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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/29276?offset=1540</link>
	<atom:link href="https://bioinformaticsonline.com/related/29276?offset=1540" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43859/mumco-is-a-simple-bash-script-that-uses-whole-genome-alignment-information-provided-by-mummer-v4-to-detect-variants</guid>
	<pubDate>Wed, 27 Apr 2022 04:34:12 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43859/mumco-is-a-simple-bash-script-that-uses-whole-genome-alignment-information-provided-by-mummer-v4-to-detect-variants</link>
	<title><![CDATA[MUM&amp;Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (v4) to detect variants.]]></title>
	<description><![CDATA[<p dir="auto">MUM&amp;Co is able to detect:<br>Deletions, insertions, tandem duplications and tandem contractions (&gt;=50bp &amp; &lt;=150kb)<br>Inversions (&gt;=1kb) and translocations (&gt;=10kb)</p><p>Address of the bookmark: <a href="https://github.com/SAMtoBAM/MUMandCo" rel="nofollow">https://github.com/SAMtoBAM/MUMandCo</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/22236/savitribai-phule-pune-university-recruitment-for-04-jrf-post-in-april-2015</guid>
  <pubDate>Mon, 27 Apr 2015 20:28:59 -0500</pubDate>
  <link></link>
  <title><![CDATA[Savitribai Phule Pune University Recruitment for 04 JRF Post in April 2015]]></title>
  <description><![CDATA[
<p>Savitribai Phule Pune University announced application for recruitment to the post of Junior Research Fellow. The candidates for the post can apply through prescribed format before 10 May 2015.<br />Description:</p>

<p>Important Date &amp; Details</p>

<p>Closing Date for Registration: 10 May 2015</p>

<p>Details of Post</p>

<p>Name of Post: Junior Research Fellow- 04 Posts</p>

<p>Pay Scale: Rs. 12,000 or 16,00+ HRA Post Graduate degree with NET (16,000+HRA) Post Graduate Degree (12,000+HRA)</p>

<p>Eligibility Criteria: M.Sc. in Microbiology/Marine Microbiology/ Marine Biotechnology/Biotechnology/Bioinformatics/Zoology or equivalent degree with minimum 60% marks or equivalent grade</p>

<p>Age Limit- Not more than 28 years</p>

<p>Organisation Name: Savitribai Phule Pune University<br />Eligibility for the post:</p>

<p>Selection Procedure: The selection procedure is through personal interview. No TA/DA will be paid for appearing in the interview.</p>

<p>How to Apply: The candidates may send their application along with CV to the Head Department of Zoology, Savitribai Phule University on or before 10 May 2015.</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44537/the-atcc-genome-portal</guid>
	<pubDate>Wed, 15 May 2024 14:24:16 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44537/the-atcc-genome-portal</link>
	<title><![CDATA[The ATCC Genome Portal]]></title>
	<description><![CDATA[<p><span>The ATCC Genome Portal (AGP,&nbsp;</span><a href="https://genomes.atcc.org/">https://genomes.atcc.org/</a><span>) is a database of authenticated genomes for bacteria, fungi, protists, and viruses held in ATCC&rsquo;s biorepository. It now includes 3,938 assemblies (253% increase) produced under ISO 9000 by ATCC. Here, we present new features and content added to the AGP for the research community.</span></p><p>Address of the bookmark: <a href="https://genomes.atcc.org/" rel="nofollow">https://genomes.atcc.org/</a></p>]]></description>
	<dc:creator>Abhi</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44489/proksee</guid>
	<pubDate>Wed, 27 Mar 2024 11:11:54 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44489/proksee</link>
	<title><![CDATA[Proksee]]></title>
	<description><![CDATA[<p><span>Proksee is an expert system for genome assembly, annotation and visualization. To begin using Proksee, provide a complete genome sequence, sequencing reads or a CGView/Proksee map JSON file.</span></p>
<fieldset><legend>Please Cite the Following</legend>
<div>Grant JR, Enns E, Marinier E, Mandal A, Herman EK, Chen C, Graham M, Van Domselaar G, and Stothard P</div>
<div><a href="https://pubmed.ncbi.nlm.nih.gov/37140037/">Proksee: in-depth characterization and visualization of bacterial genomes</a></div>
<div>Nucleic Acids Research, 2023, gkad326, https://doi.org/10.1093/nar/gkad326</div>
</fieldset><p>Address of the bookmark: <a href="https://proksee.ca/" rel="nofollow">https://proksee.ca/</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/22297/appointment-of-two-traineeships-and-two-studentships-in-bioinformatics</guid>
  <pubDate>Fri, 08 May 2015 00:24:20 -0500</pubDate>
  <link></link>
  <title><![CDATA[Appointment of two traineeships and two studentships in Bioinformatics]]></title>
  <description><![CDATA[
<p>Applications are invited for the appointment of two traineeships and two studentships in Bioinformatics for a period of six months sponsored by Department of Biotechnology, Government of India in the Bioinformatics Sub-DIC, Saraswathy Thangavelu Centre, JNTBGRI, Puthenthope, Thiruvananthapuram 695 586. The required qualifications and other details are given below.</p>

