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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/29343?offset=610</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36111/d3networktools-for-creating-d3-javascript-network-tree-dendrogram-and-sankey-graphs-from-r</guid>
	<pubDate>Fri, 06 Apr 2018 12:10:45 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36111/d3networktools-for-creating-d3-javascript-network-tree-dendrogram-and-sankey-graphs-from-r</link>
	<title><![CDATA[d3Network:Tools for creating D3 JavaScript network, tree, dendrogram, and Sankey graphs from R.]]></title>
	<description><![CDATA[<p><a href="http://bost.ocks.org/mike/">Mike Bostock</a><span>&rsquo;s&nbsp;</span><a href="http://d3js.org/">D3.js</a><span>&nbsp;is great for creating&nbsp;</span><a href="http://bl.ocks.org/mbostock/4062045">interactive network graphs</a><span>&nbsp;with JavaScript. The&nbsp;</span><a href="https://github.com/christophergandrud/d3Network">d3Network</a><span>&nbsp;package makes it easy to create these network graphs from&nbsp;</span><a href="http://www.r-project.org/">R</a><span>. The main idea is that you should able to take an R data frame with information about the relationships between members of a network and create full network graphs with one command.</span></p><p>Address of the bookmark: <a href="http://christophergandrud.github.io/d3Network/" rel="nofollow">http://christophergandrud.github.io/d3Network/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/18576/graduate-research-assistantships-university-of-nebraska-lincoln-unl</guid>
  <pubDate>Wed, 22 Oct 2014 10:05:31 -0500</pubDate>
  <link></link>
  <title><![CDATA[Graduate research assistantships @ University of Nebraska-Lincoln (UNL)]]></title>
  <description><![CDATA[
<p>Graduate research assistantships in quantitative genetics are available with Gota Morota in the Department of Animal Science at the University of Nebraska-Lincoln (UNL).</p>

<p>Current projects in the Morota lab include developing kernel-based whole-genome prediction and kernel-based genome-wide association models, polygenic modeling of binary traits, reexamining the results from quantitative genetics analysis in light of functional annotation, and extending kernel methods (such as GBLUP and RKHS) specifically tailored for diverse types of emerging omics data.</p>

<p>In addition, candidates will be expected to leverage opportunities to interact with faculty in animal genetics and biometrics at the UNL in the areas of bioinformatics, breeding, functional genomics, quantitative genetics, and molecular genetics.</p>

<p>Candidates should have a B.S. or M.S. degree in quantitative disciplines with strong background and interest in statistical computing. <br />The starting date is Fall 2015. <br />For more information about research in the Morota lab at the UNL, visit: http://www.morotalab.org</p>

<p>A letter of interest in the position, C.V., and contact information for <br />three references should be emailed to Gota Morota at . <br />Review of applications will begin immediately, and continue until the <br />positions are filled. Informal inquiries are also welcome.</p>

<p>Also, please see: http://animalscience.unl.edu/anscprospectivegraduatestudents</p>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40964/panev-an-r-package-for-a-pathway-based-network-visualization</guid>
	<pubDate>Sun, 09 Feb 2020 12:41:52 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40964/panev-an-r-package-for-a-pathway-based-network-visualization</link>
	<title><![CDATA[PANEV: an R package for a pathway-based network visualization]]></title>
	<description><![CDATA[<p><span>PANEV (PAthway NEtwork Visualizer) is an R package set for gene/pathway-based network visualization. Based on information available on KEGG, it visualizes genes within a network of multiple levels (from 1 to&nbsp;</span><em>n</em><span>) of interconnected upstream and downstream pathways. The network graph visualization helps to interpret functional profiles of a cluster of genes.</span></p>
<p><span><a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3371-7">https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3371-7</a></span></p><p>Address of the bookmark: <a href="https://github.com/vpalombo/PANEV" rel="nofollow">https://github.com/vpalombo/PANEV</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/18820/jrfsrf-at-university-of-calcutta</guid>
  <pubDate>Fri, 31 Oct 2014 08:53:10 -0500</pubDate>
  <link></link>
  <title><![CDATA[JRF/SRF at University of Calcutta]]></title>
  <description><![CDATA[
<p>Applications are invited to appear at a walk-in-interview for one post of Junior Research Fellow in the DBT(DBT Twinning NER) sponsored project entitled “Protein folding kinetics is a selection force on shaping codon usage bias in the high expression genes” in the room of the HOD, Department of Biotechnology and the Coordinator, DR. B. C. Guha Centre for Genetic Engineering and Biotechnology, University College of Science, 35 Ballygunge Circular Road, Kolkata 700019 on the 12th November, 2014 at 3:00 p.m.</p>

<p>Essential qualifications: First class M. Sc. in any branch of life sciences and qualified CSIR-UGC NET/GATE Examination.</p>

