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<channel>
	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/32018?offset=60</link>
	<atom:link href="https://bioinformaticsonline.com/related/32018?offset=60" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30966/maftools</guid>
	<pubDate>Thu, 16 Feb 2017 11:16:01 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30966/maftools</link>
	<title><![CDATA[MafTools]]></title>
	<description><![CDATA[<p>maftools - An R package to summarize, analyze and visualize MAF files. <a href="https://github.com/PoisonAlien/maftools#introduction"></a>Introduction.</p>
<p>With advances in Cancer Genomics, Mutation Annotation Format (MAF) is being widley accepted and used to store variants detected. <a href="http://cancergenome.nih.gov">The Cancer Genome Atlas</a> Project has seqenced over 30 different cancers with sample size of each cancer type being over 200. The <a href="https://wiki.nci.nih.gov/display/TCGA/TCGA+MAF+Files">resulting data</a> consisting of genetic variants is stored in the form of <a href="https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+%28MAF%29+Specification">Mutation Annotation Format</a>. This package attempts to summarize, analyze, annotate and visualize MAF files in an efficient manner either from TCGA sources or any in-house studies as long as the data is in MAF format. Maftools can also handle ICGC Simple Somatic Mutation format.</p>
<p>maftools is on <img src="https://assets-cdn.github.com/images/icons/emoji/unicode/1f449.png" alt=":point_right:" width="20" height="20" style="border: 0px;"> <a href="http://biorxiv.org/content/early/2016/05/11/052662">bioRxiv</a> <img src="https://assets-cdn.github.com/images/icons/emoji/bowtie.png" alt=":bowtie:" title=":bowtie:" width="20" height="20" style="border: 0px; text-align: absmiddle;"></p>
<p>Please cite the below if you find this tool useful for you.</p>
<p>Mayakonda, A. and H.P. Koeffler, Maftools: Efficient analysis, visualization and summarization of MAF files from large-scale cohort based cancer studies. bioRxiv, 2016. doi: <a href="http://dx.doi.org/10.1101/052662">http://dx.doi.org/10.1101/052662</a></p><p>Address of the bookmark: <a href="https://github.com/PoisonAlien/maftools" rel="nofollow">https://github.com/PoisonAlien/maftools</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/31566/software-and-tools-to-detect-structure-variation-with-long-reads</guid>
	<pubDate>Wed, 15 Mar 2017 14:31:09 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/31566/software-and-tools-to-detect-structure-variation-with-long-reads</link>
	<title><![CDATA[Software and Tools to detect structure variation with long reads !!]]></title>
	<description><![CDATA[<p>Uncovering the connection between genetics and heritable diseases requires an approach that looks at all the variant bases and types in a genome. While a PacBio&nbsp;<em>de novo</em>&nbsp;assembly resolves the most novel SV variants. 8-10X PacBio coverage of single genomes or trios reveals triple the SVs detectable by short-read data.</p><p>With&nbsp;<span style="text-decoration: underline;"><a href="http://www.pacb.com/smrt-science/">Single Molecule, Real-Time (SMRT) Sequencing</a></span>, you can access structural variations having a broad range of sizes, types, and GC content with the ability to:</p><ul>
