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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/34485?offset=160</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/29679/comparative-genomics-educational-material-and-papers-bookmarks</guid>
	<pubDate>Wed, 09 Nov 2016 16:23:30 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/29679/comparative-genomics-educational-material-and-papers-bookmarks</link>
	<title><![CDATA[Comparative genomics educational material and papers bookmarks]]></title>
	<description><![CDATA[<p><span>Alignment of the porcine genome against seven other mammalian genomes (</span><a href="http://www.nature.com/nature/journal/v491/n7424/full/nature11622.html#supplementary-information">Supplementary Information</a><span>) identified homologous synteny blocks (HSBs). Using porcine HSBs and stringent filtering criteria, 192 pig-specific evolutionary breakpoint regions (EBRs) were located. The number of porcine EBRs </span><span>is comparable to the number of bovine-lineage-specific EBRs (100) reported earlier using a slightly lower resolution (500</span><span><span>&thinsp;</span></span><span>kilobases (kb)), indicating that both lineages evolved with an average rate of ~2.1 large-scale rearrangements per million years after the divergence from a common cetartiodactyl ancestor ~60</span><span><span>&thinsp;</span></span><span>Myr ago</span><sup><a href="http://www.nature.com/nature/journal/v491/n7424/full/nature11622.html#ref2" title="Meredith, R. W. et al. Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. Science 334, 521-524 (2011)">2</a></sup><span>. This rate compares to ~1.9 rearrangements per million years within the primate lineage (</span><a href="http://www.nature.com/nature/journal/v491/n7424/full/nature11622.html#supplementary-information">Supplementary Table 11</a><span>). A total of 20 and 18 cetartiodactyl EBRs (shared by pigs and cattle) were detected using the pig and human genomes as a reference, respectively.</span></p><p>Address of the bookmark: <a href="http://www.nature.com/nature/journal/v491/n7424/abs/nature11622.html" rel="nofollow">http://www.nature.com/nature/journal/v491/n7424/abs/nature11622.html</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/33741/diya-a-bacterial-annotation-pipeline-for-any-genomics-lab</guid>
	<pubDate>Fri, 30 Jun 2017 08:48:26 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/33741/diya-a-bacterial-annotation-pipeline-for-any-genomics-lab</link>
	<title><![CDATA[DIYA: a bacterial annotation pipeline for any genomics lab]]></title>
	<description><![CDATA[<p><span>DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV</span></p>
<p><span>http://gmod.org/wiki/Diya</span></p><p>Address of the bookmark: <a href="https://sourceforge.net/projects/diyg/" rel="nofollow">https://sourceforge.net/projects/diyg/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/34929/shendurelab</guid>
  <pubDate>Thu, 28 Dec 2017 09:57:50 -0600</pubDate>
  <link></link>
  <title><![CDATA[ShendureLab]]></title>
  <description><![CDATA[
<p>The mission of our lab is to develop and apply new technologies and methods for genetics, genomics and molecular biology. Most of our work exploits next-generation DNA sequencing which is effectively emerging as a broadly enabling microscope for the measurement of biological phenomena. Our ongoing work generally falls into six areas. These are listed below as links to representative publications in each area.</p>

