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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/30555?offset=570</link>
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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>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/36630/frequent-paired-end-reads-pe-2x100-mapping-command-lines</guid>
	<pubDate>Tue, 15 May 2018 08:59:29 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/36630/frequent-paired-end-reads-pe-2x100-mapping-command-lines</link>
	<title><![CDATA[Frequent Paired-end reads (PE 2x100) mapping command lines]]></title>
	<description><![CDATA[
<p>bowtie2 -x hs37m -X 650 -q -1 r1.fq -2 r2.fq -S r12.bowtie2.sam  </p>

<p>bwa aln hs37m.fa r1.fq &gt; r1.sai &amp;&amp; bwa aln hs37m.fa r2.fq &gt; r2.sai \  <br />    &amp;&amp; bwa sampe hs37m r1.sai r2.sai r1.fq r2.fq &gt; r12.bwa.sam  </p>

<p>bwa bwasw ../index/bwa/hs37m.fa r12.fq &gt; r12.bwasw.sam  </p>

<p>gsnap -A sam -d hs37m r1.fq r2.fq &gt; r12.gsnap.sam  </p>

<p>novoalign -r Random -o SAM -f r1.fq r2.fq -i 500 50 -d hs37m-k14s3.novo &gt; r12.novo.sam  </p>

<p>smalt map -f samsoft -i 650 -o r12.smalt-k20s13.sam hs37m-k20s13 r1.fq r2.fq  </p>

<p>stampy.py -g hs37m -h hs37m -o r12.stampy.sam -M r1.fq,r2.fq  </p>

<p>soap -D hs37m.fa.index -a r1.fq -b r2.fq -l 32 -g 3 -u dummy -2 dummy -o r12.soap</p>
]]></description>
	<dc:creator>Jit</dc:creator>
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  <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>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36918/p-rna-scaffolder-a-fast-and-accurate-genome-scaffolder-using-paired-end-rna-sequencing-reads</guid>
	<pubDate>Tue, 12 Jun 2018 08:14:41 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36918/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_RNA_scaffolder, a fast and accurate tool using paired-end RNA-sequencing reads to scaffold genomes. This tool aims to improve the completeness of both protein-coding and non-coding genes. After this tool was applied to scaffolding human contigs, the structures of both protein-coding genes and circular RNAs were almost completely recovered and equivalent to those in a complete genome, especially for long proteins and long circular RNAs.<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>Jit</dc:creator>
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  <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>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37241/remilo-reference-assisted-misassembly-detection-algorithm-using-short-and-long-reads</guid>
	<pubDate>Fri, 06 Jul 2018 04:27:49 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37241/remilo-reference-assisted-misassembly-detection-algorithm-using-short-and-long-reads</link>
	<title><![CDATA[ReMILO: reference assisted misassembly detection algorithm using short and long reads.]]></title>
	<description><![CDATA[ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the initial short reads to both the contigs and reference genome, and then constructs a novel data structure called red-black multipositional de Bruijn graph to detect misassemblies. In addition, ReMILO also aligns the contigs to long reads and find their differences from the long reads to detect more misassemblies.<p>Address of the bookmark: <a href="https://github.com/songc001/remilo" rel="nofollow">https://github.com/songc001/remilo</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/14905/internship-in-computational-biology</guid>
  <pubDate>Thu, 04 Sep 2014 04:19:40 -0500</pubDate>
  <link></link>
  <title><![CDATA[Internship in Computational Biology]]></title>
  <description><![CDATA[
<p>We are looking for a motivated and autonomous intern to study gene expression in hybrid organisms. The student will work on natural hybrids of two or three different species of fungal endosymbionts of grasses. The pupose of this project is to build software allowing us to identify the genomic origin of expressed genes. To do that, the intern will have to analyze expression data (from RNA-seq) to find SNPs on the sequenced mRNAs allowing to identify from which of the parental genome the expressed gene come from. The data will have to be saved in a database using the standard BioSQL schema.</p>

<p>This job will allow the intern to become more familiar with new biological and bioinformatics tools like next generation sequencing, RNA-Seq data analysis and comparative genomics.</p>

<p>To apply for this position, send the following documents (in PDF format) to Dr Pierre-Yves Dupont (email p.y.dupont@massey.ac.nz):</p>

<p>1. A short cover letter.<br />2. A curriculum vitae, with transcript details.<br />3. The names and contact details of two referees willing to provide a confidential letter of recommendation upon request.</p>

<p>Informal enquiries are welcome. Formal applications are due by Sunday 2nd December 2012.<br />Requirements: </p>

<p>This position requires a good understanding of genetic problems, a good command of at least one scripting language (Perl, Python...), a basic knowledge of MySQL or any relational database management system. Knowledge in biological programming libraries (BioPython, BioPerl, BioRuby...), Java, C++ or any compiled language is an asset but not required. Undergraduate or Master degree is required.<br />Contact Information: </p>

<p>Dr. Pierre-Yves Dupont<br />Institute of Molecular BioSciences<br />Massey University<br />Private Bag 11 222<br />Palmerston North 4442<br />NEW ZEALAND</p>

