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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/34624?offset=120</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/42713/gggenomes-a-grammar-of-graphics-for-comparative-genomics</guid>
	<pubDate>Mon, 01 Feb 2021 14:47:32 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/42713/gggenomes-a-grammar-of-graphics-for-comparative-genomics</link>
	<title><![CDATA[gggenomes: A grammar of graphics for comparative genomics]]></title>
	<description><![CDATA[<p><span>gggenomes is a versatile graphics package for comparative genomics. It extends the popular R visualization package</span><a href="https://ggplot2.tidyverse.org/">ggplot2</a><span>&nbsp;by adding dedicated plot functions for genes, syntenic regions, etc. and verbs to manipulate the plot to, for example, quickly zoom in into gene neighborhoods.</span></p><p>Address of the bookmark: <a href="https://github.com/thackl/gggenomes" rel="nofollow">https://github.com/thackl/gggenomes</a></p>]]></description>
	<dc:creator>Surabhi Chaudhary</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/45278/the-day-we-began-reading-the-dna-of-the-world</guid>
	<pubDate>Sat, 05 Sep 2026 01:43:21 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/45278/the-day-we-began-reading-the-dna-of-the-world</link>
	<title><![CDATA[The Day We Began Reading the DNA of the World]]></title>
	<description><![CDATA[<div>Picture waking up and knowing that in one lab, a scientist is reading the DNA of a whale. In another, a team is sequencing a rare plant. Meanwhile, researchers in India are decoding the genomes of different human populations.</div><div>&nbsp;</div><div>Many organisms. Many countries. All share one remarkable goal: to understand the genetic story of life.</div><div>DNA is nature's instruction manual, written with just four letters: A, T, C, and G. For years, scientists could only read small sections of this huge book. Now, new sequencing technology lets us read entire genomes like never before.</div><div>&nbsp;</div><div>One of the most ambitious projects is the Earth BioGenome Project (EBP). Its goal is to create reference genomes for about 1.5 million known eukaryotic species. This project links genome research across continents, species, and scientific fields.</div><div>&nbsp;</div><div>But this story goes beyond just animals and plants.</div><div>&nbsp;</div><div><strong>A New Chapter in Human Genomics</strong></div><div>&nbsp;</div><div>Large human genome projects are changing how we understand our own genetic diversity.</div><div>India's GenomeIndia project has sequenced thousands of people from different populations. This work is uncovering genetic variation that global databases have often missed.</div><div>&nbsp;</div><div>Similar population-scale effSimilar large-scale projects are happening worldwide. The All of Us Research Program in the United States, Europe's 1+ Million Genomes initiative, South Korea's national genomic data program, and projects in Saudi Arabia, Australia, and Singapore are all building huge genomic resources.collect DNA.</div><div>&nbsp;</div><div>The real goal is to link genomes with health, disease, and other biological information. This creates a base for more accurate research and, in time, more personalized medicine.</div><div>&nbsp;</div><div><strong>A Race Against Time</strong></div><div>&nbsp;</div><div>There is also an important twist.</div><div>&nbsp;</div><div>We are sequencing Earth's biodiversity even as many species face growing environmental threats.</div><div>A genome alone cannot save a species, but it does keep important information about its biology, evolution, and genetic diversity. This knowledge helps scientists understand risks, guide conservation, and find traits that could help agriculture or medicine.</div><div>&nbsp;</div><div>Projects like the Darwin Tree of Life, which studies species in Britain and Ireland, and the African BioGenome Project, which is growing genomics work across Africa, are key parts of this worldwide effort.</div><div>&nbsp;</div><div>Projects to Watch</div><ol>
<li>Earth BioGenome Project (EBP) - A global effort to sequence and annotate roughly 1.5 million known eukaryotic species and create a comprehensive reference library of Earth's biodiversity.</li>
<li>Vertebrate Genomes Project (VGP) - Focuses on producing high-quality reference genomes for vertebrate species, providing a major foundation for the wider Tree of Life.</li>
<li>Darwin Tree of Life - A UK and Ireland initiative aiming to sequence approximately 70,000 species, creating a detailed genomic map of regional biodiversity.</li>
<li>African BioGenome Project (AfricaBP) - A pan-African initiative focused on sequencing Africa's biodiversity while strengthening genomics and bioinformatics capacity across the continent.</li>
<li>European Reference Genome Atlas (ERGA) - A European effort to generate high-quality reference genomes for Europe's biodiversity and connect national sequencing efforts.</li>
<li>Canada BioGenome Project - Building reference genomes for Canadian biodiversity, supporting conservation, research and the study of ecosystems.</li>
<li>California Conservation Genomics Project - Uses genomics to understand and protect California's biodiversity and help inform conservation decisions.</li>
<li>Bat1K - An ambitious global effort to sequence the genomes of all known bat species, helping scientists study their evolution, longevity, immunity and unique biology.</li>
<li>Bird 10,000 (B10K) - A global project aiming to create genome resources covering the world's bird diversity and reconstruct avian evolutionary history.</li>
<li>Global Invertebrate Genomics Alliance (GIGA) - Builds genomic resources for the enormous and genetically diverse world of invertebrates.</li>
<li>GenomeIndia - India's national human-genome initiative, designed to capture the country's extraordinary population diversity and create a reference resource for Indian genomics.</li>
<li>All of Us Research Program - A US national research program combining genomic information with health and lifestyle data at population scale.</li>
<li>1+ Million Genomes / Genome of Europe - A European effort to enable secure, cross-border use of genomic and health data and develop genome-scale resources involving more than one million people.</li>
<li>Korea National Integrated Bio Big Data Project - South Korea's large-scale national effort combining genomic and health information from a very large population cohort.</li>
<li>Saudi Genome Program - A national genomics initiative focused on genetic diseases, population genomics and precision medicine in Saudi Arabia.</li>
<li>Australian Genomics / Genomics Health Futures Mission - Australia's growing investment in genomic medicine, rare disease research and population-scale health genomics.</li>
</ol><div><strong>The Library of Life</strong></div><div>&nbsp;</div><div>The fuThe future of genomics is not just about sequencing one genome at a time. Now, it is about creating a worldwide network of genomes&mdash;human and non-human, individual and species&mdash;linked by powerful databases and advanced computational tools.ine a library without shelves.</div><div>&nbsp;</div><div>In this library, the books are genomes. The pages are made of DNA. Scientists and machines are the readers. And this library is still being written. Each genome sequenced today adds a new page to the story of life and helps us better understand our place in it.</div>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
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  <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/blog/view/43900/finding-a-mimicry-game-for-teaching-on-line-and-mentioned-general-resources</guid>
	<pubDate>Tue, 28 Jun 2022 07:32:05 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/43900/finding-a-mimicry-game-for-teaching-on-line-and-mentioned-general-resources</link>
	<title><![CDATA[Finding a mimicry game for teaching on-line and mentioned general resources]]></title>
	<description><![CDATA[<pre>Mimicry and other resources
Mimicry games:
Great Heliconius game:
http://heliconius.org/evolving_butterflies/
(See also 
https://royalsocietypublishing.org/doi/10.1098/rspb.2020.0014)
Other one, a bit less friendly:
https://ccl.northwestern.edu/netlogo/models/Mimicry
Camouflage practical
https://alexis-catherine.github.io/publication/natural-selection-and-camouflage/
(NetLogo also has one: 
https://ccl.northwestern.edu/netlogo/models/BugHuntCamouflage)
Peppered moth game:
https://askabiologist.asu.edu/peppered-moths-game/play.html

