wurmlab · yuriigr · Apr 1, 2024
diff --git a/_posts/labnews/2011-02-21-fire-ant-genome-out.markdown b/_posts/labnews/2011-02-21-fire-ant-genome-out.markdown
@@ -13,7 +13,7 @@ tags:
 - work
 ---
 
-Two papers just out! Our [Solenopsis invicta fire ant genome ](http://www.pnas.org/cgi/doi/10.1073/pnas.1009690108) paper is out in PNAS. Win! And a study  [on fire ant Odorant Binding Proteins](http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016289) in PLoS ONE. [Anurag Priyam](http://yeban.in) and are developing a [generic BLAST web interface](http://www.sequenceserver.com) in ruby. It's already super useful for our [fourmidable ant genome database](http://www.antgenomes.org), and I'm sure will be for others working with non-model organisms. (easy to use; less of a hassle to set up than gmod...). Using the server, you can [blast ant genome sequences](http://www.antgenomes.org/blast) (and predicted genes).
+Two papers just out! Our [Solenopsis invicta fire ant genome ](http://www.pnas.org/cgi/doi/10.1073/pnas.1009690108) paper is out in PNAS. Win! And a study  [on fire ant Odorant Binding Proteins](http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016289) in PLoS ONE. Anurag Priyam and are developing a [generic BLAST web interface](http://www.sequenceserver.com) in ruby. It's already super useful for our [fourmidable ant genome database](http://www.antgenomes.org), and I'm sure will be for others working with non-model organisms. (easy to use; less of a hassle to set up than gmod...). Using the server, you can [blast ant genome sequences](http://www.antgenomes.org/blast) (and predicted genes).
 
 
 
@@ -23,4 +23,4 @@ Two papers just out! Our [Solenopsis invicta fire ant genome ](http://www.pnas.o
 
 
 
-Photo of fire ants on their genome (C) [Romain Libbrecht](http://www.unil.ch/dee/page50472_en.html) & [Yannick Wurm](http://www.sbcs.qmul.ac.uk/staff/yannickwurm.html)
+Photo of fire ants on their genome (C) Romain Libbrecht & [Yannick Wurm](https://www.qmul.ac.uk/sbbs/staff/yannickwurm.html)
diff --git a/_posts/labnews/2011-06-09-june-update.markdown b/_posts/labnews/2011-06-09-june-update.markdown
@@ -6,12 +6,12 @@ layout: post
 slug: june-update
 title: May Taiwan Conf & June genome updates
 wordpress_id: 29
-categories: 
+categories:
  - labnews
 
 ---
 
-Had a great two weeks visiting [John Wang's lab at Academia Sinica, Taiwan](http://biodiv.sinica.edu.tw/en2007/index.php?pi=157), and join National Taiwan University's [International Symposium on Social Insects](http://twentomolsoc.blogspot.com/2011/03/international-symposium-on-social.html) for wonderfully stimulating talks by [Jo Billen](http://bio.kuleuven.be/ento/), [Lars Chittka](http://chittkalab.sbcs.qmul.ac.uk/), [James Nieh,](http://www-biology.ucsd.edu/labs/nieh/) [Kenji Matsuura](http://www.agr.okayama-u.ac.jp/LIECO/englishpage.html) & [Bob Vander Meer](http://ars.usda.gov/pandp/people/people.htm?personid=5796). The symposium gave me the opportunity to share some thoughts about [sequencing genomes with high throughput technologies](http://yannick.poulet.org/publications/wurm2011antGenomeBehindTheScenes.pdf) in the journal of the Taiwan Entomological Society, [Formosan Entomologist](http://140.112.100.38/english.htm).
+Had a great two weeks visiting John Wang's lab at Academia Sinica, Taiwan, and join National Taiwan University's [International Symposium on Social Insects](http://twentomolsoc.blogspot.com/2011/03/international-symposium-on-social.html) for wonderfully stimulating talks by [Jo Billen](http://bio.kuleuven.be/ento/), [Lars Chittka](http://chittkalab.sbcs.qmul.ac.uk/), [James Nieh,](http://www-biology.ucsd.edu/labs/nieh/) Kenji Matsuura & [Bob Vander Meer](http://ars.usda.gov/pandp/people/people.htm?personid=5796). The symposium gave me the opportunity to share some thoughts about [sequencing genomes with high throughput technologies](http://yannick.poulet.org/publications/wurm2011antGenomeBehindTheScenes.pdf) in the journal of the Taiwan Entomological Society, Formosan Entomologist.
 
