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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/27323?offset=890</link>
	<atom:link href="https://bioinformaticsonline.com/related/27323?offset=890" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/21794/research-associate-biotechnology-bioinformatics-in-national-research-centre-on-plant-biotechnology-%E2%80%93-new-delhi</guid>
  <pubDate>Sun, 29 Mar 2015 21:13:14 -0500</pubDate>
  <link></link>
  <title><![CDATA[Research Associate (Biotechnology, Bioinformatics) In National Research Centre on Plant Biotechnology – New Delhi]]></title>
  <description><![CDATA[
<p>Pay Scale:Rs.24000+ 30% HRA) for Ph.D. and for M. Sc Rs.23000/‐ (+ 30% HRA)<br />Educational Requirements:Ph.D. Degree in Bioinformatics/Molecular Biology/Biotechnology/ Genetics/allied sciences; or M. Sc in Bioinformatics/ Biotechnology/Life Sciences/ allied sciences with 1st division or 60% marks or equivalent overall grade point average with at least two years of research experience as evidenced from Fellowship/ Associate ship<br />Experience Requirements:2 years research experience in bioinformatic data analysis/molecular biology techniques, and high throughput DNA/RNA sequencing, and transcriptome data analysis. Research paper with IF&gt;1 will be desirable<br />+Details will be available at: http://www.nrcpb.org/sites/default/files/ICAR-NPTC%20DBT%20RA%20SRF%20interview%2024th%20March.pdf</p>

<p>No of Post: 01<br />How To Apply: Walk-in interview will be held on 24-03-2015 at 10:00 AM at NRCPB, New Delhi for filling Research Associate and Senior Research Fellow positions as mentioned below. The positions are temporary and are initially offered for a period of one year. Details such as emoluments, qualifications, application format etc., are given below. Desirous candidates should report for interview latest by 10:30 AM with the application in the prescribed format, copies and originals of certificates, thesis and documents. No TA/DA will be provided for attending the interview<br />General Instructions: The positions are purely temporary, on a contractual basis and are initially offered for one year. The period and duration of the scheme is tentative and the same may change. The person employed will have no right to claim employment or engagement in ICAR at the end of the contract period. No TA/DA will be provided for appearing in the interview. Persons already in employment should bring “No Objection Certificate” from their present employer. The candidates must bring with them five copies of the CV in the format given below along with original documents such as t h e s i s , degree certificates, marks sheets, publications, experience certificate etc. for verification and one set of self attested copy of all certificates. The decision of the Project Director of this Institute will be final and binding in all aspects. In case of any disputes, it will be resolved within the jurisdiction of New Delhi Court only.<br />Detail of Interview: 24-03-2015<br />Age Limit: 35 Years<br />Contact Details: Ph: 011-25848783; Fax: 25843984</p>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/10379/your-stressdepression-came-from-ancestor</guid>
	<pubDate>Sun, 04 May 2014 18:46:20 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/10379/your-stressdepression-came-from-ancestor</link>
	<title><![CDATA[Your stress/depression came from ancestor]]></title>
	<description><![CDATA[<p>"A study published in&nbsp;<em>Nature Neuroscience</em>&nbsp;finds that stress in early life alters the production of small RNAs, called microRNAs, in the sperm of mice. The mice show depressive behaviours that persist in their progeny."</p><p>Source:</p><p>http://www.nature.com/news/sperm-rna-carries-marks-of-trauma-1.15049</p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/22147/research-associate-bioinformatics-job-position-in-nipgr</guid>
  <pubDate>Sun, 19 Apr 2015 14:55:19 -0500</pubDate>
  <link></link>
  <title><![CDATA[Research Associate Bioinformatics job position in NIPGR]]></title>
  <description><![CDATA[
<p>NIPGR Recruitment 2015 – Apply for Research Associate Posts</p>