General resources
The always popular Populus:
https://cbs.umn.edu/populus/overview
Drift &amp; Gene Flow 
https://cartwrig.ht/apps/genie/
(Cock van Oosterhout has a great ppt to lead students through this)
See also https://cartwrig.ht/apps/redlynx/
https://demonstrations.wolfram.com/ReplicatorMutatorDynamicsWithThreeStrategies/
NetLogo:
http://ccl.northwestern.edu/netlogo/models/index.cgi
Population Genetics:
https://www.radford.edu/~rsheehy/Gen_flash/popgen/
Evolution in general
https://evolution.berkeley.edu/evolibrary/home.php
Mitochondrial Eve:
https://projects.ncsu.edu/cals/gn/ex/mit-eve.html
Y chromosomes:
https://projects.ncsu.edu/cals/gn/ex/y-chrom.html
A professional online package from Michael Kasumovic:
https://arludo.com/
a compilation of resources:
https://planted.botany.org/index.php?P=Home
Finally, Donald Forsdyke has some great on-line videos explaining
evolutionary principles (occasionally in a fake Scottish accent):
http://post.queensu.ca/~forsdyke/videolectures.htm
</pre><p>&nbsp;</p>]]></description>
	<dc:creator>Shruti Paniwala</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/43980/useful-link-to-teach-evolution</guid>
	<pubDate>Wed, 05 Oct 2022 18:29:30 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/43980/useful-link-to-teach-evolution</link>
	<title><![CDATA[Useful link to teach evolution !]]></title>
	<description><![CDATA[<pre>Mimicry and other resources
Mimicry games:
Great Heliconius game:
http://heliconius.org/evolving_butterflies/
(See also 
https://royalsocietypublishing.org/doi/10.1098/rspb.2020.0014)
Other one, a bit less friendly:
https://ccl.northwestern.edu/netlogo/models/Mimicry
Camouflage practical
https://alexis-catherine.github.io/publication/natural-selection-and-camouflage/
(NetLogo also has one: 
https://ccl.northwestern.edu/netlogo/models/BugHuntCamouflage)
Peppered moth game:
https://askabiologist.asu.edu/peppered-moths-game/play.html

