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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/27323?offset=480</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/13415/genomics-and-sequencing-approach-for-identification-of-biomarkers-to-assess-the-efficacy-of-tgf-%CE%B2ri-inhibitors-of-liver-cancer-in-vivo</guid>
	<pubDate>Tue, 05 Aug 2014 13:55:32 -0500</pubDate>
	<link>https://bioinformaticsonline.com/file/view/13415/genomics-and-sequencing-approach-for-identification-of-biomarkers-to-assess-the-efficacy-of-tgf-%CE%B2ri-inhibitors-of-liver-cancer-in-vivo</link>
	<title><![CDATA[Genomics and sequencing approach for identification of biomarkers to assess the efficacy of TGF-βRI inhibitors (of liver cancer) in vivo]]></title>
	<description><![CDATA[<p>Liver cancer is third leading cause of deaths and fourth most frequent occuring cancer worldwide. There are multiple signaling pathways responsible for causing cancer amongst which TGFb is most important cytokine whose signaling pathway promote cancer. However, main problem is to cure this cancer at late stage where we still have no treatment strategy to tackle this deadly cancer. &nbsp;Hence we need to find out new therapeutic target. One way is to look the relationships between mRNA, methylation and miRNA data of patients with different pathological conditions (cancer vs control either with inhibitor/not). MiRNA is small RNA molecules known to inhibit mRNA expression of particular gene by binding improperly to 3'UTR region of a gene and hence block binding of TF /translation of gene. CpG regions is known to located at promoter region of gene (5' UTR) and usually hypomethylated which allow to gene to transcribe and translate however sometime this region become hyper-methylated thats prevent expression of host gene. Thus , integration of these three data reveal new targets and pathways important for causing or preventing cancer and also reveal biomarker thats check the effects of inhibitor on signaling pathway underlying liver cancer.</p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/13415" length="26423" type="image/jpeg" />
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/21095/ra-walk-in-interview-actrec</guid>
  <pubDate>Mon, 09 Feb 2015 01:06:16 -0600</pubDate>
  <link></link>
  <title><![CDATA[RA WALK-IN-INTERVIEW @ ACTREC]]></title>
  <description><![CDATA[
<p>No. ACTREC/Advt./ 7 /2015</p>

<p>Title of the Project<br />Research Associate<br />(One position)<br />DBTs Biotechnology/Bioinformatics training centre<br />PI Dr. Ashok Varma	</p>

<p>Duration of the Project Six Months from the date of appointment, can be extended further for six month.</p>

<p>Date &amp; Time: 17th February, 2015 at 10.00 a.m.</p>

<p>Venue: Meeting Room, 3rd floor, Khanolkar Shodhika, ACTREC</p>

<p>Essential Qualifications and Experience:</p>

<p>Ph.D. Degree in Basic Sciences from recognized University. Research experience in Bioinformatics or on gene cloning, protein purification, and crystallization.</p>

<p>*M.Sc. degree obtained after a one year course will not be considered.</p>

<p>Selected candidate will have to join at the earliest.</p>

<p>Consolidated Salary: Rs.28,600/- p.m. {Rs.22,000/- + 30% HRA}</p>

<p>The work progress of the candidate will be monitored and extension after 6 months will depend on satisfactory progress of the work.</p>

<p>Candidates fulfilling these requirements should pre-register by sending their application in the prescribed format with recent CV and contact details of 2 referees by e-mail to ‘program.office@actrec.gov.in’ latest by 17.00 hrs on 12-02-2015.<br />The interviews would be held on 17th February, 2015 and will be only for the pre-registered candidates. Candidates should report between 09.30 to 10.00 a.m. in Steno Pool, 3rd floor, Khanolkar Shodhika, ACTREC, Kharghar, Navi Mumbai.<br />No T.A./D.A. will be admissible for attending the interview.</p>

<p>At the time of Interview the candidate should bring original certificates along with CV with contact details of 2 referees and submit the photocopies (attested) of the certificates, with a recent passport size photograph.</p>

<p>All correspondence should be strictly made only to ‘program.office@actrec.gov.in’ as indicated.</p>

