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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/44525?offset=20</link>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/4546/sowdhamini-lab</guid>
  <pubDate>Sun, 15 Sep 2013 09:19:12 -0500</pubDate>
  <link></link>
  <title><![CDATA[SOWDHAMINI Lab]]></title>
  <description><![CDATA[
<p>Genome sequencing projects have enormous potential for benefiting human endeavors. However, just as acquiring a language's vocabulary does not enable one to speak it, databases that list the amino acid composition of proteins do not directly tell us much about these proteins' higher-level structure and function. The most productive way to indirectly exploit these databases has been to start with the small number of proteins that are fully-characterised and to assume that other "similar" proteins will have a related structure and function. Proteins with very similar amino acid sequence are "no-brainers", but the real test, which our group largely focuses on, is to detect the "essential" similarity in proteins whose non-critical sections have experienced random rearrangements during evolution. In such cases functionally similar proteins may have less than 25% sequence overlap.</p>

<p>More @ http://www.ncbs.res.in/sowdhamini/groups_sowdhamini.htm</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37794/mimicree2-genome-wide-forward-simulations-of-evolve-and-resequencing-studies</guid>
	<pubDate>Fri, 28 Sep 2018 09:21:14 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37794/mimicree2-genome-wide-forward-simulations-of-evolve-and-resequencing-studies</link>
	<title><![CDATA[MimicrEE2: Genome-wide forward simulations of Evolve and Resequencing studies]]></title>
	<description><![CDATA[<p><span>MimicrEE2, a multi-threaded Java program for genome-wide forward simulations of evolving populations. MimicrEE2 enables the convenient usage of available genomic resources, supports biological particulars of model organism frequently used in E&amp;R studies and offers a wide range of different adaptive models (selective sweeps, polygenic adaptation, epistasis). MimicrEE2 runs on any computer with Java installed. It is distributed under the GPLv3 license at&nbsp;</span><a href="https://sourceforge.net/projects/mimicree2/">https://sourceforge.net/projects/mimicree2/</a><span>.</span></p><p>Address of the bookmark: <a href="https://sourceforge.net/projects/mimicree2/" rel="nofollow">https://sourceforge.net/projects/mimicree2/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40140/alf-a-simulation-framework-for-genome-evolution</guid>
	<pubDate>Tue, 22 Oct 2019 22:05:58 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40140/alf-a-simulation-framework-for-genome-evolution</link>
	<title><![CDATA[ALF--a simulation framework for genome evolution.]]></title>
	<description><![CDATA[<p style="color: #000000; font-size: small; font-style: normal; font-weight: 400; text-align: -webkit-left;"><span style="color: #4d4d4d; font-size: small; font-style: normal; font-weight: 400; text-align: left; background-color: #ffffff; float: none;">Artificial Life Framework (ALF)</span> simulates a root genome into a number of related genomes. Result files include the resulting gene sequences, true tree and true MSAs. A description of ALF can be found in the following article:</p>
<p style="color: #000000; font-size: small; font-style: normal; font-weight: 400; text-align: -webkit-left;">Daniel A Dalquen, Maria Anisimova, Gaston H Gonnet, Christophe Dessimoz: ALF - A Simulation Framework for Genome Evolution.<span>&nbsp;</span><em>Mol Biol Evol</em>, 29(4):1115-1123, April 2012.<br><a href="http://mbe.oxfordjournals.org/content/29/4/1115" target="_blank">http://mbe.oxfordjournals.org/content/29/4/1115</a></p><p>Address of the bookmark: <a href="http://alfsim.org/#index" rel="nofollow">http://alfsim.org/#index</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/42907/lecturer-in-evolutionary-biology-bioinformatics-at-department-of-zoology-te-tari-matai-kararehe-division-of-sciences-te-rohe-a-ahikaroa</guid>
  <pubDate>Tue, 23 Feb 2021 02:05:15 -0600</pubDate>
  <link></link>
  <title><![CDATA[Lecturer in Evolutionary Biology (Bioinformatics) at DEPARTMENT of ZOOLOGY | TE TARI MĀTAI KARAREHE DIVISION of SCIENCES | TE ROHE A AHIKAROA]]></title>
  <description><![CDATA[
<p>DEPARTMENT of ZOOLOGY | TE TARI MĀTAI KARAREHE<br />DIVISION of SCIENCES | TE ROHE A AHIKAROA</p>

<p>Applications are invited for the position of Lecturer in Evolutionary Biology (Bioinformatics).</p>

<p>We are seeking a person with a relevant doctorate, and demonstrated potential to develop as an outstanding researcher and teacher in evolutionary bioinformatics in the Department of Zoology. The position affords an exciting opportunity for an emerging scholar to research and teach in a vibrant and diverse Department. The successful candidate will develop a transformative and collaborative research program, supporting the university's commitment to excellence in research.</p>

