95 lines
No EOL
11 KiB
HTML
95 lines
No EOL
11 KiB
HTML
|
|
|
|
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
<html xmlns="http://www.w3.org/1999/xhtml" lang="en">
|
|
<head>
|
|
<meta name="title" property="og:title" content="CGR Impact Spotlight: Bioinformatics-PMID36124807">
|
|
<meta name="type" property="og:type" content="website">
|
|
<meta name="image" property="og:image" content="https://www.nlm.nih.gov/images/NLMgeneric.jpg">
|
|
<meta name="image:alt" property="og:image:alt" content="National Library of Medicine (NLM)">
|
|
|
|
<meta name="twitter:card" content="summary_large_image">
|
|
<meta name="twitter:site" content="@NLM_NIH">
|
|
<meta name="twitter:title" content="CGR Impact Spotlight: Bioinformatics-PMID36124807">
|
|
<meta name="twitter:image" content="https://www.nlm.nih.gov/images/NLMgeneric.jpg">
|
|
<meta name="twitter:image:alt" content ="National Library of Medicine (NLM)">
|
|
|
|
|
|
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
|
<link rel="schema.DC" href="//purl.org/dc/elements/1.1/" title="The Dublin Core metadata Element Set"/> <title>CGR Impact Spotlight: Bioinformatics-PMID36124807</title>
|
|
<link rel="schema.DC" href="http://purl.org/dc/elements/1.1/" title="The Dublin Core metadata Element Set" />
|
|
<meta name="DC.Title" content="CGR Impact Spotlight: Bioinformatics-PMID36124807" />
|
|
|
|
<meta name="DC.Publisher" content="U.S. National Library of Medicine" />
|
|
<meta name="DC.Date.Issued" content="2023-08-28" />
|
|
<meta name="DC.Date.Modified" content="2023-08-28" />
|
|
<meta name="NLMDC.Date.LastReviewed" content="2023-08-28" />
|
|
<meta name="NLM.Contact.Email" content="conferences@ncbi.nlm.nih.gov" />
|
|
<meta name="DC.Type" content="Other" />
|
|
<meta name="DC.Rights" content="Public Domain" />
|
|
<meta name="DC.Language" content="eng" />
|
|
|
|
<!-- Google Tag Manager -->
|
|
<script>(function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start': new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='//www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-MT6MLL');</script>
|
|
<!-- End Google Tag Manager -->
|
|
</head>
|
|
|
|
<body>
|
|
<!-- Google Tag Manager -->
|
|
<noscript><iframe src="//www.googletagmanager.com/ns.html?id=GTM-MT6MLL" height="0" width="0" style="display:none;visibility:hidden" title="googletagmanager"></iframe></noscript>
|
|
<!-- End Google Tag Manager -->
|
|
|
|
<!-- ************************* Content start ************************* -->
|
|
|
|
<a title="Link to the NIH Comparative Genome Resource (CGR) homepage" href="https://www.ncbi.nlm.nih.gov/datasets/cgr/"><img style="display: block; margin-left: auto; margin-right: auto;" src="/ncbi/cgr-impactspotlights/assets/impactspotlight-header.svg" alt="CGR Impact Spotlight header image" width="99.97%" /></a><br /><br /><br />
|
|
<table style="border-collapse: collapse; width: 95%;" border="0">
|
|
<tbody>
|
|
<tr>
|
|
<td style="width: 20%; vertical-align: top;"><a title="Link to the publication on the Journal site" href="https://academic.oup.com/bioinformatics/article/38/Supplement_2/ii168/6702016" target="_blank" rel="noopener"><img style="border-style: groove; float: left; margin: 20px 25px 40px 25px;" src="/ncbi/cgr-impactspotlights/assets/bioinformatics-v38-coverimage.png" alt="Cover image of Bioinformatics Journal volume 38" width="250 px" /></a></td>
|
|
<td style="width: 75%; vertical-align: top;">
|
|
<h2><span style="font-family: helvetica, arial, sans-serif;">Research Summary</span></h2>
|
|
