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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/29614?offset=180</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/39213/flye-fast-and-accurate-de-novo-assembler-for-single-molecule-sequencing-reads</guid>
	<pubDate>Tue, 02 Apr 2019 21:54:55 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/39213/flye-fast-and-accurate-de-novo-assembler-for-single-molecule-sequencing-reads</link>
	<title><![CDATA[Flye: Fast and accurate de novo assembler for single molecule sequencing reads]]></title>
	<description><![CDATA[<p><span>Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Flye also includes a special mode for metagenome assembly.</span></p><p>Address of the bookmark: <a href="https://github.com/fenderglass/Flye" rel="nofollow">https://github.com/fenderglass/Flye</a></p>]]></description>
	<dc:creator>BioJoker</dc:creator>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/17504/postdoc-scientist-bioinformatics-at-ccmb</guid>
  <pubDate>Fri, 26 Sep 2014 19:58:41 -0500</pubDate>
  <link></link>
  <title><![CDATA[PostDoc Scientist Bioinformatics at CCMB]]></title>
  <description><![CDATA[
<p>1. Project Assistant/Junior Research Fellow/ Project Fellow [PA_JRF_PF]</p>

<p>a) M.Sc/or equivalent in biological sciences/related areas [Position Code: PA_JRF_PF_a]<br />b) B.E/B.Tech/ M.Sc in biotechnology/bioinformatics/computer science/Chemistry/Physics or MCA [Position Code: PA_JRF_PF_b]<br />c) M.Sc/or equivalent in wildlife sciences/ecology/environmental sciences or MBBS/BVSc/MVSc. [Position Code: PA_JRF_PF_c]</p>

<p>(Candidates with result awaited are NOT eligible to apply)</p>

<p>Upper Age limit 28years</p>

<p>Rs.12000 / Rs.16000 (as sanctioned by the funding agency)</p>

<p>2. Post Doctoral Fellow/Research Associate in multiple research areas [PDF_RA]</p>

<p>Ph.D. (submitted/awarded) in any branch of biological Sciences. Candidates with Ph.D. in other sciences are also encouraged to apply.</p>

<p>Experience in molecular biology, biochemistry, structural biology, cell biology, infectious disease, conservation genetics, veterinary science, reproductive biology, and molecular diagnostics is desired but not mandatory.</p>

<p>[Position Code: PDF_RA]</p>

<p>UpperAge limit 35years</p>

<p>Rs. 22000- 26000 (as sanctioned by the funding agency)</p>

<p>3. Post Doctoral Scientist Fellow [PDSF]</p>

<p>Ph.D in any of the following areas: bioinformatics, next generation sequencing, high throughput data analysis, proteomics, bio-statistics, computer science, information technology, computer hardware and networking/clustering, parallel processing.<br />[Position Code: PDSF]</p>

<p>Upper Age limit 40 years</p>

<p>Rs. 40000 consolidated (as sanctioned by the funding agency)</p>

<p>Download Application: Last date for apply online: 09th Oct 2014</p>

<p>Advertisement: www.ccmb.res.in//index.php?view=notifications&amp;mid=0&amp;id=71&amp;nid=38</p>

<p>Apply online http://www.ccmb.res.in/positions/temp_notif/online_form.html</p>

<p>More at http://www.ccmb.res.in//index.php?view=notifications&amp;mid=0&amp;id=71&amp;nid=38</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/17652/arraygen-bioinformatics-genomics-group</guid>
  <pubDate>Sun, 28 Sep 2014 14:09:55 -0500</pubDate>
  <link></link>
  <title><![CDATA[ArrayGen Bioinformatics Genomics Group]]></title>
  <description><![CDATA[
<p>ArrayGen is a global bioinformatics company which is a one stop solution for microarray designing and genomics data analysis. Our novel Array Design Approach Strategy (ADAS) aims to condense the time lag between demands of scientific community and manufacture industry, thereby expediting research processes.</p>

