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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/44742?offset=50</link>
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	<description><![CDATA[]]></description>
	
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41328/deephic-a-generative-adversarial-network-for-enhancing-hi-c-data-resolution</guid>
	<pubDate>Tue, 03 Mar 2020 01:12:47 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41328/deephic-a-generative-adversarial-network-for-enhancing-hi-c-data-resolution</link>
	<title><![CDATA[DeepHiC: A Generative Adversarial Network for Enhancing Hi-C Data Resolution]]></title>
	<description><![CDATA[<p><strong>DeepHiC</strong> is a GAN-based model for enhancing Hi-C data resolution. We developed this server for helping researchers to enhance their own low-resolution data by a few steps of clicks. <em>Ab initio</em> training could be performed according to our published <a href="https://github.com/omegahh/DeepHiC">code</a>. We provided trained models for various depth of low-coverage sequencing Hi-C data. The depth of input data is estimated by its distribution comparing with those of the downsampled Hi-C data we used in training</p><p>Address of the bookmark: <a href="http://sysomics.com/deephic" rel="nofollow">http://sysomics.com/deephic</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43374/reference-sequence-resource</guid>
	<pubDate>Wed, 15 Sep 2021 21:15:22 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43374/reference-sequence-resource</link>
	<title><![CDATA[Reference Sequence Resource!]]></title>
	<description><![CDATA[<p><span>The ENCODE project uses Reference Genomes from&nbsp;</span><a href="http://www.ncbi.nlm.nih.gov/genome/browse/reference/">NCBI</a><span>&nbsp;or&nbsp;</span><a href="http://hgdownload.cse.ucsc.edu/downloads.html">UCSC</a><span>&nbsp;to provide a consistent framework for mapping high-throughput sequencing data.&nbsp;In general, ENCODE data are mapped consistently to 2 human (GRCH38, hg19) and 2 mouse (mm9/mm10) genomes for historical comparability.&nbsp;</span><em>Drosophia melanogaster</em><span>&nbsp;experiments are mapped to either dm3 or dm6 and&nbsp;</span><em>Caenorhabdilis elegans&nbsp;</em><span>experiments are mapped to ce10 or ce11.&nbsp;T</span></p><p>Address of the bookmark: <a href="https://www.encodeproject.org/data-standards/reference-sequences/" rel="nofollow">https://www.encodeproject.org/data-standards/reference-sequences/</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/42570/breeding-insight</guid>
	<pubDate>Wed, 06 Jan 2021 19:49:21 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/42570/breeding-insight</link>
	<title><![CDATA[Breeding Insight]]></title>
	<description><![CDATA[<p><span><span>Breeding Insight&nbsp;at Cornell University will leverage recent improvements in genomics and open source informatics components, and in&nbsp;partnership with small breeding programs, will enable these programs to harness&nbsp;&nbsp;powerful digital tools to accelerate their genetic gains</span></span></p>
<p><span>Breeding Insight is funded by&nbsp;the&nbsp;</span><span><a href="https://www.ars.usda.gov/about-ars/" target="_blank">U.S. Department of Agriculture (USDA) Agricultural Research Service (ARS)</a></span><span>&nbsp;through Cornell University. The USDA ARS delivers scientific solutions to national and global agricultural challenges. As a global leader&nbsp;in agricultural discovery through scientific excellence, ARS is committed to delivering cutting-edge, scientific tools and innovative solutions for American farmers, producers, industry, and communities to support the nourishment and well-being of all people; sustaining our nation&rsquo;s agroecosystems and natural resources; and ensuring the economic competitiveness and excellence of our agriculture.</span></p><p>Address of the bookmark: <a href="https://www.breedinginsight.org/" rel="nofollow">https://www.breedinginsight.org/</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/43768/summer-school-open-to-phd-students</guid>
  <pubDate>Wed, 02 Feb 2022 06:08:35 -0600</pubDate>
  <link></link>
  <title><![CDATA[Summer school open to PhD students]]></title>
  <description><![CDATA[
<p>Some PhD students are organizing a summer school open to PhD students with different backgrounds and interests.</p>