<p>Developing New Molecular Methods</p>

<p>Genomic Approaches to Developmental Biology</p>

<p>Massively Parallel Functional Genomics</p>

<p>Translating Genomics to the Clinic</p>

<p>Genetic Basis of Human Disease</p>

<p>Genome Sequencing Technologies</p>

<p>http://krishna.gs.washington.edu/index.html<br />http://www.gs.washington.edu/faculty/shendure.htm</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37257/asar-advanced-metagenomic-sequence-analysis-in-r</guid>
	<pubDate>Mon, 09 Jul 2018 05:20:50 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37257/asar-advanced-metagenomic-sequence-analysis-in-r</link>
	<title><![CDATA[ASAR: Advanced metagenomic Sequence Analysis in R]]></title>
	<description><![CDATA[<p><span>An interactive data analysis tool for selection, aggregation and visualization of metagenomic data is presented. Functional analysis with a SEED hierarchy and pathway diagram based on KEGG orthology based upon MG-RAST annotation results is available.</span></p>
<p><span><span>To read the manual, please click the link&nbsp;</span><a href="https://askarbek-orakov.github.io/ASAR/">https://askarbek-orakov.github.io/ASAR/</a></span></p><p>Address of the bookmark: <a href="https://github.com/Askarbek-orakov/ASAR" rel="nofollow">https://github.com/Askarbek-orakov/ASAR</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40955/the-global-alliance-for-genomics-and-health-ga4gh</guid>
	<pubDate>Sat, 08 Feb 2020 07:37:31 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40955/the-global-alliance-for-genomics-and-health-ga4gh</link>
	<title><![CDATA[The Global Alliance for Genomics and Health (GA4GH)]]></title>
	<description><![CDATA[<p>The Global Alliance for Genomics and Health (GA4GH) is a policy-framing and technical standards-setting organization, seeking to enable responsible genomic data sharing within a <a href="https://www.ga4gh.org/genomic-data-toolkit/regulatory-ethics-toolkit/framework-for-responsible-sharing-of-genomic-and-health-related-data/">human rights framework</a>.</p>
<p>GA4GH core funders and sponsors enable our work and allow us to convene the international genomic data sharing community.</p>
<p>https://www.ga4gh.org/</p><p>Address of the bookmark: <a href="https://www.ga4gh.org/" rel="nofollow">https://www.ga4gh.org/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/42490/bioinformatics-scientist-%E2%80%93-icmr-computational-genomics-centre</guid>
  <pubDate>Sat, 26 Dec 2020 10:18:29 -0600</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics Scientist – ICMR Computational Genomics Centre]]></title>
  <description><![CDATA[
<p>ICMR invites online applications, from Indian Citizens, up to 8th January 2020 till 5:30 PM to fill up the following post to be filled purely on a temporary basis under “ICMR Computational Genomics Centre” under Dr. Harpreet Singh, Head, Division of Biomedical Informatics (BMI), ICMR HQRS, New Delhi 110029.<br />The Terms &amp; Conditions for the post are as follows:</p>

<p>a) Scientist-B – UR (2 posts-Bioinformatics) on consolidated salary of Rs.48,000/- pm + HRA</p>

<p>b) Scientist C – UR (1 post -Bioinformatics) on consolidated salary of Rs. 51,000 pm+ HRA</p>

<p>c) Scientist B- UR (2 post-Statistics) on a consolidated salary of Rs.48,000/- pm +HRA</p>

<p>d) Computer Programmer 1 post UR &amp; 1 post SC on a consolidated salary of Rs. 32,500/- pm</p>

<p>e) Research Assistant -UR 1 post on a consolidated salary of Rs. 31,000/- pm</p>

