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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/41991?offset=1060</link>
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	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44900/pegas-a-comprehensive-bioinformatic-solution-for-pathogenic-bacterial-genomic-analysis</guid>
	<pubDate>Mon, 01 Sep 2025 01:18:10 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44900/pegas-a-comprehensive-bioinformatic-solution-for-pathogenic-bacterial-genomic-analysis</link>
	<title><![CDATA[PeGAS: A Comprehensive Bioinformatic Solution for Pathogenic Bacterial Genomic Analysis]]></title>
	<description><![CDATA[<p><span>This is PeGAS, a powerful bioinformatic tool designed for the seamless quality control, assembly, and annotation of Illumina paired-end reads specific to pathogenic bacteria. This tool integrates state-of-the-art open-source software to provide a streamlined and efficient workflow, ensuring accurate insights into the genomic makeup of pathogenic microbial strains.</span></p>
<p><span><img src="https://github.com/liviurotiul/PeGAS/raw/main/Features.png" alt="image" style="border: 0px;"></span></p><p>Address of the bookmark: <a href="https://github.com/liviurotiul/PeGAS" rel="nofollow">https://github.com/liviurotiul/PeGAS</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/38642/thank-you-email-after-bioinformatics-interview</guid>
	<pubDate>Tue, 08 Jan 2019 15:37:33 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/38642/thank-you-email-after-bioinformatics-interview</link>
	<title><![CDATA[Thank You Email After Bioinformatics Interview !]]></title>
	<description><![CDATA[<p>A good interview thank you email or note should contain three essential pieces:</p><p>a) Show appreciation for their time and thank them</p><p>b) Mention something specific you talked about in the interview, so they know it&rsquo;s not a cut &amp; paste email</p><p>c) Express interest in the position and tell them you&rsquo;re excited to learn more</p><p>d)&nbsp;Invite them to contact you if they have any questions/concerns, or need clarification on anything discussed</p><p>First sample:</p><blockquote><p>Dear Dr XYZ<br />I enjoyed speaking with you today about the XXX position&nbsp;at the X Lab, Uni. The job seems to be an excellent match for my&nbsp;skills and interests.<br /><br />The lab loaded with new updated technology and international experts,&nbsp;that you informed while interviewing confirmed my desire to work with&nbsp;X lab.<br /><br />In addition to my enthusiasm, I will bring to the position strong&nbsp;writing skills, assertiveness, and the ability to encourage others to&nbsp;work cooperatively with the group<br /><br />I appreciate the time you took to interview me. I am very interested&nbsp;in working with you and look forward to hearing from you regarding&nbsp;this position.<br /><br />Sincerely,<br />XXX</p></blockquote><p>Second sample:</p><p>&nbsp;</p><blockquote><p>Dear Dr XXX,</p><p>I wanted to take a second to thank you for your time . I enjoyed our conversation about and enjoyed learning about the position overall.</p><p>It sounds like an exciting opportunity, and an opportunity I could succeed and excel in! I&rsquo;m looking forward to hearing any updates you can share, and don&rsquo;t hesitate to contact me if you have any questions or concerns in the meantime.</p><p>Thanks again for the great conversation .</p><p>Best Regards,<br />XXX</p></blockquote>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/34463/single-cell-rnaseq-data-analysis-tutorial</guid>
	<pubDate>Mon, 27 Nov 2017 16:24:29 -0600</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/34463/single-cell-rnaseq-data-analysis-tutorial</link>
	<title><![CDATA[Single Cell RNAseq data analysis tutorial !!]]></title>
	<description><![CDATA[<ul>
<li>A major breakthrough (replaced microarrays) in the late 00&rsquo;s and has been widely used since</li>
<li>Measures the&nbsp;average expression level&nbsp;for each gene across a large population of input cells</li>
<li>Useful for comparative transcriptomics, e.g.&nbsp;samples of the same tissue from different species</li>
<li>Useful for quantifying expression signatures from ensembles, e.g.&nbsp;in disease studies</li>
<li>Insufficient&nbsp;for studying heterogeneous systems, e.g.&nbsp;early development studies, complex tissues (brain)</li>
<li>Does&nbsp;not&nbsp;provide insights into the stochastic nature of gene expression</li>