<p>NIPGR is commonly known as National Institute of Plant Genome Research. Recently, it’s great opportunity for those candidates who are interested to do job in NIPGR. National Institute of Plant Genome Research (NIPGR) had found to build a bridge between the branches of natural sciences and due this connection it is steeping on the heaps of success. Its objectives to preserve, research, production and the advancement in the trait are very clear and also being appreciated by the nation and had been contributing for the further enrichment of the institute. NIPGR had announced the recruitment to further make improvements and amendments by the young potential in their panel. The recruitment is being announced for the post is mentioned below. We are giving a complete information to applicants for find their eligibility as per desired post under NIPGR Recruitment 2015 project but if the candidates are not satisfied with this information then they can download an official advertisement of NIPGR recruitment 2015 from the link defined ahead under the head of reference.</p>

<p>NIPGR Recruitment 2015 for the 1 post of Research Associate: National Institute of Plant Genome Research (NIPGR) had instigated the progression of the recruitment and this process is linked thoroughly so as the 1 post of Research Associate. Applicants are associated and linked with the education to be PHD degree in the life science, biotechnology, bioinformatics or molecular biology. Applicants are associated with the dispatch of the application along with the required certificates so as on the date of 24th Feb 2015.</p>

<p>The recruitment notification and application @ http://www.nipgr.res.in/careers/vacancies_latest.php#</p>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/34221/alignment-free-sequence-comparison-tools-available-for-next-generation-sequencing-data-analysis</guid>
	<pubDate>Tue, 07 Nov 2017 05:33:33 -0600</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/34221/alignment-free-sequence-comparison-tools-available-for-next-generation-sequencing-data-analysis</link>
	<title><![CDATA[Alignment-free sequence comparison tools available for next-generation sequencing data analysis]]></title>
	<description><![CDATA[<div><p><span>kallisto</span></p></div><div><p>Transcript abundance quantification from RNA-seq data (uses pseudoalignment for rapid determination of read compatibility with targets)</p><p>Software (C++)</p><p><a href="https://pachterlab.github.io/kallisto/">https://pachterlab.github.io/kallisto/</a></p><p>Sailfish</p><p>Estimation of isoform abundances from reference sequences and RNA-seq data (<em>k</em>-mer based)</p><p>Software (C++)</p><p><a href="http://www.cs.cmu.edu/~ckingsf/software/sailfish/">http://www.cs.cmu.edu/~ckingsf/software/sailfish/</a></p><p>Salmon</p><p>Quantification of the expression of transcripts using RNA-seq data (uses&nbsp;<em>k</em>-mers)</p><p><a href="https://combine-lab.github.io/salmon/">https://combine-lab.github.io/salmon/</a></p><p>RNA-Skim</p><p>RNA-seq quantification at transcript-level (partitions the transcriptome into disjoint transcript clusters; uses&nbsp;<em>sig</em>-mers, a special type of&nbsp;<em>k</em>-mers)</p><p>Software (C++)</p><p><a href="http://www.csbio.unc.edu/rs/">http://www.csbio.unc.edu/rs/</a></p><p>Variant calling</p><p>ChimeRScope</p><p>Fusion transcript prediction using gene&nbsp;<em>k</em>-mers profiles of the RNA-seq paired-end reads</p><p>Software (Java)</p><p><a href="https://github.com/ChimeRScope/ChimeRScope/wiki">https://github.com/ChimeRScope/ChimeRScope/wiki</a></p><p>FastGT</p><p>Genotyping of known SNV/SNP variants directly from raw NGS sequence reads by counting unique&nbsp;<em>k</em>-mers</p><p>Software (C)</p><p><a href="https://github.com/bioinfo-ut/GenomeTester4/">https://github.com/bioinfo-ut/GenomeTester4/</a></p><p>Phy-Mer</p><p>Reference-independent mitochondrial haplogroup classifier from NGS data (<em>k</em>-mer based)</p><p>Software (Python)</p><p><a href="https://github.com/danielnavarrogomez/phy-mer">https://github.com/danielnavarrogomez/phy-mer</a></p><p>LAVA</p><p>Genotyping of known SNPs (dbSNP and Affymetrix's Genome-Wide Human SNP Array) from raw NGS reads (<em>k</em>-mer based)</p><p>Software (C)</p><p><a href="http://lava.csail.mit.edu/">http://lava.csail.mit.edu/</a></p><p>MICADo</p><p>Detection of mutations in targeted third-generation NGS data (can distinguish patients&rsquo; specific mutations; algorithm uses&nbsp;<em>k</em>-mers and is based on colored de Bruijn graphs)</p><p>Software (Python)</p><p><a href="http://github.com/cbib/MICADo">http://github.com/cbib/MICADo</a></p><p>General mapper</p><p>Minimap</p><p>Lightweight and fast read mapper and read overlap detector (uses the concept of &ldquo;minimazers&rdquo;, a special type of&nbsp;<em>k</em>-mers)</p><p>Software (C)</p><p><a href="https://github.com/lh3/minimap">https://github.com/lh3/minimap</a></p><p>Assembly</p><p>De novo genome assembly</p><p>MHAP</p><p>Produces highly continuous assembly (fully