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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/5812?</link>
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	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/4763/inner-life-of-a-cell-full-versionmkv</guid>
	<pubDate>Mon, 23 Sep 2013 18:09:41 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/4763/inner-life-of-a-cell-full-versionmkv</link>
	<title><![CDATA[Inner Life Of A Cell - Full Version.mkv]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/yKW4F0Nu-UY" frameborder="0" allowfullscreen></iframe>Работа аппарата Гольджи и ЭПС при дифференцировке лейкоцита]]></description>
	
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	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/5731/influenza-animation-flu-virus-mechanism</guid>
	<pubDate>Thu, 17 Oct 2013 19:43:13 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/5731/influenza-animation-flu-virus-mechanism</link>
	<title><![CDATA[Influenza animation - flu virus mechanism]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/YSgkoldBNkI" frameborder="0" allowfullscreen></iframe>Animation of the mechanism of an influenza virus and how Crucell's antibodies target the HA1 proteins on the virus and prevent further spread of influenza. 

Client: Crucell
Direction, Design & Animation: Daniel Lim, 2Preform
Music & Sound Design: Javier Barrero, Logical Disorder
Production Company: David Hager, All Terrain Media]]></description>
	
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	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/4633/cancer-growth-animation</guid>
	<pubDate>Fri, 20 Sep 2013 06:16:51 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/4633/cancer-growth-animation</link>
	<title><![CDATA[Cancer Growth Animation]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/WXTsxPPcTEs" frameborder="0" allowfullscreen></iframe>This video demonstrates how cancer growth happens in human body.]]></description>
	
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	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/5580/pharmacogenomics-at-mayo-clinic</guid>
	<pubDate>Mon, 14 Oct 2013 16:21:45 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/5580/pharmacogenomics-at-mayo-clinic</link>
	<title><![CDATA[Pharmacogenomics at Mayo Clinic]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/fGjG_9EEeeA" frameborder="0" allowfullscreen></iframe>The right drug, at the right dose, for the right patient. Mayo Clinic uses the latest technologies to understand how drugs will work in individual patients, maximizing drug efficacy and minimizing the potential for side effects.]]></description>
	
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	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/5934/retrovirus-replication-3d-animation</guid>
	<pubDate>Sat, 26 Oct 2013 09:07:25 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/5934/retrovirus-replication-3d-animation</link>
	<title><![CDATA[Retrovirus Replication 3D Animation]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/HhhRQ4t95OI" frameborder="0" allowfullscreen></iframe>The example used is the HIV Lentivirus. This video does a great job describing "complex" retrovirus transcription in a visually appealing way that is sufficient in detail for upper level coursework and possibly graduate coursework.
 * Modes of action for some anti-viral drugs are also described.

NOTE:  The viral genome in the form of DNA stays in the cell's chromosome! This is the predominant reason for the persistence of retroviral infections.]]></description>
	
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	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/13878/janet-iwasa-how-animations-can-help-scientists-test-a-hypothesis</guid>
	<pubDate>Sun, 10 Aug 2014 15:26:04 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/13878/janet-iwasa-how-animations-can-help-scientists-test-a-hypothesis</link>
	<title><![CDATA[Janet Iwasa: How animations can help scientists test a hypothesis]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/YvyeI-Axb70" frameborder="0" allowfullscreen></iframe>3D animation can bring scientific hypotheses to life. Molecular biologist (and TED Fellow) Janet Iwasa introduces a new open-source animation software designed just for scientists.