<p>More at https://projectjobs.icmr.org.in/sccbioinformatics/uploads/recruitment/Adv_BMI_24122020.pdf</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43362/machine-learning-for-genomics</guid>
	<pubDate>Thu, 09 Sep 2021 11:26:32 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43362/machine-learning-for-genomics</link>
	<title><![CDATA[Machine Learning for Genomics]]></title>
	<description><![CDATA[<h3>Module 1: Statistics for genomics (2-8 August 2021)</h3>
<ul>
<li>A simple intro to statistical distributions</li>
<li>hypothesis testing</li>
<li>linear models.</li>
</ul>
<p>reading:&nbsp;<a href="http://compgenomr.github.io/book/stats.html">http://compgenomr.github.io/book/stats.html</a></p>
<p>slides:&nbsp;<a href="https://github.com/BIMSBbioinfo/compgen2021/tree/main/week1/compgen2021_stats.pdf">https://github.com/BIMSBbioinfo/compgen2021/tree/main/week1/compgen2021_stats.pdf</a></p>
<p>exercises+code:&nbsp;<a href="https://github.com/BIMSBbioinfo/compgen2021/tree/main/week1/">https://github.com/BIMSBbioinfo/compgen2021/tree/main/week1/</a></p>
<h3><a href="https://github.com/BIMSBbioinfo/compgen2021#module-2-unsupervised-learning-for-genomics-9-15-august-2021"></a>Module 2: Unsupervised learning for genomics (9-15 August 2021)</h3>
<ul>
<li>Understanding basic intuition behind machine learning approaches.</li>
<li>Using unsupervised learning to cluster and visualise data points</li>
<li>Dimension reduction techniques for visualisation and as input to clustering methods</li>
</ul>
<p>reading:&nbsp;<a href="http://compgenomr.github.io/book/unsupervisedLearning.html">http://compgenomr.github.io/book/unsupervisedLearning.html</a></p>
<p>slides:&nbsp;<a href="https://github.com/BIMSBbioinfo/compgen2021/tree/main/week2/compgen2021_unsupervisedLearning.pdf">https://github.com/BIMSBbioinfo/compgen2021/tree/main/week2/compgen2021_unsupervisedLearning.pdf</a></p>
<p>exercises+code:&nbsp;<a href="https://github.com/BIMSBbioinfo/compgen2021/tree/main/week2/">https://github.com/BIMSBbioinfo/compgen2021/tree/main/week2/</a></p>
<h3><a href="https://github.com/BIMSBbioinfo/compgen2021#module-3-supervised-learning-for-genomics-16-22-august-2021"></a>Module 3: Supervised learning for genomics (16-22 August 2021)</h3>
<ul>
<li>Understanding and using supervised learning methods for predictive purposes</li>
<li>How to measure prediction performance</li>
<li>Understand and use cross-validation and related concepts</li>
</ul>
<p>reading:&nbsp;<a href="http://compgenomr.github.io/book/supervisedLearning.html">http://compgenomr.github.io/book/supervisedLearning.html</a></p>
<p>slides:&nbsp;<a href="https://github.com/BIMSBbioinfo/compgen2021/tree/main/week3/compgen2021_supervisedLearning.pdf">https://github.com/BIMSBbioinfo/compgen2021/tree/main/week3/compgen2021_supervisedLearning.pdf</a></p>
<p>exercises+code:&nbsp;<a href="https://github.com/BIMSBbioinfo/compgen2021/tree/main/week3/">https://github.com/BIMSBbioinfo/compgen2021/tree/main/week3/</a></p>
<p>https://github.com/BIMSBbioinfo/compgen2021</p><p>Address of the bookmark: <a href="https://github.com/BIMSBbioinfo/compgen2021" rel="nofollow">https://github.com/BIMSBbioinfo/compgen2021</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/44727/postdoctoral-scholar-in-bacterial-evolution-at-pathogen-and-microbiome-institute-at-northern-arizona-university</guid>
  <pubDate>Fri, 13 Dec 2024 12:49:16 -0600</pubDate>
  <link></link>
  <title><![CDATA[Postdoctoral Scholar in Bacterial Evolution at Pathogen and Microbiome Institute at Northern Arizona University]]></title>
  <description><![CDATA[
<p>We are pleased to announce a Postdoctoral Scholar position to study<br />bacterial evolution at the Pathogen and Microbiome Institute at<br />Northern Arizona University with Professor Paul Keim. The scholar<br />will have the opportunity also work with Professor Sam Sheppard at<br />The University of Oxford on joint projects. See our recent paper<br />on interspecific gene flow in Campylobacter. (DOI:<br />https://doi.org/10.1128/mbio.00581-24)</p>

<p>The job description: "This research position focuses on the science<br />of bacterial evolution. It will consist of researching theoretical<br />principles, but could include translational applications. Phylogenomic<br />and bioinformatic analysis of bacterial populations in nature or<br />in laboratory experiments will be a key component of the work. Prior<br />experience is an asset though training will be possible at PMI.<br />Likewise, laboratory microbiological, molecular, and biochemical<br />skills are an asset though not essential. Communication and critical<br />thinking skills are essential for performing the work and for<br />communicating to the local and international scientific communities.<br />Participating in team or independent grant writing to obtain research<br />funding will be required. Student mentoring is a part of the NAU<br />mission and is a partial expectation."</p>

<p>https://hr.peoplesoft.nau.edu/psp/ph92prta/EMPLOYEE/HRMS/c/HRS_HRAM.HRS_APP_SCHJOB.GBL?Page=HRS_APP_JBPST&amp;Action=U&amp;FOCUS=Applicant&amp;SiteId=1&amp;JobOpeningId=608024&amp;PostingSeq=1</p>

<p>Northern Arizona University is located in Flagstaff, Arizona, a<br />beautiful mountain town with a surprisingly vibrant restaurant<br />scene. Located a little over an hour from the Grand Canyon and ~45<br />min from Sedona, Flagstaff is a hiker's paradise. In fact, the city<br />of Flagstaff operates more than 50 miles of unpaved trails and there<br />are, on average, 266 sunny days per year with which to enjoy them.<br />At 7000 ft in elevation, Flagstaff experiences all four seasons,<br />but thesummers are mild and, in the winter, you can be on the ski<br />slopes within 30 min! https://www.flagstaffarizona.org/</p>