<p>Several sessions and workshops will be held within five focus groups, and one common theme: mountain research.</p>

<p>The summer school will take place in Obergurgl, in the middle of the Austrian Alps, September 5-9.</p>

<p>Abstract submission is now open, until February 16th: https://www.imc2022.info/summerschool/</p>

<p>The summer school takes place in the context of the International Mountain Conference 2022, Innsbruck, Austria: https://www.imc2022.info/</p>

<p>Please feel free to spread the word among potentially interested colleagues and PhD students.</p>

<p>"Capponi, Lisa"</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/29998/csir-nehru-science-postdoctoral-research-fellowship</guid>
  <pubDate>Tue, 29 Nov 2016 12:34:59 -0600</pubDate>
  <link></link>
  <title><![CDATA[CSIR Nehru Science Postdoctoral Research Fellowship]]></title>
  <description><![CDATA[
<p>CSIR Nehru Science Postdoctoral Research Fellowship</p>

<p>About Fellowship: <br />CSIR Nehru Science Postdoctoral Research Fellowship Scheme is an Research Fellowship awarded/given by HRD Ministry, Govt. of India every year to more than 100 fellows.</p>

<p>It was started to identify promising and young researchers with novel ideas and provide them research opportunities in the areas of basic science, engineering, medicine &amp; agriculture.</p>

<p>The fellowship aims at facilitating their transition from mentored to independent research career.</p>

<p>In addition, check these ICTS Research Fellowships:<br />1.) Max-Planck Partner Group Fellowships 2017-18<br />2.) ICTS-Simons Postdoctoral Fellowships 2017<br />3.) ICTS Post Doctoral Fellowships 2017<br />4.) Airbus Prize Postdoctoral Fellowship 2017-18</p>

<p>Eligibility: To be eligible for this fellowship, you:<br />1.) PhD degree (within 3 years of award of PhD degree), OR<br />2.) Those who have submitted PhD theses.<br />3.) Applicants should have research publications in good impact factor SCI journals.<br />4.) Indian nationals, Persons of Indian Origin (PIO) &amp; Overseas Citizen of India (OCI), a can also apply.<br />5.) Maximum Age Limit: 32 years.</p>

<p>Duration: <br />– 2 Years.<br />– extendable for a maximum of 1 more year based on performance.</p>

<p>Remuneration: <br />– Rs. 50,000/- per month plus House Rent Allowance (HRA)<br />– A contingency grant of Rs. 3.0 lakh per annum.<br />– 25% of the contingency grant can be used for domestic and international travel.</p>

<p>Mode of Selection: You can apply throughout the year, but selection will be made twice a year, in June and December.</p>

<p>How to Apply: <br />– Read the instructions, given at Annexure-I in this PDF file.<br />– And, application form is given as, Annexure-II.<br />– Fill the form &amp; send it to the given address in the PDF file.</p>

<p>Deadline: Rolling Deadline (Applications accepted throughout the year)</p>

<p>Also See: Research Internship/ Fellowship in India:<br />1.) IIT Bombay Research Internship Awards Programme 2016-17<br />2.) IIT Delhi Internship Program 2016-17<br />3.) DAAD WISE – International Internship in Germany<br />4.) Summer Research Fellowship Programme| JNCASR Bangalore<br />5.) Indian Academy of Sciences Summer Internships 2017<br />6.) Winter Internship – IIT Bombay NPDE-TCA<br />7.) Viterbi – India Program 2017 | Research Internship in US<br />8.) Internship – Centre for Stem Cell Research, Vellore</p>

<p>Accommodation &amp; other benefits: <br />– Accommodation may be provided by CSIR, if available.<br />– Medical benefits as per CSIR norms.</p>

