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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/2261?offset=430</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/28997/braker-pipeline-for-fully-automated-prediction-of-protein-coding-genes-with-genemark-eset-and-augustus-in-novel-eukaryotic-genomes</guid>
	<pubDate>Thu, 01 Sep 2016 08:02:59 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/28997/braker-pipeline-for-fully-automated-prediction-of-protein-coding-genes-with-genemark-eset-and-augustus-in-novel-eukaryotic-genomes</link>
	<title><![CDATA[BRAKER: pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes]]></title>
	<description><![CDATA[<p><span>Gene finding in eukaryotic genomes is notoriously difficult to automate. The task is to design a work flow with a minimal set of tools that would reach state-of-the-art performance across a wide range of species. GeneMark-ET is a gene prediction tool that incorporates RNA-Seq data into unsupervised training and subsequently generates ab initio gene predictions. AUGUSTUS is a gene finder that usually requires supervised training and uses information from RNA-Seq reads in the prediction step. Complementary strengths of GeneMark-ET and AUGUSTUS provided motivation for designing a new combined tool for automatic gene prediction.</span></p>
<p>http://www.ncbi.nlm.nih.gov/pubmed/26559507</p><p>Address of the bookmark: <a href="http://bioinf.uni-greifswald.de/bioinf/braker/" rel="nofollow">http://bioinf.uni-greifswald.de/bioinf/braker/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30168/gene-synteny-database</guid>
	<pubDate>Fri, 16 Dec 2016 11:09:39 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30168/gene-synteny-database</link>
	<title><![CDATA[Gene Synteny Database]]></title>
	<description><![CDATA[<p>Comparative genomics remains a pivotal strategy to study the evolution of gene organization, and this primacy is reinforced by the growing number of full genome sequences available in public repositories. Despite this growth, bioinformatic tools available to visualize and compare genomes and to infer evolutionary events remain restricted to two or three genomes at a time, thus limiting the breadth and the nature of the question that can be investigated. Here we present Genomicus, a new synteny browser that can represent and compare unlimited numbers of genomes in a broad phylogenetic view. In addition, Genomicus includes reconstructed ancestral gene organization, thus greatly facilitating the interpretation of the data.</p>
<p><strong>Availability:</strong>&nbsp;Genomicus is freely available for online use at&nbsp;<a href="http://www.dyogen.ens.fr/genomicus" target="pmc_ext">http://www.dyogen.ens.fr/genomicus</a>&nbsp;while data can be downloaded at&nbsp;<a href="ftp://ftp.biologie.ens.fr/pub/dyogen/genomicus" target="pmc_ext">ftp://ftp.biologie.ens.fr/pub/dyogen/genomicus</a></p>
<p><strong>Contact:</strong>&nbsp;<a href="mailto:dev@null">rf.sne.eigoloib@crh</a></p><p>Address of the bookmark: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2853686/" rel="nofollow">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2853686/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials</guid>
	<pubDate>Thu, 29 Aug 2013 09:23:51 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials</link>
	<title><![CDATA[Bioinformatics Algorithm Demonstrations and Tutorials]]></title>
	<description><![CDATA[<p>Abstract</p>
<p>This project presents demonstrations of selected computer science algorithms important in&nbsp;bioinformatics, implemented in the spreadsheet program Microsoft Excel. Spreadsheets provide an&nbsp;interesting platform for demonstration of algorithms, since various steps of the calculations can be&nbsp;exposed in a manner that is easily comprehensible to users with little programming experience. The&nbsp;algorithms demonstrated include two approaches to approximate string matching (dynamic programming&nbsp;and Shift-AND numeric approximate matching), Hierarchical Clustering (used in phylogenetic studies&nbsp;and microarray analysis of gene expression), a Naive Bayes Classifier for simulated microarray gene&nbsp;expression data, and a simple Neural Network. These demonstrations are designed to serve as&nbsp;instructional aids in bioinformatics courses.</p>
<p>Tutorial @&nbsp;http://www.cybertory.org/downloads/bae/BioinformaticsAlgorithmsInExcel.zip</p>
<p>One of the best resource for online bioinformatics learning is https://stepic.org/Bioinformatics-Algorithms-2 Enjoy the online learning.</p>
<p>Reference :&nbsp;cybertory</p>
<blockquote>
<p><span>" Please add your favourite bioinformatics algorithms and tutorial links below in the comment section, for the benefit of bioinformatics and computational biology community ".&nbsp;</span></p>
</blockquote><p>Address of the bookmark: <a href="http://www.cybertory.org/downloads/bae/BioinformaticsAlgorithmsExcelDoc.pdf" rel="nofollow">http://www.cybertory.org/downloads/bae/BioinformaticsAlgorithmsExcelDoc.pdf</a></p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/23498/algorithms-for-dna-sequencing-course-offered-each-month</guid>
	<pubDate>Sun, 26 Jul 2015 01:57:02 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/23498/algorithms-for-dna-sequencing-course-offered-each-month</link>
	<title><![CDATA[Algorithms for DNA Sequencing (course offered each month)]]></title>
	<description><![CDATA[<p>"<span>We will learn computational methods -- algorithms and data structures -- for analyzing DNA sequencing data. We will learn a little about DNA, genomics, and how DNA sequencing is used. We will use Python to implement key algorithms and data structures and to analyze real genomes and DNA sequencing datasets."</span></p>
<p><span>Source :&nbsp;https://www.coursera.org/course/ads1</span></p>
<p>&nbsp;</p><p>Address of the bookmark: <a href="https://www.coursera.org/course/ads1" rel="nofollow">https://www.coursera.org/course/ads1</a></p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/44400/pevzner-lab</guid>
  <pubDate>Thu, 02 Nov 2023 05:39:26 -0500</pubDate>
  <link></link>
  <title><![CDATA[Pevzner Lab !]]></title>
  <description><![CDATA[
<p>The laboratory works on genome sequencing, immunoproteogenomics, antibiotics sequencing, and comparative genomics - computational technologies that enabled new applications and allowed scientists to attack biological problems that remained beyond the reach of previous techniques.</p>