resolved chromosome arms) from third-generation long and noisy reads (10 kbp) using a dimensionality reduction technique MinHash</p><p>Software (Java)</p><p><a href="https://github.com/marbl/MHAP">https://github.com/marbl/MHAP</a></p><p>Miniasm</p><p>Assembler of long noisy reads (SMRT, ONT) using the Overlap-Layout Consensus (OLC) approach without the necessity of an error correction stage (uses minimap)</p><p>Software (C)</p><p><a href="https://github.com/lh3/miniasm">https://github.com/lh3/miniasm</a></p><p>LINKS</p><p>Scaffolding genome assembly with error-containing long sequence (e.g., ONT or PacBio reads, draft genomes)</p><p>Software (Perl)</p><p><a href="https://github.com/warrenlr/LINKS/">https://github.com/warrenlr/LINKS/</a></p><p>Read clustering</p><p>afcluster</p><p>Clustering of reads from different genes and different species based on&nbsp;<em>k</em>-mer counts</p><p>Software (C++)</p><p><a href="https://github.com/luscinius/afcluster">https://github.com/luscinius/afcluster</a></p><p>QCluster</p><p>Clustering of reads with alignment-free measures (<em>k</em>-mer based) and quality values</p><p>Software (C++)</p><p><a href="http://www.dei.unipd.it/~ciompin/main/qcluster.html">http://www.dei.unipd.it/~ciompin/main/qcluster.html</a></p><p>Reads error correction</p><p>Lighter</p><p>Correction of sequencing errors in raw, whole genome sequencing reads (<em>k</em>-mer based)</p><p>Software (C++)</p><p><a href="https://github.com/mourisl/Lighter">https://github.com/mourisl/Lighter</a></p><p>QuorUM</p><p>Error corrector for Illumina reads using k-mers</p><p>Software (C++)</p><p><a href="https://github.com/gmarcais/Quorum">https://github.com/gmarcais/Quorum</a></p><p>Trowel</p><p>Software (C++)</p><p><a href="https://sourceforge.net/projects/trowel-ec/">https://sourceforge.net/projects/trowel-ec/</a></p><p>Metagenomics</p><p>Assembly-free phylogenomics</p><p>AAF</p><p>Phylogeny reconstruction directly from unassembled raw sequence data from whole genome sequencing projects; provides bootstrap support to assess uncertainty in the tree topology (<em>k</em>-mer based)</p><p>Software (Python)</p><p><a href="https://github.com/fanhuan/AAF">https://github.com/fanhuan/AAF</a></p><p>kSNP v3</p><p>Reference-free SNP identification and estimation of phylogenetic trees using SNPs (based on&nbsp;<em>k</em>-mer analysis)</p><p>Software (C)</p><p><a href="https://sourceforge.net/projects/ksnp/files/">https://sourceforge.net/projects/ksnp/files/</a></p><p>NGS-MC</p><p>Phylogeny of species based on NGS reads using alignment-free sequence dissimilarity measures d2* and d2&nbsp;S&nbsp;under different Markov chain models (using&nbsp;<em>k</em>-words)</p><p>R package</p><p><a href="http://www-rcf.usc.edu/~fsun/Programs/NGS-MC/NGS-MC.html">http://www-rcf.usc.edu/~fsun/Programs/NGS-MC/NGS-MC.html</a></p><p>Species identification/taxonomic profiling</p><p>CLARK</p><p>Taxonomic classification of metagenomic reads to known bacterial genomes using&nbsp;<em>k</em>-mer search and LCA assignment</p><p>Software (C++)</p><p><a href="http://clark.cs.ucr.edu/">http://clark.cs.ucr.edu/</a></p><p>FOCUS</p><p>Reports organisms present in metagenomic samples and profiles their abundances (uses composition-based approach and non-negative least squares for prediction)</p><p>Web service Software (Python)</p><p><a href="http://edwards.sdsu.edu/FOCUS/">http://edwards.sdsu.edu/FOCUS/</a></p><p>GSM</p><p>Estimation of abundances of microbial genomes in metagenomic samples (<em>k</em>-mer based)</p><p>Software (Go)</p><p><a href="https://github.com/pdtrang/GSM">https://github.com/pdtrang/GSM</a></p><p>Mash</p><p>Species identification using assembled or unassembled Illumina, PacBio, and ONT data (based on MinHash dimensionality-reduction technique)</p><p>Software (C++)</p><p><a href="https://github.com/marbl/mash">https://github.com/marbl/mash</a></p><p>Kraken</p><p>Taxonomic assignment in metagenome analysis by exact&nbsp;<em>k</em>-mer search; LCA assignment of short reads based on a comprehensive sequence database</p><p>Software (C++)</p><p><a href="https://ccb.jhu.edu/software/kraken/">https://ccb.jhu.edu/software/kraken/</a></p><p>LMAT</p><p>Assignment of taxonomic labels to reads by&nbsp;<em>k</em>-mers searches in precomputed database</p><p>Software (C++/Python)</p><p><a href="https://sourceforge.net/projects/lmat/">https://sourceforge.net/projects/lmat/</a></p><p>stringMLST</p><p><em>k</em>-mer-based tool for MLST directly from the genome sequencing reads</p><p>Software (Python)</p><p><a