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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/42359?offset=260</link>
	<atom:link href="https://bioinformaticsonline.com/related/42359?offset=260" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/2518/genome-browsers</guid>
	<pubDate>Fri, 16 Aug 2013 19:04:47 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/2518/genome-browsers</link>
	<title><![CDATA[Genome Browsers]]></title>
	<description><![CDATA[<p>Genome Browser is the platform/database used for searching and retreiving sequences and annotation of genomes belong to various eukaryotes, prokaryotes, etc.</p><p>Following are the weblink for different available browsers:</p><p><a href="http://www.ensembl.org/index.html">http://www.ensembl.org/index.html</a></p><p><a href="http://ensemblgenomes.org/">http://ensemblgenomes.org/</a></p><p><a href="http://genome.ucsc.edu/">http://genome.ucsc.edu/</a></p><p><a href="http://www.ncbi.nlm.nih.gov/genome">http://www.ncbi.nlm.nih.gov/genome</a></p><p><a href="http://www.ebi.ac.uk/genomes/">http://www.ebi.ac.uk/genomes/</a></p><p><a href="http://flybase.org/">http://flybase.org/</a></p><p><a href="http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi">http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi</a></p><p><a href="http://www.sanger.ac.uk/resources/databases/">http://www.sanger.ac.uk/resources/databases/</a></p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/4297/how-genes-are-regulated-transcription-factors</guid>
	<pubDate>Thu, 05 Sep 2013 16:54:19 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/4297/how-genes-are-regulated-transcription-factors</link>
	<title><![CDATA[How Genes are Regulated: Transcription Factors]]></title>
	<description><![CDATA[<iframe src="http://player.vimeo.com/video/30034882?byline=0" width="" height="" frameborder="0" webkitAllowFullScreen allowFullScreen></iframe>Each cell in our body inherits the same master copy of DNA, but different cell types use it differently. Transcription Factors help influence which genes are used in which cell. Understanding how these dynamic proteins physically interact with DNA allows us to better understand and model their binding to DNA and their regulation of gene expression.  Scientific Direction by the Wasserman Lab at the University of British Columbia: http://www.cmmt.ubc.ca/research/investigators/wasserman/lab  Animation and editing by Blair Lyons of Stroma Studios: http://www.stromastudios.com]]></description>
	
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/4943/molecular-genetics-lecture</guid>
	<pubDate>Fri, 27 Sep 2013 04:24:45 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/4943/molecular-genetics-lecture</link>
	<title><![CDATA[Molecular Genetics Lecture]]></title>
	<description><![CDATA[<p><span>"Robert Sapolsky makes interdisciplinary connections between behavioral biology and molecular genetic influences. He relates protein synthesis and point mutations to microevolutionary change, and discusses conflicting theories of gradualism and punctuated equilibrium and the influence of epigenetics on development theories."&nbsp;</span></p>
<p><span>"<span><strong>Robert Sapolsky</strong> is an American neuroendocrinologist, professor of biology, neuroscience, and neurosurgery at Stanford University, researcher and author" ----Wikipedia</span></span></p><p>Address of the bookmark: <a href="http://www.youtube.com/watch?v=_dRXA1_e30o" rel="nofollow">http://www.youtube.com/watch?v=_dRXA1_e30o</a></p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/8639/edit-dna</guid>
	<pubDate>Wed, 05 Mar 2014 02:27:54 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/8639/edit-dna</link>
	<title><![CDATA[Edit DNA !!!]]></title>