<li>Uncover missing heritability linked to structural variation</li>
<li>Unambiguously identify genomic context and variant breakpoints at the sequence level to unravel the genetic etiology of disease</li>
<li>Resolve structural variation across the complete size spectrum with basepair resolution</li>
</ul><p>Following are the SV tools, which can assist you to achieve your goal.</p><p><strong>Sniffles:</strong>&nbsp;Structural variation caller using third generation sequencing</p><p>Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Please note the current version of Sniffles requires sorted output from BWA-MEM (use -M and -x parameter) or NGM-LR with the optional SAM attributes enabled!&nbsp;</p><p>More at&nbsp;https://github.com/fritzsedlazeck/Sniffles</p><p><strong style="font-size: 12.8px;"><br />MultiBreak-SV:</strong> It identifies structural variants from next-generation paired end data, third-generation long read data, or data from a combination of sequencing platforms.</p><p>There are two pieces of software in this release: (1) a pre-processor that takes machineformat (.m5) BLASR files, and (2) MultiBreak-SV. For installation and usage instructions, see doc/MultiBreakSV-Manual.txt.</p><p>More at&nbsp;https://github.com/raphael-group/multibreak-sv</p><p><strong style="font-size: 12.8px;"><br />Parliament:</strong>&nbsp;A Structural Variation Tool. Why ask a single sv-detection approach to find every variant when you can have a parliament of tools deciding?</p><p>Publication about the algorithm and &ldquo;&hellip;the first long-read characterization of structural variation in a diploid human personal genome&hellip;&rdquo; (HS1011) -&nbsp;<a href="http://www.biomedcentral.com/1471-2164/16/286">&ldquo;Assessing structural variation in a personal genome&mdash;towards a human reference diploid genome&rdquo;</a></p><p>More at&nbsp;https://sourceforge.net/projects/parliamentsv/</p><p>https://www.dnanexus.com/papers/Parliament_Info_Sheet.pdf</p><p><br /><strong>PBHoney:</strong>&nbsp;the structural variation discovery tool&nbsp;<br /><br />PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). PBHoney considers both intra-read discordance and soft-clipped tails of long reads to identify structural variants.</p><p>Read The Paper&nbsp;<a href="http://www.biomedcentral.com/1471-2105/15/180/abstract" target="_blank">http://www.biomedcentral.com/1471-2105/15/180/abstract</a></p><p>More at&nbsp;https://sourceforge.net/projects/pb-jelly/</p><p><strong><br />SMRT-SV:</strong> Structural variant and indel caller for PacBio reads</p><p>Structural variant (SV) and indel caller for PacBio reads based on methods from&nbsp;<a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13907.html">Chaisson et al. 2014</a>.</p><p>SMRT-SV provides an official software package for tools described in&nbsp;<a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13907.html">Chaisson et al. 2014</a>&nbsp;and adds several key features including the following.</p><ul>
<li>Unified variant calling user interface with built-in cluster compute support</li>
<li>Small indel calling (2-49 bp)</li>
<li>Improved inversion calling (<code>screenInversions</code>)</li>
<li>Quality metric for SV calls based on number of local assemblies supporting each call</li>
