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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/39213?offset=410</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/17885/international-conference-on-bioinformatics-models-methods-and-algorithms</guid>
	<pubDate>Sun, 05 Oct 2014 11:42:52 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/17885/international-conference-on-bioinformatics-models-methods-and-algorithms</link>
	<title><![CDATA[International Conference on Bioinformatics Models, Methods and Algorithms]]></title>
	<description><![CDATA[<p><span>The purpose of the International Conference on Bioinformatics Models, Methods and Algorithms is to bring together researchers and practitioners interested in the application of computational systems and information technologies to the field of molecular biology, including for example the use of statistics and algorithms to understanding biological processes and systems, with a focus on new developments in genome bioinformatics and computational biology. Areas of interest for this community include sequence analysis, biostatistics, image analysis, scientific data management and data mining, machine learning, pattern recognition, computational evolutionary biology, computational genomics and other related fields.</span></p>
<p><span><span>Position Paper Submission Extension:</span><span>&nbsp;</span><span>October 9, 2014</span><span>&nbsp;</span><br><span>Regular Paper Authors Notification:</span><span>&nbsp;</span><span>November 3, 2014</span><span>&nbsp;</span><br><span>Position Paper Authors Notification:</span><span>&nbsp;</span><span>November 6, 2014</span><span>&nbsp;</span><br><span>Regular and Position Paper Camera Ready and Registration:</span><span>&nbsp;</span><span>November 17, 2014</span><span>&nbsp;</span></span></p><p>Address of the bookmark: <a href="http://www.bioinformatics.biostec.org/" rel="nofollow">http://www.bioinformatics.biostec.org/</a></p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34396/pore-an-r-package-for-the-visualization-and-analysis-of-nanopore-sequencing-data</guid>
	<pubDate>Thu, 23 Nov 2017 09:55:57 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34396/pore-an-r-package-for-the-visualization-and-analysis-of-nanopore-sequencing-data</link>
	<title><![CDATA[poRe: an R package for the visualization and analysis of nanopore sequencing data]]></title>
	<description><![CDATA[<p><strong>Motivation:</strong>&nbsp;The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the bioinformatics community will need to design and build a suite of tools specifically for MinION data.</p>
<p><strong>Results:</strong>&nbsp;Here we present poRe, a package for R that enables users to manipulate, organize, summarize and visualize MinION nanopore sequencing data. As a package for R, poRe has been tested on Windows, Linux and MacOSX. Crucially, the Windows version allows users to analyse MinION data on the Windows laptop attached to the device.</p>
<p><strong>Availability and implementation:</strong>&nbsp;poRe is released as a package for R at&nbsp;<a href="http://sourceforge.net/projects/rpore/" target="">http://sourceforge.net/projects/rpore/</a>&nbsp;. A tutorial and further information are available at&nbsp;<a href="https://sourceforge.net/p/rpore/wiki/Home/" target="">https://sourceforge.net/p/rpore/wiki/Home/</a></p>
<p><strong>Contact:</strong><a href="mailto:mick.watson@roslin.ed.ac.uk" target="">mick.watson@roslin.ed.ac.uk</a></p><p>Address of the bookmark: <a href="https://academic.oup.com/bioinformatics/article/31/1/114/2365693" rel="nofollow">https://academic.oup.com/bioinformatics/article/31/1/114/2365693</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36806/manta-rapid-detection-of-structural-variants-and-indels-for-germline-and-cancer-sequencing-applications</guid>
	<pubDate>Mon, 28 May 2018 09:41:39 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36806/manta-rapid-detection-of-structural-variants-and-indels-for-germline-and-cancer-sequencing-applications</link>
	<title><![CDATA[Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications.]]></title>
	<description><![CDATA[Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow.<p>Address of the bookmark: <a href="https://github.com/Illumina/manta" rel="nofollow">https://github.com/Illumina/manta</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37527/nanopack-visualizing-and-processing-long-read-sequencing-data</guid>
	<pubDate>Fri, 10 Aug 2018 18:41:34 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37527/nanopack-visualizing-and-processing-long-read-sequencing-data</link>
	<title><![CDATA[NanoPack: visualizing and processing long-read sequencing data]]></title>
