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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/19631?offset=840</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/29652/bioistats-ppt</guid>
	<pubDate>Tue, 08 Nov 2016 07:09:01 -0600</pubDate>
	<link>https://bioinformaticsonline.com/file/view/29652/bioistats-ppt</link>
	<title><![CDATA[Bioistats PPT]]></title>
	<description><![CDATA[<p>Basics concepts of&nbsp;Probability: The Study of Randomness</p><p>Biostatistics is the application of statistics to a wide range of topics in biology. The science of biostatistics encompasses the design of biological experiments, especially in medicine, pharmacy, agriculture and fishery; the collection, summarization, and analysis of data from those experiments; and the interpretation of, and inference from, the results. A major branch of this is medical biostatistics, which is exclusively concerned with medicine and health.</p>]]></description>
	<dc:creator>Jit</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/29652" length="1663809" type="application/pdf" />
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/29679/comparative-genomics-educational-material-and-papers-bookmarks</guid>
	<pubDate>Wed, 09 Nov 2016 16:23:30 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/29679/comparative-genomics-educational-material-and-papers-bookmarks</link>
	<title><![CDATA[Comparative genomics educational material and papers bookmarks]]></title>
	<description><![CDATA[<p><span>Alignment of the porcine genome against seven other mammalian genomes (</span><a href="http://www.nature.com/nature/journal/v491/n7424/full/nature11622.html#supplementary-information">Supplementary Information</a><span>) identified homologous synteny blocks (HSBs). Using porcine HSBs and stringent filtering criteria, 192 pig-specific evolutionary breakpoint regions (EBRs) were located. The number of porcine EBRs </span><span>is comparable to the number of bovine-lineage-specific EBRs (100) reported earlier using a slightly lower resolution (500</span><span><span>&thinsp;</span></span><span>kilobases (kb)), indicating that both lineages evolved with an average rate of ~2.1 large-scale rearrangements per million years after the divergence from a common cetartiodactyl ancestor ~60</span><span><span>&thinsp;</span></span><span>Myr ago</span><sup><a href="http://www.nature.com/nature/journal/v491/n7424/full/nature11622.html#ref2" title="Meredith, R. W. et al. Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. Science 334, 521-524 (2011)">2</a></sup><span>. This rate compares to ~1.9 rearrangements per million years within the primate lineage (</span><a href="http://www.nature.com/nature/journal/v491/n7424/full/nature11622.html#supplementary-information">Supplementary Table 11</a><span>). A total of 20 and 18 cetartiodactyl EBRs (shared by pigs and cattle) were detected using the pig and human genomes as a reference, respectively.</span></p><p>Address of the bookmark: <a href="http://www.nature.com/nature/journal/v491/n7424/abs/nature11622.html" rel="nofollow">http://www.nature.com/nature/journal/v491/n7424/abs/nature11622.html</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/29849/ra-bioinformatics-at-national-institute-of-cancer-prevention-research-icmr</guid>
  <pubDate>Thu, 17 Nov 2016 04:11:09 -0600</pubDate>
  <link></link>
  <title><![CDATA[RA Bioinformatics at NATIONAL INSTITUTE OF CANCER PREVENTION &amp; RESEARCH (ICMR)]]></title>
  <description><![CDATA[
<p>NATIONAL INSTITUTE OF CANCER PREVENTION &amp; RESEARCH (ICMR)</p>

<p>Noida 201301 (U.P)</p>

<p>Applications are invited upto 21.11.2016 from interested candidates as per details available on NICPR website (www.nicpr.res.in)/ ICMR website (www.icmr.nic.in) to fill up following temporary position in the time bound DHR Project entitled “Next generation EGFR inhibitor identification using ligand based QSAR technique” under Dr. Subhash M. Agarwal, Scientist-D, Division of Bioinformatics.</p>

<p>Research Assistant (One)</p>

<p>Rs.27000/- p.m. (Fixed/temporary)</p>

<p>Essential: M.Sc. in Bioinformatics or related field.</p>

<p>Desirable: Experience in QSAR and structure based drug designing.</p>

<p>More Info : www.icmr.nic.in/icmrnews/NICPR_Advertisement%20for%20RA.pdf</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/29998/csir-nehru-science-postdoctoral-research-fellowship</guid>
  <pubDate>Tue, 29 Nov 2016 12:34:59 -0600</pubDate>
  <link></link>
  <title><![CDATA[CSIR Nehru Science Postdoctoral Research Fellowship]]></title>
  <description><![CDATA[
<p>CSIR Nehru Science Postdoctoral Research Fellowship</p>

<p>About Fellowship: <br />CSIR Nehru Science Postdoctoral Research Fellowship Scheme is an Research Fellowship awarded/given by HRD Ministry, Govt. of India every year to more than 100 fellows.</p>