 
 
@@ -21,9 +21,9 @@ Had a great two weeks visiting [John Wang's lab at Academia Sinica, Taiwan](http
 
 
 
-
 
 
 
 
-In genomic news, the _Acromyrmex echinatior _leafcutter ant genome, led by [Sanne Nygaard](http://www1.bio.ku.dk/english/research/oe/cse/personer/sanne/) & [Koos Boosma](http://www1.bio.ku.dk/english/research/oe/cse/personer/koos/) is _in press_!  The data are already on [Fourmidable](http://www.antgenomes.org); and Fourmdiable's [ant genome BLAST interface](http://www.antgenomes.org) was updated to the latest [SequenceServer](http://www.sequenceserver.com).
+
+In genomic news, the _Acromyrmex echinatior _leafcutter ant genome, led by Sanne Nygaard & Koos Boosma is _in press_!  The data are already on [Fourmidable](http://www.antgenomes.org); and Fourmdiable's [ant genome BLAST interface](http://www.antgenomes.org) was updated to the latest [SequenceServer](http://www.sequenceserver.com).
diff --git a/_posts/labnews/2011-07-03-shenzhen-social-insect-conference.markdown b/_posts/labnews/2011-07-03-shenzhen-social-insect-conference.markdown
@@ -6,12 +6,12 @@ layout: post
 slug: shenzhen-social-insect-conference
 title: Social insect genomics conference 2011
 wordpress_id: 41
-categories: 
+categories:
  - labnews
  - genomics
 ---
 
-Many interesting talks and stimulating discussions during [Shenzhen's Social Insect Genomics Conference](http://ldl.genomics.org.cn/event/conference.jsp?conId=31) which coincided with the release of Sanne Nygaard's [_Acromyrmex echinatior_ leaf-cutter ant genome paper](http://www.genome.org/cgi/doi/10.1101/gr.121392.111) showing adaptations linked to fungal farming. More excitement is on its way with next generation sociogenetics projects bubbling up around the world & across the phylogeny!
+Many interesting talks and stimulating discussions during Shenzhen's Social Insect Genomics Conference which coincided with the release of Sanne Nygaard's [_Acromyrmex echinatior_ leaf-cutter ant genome paper](http://www.genome.org/cgi/doi/10.1101/gr.121392.111) showing adaptations linked to fungal farming. More excitement is on its way with next generation sociogenetics projects bubbling up around the world & across the phylogeny!
 
 
 