	<description><![CDATA[<p>The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at&nbsp;<a href="https://github.com/wdecoster/nanopack" target="">https://github.com/wdecoster/nanopack</a>, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Windows 10 subsystem for Linux and are available as a graphical user interface, a web service at&nbsp;<a href="http://nanoplot.bioinf.be/" target="">http://nanoplot.bioinf.be</a>&nbsp;and command line tools.</p>
<p>&nbsp;https://academic.oup.com/bioinformatics/article/34/15/2666/4934939</p><p>Address of the bookmark: <a href="https://github.com/wdecoster/nanoQC" rel="nofollow">https://github.com/wdecoster/nanoQC</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/38649/ngs-platforms-launched-by-bgi%E2%80%99s-mgi-tech</guid>
	<pubDate>Thu, 10 Jan 2019 04:42:06 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/38649/ngs-platforms-launched-by-bgi%E2%80%99s-mgi-tech</link>
	<title><![CDATA[NGS Platforms launched by BGI’s MGI Tech]]></title>
	<description><![CDATA[<p>MGI Tech Co., Ltd. (MGI), a subsidiary of BGI Group, is committed to enabling effective and affordable healthcare solutions for all. Based on its proprietary technology, MGI produces sequencing devices, equipment, consumables and reagents to support life science research, medicine and healthcare. MGI's multi-omics platforms include genetic sequencing, mass spectrometry and medical imaging. Providing real-time, comprehensive, life-long solutions, its mission&nbsp;is to&nbsp;develop and promote advanced life science tools for future healthcare.</p><p>MGI, a subsidiary of global genomics leader BGI Group, announced pricing and its first early access customer for the new ultra high-throughput sequencer, MGISEQ-T7, saying it has driven down sequencing cost to&nbsp;$5&nbsp;per gigabyte, with exceptionally high accuracy. Such innovations are helping more people to realize the benefits of genomic information.</p><p>In October, MGI launched the MGISEQ-T7, a highly flexible production-scale platform that is the most powerful sequencer to date. It can produce as many as 60 whole human genomes in one day. The instrument sells for&nbsp;$1 million.</p><p>The T7 enables simultaneous but independent operation of up to four flow cells, which means different applications such as single-cell RNA sequencing, whole exome sequencing and whole genome sequencing can be run in different flow cells at the same time. This helps to reduce costs, allowing MGI to offer the most competitive sequencing price in the market.</p><p><span>Powered by DNBseq&trade;, MGISEQ delivers quality data with accuracy for SNP and Indel calling rate of 99.9% and 99%, respectively, along with decreased duplication rate down to less than 2 percent, and almost zero Index mis-assignment rate.</span></p><p><span><span>SOURCE MGI</span></span></p><p>https://www.bgi.com/global/company/news/bgis-mgi-tech-launches-two-new-ngs-platforms/</p><p>http://en.mgitech.cn/</p>]]></description>
	<dc:creator>Jit</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/41039/phd-position-in-translational-medicine</guid>
  <pubDate>Sat, 15 Feb 2020 06:07:19 -0600</pubDate>
  <link></link>
  <title><![CDATA[PhD position in Translational Medicine]]></title>
  <description><![CDATA[
<p>https://www.jobvector.de/jobs-stellenangebote/biologie-life-sciences/wissenschaftliche-r-mitarbeiter-in/phd-position-translational-medicine-129981.html?suid=1b510358c7578e8f75cf04a464fc21a404a574ca</p>

<p>Essential experience / qualifications:<br />Master / Diploma in Biology, Biochemistry, Molecular Medicine or similar; solid knowledge of molecular and cell biological techniques; good English knowledge</p>

<p>Applications:<br />Please send your application (including CV, letter of motivation, contact information of two references, and list of publication) by 13.03.2020 at the latest to:</p>

<p>Universitätsklinikum Erlangen<br />Chirurgische Klinik<br />Translational Research Center<br />Prof. Dr. rer. nat. Michael Stürzl<br />Schwabachanlage 12<br />91054 Erlangen<br />E-Mail: michael.stuerzl@uk-erlangen.de</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44659/figeno-tool-for-plotting-sequencing-data-along-genomic-coordinates</guid>
	<pubDate>Tue, 17 Sep 2024 02:28:15 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44659/figeno-tool-for-plotting-sequencing-data-along-genomic-coordinates</link>
	<title><![CDATA[Figeno: Tool for plotting sequencing data along genomic coordinates.]]></title>
	<description><![CDATA[<p><span>Tool for plotting sequencing data along genomic coordinates.</span></p>
<div>
<pre><code>FIGENO is a
  FIGure
    GENerator
for GENOmics</code></pre>
</div>
<p dir="auto">With figeno, you can plot various types of sequencing data along genomic coordinates. Video overview:&nbsp;<a href="https://www.youtube.com/watch?v=h1cBeXoSYTA">https://www.youtube.com/watch?v=h1cBeXoSYTA</a>.</p>