<li>Higher sensitivity for SV calls using tiled local assemblies across the entire genome instead of "signature" regions</li>
<li>Genotyping of SVs with Illumina paired-end reads from WGS samples</li>
</ul><p>More at&nbsp;https://github.com/EichlerLab/pacbio_variant_caller</p>]]></description>
	<dc:creator>Archana Malhotra</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/32131/wgs-celera-assembler-version-83rc2</guid>
	<pubDate>Mon, 10 Apr 2017 04:45:40 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32131/wgs-celera-assembler-version-83rc2</link>
	<title><![CDATA[WGS Celera Assembler version 8.3rc2]]></title>
	<description><![CDATA[<p>These are release notes for Celera Assembler version 8.3rc2, which was released on May 24, 2015.<br><br>This distribution package provides a stable, tested, documented version of the software.&nbsp; The distribution is usable on most Unix-like platforms, and some platforms have pre-compiled binary distributions ready for installation.<br><br>The source code package includes full source code (revision 4627), Makefiles, and scripts.&nbsp; A subset of the kmer package (http://kmer.sourceforge.net/, version r1994), used by some modules of Celera Assembler, is included.&nbsp; This distribution includes [http://samtools.sourceforge.net/ SAMtools], [http://www.cbcb.umd.edu/software/jellyfish/ Jellyfish 2.0], [https://github.com/pbjd/pbutgcns PBUTGCNS], [https://github.com/PacificBiosciences/pbdagcon PBDAGCON], [https://github.com/PacificBiosciences/BLASR BLASR], and parts of the [https://github.com/PacificBiosciences/FALCON/tree/v0.1.3 Falcon assembler].<br><br>Full documentation can be found online at http://wgs-assembler.sourceforge.net/.</p>
<p>Interesting scripts within it</p>
<p>urbe@urbo214b[bin] ls&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;&nbsp;&nbsp; []<br>-rwxrwxr-x 1 urbe urbe&nbsp; 11K Apr 10 11:41 addCNSToStore<br>-rwxrwxr-x 1 urbe urbe 575K Apr 10 11:41 addReadsToUnitigs<br>-rwxrwxr-x 1 urbe urbe 128K Apr 10 11:41 analyzeBest<br>-rwxrwxr-x 1 urbe urbe 257K Apr 10 11:41 analyzePosMap<br>-rwxrwxr-x 1 urbe urbe 1,5M Apr 10 11:41 analyzeScaffolds<br>-rwxrwxr-x 1 urbe urbe 224K Apr 10 11:41 asmOutputFasta<br>-rwxrwxr-x 1 urbe urbe 448K Apr 10 11:41 asmOutputStatistics<br>-rwxrwxr-x 1 urbe urbe 2,4K Apr 10 11:41 asmToAGP.pl<br>-rwxrwxr-x 1 urbe urbe 7,6M Apr 10 11:41 blasr<br>-rwxrwxr-x 1 urbe urbe 1,6M Apr 10 11:41 bogart<br>-rwxrwxr-x 1 urbe urbe 183K Apr 10 11:41 bogus<br>-rwxrwxr-x 1 urbe urbe 272K Apr 10 11:41 bogusness<br>-rwxrwxr-x 1 urbe urbe 247K Apr 10 11:41 buildPosMap<br>-rwxrwxr-x 1 urbe urbe 213K Apr 10 11:41 buildRefContigs<br>-rwxrwxr-x 1 urbe urbe 990K Apr 10 11:41 buildUnitigs<br>-rwxrwxr-x 1 urbe urbe&nbsp; 18K Apr 10 11:41 ca2ace.pl<br>-rwxrwxr-x 1 urbe urbe&nbsp; 12K Apr 10 11:41 caqc_help.ini<br>-rwxrwxr-x 1 urbe urbe&nbsp; 61K Apr 10 11:41 caqc.pl<br>-rwxrwxr-x 1 urbe urbe&nbsp; 23K Apr 10 11:41 cat-corrects<br>-rwxrwxr-x 1 urbe urbe&nbsp; 24K Apr 10 11:41 cat-erates<br>-rwxrwxr-x 1 urbe urbe 1,9M Apr 10 11:41 cgw<br>-rwxrwxr-x 1 urbe urbe 1,4M Apr 10 11:41 cgwDump<br>-rwxrwxr-x 1 urbe urbe 204K Apr 10 11:41 chimChe<br>-rwxrwxr-x 1 urbe urbe 201K Apr 10 11:40 chimera<br>-rwxrwxr-x 1 urbe urbe 220K Apr 10 11:41 classifyMates<br>-rwxrwxr-x 1 urbe