<p>https://bioalgorithms.ucsd.edu/research4.html</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/32379/enrichr-a-comprehensive-gene-set-enrichment-analysis</guid>
	<pubDate>Thu, 27 Apr 2017 05:42:09 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32379/enrichr-a-comprehensive-gene-set-enrichment-analysis</link>
	<title><![CDATA[Enrichr: a comprehensive gene set enrichment analysis]]></title>
	<description><![CDATA[<p><span>Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gene set libraries available for analysis and download. In total, Enrichr currently contains 180 184 annotated gene sets from 102 gene set libraries. New features have been added to Enrichr including the ability to submit fuzzy sets, upload BED files, improved application programming interface and visualization of the results as clustergrams. Overall, Enrichr is a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries. Enrichr is freely available at:&nbsp;</span><a href="http://amp.pharm.mssm.edu/Enrichr" target="">http://amp.pharm.mssm.edu/Enrichr</a><span>.</span></p>
<p>https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw377</p><p>Address of the bookmark: <a href="http://amp.pharm.mssm.edu/Enrichr/" rel="nofollow">http://amp.pharm.mssm.edu/Enrichr/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/915/researcher-in-computer-sciencebiology</guid>
  <pubDate>Mon, 15 Jul 2013 18:38:40 -0500</pubDate>
  <link></link>
  <title><![CDATA[Researcher in computer science/biology]]></title>
  <description><![CDATA[
<p>Researcher in Computer Science at the Computational Biology Unit - temporary employment</p>