	<description><![CDATA[<p>A genome-engineering tool known as Crispr may allow scientists to alter the DNA of humans, animals and plants, a research breakthrough that promises to make a significant impact on science and fighting diseases, according to a <a href="http://www.nytimes.com/2014/03/04/health/a-powerful-new-way-to-edit-dna.html">March 3 story in the <em>New York Times</em></a>. Scientists hope Crispr might also be used for genomic surgery, as it were, to correct errant genes that cause disease.</p><p>A rescently publication paper ( http://jb.asm.org/content/169/12/5429.long )shows significance of an unusual repeated DNA sequences next to a gene in a common bacterium, and their scientific significance. The sequences, it turns out, are part of a sophisticated immune system that bacteria use to fight viruses. And that system, whose very existence was unknown until about seven years ago, may provide scientists with unprecedented power to rewrite the code of life. This means a genome can be edited, much as a writer might change words or fix spelling errors. It allows &ldquo;customizing the genome of any cell or any species at will,&rdquo;.</p><p>Reference:</p><p>http://www.prweb.com/releases/2014/03/prweb11636031.htm</p><p>http://www.nytimes.com/2014/03/04/health/a-powerful-new-way-to-edit-dna.html?hpw&amp;rref=health</p><p>http://jb.asm.org/content/169/12/5429.long</p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/23838/scripted-dna</guid>
	<pubDate>Mon, 17 Aug 2015 17:44:04 -0500</pubDate>
	<link>https://bioinformaticsonline.com/file/view/23838/scripted-dna</link>
	<title><![CDATA[Scripted DNA !!!]]></title>
	<description><![CDATA[<p>As per bioinformatician DNA is partially scripted ;) You dont believe in it. Please have a look at image carefully:)</p>]]></description>
	<dc:creator>Jit</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/23838" length="13498" type="image/gif" />
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/33874/dna-testing-companies-around-the-globe</guid>
	<pubDate>Thu, 13 Jul 2017 04:44:03 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/33874/dna-testing-companies-around-the-globe</link>
	<title><![CDATA[DNA testing companies around the globe !]]></title>
	<description><![CDATA[<p>It was realized in the 1940s that DNA molecules are passed down through the generations of a family. In 1953 Watson and Crick elucidated the chemical structure of this molecule as a twisted ladder (a &lsquo;helix&rsquo;) made of two strands. DNA occurs in all the cells of our body, it is our blueprint! The strands of DNA contain information in the form of a code, which in turn determines our individual traits and characteristics. This code, the genetic code, is the order of four types of DNA building block. When the two strands of DNA separate, each building block (&lsquo;base&rsquo;) accurately templates a corresponding base on the newly made strand of DNA so that information is not lost but is instead duplicated and preserved.</p><p>Testing for similarities between DNA (deoxyribonucleic acid) samples from two people allows family relationships to be established &ndash; or disproved &ndash; to an extraordinarily high degree of certainty. A common use for a DNA test is to establish if a man is the biological father of a child; this is known as a paternity test. However, there are other uses for the science of DNA testing (also called genotyping), these include forensic analysis of human DNA samples, and tracking relationships amongst domesticated animals.</p><p>The order in which the bases occur in DNA is referred to as the DNA sequence. Each person is unique and just as people differ in their fingerprints, they also have a unique and slightly different DNA sequence. Half of a person&rsquo;s DNA is received from their mother, and half is received from the father. However, while fingerprints have no value for establishing family relationships, the minor variations in DNA sequence are extraordinarily useful for this purpose. All cells of our body contain DNA, skin cells from the lining of the cheek provide a simple and convenient source of material.</p><p>DNA is purified from these cells and the minor variations are read out as a type of bar-code by a machine. When the net DNA &lsquo;barcodes&rsquo; from family members are lined up next to each other it becomes clear when a child is related to biological parents because half the stripes in the bar-code like signature will line up with those of the mother, and half will line up with those of the father. On the other hand, in the absence of a biological relationship, the DNA signatures from a child and from a potential parent are not found to have 50% in common. It may be appreciated that DNA testing is the most convenient and scientifically accurate method of determining relationships between people.</p><p>Following are the list of companies who qssist in DNA testing:</p><h2><span>DNA testing companies</span></h2><ul>