diff --git a/_posts/labnews/2011-12-01-Solenopsis-invicta-fire-ant-genome-paper.markdown b/_posts/labnews/2011-12-01-Solenopsis-invicta-fire-ant-genome-paper.markdown
@@ -24,7 +24,7 @@ categories:
             <dt>31.01.2011</dt>
             <dd><a href="http://asunews.asu.edu/20110201_4antgenomes">Arizona State University: <strong>New quartet of ant genomes advanced by experts</strong></a><a href="{{ site.url }}/pressCoverage/pressRelease/2011-01-31-ASUPressRelease4genomes.pdf"> [pdf]</a></dd>
             <dt>02.02.2011</dt>
-            <dd><a href="http://www.isb-sib.ch/news-a-events/news/463.html">Swiss Institute of Bioinformatics: <strong>Fire ant: The biggest genome ever sequenced in Switzerland </strong></a><a href="{{ site.url }}/pressCoverage/pressRelease/2011-02-01-FireAntPressReleaseEng.pdf"> [pdf]</a></dd>
+            <dd>Swiss Institute of Bioinformatics: <strong>Fire ant: The biggest genome ever sequenced in Switzerland </strong><a href="{{ site.url }}/pressCoverage/pressRelease/2011-02-01-FireAntPressReleaseEng.pdf"> [pdf]</a></dd>
         </dl>
         <h4>Scientific Coverage</h4>
         <dl>
@@ -42,25 +42,25 @@ categories:
         <h4>Traditional News Media</h4>
         <dl>
             <dt>04.02.2011</dt>
-            <dd><span class="highlight"><a href="http://www.24heures.ch/genome-nouvelle-arme-contre-vilaines-fourmis-2011-02-04">Tribune de Geneve: <strong>Le genome, nouvelle arme contre les vilaines fourmis</strong></a><a href="{{ site.url }}/pressCoverage/normalPress/2011-02-04-TribunedeGeneve.pdf"> [pdf]</a></span></dd>
+            <dd><span class="highlight">Tribune de Geneve: <strong>Le genome, nouvelle arme contre les vilaines fourmis</strong><a href="{{ site.url }}/pressCoverage/normalPress/2011-02-04-TribunedeGeneve.pdf"> [pdf]</a></span></dd>
             <dt>01.02.2011</dt>
             <dd><span class="highlight"><a href="http://www.myscience.ch/wire/fourmi_de_feu_le_plus_grand_genome_jamais_sequence_en_suisse-2011-unil">myScience: <strong>Fourmi de feu: le plus grand genome jamais sequence en Suisse</strong></a><a href="{{ site.url }}/pressCoverage/normalPress/2011-02-01-mySciencePortal-AntGenome.pdf"> [pdf]</a></span></dd>
             <dt>01.02.2011</dt>
-            <dd><a href="http://www.tdg.ch/universite-lausanne-genome-fourmi-feu-sequence-2011-02-01">Tribune de Geneve: <strong>Universite? de Lausanne: le genome de la fourmi de feu sequence</strong></a><a href="{{ site.url }}/pressCoverage/normalPress/2011-02-01-TribunedeGeneve.pdf"> [pdf]</a></dd>
+            <dd>Tribune de Geneve: <strong>Universite? de Lausanne: le genome de la fourmi de feu sequence</strong><a href="{{ site.url }}/pressCoverage/normalPress/2011-02-01-TribunedeGeneve.pdf"> [pdf]</a></dd>
             <dt>01.02.2011</dt>
             <dd><a href="http://www.lematin.ch/actu/suisse/universite-lausanne-genome-fourmi-feu-sequence-381142">Le Matin: <strong>Universite de Lausanne: le genome de la fourmi de feu sequence</strong></a><a href="{{ site.url }}/pressCoverage/normalPress/2011-02-01-lematin.pdf"> [pdf]</a> </dd>
             <dt>01.02.2011</dt>
             <dd><a href="http://bazonline.ch/wissen/natur/Forscher-entschluesseln-das-Erbgut-von-drei-Ameisenarten/story/26371516">TagesAngzeiger: <strong>Forscher entschlusseln das Erbgut von drei Ameisenarten</strong></a><a href="{{ site.url }}/pressCoverage/normalPress/2011-02-01-tagesAnzeiger-AntGenome.pdf"> [pdf]</a> </dd>
             <dt>01.02.2011</dt>
             <dd><a href="http://bazonline.ch/wissen/natur/Forscher-entschluesseln-das-Erbgut-von-drei-Ameisenarten/story/26371516">Basler Zeitung: <strong>Forscher entschlusseln das Erbgut von drei Ameisenarten</strong></a><a href="{{ site.url }}/pressCoverage/normalPress/2011-02-01-baslerZeitungAntGenome.pdf"> [pdf]</a> </dd>
