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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/44659?offset=80</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/3885/precision-medicine</guid>
	<pubDate>Sat, 24 Aug 2013 15:47:03 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/3885/precision-medicine</link>
	<title><![CDATA[Precision Medicine]]></title>
	<description><![CDATA[<p>Coupling established clinical&ndash;pathological indexes with state-of-the-art molecular profiling to create diagnostic, prognostic, and therapeutic strategies precisely tailored to each patient's requirements &mdash; hence the term &ldquo;Precision medicine&rdquo;&nbsp;</p>
<p>Source:<a href="http://www.nejm.org/doi/full/10.1056/NEJMp1114866">http://www.nejm.org/doi/full/10.1056/NEJMp1114866</a></p>
<p><strong>Another video on precision medicine</strong>:</p>
<p><a href="http://www.youtube.com/watch?v=Pi8W0yOXnzE">http://www.youtube.com/watch?v=Pi8W0yOXnzE</a></p>
<p>Precision Medicine basically intergrates bioinformatics, genomics , genetics, molecular biology and nanotechnology to deliver precise cure/diagnotics to a specific patient.</p>
<p>Examples:</p>
<ul>
<li><span>The drug imatinib (Gleevec) designed to inhibit an altered enzyme produced by a fused version of two genes found in chronic myelogenous leukemia.</span></li>
<li><span>The breast cancer drug trastuzumab (Herceptin) works only for women whose tumors have a particular genetic profile called HER-2 positive.</span></li>
</ul>
<p><span>E.g. source :</span></p>
<p><span><a href="http://www.bionews-tx.com/news/2013/08/15/how-the-impact-of-cancer-genomics-on-precision-medicine-is-revolutionizing-cancer-treatment/">http://www.bionews-tx.com/news/2013/08/15/how-the-impact-of-cancer-genomics-on-precision-medicine-is-revolutionizing-cancer-treatment/</a></span></p><p>Address of the bookmark: <a href="http://www.cbsnews.com/video/watch/?id=50149783n" rel="nofollow">http://www.cbsnews.com/video/watch/?id=50149783n</a></p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/3029/bioinformatics-market-in-india</guid>
	<pubDate>Fri, 23 Aug 2013 07:08:49 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/3029/bioinformatics-market-in-india</link>
	<title><![CDATA[Bioinformatics market in India]]></title>
	<description><![CDATA[<div><strong>Key Topics Covered in the Report:</strong></div>
<ul>
<li>The market size of the Indian Bioinformatics Industry , FY&rsquo;2007-FY&rsquo;2013</li>
<li>Market segmentation of India bioinformatics industry by application by sectors, FY&rsquo;2007-FY&rsquo;2013</li>
<li>Market Segmentation of India bioinformatics industry by products and services,FY&rsquo;2007-FY&rsquo;2013</li>
<li>Market Segmentation of India bioinformatics industry by applications of bioinformatics ,FY&rsquo;2007-FY&rsquo;2013</li>
<li>India bioinformatics industry trends and developments</li>
<li>Government regulations and initiatives of India bioinformatics industry</li>
<li>Major bioinformatics research institutes in India</li>
<li>Market Share of leading players in bioinformatics industry in India,FY&rsquo;2013</li>
<li>Company profiles of major players in India bioinformatics industry</li>
<li>Future outlook and projections on the basis of revenue in India bioinformatics market, FY&rsquo;2014-FY&rsquo;2018</li>
</ul>
<p>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;(Source: Ken Research)</p><p>Address of the bookmark: <a href="http://www.kenresearch.com/healthcare/biotechnology/india-bioinformatics-industry-research-report/392-91.html" rel="nofollow">http://www.kenresearch.com/healthcare/biotechnology/india-bioinformatics-industry-research-report/392-91.html</a></p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/4184/zombies-like-bacteria</guid>
	<pubDate>Tue, 03 Sep 2013 08:44:15 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/4184/zombies-like-bacteria</link>
	<title><![CDATA[Zombies like bacteria!!!]]></title>
	<description><![CDATA[<p>Do you believe in Zombies stories &hellip; Hmm confused? Don&rsquo;t worry there is a news for you. Scientists from the Integrated Ocean Drilling Program have announced the findings &nbsp;of the long-lived bacteria, reproducing only once every 10,000 years, which have been found in rocks 2.5km (1.5 miles) below the ocean floor that are as much as 100 million years old.</p><p><span>" the microbes exist in very low concentrations, of around 1,000 microbes in every tea spoon full of rock, compared with billions or trillions of bacteria that would typically be found in the same amount of soil at Earth's surface."</span></p><p><span>Reference:</span></p><p><span><a href="http://www.bbc.co.uk/news/science-environment-23855436">http://www.bbc.co.uk/news/science-environment-23855436</a></span></p><p>&nbsp;</p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/5350/introduction-of-epigenomics</guid>
	<pubDate>Sun, 06 Oct 2013 04:59:30 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/5350/introduction-of-epigenomics</link>
	<title><![CDATA[Introduction of Epigenomics]]></title>
	<description><![CDATA[<ul>
<li><a href="http://www.genome.gov/27532724#al-1">What is the epigenome?</a></li>
<li><a href="http://www.genome.gov/27532724#al-2">What does the epigenome do?</a></li>
<li><a href="http://www.genome.gov/27532724#al-3">What makes up the epigenome?</a></li>
<li><a href="http://www.genome.gov/27532724#al-4">Is the epigenome inherited?</a></li>
<li><a href="http://www.genome.gov/27532724#al-5">What is imprinting?</a></li>
<li><a href="http://www.genome.gov/27532724#al-6">Can the epigenome change?</a></li>
<li><a href="http://www.genome.gov/27532724#al-7">What makes the epigenome change?</a></li>
<li><a href="http://www.genome.gov/27532724#al-8">How do changes in the epigenome contribute to cancer?</a></li>
<li><a href="http://www.genome.gov/27532724#al-9">How are researchers exploring the epigenome?</a></li>
</ul><p>Address of the bookmark: <a href="http://www.genome.gov/27532724" rel="nofollow">http://www.genome.gov/27532724</a></p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/6302/a-allele-of-slc24a5-gene-is-found-to-be-responsible-for-variation-in-skin-color-of-south-east-asians-and-europeans</guid>
	<pubDate>Tue, 12 Nov 2013 21:02:27 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/6302/a-allele-of-slc24a5-gene-is-found-to-be-responsible-for-variation-in-skin-color-of-south-east-asians-and-europeans</link>
	<title><![CDATA[A-allele of SLC24A5 gene is found to be responsible for variation in skin color of South-East Asians and Europeans]]></title>