<p>http://massey.genomicus.com/<br />p.y.dupont@massey.ac.nz</p>

<p>Information about the Institute of Molecular BioSciences (http://imbs.massey.ac.nz/) and the Computational Biology Research Group (http://massey.genomicus.com/) is available online. For more information about the position, you can contact Dr Pierre-Yves Dupont (email p.y.dupont@massey.ac.nz).</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/16158/bioinformatics-position-at-irccs-casa-sollievo-della-sofferenza</guid>
  <pubDate>Wed, 10 Sep 2014 14:25:34 -0500</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics position at IRCCS Casa Sollievo della Sofferenza]]></title>
  <description><![CDATA[
<p>The bioinformatics unit at IRCCS Casa Sollievo della Sofferenza - Mendel laboratory in Rome is looking for one young bioinformatician with specific experience and/or interest in the analysis of genomics and transcriptomic data.</p>

<p>The candidate will be mainly in charge of developing research on Gene Expression/SNP Arrays data, NGS whole -exome and -transcriptome datasets and biological networks in the contexts of genetic diseases, innovative therapies and regenerative medicine. Main activities will be: (i) data analysis (short-reads mapping, genomics aberrations discovery and annotation, variants pathogenicity detection); (ii) functional/pathway enrichment analysis; (iii) biological networks analysis (artificial knockout, redundancy and lethality analysis, gene set essentiality); (iv) developing of ad-hoc software solutions/routines on clusters of CPUs and GPUs.</p>

<p>The correct cultural background (training in Biology / Computer Science / Statistics or a mix of the three) and a strong interest in working in high throughput data analysis will be considered at the same level of specific experience in the above-mentioned fields.</p>

<p>Knowledge of molecular modeling and simulation and willingness to learn one or more of these languages: python, perl, R, Java, C++, C# is a golden plus. Good knowledge of Scientific English will be positively evaluated for this position, together with good presentation and teamwork skills.</p>

<p>Candidates should send:<br />• a cover letter explaining the role they would like to undertake within the Center, even if it is not listed in this job adv, stating clearly why they would be a good fit to the proposed role, and what they would bring to the Center in terms of expertise, ideas, talent;<br />• a CV including a list of publications;<br />• List of referees.</p>

<p>A CV with one professional reference, details on educational background and of the biological and/or bioinformatic and/or data analysis skills and experience should be sent by email for a preliminary selection to: Tommaso Mazza t.mazza@css-mendel.it</p>
]]></description>
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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>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/17187/urdip-bioinformatics-rajrf-vacancies</guid>
  <pubDate>Sat, 20 Sep 2014 20:52:56 -0500</pubDate>
  <link></link>
  <title><![CDATA[URDIP Bioinformatics RA/JRF Vacancies]]></title>
  <description><![CDATA[
<p>CSIR - UNIT FOR RESEARCH AND DEVELOPMENT OF INFORMATION PRODUCTS (CSIR- URDIP)</p>

<p>Adv. No. URDIP/ 6/2014</p>

<p>Opportunity for young Bioinformatics Professionals to make a career in the area of Intellectual Property CSIR has set up a Unit for Research and Development of Information Products (CSIR-URDIP) at Pune to work in the area of scientific informatics. One of the major focus areas of research work at CSIR-URDIP is PATENT INFORMATICS. With the increasing applications of Bioinformatics in the areas of life sciences industry such as Agriculture and Health Care (Diagnostics and Drugs), the output of research in these area is being protected by different forms of Intellectual Property rights. Realizing the importance of IP in the Bioinformatics field, Department of Biotechnology (DBT) has sanctioned a project on “Development, Facilitation and Harvesting of Bioinformatics related Intellectual Property” at CSIR-URDIP.</p>

<p>The project will involve application of Patent Informatics tools and techniques to Bioinformatics (including creation of patent landscapes, preparation of techno-legal reports of patentability, freedom to operate studies) to help protect IPRs and develop and conduct training programmes on IPRs related to Bioinformatics.</p>

<p>CSIR-URDIP invites applications from young Bioinformatics professionals to work on this emerging area which offers challenging opportunities and attractive career possibilities in future.</p>

<p>Position I: Research Associate</p>

<p>No of Positions: One</p>

<p>Consolidated amount Payable: Rs. 22,000/- per month + 20% HRA= Rs.26,400</p>

<p>Qualification:  PhD in Bioinformatics. In exceptional cases, candidature of M. Tech. candidates with First class in Bioinformatics with three years of relevant work experience will also be considered.</p>

<p>Age Limit: 35 years. The age should not exceed the limit indicated as on a closing date of receipt of completed application form.</p>

<p>Upper age limit is relaxable for 5 years for SC/ST, OBC, Physically handicapped and female candidates as per CSIR/Government of India rules.</p>

<p>Position II: Junior Research Fellow</p>

<p>No of Positions: one</p>

<p>Consolidated amount Payable: Rs. 16,000/- + 20% HRA = 19,200</p>

<p>Qualification: M.Sc / BE or equivalent in Bioinformatics with minimum of 55% marks in aggregate Job requirement: Scientific literature and patent search, analysis and Report Writing</p>

<p>Preference: Preference will be given to candidates with knowledge of patents and or 1-2 years of experience + Knowledge of Computers (MS Excel + Word Processing)</p>

<p>Age Limit: 28 years. The age should not exceed the limit indicated as on a closing date of receipt of completed application form.</p>

<p>For details please visit our website (www.urdip.res.in/careers) for further details and apply online by 30th September, 2014.</p>

<p>Advertisement: http://www.urdip.res.in/download/Advt6_2014.pdf</p>
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