<p>Position 1: Traineeship<br />Monthly fellowship (in rupee): 5,000/-<br />No. of vacancies: Two<br />Required Qualification: First Class M.Sc Bioinformatics/ Biotechnology/ Botany</p>

<p>Position 2: Studentship<br />Monthly fellowship (in rupee): 5,000/-<br />No. of vacancies: Two<br />Required Qualification: M.Phil/M.Tech Bioinformatics/ Biotechnology/ any branch of Life Science students for doing their thesis work in the area of Bioinformatics.</p>

<p>Age limit as on 1.1.2015, 28 years. Age relaxation will be provided for SC, ST, OBC candidates as per Govt. norms.</p>

<p>Interested candidates may appear for walk-in-interview on 15th May 2015 at 10.30 am at JNTBGRI, Palode, Thiruvananthapuram. The candidate should report to the Office at Palode before 10.00 am.</p>

<p>More at http://jntbgri.res.in/news/appointment-of-two-traineeships-and-two-studentships-in-bioinformatics/</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44628/uncovar-workflow-for-transparent-and-robust-virus-variant-calling-genome-reconstruction-and-lineage-assignment</guid>
	<pubDate>Mon, 05 Aug 2024 23:01:29 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44628/uncovar-workflow-for-transparent-and-robust-virus-variant-calling-genome-reconstruction-and-lineage-assignment</link>
	<title><![CDATA[UnCoVar: Workflow for Transparent and Robust Virus Variant Calling, Genome Reconstruction and Lineage Assignment]]></title>
	<description><![CDATA[<p>UnCoVar: Workflow for Transparent and Robust Virus Variant Calling, Genome Reconstruction and Lineage Assignment</p>
<ul>
<li>
<p>Using state of the art tools, easily extended for other viruses</p>
</li>
<li>
<p>Tool and database updates for critical components via Conda</p>
</li>
<li>
<p>Built using modern design patterns with Conda and Snakemake</p>
</li>
<li>
<p>Extensible and easy to customize</p>
</li>
<li>
<p>Submission Ready Genomes</p>
</li>
<li>
<p>Customizable reporting with comprehensive visualization</p>
</li>
</ul>
<p>https://ikim-essen.github.io/uncovar/</p>
<p>Github&nbsp;https://github.com/IKIM-Essen/uncovar</p>
<p>&nbsp;</p>
<p>&nbsp;</p><p>Address of the bookmark: <a href="https://ikim-essen.github.io/uncovar/" rel="nofollow">https://ikim-essen.github.io/uncovar/</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/22393/narcis-fernandez-fuentes-lab</guid>
  <pubDate>Mon, 25 May 2015 07:30:00 -0500</pubDate>
  <link></link>
  <title><![CDATA[Narcis Fernandez-Fuentes Lab]]></title>
  <description><![CDATA[
<p>Welcome to our web-site compiling all the research-related activities of the group. Our research interests relate to a number of areas within Bioinformatics. We have a long-standing interest in protein structure prediction and structure-to-function relationships. We work in the study of biomolecular interactions, modeling of protein complexes, the study and characterization of protein-protein interactions, peptide design, modeling of genetic variation, structure-based protein design and different aspects of Plant Bioinformatics. Take a look at the our databases and servers and the list of publications for more information.</p>