<p>For more details: <br />– Check this PDF Notification of Fellowship.<br />– List of CSIR Labs &amp; their work/activities can be seen at www.csir.res.in.</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44749/2024s-top-10-science-breakthroughs-innovations-shaping-our-future</guid>
	<pubDate>Mon, 30 Dec 2024 11:22:21 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44749/2024s-top-10-science-breakthroughs-innovations-shaping-our-future</link>
	<title><![CDATA[2024&#039;s Top 10 Science Breakthroughs: Innovations Shaping Our Future]]></title>
	<description><![CDATA[<p>The year 2024 has been marked by remarkable scientific advancements across various disciplines, each contributing to a deeper understanding of our universe, our planet, and ourselves. Here are ten of the most intriguing breakthroughs that have captured the world's attention:</p><p><strong>James Webb Space Telescope's Revelations:</strong> Since its launch, the James Webb Space Telescope has provided unprecedented insights into the cosmos, unveiling details about the early universe and distant galaxies that were previously beyond our reach.</p><p><strong>Re-establishing Contact with Voyager 1:</strong> In a testament to human ingenuity, scientists successfully re-established communication with Voyager 1, the spacecraft launched in 1977 now traversing interstellar space, offering data from the far reaches of our solar system.</p><p><strong>Advancements in Human Biology:</strong> The global cell atlas project released its initial findings, mapping human cells with unprecedented detail, akin to a "Google Maps for the body." Additionally, the first complete map of a fruit fly's brain was unveiled, promising new insights into neurological diseases.</p><p><strong>Public Health Milestones:</strong> The rollout of the first malaria vaccines and the commencement of late-stage clinical trials for a new tuberculosis vaccine&mdash;the first in over a century&mdash;marked significant strides in combating these diseases. Efforts against HIV/AIDS also showed promising progress, particularly in Africa.</p><p><strong>Weight-Loss Drugs' Expanded Potential:</strong> Medications initially developed for weight loss demonstrated potential in treating a range of other diseases, indicating a broader therapeutic application than previously anticipated.</p><p><strong>Robotics and Quantum Computing:</strong> Technological advancements brought robots capable of performing more complex tasks and moved quantum computing closer to practical, real-world applications, heralding a new era in computing and automation.</p><p><strong>Synthetic Biology Concerns:</strong> Leading researchers, including Nobel laureates, raised alarms about the potential risks associated with synthetic biology, particularly the creation of "mirror bacteria," underscoring the need for careful regulation in this rapidly evolving field.</p><p><strong>Climate Change Insights:</strong> Studies indicated that global CO₂ emissions plateaued with only a 0.1% increase in 2023, suggesting a potential turning point in emission trends. However, concerns about climate tipping points, such as the Atlantic Meridional Overturning Current, highlighted the urgency for continued action.</p><p>New Antibiotic Class Discovered: A novel class of antibiotics targeting multi-drug resistant bacteria was discovered, offering hope in the fight against antibiotic-resistant infections.</p>]]></description>
	<dc:creator>LEGE</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34396/pore-an-r-package-for-the-visualization-and-analysis-of-nanopore-sequencing-data</guid>
	<pubDate>Thu, 23 Nov 2017 09:55:57 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34396/pore-an-r-package-for-the-visualization-and-analysis-of-nanopore-sequencing-data</link>
	<title><![CDATA[poRe: an R package for the visualization and analysis of nanopore sequencing data]]></title>
	<description><![CDATA[<p><strong>Motivation:</strong>&nbsp;The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the bioinformatics community will need to design and build a suite of tools specifically for MinION data.</p>
<p><strong>Results:</strong>&nbsp;Here we present poRe, a package for R that enables users to manipulate, organize, summarize and visualize MinION nanopore sequencing data. As a package for R, poRe has been tested on Windows, Linux and MacOSX. Crucially, the Windows version allows users to analyse MinION data on the Windows laptop attached to the device.</p>
<p><strong>Availability and implementation:</strong>&nbsp;poRe is released as a package for R at&nbsp;<a href="http://sourceforge.net/projects/rpore/" target="">http://sourceforge.net/projects/rpore/</a>&nbsp;. A tutorial and further information are available at&nbsp;<a href="https://sourceforge.net/p/rpore/wiki/Home/" target="">https://sourceforge.net/p/rpore/wiki/Home/</a></p>
<p><strong>Contact:</strong><a href="mailto:mick.watson@roslin.ed.ac.uk" target="">mick.watson@roslin.ed.ac.uk</a></p><p>Address of the bookmark: <a href="https://academic.oup.com/bioinformatics/article/31/1/114/2365693" rel="nofollow">https://academic.oup.com/bioinformatics/article/31/1/114/2365693</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/35249/gpopsim-a-simulation-tool-for-whole-genome-genetic-data</guid>
	<pubDate>Wed, 17 Jan 2018 03:47:46 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/35249/gpopsim-a-simulation-tool-for-whole-genome-genetic-data</link>
	<title><![CDATA[GPOPSIM: a simulation tool for whole-genome genetic data]]></title>
	<description><![CDATA[<p><span>GPOPSIM is a simulation tool for pedigree, phenotypes, and genomic data, with a variety of population and genome structures and trait genetic architectures. It provides flexible parameter settings for a wide discipline of users, especially can simulate multiple genetically correlated traits with desired genetic parameters and underlying genetic architectures.</span></p><p>Address of the bookmark: <a href="https://github.com/SCAU-AnimalGenetics/GPOPSIM" rel="nofollow">https://github.com/SCAU-AnimalGenetics/GPOPSIM</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36833/bfc-a-standalone-high-performance-tool-for-correcting-sequencing-errors-from-illumina-sequencing-data</guid>
	<pubDate>Thu, 31 May 2018 09:35:23 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36833/bfc-a-standalone-high-performance-tool-for-correcting-sequencing-errors-from-illumina-sequencing-data</link>
	<title><![CDATA[BFC: a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data]]></title>
	<description><![CDATA[BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes.