</ul><p>Following are the useful links:</p><p><a href="http://hemberg-lab.github.io/scRNA.seq.course/scRNA-seq-course.pdf" target="_blank">Single Cell RNAseq data analysis Tutorial</a></p><p><a href="https://f1000research.com/articles/5-2122/v2" target="_blank">A step-by-step workflow for low-level analysis of single-cell RNA-seq data</a></p><p><a href="https://www.bioconductor.org/help/workflows/simpleSingleCell/" target="_blank">A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor</a></p><p>SCell: single-cell RNA-seq analysis software</p><p><a href="https://github.com/diazlab/SCell">https://github.com/diazlab/SCell</a></p><p>Beta-Poisson model for single-cell RNA-seq data analyses</p><p><a href="https://github.com/nghiavtr/BPSC">https://github.com/nghiavtr/BPSC</a></p><p>Sincera: A Computational Pipeline for Single Cell RNA-Seq Profiling Analysis</p><p><a href="https://research.cchmc.org/pbge/sincera.html">https://research.cchmc.org/pbge/sincera.html</a></p><p>SC3 &ndash; consensus clustering of single-cell RNA-Seq data</p><p><a href="http://biorxiv.org/content/early/2016/09/02/036558">http://biorxiv.org/content/early/2016/09/02/036558</a></p><p>Citrus: A toolkit for single cell sequencing analysis</p><p><a href="http://biorxiv.org/content/early/2016/09/14/045070">http://biorxiv.org/content/early/2016/09/14/045070</a></p><p>Single-Cell Resolution of Temporal Gene Expression during Heart Development</p><p><a href="http://www.cell.com/developmental-cell/fulltext/S1534-5807%2816%2930682-7">http://www.cell.com/developmental-cell/fulltext/S1534-5807(16)30682-7</a></p><p>Scalable latent-factor models applied to single-cell RNA-seq data separate biological drivers from confounding effects</p><p><a href="http://biorxiv.org/content/early/2016/11/15/087775">http://biorxiv.org/content/early/2016/11/15/087775</a></p><p>Single cell transcriptomes identify human islet cell signatures and reveal cell-type-specific expression changes in type 2 diabetes</p><p><a href="http://genome.cshlp.org/content/early/2016/11/18/gr.212720.116.abstract">http://genome.cshlp.org/content/early/2016/11/18/gr.212720.116.abstract</a></p><p>SCODE: An efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation</p><p><a href="http://biorxiv.org/content/early/2016/11/21/088856">http://biorxiv.org/content/early/2016/11/21/088856</a></p><p>SCOUP is a probabilistic model to analyze single-cell expression data during differentiation</p><p><a href="https://github.com/hmatsu1226/SCOUP">https://github.com/hmatsu1226/SCOUP</a></p><p>scLVM is a modelling framework for single-cell RNA-seq data</p><p><a href="https://github.com/PMBio/scLVM">https://github.com/PMBio/scLVM</a></p><p>Selective Locally linear Inference of Cellular Expression Relationships (SLICER) algorithm for inferring cell trajectories</p><p><a href="https://github.com/jw156605/SLICER">https://github.com/jw156605/SLICER</a></p><p>SinQC: A Method and Tool to Control Single-cell RNA-seq Data Quality</p><p><a href="http://www.morgridge.net/SinQC.html">http://www.morgridge.net/SinQC.html</a></p><p>TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis</p><p><a href="https://github.com/zji90/TSCAN">https://github.com/zji90/TSCAN</a></p><p>Visualization and cellular hierarchy inference of single-cell data using SPADE</p><p><a href="http://www.nature.com/nprot/journal/v11/n7/full/nprot.2016.066.html">http://www.nature.com/nprot/journal/v11/n7/full/nprot.2016.066.html</a></p><p>OEFinder: Identify ordering effect genes in single cell RNA-seq data</p><p><a href="https://github.com/lengning/OEFinder">https://github.com/lengning/OEFinder</a></p>]]></description>
	<dc:creator>Robert M Willioms</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/40228/bioinformatics-services-cro-services</guid>
	<pubDate>Wed, 06 Nov 2019 00:33:11 -0600</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/40228/bioinformatics-services-cro-services</link>
	<title><![CDATA[Bioinformatics Services / CRO Services]]></title>
	<description><![CDATA[<p>RASA is set to provide premium technical and scientific services in a form of solutions, product development and training. .We are also very proficient in providing the high quality Research &amp; Development services in life science informatics field like Next Generation Sequencing (NGS) Data Analysis,Computational Drug Discovery, Bioinformatics, Chemo-informatics and BIO-IT.</p><p>RASA offers faster, better and cost effective cutting edge technology solutions to chemical and life science research and industry. We provide our customers with A seamless model of wide expertise and comprehensive platforms. Our Value is to take our customers</p>]]></description>
	<dc:creator>RASA Life Sciences</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/40503/3-phd-positions-available-in-the-area-of-bioinformaticscomputational-biology-at-ulsteracuk</guid>
  <pubDate>Thu, 02 Jan 2020 12:41:10 -0600</pubDate>
  <link></link>
  <title><![CDATA[3 PhD positions available in the area of Bioinformatics/Computational Biology at ulster.ac.uk]]></title>
  <description><![CDATA[
<p>3 PhD positions available in the area of Bioinformatics/Computational Biology, Machine Learning (ML)/Artificial Intelligence (AI), Biomarker Discovery, Stratified/Personalized Medicine in Mental Health, Diabetes and Multimorbidity. Please see details (weblinks) below:</p>