<p>Your skills and experience</p>

<p>A PhD with a background in analysis of high-throughput sequencing data and evolutionary biology.<br />Knowledge of and familiarity with a range of bioinformatics skills, concepts, and practices as they relate to the biology of animals, including genomic, transcriptomic and metabarcoding data analyses.<br />A strong interest, and experience, in research and teaching of bioinformatics and evolutionary genomics.<br />An ability to contribute to teaching and learning environments that support engagement of students and staff with bioinformatics and genomics.<br />Be committed to and or have established connections or track record of working with national and local bioinformaticians. <br />Be committed to being a productive collaborator with a track record of working collegially.<br />Further details</p>

<p>This is a confirmation-path (tenure track) position at the level of Lecturer. The successful candidate is expected to take up duties by 1 July 2021.</p>

<p>To see a full job description and to apply online go to: https://otago.taleo.net/careersection/2/jobdetail.ftl?job=2100342</p>
]]></description>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44219/chromosome-breakpoint-a-breakup-to-remember</guid>
	<pubDate>Tue, 07 Mar 2023 13:31:54 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44219/chromosome-breakpoint-a-breakup-to-remember</link>
	<title><![CDATA[Chromosome breakpoint - a breakup to remember]]></title>
	<description><![CDATA[<div><div><div><div><div><div><div><div><div><div><p>Chromosome breakpoint refers to the physical location where a chromosome is broken and rearranged. Chromosome breakage can occur spontaneously or be induced by environmental factors such as radiation, chemicals, or viruses. The rearrangement of genetic material resulting from a chromosome breakpoint can have important consequences, including the development of genetic diseases, chromosomal abnormalities, or cancer.</p><p>Chromosome breakpoints can occur in two ways: interstitial or terminal. Interstitial breakpoints occur within the chromosome, while terminal breakpoints occur at the end of the chromosome. Terminal breakpoints can lead to the loss of genetic material, whereas interstitial breakpoints can result in the duplication or deletion of genetic material.</p><p>Chromosome breakpoints can be detected using a variety of techniques, including cytogenetic analysis, fluorescence in situ hybridization (FISH), and molecular methods such as polymerase chain reaction (PCR) and next-generation sequencing (NGS). These techniques can also help identify the exact location of the breakpoint and the nature of the rearrangement, such as translocations, inversions, deletions, or duplications.</p><p>Translocations are one of the most common types of chromosome rearrangements caused by breakpoints. In a translocation, genetic material is exchanged between two different chromosomes, resulting in a balanced or unbalanced distribution of genetic material. Unbalanced translocations can cause genetic diseases or developmental abnormalities, while balanced translocations can be inherited without any apparent phenotypic effects.</p><p>Inversions occur when a chromosome segment is inverted, resulting in a change in the order of genetic material. Inversions can be pericentric, involving the centromere, or paracentric, not involving the centromere. Inversions can cause genetic diseases or phenotypic effects if they disrupt the function of essential genes or regulatory elements.</p><p>Deletions and duplications are caused by interstitial breakpoints that result in the loss or gain of genetic material. Deletions can cause genetic diseases or developmental abnormalities if they involve essential genes or regulatory elements. Duplications can also have phenotypic effects, depending on the location and size of the duplicated segment.</p><p>Chromosome breakpoints can also be involved in the formation of complex chromosomal rearrangements, such as ring chromosomes or dicentric chromosomes. These complex rearrangements can have important clinical implications, as they can cause genetic diseases or cancer.</p><p>In conclusion, chromosome breakpoints are important genetic events that can lead to the rearrangement of genetic material and have important clinical implications. The detection and characterization of chromosome breakpoints using cytogenetic, molecular, and genomic methods are essential for the diagnosis, prognosis, and treatment of genetic diseases and cancer. Further research is needed to understand the molecular mechanisms underlying chromosome breakage and to develop new therapies targeting these events.</p></div></div></div></div></div></div></div></div></div></div>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/2699/translational-bioinformatics-transforming-300-billion-points-of-data</guid>
	<pubDate>Tue, 20 Aug 2013 19:03:47 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/2699/translational-bioinformatics-transforming-300-billion-points-of-data</link>
	<title><![CDATA[Translational Bioinformatics: Transforming 300 Billion Points of Data]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/o4KNG7nd938" frameborder="0" allowfullscreen></iframe>Translational Bioinformatics: Transforming 300 Billion Points of Data into Diagnostics, Therapeutics, and New Insights into Disease      
      
Air date:  Wednesday, June 20, 2012, 3:00:00 PM
Time displayed is Eastern Time, Washington DC Local  
 
Description:  There is an urgent need to translate genome-era discoveries into clinical utility, but the difficulties in making bench-to-bedside translations haven't been well described. The nascent field of translational bioinformatics may help. Dr. Butte's lab at Stanford University builds and applies tools that convert more than 300 billion points of molecular, clinical, and epidemiological data (measured by researchers and clinicians over the past decade) into diagnostics, therapeutics, and new insights into disease. Dr. Butte, a bioinformatician and pediatric endocrinologist, will highlight his lab's work on using publicly available molecular measurements to find new uses for drugs, discovering new treatable mechanisms of disease in type 2 diabetes, and evaluating patients presenting with whole genomes sequenced. 