urbe 201K Apr 10 11:41 classifyMatesApply<br>-rwxrwxr-x 1 urbe urbe 215K Apr 10 11:41 classifyMatesPairwise<br>-rwxrwxr-x 1 urbe urbe 366K Apr 10 11:41 computeCoverageStat<br>-rwxrwxr-x 1 urbe urbe 9,8K Apr 10 11:41 convert-fasta-to-v2.pl<br>-rwxrwxr-x 1 urbe urbe&nbsp; 48K Apr 10 11:41 convertOverlap<br>-rwxrwxr-x 1 urbe urbe 119K Apr 10 11:41 convertSamToCA<br>-rwxrwxr-x 1 urbe urbe&nbsp; 20K Apr 10 11:41 convertToPBCNS<br>-rwxrwxr-x 1 urbe urbe 197K Apr 10 11:41 correct-frags<br>-rwxrwxr-x 1 urbe urbe 259K Apr 10 11:41 correct-olaps<br>-rwxrwxr-x 1 urbe urbe 520K Apr 10 11:41 correctPacBio<br>-rwxrwxr-x 1 urbe urbe 540K Apr 10 11:41 ctgcns<br>-rwxrwxr-x 1 urbe urbe 162K Apr 10 11:40 deduplicate<br>-rwxrwxr-x 1 urbe urbe&nbsp; 37K Apr 10 11:41 demotePosMap<br>-rwxrwxr-x 1 urbe urbe 1,5M Apr 10 11:41 dumpCloneMiddles<br>-rwxrwxr-x 1 urbe urbe 124K Apr 10 11:41 dumpPBRLayoutStore<br>-rwxrwxr-x 1 urbe urbe 1,3M Apr 10 11:41 dumpSingletons<br>-rwxrwxr-x 1 urbe urbe 171K Apr 10 11:41 erate-estimate<br>-rwxrwxr-x 1 urbe urbe 221K Apr 10 11:40 estimate-mer-threshold<br>-rwxrwxr-x 1 urbe urbe 1,5M Apr 10 11:41 extendClearRanges<br>-rwxrwxr-x 1 urbe urbe 1,3M Apr 10 11:41 extendClearRangesPartition<br>-rwxrwxr-x 1 urbe urbe 205K Apr 10 11:40 extractmessages<br>-rwxrwxr-x 1 urbe urbe 7,2M Apr 10 11:41 falcon_sense<br>-rwxrwxr-x 1 urbe urbe 9,8K Apr 10 11:41 fastaToCA<br>-rwxrwxr-x 1 urbe urbe 124K Apr 10 11:40 fastqAnalyze<br>-rwxrwxr-x 1 urbe urbe 137K Apr 10 11:40 fastqSample<br>-rwxrwxr-x 1 urbe urbe&nbsp; 62K Apr 10 11:40 fastqSimulate<br>-rwxrwxr-x 1 urbe urbe 121K Apr 10 11:40 fastqSimulate-sort<br>-rwxrwxr-x 1 urbe urbe 246K Apr 10 11:40 fastqToCA<br>-rwxrwxr-x 1 urbe urbe 140K Apr 10 11:41 filterOverlap<br>-rwxrwxr-x 1 urbe urbe 341K Apr 10 11:40 finalTrim<br>-rwxrwxr-x 1 urbe urbe 228K Apr 10 11:41 fixUnitigs<br>-rwxrwxr-x 1 urbe urbe 147K Apr 10 11:40 fragmentDepth<br>-rwxrwxr-x 1 urbe urbe&nbsp; 29K Apr 10 11:41 fragsInVars<br>-rwxrwxr-x 1 urbe urbe 545K Apr 10 11:41 frgs2clones<br>-rwxrwxr-x 1 urbe urbe 398K Apr 10 11:40 gatekeeper<br>-rwxrwxr-x 1 urbe urbe 139K Apr 10 11:40 gatekeeperbench<br>-rwxrwxr-x 1 urbe urbe 167K Apr 10 11:40 gkpStoreCreate<br>-rwxrwxr-x 1 urbe urbe 147K Apr 10 11:40 gkpStoreDumpFASTQ<br>-rwxrwxr-x 1 urbe urbe 184K Apr 10 11:41 greedyFragmentTiling<br>-rwxrwxr-x 1 urbe urbe 1,6K Apr 10 11:41 greedy_layout_to_IUM<br>-rwxrwxr-x 1 urbe urbe 142K Apr 10 11:40 initialTrim<br>-rwxrwxr-x 1 urbe urbe 967K Apr 10 11:41 jellyfish<br>-rwxrwxr-x 1 urbe urbe 219K Apr 10 11:41 markRepeatUnique<br>-rwxrwxr-x 1 urbe urbe 273K Apr 10 11:40 markUniqueUnique<br>-rwxrwxr-x 1 urbe urbe 114K Apr 10 11:40 mercy<br>-rwxrwxr-x 1 urbe urbe 3,8K Apr 10 11:41 mergeqc.pl<br>-rwxrwxr-x 1 urbe urbe 422K Apr 10 11:40 merTrim<br>-rwxrwxr-x 1 urbe urbe 125K Apr 10 11:40 merTrimApply<br>-rwxrwxr-x 1 urbe urbe 376K Apr 10 11:40 meryl<br>-rwxrwxr-x 1 urbe urbe 176K Apr 10 11:41 metagenomics_ovl_analyses<br>-rwxrwxr-x 1 urbe urbe 297K Apr 10 11:41 olap-from-seeds<br>-rwxrwxr-x 1 urbe urbe 275K Apr 10 11:41 outputLayout<br>-rwxrwxr-x 1 urbe urbe 229K Apr 10 11:41 overlapInCore<br>-rwxrwxr-x 1 urbe urbe 144K Apr 10 11:40 overlap_partition<br>-rwxrwxr-x 1 urbe urbe 179K Apr 10 11:41 overlapStats<br>-rwxrwxr-x 1 urbe urbe 179K Apr 10 11:41 overlapStore<br>-rwxrwxr-x 