<p dir="auto"><a href="https://github.com/CompEpigen/figeno/blob/main/docs/content/images/figeno.png" target="_blank"><img src="https://github.com/CompEpigen/figeno/raw/main/docs/content/images/figeno.png" alt="figeno" style="border: 0px;"></a></p><p>Address of the bookmark: <a href="https://github.com/CompEpigen/figeno" rel="nofollow">https://github.com/CompEpigen/figeno</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/40497/artificial-intelligence-is-more-accurate-than-doctors-in-diagnosing-breast-cancer</guid>
	<pubDate>Wed, 01 Jan 2020 22:12:34 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/40497/artificial-intelligence-is-more-accurate-than-doctors-in-diagnosing-breast-cancer</link>
	<title><![CDATA[Artificial intelligence is more accurate than doctors in diagnosing breast cancer]]></title>
	<description><![CDATA[<p>Artificial intelligence is more accurate than doctors in diagnosing breast cancer from mammograms, a study in the journal Nature suggests.</p><p>An international team, including researchers from&nbsp;<a href="https://health.google/" target="_blank">Google Health</a>&nbsp;and&nbsp;<a href="https://www.imperial.ac.uk/news/183293/research-collaboration-aims-improve-breast-cancer/" target="_blank">Imperial College London</a>, designed and trained a computer model on X-ray images from nearly 29,000 women.</p><p>The algorithm&nbsp;<a href="https://nature.com/articles/s41586-019-1799-6" target="_blank">outperformed six radiologists</a>&nbsp;in reading mammograms.</p><p>AI was still as good as two doctors working together.</p><p>Unlike humans, AI is tireless. Experts say it could improve detection. Read More:&nbsp;<a href="https://www.bbc.com/news/health-50857759" target="_blank">https://www.bbc.com/news/health-50857759</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44894/dna2bit-an-ultra-fast-and-accurate-genomic-distance-estimation-software</guid>
	<pubDate>Sun, 31 Aug 2025 06:24:58 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44894/dna2bit-an-ultra-fast-and-accurate-genomic-distance-estimation-software</link>
	<title><![CDATA[dna2bit: an ultra-fast and accurate genomic distance estimation software]]></title>
	<description><![CDATA[<p><span>dna2bit is a software tool developed in C++11, leveraging the capabilities of OpenMP for parallel computing and the popcount technique for efficient bit manipulation. It has been thoroughly tested using the g++ and clang compilers on both Linux and MacOS platforms.</span></p><p>Address of the bookmark: <a href="https://github.com/lijuzeng/dna2bit" rel="nofollow">https://github.com/lijuzeng/dna2bit</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/44515/cleaner-blast-databases-for-more-accurate-results</guid>
	<pubDate>Tue, 23 Apr 2024 01:23:08 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/44515/cleaner-blast-databases-for-more-accurate-results</link>
	<title><![CDATA[Cleaner BLAST Databases for More Accurate Results]]></title>
	<description><![CDATA[<p>Do you use&nbsp;<a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=blast-cleaner-20240422">BLAST</a><span style="font-size: 12.8px; font-weight: normal;">&nbsp;to identify a sequence or the evolutionary scope of a gene? That can be challenging if contaminated and misclassified sequences are in the BLAST databases and show up in your search results. To address</span><span style="font-size: 12.8px; font-weight: normal;">&nbsp;this problem</span><span style="font-size: 12.8px; font-weight: normal;">, we now use the NCBI quality assurance tools listed below to systematically remove these misleading sequences from the default nucleotide (nt) and protein (nr) BLAST databases.</span><span style="font-size: 12.8px; font-weight: normal;">&nbsp;</span></p><div><ul>
<li><a href="https://github.com/ncbi/fcs">Foreign Contamination Screen tool for genome cross-species screening (FCS-GX)</a>&nbsp;detects contamination from foreign organisms in genomes and other sequences using the genome cross-species aligner (GX)&nbsp;</li>
<li><a href="https://ncbiinsights.ncbi.nlm.nih.gov/2022/05/27/ani-for-assembly-validation?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=blast-cleaner-20240422">Average Nucleotide Identity (ANI)</a>&nbsp;evaluates the taxonomic classification of prokaryotic genome assemblies. Sequences from genomes marked up as &lsquo;unverified source organism&rsquo; are considered suspect and removed.&nbsp;</li>
</ul><p>Ref&nbsp;https://ncbiinsights.ncbi.nlm.nih.gov/2024/04/22/cleaner-blast-databases-more-accurate-results/</p></div>]]></description>
	<dc:creator>LEGE</dc:creator>
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