<p>1. https://www.ulster.ac.uk/doctoralcollege/find-a-phd/510894<br />2. https://www.ulster.ac.uk/doctoralcollege/find-a-phd/511458<br />3. https://www.ulster.ac.uk/doctoralcollege/find-a-phd/512618</p>

<p>Looking for students with good computational/programming skills (preferable in Linux/Shell, Python and/or R) and knowledge in computational biology and statistics. However, students from more biology oriented background but strong interest to learn bioinformatics and programming are also encouraged to apply.</p>

<p>Informal inquiries are welcomed at: p.shukla@ulster.ac.uk</p>

<p>Dr Priyank Shukla PhD FHEA FCHERP<br />Lecturer (Asst Prof) in Stratified Medicine (Bioinformatics)</p>

<p>Northern Ireland Centre for Stratified Medicine<br />Biomedical Sciences Research Institute<br />University of Ulster (Magee Campus)<br />C-TRIC Building, Altnagelvin Area Hospital<br />Glenshane Road, Derry/Londonderry<br />BT47 6SB, Northern Ireland, United Kingdom</p>

<p>T: +44 28 7167 5690<br />E: p.shukla@ulster.ac.uk<br />W: https://www.ulster.ac.uk/staff/p-shukla</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/42263/data-steward-research-development-specialist-at-at-the-luxembourg-centre-for-systems-biomedicine-lcsb</guid>
  <pubDate>Sun, 25 Oct 2020 22:36:38 -0500</pubDate>
  <link></link>
  <title><![CDATA[Data Steward / Research &amp; Development Specialist at at the Luxembourg Centre for Systems Biomedicine (LCSB)]]></title>
  <description><![CDATA[
<p>Applications should be addressed online to: Prof. Dr. Reinhard Schneider, Head of the Bioinformatics Core Facility</p>

<p>For further information, please contact: Dr. Pinar Alper (pinar.alper@uni.lu)</p>

<p>Applications should be submitted online and include:</p>

<p>A detailed curriculum vitae<br />Cover letter mentioning the reference number<br />List of publications/software projects<br />Description of past experience and future interests<br />Names and addresses of three referees<br />Early application is highly encouraged, as the applications will be processed upon reception. Please apply ONLINE formally through the HR system. Applications by email will not be considered.</p>