1 urbe urbe 153K Apr 10 11:41 overlapStoreBucketizer<br>-rwxrwxr-x 1 urbe urbe 175K Apr 10 11:41 overlapStoreBuild<br>-rwxrwxr-x 1 urbe urbe&nbsp; 33K Apr 10 11:41 overlapStoreIndexer<br>-rwxrwxr-x 1 urbe urbe&nbsp; 48K Apr 10 11:41 overlapStoreSorter<br>-rwxrwxr-x 1 urbe urbe 604K Apr 10 11:40 overmerry<br>lrwxrwxrwx 1 urbe urbe&nbsp;&nbsp;&nbsp; 4 Apr 10 11:41 pacBioToCA -&gt; PBcR<br>-rwxrwxr-x 1 urbe urbe 131K Apr 10 11:41 PBcR<br>-rwxrwxr-x 1 urbe urbe 2,9M Apr 10 11:41 pbdagcon<br>-rwxrwxr-x 1 urbe urbe 1,9M Apr 10 11:41 pbutgcns<br>-rwxrwxr-x 1 urbe urbe 201K Apr 10 11:40 remove_fragment<br>-rwxrwxr-x 1 urbe urbe 153K Apr 10 11:40 removeMateOverlap<br>-rwxrwxr-x 1 urbe urbe 2,5K Apr 10 11:41 replaceUIDwithName-fastq<br>-rwxrwxr-x 1 urbe urbe 1,2K Apr 10 11:41 replaceUIDwithName-posmap<br>-rwxrwxr-x 1 urbe urbe 1,3M Apr 10 11:41 resolveSurrogates<br>-rwxrwxr-x 1 urbe urbe 139K Apr 10 11:41 rewriteCache<br>-rwxrwxr-x 1 urbe urbe 232K Apr 10 11:41 runCA<br>-rwxrwxr-x 1 urbe urbe&nbsp; 88K Apr 10 11:41 runCA-dedupe<br>-rwxrwxr-x 1 urbe urbe&nbsp; 14K Apr 10 11:41 runCA-overlapStoreBuild<br>-rwxrwxr-x 1 urbe urbe 3,6K Apr 10 11:41 run_greedy.csh<br>-rwxrwxr-x 1 urbe urbe 297K Apr 10 11:40 sffToCA<br>-rwxrwxr-x 1 urbe urbe&nbsp; 13K Apr 10 11:40 show-corrects<br>-rwxrwxr-x 1 urbe urbe 557K Apr 10 11:41 splitUnitigs<br>-rwxrwxr-x 1 urbe urbe 1,4M Apr 10 11:41 terminator<br>drwxrwxr-x 2 urbe urbe 4,0K Apr 10 11:41 TIGR<br>-rwxrwxr-x 1 urbe urbe 526K Apr 10 11:41 tigStore<br>-rwxrwxr-x 1 urbe urbe&nbsp; 35K Apr 10 11:41 tracearchiveToCA<br>-rwxrwxr-x 1 urbe urbe&nbsp; 35K Apr 10 11:41 tracedb-to-frg.pl<br>-rwxrwxr-x 1 urbe urbe&nbsp; 44K Apr 10 11:41 trimFastqByQVWindow<br>-rwxrwxr-x 1 urbe urbe&nbsp; 18K Apr 10 11:40 uidclient<br>-rwxrwxr-x 1 urbe urbe 589K Apr 10 11:41 unitigger<br>-rwxrwxr-x 1 urbe urbe&nbsp; 42K Apr 10 11:40 upgrade-v8-to-v9<br>-rwxrwxr-x 1 urbe urbe&nbsp; 42K Apr 10 11:40 upgrade-v9-to-v10<br>-rwxrwxr-x 1 urbe urbe&nbsp; 854 Apr 10 11:41 utg2fasta<br>-rwxrwxr-x 1 urbe urbe 731K Apr 10 11:41 utgcns<br>-rwxrwxr-x 1 urbe urbe 561K Apr 10 11:41 utgcnsfix<br><br><br></p><p>Address of the bookmark: <a href="http://wgs-assembler.sourceforge.net/wiki/index.php/Main_Page" rel="nofollow">http://wgs-assembler.sourceforge.net/wiki/index.php/Main_Page</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/43272/bioinformatics-head-bioinformatics-manager-iii-cancer-genomics-research-laboratory-at-frederick-national-laboratory</guid>
  <pubDate>Wed, 18 Aug 2021 00:19:48 -0500</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics Head (Bioinformatics Manager III), Cancer Genomics Research Laboratory at  Frederick National Laboratory]]></title>
  <description><![CDATA[
<p>Frederick National Laboratory seeking an enthusiastic, creative, and seasoned bioinformatics professional to join our leadership team and direct the exceptional Bioinformatics Group at the Cancer Genomics Research Laboratory (CGR).  CGR has a diverse team of bioinformatics and computational scientists that support all areas of bioinformatics and data analysis (infrastructure, data QC, pipeline development and maintenance, data curation and sharing, methodology development, statistical analyses, machine learning approaches, and scientific interpretation).</p>

