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---
layout: page
title: Ants, Genomes & Evolution Lab @ Queen Mary University London
comments: false
---
<div class="row">
<div class="column col-sm-8 col-md-8">
<div id="section1" class="row">
<div class="col-sm-12">
<h3>Evolutionary genomics of social insects</h3>
</div>
<div class="col-md-7">
<p>Extensive theoretical work has explained how and why complex societies evolve. However, only little is known about the genes and molecular mechanisms responsible for social phenotypes.</p>
<p>We have been identifying genes and mechanisms involved in the evolution of insect societies using modern genomics approaches, combining comparative genomics and transcriptomics with population genomics and behavioral experiments.</p>
<btn id="section1-more-btn" onclick="$('#section1-extra').show();$('#section1-more-btn').hide();" class="btn btn-default btn-sm">Read More</btn>
</div>
<div class="col-md-5 hidden-xs hidden-sm">
<img src="{{ site.url }}/img/frontpage/fireants-ongenome480w.jpg" class="img-rounded img-responsive center-block" alt="fire ants on the genomic sequence of their social chromosome">
</div>
<div id="section1-extra" class="col-sm-12" style="display:none;">
<p> We are interested in themes including the genetics of behavior, the interplay between social evolution and genome evolution, and the molecular mechanisms responsible for differences between castes.</p>
<p>For example we:</p>
<ul>
<li>discovered that the number of queens accepted in a fire ant colony is determined by variants of a social chromosome (<a href="http://dx.doi.org/10.1038/nature11832">Nature 2013</a>).</li>
<li>characterized the genomic features of the variants of the social chromosome, showing high genetic diversity between them (<a href="http://onlinelibrary.wiley.com/doi/10.1111/mec.14054/abstract">Mol Ecol</a>).</li>
<li>sequenced and analyzed the genome of the invasive red fire ant <em>Solenopsis invicta</em> (<a href="http://dx.doi.org/10.1073/pnas.1009690108">PNAS 2011</a>).</li>
<li>described the gene expression changes that occur in a virgin queen when she is given the opportunity of replacing her mother (Mol Ecol 2010).</li>
<li>examined selective regime (positive vs. neutral selection) and fate of duplicated genes (conserved vs. subfunctionalized vs. neofunctionalization) for gene families including <a href="http://rspb.royalsocietypublishing.org/content/280/1758/20122968">sex-determination loci (tranfsormer/feminiser)</a>, <a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0045715">clock genes</a>, <a href="http://www.nature.com/hdy/journal/v110/n6/full/hdy2012122a.html">chemosensory proteins (CSPs)</a>, <a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0016289">olfactory binding proteins (OBPs)</a>, <a href="http://dx.doi.org/10.1073/pnas.1009690108">olfactory receptors</a> and <a href="http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003730">vitellogenin genes</a>.</li>
</ul>
<btn id="section1-less-btn" onclick="$('#section1-extra').hide();$('#section1-more-btn').show();" class="btn btn-default btn-sm">Read Less</btn>
</div>
<div class="col-md-5 visible-xs-inline visible-sm-inline">
<img src="{{ site.url }}/img/frontpage/fireants-ongenome480w.jpg" class="img-rounded img-responsive center-block" alt="fire ants on the genomic sequence of their social chromosome">
</div>
</div>
<div class="clearfix"></div>
<hr>
<div id="section2" class="row">
<div class="col-sm-12">
<h3>Genome bioinformatics</h3>
</div>
<div class="col-md-7">
<p>The recent 10,000-fold drop in the cost of DNA sequencing means that any lab can sequence anything - and lots of it. This brings exciting opportunities but also new challenges, in particular with regards to data handling, data analysis and visualization.</p>
<p>We develop innovative tools and approaches to facilitate modern biological work on established and emerging model organisms. We pay special attention to visualization and user experience.</p>
<btn id="section2-more-btn" onclick="$('#section2-extra').show();$('#section2-more-btn').hide();" class="btn btn-default btn-sm">Read More</btn>
</div>
<div class="col-md-5 hidden-xs hidden-sm">
<img src="{{ site.url }}/img/frontpage/analyze-final.gif" class="img-rounded img-responsive center-block" alt="how tools should be">
</div>
<div id="section2-extra" class="col-sm-12" style="display:none;">
<ul>
<li>BLAST is the most commonly used bioinformatics tool. But setting it up for private data and using it is counter-intuitive. Furthermore the standard graphical user interfaces for BLAST are clunky. We developed <a href="http://www.sequenceserver.com">SequenceServer</a> to overcome these hurdles. </li>
<li>Sequencing genomes has become straightforward. But correctly identifying genes in a genome sequence remains challenging. This is a huge problem for multi-species multi-gene analyses on emerging model organisms (trash in trash out).