<li><a href="https://isogg.org/wiki/23andMe" title="23andMe">23andMe</a>&nbsp;(admixture, adoption, deep ancestry, genealogy) (health and trait reports also available in some countries)</li>
<li><a href="https://24genetics.com/">24 genetics</a>&nbsp;(admixture, exome sequencing, health, paternity, pharmacogenetics, whole genome sequencing) A company catering for the Spanish market</li>
<li><a href="http://www.africanancestry.com/">African Ancestry</a>&nbsp;(deep ancestry)</li>
<li><a href="http://www.africandna.com/">AfricanDNA</a>&nbsp;(<a href="https://isogg.org/wiki/Family_Tree_DNA" title="Family Tree DNA">FTDNA</a>&nbsp;affiliate) (admixture, deep ancestry, genealogy)</li>
<li><a href="https://isogg.org/wiki/AncestrybyDNA" title="AncestrybyDNA">AncestrybyDNA</a>&nbsp;(admixture, deep ancestry)</li>
<li><a href="https://isogg.org/wiki/AncestryDNA" title="AncestryDNA">AncestryDNA</a>, a subsidiary of Ancestry.com (admixture, adoption, genealogy)</li>
<li><a href="https://atlas.ru/">Atlas Biomed</a>&nbsp;(deep ancestry, diet, health and traits, sport) A test catering for the Russian market</li>
<li><a href="https://isogg.org/wiki/BritainsDNA" title="BritainsDNA">BritainsDNA</a>&nbsp;(formerly Ethnoancestry) (admixture, deep ancestry)</li>
<li><a href="https://isogg.org/wiki/Centrillion_Biosciences" title="Centrillion Biosciences">Centrillion Biosciences</a>&nbsp;(aka TribeCode) (admixture, deep ancestry)</li>
<li>CymruDNAWales - see&nbsp;<a href="https://isogg.org/wiki/BritainsDNA" title="BritainsDNA">BritainsDNA</a></li>
<li><a href="https://www.dantelabs.com/">Dante Labs</a>&nbsp;(exome sequencing, health, whole genome sequencing) A test aimed at the European market</li>
<li><a href="http://www.dnaancestry.ae/">DNA Ancestry and Family Origin</a>&nbsp;(<a href="https://isogg.org/wiki/Family_Tree_DNA" title="Family Tree DNA">FTDNA</a>&nbsp;affiliate in the Middle East) (admixture, adoption, deep ancestry, full mtDNA sequencing, genealogy)</li>
<li><a href="http://dnaconsultants.com/">DNA Consultants</a>&nbsp;(admixture, deep ancestry)</li>
<li><a href="https://isogg.org/wiki/DNA_Tribes" title="DNA Tribes">DNA Tribes</a>&nbsp;(admixture)</li>
<li><a href="https://www.dna-worldwide.com/">DNA Worldwide</a>&nbsp;(formerly a&nbsp;<a href="https://isogg.org/wiki/Family_Tree_DNA" title="Family Tree DNA">FTDNA partner</a>. See also&nbsp;<a href="https://www.livingdna.com/">Living DNA</a>)</li>
<li>Ethnoancestry - see&nbsp;<a href="https://isogg.org/wiki/BritainsDNA" title="BritainsDNA">BritainsDNA</a></li>
<li><a href="https://isogg.org/wiki/Family_Tree_DNA" title="Family Tree DNA">Family Tree DNA</a>&nbsp;(admixture, adoption, deep ancestry, full mtDNA sequencing, genealogy, Y chromosome sequencing)</li>
<li><a href="https://isogg.org/wiki/Full_Genomes_Corporation" title="Full Genomes Corporation">Full Genomes Corporation</a>&nbsp;(whole genome sequencing, Y-chromosome sequencing)</li>
<li><a href="https://isogg.org/wiki/Gene_by_Gene" title="Gene by Gene">Gene by Gene</a>&nbsp;- the parent company of&nbsp;<a href="https://isogg.org/wiki/Family_Tree_DNA" title="Family Tree DNA">Family Tree DNA</a>&nbsp;which now incorporates the companies previously known as DNA Traits, DNA DTC and DNA Findings (research, health, exome sequencing, whole genome sequencing)</li>
<li><a href="https://isogg.org/wiki/Genebase" title="Genebase">Genebase</a>&nbsp;(deep ancestry, genealogy)</li>
<li><a href="https://www.genotek.ru/">GenoTek</a>&nbsp;(admixture, genealogy, diet and fitness, family planning, health, talents and sports) A company catering for the Russian market</li>
<li><a href="https://isogg.org/wiki/Genographic_Project" title="Genographic Project">Genographic Project</a>&nbsp;(admixture, deep ancestry)</li>
