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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/27427?offset=1370</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/13226/you-and-your-friend-have-similar-dna</guid>
	<pubDate>Sun, 27 Jul 2014 20:44:05 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/13226/you-and-your-friend-have-similar-dna</link>
	<title><![CDATA[You and your friend have similar DNA !!!]]></title>
	<description><![CDATA[<p>New research out of Massachusetts claims that people often choose friends that are similar to them in genetics and they are more accurate than you might suppose. A study published on PNAS&nbsp;http://www.pnas.org/content/111/Supplement_3/10796.full found that people are apt to pick friends who are genetically similar to themselves - so much so that friends tend to be as alike at the genetic level as a person's fourth cousin.</p><div style="text-align: center;"><img src="http://i.kinja-img.com/gawker-media/image/upload/s--CwLwHa43--/18fbmlokxcmqcjpg.jpg" alt="image" width="300" height="271" style="border: 0px; border: 0px;"></div><p>Scientists with a long-running Framingham Heart Study looked at 1,932 people (examination of about 1.5 million markers of genetic variations), comparing unrelated friends to unrelated strangers. They found that friends shared about 1% of their genes &mdash; a percentage much higher than those shared with strangers.This new findings made it clear that people have more DNA in common with those who are selected as friends than with strangers in the same population.&nbsp;</p><p>The genes that lined up the most were olfactory genes, which deal with smell. The ones that lined up the least were immune system genes. The researchers weren't sure why that happened :/. Olfactory genes might be a straightforward explanation: People who like the same smells tend to be drawn to similar environments, where they meet others with the same tendencies.</p><p>Reference:</p><p>http://www.pnas.org/content/111/Supplement_3/10796.full</p><p>Image : http://i.kinja-img.com</p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/36952/getoptspl-file</guid>
	<pubDate>Fri, 15 Jun 2018 04:43:03 -0500</pubDate>
	<link>https://bioinformaticsonline.com/file/view/36952/getoptspl-file</link>
	<title><![CDATA[getopts.pl file]]></title>
	<description><![CDATA[
<p>SSPACE_longread complain for getopts.pl file. </p>

<p>To resolve this, download and have in SSPACED-Longreads folder. </p>

<p>Cheers :)</p>
]]></description>
	<dc:creator>Jit</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/36952" length="942" type="text/plain" />
</item>

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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/13338/protein-function-annotation-and-machine-learning-upmc-paris-france</guid>
  <pubDate>Sat, 02 Aug 2014 01:22:52 -0500</pubDate>
  <link></link>
  <title><![CDATA[Protein function annotation and machine learning - UPMC - Paris, France]]></title>
  <description><![CDATA[
<p>Protein function annotation and machine learning - UPMC - Paris, France</p>

<p>Job Description: We are interested in finding an excellent postdoc with interests in protein functional annotation, machine learning and computer grids. The position is open for 3.5 years at the Université Pierre et Marie Curie, in the heart of paris.</p>

<p>Research topic: Protein function annotation, multiple probabilistic models, domain architecture, machine learning, combinatorial optimization, computer grid.</p>

<p>Title: A novel integrative platform for large scale protein annotation that exploits a multitude of diversified probabilistic models in several protein signature databases.</p>

<p>We propose a novel integrated approach for large scale protein annotation that will exploit an unprecedented amount of genomic data as well as sophisticated machine learning techniques and combinatorial optimization approaches taking advantages of High Performance Computing (HPC) environments. The idea is to uncover as much as possible the evolutionary processes of protein sequences that took place throughout the whole tree of life and that affected the evolution of a protein family. We have already demonstrated in a previous work that the problem of functional annotation is inherent to the ability of uncovering such paths. Now, we shall extend this approach to large scale genome annotation by considering 11 different protein databases, constituted by about 10^9 protein sequences, and by producing a large pool of diversified probabilistic models coding for about 10^7 evolutionary protein pathways. Such models will be used to search for specific domains in genomes to be annotated. Our previous methodology needs to be fundamentally improved to deal with this large amount of biological data. In this project, we shall work on the algorithms to reduce the space of models and the search complexity, and we shall implement some important algorithmic changes towards the realization of a powerful integrated annotation tool.</p>

<p>Where: This project is run on the Laboratoire de Biologie Computationnelle et Quantitative UMR7238 CNRS-UPMC – Analytical Genomics team, headed by A.Carbone. It is co-advised with Pierre-Henri Wuillemin, Laboratoire d’Informatique de Paris 6 – Equipe DECISION.</p>