<p>Desirable qualifications: Practical experience in biochemical and biophysical studies of proteins</p>

<p>Emoluments: as per DBT norms</p>

<p>The project is tenable for two years, initially for one year.</p>

<p>Age: Below 28 years (relaxable in the case of SC/ST/OBC/women candidates)</p>

<p>Candidates are requested to bring two sets of complete applications on plain paper furnishing bio-data and copies of attested certificates along with originals (for verification) on the date of interview.</p>

<p>No TA/DA is admissible for candidates appearing at the interview.</p>

<p>Dr. Rajat Banerjee<br />Assistant Professor<br />Department of Biotechnology and<br />Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology<br />University College of Science<br />35, Ballygunge Circular Road<br />Kolkata 700019</p>

<p>Advertisement: www.caluniv.ac.in/news/jrf_biotech_2.pdf</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/3918/the-human-genome-project-video-3d-animation-introduction-low</guid>
	<pubDate>Sat, 24 Aug 2013 19:01:19 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/3918/the-human-genome-project-video-3d-animation-introduction-low</link>
	<title><![CDATA[The Human Genome Project Video   3D Animation Introduction Low)]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/YxoQFSBwyms" frameborder="0" allowfullscreen></iframe>]]></description>
	
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/19085/jrf-in-bioinformatics-pondicherry-university</guid>
  <pubDate>Sat, 08 Nov 2014 14:34:48 -0600</pubDate>
  <link></link>
  <title><![CDATA[JRF in Bioinformatics @ Pondicherry University]]></title>
  <description><![CDATA[
<p>Eager to get JRF job in Puducherry? Pondicherry University, School of Life Sciences, Centre for Bioinformatics has issued notification to fill the vacancy of JRF for DST sponsored research project entitled "Design and discovery of aurora kinase inhibitors as anti cancer drugs; application of computer aided drug design". It is good chance to get job with Pondicherry University and secure your future. Learn eligibility criteria and apply on or before 21.11.2014.</p>

<p>Required Skills:	no special skills required for this job post<br />Required Experience:	<br />Experience in computer aided drug design and or biochemical testing of natural or synthetic compounds is desired<br />Required Education:	<br />M.Sc. / M.Tech.</p>

<p>Required Job Profile:<br />Candidate must possess M.Sc. in bioinformatics or computational biology or biotechnology or any branch of life sciences or pharmacology or chemical sciences or M.Tech. in any branch of life sciences with at least fifty five percent marks with NET or GATE.</p>

<p>Desired Job Profile:<br />Candidate having experience in computer aided drug design and or biochemical testing of natural or synthetic compounds.</p>

<p>How to apply:<br />Eligible and interested candidates should need to appear for walk-in interview on 21.11.2014 at 1700 hrs at the above mentioned address.</p>

<p>Contact<br />Pondicherry University<br />Dr. S. Mohane Coumar, Assistant Professor &amp; Project Investigator, Centre for Bioinformatics, Pondicherry University, Puducherry 605 014<br />Email:registrar@pondiuni.edu.in<br />Phone:	0413-2655175</p>