General resources
The always popular Populus:
https://cbs.umn.edu/populus/overview
Drift &amp; Gene Flow 
https://cartwrig.ht/apps/genie/
(Cock van Oosterhout has a great ppt to lead students through this)
See also https://cartwrig.ht/apps/redlynx/
https://demonstrations.wolfram.com/ReplicatorMutatorDynamicsWithThreeStrategies/
NetLogo:
http://ccl.northwestern.edu/netlogo/models/index.cgi
Population Genetics:
https://www.radford.edu/~rsheehy/Gen_flash/popgen/
Evolution in general
https://evolution.berkeley.edu/evolibrary/home.php
Mitochondrial Eve:
https://projects.ncsu.edu/cals/gn/ex/mit-eve.html
Y chromosomes:
https://projects.ncsu.edu/cals/gn/ex/y-chrom.html
A professional online package from Michael Kasumovic:
https://arludo.com/
a compilation of resources:
https://planted.botany.org/index.php?P=Home
Finally, Donald Forsdyke has some great on-line videos explaining
evolutionary principles (occasionally in a fake Scottish accent):
http://post.queensu.ca/~forsdyke/videolectures.htm</pre>]]></description>
	<dc:creator>Abhi</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/view/119</guid>
	<pubDate>Wed, 10 Jul 2013 14:35:34 -0500</pubDate>
	<link>https://bioinformaticsonline.com/view/119</link>
	<title><![CDATA[Which are the best statistical programming languages to study for a bioinformatician?]]></title>
	<description><![CDATA[<p><span>In Bio-informatics based&nbsp;genome sequencing and predicting metabolic pathways&nbsp;research jobs&nbsp;I used Matlab, SAS, SPSS, R and several Bioconductor packages. Matlab had a lot of powerful tools and was easy to use, whereas SPSS is for non-programmers and R need programming skills. I am wondering what other people think is best? or there might not be one specific language but a few that lend themselves best to Bio-informatics work that is math heavy and deals with a large amount of data.</span></p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>

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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/857/smyth-lab</guid>
  <pubDate>Sun, 14 Jul 2013 12:26:18 -0500</pubDate>
  <link></link>
  <title><![CDATA[Smyth Lab]]></title>
  <description><![CDATA[
<p>Statistical functional genomics in experimental medicine<br />The genome projects and the accelerated development of high-throughput genomic technologies such as microarrays have revolutionised biology. Making the most of this revolution requires the marriage of researchers from mathematical and biological backgrounds.</p>

<p>Research Area:<br />Linear models for microarray data<br />Digital gene expression technologies<br />Detection of molecular pathways<br />Bioinformatics resources for medical research</p>

<p>Link @ http://www.wehi.edu.au/faculty_members/professor_gordon_smyth/</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/914/welch-lab</guid>
  <pubDate>Mon, 15 Jul 2013 18:21:13 -0500</pubDate>
  <link></link>
  <title><![CDATA[Welch Lab]]></title>
  <description><![CDATA[
<p>They are based in the Department of Genetics at the University of Cambridge. </p>

<p>The research covers diverse areas of evolutionary biology, and molecular evolution in particular. It combines theoretical and empirical approaches, and particularly evolutionary inference from genome sequence data.</p>

<p>Links @ http://www.gen.cam.ac.uk/research/welch/GroupPage/Home.html</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/1466/iscb-asia-2013-translational-bioinformatics-conference</guid>
  <pubDate>Thu, 08 Aug 2013 06:31:32 -0500</pubDate>
  <link></link>
  <title><![CDATA[ISCB-Asia 2013 Translational Bioinformatics Conference]]></title>
  <description><![CDATA[
<p>ISCB-Asia 2013<br />Translational Bioinformatics Conference<br />Seoul, Korea<br />October 2 - 4, 2013</p>

<p>For more information visit: http://www.snubi.org/TBC2013/</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/1491/2013-nextgen-genomics-bioinformatics-technologies-ngbt-conference-new-delhi-india</guid>
  <pubDate>Thu, 08 Aug 2013 16:21:16 -0500</pubDate>
  <link></link>
  <title><![CDATA[2013 NextGen Genomics &amp; Bioinformatics Technologies (NGBT) Conference, New Delhi, INDIA]]></title>
  <description><![CDATA[
<p>2013 NextGen Genomics &amp; Bioinformatics Technologies (NGBT) Conference</p>

<p>SciGenom Research Foundation (SGRF) and Institute of Genomics and Integrative Biology (IGIB) are pleased to host the Next-Generation Sequencing and Bioinformatics for Genomics &amp; Healthcare conference.</p>

<p>In the ten years since the first human reference genome was completed for US$3 billion the sequencing technologies have radically changed leading to great reduction in sequencing cost. Today a human genome can be sequenced for under US$ 5000 in less than two weeks. It is expected that by the end of 2015 the cost of sequencing a human genome will drop to below thousand dollars. The next generation sequencing technologies over the past five years have enabled a large number of genomic studies that impact human health and disease. Also, this has made possible the growth of microbial, animal and plant genomics studies. While the data production has increased at a rapid pace challenges remain in analyzing and understanding the data. The conference will cover the next generation sequencing (NGS) technologies, bioinformatics for NGS and applications of NGS in many areas including personalized medicine.</p>

<p>For more info : http://www.scigenomconferences.com/2013/default.php</p>
]]></description>
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