<li><a href="http://www.genos.co/">Genos Research Inc</a>&nbsp;(DTC whole exome sequencing; consumer focused healthcare big data spin out from Complete Genomics; Note: no genetic genealogy focus or tools)</li>
<li><a href="http://www.guardiome.com/">Guardiome</a>&nbsp;(admixture, whole genome sequencing and interpretation)</li>
<li><a href="https://www.helix.com/">Helix</a>&nbsp;(exome sequencing) US supplier of the&nbsp;<a href="https://isogg.org/wiki/Genographic_Project" title="Genographic Project">Genographic Project</a>&nbsp;Geno 2.0 Next Generation test</li>
<li><a href="http://www.igenea.com/">iGENEA</a>&nbsp;(<a href="https://isogg.org/wiki/Family_Tree_DNA" title="Family Tree DNA">FTDNA</a>&nbsp;affiliate) (admixture, deep ancestry, genealogy)</li>
<li>IrelandsDNA - See&nbsp;<a href="https://isogg.org/wiki/BritainsDNA" title="BritainsDNA">BritainsDNA</a>&nbsp;(formerly Ethnoancestry)</li>
<li><a href="https://isogg.org/wiki/BritainsDNA" title="BritainsDNA">MyDNA Global</a>&nbsp;- a new name for&nbsp;<a href="https://isogg.org/wiki/BritainsDNA" title="BritainsDNA">BritainsDNA</a></li>
<li><a href="https://www.livingdna.com/">Living DNA</a>&nbsp;(admixture, deep ancestry) See also&nbsp;<a href="https://www.dna-worldwide.com/">DNA Worldwide</a></li>
<li><a href="https://www.myheritage.com/dna">MyHeritage DNA</a>&nbsp;(admixture, genealogy)</li>
<li><a href="https://isogg.org/wiki/Oxford_Ancestors" title="Oxford Ancestors">Oxford Ancestors</a>&nbsp;(deep ancestry)</li>
<li><a href="http://www.rootsforreal.com/">Roots for Real</a>&nbsp;(admixture, deep ancestry)</li>
<li><a href="https://isogg.org/wiki/ScotlandsDNA" title="ScotlandsDNA">ScotlandsDNA</a>&nbsp;- (formerly Ethnoancestry) (admixture, deep ancestry)</li>
<li><a href="https://isogg.org/wiki/Sorenson_Genomics" title="Sorenson Genomics">Sorenson Genomics</a>&nbsp;(laboratory services)</li>
<li><a href="http://www.suregenomics.com/">Sure Genomics</a>&nbsp;(whole genome sequencing and interpretation)</li>
<li>TribeCode See&nbsp;<a href="https://isogg.org/wiki/Centrillion_Biosciences" title="Centrillion Biosciences">Centrillion Biosciences</a></li>
<li><a href="https://www.veritasgenetics.com/">Veritas Genetics</a>&nbsp;(whole genome sequencing and interpretation)</li>
<li><a href="http://xcode.in/">Xcode</a>&nbsp;(Diet and Fitness, Precision medicine, Genotyping, Sequencing, Interpretation)</li>
<li>YorkshiresDNA - See&nbsp;<a href="https://isogg.org/wiki/BritainsDNA" title="BritainsDNA">BritainsDNA</a>&nbsp;(formerly Ethnoancestry)</li>
<li><a href="https://www.wegene.com/">WeGene</a>&nbsp;(admixture, deep ancestry, health, sports, traits) A test tailored for the East Asian market</li>
<li><a href="https://isogg.org/wiki/YSEQ" title="YSEQ">YSEQ</a>&nbsp;(custom Y-SNPs, Y-STRs, SNP panels, whole genome sequencing)</li>
</ul>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34867/magic-blast-a-tool-for-mapping-large-next-generation-rna-or-dna-sequencing-runs-against-a-whole-genome-or-transcriptome</guid>
	<pubDate>Tue, 26 Dec 2017 22:23:39 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34867/magic-blast-a-tool-for-mapping-large-next-generation-rna-or-dna-sequencing-runs-against-a-whole-genome-or-transcriptome</link>
	<title><![CDATA[Magic-BLAST: a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.]]></title>
	<description><![CDATA[<p>Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of RNA-seq, locating the candidate introns and adding up the score of all exons. This is very different from other versions of BLAST, where each exon is scored as a separate hit and read-pairing is ignored.</p>
<p>Magic-BLAST incorporates within the NCBI BLAST code framework ideas developed in the NCBI Magic pipeline, in particular hit extensions by local walk and jump&nbsp;<a href="http://www.ncbi.nlm.nih.gov/pubmed/26109056">(http://www.ncbi.nlm.nih.gov/pubmed/26109056)</a>, and recursive clipping of mismatches near the edges of the reads, which avoids accumulating artefactual mismatches near splice sites and is needed to distinguish short indels from substitutions near the edges.</p><p>Address of the bookmark: <a href="https://ncbi.github.io/magicblast/" rel="nofollow">https://ncbi.github.io/magicblast/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36456/alpaca-a-hybrid-strategy-for-assembly-of-genomic-dna-shotgun-sequencing-reads</guid>