<p>Start date: September 1st, 2014<br />Contact Person: Alessandra Carbone<br />Contact: alessandra.carbone@lip6.fr</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37223/chopstitch-exon-annotation-and-splice-graph-construction-using-transcriptome-assembly-and-whole-genome-sequencing-data</guid>
	<pubDate>Tue, 03 Jul 2018 04:14:52 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37223/chopstitch-exon-annotation-and-splice-graph-construction-using-transcriptome-assembly-and-whole-genome-sequencing-data</link>
	<title><![CDATA[ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data]]></title>
	<description><![CDATA[ChopStitch is a new method for finding putative exons and constructing splice graphs using an assembled transcriptome and whole genome shotgun sequencing (WGSS) data. ChopStitch identifies exon-exon boundaries in de novo assembled RNA-seq data with the help of a Bloom filter that represents the k-mer spectrum of WGSS reads. The algorithm also detects base substitutions in transcript sequences corresponding to sequencing or assembly errors, haplotype variations, or putative RNA editing events. The primary output of our tool is a FASTA file containing putative exons. Further, exon edges are interrogated for alternative exon-exon boundaries to detect transcript isoforms, which are reported as splice graphs in dot output format.<p>Address of the bookmark: <a href="https://github.com/bcgsc/ChopStitch" rel="nofollow">https://github.com/bcgsc/ChopStitch</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>

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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/14050/assistant-professor-in-bioinformatics-at-indian-institute-of-technology-delhi</guid>
  <pubDate>Fri, 15 Aug 2014 06:16:06 -0500</pubDate>
  <link></link>
  <title><![CDATA[Assistant Professor 	in Bioinformatics at Indian Institute of Technology Delhi]]></title>
  <description><![CDATA[
<p>Indian Institute of Technology Delhi Hauz Khas ,New Delhi – 110016</p>

<p>ROLLING ADVERTISEMENT NO. 01/2014(E-1)<br />ADVERTISEMENT FOR THE POSITIONS OF ASSISTANT PROFESSOR CANDIDATES CAN APPLY ANY TIME DURING THE YEAR.</p>

<p>IIT Delhi invites applications from qualified Indian Nationals, Persons of Indian Origin (PIOs) and Overseas Citizens of India (OCIs) for the following positions in the various Departments/Centres/Schools (in the fields<br />mentioned alongwith them):<br />Post Pay Band Assistant Professor and Assistant Professor (on Contract) Rs.15600-39100 (PB-3) (Minimum pay of Rs.30000/-)+ AGP Rs.8000/-</p>

<p>The following norms will be followed for fixing the basic pay + AGP for Assistant Professors appointed on<br />contract with Ph.D but experience of 3 years or less:-<br />Type Qualification &amp; Experience on the date of joining<br />Assistant Professor (Contract) PB3 (Rs. 15,600-39,100).</p>

<p>MINIMUM QUALIFICATIONS AND EXPERIENCE:<br />Ph.D. with First class at the preceding degree or equivalent in the appropriate branch with very good academic record throughout. A minimum of three years industrial/research/teaching experience, excluding however, the experience gained while Pursuing Ph. D. The candidates should preferably be below<br />35 years of age for male and 38 years for female ( to be relaxed by 5 years in case of persons with physical disability, SC/ST and 3 years in case of OBC-NCL).</p>

<p>Qualified persons include:<br />(a) Indian Nationals,<br />(b) Foreign Nationals who are “Persons of Indian Origin” (PIO) or Overseas<br />Citizens of India (OCI), in whose case, if selected, permission will be sought from Govt. of India<br />before he/she can join IIT Delhi, or<br />(c) Other Foreign Nationals, in whose case, if selected, appointment will be on a contract basis for up to 5 (five) years subject to permission from the Govt. of India before he/she can join IIT Delhi.<br />(d) Institute specifically encourages applicants from SC/ST/OBC category as well as persons<br />with disability to apply for these positions. </p>

<p>AMAR NATH &amp; SHASHI KHOSLA SCHOOL OF INFORMATION TECHNOLOGY:<br />Computational Neuroscience, Medical Applications of Information Technologies, Computational &amp; Systems Biology, Machine to Machine (M2M) Technologies, Embedded Systems &amp; Sensors, Computer Security.<br />KUSUMA SCHOOL OF BIOLOGICAL SCIENCES:<br />In-silico Biology Applications, Systems Biology, Infection Biology, Neurodegeneration. </p>

<p>More at http://www.iitd.ac.in/sites/default/files/jobs/faculty/spl-areas-rolling-advt.pdf</p>