             <dt>01.02.2011</dt>
-            <dd><a href="http://www.swissinfo.ch/eng/science_technology/Genome_research_could_combat_ant_pest_.html?cid=29387808">SwissInfo: <strong>Genome research could combat ant pest</strong></a><a href="{{ site.url }}/pressCoverage/normalPress/2011-02-01-swissinfoch.pdf"> [pdf]</a> </dd>
+            <dd>SwissInfo: <strong>Genome research could combat ant pest</strong><a href="{{ site.url }}/pressCoverage/normalPress/2011-02-01-swissinfoch.pdf"> [pdf]</a> </dd>
             <dt>01.02.2011</dt>
             <dd><a href="http://www.derbund.ch/wissen/natur/Forscher-entschluesseln-das-Erbgut-von-drei-Ameisenarten/story/26371516">Der Bund : <strong>Forscher entschlusseln das Erbgut von drei Ameisenarten</strong></a><a href="{{ site.url }}/pressCoverage/normalPress/2011-02-01-derbund-ch.pdf"> [pdf]</a> </dd>
             <dt>01.02.2011</dt>
-            <dd><a href="http://tt.bernerzeitung.ch/wissen/natur/Forscher-entschluesseln-das-Erbgut-von-drei-Ameisenarten/story/26371516">Thuner Tagblatt: <strong>Forscher entschlusseln das Erbgut von drei Ameisenarten</strong></a><a href="{{ site.url }}/pressCoverage/normalPress/2011-02-01-thunerTagblatt.pdf"> [pdf]</a> </dd>
+            <dd>Thuner Tagblatt: <strong>Forscher entschlusseln das Erbgut von drei Ameisenarten</strong><a href="{{ site.url }}/pressCoverage/normalPress/2011-02-01-thunerTagblatt.pdf"> [pdf]</a> </dd>
             <dt>01.02.2011</dt>
-            <dd><a href="http://www.24heures.ch/universite-lausanne-genome-fourmi-feu-sequence-2011-02-01">24heures: <strong>Universite de Lausanne: le genome de la fourmi de feu sequence</strong></a><a href="{{ site.url }}/pressCoverage/normalPress/2011-01-02-24heures.pdf"> [pdf]</a> </dd>
+            <dd>24heures: <strong>Universite de Lausanne: le genome de la fourmi de feu sequence</strong><a href="{{ site.url }}/pressCoverage/normalPress/2011-01-02-24heures.pdf"> [pdf]</a> </dd>
             <dt>02.02.2011</dt>
             <dd><a href="http://www.tsr.ch/info/suisse/1105502-rsr-matinale-speciale-1ere-partie-27-fevrier-journal-du-matin.html">Radio Suisse Romande: <strong>informations matinales</strong></a></dd>
         </dl>
@@ -71,9 +71,9 @@ categories:
             <dt>01.02.2011</dt>
             <dd><span class="highlight"><a href="http://www.genomeweb.com/sequencing/international-teams-publish-three-new-ant-genome-studies">GenomeWeb: <strong>International Teams Publish Three New Ant Genome Studies</strong></a><a href="{{ site.url }}/pressCoverage/mentionedWithOthers/2011-02-01-GenomeWeb-withsinvictaquotes.pdf"> [pdf]</a></span></dd>
             <dt>01.02.2011</dt>
-            <dd><a href="http://articles.sfgate.com/2011-02-01/news/27093366_1_argentine-ants-neil-d-tsutsui-leaf-cutter">SF Chronicle: <strong>Ants' genome project might unlock mysteries</strong></a><a href="{{ site.url }}/pressCoverage/mentionedWithOthers/2011-02-01-SFGate-SFChronicle.pdf"> [pdf]</a> </dd>
+            <dd>SF Chronicle: <strong>Ants' genome project might unlock mysteries</strong><a href="{{ site.url }}/pressCoverage/mentionedWithOthers/2011-02-01-SFGate-SFChronicle.pdf"> [pdf]</a> </dd>
             <dt>01.02.2011</dt>
-            <dd><a href="http://www.futurity.org/science-technology/genome-of-menacing-ant-sequenced/">Futurity: <strong>Genomes of menacing ants sequenced</strong></a><a href="{{ site.url }}/pressCoverage/mentionedWithOthers/2011-01-31-futurity.pdf"> [pdf]</a> </dd>
+            <dd>Futurity: <strong>Genomes of menacing ants sequenced</strong><a href="{{ site.url }}/pressCoverage/mentionedWithOthers/2011-01-31-futurity.pdf"> [pdf]</a> </dd>
         </dl>
     </div>
     <div class="column col-sm-1 col-md-1"></div>