href="http://jordan.biology.gatech.edu/page/software/stringMLST">http://jordan.biology.gatech.edu/page/software/stringMLST</a></p><p>Taxonomer</p><p><em>k</em>-mer-based ultrafast metagenomics tool for assigning taxonomy to sequencing reads from clinical and environmental samples</p><p>Web service</p><p><a href="http://taxonomer.iobio.io/">http://taxonomer.iobio.io/</a></p><p>Other</p><p>d2-tools</p><p>Word-based (<em>k</em>-tuple) comparison (pairwise dissimilarity matrix using d2S measure) of metatranscriptomic samples from NGS reads</p><p>Software (Python/R)</p><p><a href="https://code.google.com/p/d2-tools/">https://code.google.com/p/d2-tools/</a></p><p>VirHostMatcher</p><p>Prediction of hosts from metagenomic viral sequences based on ONF using various distance measures (e.g., d2)</p><p>Software (C++)</p><p><a href="https://github.com/jessieren/VirHostMatcher">https://github.com/jessieren/VirHostMatcher</a></p><p>MetaFast</p><p>Statistics calculation of metagenome sequences and the distances between them based on assembly using de Bruijn graphs and Bray&ndash;Curtis dissimilarity measure</p><p>Software (Java)</p><p><a href="https://github.com/ctlab/metafast">https://github.com/ctlab/metafast</a></p></div>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/22073/bcil-bioinformatics-bitp-application</guid>
	<pubDate>Fri, 17 Apr 2015 04:34:56 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/22073/bcil-bioinformatics-bitp-application</link>
	<title><![CDATA[BCIL Bioinformatics BITP Application !!]]></title>
	<description><![CDATA[<p>BCIL Bioinformatics BITP Application Form 2015 logoGrab latest Information! Biotech Consortium India Limited has announced a notification for offering admission in Biotech Industrial Training Program. The organization has invited online application from 7th April 2015 BCIL Admission 2015. BCIL has conducted an entrance exam which is scheduled on 20th June 2015. Candidates those who are looking for this program just go for it and don&rsquo;t miss this opportunity.<br /><br />To apply for Biotech Industrial Training Programme the candidates should have 50% marks in B.Tech/BE/M.Tech Degree in Bio technology, bio process technology and other related disciplines form any recognized institution. The organization has decided application fee of Rs.500/- for all candidates and that should be paid through demand draft. Applicants who satisfy the organization requirement, they can take their steps forward.<br /><br />Candidates should submit the online application before 10th May 2015. After registering the online application you need to take the hard copy of it and send through post. Print out of this application should be reached before 15th May 2015. All the latest updates like selection process, exam syllabus and other related information are updated soon at the main URL of the department and aspirants should keep in touch with this site. Further details of BCIL Bioinformatics BITP Application Form 2015 are explained below.<br /><br />Organization: Biotech Consortium India Limited<br /><br />Website URL: www.bcil.nic.in<br /><br />Location: New Delhi<br /><br />Course Name: Biotech Industrial Training Program<br /><br />Exam Name: BCIL Entrance Exam<br /><br />Educational Details: Applicants should complete their B.Tech/M.Tech/BE programs in Neuro- Science, Agricultural, Bio technology, bio process technology and other related disciplines having 50% aggregate from any authorized university.<br /><br />Application Fee: For all candidates application fee is Rs.500/- and it will be paid through Demand Draft drawn in favour of BCIL, New Delhi.<br /><br />How to Apply: Candidates who are willing to apply for this program they can apply through online mode. Then send the hard copy of registered application form to through post.<br /><br />Important Dates<br /><br />Opening Date of Submission Online Application Form: 7h April 2015<br /><br />Closing Date of Submission of Online Application Form: 10th May 2015<br /><br />Last Date of Receipt of Application Form: 15th May 2015<br /><br />Exam Date: 20th June 2015</p><p>More at http://bcil.nic.in/default.htm</p>]]></description>
	<dc:creator>Pranjali Yadav</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34914/ra-assembler-a-de-novo-dna-assembler-for-third-generation-sequencing-data</guid>
	<pubDate>Wed, 27 Dec 2017 20:36:54 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34914/ra-assembler-a-de-novo-dna-assembler-for-third-generation-sequencing-data</link>
	<title><![CDATA[Ra assembler - a de novo DNA assembler for third generation sequencing data]]></title>