<p>Advertisement: www.actrec.gov.in/data%20files/2015/AV-RA-DBT-28-1-15.docx</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/32948/simba-a-web-tool-for-managing-bacterial-genome-assembly-generated-by-ion-pgm-sequencing-technology</guid>
	<pubDate>Tue, 23 May 2017 05:28:56 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32948/simba-a-web-tool-for-managing-bacterial-genome-assembly-generated-by-ion-pgm-sequencing-technology</link>
	<title><![CDATA[SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology]]></title>
	<description><![CDATA[<p><span>SIMBA</span><span>, SImple Manager for Bacterial Assemblies, is a Web interface for managing assembly projects of bacterial genomes. SIMBA was created to assist bioinformaticians to assemble bacterial genomes sequenced with NextGeneration Sequencing (NGS) platforms quickly, easily and effectively. SIMBA also is open source tool, i.e., can be freely downloaded, shared and modified.</span></p>
<p>https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1344-7</p><p>Address of the bookmark: <a href="http://ufmg-simba.sourceforge.net/" rel="nofollow">http://ufmg-simba.sourceforge.net/</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/21242/summer-intern-research-bioinformatics</guid>
  <pubDate>Mon, 16 Feb 2015 12:26:32 -0600</pubDate>
  <link></link>
  <title><![CDATA[Summer Intern - Research Bioinformatics]]></title>
  <description><![CDATA[
<p>Be proficient in LINUX, know perl or python, understand biology and Next Generation Sequencing.<br />The intern will port Agile Assay Design pipelines into Galaxy.<br />The intern will also learn to develope his/her own bioinformatics pipelines for PCR or NGS data analysis.</p>

<p>Who you are<br />You’re someone who wants to influence your own development. You’re looking for a company where you have the opportunity to pursue your interests across functions and geographies. Where a job title is not considered the final definition of who you are, but the starting point.</p>

<p>Qualifications:<br />Major: Bioinformatcis or biology major who is interested and wants to learn Biocomputing, At least 2 years of college.<br />Basic knowledge of LINUX and programming, e.g., perl, python, XML.</p>

<p>More at http://www.roche.com/careers/jobs/jobsearch/job.htm?id=E-00437679&amp;locale=en&amp;title=Summer%20Intern%20-%20Research%20Bioinformatics</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34515/metasim-a-sequencing-simulator-for-genomics-and-metagenomics</guid>
	<pubDate>Mon, 04 Dec 2017 07:18:20 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34515/metasim-a-sequencing-simulator-for-genomics-and-metagenomics</link>
	<title><![CDATA[MetaSim A Sequencing Simulator for Genomics and Metagenomics.]]></title>
	<description><![CDATA[<p><span>Our software can be used to&nbsp;</span><strong>generate collections of synthetic reads</strong><span>&nbsp;that reflect the diverse taxonomical composition of typical metagenome data sets. Based on a database of given genomes, the program allows the user to&nbsp;</span><strong>design a metagenome</strong><span>&nbsp;by specifying the number of genomes present at different levels of the NCBI taxonomy, and then to collect reads from the metagenome using a&nbsp;</span><strong>simulation of a number of different sequencing technologies</strong><span>. A population sampler optionally produces evolved sequences based on source genomes and a given evolutionary tree.&nbsp;</span></p><p>Address of the bookmark: <a href="http://ab.inf.uni-tuebingen.de/software/metasim/" rel="nofollow">http://ab.inf.uni-tuebingen.de/software/metasim/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/21436/jrf-bioinformatics-iisr-kozhikode</guid>
  <pubDate>Tue, 24 Feb 2015 08:44:17 -0600</pubDate>
  <link></link>
  <title><![CDATA[JRF Bioinformatics @ IISR, Kozhikode]]></title>
  <description><![CDATA[
<p>JRF Bioinformatics Jobs recruitment in Indian Institute of Spices Research on temporary basis</p>

<p>Name of the Scheme : Distributed Information Sub Centre – DISC</p>

<p>Qualifications :  M.Sc/ B Tech in Bioinformatics with NET/GATE or M Tech in Bioinformatics</p>