diff --git a/_posts/labnews/2012-02-07-new-publications-new-job.markdown b/_posts/labnews/2012-02-07-new-publications-new-job.markdown
@@ -6,27 +6,27 @@ layout: post
 slug: new-publications-new-job
 title: New publications & New job
 wordpress_id: 67
-categories: 
+categories:
  - labnews
  - genomics
 ---
 
 New year, new country, new job:  I am now a [Lecturer](http://en.wikipedia.org/wiki/Lecturer#United_Kingdom) at [Queen Mary University of London](http://www.qmul.ac.uk/). I will continue to use genomics and bioinformatics approaches to examine the interplay between social evolution and genome evolution. Get in touch if you're interested in working with me in a great place.
 
-[![Queen mary qmul logo blue]({{ site.url }}/img/news/queen_mary_qmul_logo_blue.gif)](http://www.sbcs.qmul.ac.uk/staff/yannickwurm.html)
+[![Queen mary qmul logo blue]({{ site.url }}/img/news/queen_mary_qmul_logo_blue.gif)](https://www.qmul.ac.uk/sbbs/staff/yannickwurm.html)
 
 And a few nice papers on which I am coauthor are now out.
 
 
 
 
-  * [PNAS: Relaxed selection is a precursor to the evolution of phenotypic plasticity](http://yannick.poulet.org/publications/hunt2011phenotypicPlasticity.pdf). Led by [Brendan Hunt](http://www.goodismanlab.biology.gatech.edu/hunt/) at Georgia Tech
+  * [PNAS: Relaxed selection is a precursor to the evolution of phenotypic plasticity](http://yannick.poulet.org/publications/hunt2011phenotypicPlasticity.pdf). Led by Brendan Hunt at Georgia Tech
 
 
   * [Bioinformatics: Visualization and quality assessment of de novo genome assemblies](http://yannick.poulet.org/publications/Bioinformatics-2011-Riba-Grognuz-3425-6.pdf) - led by [Oksana Riba-Grognuz](http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CCIQFjAA&url=http%3A%2F%2Fwww.unil.ch%2Fdee%2Fpage81073_en.html&ei=fRcxT9HTMMi_0QWrhNSzBw&usg=AFQjCNE8Ei6RfZ8mIpMA03zncpmkodTzbg&sig2=7AxdNSLp5YWPl93zXvcf5Q) - [Source code available](https://github.com/ksanao/TGNet).
 
 
-  * [Trends in Genetics: The genomic impact of 100 million years of social evolution in seven ant species](http://yannick.poulet.org/publications/TiG2011.pdf). Reviews some of the findings from the [ant genome projects](http://www.antgenomes.org) & lays the foundation for coming analyses. [Romain Libbrecht](http://www.unil.ch/dee/page50472_en.html) & I made the photo that was selected as cover image!
+  * [Trends in Genetics: The genomic impact of 100 million years of social evolution in seven ant species](http://yannick.poulet.org/publications/TiG2011.pdf). Reviews some of the findings from the [ant genome projects](http://www.antgenomes.org) & lays the foundation for coming analyses. Romain Libbrecht & I made the photo that was selected as cover image!
 
 
 [![TIGs ant genomes]({{ site.url }}/img/news/TIGs_ant_genomes.png)](http://www.antgenomes.org)
diff --git a/...-02-18-oxford-nanopore-sequencing-a-revolution-for-non-model-organisms.markdown b/...-02-18-oxford-nanopore-sequencing-a-revolution-for-non-model-organisms.markdown
@@ -21,7 +21,7 @@ Exciting announcement of a new dirt-cheap machine-less DNA sequencing technology
   * it supposedly provide 100,000bp long reads. This will eliminate [most scaffolding issues]({{ site.url }}/news/2011-09-21-genome-analyses-for-non-model-organisms/) we have with assembling _de novo _genome sequence.
 
 
-  * using the [USB thumb-chip version](http://www.nanoporetech.com/technology/minion-a-miniaturised-sensing-instrument), no machine is required. Thus when you are [out in the field](http://vimeo.com/21287431), you can sequence right then and there - a potential workaround for worrying about tissue sample export permits... at least until new regulations appear!
+  * using the USB thumb-chip version, no machine is required. Thus when you are [out in the field](http://vimeo.com/21287431), you can sequence right then and there - a potential workaround for worrying about tissue sample export permits... at least until new regulations appear!
 
