giffordlabcvr/DIGS-tool">DIGS</a> is maintained by <a href="https://github.com/giffordlabcvr">giffordlabcvr</a>.</span>

<span class="site-footer-credits">This page was generated by <a href="https://pages.github.com">GitHub Pages</a> using the <a href="https://github.com/jasonlong/cayman-theme">Cayman theme</a> by <a href="https://twitter.com/jasonlong">Jason Long</a>.</span>
</footer>


</section>


</body>

</html>









1 change: 1 addition & 0 deletions website/user-guide/user-guide.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@ <h2 class="project-tagline">Database-Integrated Genome Screening</h2>
<a href="./explore.html" class="btn">Background</a>
<a href="https://github.com/giffordlabcvr/DIGS-tool/zipball/master" class="btn">Download</a>
<a target="_blank" href="https://github.com/giffordlabcvr/DIGS-tool" class="btn">GitHub</a>
<a href="./publications.html" class="btn">Publications</a>
<a target="_blank" href="https://twitter.com/DigsTool" class="btn">Twitter</a>

</section>
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