<p>ArrayGen specializes in Genomics data analysis and research, as we believe in the level of precision, predictability, benchmark-ability, and data analysis capability of genomics data over other forms of biological data. ArrayGen constantly strives to develop new solutions, and plug the existing gaps in the technological advancement of the field.</p>

<p>More http://www.arraygen.com/</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/17873/postdoc-position-in-protein-annotation-and-machine-learning-paris-france</guid>
  <pubDate>Sat, 04 Oct 2014 08:10:45 -0500</pubDate>
  <link></link>
  <title><![CDATA[Postdoc position in protein annotation and machine learning - Paris, France]]></title>
  <description><![CDATA[
<p>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>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>The postdoc will be payed under a contract of Ingénieur de Recherche lasting 3.5 years and it is available from September 1st, 2014.</p>

<p>Group Web Page: http://www.lcqb.upmc.fr/AnalGenom/home.html</p>

<p>Ref. E-Mail: Alessandra Carbone alessandra.carbone@lip6.fr</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43254/quasr-quantification-and-annotation-of-short-reads-in-r</guid>
	<pubDate>Fri, 13 Aug 2021 07:44:05 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43254/quasr-quantification-and-annotation-of-short-reads-in-r</link>
	<title><![CDATA[QuasR: Quantification and annotation of short reads in R]]></title>
	<description><![CDATA[<p>The <em><a href="https://bioconductor.org/packages/3.14/QuasR">QuasR</a></em> package (short for <em>Qu</em>antify and <em>a</em>nnotate <em>s</em>hort reads in <em>R</em>) integrates the functionality of several <strong>R</strong> packages (such as <em><a href="https://bioconductor.org/packages/3.14/IRanges">IRanges</a></em> <span>(Lawrence et al. 2013)</span> and <em><a href="https://bioconductor.org/packages/3.14/Rsamtools">Rsamtools</a></em>) and external software (e.g.&nbsp;<code>bowtie</code>, through the <em><a href="https://bioconductor.org/packages/3.14/Rbowtie">Rbowtie</a></em> package, and <code>HISAT2</code>, through the <em><a href="https://bioconductor.org/packages/3.14/Rhisat2">Rhisat2</a></em> package). The package aims to cover the whole analysis workflow of typical high throughput sequencing experiments, starting from the raw sequence reads, over pre-processing and alignment, up to quantification. A single <strong>R</strong> script can contain all steps of a complete analysis, making it simple to document, reproduce or share the workflow containing all relevant details.</p><p>Address of the bookmark: <a href="https://www.bioconductor.org/packages/devel/bioc/vignettes/QuasR/inst/doc/QuasR.html" rel="nofollow">https://www.bioconductor.org/packages/devel/bioc/vignettes/QuasR/inst/doc/QuasR.html</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>

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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/22403/ryan-e-mills-lab</guid>
  <pubDate>Tue, 26 May 2015 09:29:24 -0500</pubDate>
  <link></link>
  <title><![CDATA[Ryan E. Mills Lab]]></title>
  <description><![CDATA[
<p>Our research group is primarily focused on the analysis of whole genome sequence data to identify genetic variation (primarily structural variation) and examine their potential functional impact in disease phenotypes. We are particularly interested in analyzing complex regions of the genome that are not easily resolved through modern sequencing approaches and which may exhibit interesting mechanistic origins.</p>

<p>We are also interested in the large-scale integration of genomic, expression, methylation and proteomic data sets, as well as the application of whole genome sequence analysis in clinical diagnostics. </p>

<p>More at http://millslab.ccmb.med.umich.edu/index.html</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/23149/raphael-lab</guid>
  <pubDate>Sat, 04 Jul 2015 19:05:29 -0500</pubDate>
  <link></link>
  <title><![CDATA[Raphael Lab]]></title>
  <description><![CDATA[
<p>Raphael Lab research is focused on Bioinformatics and Computational Biology.</p>

<p>Current research interests include next-generation DNA sequencing, structural variation, genome rearrangements in cancer and evolution, and network analysis of somatic mutations in cancer. Earlier research included topics in comparative genomics, multiple sequence alignment, and motif finding.</p>