<p>More at http://www.pondiuni.edu.in/sites/default/files/JRF-bioinfor-041114.pdf</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/21150/webinar-on-an-integrated-rna-and-dna-approach-to-unravel-genetic-regulation-in-cancer</guid>
	<pubDate>Wed, 11 Feb 2015 04:59:57 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/21150/webinar-on-an-integrated-rna-and-dna-approach-to-unravel-genetic-regulation-in-cancer</link>
	<title><![CDATA[Webinar on 'An integrated RNA and DNA approach to unravel genetic regulation in cancer']]></title>
	<description><![CDATA[<div><p><strong>Webinar on 'An integrated RNA and DNA approach to unravel genetic regulation in cancer'</strong></p><p><strong>Abstract</strong></p><p>Whole exome DNA sequencing (WES) or whole genome DNA sequencing (WGS) allows detection of mutations and polymorphisms in all exonic and genomic regions, respectively, while messenger RNA sequencing (RNA-Seq) enables quantitative analysis of gene expression. Mutations in the genome result in diverse transcriptional aberrations that can be missed in a stand-alone WES/WGS analysis. An integration of DNA variant analysis and RNA-Seq analysis enables one to investigate the consequences of genomic changes in the RNA transcripts including germline and somatic changes, imprinting, RNA editing and allele specific expression (ASE). In this webinar, we will demonstrate this integrated approach using Strand NGS to identify high confidence mutations, RNA editing events and ASE in cancer.</p><p><strong>Webinar Details</strong></p><table width="100%" border="1" cellspacing="0" cellpadding="0">
<tbody>
<tr>
<td valign="top">
<p style="text-align: center;"><br /> <strong>Sessions</strong></p>
</td>
<td valign="top">
<p style="text-align: center;"><a href="http://www.strand-ngs.com/webinar_registration"><strong>San Francisco Time<br /> (PST)</strong></a></p>
</td>
<td valign="top">
<p style="text-align: center;"><a href="http://www.strand-ngs.com/webinar_registration"><strong>Tokyo Time<br /> (GMT+09:00)</strong></a></p>
</td>
<td valign="top">
<p style="text-align: center;"><a href="http://www.strand-ngs.com/webinar_registration"><strong>Berlin Time<br /> (GMT+01:00)</strong></a></p>
</td>
<td valign="top">
<p style="text-align: center;"><a href="http://www.strand-ngs.com/webinar_registration"><strong>Mumbai Time<br /> (GMT+05:30)</strong></a></p>
</td>
</tr>
<tr>
<td>
<p style="text-align: center;"><a href="http://www.strand-ngs.com/webinar_registration"><strong>Session 1</strong></a></p>
</td>
<td valign="top">
<p style="text-align: center;">25 Feb&nbsp;<br /> 12:30 AM</p>
</td>
<td>
<p style="text-align: center;">25 Feb&nbsp;<br /> 5:30 PM</p>
</td>
<td>
<p style="text-align: center;">25 Feb&nbsp;<br /> 9:30 AM</p>
</td>
<td>
<p style="text-align: center;">25 Feb&nbsp;<br /> 2:00 PM</p>
</td>
</tr>
<tr>
<td valign="top">
<p style="text-align: center;"><a href="http://www.strand-ngs.com/webinar_registration"><strong>Session 2</strong></a></p>
</td>
<td valign="top">
<p style="text-align: center;">25 Feb&nbsp;<br /> 9:00 AM</p>
</td>
<td>
<p style="text-align: center;">26 Feb<br /> 2:00 AM</p>
</td>
<td>
<p style="text-align: center;">25 Feb&nbsp;<br /> 6:00 PM</p>
</td>
<td>
<p style="text-align: center;">25 Feb&nbsp;<br /> 10:30 PM</p>
</td>
</tr>
</tbody>
</table><p><strong style="font-size: 12.8000001907349px;">Register here: </strong><a href="http://www.strand-ngs.com/webinar_registration">http://www.strand-ngs.com/webinar_registration</a></p><p><strong>About Speaker:</strong></p><p>Dr. Veena Hedatale, has a PhD in Plant Genetics from The Radboud University, Netherlands focused on meiosis and recombination. Her prior academic experience at Cornell University was on genetic mapping and gene transformation in Rice. She has worked with Monsanto, and contributed to data mining, database development as well as gene/promoter/pathway discovery for traits related to yield and stress in crop species. At Strand, Veena has worked on Pharmacogenomic analysis of targets and Gene family analysis projects. Currently, she is part of the Strand NGS Application Science team and is involved in the analysis of next generation sequencing data.</p><p>Please feel free to contact us 24/5, for availing free online training or if you have any questions.</p></div><div><p><strong style="font-size: 12.8000001907349px;">Email:</strong> sales@strandngs.com</p><p><strong>Phone (USA):</strong> 1-800-752-9122</p><p><strong>Phone (ROW):</strong> +1-650-353-5060</p><p>&nbsp;</p></div>]]></description>
	<dc:creator>Yeshodari</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/19091/phd-opportunity-aicadd-fellowship-mhrd-govt-of-india-of-university-of-kerala</guid>
  <pubDate>Sat, 08 Nov 2014 15:16:24 -0600</pubDate>
  <link></link>
  <title><![CDATA[PhD opportunity / AiCADD fellowship (MHRD, Govt. of India) of University of Kerala.]]></title>
  <description><![CDATA[
<p>No. DCB/DBT-BIF/229 /14-15                                                                                     07-11-2014</p>

<p>Applications are invited for the AiCADD fellowship (MHRD, Govt. of India) of University of Kerala.</p>

<p>The terms and conditions of the fellowship is given below:</p>

<p>Ø The AiCADD PhD Fellowship scheme will be available for the students registered for full-time research      or   intending to register and pursue full time research at SIUCEB in frontier areas of bioinformatics,    computational biology, systems biology and closely allied areas with focus on Ayur-Informatics. </p>

<p>  Ø  The fellowships will be widely announced and open to students irrespective of geographical consideration.</p>

<p>  Ø  Candidates availing of this fellowship shall not be in receipt of any other fellowships concurrently.</p>

<p>  Ø  Researchers will be selected on the basis of research aptitude test and personal interview.</p>

<p>  Ø  Each selected student will be eligible for a monthly fellowship of Rs. 10,000/- for the 1st and 2nd year and Rs. 12,000/- for the 3rd year.</p>