<p>It was started to identify promising and young researchers with novel ideas and provide them research opportunities in the areas of basic science, engineering, medicine &amp; agriculture.</p>

<p>The fellowship aims at facilitating their transition from mentored to independent research career.</p>

<p>In addition, check these ICTS Research Fellowships:<br />1.) Max-Planck Partner Group Fellowships 2017-18<br />2.) ICTS-Simons Postdoctoral Fellowships 2017<br />3.) ICTS Post Doctoral Fellowships 2017<br />4.) Airbus Prize Postdoctoral Fellowship 2017-18</p>

<p>Eligibility: To be eligible for this fellowship, you:<br />1.) PhD degree (within 3 years of award of PhD degree), OR<br />2.) Those who have submitted PhD theses.<br />3.) Applicants should have research publications in good impact factor SCI journals.<br />4.) Indian nationals, Persons of Indian Origin (PIO) &amp; Overseas Citizen of India (OCI), a can also apply.<br />5.) Maximum Age Limit: 32 years.</p>

<p>Duration: <br />– 2 Years.<br />– extendable for a maximum of 1 more year based on performance.</p>

<p>Remuneration: <br />– Rs. 50,000/- per month plus House Rent Allowance (HRA)<br />– A contingency grant of Rs. 3.0 lakh per annum.<br />– 25% of the contingency grant can be used for domestic and international travel.</p>

<p>Mode of Selection: You can apply throughout the year, but selection will be made twice a year, in June and December.</p>

<p>How to Apply: <br />– Read the instructions, given at Annexure-I in this PDF file.<br />– And, application form is given as, Annexure-II.<br />– Fill the form &amp; send it to the given address in the PDF file.</p>

<p>Deadline: Rolling Deadline (Applications accepted throughout the year)</p>

<p>Also See: Research Internship/ Fellowship in India:<br />1.) IIT Bombay Research Internship Awards Programme 2016-17<br />2.) IIT Delhi Internship Program 2016-17<br />3.) DAAD WISE – International Internship in Germany<br />4.) Summer Research Fellowship Programme| JNCASR Bangalore<br />5.) Indian Academy of Sciences Summer Internships 2017<br />6.) Winter Internship – IIT Bombay NPDE-TCA<br />7.) Viterbi – India Program 2017 | Research Internship in US<br />8.) Internship – Centre for Stem Cell Research, Vellore</p>

<p>Accommodation &amp; other benefits: <br />– Accommodation may be provided by CSIR, if available.<br />– Medical benefits as per CSIR norms.</p>

<p>For more details: <br />– Check this PDF Notification of Fellowship.<br />– List of CSIR Labs &amp; their work/activities can be seen at www.csir.res.in.</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30018/bipype</guid>
	<pubDate>Thu, 01 Dec 2016 08:47:38 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30018/bipype</link>
	<title><![CDATA[bipype]]></title>
	<description><![CDATA[<p><span>Bipype is a very useful program, which prepare a lot of types of bioinformatics analyses. There are three input options: amplicons, WGS (whole genome sequences) and metatranscriptomic data. If amplicons are input data, then bipype does reconstruction and pairs merging. After that biodiversity is searching. There are two types of searching depending on the amplicons types (ITS or 16S). If WGS are chosen, then bipype finds the SA coordinates of the input reads and generates alignments in the SAM format given single-end reads, aligns reads to reference sequence(s). All of these analyses will be shown with Krona program, which allows to show hierarchical data with pie charts.</span></p><p>Address of the bookmark: <a href="https://readthedocs.org/projects/bipype/" rel="nofollow">https://readthedocs.org/projects/bipype/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/30334/postdoc-at-ubritishcolumbia-in-troutgenomics</guid>
  <pubDate>Thu, 22 Dec 2016 08:18:46 -0600</pubDate>
  <link></link>
  <title><![CDATA[Postdoc at UBritishColumbia in TroutGenomics]]></title>
  <description><![CDATA[
<p>Landscape Genomics Postdoc at UBC A research team at the University of British Columbia’s Department of Zoology and Biodiversity Research Centre is seeking a postdoctoral researcher in landscape genetics of native rainbow trout (Oncorhynchus mykiss). </p>

<p>This project is part of a larger Genome Canada project on genetics and physiology of adaptation to climate change in rainbow trout, and the population genomics component is in the labs of Eric Taylor and Michael Whitlock. The landscape genomics component primarily involves whole genome sequencing approaches to understanding the genomic basis of adaptation to features of habitat, but also to provide insights into phylogeography and the influence of watershed structure on population subdivision in rainbow trout. A PhD in a related field with expertise in basic theory and bioinformatic analysis of population genomics data is required. </p>