TEDTalks is a daily video podcast of the best talks and performances from the TED Conference, where the world's leading thinkers and doers give the talk of their lives in 18 minutes (or less). Look for talks on Technology, Entertainment and Design -- plus science, business, global issues, the arts and much more.
Find closed captions and translated subtitles in many languages at http://www.ted.com/translate

Follow TED news on Twitter: http://www.twitter.com/tednews
Like TED on Facebook: https://www.facebook.com/TED

Subscribe to our channel: http://www.youtube.com/user/TEDtalksDirector]]></description>
	
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/4357/flow-cytometry-data-analysis</guid>
	<pubDate>Sat, 07 Sep 2013 18:09:48 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/4357/flow-cytometry-data-analysis</link>
	<title><![CDATA[Flow cytometry data analysis]]></title>
	<description><![CDATA[<p>Flow cytometry&nbsp;is a&nbsp;biophysical laser based instrument used in various purposes like&nbsp;cell counting,&nbsp;cell sorting,&nbsp;biomarker&nbsp;detection, etc.</p>
<p>More on this:</p>
<p><a href="http://bioinformatics.ca/workshops/2013/flow-cytometry-data-analysis-using-r-2013">http://bioinformatics.ca/workshops/2013/flow-cytometry-data-analysis-using-r-2013</a></p>
<p><a href="http://pyvideo.org/video/1234/fcm-a-python-library-for-flow-cytometry">http://pyvideo.org/video/1234/fcm-a-python-library-for-flow-cytometry</a></p><p>Address of the bookmark: <a href="http://www.ehu.es/biologiacomputacional/reprints/nmeth.2365.pdf" rel="nofollow">http://www.ehu.es/biologiacomputacional/reprints/nmeth.2365.pdf</a></p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/34463/single-cell-rnaseq-data-analysis-tutorial</guid>
	<pubDate>Mon, 27 Nov 2017 16:24:29 -0600</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/34463/single-cell-rnaseq-data-analysis-tutorial</link>
	<title><![CDATA[Single Cell RNAseq data analysis tutorial !!]]></title>
	<description><![CDATA[<ul>
<li>A major breakthrough (replaced microarrays) in the late 00&rsquo;s and has been widely used since</li>
<li>Measures the&nbsp;average expression level&nbsp;for each gene across a large population of input cells</li>
<li>Useful for comparative transcriptomics, e.g.&nbsp;samples of the same tissue from different species</li>
<li>Useful for quantifying expression signatures from ensembles, e.g.&nbsp;in disease studies</li>
<li>Insufficient&nbsp;for studying heterogeneous systems, e.g.&nbsp;early development studies, complex tissues (brain)</li>
<li>Does&nbsp;not&nbsp;provide insights into the stochastic nature of gene expression</li>
</ul><p>Following are the useful links:</p><p><a href="http://hemberg-lab.github.io/scRNA.seq.course/scRNA-seq-course.pdf" target="_blank">Single Cell RNAseq data analysis Tutorial</a></p><p><a href="https://f1000research.com/articles/5-2122/v2" target="_blank">A step-by-step workflow for low-level analysis of single-cell RNA-seq data</a></p><p><a href="https://www.bioconductor.org/help/workflows/simpleSingleCell/" target="_blank">A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor</a></p><p>SCell: single-cell RNA-seq analysis software</p><p><a href="https://github.com/diazlab/SCell">https://github.com/diazlab/SCell</a></p><p>Beta-Poisson model for single-cell RNA-seq data analyses</p><p><a href="https://github.com/nghiavtr/BPSC">https://github.com/nghiavtr/BPSC</a></p><p>Sincera: A Computational Pipeline for Single Cell RNA-Seq Profiling Analysis</p><p><a href="https://research.cchmc.org/pbge/sincera.html">https://research.cchmc.org/pbge/sincera.html</a></p><p>SC3 &ndash; consensus clustering of single-cell RNA-Seq data</p><p><a href="http://biorxiv.org/content/early/2016/09/02/036558">http://biorxiv.org/content/early/2016/09/02/036558</a></p><p>Citrus: A toolkit for single cell sequencing analysis</p><p><a href="http://biorxiv.org/content/early/2016/09/14/045070">http://biorxiv.org/content/early/2016/09/14/045070</a></p><p>Single-Cell Resolution of Temporal Gene Expression during Heart Development</p><p><a