<p>More at http://www.bioinsilico.org/</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44770/nvidia-and-arc-institute-unveil-evo-2-a-breakthrough-ai-for-dna-design</guid>
	<pubDate>Fri, 21 Feb 2025 10:39:47 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44770/nvidia-and-arc-institute-unveil-evo-2-a-breakthrough-ai-for-dna-design</link>
	<title><![CDATA[NVIDIA and Arc Institute Unveil Evo 2: A Breakthrough AI for DNA Design]]></title>
	<description><![CDATA[<p>NVIDIA and the Arc Institute have introduced <strong style="font-size: 12.8px;">Evo 2</strong>, a groundbreaking AI model designed to <strong style="font-size: 12.8px;">understand, predict, and generate DNA sequences</strong>. This marks a major advancement in computational biology, offering scientists an unprecedented tool to decode the genetic blueprint of life and even design entirely new biological systems.</p><h3><strong>The Power of Evo 2: AI Meets DNA</strong></h3><p>Evo 2 is <strong>the largest AI model for biology ever created</strong>, trained on an astonishing <strong>9.3 trillion DNA "letters"</strong> (nucleotides) carefully selected from genomes spanning the entire tree of life. This massive dataset ensures that Evo 2 can recognize patterns and relationships in genetic sequences at an unparalleled scale.</p><p>For the first time, scientists can <strong>design DNA with AI</strong>, moving beyond simple sequence analysis to active DNA generation. Evo 2 enables researchers to <strong>predict, modify, and even create entire genetic sequences</strong>, opening new possibilities in medicine, agriculture, and synthetic biology.</p><h3><strong>Decoding the Dark Genome</strong></h3><p>One of the biggest challenges in genetics is understanding the <strong>non-coding regions</strong> of DNA&mdash;vast stretches of the genome that do not code for proteins but play crucial roles in regulating gene expression. These regions control when and how genes are activated, influencing everything from development to disease.</p><p>Evo 2 is designed to <strong>decode these non-coding elements</strong>, helping researchers uncover their functions and use this knowledge to develop gene-based therapies, synthetic life forms, and precision agriculture solutions.</p><h3><strong>From Reading DNA to Writing It</strong></h3><p>To put Evo 2&rsquo;s impact into perspective:</p><ul>
<li><strong>Previous AI models could "read" DNA</strong> like a book, analyzing genetic sequences and identifying patterns.</li>
<li><strong>Evo 2 can "write" entirely new DNA</strong>, designing functional genes, chromosomes, and even full genomes from scratch.</li>
</ul><p>This means scientists can now <strong>engineer biological systems with AI</strong>, designing new proteins, metabolic pathways, and genetic circuits to address real-world challenges.</p><h3><strong>A Step Toward Generative Biology</strong></h3><p>The Arc Institute describes Evo 2 as a major step toward <strong>"generative biology"</strong>&mdash;a revolutionary approach where AI is used to create <strong>novel biological structures</strong> rather than just analyzing existing ones. This could lead to breakthroughs such as:</p><ul>
<li><strong>New medicines</strong>: AI-generated enzymes and proteins tailored for targeted therapies.</li>
<li><strong>Disease-resistant crops</strong>: Genetically optimized plants for higher yield and climate resilience.</li>
<li><strong>Synthetic organisms</strong>: Custom-designed microbes for bioremediation, biofuel production, and industrial applications.</li>
</ul><h3><strong>An Open-Source Revolution</strong></h3><p>Unlike many proprietary AI models, <strong>Evo 2 is open source</strong>, making its capabilities accessible to researchers worldwide. This democratization of AI-driven biology means that scientists from different disciplines can <strong>collaborate, experiment, and innovate</strong>, accelerating discoveries in genetic engineering and synthetic biology.</p><p>With Evo 2, the boundaries of what&rsquo;s possible in <strong>DNA design, genetic engineering, and biological innovation</strong> are being redrawn. The future of life sciences is no longer just about understanding life&rsquo;s code&mdash;it&rsquo;s about writing it.</p>]]></description>
	<dc:creator>BioStar</dc:creator>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/22431/genomic-scientist-at-udsc</guid>
  <pubDate>Thu, 28 May 2015 19:14:23 -0500</pubDate>
  <link></link>
  <title><![CDATA[Genomic Scientist at UDSC]]></title>
  <description><![CDATA[
<p>Centre for Genetic Manipulation of Crop Plants</p>