<span style="font-family: helvetica, arial, sans-serif;"><a title="Link to the Bartoszewicz, et al. citation in PubMed" href="https://pubmed.ncbi.nlm.nih.gov/36124807/" target="_blank" rel="noopener"><strong><span style="color: #236fa1;"><img style="margin-right: 5px; margin-left: 5px; float: left;" src="/ncbi/cgr-impactspotlights/assets/pubmed-icon.png" alt="PubMed icon" width="60" /></span></strong></a><a href="https://pubmed.ncbi.nlm.nih.gov/36124807/" target="_blank" rel="noopener">Publication (PMID: 36124807)</a> Bartoszewicz JM, Nasri F, Nowicka M, Renard BY. Detecting DNA of novel fungal pathogens using ResNets and a curated fungi-hosts data collection. Bioinformatics. 2022 Sep 16;38(Suppl_2):ii168-ii174. doi: 10.1093/bioinformatics/btac495.<br /><br /><strong>Topic: </strong>Bioinformatics resource development<br /><br />Researchers created a <a href="https://dacs-hpi.gitlab.io/pathogenic-fungi/" target="_blank" rel="noopener">curated database</a> of fungal host-range data linked to publicly available genomes. Using custom neural networks trained on <a href="https://zenodo.org/record/5711877#.ZDQPP-zMJqv" target="_blank" rel="noopener">these data</a>, they showed that this combination of genomic and host information can be used to predict pathogenicity using both sequence homology and deep-learning approaches.<br /><br />The researchers’ database contains over 1600 genomes linked to host and disease phenotype metadata from multiple existing databases. They found that their neural networks could accurately detect fungal pathogens in Next Generation Sequencing (NGS) datasets. The trained models predicted pathogenicity and whether a fungus infects humans vs. other hosts. They also developed models capable of identifying novel fungal, viral, and bacterial pathogens in human-derived samples.<br /></span></td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
<br />
|
|
<table style="border-collapse: collapse; width: 100%; background-color: #c2e0f4;" border="0" cellpadding="25px">
|
|
<tbody>
|
|
<tr>
|
|
<td style="width: 90%; vertical-align: top;">
|
|
<h2><span style="font-family: helvetica, arial, sans-serif;">Potential CGR Impact on Research</span></h2>
|
|
<span style="color: #236fa1;"><span style="font-family: helvetica, arial, sans-serif; color: #34495e;"><em><strong>The following are examples of how CGR resources and capabilities could impact this study.</strong></em></span> <br /><br /><span style="font-family: helvetica, arial, sans-serif; font-size: 12pt;"><strong><a href="https://www.ncbi.nlm.nih.gov/datasets/" target="_blank" rel="noopener">NCBI Datasets</a><span style="color: #34495e;">:</span></strong><span style="color: #34495e;"> NCBI Datasets: Researchers could automatically produce tabular-formatted metadata (and only for specified relevant fields) for a large list of taxa using NCBI Datasets. NCBI Datasets reports by taxon or genome would help researchers easily add information about assembly quality or status of included genomes, which could then be used to assess the effects of genome quality on results. The researchers could then use NCBI Datasets reports/assembled genomes to better understand taxonomic bias or gaps in the genomes available for the taxonomic group. Researchers could programmatically pull target genomes and metadata using command line tools or an API connection. Data pulls could be easily performed at regular intervals and fit specified characteristics, including newly added data.</span></span><br /><br /></span></td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
<br /><!-----------------footer-----------------> <br />
|
|
<div>
|
|
<table style="border-collapse: collapse; width: 100%; height: 72px; background-color: #ced4d9;" border="0" cellpadding="5px">
|
|
<tbody>
|
|
<tr style="height: 25px;">
|
|
<td style="width: 30%; padding-left: 20px; height: 72px; vertical-align: middle;" rowspan="2"><span style="font-family: helvetica, arial, sans-serif;"><a title="Link to NCBI website homepage" href="https://www.ncbi.nlm.nih.gov" target="_blank" rel="noopener"><img src="/ncbi/cgr-impactspotlights/assets/nih-nlm-ncbi-two-color.png" alt="NLM NCBI Logo" width="100%" /></a></span></td>