	<description><![CDATA[<p><strong>Key finding</strong>:</p><ol>
<li><span>rs1426654 SNP of <em>SLC24A5</em>&nbsp;gene is decider of skin pigmentation variation in South Asia</span></li>
<li><span><span>rs1426654-A allele is widely spread throughout the Indian subcontinent&nbsp;</span></span></li>
<li><span>Skin pigmentation is also account by the combination of processes like selection and demographic history of populations affected by their language and origin</span></li>
<li><span><span>Sign of positive selection in Europeans, Middle East, Pakistan, Central Asia and North India but not in South India</span></span></li>
<li><span><span>In European , A-allele is almost reached to fixation</span></span></li>
</ol><p><span><span><strong>Paper</strong>:</span></span></p><p><span><span><a href="http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003912">http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003912</a></span></span></p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/10379/your-stressdepression-came-from-ancestor</guid>
	<pubDate>Sun, 04 May 2014 18:46:20 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/10379/your-stressdepression-came-from-ancestor</link>
	<title><![CDATA[Your stress/depression came from ancestor]]></title>
	<description><![CDATA[<p>"A study published in&nbsp;<em>Nature Neuroscience</em>&nbsp;finds that stress in early life alters the production of small RNAs, called microRNAs, in the sperm of mice. The mice show depressive behaviours that persist in their progeny."</p><p>Source:</p><p>http://www.nature.com/news/sperm-rna-carries-marks-of-trauma-1.15049</p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/33826/geneprof-analysis-of-high-throughput-sequencing-experiment</guid>
	<pubDate>Wed, 05 Jul 2017 16:47:05 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/33826/geneprof-analysis-of-high-throughput-sequencing-experiment</link>
	<title><![CDATA[GeneProf: analysis of high-throughput sequencing experiment]]></title>
	<description><![CDATA[<div>GeneProf is a web-based, graphical software suite that allows users to analyse data produced using high-throughput sequencing platforms (RNA-seq and ChIP-seq; "Next-Generation Sequencing" or NGS): Next-gen analysis for next-gen data!</div>
<p>Some of GeneProf's highlights include:</p>
<ul>
<li><strong>Easy-to-use web-based interface:</strong>Access your data at any time from any computer with a working internet connection -- no need to install software! (cp.&nbsp;<a href="https://www.geneprof.org/GeneProf/help_introduction.jsp#section:SystemRequirements">Section 'System Requirements'</a>).</li>
<li><strong>Analysis wizards make your life easy:</strong>Step-by-step workflows make it easy to analyse high-throughput data within a minimum of hands-on time. (cp.&nbsp;<a href="https://www.geneprof.org/GeneProf/help_conceptsexplained.jsp#subconcept:AnalysisWizards">SubConcept 'Analysis Wizards'</a>).</li>
<li><strong>Versatile modules:</strong>Advanced users and data analysis experts benefit from GeneProf's broad range of analysis modules, which can be combined freely into sophisticated workflows (cp.&nbsp;<a href="https://www.geneprof.org/GeneProf/help_conceptsexplained.jsp#concept:Workflows">Concept 'Workflows'</a>).</li>
<li><strong>Integrated Analysis:</strong>Analysis of&nbsp;<em>ChIP-seq</em>&nbsp;and&nbsp;<em>RNA-seq</em>&nbsp;data in one place, plus support for the integration of other external data (e.g. from microarrays).</li>
<li><strong>Comprehensive Resource:</strong>GeneProf provides a comprehensive resource of&nbsp;<em>fully analyzed</em>&nbsp;next-generation sequencing data. Experimental results can be easily accessed and compared and the analysis procedures employed to produce the data are fully transparent (cp.&nbsp;<a href="https://www.geneprof.org/GeneProf/help_tutorials.jsp#tutorial:ExaminingPublicNext-GenDatausingGeneProf">Tutorial 'Examining Public Next-Gen Data..'</a>).</li>
<li><strong>Extensibility:</strong>Algorithm developers and computer programmers can develop their own modules and extend GeneProf. Existing software can be easily wrapped in the workflow framework (cp.&nbsp;<a href="https://www.geneprof.org/GeneProf/help_advancedtopics.jsp#section:ModuleDevelopment:AddingnewFunctionalitytoGeneProf">Section 'Module Development: Adding new..'</a>) and data from GeneProf may be used externally (cp.&nbsp;<a href="https://www.geneprof.org/GeneProf/help_advancedtopics.jsp#section:WebAPI:RetrievingDatafromGeneProf">Section 'Web API: Retrieving Data from ..'</a>).</li>
</ul>
<p>&nbsp;</p>
<p>GeneProf is academic software developed at the&nbsp;<a href="http://www.crm.ed.ac.uk/">Centre for Regenerative Medicine</a>&nbsp;/&nbsp;<a href="http://www.crm.ed.ac.uk/about/institute-stem-cell-research">Institute for Stem Cell Research</a>,&nbsp;<a href="http://www.ed.ac.uk/">University of Edinburgh</a>&nbsp;and has benefited from funding by the&nbsp;<a href="http://www.mrc.ac.uk/">Medical Research Council</a>&nbsp;and the&nbsp;<a href="http://www.eurosystemproject.eu/">EU Framework 7 Project "EuroSyStem"</a>.</p><p>Address of the bookmark: <a href="https://www.geneprof.org/GeneProf/index.jsp" rel="nofollow">https://www.geneprof.org/GeneProf/index.jsp</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/34711/1mb-long-dna-with-nanopore-technology</guid>
	<pubDate>Tue, 19 Dec 2017 18:49:28 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/34711/1mb-long-dna-with-nanopore-technology</link>
	<title><![CDATA[1mb long DNA with Nanopore technology]]></title>
	<description><![CDATA[<p>The first continuous DNA read of more than a million bases (&gt;1Mb) has been achieved, using Oxford Nanopore sequencing technology. Congratulations to Martin Smith and collaborators! Read more: http://bit.ly/2j5TNCO</p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36621/hapcut2-robust-and-accurate-haplotype-assembly-for-diverse-sequencing-technologies</guid>
	<pubDate>Tue, 15 May 2018 07:35:26 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36621/hapcut2-robust-and-accurate-haplotype-assembly-for-diverse-sequencing-technologies</link>
	<title><![CDATA[HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies]]></title>
	<description><![CDATA[HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy. We found that previously described haplotype assembly methods are specialized for specific read technologies or protocols, with slow or inaccurate performance on others. With this in mind, HapCUT2 is designed for speed and accuracy across diverse sequencing technologies, including but not limited to:

NGS short reads (Illumina HiSeq)
clone-based sequencing (Fosmid or BAC clones)
SMRT reads (PacBio)
Oxford Nanopore reads
10X Genomics Linked-Reads
proximity-ligation (Hi-C) reads
high-coverage sequencing (&gt;40x coverage-per-SNP) using above technologies
combinations of the above technologies (e.g. scaffold long reads with Hi-C reads)
See below for specific examples of command line options and best practices for some of these technologies.

NOTE: At this time HapCUT2 is for diploid organisms only. VCF input should contain diploid variants.

If you use HapCUT2 in your research, please cite:

Edge, P., Bafna, V. &amp; Bansal, V. HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies. Genome Res. gr.213462.116 (2016). doi:10.1101/gr.213462.116<p>Address of the bookmark: <a href="https://github.com/vibansal/HapCUT2" rel="nofollow">https://github.com/vibansal/HapCUT2</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36895/npscarf-real-time-scaffolder-using-spades-contigs-and-nanopore-sequencing-reads</guid>
	<pubDate>Mon, 11 Jun 2018 05:14:57 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36895/npscarf-real-time-scaffolder-using-spades-contigs-and-nanopore-sequencing-reads</link>
	<title><![CDATA[npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads]]></title>
	<description><![CDATA[npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for microbial datasets. In real-time mode, it can be integrated with simple structural analyses such as gene ordering, plasmid forming.<p>Address of the bookmark: <a href="http://japsa.readthedocs.io/en/latest/tools/jsa.np.npscarf.html" rel="nofollow">http://japsa.readthedocs.io/en/latest/tools/jsa.np.npscarf.html</a></p>]]></description>
	<dc:creator>Shruti Paniwala</dc:creator>
</item>

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