<p>http://www.iitd.ac.in/content/faculty-positions</p>
]]></description>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37650/p-rna-scaffolder-a-fast-and-accurate-genome-scaffolder-using-paired-end-rna-sequencing-reads</guid>
	<pubDate>Fri, 07 Sep 2018 05:19:06 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37650/p-rna-scaffolder-a-fast-and-accurate-genome-scaffolder-using-paired-end-rna-sequencing-reads</link>
	<title><![CDATA[P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads]]></title>
	<description><![CDATA[<p><span>P_RNA_scaffolder is a novel scaffolding tool using Pair-end RNA-seq to scaffold genome fragments. The method is suitable for most genomes. The program could utilize Illumina Paired-end RNA-sequencing reads from target speciesies. Our method provides another practical alternative to existing mate-pair_based approaches or other Protein-based approaches (for instance,&nbsp;</span><a href="http://www.fishbrowser.org/software/PEP_scaffolder/">PEP_scaffolder&nbsp;</a><span>) for scaffolding genome sequences. The most important feature of this method is to improve the completeness of gene regions and long-coding gene regions (for instance,&nbsp;</span><a href="http://circrna.org/">circRNA</a><span>).</span></p><p>Address of the bookmark: <a href="http://www.fishbrowser.org/software/P_RNA_scaffolder/#" rel="nofollow">http://www.fishbrowser.org/software/P_RNA_scaffolder/#</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/14272/lecturersenior-lecturer-level-bc-in-bioinformatics</guid>
  <pubDate>Fri, 22 Aug 2014 12:45:52 -0500</pubDate>
  <link></link>
  <title><![CDATA[Lecturer/Senior Lecturer (Level B/C) in Bioinformatics]]></title>
  <description><![CDATA[
<p>Lecturer/Senior Lecturer (Level B/C) in Synthetic Biology, Research Fellow (Level B) in Synthetic Biology &amp; Lecturer/Senior Lecturer (Level B/C) in Bioinformatics</p>

<p>Apply now Job no: 494553<br />Work type: Continuing full time<br />Vacancy type: External Vacancy, Internal Vacancy<br />Categories: Academic - Teaching and Research</p>

<p>The Faculty of Science is launching a new and innovative branch of biological science at Macquarie University – Synthetic Biology. Synthetic biology combines engineering principles with molecular biological approaches to design and construct biological devices and systems. Recent highlights in this field include the design and synthesis of a functional bacterial genome and a yeast chromosome, and generation of synthetic bacterial cells. The rational synthesis of "designer" organisms yield important insights into how organisms work and has the potential to revolutionise biotechnological applications in areas such as bioenergy and biomanufacturing.</p>

<p>Find more at http://jobs.mq.edu.au/cw/en/job/494553/lecturersenior-lecturer-level-bc-in-synthetic-biology-research-fellow-level-b-in-synthetic-biology-lecturersenior-lecturer-level-bc-in-bioinformatics</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38006/scribl-html5-canvas-genomics-graphic-library</guid>
	<pubDate>Thu, 25 Oct 2018 09:38:53 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38006/scribl-html5-canvas-genomics-graphic-library</link>
	<title><![CDATA[Scribl : HTML5 canvas genomics graphic library]]></title>
	<description><![CDATA[<p>Scribl is a javascript, Canvas-based graphics library that easily generates biological visuals of genomic regions, alignments, and assembly data. Scribl can also be used in conventional offline pipelines, since everything needed to generate charts can be contained in a single html file.</p>
<p>&nbsp;</p><p>Address of the bookmark: <a href="http://chmille4.github.io/Scribl/" rel="nofollow">http://chmille4.github.io/Scribl/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/14758/phd-opportunity-at-universite-de-liege-belgium</guid>
  <pubDate>Mon, 01 Sep 2014 17:16:22 -0500</pubDate>
  <link></link>
  <title><![CDATA[PhD opportunity at Université de Liège - Belgium]]></title>
  <description><![CDATA[
<p>The Bioinformatics and Systems Biology Unit of Université de Liège (Belgium) is looking for a highly motivated master student with programming skills for a PhD thesis project (4 years, fully funded) with the goal of designing computational tools that use literature, genomic and structural data in order to infer regulatory and metabolic networks.  </p>

<p>Applicants are invited to send their resume and a recommendation letter to Prof. Patrick Meyer (more details at   www.biosys.ulg.ac.be )</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38053/swgis-v20-a-seqword-genomic-island-sniffer</guid>
	<pubDate>Thu, 01 Nov 2018 12:35:52 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38053/swgis-v20-a-seqword-genomic-island-sniffer</link>
	<title><![CDATA[swgis v2.0 : a seqword genomic island sniffer]]></title>
	<description><![CDATA[<p><strong>swgis v2.0</strong>&nbsp;is the modified version of the seqword genomic island sniffer. this version is specifically optimized for predicting genomic islands in eukaryotic genomes. swgis v2.0 was tested on several eukaryotic species of different lineages. all identified genomic islands were deposited in the&nbsp;<a href="http://eugi.bi.up.ac.za/" title="Go to EuGI database">eugi database</a>.</p>
<p><a href="http://eugi.bi.up.ac.za/download_swgis/swgisv2.0.zip" title="Download SWGIS v2.0">download swgis v2.0</a></p><p>Address of the bookmark: <a href="http://eugi.bi.up.ac.za/eugi_download_swgis.php" rel="nofollow">http://eugi.bi.up.ac.za/eugi_download_swgis.php</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
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