<p>The Department of Informatics is a vacant position as a researcher in computer science, related to Computational Biology Unit (CBU), for 3 years.<br /> <br />The position is part of CBU Service Group and will focus on bioinformatic analysis project and especially the analysis of high-throughput data, including NGS (sequencing), and proteomics data.<br /> <br />The successful candidate will be part of the Norwegian bioinformatics platform's national helpdesk within the project ELIXIR.NO<br /> <br />Applicants must hold a PhD in a relevant subject such as computer science, mathematics, molecular biology and also possess expertise and experience in bioinformatics statistics and analysis of data from high-throughput molecular experiment.<br /> <br />Basic programming or scripting skills are required. Experience in Python, R, Perl, Linux-based operating systems and moreover knowledge of databases and web programming will be a strength for applicants.<br /> <br />We expect enthusiasm and independence and moreover the ability to work in an interdisciplinary team environment.<br /> <br />Good knowledge of English is required.<br /> <br />Salaries start at level 57 (code 1109/LR 24.1) by appointment. Further promotion occurs after<br />service seniority in the position (at grade 57-65). Of particularly highly qualified applicants may be considered a higher salary.<br /> <br />Further information about the position is available from the chair of the CBU, <br />Professor Inge Jonassen, e-mail: Inge.Jonassen @ ii.uib.no<br /> <br />The successful applicant must comply with the guidelines that apply at any given time the position.<br /> <br />State employment shall as far as possible reflect the diversity of the population. It is therefore an objective to achieve a balanced age and sex composition and the recruitment of persons with immigrant backgrounds. Persons with immigrant background are requested to apply for the position.<br /> <br />Women are particularly encouraged to apply. If the experts find that several applicants have approximately equivalent qualifications, the rules on equal in the Personnel Regulations for Academic Positions will be applied.<br /> <br />University of Bergen applies the principles of public openness when recruiting staff to scientific positions.<br /> <br />Information about the applicant may be made public even though the applicant has requested not to be named in the list of applicants. If the request does not host admitted to the result, the applicant shall be notified of this.<br /> <br />Send application, CV, certificates, diplomas, undergraduate work and a list of publications (list of publications) online by clicking on https://www.jobbnorge.no/jobbsoknet/login.aspx?returnurl=/jobbsoknet/jobapplication.aspx?jobid=95196<br /> <br />You need to upload certified translations into English or a Scandinavian language of appendices, such as diplomas and transcripts.<br /> <br />Applications sent by email to individuals at the institute will not be considered.<br /> <br />Deadline: 9 August 2013</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/1515/list-of-pharmacogenomics-companies-in-india</guid>
	<pubDate>Fri, 09 Aug 2013 13:26:56 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/1515/list-of-pharmacogenomics-companies-in-india</link>
	<title><![CDATA[List of pharmacogenomics companies in India]]></title>
	<description><![CDATA[<p>pharmacogenomics companies in India are making their good impacts. Here is the list of few pharmacogenomics companies. Please add more if not mentioned here.</p><p>Genomics in India <br /><a href="http://www.ganitlabs.in/">www.ganitlabs.in</a> <br /><a href="http://www.sandor.co.in/">www.sandor.co.in</a> <br /><a href="http://www.igib.res.in/">www.igib.res.in</a> <br /><a href="http://www.genotypic.co.in/">www.genotypic.co.in</a> <br /><a href="http://www.ocimumbio.com/">www.ocimumbio.com</a> <br /><a href="http://www.abcgenomics.com/">www.abcgenomics.com</a> <br /><a href="http://www.xcelrisgenomics.com/">www.xcelrisgenomics.com</a> <br /><a href="http://www.ayugen.com/">www.ayugen.com</a> <br /><a href="http://www.geneombiotech.com/">www.geneombiotech.com</a></p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/2001/the-ontario-institute-for-cancer-research-oicr-genomics-lab-toronto-canada</guid>
  <pubDate>Mon, 12 Aug 2013 01:43:13 -0500</pubDate>
  <link></link>
  <title><![CDATA[The Ontario Institute for Cancer Research (OICR) Genomics Lab , Toronto, Canada.]]></title>
  <description><![CDATA[
<p>The Human Genome Project led to the development of a wide array of technologies to screen the genome and its products (genes, proteins, metabolites) and molecules that interact with these products (chemicals, RNAi). The existence of these tools resulted in the creation of facilities that use robotics and informatics to generate high-throughput screens of DNA, RNA, protein, tissue, chemicals and other substances.</p>

<p>The genomics platform uses cancer genome sequencing and other high-throughput techniques to identify genes critical to the development of cancer and anomalies in the genomic profile of the tumours.</p>

<p>For more info visit : http://oicr.on.ca/</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/6458/bigre-lab</guid>
  <pubDate>Sun, 17 Nov 2013 10:35:49 -0600</pubDate>
  <link></link>
  <title><![CDATA[BIGRE Lab]]></title>
  <description><![CDATA[
<p>The Laboratoire de Bioinformatique des Génomes et des Réseaux (Genome and Network Bioinformatics) is specialized in the conception, implementation, evaluation and application of bioinformatics approaches for the analysis of genome, transcriptome, proteome and metabolism.<br />Our main activities include</p>

<p>Analysis of regulatory sequences (RSAT project)<br />Classification and analysis of mobile genetic elements (ACLAME project).<br />Analysis of molecular interaction networks (NeAT project)<br />Inference of metabolic pathways from genomic and post-genomic data <br />(metabolic pathfinding, see also metabolic pathfinding in NeAT)<br />Critical assesment of protein interactions (CAPRI)</p>

<p>Lab Page http://www.bigre.ulb.ac.be/</p>
]]></description>
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