<p>More athttp://compbio.cs.brown.edu/</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/23633/biorg</guid>
  <pubDate>Tue, 04 Aug 2015 20:52:52 -0500</pubDate>
  <link></link>
  <title><![CDATA[BioRG]]></title>
  <description><![CDATA[
<p>This research group works on problems from the fields of Bioinformatics, Biotechnology, Data Mining, and Information Retrieval. The group's research projects includes Comparative Genomics of Bacterial genomes, Metagenomics, Genomic databases, Pattern Discovery in sequences and structures, micro-array data analysis, prediction of regulatory elements, primer design, probe design, phylogenetic analysis, medical image processing, image analysis, data integration, data mining, information retrieval, knowledge discovery in electronic medical records, and more. </p>

<p>More at http://biorg.cis.fiu.edu/</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/25284/rajiv-gandhi-centre-for-biotechnology-rgcb-invites-applications-for-the-following-three-faculty-scientist</guid>
  <pubDate>Tue, 24 Nov 2015 22:13:16 -0600</pubDate>
  <link></link>
  <title><![CDATA[Rajiv Gandhi Centre for Biotechnology (RGCB) invites applications for the following three faculty scientist]]></title>
  <description><![CDATA[
<p>Scientist Positions<br />Advt. No.RGCB Advt./SCI 2015/1<br /> <br />November 11, 2015</p>

<p>Rajiv Gandhi Centre for Biotechnology (RGCB) invites applications for the following three faculty scientist positions:</p>

<p>Scientist E-II or F in Bioinformatics &amp; Computational Biology</p>

<p>SCIENTIST E-II OR F IN COMPUTATIONAL BIOLOGY &amp; BIOINFORMATICS</p>

<p>Highly motivated and innovative individual who will pursue basic research, solve biological problems with emphasis on computational and quantitative experimental methods and build active bridges to translational research. The scientist will also provide computational biology support to ongoing research programs in disease biology, provide assistance to analyze complex data sets generated by RGCB scientists and collaborators inclusive of including high dimensional “omics” data and next generation sequencing data, such as whole genome, exome, RNA-seq and ChIP-seq as well as provide leadership for high quality training for junior scientists and regular teaching programs of the institute. Areas of research of interest to RGCB include but are not limited to computational, systems, or quantitative biology with applications to cell biology, developmental biology, metabolism, genomics, proteomics, biophysics, biological information systems, network pharmacology, drug design and cancer research. The scientist’s responsibilities include efforts for the integration of DNA variant annotation with statistical genetic analysis methods including linkage, imputation and association methods, adopting novel and innovative methodologies to analyze, integrate and interpret high dimensional data sets, provision of annotation to robust genetics and genomics findings using several data sources and methods, data management of exploratory clinical and R&amp;D studies in partnership with other lines of genetic data generated from internal and external studies, delivery and documentation of genomic information to support genetic studies, ensuring high-quality genetic and genomic data is incorporated into exploratory- clinical research programs, developing tools that make maximum use of multiple data sources to support annotation of DNA variation and contributes to systems biology initiatives within RGCB </p>

<p>More at http://rgcb.res.in/scientist-positions/</p>

<p>Application Form http://rgcb.res.in/wp-content/uploads/2015/11/APPLICATION-FORMAT-FOR-SCIENTISTS.docx</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/26525/ensembl-comparative-genomics-resources</guid>
	<pubDate>Sun, 28 Feb 2016 17:10:20 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/26525/ensembl-comparative-genomics-resources</link>
	<title><![CDATA[Ensembl comparative genomics resources]]></title>
	<description><![CDATA[<div>
<p>The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available.</p>
<p><strong>Database URL:</strong> <a href="http://www.ensembl.org" target="pmc_ext">http://www.ensembl.org</a>.</p>
</div><p>Address of the bookmark: <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4761110/" rel="nofollow">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4761110/</a></p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
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