 
 
@@ -31,7 +31,7 @@ Exciting announcement of a new dirt-cheap machine-less DNA sequencing technology
 
 
 
- 
+
 
 
 

diff --git a/_posts/labnews/2013-12-22-news.markdown b/_posts/labnews/2013-12-22-news.markdown
@@ -5,18 +5,17 @@ date: 2013-12-22 17:07:12
 layout: post
 slug: 2013-nonews
 title: Long time no update
-categories: 
+categories:
  - labnews
  - teaching
 ---
-No real update here for a while! Major events include: 
+No real update here for a while! Major events include:
 
  * Publication of our [social chromosome paper in Nature](http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11832.html)
- * BBSRC & NESCent funding to [crowdsource gene curation](http://afra.sbcs.qmul.ac.uk)
+ * BBSRC & NESCent funding to crowdsource gene curation
  * Google Summer of Code funding to help [identify problematic gene predictions](https://github.com/monicadragan/GeneValidator)
  * Support form the [Software Sustainability Institute](http://software.ac.uk)
  * [Lots of teaching](/teaching/)
- * Some wonderful new [team members](/team), visitors, [colleagues](http://www.sbcs.qmul.ac.uk/people/index.html) & collaborators.
-
-Perhaps hope for more regular updates in 2014? We'll see. 
+ * Some wonderful new [team members](/team), visitors, [colleagues](https://www.qmul.ac.uk/sbbs/people/index.html) & collaborators.
 
+Perhaps hope for more regular updates in 2014? We'll see.
diff --git a/_posts/labnews/2013-12-23-vacancies.markdown b/_posts/labnews/2013-12-23-vacancies.markdown
@@ -14,11 +14,11 @@ categories:
 Positions to be filled:
 
  * [Postdoc (renewable for up to 3 years) of genomics, transcriptomics, bioinformatics & population genomics work involving pollinators](/news/2014-10-31-pollinator-population-genomicist). This will be in collaboration with [Richard Gill](http://www3.imperial.ac.uk/people/r.gill) at Imperial College Silwood Park.
- * Two four-year PhD positions available as part of [NERC's London Doctoral Training Program](http://www.sbcs.qmul.ac.uk/prospectivestudents/research/nercdtpstudentships/118400.html):
-   * [Social Chromosome Evolution](http://london-nerc-dtp.org/2013/11/27/social-chromosome-evolution/) co-supervised with [Judith Mank](http://www.ucl.ac.uk/mank-group/people.htm)
-   * [Evolutionary Genomics in Ants](http://london-nerc-dtp.org/2013/11/27/evolutionary-genomics-in-ants/) co-supervised by [Steve Rossiter](http://www.sbcs.qmul.ac.uk/staff/stephenrossiter.html)
+ * Two four-year PhD positions available as part of NERC's London Doctoral Training Program:
+   * Social Chromosome Evolution co-supervised with Judith Mank
+   * Evolutionary Genomics in Ants co-supervised by [Steve Rossiter](https://www.qmul.ac.uk/sbbs/staff/stephenrossiter.html)
 
 
 Please get in touch by email with a CV for more details. NERC PhD application deadline is mid-February. Cheers, Yannick.
 
-<a href="http://www.sbcs.qmul.ac.uk/prospectivestudents/research/nercdtpstudentships/118400.html"><img src="{{site.url }}/img/logos/nerc-logo-large.jpg" width="200" alt="NERC logo"></a>
+<img src="{{site.url }}/img/logos/nerc-logo-large.jpg" width="200" alt="NERC logo">
Original file line number	Diff line number	Diff line change
Expand Up		@@ -21,7 +21,7 @@ Exciting announcement of a new dirt-cheap machine-less DNA sequencing technology
		* it supposedly provide 100,000bp long reads. This will eliminate [most scaffolding issues]({{ site.url }}/news/2011-09-21-genome-analyses-for-non-model-organisms/) we have with assembling _de novo _genome sequence.


		* using the [USB thumb-chip version](http://www.nanoporetech.com/technology/minion-a-miniaturised-sensing-instrument), no machine is required. Thus when you are [out in the field](http://vimeo.com/21287431), you can sequence right then and there - a potential workaround for worrying about tissue sample export permits... at least until new regulations appear!
		* using the USB thumb-chip version, no machine is required. Thus when you are [out in the field](http://vimeo.com/21287431), you can sequence right then and there - a potential workaround for worrying about tissue sample export permits... at least until new regulations appear!



Expand All		@@ -31,7 +31,7 @@ Exciting announcement of a new dirt-cheap machine-less DNA sequencing technology








Expand Down