	<description><![CDATA[<p>Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS).</p>
<p>Ra is in development since 2014 in the form of several separate components that used to be run individually.<br>This project aims to ease the usage of Ra by integrating it into a complete de novo assembly tool.</p>
<p>Unlike other state-of-the-art assemblers,&nbsp;<span>Ra does not have an error correction step.</span>&nbsp;Instead, it relies on detecting overlaps using a very sensitive and specific overlapper ("graphmap -w owler",&nbsp;<a href="https://github.com/isovic/graphmap">https://github.com/isovic/graphmap</a>) and constructing and reducing an overlap graph (Ra layout,&nbsp;<a href="https://github.com/mariokostelac/ra">https://github.com/mariokostelac/ra</a>).</p><p>Address of the bookmark: <a href="https://github.com/mariokostelac/ra-integrate/" rel="nofollow">https://github.com/mariokostelac/ra-integrate/</a></p>]]></description>
	<dc:creator>biogeek</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/22024/research-associate-bioinformatics-job-position-in-indian-agricultural-statistics-research-institute-iasri-pusa-new-delhi</guid>
  <pubDate>Tue, 14 Apr 2015 11:57:13 -0500</pubDate>
  <link></link>
  <title><![CDATA[Research Associate Bioinformatics job position in Indian Agricultural Statistics Research Institute (IASRI), Pusa, New Delhi]]></title>
  <description><![CDATA[
<p>Indian Agricultural Statistics Research Institute is inviting applications from indian citizens for recruiting following posts:</p>

<p>Vacancies:<br />Research Associate-02<br />Age Limits:<br />Candidates age limit should be not more than 40 years as on date of interview.<br />Qualification:<br />Candidates should possess Ph.D in Bioinformatics/Agricultural Statistics/Statistics/Computer Science/Computer Application or equivalent.<br />Selection Process:<br />Selection will be based on interview.<br />How to Apply:<br />Eligible candidates may attend for interview along with application in prescribed format, recent passport size photograph pasted on the application form, bio-data, original certificates and self attested copies of relevant documents, all experience certificates, testimonials etc, held at Indian Agricultural Statistics Research Institute, Pusa, New Delhi on 18-04-2015 at 10:30 AM.<br />Last Date:<br />18-04-2015</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36806/manta-rapid-detection-of-structural-variants-and-indels-for-germline-and-cancer-sequencing-applications</guid>
	<pubDate>Mon, 28 May 2018 09:41:39 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36806/manta-rapid-detection-of-structural-variants-and-indels-for-germline-and-cancer-sequencing-applications</link>
	<title><![CDATA[Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications.]]></title>
	<description><![CDATA[Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow.<p>Address of the bookmark: <a href="https://github.com/Illumina/manta" rel="nofollow">https://github.com/Illumina/manta</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/22044/binc-sample-question-paper</guid>
	<pubDate>Thu, 16 Apr 2015 09:12:39 -0500</pubDate>
	<link>https://bioinformaticsonline.com/file/view/22044/binc-sample-question-paper</link>
	<title><![CDATA[BINC Sample Question Paper !!!]]></title>
	<description><![CDATA[<p>BINC sample question paper for round ONE.</p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/22044" length="1260" type="text/plain" />
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37498/nextsv-a-meta-caller-for-structural-variants-from-low-coverage-long-read-sequencing-data</guid>
	<pubDate>Mon, 06 Aug 2018 17:24:53 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37498/nextsv-a-meta-caller-for-structural-variants-from-low-coverage-long-read-sequencing-data</link>
	<title><![CDATA[NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data]]></title>
	<description><![CDATA[<p>NextSV, a meta SV caller and a computational pipeline to perform SV calling from low coverage long-read sequencing data. NextSV integrates three aligners and three SV callers and generates two integrated call sets (sensitive/stringent) for different analysis purpose. The output of NextSV is in ANNOVAR-compatible bed format. Users can easily perform downstream annotation using ANNOVAR and disease gene discovery using Phenolyzer.</p>
<p>&nbsp;</p>
<h2>&nbsp;</h2><p>Address of the bookmark: <a href="https://github.com/Nextomics/NextSV" rel="nofollow">https://github.com/Nextomics/NextSV</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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