	<pubDate>Mon, 30 Apr 2018 04:38:40 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36456/alpaca-a-hybrid-strategy-for-assembly-of-genomic-dna-shotgun-sequencing-reads</link>
	<title><![CDATA[ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.]]></title>
	<description><![CDATA[<p><span>ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set.&nbsp;</span></p>
<p><span>Detail paper at&nbsp;https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3927-8</span></p><p>Address of the bookmark: <a href="https://github.com/VicugnaPacos/ALPACA" rel="nofollow">https://github.com/VicugnaPacos/ALPACA</a></p>]]></description>
	<dc:creator>Seema Singh</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37915/dna-nucleotide-counter</guid>
	<pubDate>Fri, 12 Oct 2018 04:37:01 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37915/dna-nucleotide-counter</link>
	<title><![CDATA[DNA Nucleotide Counter]]></title>
	<description><![CDATA[<p style="margin: 2px 5px 4px 6px; color: #000011; font-size: 12px; font-style: normal; font-weight: 400; text-align: justify;">DNA Nucleotide Counter is delivered in a DNA Baser package together with other free molecular biology tools.<span>&nbsp;</span><a href="http://www.dnabaser.com/download/biology-tools-package-download-count.html">Download</a><span>&nbsp;</span>the package and double click it. The programs inside the package will be extracted to the destination folder (specified by you). Go to the destination folder&nbsp;and double click the program you want to use.</p>
<p style="margin: 2px 5px 4px 6px; color: #000011; font-size: 12px; font-style: normal; font-weight: 400; text-align: justify;">It<span>&nbsp;</span><a href="http://www.dnabaser.com/download/install-anywhere.html">installs in any computer</a><span>&nbsp;</span>even if you don't have administrator rights!</p><p>Address of the bookmark: <a href="http://www.dnabaser.com/download/DNA-Counter/index.html" rel="nofollow">http://www.dnabaser.com/download/DNA-Counter/index.html</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/40566/the-el-sherif-group-chair-of-developmental-biology-department-of-biology-phd-position</guid>
  <pubDate>Sun, 19 Jan 2020 10:06:37 -0600</pubDate>
  <link></link>
  <title><![CDATA[The El-Sherif Group, Chair of Developmental Biology, Department of Biology - PhD Position]]></title>
  <description><![CDATA[
<p>El-Sherif lab studies how genes are regulated to mediate patterning in Development. We use live and super-resolution imaging in addition to computational modeling to understand transcription dynamics at the single-cell level in three model systems: the fruit fly Drosophila melanogaster, the beetle Tribolium castaneum, and embryonic bodies derived from embryonic mouse stem cells.</p>

<p>In this project, you will use single-molecule techniques to label mRNA and DNA in (live and fixed) Drosophila embryos and fixed embryonic bodies. You will also use super-resolution microscopy to visualize protein condensates. Co-localization dynamics reflecting DNA-protein bindings and DNA looping events will be detected, analyzed, and used to test computational models of gene transcription.</p>

<p>Qualification:<br />MSc degree (or equivalent) in Biology, Biophysics, or Bioengineering</p>

<p>Experience in one or more of these areas: (1) molecular cloning, (2) imaging, (3) image analysis (using Matlab/Python/Java), (4) microfluidics, and (5) computational modeling.</p>

<p>How to Apply?<br />Send (1) your CV, (2) summary of research experience, and (3) email addresses of at least 2 references to ezzat.el-sherif@fau.de. Title your email ‘Transcription PhD Position’.</p>

<p>salary Grade.: E13<br />Total Time: 3 Jahre<br />Start: 01.01.2020.<br />End: 31.3.2020.</p>

<p>Address:<br />Dr. El-Sherif, Ezzat<br />Department Biologie<br />Professur für Zoologie (Entwicklungsbiologie) (Prof. Dr. Klingler)<br />Telefon 09131/85-28068, Fax 09131/85-28040, E-Mail: ezzat.el-sherif@fau.de</p>
]]></description>
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