<p>Number of posts : One</p>

<p>Emoluments : Rs. 25,000/-</p>

<p>Upper age limit : 35 years for Men &amp; 40 years for Women as on date of Interview<br />How to apply</p>

<p>Date of Interview : 12-03-2015 at 10.00 AM. All relevant certificates (in original) and bio data, No objection certificate in case he/she is employed elsewhere and experience certificate in original (if any) need to be produced at the time of interview.</p>

<p>More at http://spices.res.in/index.php?option=com_content&amp;view=article&amp;id=263</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41452/apollo-a-sequencing-technology-independent-scalable-and-accurate-assembly-polishing-algorithm</guid>
	<pubDate>Mon, 16 Mar 2020 10:09:26 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41452/apollo-a-sequencing-technology-independent-scalable-and-accurate-assembly-polishing-algorithm</link>
	<title><![CDATA[Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm]]></title>
	<description><![CDATA[<p><span>Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies of genomes of any size. Described by Firtina et al. (preliminary version at&nbsp;</span><a href="https://arxiv.org/pdf/1902.04341.pdf">https://arxiv.org/pdf/1902.04341.pdf</a></p>
<p>More at&nbsp;<a href="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa179/5804978?rss=1">https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa179/5804978?rss=1</a></p><p>Address of the bookmark: <a href="https://github.com/CMU-SAFARI/Apollo" rel="nofollow">https://github.com/CMU-SAFARI/Apollo</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/21444/a-guide-for-complete-r-beginners-installing-r-packages</guid>
	<pubDate>Tue, 24 Feb 2015 20:23:34 -0600</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/21444/a-guide-for-complete-r-beginners-installing-r-packages</link>
	<title><![CDATA[A guide for complete R beginners :- Installing R packages]]></title>
	<description><![CDATA[<p>Part of the reason R has become so popular is the vast array of packages available at the <a href="http://cran.r-project.org/" target="_blank">cran</a> and <a href="http://www.bioconductor.org/" target="_blank">bioconductor</a> repositories. In the last few years, the number of packages has grown <a href="http://blog.revolutionanalytics.com/2010/09/what-can-other-languages-learn-from-r.html" target="_blank">exponentially</a>!</p><p>This is a short post giving steps on how to actually install R packages. Let&rsquo;s suppose you want to install the <a href="http://had.co.nz/ggplot2/" target="_blank">ggplot2</a> package. Well nothing could be easier. We just fire up an R shell and type:<br /><code><br />&gt; install.packages("ggplot2")</code></p><p>In theory the package should just install, however:</p><ul>
<li>if you are using Linux and don&rsquo;t have root access, this command won&rsquo;t work.</li>
<li>you will be asked to select your local mirror, i.e. which server should you use to download the package.</li>
</ul><h4>Installing packages without root access</h4><p>First, you need to designate a directory where you will store the downloaded packages. On my machine, I use the directory <code>/data/Rpackages/</code> After creating a package directory, to install a package we use the command:<br /><code><br />&gt; install.packages("ggplot2"</code><code>, lib="/data/Rpackages/")<br />&gt; library(ggplot2, lib.loc="/data/Rpackages/")<br /></code></p><p>It&rsquo;s a bit of a pain having to type <code>/data/Rpackages/</code> all the time. To avoid this burden,&nbsp; we create a file <code>.Renviron</code> in our home area, and add the line <code>R_LIBS=/data/Rpackages/</code> to it. This means that whenever you start R, the directory <code>/data/Rpackages/</code> is added to the list of places to look for R packages and so:</p><p><code>&gt; install.packages("ggplot2"</code><code>)<br />&gt; library(ggplot2)</code></p><p>just works!</p><h4>Setting the repository</h4><p>Every time you install a R package, you are asked which repository R should use. To set the repository and avoid having to specify this at every package install, simply:</p><ul>
<li>create a file <code>.Rprofile</code> in your home area.</li>
<li>Add the following piece of code to it:</li>
</ul><p><code><br />cat(".Rprofile: Setting UK repositoryn")<br />r = getOption("repos") # hard code the UK repo for CRAN<br />r["CRAN"] = "http://cran.uk.r-project.org"<br />options(repos = r)<br />rm(r)<br /></code></p><p>I found this tip in a stackoverflow <a href="http://stackoverflow.com/questions/1189759/expert-r-users-whats-in-your-rprofile/1189826#1189826" target="_blank">answer </a>.</p>]]></description>
	<dc:creator>Archana Malhotra</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/view/1906</guid>
	<pubDate>Sun, 11 Aug 2013 11:13:58 -0500</pubDate>
	<link>https://bioinformaticsonline.com/view/1906</link>
	<title><![CDATA[Compressive Genomics]]></title>
	<description><![CDATA[<p>The key to finding a solution is to notice that most&nbsp;<a href="http://www.i-programmer.info/news/181-algorithms/4537-a-new-dna-sequence-search-compressive-genomics.html">genomic</a>sequences differ by very little. It may well be that the number of complete genome sequences being stored is increasing rapidly, but the actual amount of new data is very small. In other words, a single DNA sequence isn't particularly compressible but a set of sequences shares so much in common that the redundancy can be used to store them in a much smaller storage space. (Source:e-article from&nbsp;Alex Armstrong)</p><p><a href="http://www.i-programmer.info/news/181-algorithms/4537-a-new-dna-sequence-search-compressive-genomics.html">http://www.i-programmer.info/news/181-algorithms/4537-a-new-dna-sequence-search-compressive-genomics.html</a></p><p><a href="http://en.wikipedia.org/wiki/Compression_of_Genomic_Re-Sequencing_Data">http://en.wikipedia.org/wiki/Compression_of_Genomic_Re-Sequencing_Data</a></p><p><a href="http://www.nature.com/nbt/journal/v30/n7/full/nbt.2241.html">http://www.nature.com/nbt/journal/v30/n7/full/nbt.2241.html</a></p><p><a href="http://bioinformatics.oxfordjournals.org/content/29/13/i283.full">http://bioinformatics.oxfordjournals.org/content/29/13/i283.full</a></p><p><a href="http://groups.csail.mit.edu/cb/cast/">http://groups.csail.mit.edu/cb/cast/</a></p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/21830/research-associate-bioinformatics-job-position-in-indian-agricultural-statistics-research-institute-iasri</guid>
  <pubDate>Tue, 31 Mar 2015 20:45:14 -0500</pubDate>
  <link></link>
  <title><![CDATA[Research Associate Bioinformatics job position in Indian Agricultural Statistics Research Institute (IASRI)]]></title>
  <description><![CDATA[
<p>Research Associate Bioinformatics job position in Indian Agricultural Statistics Research Institute (IASRI)</p>