<p>*gn=gender neutral.</p>

<p>More at https://recruitment.uni.lu/en/details.html?nPostingId=54616&amp;nPostingTargetId=74219&amp;id=QMUFK026203F3VBQB7V7VV4S8&amp;LG=UK&amp;mask=karriereseiten&amp;sType=Social%20Recruiting</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40611/deepvariant-an-analysis-pipeline-that-uses-a-deep-neural-network-to-call-genetic-variants-from-next-generation-dna-sequencing-data</guid>
	<pubDate>Sat, 25 Jan 2020 13:28:09 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40611/deepvariant-an-analysis-pipeline-that-uses-a-deep-neural-network-to-call-genetic-variants-from-next-generation-dna-sequencing-data</link>
	<title><![CDATA[DeepVariant : an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.]]></title>
	<description><![CDATA[<p><span>DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.</span></p>
<p><span><span>DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant relies on&nbsp;</span><a href="https://github.com/google/nucleus">Nucleus</a><span>, a library of Python and C++ code for reading and writing data in common genomics file formats (like SAM and VCF) designed for painless integration with the&nbsp;</span><a href="https://www.tensorflow.org/">TensorFlow</a><span>&nbsp;machine learning framework.</span></span></p>
<p><span><a href="https://ai.googleblog.com/2017/12/deepvariant-highly-accurate-genomes.html">https://ai.googleblog.com/2017/12/deepvariant-highly-accurate-genomes.html</a></span></p>
<p><span><a href="https://www.biorxiv.org/content/10.1101/092890v6">https://www.biorxiv.org/content/10.1101/092890v6</a></span></p>
<p><span><img src="https://4.bp.blogspot.com/-2KlXZO60sWE/WiGc8qlZfxI/AAAAAAAACOs/s1pNiKI8jsAvJLr1E_po5udDO8eObm_awCLcBGAs/s640/image3.png" width="640" height="427" alt="image" style="border: 0px;"></span></p><p>Address of the bookmark: <a href="https://github.com/google/deepvariant" rel="nofollow">https://github.com/google/deepvariant</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41209/juicebox-visualization-and-analysis-software-for-hi-c-data</guid>
	<pubDate>Fri, 21 Feb 2020 00:33:38 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41209/juicebox-visualization-and-analysis-software-for-hi-c-data</link>
	<title><![CDATA[Juicebox: Visualization and analysis software for Hi-C data]]></title>
	<description><![CDATA[<p>Juicebox is visualization software for Hi-C data. This distribution includes the source code for Juicebox,&nbsp;<a href="https://github.com/theaidenlab/juicer/wiki/Download">Juicer Tools</a>, and&nbsp;<a href="https://aidenlab.org/assembly/">Assembly Tools</a>.&nbsp;<a href="https://github.com/theaidenlab/juicebox/wiki/Download">Download Juicebox here</a>, or use&nbsp;<a href="https://aidenlab.org/juicebox">Juicebox on the web</a>. Detailed documentation is available&nbsp;<a href="https://github.com/theaidenlab/juicebox/wiki">on the wiki</a>. Instructions below pertain primarily to usage of command line tools and the Juicebox jar files.</p>
<p>Juicebox can now be used to visualize and interactively (re)assemble genomes. Check out the Juicebox Assembly Tools Module website&nbsp;<a href="https://aidenlab.org/assembly">https://aidenlab.org/assembly</a>&nbsp;for more details on how to use Juicebox for assembly.</p>
<p>GUI at&nbsp;<a href="https://aidenlab.org/juicebox/">https://aidenlab.org/juicebox/</a></p><p>Address of the bookmark: <a href="https://github.com/aidenlab/Juicebox" rel="nofollow">https://github.com/aidenlab/Juicebox</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/42308/icmr-scientist-jobs-for-biotechlife-sciencebiology-bioinformatics</guid>
  <pubDate>Tue, 10 Nov 2020 18:45:49 -0600</pubDate>
  <link></link>
  <title><![CDATA[ICMR Scientist Jobs For Biotech/Life Science/Biology &amp; Bioinformatics]]></title>
  <description><![CDATA[
<p>CMR welcomes on-line applications up to 5th December 2020 till 5:30 PM to fill out the vacancies of 42 Scientist’ E’ (Medical), 01 Scientist ‘E’ (Non-Medical), 16 Scientist ‘D’ (Medical) and also 06 Scientist ‘D’ (Non-Medical) from Indian Citizens for appointment on regular basis under Direct Recruitment with all India transfer liability under the Council.</p>

<p>Post I</p>

<p>Name of the Post: Scientist-E (Non-Medical)</p>

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

<p>Upper Age limit: 50 years</p>

<p>Post II</p>

<p>Name of the Post: Scientist-D (Non-Medical)</p>

<p>Number of positions: Six</p>

<p>Upper Age limit: 45 years</p>

<p>Fee:</p>

<p>Application Fee of Rs. 1500/- (Rupees one thousand five hundred only) is needed. SC / ST / Women/ PWD/ EWS applicants are exempted from application fee. Application Fee is to be paid by candidates through online web link given up the application. Application fees when paid will certainly not be reimbursed under any situations.</p>

<p>How to apply:</p>

<p>i) Candidates should apply online on https://recruit.icmr.org.in. A separate application needs to be submitted for every post, with the required application fee.</p>

<p>ii) Following self-attested documents are required to be uploaded together with the application:<br />a) Proof of Date of Birth.<br />b) Educational qualifications.<br />c) Experience.</p>

<p>More at https://recruit.icmr.org.in/assets/uploads/advertisement/ICMR_Advertisement_06112020.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41996/wgd%E2%80%94simple-command-line-tools-for-the-analysis-of-ancient-whole-genome-duplications</guid>
	<pubDate>Thu, 23 Jul 2020 05:49:45 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41996/wgd%E2%80%94simple-command-line-tools-for-the-analysis-of-ancient-whole-genome-duplications</link>
	<title><![CDATA[wgd—simple command line tools for the analysis of ancient whole-genome duplications]]></title>
	<description><![CDATA[<p><span>wgd is a easy to use command-line tool for<span>&nbsp;</span></span><em>K</em><sub>S</sub><span><span>&nbsp;</span>distribution construction named wgd. The wgd suite provides commonly used<span>&nbsp;</span></span><em>K</em><sub>S</sub><span><span>&nbsp;</span>and colinearity analysis workflows together with tools for modeling and visualization, rendering these analyses accessible to genomics researchers in a convenient manner.</span></p>
<p><a href="https://academic.oup.com/bioinformatics/article/35/12/2153/5162749">https://academic.oup.com/bioinformatics/article/35/12/2153/5162749</a></p><p>Address of the bookmark: <a href="https://github.com/arzwa/wgd" rel="nofollow">https://github.com/arzwa/wgd</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
</item>

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