<p>The position is available for one year with renewal for up to three additional years. Salary is $55,000 per year plus benefits. To apply, please send a brief cover letter summarizing your qualifications for the position, a CV, and the names, addresses, phone numbers and emails of three references. </p>

<p>Review of applications will begin January 16, 2017. Address application materials to etaylor@zoology.ubc.ca to whom any questions can also be addressed. etaylor@zoology.ubc.ca</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30375/mauve-a-system-for-constructing-multiple-genome-alignments-in-the-presence-of-large-scale-evolutionary-events-such-as-rearrangement-and-inversion</guid>
	<pubDate>Sat, 24 Dec 2016 09:20:53 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30375/mauve-a-system-for-constructing-multiple-genome-alignments-in-the-presence-of-large-scale-evolutionary-events-such-as-rearrangement-and-inversion</link>
	<title><![CDATA[Mauve: a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion]]></title>
	<description><![CDATA[<p>Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignments provide a basis for research into comparative genomics and the study of genome-wide evolutionary dynamics.</p>
<p>Mauve has been developed with the idea that a multiple genome aligner should require only modest computational resources. It employs algorithmic techniques that scale well in the lengths of sequences being aligned. For example, a pair of&nbsp;<em>Y. pestis</em>&nbsp;genomes can be aligned in under a minute, while a group of 9 divergent Enterobacterial genomes can be aligned in a few hours. However, the current algorithm&rsquo;s compute time (progressiveMauve) scales cubically in the number of genomes to align, making it unsuitable for datasets containing more than 50-100 bacterial genomes.</p><p>Address of the bookmark: <a href="http://darlinglab.org/mauve/mauve.html" rel="nofollow">http://darlinglab.org/mauve/mauve.html</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/30744/binc-2017</guid>
	<pubDate>Wed, 01 Feb 2017 09:36:22 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/30744/binc-2017</link>
	<title><![CDATA[BINC 2017]]></title>
	<description><![CDATA[<p><span>Pondicherry University,Puducherry,on behalf of Department of Biotechnology, Government of India, conducted the BINC examination in&nbsp;</span><span style="color: blue;">2015 and 2016.&nbsp;</span><span>The objective of this examination is to certify bioinformatics professionals, trained formally as well as self-trained.</span><span style="color: blue;">Registration for BINC 2017 examination will open from January 29,2017 to February 28,2017.</span><span>&nbsp;</span></p><p><span>Pondicherry University, Puducherry has been identified as a nodal agency by the Department of Biotechnology, Govt. of India to coordinate this examination along with nine centres namely, </span></p><p><span>Pune University, Pune; </span></p><p><span>Anna University, Chennai; </span></p><p><span>Bose Institute, Kolkata; </span></p><p><span>Institute of Bioinformatics &amp; Applied Biotechnology, Bangalore; </span></p><p><span>North-Eastern Hill University, Shillong, University of Hyderabad, Hyderabad; </span></p><p><span>University of Kerala, Thiruvananthapuram; </span></p><p><span>Jawaharlal Nehru University, New Delhi and </span></p><p><span>Assam Agricultural University, Guwahati.</span><span style="color: blue;"><strong>&nbsp;</strong></span></p><p><span style="color: blue;"><strong>In the BINC 2015 and 2016 examination, 23 candidates and five candidates were certified respectively.</strong></span><span>&nbsp;DBT has agreed to fund Research fellowships for all the BINC qualified Indian nationals to pursue Ph.D. in Indian Institutes/Universities. </span></p><p><span>Note that the candidate must possess a postgraduate degree(or equivalent) &amp; meet the criteria of the institutes/universities in order to avail research fellowship. </span></p><p><span>In addition, cash prize of Rs. 10,000/- will be awarded to the top 10 BINC qualifiers.</span></p><p><span>More at&nbsp;http://www.pondiuni.edu.in/exams/binc/</span></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/30889/phd-program-in-computer-science-at-university-of-essex</guid>
  <pubDate>Sat, 11 Feb 2017 13:11:36 -0600</pubDate>
  <link></link>
  <title><![CDATA[PhD program in Computer Science at University of Essex]]></title>
  <description><![CDATA[
<p>As part of the PhD program in Computer Science at University of Essex, I am looking for a PhD student in computational and synthetic biology.<br />The ideal candidate is interested in designing new biological design automation methods for genome scale projects and/or network modelling of genomic, transcriptomic and proteomic data.<br />Candidates interested in developing optimization algorithms for biological problems are encouraged to apply as well.<br />A summary of the research work in the lab can be found on o this page.</p>

<p>Candidates interested in the position should contact me in advance by email to: g.stracquadanio@essex.ac.uk</p>

<p>The deadline for the application is 28/02/2017; info about the application can be found on the Essex CSEE website.</p>
]]></description>
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	<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>
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