<p>More at https://leidosbiomed.csod.com/ats/careersite/jobdetails.aspx?site=4&amp;c=leidosbiomed&amp;id=2040</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/5209/anders-krogh-lab</guid>
  <pubDate>Mon, 30 Sep 2013 19:07:40 -0500</pubDate>
  <link></link>
  <title><![CDATA[Anders Krogh Lab]]></title>
  <description><![CDATA[
<p>In a lot of my work in bioinformatics, I have been using hidden Markov models (HMMs). As a postdoc with David Haussler at UCSC we developed the so-called profile HMMs (refs). Since then I have applied HMMs to membrane proteins (refs) and gene identification (refs) and have worked on methods for such things as discriminative estimation of HMMs (refs) and alternative decoding algorithms etc. (refs).</p>

<p>Now my main interests are in gene regulation, where we work on promoter analysis; non-coding RNA, where miRNAs and structure prediction are the main areas; and protein structure, where the group is working on methods for structure prediction from sequence. To read more about these topics, please see the research pages. </p>

<p>Lab page @ http://wiki.binf.ku.dk/User:Krogh</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43943/bioinformatics-tutorial</guid>
	<pubDate>Mon, 22 Aug 2022 23:56:22 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43943/bioinformatics-tutorial</link>
	<title><![CDATA[Bioinformatics Tutorial !]]></title>
	<description><![CDATA[<p>This site aims to be a useful resource for bioinformatics beginners. Feel free to jump right in with the section most relevant to you, and if you're not sure, then the place to start is definitely Unix <p>Address of the bookmark: <a href="https://astrobiomike.github.io/" rel="nofollow">https://astrobiomike.github.io/</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/4946/crcri-bioinfomatics-walk-in-on-08102013</guid>
  <pubDate>Fri, 27 Sep 2013 10:59:53 -0500</pubDate>
  <link></link>
  <title><![CDATA[CRCRI Bioinfomatics Walk In on 08.10.2013]]></title>
  <description><![CDATA[
<p>Walk-in-Interview for recruitment of one Project Fellow for a period of 10 months purely on temporary basis is proposed to be held at Central Tuber Crops Research Institute, Sreekariyam, Thiruvananthapuram for a KSCSTE funded project entitled “PARTICIPATORY DEVELOPMENT OF A WEB BASED USER FRIENDLY CASSAVA EXPERT SYSTEM”</p>