The BFC algorithm is a variant of the classical spectrum alignment algorithm introduced by Pevzner et al (2001). It uses an exhaustive search to find a k-mer path through a read that minimizes a heuristic objective function jointly considering penalties on correction, quality and k-mer support. This algorithm was first implemented in my fermi assembler and then refined a few times in fermi, fermi2 and now in BFC. In the k-mer counting phase, BFC uses a blocked bloom filter to filter out most singleton k-mers and keeps the rest in a hash table (Melsted and Pritchard, 2011). The use of bloom filter is how BFC is named, though other correctors such as Lighter and Bless actually rely more on bloom filter than BFC.

https://github.com/lh3/bfc<p>Address of the bookmark: <a href="https://github.com/lh3/bfc" rel="nofollow">https://github.com/lh3/bfc</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37527/nanopack-visualizing-and-processing-long-read-sequencing-data</guid>
	<pubDate>Fri, 10 Aug 2018 18:41:34 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37527/nanopack-visualizing-and-processing-long-read-sequencing-data</link>
	<title><![CDATA[NanoPack: visualizing and processing long-read sequencing data]]></title>
	<description><![CDATA[<p>The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at&nbsp;<a href="https://github.com/wdecoster/nanopack" target="">https://github.com/wdecoster/nanopack</a>, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Windows 10 subsystem for Linux and are available as a graphical user interface, a web service at&nbsp;<a href="http://nanoplot.bioinf.be/" target="">http://nanoplot.bioinf.be</a>&nbsp;and command line tools.</p>
<p>&nbsp;https://academic.oup.com/bioinformatics/article/34/15/2666/4934939</p><p>Address of the bookmark: <a href="https://github.com/wdecoster/nanoQC" rel="nofollow">https://github.com/wdecoster/nanoQC</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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