<p>Department of Genetics</p>

<p>University of Delhi South Campus</p>

<p>NEW DELHI – 110 021</p>

<p>WALK-IN-INTERVIEW FOR THE TEMPORARY POSITIONS OF RESEACH SCIENTIT &amp; LAB / FIELD ATTENDANT</p>

<p>1 Research Scientist (RS) – 3</p>

<p>    DBT, Ph. D.</p>

<p>    Experience on DNA Markers, plant genome mapping and bioinformatics</p>

<p>    Salary: 60,000 (Consolidated) + 5% annual increment</p>

<p>    Date and time: 25.06.2015 at 10:30 AM</p>

<p>These temporary positions have been sanctioned in a DBT funded project for the Phase II on ‘Centre of Excellence on genome mapping and molecular breeding of Brassicas.’</p>

<p>The applicants are requested to register their names on the day of interview in the First Floor, Biotech Centre, Centre for Genetic Manipulation of Crop Plants, Department of Genetics before the stipulated time for the interview. Only the registered eligible candidates will be interviewed on the day in the Committee Room.</p>

<p>Applicants are requested to bring all related documents, in original and a set of photocopy, for verification.</p>

<p>No TA/DA will be paid for attending the interview.</p>

<p>Advertisement:</p>

<p>www.du.ac.in/du/index.php?mact=News,cntnt01,detail,0&amp;cntnt01articleid=5492&amp;cntnt01returnid=83</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/45251/aurora-a-new-detective-for-bacterial-genomes</guid>
	<pubDate>Fri, 21 Aug 2026 11:31:00 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/45251/aurora-a-new-detective-for-bacterial-genomes</link>
	<title><![CDATA[Aurora: A New Detective for Bacterial Genomes]]></title>
	<description><![CDATA[<p>Imagine trying to solve a mystery with thousands of clues&mdash;but some of the clues are labelled incorrectly.</p><p>That is the challenge researchers face when studying how bacteria adapt to different environments. A bacterial gene may appear to be linked to a particular habitat, when the real reason is simply that closely related bacteria happen to live there.</p><p>In their 2025 Genome Biology paper, Bujdo&scaron;, Walter, and O&rsquo;Toole introduce aurora, a machine-learning tool designed to tackle this problem.</p><p>Aurora identifies potentially mislabeled or unusual bacterial strains before performing genome-wide association studies (GWAS). By cleaning up the dataset and accounting for bacterial evolutionary relationships, it can help researchers find genetic features that are more genuinely connected to habitat adaptation.</p><p>The researchers tested aurora using simulated and real bacterial datasets and found that it could recover important genetic associations even when datasets contained misleading labels.</p><p>The bigger lesson is simple: better biological discoveries often begin with better data.</p><p>Aurora gives researchers a new way to separate real genetic clues from misleading ones&mdash;and could help us better understand how bacteria adapt, survive, and evolve in the environments they call home.</p><p>Based on Bujdo&scaron; et al., &ldquo;aurora: a machine learning GWAS tool for analyzing microbial habitat adaptation,&rdquo; Genome Biology (2025).[Read the original paper](https://link.springer.com/article/10.1186/s13059-025-03524-7?)</p>]]></description>
	<dc:creator>BioStar</dc:creator>
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