<p>As mentioned, joint projects with Professor Sheppard at Oxford<br />University are possible, including travel to his laboratory in the<br />United Kingdom. https://www.biology.ox.ac.uk/people/samuel-sheppard</p>

<p>Contact Information:<br />Paul.Keim@nau.edu</p>

<p>Paul S. Keim, Ph.D.<br />Regents Professor, &amp;<br />Cowden Endowed Chair of Microbiology<br />Northern Arizona University<br />Flagstaff, AZ 86011-4073</p>

<p>Paul S Keim</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/45133/postdoctoral-position-in-evolutionary-genomics-and-bioinformatics-at-the-center-for-interdisciplinary-neuroscience-at-university-of-valparaiso-valparaiso-chile</guid>
  <pubDate>Wed, 22 Apr 2026 02:36:00 -0500</pubDate>
  <link></link>
  <title><![CDATA[Postdoctoral Position in Evolutionary Genomics and Bioinformatics, at the Center for Interdisciplinary Neuroscience at University of Valparaiso, Valparaiso, Chile.]]></title>
  <description><![CDATA[
<p>The Center for Interdisciplinary Neuroscience of Valparaiso (CINV)<br />in Valparaiso, Chile, invites postdoctoral researchers to apply for<br />a Postdoctoral Fellowship focusing on understanding the evolution of<br />genes and molecular pathways that play a role on inflammatory processes<br />driving diseases affecting the central nervous system.</p>

<p>The postdoctoral researcher will contribute to this project using<br />a combination of evolutionary and comparative genomics, as well as a<br />diverse set of bioinformatic approaches for data analysis and integration<br />(e.g., transcriptomics, genomics, phenotypic data). This position offers<br />a unique opportunity to integrate diverse state-of-the-art genomic and<br />phenotypic datasets across different model organisms to understand the<br />role of genes, molecular pathways in the origin of complex diseases.</p>

<p>CINV provides a highly collaborative and multidisciplinary environment<br />using a variety of computational and experimental approaches,<br />including genetically tractable animal models as well as expertise in<br />genetics, behavior, glia-neuron communication, metabolism, biophysics,<br />genomics, bioinformatics, host-microbe communication, and biomolecular<br />modelling. The new postdoc will be part of one of our labs which focuses<br />more generally on the intersection between molecular evolution and<br />disease biology.</p>

<p>Required qualifications are a PhD in evolutionary biology, computational<br />biology, bioinformatics, or closely related fields. Candidates must have<br />excellent verbal and written communication skills (working language<br />is English), as well as an established record of productivity (e.g.,<br />at least one previous peer-reviewed publication). Candidates with a<br />past record of publications in bioinfomatics, computational biology,<br />population genetics or evolutionary genomics are strongly preferred. Ideal<br />candidates should have experience in analyzing genomic and phenomic<br />data, performing comparative evolution or population genomic analyses,<br />as well as in collaborating with experimentalists.</p>

<p>Interested candidates should first contact Evandro Ferrada at<br />. Please include the following: (1) a cover<br />letter addressing your interest in the position and how your expertise<br />meets the position requirements, (2) a CV, (3) contact information of<br />at least 2 references. A short online interview will follow to discuss<br />specific proposals. Candidate materials will be reviewed as soon as<br />possible until the position is filled.</p>

<p>For further information, please visit:<br />https://cinv.uv.cl/cinv-postdoctoral-fellowship-program-2026/</p>

<p>Dr. Evandro Ferrada<br />Associate Profesor</p>

<p>Centro Interdisciplinario de Neurociencia (CINV)</p>

<p>Facultad de Ciencias, Universidad de Valpara�so.</p>

<p>Pasaje Harrington 287, Playa Ancha, Valpara�so, Chile.</p>

<p>Tel.  +56 (32) 250 8453</p>

<p>www.cinv.cl</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/45309/ley-lab</guid>
  <pubDate>Fri, 11 Sep 2026 13:21:10 -0500</pubDate>
  <link></link>
  <title><![CDATA[Ley Lab !]]></title>
  <description><![CDATA[
<p>Research Program aims to elucidate how gut microbial species relate to genotypic differences between human individuals, to identify bacterial and archaeal species that share an evolutionary history with humans, and to determine the molecular basis of long-term host-microbial relationships. We approach these aims through a combination of population-level observations and laboratory-based molecular-level investigations. We link inter-microbial and microbial-host interactions at the molecular scale to patterns at population and evolutionary scales. </p>

<p>More at https://leylab.com/</p>
]]></description>
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