<ul>
<li>We developed <a href="/tools/genevalidator/">GeneValidator</a> for automated identification and visualization of problems with gene predictions.</li>
<li>Many gene predictions need to be inspected and manually fixed before performing analyses. We are developing infrastructure to <a href="http://afra.sbcs.qmul.ac.uk">crowd-source gene curation to students as part of improved learning experience</a>. </li>
</ul>
</li>
<li>Because genomics data types and analysis algorithms remain young, many analyses require jumping back and forth between multiple tools. The tools themselves are young, can be challenging to install and can require frequent updates. But for reproducibility a given project may want to stick to specific versions of specific tools. Based on the <a href="http://docker.io/">docker</a> container architecture, <a href="https://github.com/yeban/oswitch">oSwitch enables lightweight switching from one virtual operating system to another</a>. It is a powerful tool for pipelines and for hacking.
<li>We are also developping <a href="http://www.bionode.io/">BioNode</a>, an Open Source community to build highly reusable tools and code for bioinformatics by leveraging the Node.JS ecosystem. We want to process big genomic data using Node.JS Streams. We welcome all kinds of contributions at all levels of experience.
</li>
</ul>
<btn id="section2-less-btn" onclick="$('#section2-extra').hide();$('#section2-more-btn').show();" class="btn btn-default btn-sm">Read Less</btn>
</div>
<div class="col-md-5 visible-xs-inline visible-sm-inline">
<img src="{{ site.url }}/img/frontpage/analyze-final.gif" class="img-rounded img-responsive center-block" alt="how tools should be">
</div>
</div>
<div class="clearfix"></div>
<hr>
<div id="section3" class="row">
<div class="col-sm-12">
<h3>Pollinator health</h3>
</div>
<div class="col-md-7">
<p>
Pollinators (bees in particular) are essential for preserving biodiversity and ensuring agricultural yields, thus their worldwide decline poses important risks. Taking inspiration from biomedical approaches for understanding cancer biology, we are using modern molecular tools to determine how pollinators are affected by changing environments (e.g., pesticide exposure, habitat loss, changing climates) and their ability to cope with such changes.
</p>
<p>
We recently began sequencing hundreds of pollinator genomes and are performing population genomics analyses.
</p>
</div>
<div class="col-md-5 hidden-xs hidden-sm">
<img src="{{ site.url }}/img/frontpage/bumblebee-240.jpg" class="img-rounded img-responsive center-block" alt="bumblebee on flower">
</div>
</div>
</div>
<div class="col-sm-4 col-md-4">
<h3>Latest news</h3>
<ul style="list-style-type: none; padding-left: 5px; border-bottom: 1px solid #eee">
{% for post in site.categories.labnews offset: 0 limit: 3 %}
<li>
<strong><a href="{{ site.url }}{{ post.url }}">{{ post.title }}</a></strong> <br>{{ post.date | date: "%B %e, %Y" }}</br></p>
</li>
{% endfor %}
</ul>
<ul class="fa-ul">
<li><i class="fa-li fa fa-sign-in"></i><a href="/postdoc_phd_positions"><h3>Joining the lab</h3></a></li>
</ul>
<hr/>
<h3>Contact</h3>
{% include contact.html %}
<hr/>
<a href="/map">
<img src="/img/map.png" width="100%"/>
</a>
<p style="text-align:center;">[<a href="/map">Larger Map & Local Directions</a>]</p>
<hr/>
<div class="row text-center">
<a class="twitter-timeline" data-width="300" data-height="400" data-dnt="true" href="https://twitter.com/yannick__">Twitter feed</a> <script async src="//platform.twitter.com/widgets.js" charset="utf-8"></script>
</div>
</div>
<br>
<div class="clearfix"></div>
<br>
<hr>
<div class="row">
<div class="col-sm-12 col-md-12">
<p>We are grateful for support from our funders:</p>
<img class="img-responsive" src="{{ site.url }}/img/logos/allstuck-bw.png" alt="funding bodies" style="max-height: 200px;">
</div>
<!-- <h3>Misc</h3>
<ul>
<li><a href="http://www.antgenomes.org">BLAST search ant genomes</a></li>
<li>Generic easy to deploy <a href="http://www.sequenceserver.com">local blast web server frontend (alternative to NCBI's wwwblast)</a></li>
<li>And: <a href="http://github.com/yannickwurm/">github</a>, <a href="http://del.icio.us/shihan">del.icio.us</a>, <a href="http://www.linkedin.com/in/sectgenomics">LinkedIn</a>, <a href="http://profile.to/yannickwurm">Facebook</a>, <a href="http://www.myspace.com/yannick.wurm">MySpace</a>, <a href="http://twitter.com/yannick__">Twitter</a>, skype, msn, icq...</li>
<li>Unsponsored advertising: <a
href="http://www.karatelausanne.com/" title="Karaté
traditionnel">Shotokan Karate in Lausanne</a>, <a
href="http://www.danielefraboulet.com" title="belles aquarelles">My
Mom's great Watercolor art</a>, <a
href="http://indraaziz.net">Jakarta Music</a>.</li>
<li><a
href="/archive.php">Some old stuff.</a></li>
<li><a
href="http://www.ownersdirect.co.uk/italy/it3092.htm">Beautiful
countryside vacation rental near Florence, Tuscany</a></li>
<li><a href="http://www.danielefraboulet.com">Cours de peinture/aquarelle à Lausanne</a></li>
</ul>
-->
</div>
<!-- LocalWords: visualisation SequenceServer genomes genome curation html Sk
-->
<!-- LocalWords: genomics
-->