<p>  Ø  Candidates must register for PhD within one year of joining, failing which the fellowship will have to be    remitted back.</p>

<p>  Ø  Candidates receiving the fellowship shall submit bi-annual reports of progress and the continuation of the fellowship will be based on the evaluation of the same.</p>

<p>  Ø  Candidates are also required to take up academic duties including teaching upto a maximum of 6 hours     per week, as directed by AiCADD Principal Investigator.</p>

<p> Interested candidates may please forward their application along with resume on or before 15th November 2014 in the following address. Principal Investigator, AiCADD Centre, Dept. of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram - 695581.</p>

<p>More at https://sites.google.com/site/centreforbioinformatics/announcements</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/29407/live-webinar-on-rna-seq-data-analysis-on-9-nov-2016</guid>
	<pubDate>Wed, 19 Oct 2016 05:25:27 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/29407/live-webinar-on-rna-seq-data-analysis-on-9-nov-2016</link>
	<title><![CDATA[Live Webinar on RNA-Seq Data Analysis on 9 Nov 2016]]></title>
	<description><![CDATA[<p><strong><a href="http://www.strand-ngs.com/webinar_registration">Live Webinar on RNA-Seq Data Analysis</a></strong></p><p><a href="http://www.strand-ngs.com/webinar_registration">Abstract: </a>Strand NGS supports an extensive workflow for the analysis and visualization of RNA-Seq data. The workflow includes Transcriptome / Genome alignment, Differential expression analysis with Statistical approach and Splicing events detection. Strand NGS also supports novel discovery like identification of novel genes, exons and Novel splice junctions, alongside it can also detect gene fusion events. Further downstream analysis such as GO and pathway analysis can be performed on the set of interesting genes. The product has an option to create pipelines for time consuming jobs which automates analysis and leaves more time for end data interpretation. This webinar will give an overview of the features in the RNA-Seq data analysis workflow in Strand NGS and also highlights on parameters within each feature that can be optimized depending on datasets and analysis needs.</p><p><a href="http://www.strand-ngs.com/webinar_registration">Speaker:</a> Mr. Sugandan Sivamani, Senior Application Scientist, Strand Life Sciences</p><p>Date: 9th Nov, <a href="http://www.strand-ngs.com/webinar_registration">Session 1</a> for SAPK/ APFO: 2:30 PM IST Date: 9th Nov, <a href="http://www.strand-ngs.com/webinar_registration">Session 2</a> for AFO/ EMEA: 9:00 AM PST</p><p>Register here <a href="http://www.strand-ngs.com/webinar_registration">http://www.strand-ngs.com/webinar_registration</a></p>]]></description>
	<dc:creator>Strand</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/33486/quick-next-generation-sequencing-ngs-terms-definition</guid>
	<pubDate>Fri, 09 Jun 2017 04:52:26 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/33486/quick-next-generation-sequencing-ngs-terms-definition</link>
	<title><![CDATA[Quick next generation sequencing (NGS) terms definition]]></title>
	<description><![CDATA[<p><strong>fragment size:</strong><span>&nbsp;the Illumina WGS protocol generates paired-end reads from both ends of longer fragments. The lengths of these fragments are assumed to be sampled from a normal distribution. Therefore, in the absence of structural variants, mapping locations of the paired ends span within an interval [&delta;min,&delta;max]. Most (&gt;90%) of paired-end reads are sampled from no-SV regions, therefore the fragment size distribution can be learned empirically for each WGS data set separately.</span><br /><br /><strong>concordant reads:</strong><span>&nbsp;a read pair is called concordant if they can be mapped to the reference genome as &ldquo;expected&rdquo;: (a) mapped to opposing strands where the upstream read is mapped to the forward strand and the downstream read is mapped to the reverse strand2, (b) the distance between ends is between the minimum and maximum expected fragment size.</span><br /><br /><strong>discordant reads:</strong><span>&nbsp;briefly, any non-concordant read pair is considered discordant. Note that, by definition, the discordant read pairs signal potential SVs. The sequence signature produced by these type of reads is known as read-pair signature.</span><br /><br /><strong>split reads:</strong><span>&nbsp;a read that can only be mapped to the reference genome by breaking into two sub-reads is called a split-read. These types of reads also indicate a potential SV or a short insertion or deletion (indel).</span><br /><br /><strong>read depth:</strong><span>&nbsp;number of reads that map within a region of the genome. Overall genome-wide read depth is also referred to as depth of coverage. It is expected that the number of reads that &ldquo;cover&rdquo; each base-pair to follow a Poisson distribution. Therefore, if the read depth over a certain region deviates significantly from this distribution, it signals for a potential copy number variation (CNV).</span></p>]]></description>
	<dc:creator>Neel</dc:creator>
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