href="http://www.cell.com/developmental-cell/fulltext/S1534-5807%2816%2930682-7">http://www.cell.com/developmental-cell/fulltext/S1534-5807(16)30682-7</a></p><p>Scalable latent-factor models applied to single-cell RNA-seq data separate biological drivers from confounding effects</p><p><a href="http://biorxiv.org/content/early/2016/11/15/087775">http://biorxiv.org/content/early/2016/11/15/087775</a></p><p>Single cell transcriptomes identify human islet cell signatures and reveal cell-type-specific expression changes in type 2 diabetes</p><p><a href="http://genome.cshlp.org/content/early/2016/11/18/gr.212720.116.abstract">http://genome.cshlp.org/content/early/2016/11/18/gr.212720.116.abstract</a></p><p>SCODE: An efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation</p><p><a href="http://biorxiv.org/content/early/2016/11/21/088856">http://biorxiv.org/content/early/2016/11/21/088856</a></p><p>SCOUP is a probabilistic model to analyze single-cell expression data during differentiation</p><p><a href="https://github.com/hmatsu1226/SCOUP">https://github.com/hmatsu1226/SCOUP</a></p><p>scLVM is a modelling framework for single-cell RNA-seq data</p><p><a href="https://github.com/PMBio/scLVM">https://github.com/PMBio/scLVM</a></p><p>Selective Locally linear Inference of Cellular Expression Relationships (SLICER) algorithm for inferring cell trajectories</p><p><a href="https://github.com/jw156605/SLICER">https://github.com/jw156605/SLICER</a></p><p>SinQC: A Method and Tool to Control Single-cell RNA-seq Data Quality</p><p><a href="http://www.morgridge.net/SinQC.html">http://www.morgridge.net/SinQC.html</a></p><p>TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis</p><p><a href="https://github.com/zji90/TSCAN">https://github.com/zji90/TSCAN</a></p><p>Visualization and cellular hierarchy inference of single-cell data using SPADE</p><p><a href="http://www.nature.com/nprot/journal/v11/n7/full/nprot.2016.066.html">http://www.nature.com/nprot/journal/v11/n7/full/nprot.2016.066.html</a></p><p>OEFinder: Identify ordering effect genes in single cell RNA-seq data</p><p><a href="https://github.com/lengning/OEFinder">https://github.com/lengning/OEFinder</a></p>]]></description>
	<dc:creator>Robert M Willioms</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/3917/the-story-of-you-encode-and-the-human-genome</guid>
	<pubDate>Sat, 24 Aug 2013 18:49:03 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/3917/the-story-of-you-encode-and-the-human-genome</link>
	<title><![CDATA[The Story of You: ENCODE and the human genome]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/TwXXgEz9o4w" frameborder="0" allowfullscreen></iframe><p>Ever since a monk called Mendel started breeding pea plants we've been learning about our genomes. In 1953, Watson, Crick and Franklin described the structure of the molecule that makes up our genomes: the DNA double helix. Then, in 2001, scientists wrote down the entire 3-billion letter code contained in the average human genome. Now they're trying to interpret that code; to work out how it's used to make different types of cells and different people. The ENCODE project, as it's called, is the latest chapter in the story of you. To read the ENCODE research papers and more, visit http://www.nature.com/ENCODE</p>]]></description>
	
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	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/4634/immune-response-to-cancer-cells-awesome</guid>
	<pubDate>Fri, 20 Sep 2013 06:20:47 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/4634/immune-response-to-cancer-cells-awesome</link>
	<title><![CDATA[Immune response to cancer cells! AWESOME]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/C6YuBh-wAPQ" frameborder="0" allowfullscreen></iframe><p>Awesome viddeo explaining the way in which the antibody, HuLuc 63, appears to induce anti-tumor effects by binding to a protein that is only expressed on the surface of myeloma cells. This initiates antibody-dependent cellular cytotoxicity activity that kills myeloma cells and leaves healthy cells intact.</p>]]></description>
	
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