<p>Salary: Rs. 10,000/- per month.</p>

<p>Age limit: 35 for men and 40 for women &amp; SC/ST.</p>

<p>Qualification: First class in M. Sc (Agriculture)/MCA/M.Sc (IT)/ M. Sc (Computer Application)/M.Sc (Bioinformatics)/M.Sc (Geoinformatics).</p>

<p>Desirable: Two years experience in web design and web programming.</p>

<p>Date &amp; time of interview: 08.10.2013, 10 am</p>

<p>Interested candidates may appear for an interview at this institute along with their application in plain paper containing the following particulars viz. (1) Name (2) Father/Husband/Guardian’s Name (3) date of birth &amp; age as on 01.10.2013 (4) Permanent address (5) Address for communication (6) Email address and Telephone No. with code (7) Qualification (8) National fellowship like ICAR/CSIR/UGC etc. if any (9) Whether SC/ST/OBC (10) Details of experience (Attested copies of degree certificate, proof of age, mark sheets). Original certificates should be produced for verification.</p>

<p>No TA/DA will be admissible to the candidates attending the test. The selected candidate will have to join immediately.</p>

<p>Advertisement: http://www.ctcri.org/careers/mithra_SRF.doc</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/44226/rotifers-lab</guid>
  <pubDate>Wed, 08 Mar 2023 23:23:14 -0600</pubDate>
  <link></link>
  <title><![CDATA[Rotifers Lab]]></title>
  <description><![CDATA[
<p>For scientists in the MBL’s Gribble Lab, the rotifer (Brachionus manjavacas) is used as a model organism to study evolution, stress responses, the biology of aging, and maternal effects. Rotifers are small, easy to grow in the lab, have a short lifespan, and share many of their genes with humans. That makes them ideal specimens in which to address questions relevant to human health as well as understand basic biological and evolutionary processes. Brachionus rotifers produces eggs that can be completely dried and frozen for decades, then hatch within a day when exposed to water and light.</p>

<p>https://www.mbl.edu/research/research-organisms/rotifer<br />https://gribblebiolab.org/</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/5187/bioinformatics-algorithms-part-1-with-pavel-pevzner-phillip-e-c-compeau</guid>
	<pubDate>Mon, 30 Sep 2013 11:34:09 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/5187/bioinformatics-algorithms-part-1-with-pavel-pevzner-phillip-e-c-compeau</link>
	<title><![CDATA[Bioinformatics Algorithms (Part 1)  with Pavel  Pevzner, Phillip E. C. Compeau,]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/t5t_nfzdzEg" frameborder="0" allowfullscreen></iframe><p>The course Bioinformatics Algorithms (Part 1) by Pavel Pevzner, Phillip E. C. Compeau, and Nikolay Vyahhi from University of California, San Diego will be offered free of charge to everyone on the Coursera platform. Sign up at http://www.coursera.org/course/bioinformatics.</p>]]></description>
	
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/5255/walk-in-interview-indian-agricultural-statistics-research-institute</guid>
  <pubDate>Wed, 02 Oct 2013 15:40:17 -0500</pubDate>
  <link></link>
  <title><![CDATA[Walk-in-Interview @ Indian Agricultural Statistics Research Institute]]></title>
  <description><![CDATA[
<p>Indian Agricultural Statistics Research Institute<br />Library Avenue, Pusa, New Delhi – 110012</p>

<p>Walk-in-Interview</p>

<p>Walk-in-interview will be held on October 5, 2013 at 10:00 A.M. at IASRI, New Delhi for a project “A New Distributed Computing Framework for Data Mining” funded by Department of Electronics and Information Technology, Government of India for the following posts. The appointment will be on contractual basis upto 14th October, 2015 or till the termination of the project whichever is earlier and the incumbent shall not have any claim for regular appointment under ICAR.</p>

<p>Research Associate</p>

<p>    Ph.D. in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent or</p>

<p>    Post-Graduation in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent with 1st Division and at least two years of research experience</p>

<p>     Knowledge of Statistical Analysis /Bioinformatics tools for computational genomics.</p>

<p>     Knowledge of R/Perl programming language</p>

<p>Research Associate</p>

<p>    Ph.D. in Computer Science/ Computer Application / Bioinformatics/ Agricultural<br />    Statistics/ Statistics or equivalent or</p>

<p>    Post-Graduation in Computer Science/ Computer Application /Bioinformatics/ Agricultural Statistics/ Statistics or equivalent with 1st Division and at least two years of research experience</p>

<p>     Expertise in Java programming.<br />     Knowledge of system administration and networking under Linux environment.<br />     Knowledge of parallel programming and cluster computing.</p>

<p>Emoluments for Research Associate: Consolidated Rs:24000/- per month + HRA (for Ph.D. Degree holders) and Rs:23000/- per month + HRA (for Master’s Degree holders)</p>

<p>Age Limit: Age should be not more than 40 years (5 years relaxation for  SC/ST/women candidates and 3 years for OBC candidates as on date of interview).</p>

<p>Interested candidates are requested to appear for Walk-in-Interview on the date and time as specified above in Room No. 106, Training Cum Administrative Block of the Institute along with their application giving bio-data with attested copies of certificates, degrees, testimonials, etc. and one passport size photograph.</p>

<p>Original certificates/ Degrees are needed to be produced at the time of interview.</p>

<p>No T.A. /D.A. will be paid for appearing in the interview.</p>

<p>Advertisement: http://www.iasri.res.in/employment/employment.htm</p>
]]></description>
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