<p>Qualification : Ph.D. in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application/ Life Science/ Biotechnology/ Agricultural Science or equivalent. Desirable: Knowledge of Statistical and Computational Genomics/ Proteomics/ Bioinformatics OR Post-Graduation in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application/ Life Science/ Biotechnology/ Agricultural Science or equivalent with 1st Division or 60% marks or equivalent with at least two years of research experience. Desirable:Expertise on use of various software/ tool.</p>

<p>No.of Post: 2</p>

<p>Emoluments for RA: Consolidated Rs. 24000/- per month + 30% HRA for Ph.D holders and consolidated Rs. 23000/- per month + 30% HRA for Master Degree.</p>

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

<p>Interested candidates are invited to appear for Walk-In interview at Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi -110012, along with filled in application form , all the original certificates from matriculation onwards, Ph.D. or M.Sc. certificate (as the case may be) must be produced at the time of interview in either original or provisional, Bio-Data, attested copies of all experience certificates, testimonials etc., one passport size photograph and one set of the self-attested photocopies of all the required certificates from matriculation onwards and an attested copy of recent passport size photograph pasted onto the application form. Walk-in interview will be held on 16th April, 2015 at 10:30 a.m.</p>

<p>Click Here for Job Details &amp; Application Form http://www.iasri.res.in/employment/employment.htm</p>
]]></description>
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