|
|
<td style="width: 2%; height: 36px;"> </td>
|
|
<td style="width: 12%; vertical-align: middle; height: 36px;"><span style="font-family: helvetica, arial, sans-serif;"><a style="color: #7e8c8d;" title="CGR Email List" href="https://public.govdelivery.com/accounts/USNLMOCPL/subscriber/new?topic_id=USNLMOCPL_50" target="_blank" rel="noopener"><img style="float: right;" src="/ncbi/cgr-impactspotlights/assets/email-icon.png" alt="email icon" width="40" /></a></span></td>
|
|
<td style="width: 16%; vertical-align: middle; height: 36px;"><a style="text-decoration: none;" title="CGR Mailing List" href="https://public.govdelivery.com/accounts/USNLMOCPL/subscriber/new?topic_id=USNLMOCPL_50" target="_blank" rel="noopener"><span style="font-family: helvetica, arial, sans-serif;"><strong><span style="font-size: 12pt; color: #7e8c8d;">Join our mailing list</span></strong></span></a></td>
|
|
<td style="width: 12%; vertical-align: middle; height: 36px;"><span style="font-family: helvetica, arial, sans-serif;"><a title="Link to NCBI Twitter (X) Feed" href="https://www.twitter.com/ncbi" target="_blank" rel="noopener"><img style="float: right;" src="/ncbi/cgr-impactspotlights/assets/follow-icon.png" alt="thumbs up icon" width="40" /></a></span></td>
|
|
<td style="width: 16%; height: 36px;"><a style="text-decoration: none;" title="Link to NCBI's Twitter (X) Feed" href="https://www.twitter.com/ncbi" target="_blank" rel="noopener"><span style="font-family: helvetica, arial, sans-serif;"><strong><span style="font-size: 12pt; color: #7e8c8d; text-decoration: none;">Follow us on social</span></strong></span></a></td>
|
|
<td style="width: 2%; height: 36px; vertical-align: middle;"> </td>
|
|
</tr>
|
|
<tr style="height: 25px;">
|
|
<td style="width: 2%; height: 36px;"> </td>
|
|
<td style="width: 12%; vertical-align: middle; height: 36px;"><span style="font-family: helvetica, arial, sans-serif;"><a href="mailto:cgr@nlm.nih.gov" target="_blank" rel="noopener"><img style="float: right;" src="/ncbi/cgr-impactspotlights/assets/contact_us-icon.png" alt="contact us icon" width="42" /></a></span></td>
|
|
<td style="width: 16%; vertical-align: middle; height: 36px;"><a style="text-decoration: none;" title="Open up an Email to CGR" href="mailto:cgr@nlm.nih.gov" target="_blank" rel="noopener"><span style="font-family: helvetica, arial, sans-serif;"><strong><span style="font-size: 12pt; color: #7e8c8d; text-decoration: none;">Contact us</span></strong></span></a></td>
|
|
<td style="width: 5.11921%; height: 36px;"><span style="font-family: helvetica, arial, sans-serif;"><a title="Link to the NIH CGR homepage" href="https://www.ncbi.nlm.nih.gov/cgr" target="_blank" rel="noopener"><img style="float: right;" src="/ncbi/cgr-impactspotlights/assets/website-icon.png" alt="website icon" width="41" /></a></span></td>
|
|
<td style="width: 16%; vertical-align: middle; height: 36px;"><a style="text-decoration: none;" title="Link to the CGR website homepage" href="https://www.ncbi.nlm.nih.gov/cgr"><span style="font-family: helvetica, arial, sans-serif;"><strong><span style="font-size: 12pt; color: #7e8c8d; text-decoration: none;">Visit our CGR website</span></strong></span></a></td>
|
|
<td style="width: 6%; height: 36px;"> </td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
</div>
|
|
|
|
<!--*****************************Content end*******************************-->
|
|
<script src="//assets.nlm.nih.gov/jquery/jquery-latest.min.js"></script>
|
|
<script src="/core/nlm-notifyExternal/1.0/nlm-notifyExternal.min.js"></script>
|
|
</body>
|
|
</html>
|
|
|