The NIH Wednesday Afternoon Lecture Series includes weekly scientific talks by some of the top researchers in the biomedical sciences worldwide. 

For more information, visit: 
The NIH Director's Wednesday Afternoon Lecture Series  
Author:  Atul Butte, M.D., Ph.D., Stanford University  
Runtime:  01:07:42  
Permanent link:  http://videocast.nih.gov/launch.asp?17321]]></description>
	
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/32868/pollux-platform-independent-error-correction-of-single-and-mixed-genomes</guid>
	<pubDate>Fri, 19 May 2017 09:41:27 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32868/pollux-platform-independent-error-correction-of-single-and-mixed-genomes</link>
	<title><![CDATA[Pollux: platform independent error correction of single and mixed genomes]]></title>
	<description><![CDATA[<p><span>Pollux: General-purpose error corrector that corrects errors introduced by Illumina, Ion Torrent, and Roche 454 sequencing technologies and can be applied to single- or mixed-genome data. In addition to correcting substitution errors, we locate and correct insertion, deletion, and homopolymer errors while remaining sensitive to low coverage areas of sequencing projects. Using published data sets, we correct 94% of Illumina MiSeq errors, 88% of Ion Torrent PGM errors, 85% of Roche 454 GS Junior errors. Introduced errors are 20 to 70 times more rare than successfully corrected errors. Furthermore, we show that the quality of assemblies improves when reads are corrected by our software.</span></p>
<p><span>https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-014-0435-6</span></p><p>Address of the bookmark: <a href="https://github.com/emarinier/pollux" rel="nofollow">https://github.com/emarinier/pollux</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36597/gappadder-a-sensitive-approach-for-closing-gaps-on-draft-genomes-with-short-sequence-reads</guid>
	<pubDate>Mon, 14 May 2018 05:25:48 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36597/gappadder-a-sensitive-approach-for-closing-gaps-on-draft-genomes-with-short-sequence-reads</link>
	<title><![CDATA[GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads]]></title>
	<description><![CDATA[<p><span>This software is provided ``as is&rdquo; without warranty of any kind. In no event shall the author be held responsible for any damage resulting from the use of this software. The program package, including source codes, executables, and this documentation, is distributed free of charge. If you use this program in a publication, please cite the following reference:</span><br><span>Chong Chu, Xin Li, and Yufeng Wu. "GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads." bioRxiv (2017): 125534.</span></p><p>Address of the bookmark: <a href="https://github.com/Reedwarbler/GAPPadder" rel="nofollow">https://github.com/Reedwarbler/GAPPadder</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44599/p10k-the-protist-10000-genomes</guid>
	<pubDate>Sat, 06 Jul 2024 08:29:30 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44599/p10k-the-protist-10000-genomes</link>
	<title><![CDATA[P10K: The Protist 10,000 Genomes]]></title>
	<description><![CDATA[<p><span>The Protist 10,000 Genomes (P10K) Project aims to decipher the genome sequences and construct a comprehensive database resource containing over 10,000 species of protists, encompassing representatives from every major clade. Samples were collected from diverse habitats, and the genome information was acquired through de novo sequencing, genome re-annotation, and integration of publicly available data. Serving as a centralized data portal for the project, the P10K database primarily focuses on delivering high-quality curation and facilitating efficient retrieval of protist genome data.</span></p><p>Address of the bookmark: <a href="https://ngdc.cncb.ac.cn/p10k/" rel="nofollow">https://ngdc.cncb.ac.cn/p10k/</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/33887/gview-a-java-application-for-viewing-and-examining-prokaryotic-genomes-in-a-circular-or-linear-context</guid>
	<pubDate>Fri, 14 Jul 2017 07:47:03 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/33887/gview-a-java-application-for-viewing-and-examining-prokaryotic-genomes-in-a-circular-or-linear-context</link>
	<title><![CDATA[GView: A Java application for viewing and examining prokaryotic genomes in a circular or linear context]]></title>
	<description><![CDATA[<p>GView is a Java application for viewing and examining prokaryotic genomes in a circular or linear context. It accepts standard sequence file formats and an optional style specification file to generate customizable, publication quality genome maps in bitmap and scalable vector graphics formats. GView features an interactive pan-and-zoom interface, a command-line interface for incorporation in genome analysis pipelines, and a public Application Programming Interface for incorporation in other Java applications.</p>
<p><strong>Availability:</strong>&nbsp;GView is a freely available application licensed under the GNU Public License. The application, source code, documentation, file specifications, tutorials and image galleries are available at&nbsp;<a href="http://gview.ca/" target="pmc_ext">http://gview.ca</a></p>
<p><strong>Contact:</strong>&nbsp;<a href="mailto:dev@null">ac.cg.cpsa-cahp@raalesmod.nav.yrag</a></p>
<p>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995121/</p><p>Address of the bookmark: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995121/" rel="nofollow">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995121/</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
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