Rename REHAB to journal club, migrate to jclub page, and rebuild site

Author: rossibarra

_site.yml

@@ -12,8 +12,8 @@ navbar:
       href: pubs.html
     - text: "Lab Docs"
       href: https://github.com/RILAB/lab-docs
-    - text: "R.E.H.A.B"
-      href: rehab.html
+    - text: "journal club"
+      href: jclub.html
     - text: "News"
       href: news.html
 output:

blogs/01052015.html

@@ -169,7 +169,7 @@
         <li><a href="research.html">Research</a></li>
         <li><a href="pubs.html">Publications</a></li>
         <li><a href="https://github.com/RILAB/lab-docs">Lab Docs</a></li>
-        <li><a href="rehab.html">R.E.H.A.B</a></li>
+        <li><a href="jclub.html">journal club</a></li>
         <li><a href="news.html">News</a></li>
         <li><a href="press.html">Press</a></li>
     </div><!--/.nav-collapse -->

blogs/02102015.html

@@ -169,7 +169,7 @@
         <li><a href="research.html">Research</a></li>
         <li><a href="pubs.html">Publications</a></li>
         <li><a href="https://github.com/RILAB/lab-docs">Lab Docs</a></li>
-        <li><a href="rehab.html">R.E.H.A.B</a></li>
+        <li><a href="jclub.html">journal club</a></li>
         <li><a href="news.html">News</a></li>
         <li><a href="press.html">Press</a></li>
     </div><!--/.nav-collapse -->
@@ -186,7 +186,7 @@ <h1 class="title toc-ignore">Wang et. al., 2015</h1>
 
 
 <p><a href="http://www.pnas.org/content/112/35/E4959.long">Wang <em>et. al.</em>, 2015</a> created a set of F4-F6 pure breeding lines, called hybrid mimics, which exhibit hybrid vigor similar to F1 hybrids in <em>Arabidopsis</em>. The authors compared the differentially expressed genes in F1 hybrid and the hybrid mimics and found similar expression pattern between them. The authors proposed that the altered expression could be a consequence of trans-regulation of genes or epigenetic modifications.</p>
-<p>In general, during R-I lab <a href="http://www.rilab.org/rehab.html">R.E.H.A.B.</a> discussion, most of us liked the paper. It was well written with explicit figures. The authors selected rosette diameter as a trait of interest. With the selection intensity of 4-10%, they were able to create F4-F6 hybrid mimics, which provided evidence to argue against early criticism about the complementation of deleterious alleles in explaining heterosis. The early idea was that if the complementation hypothesis were true, it should be possible to create a hybrid-like inbred line with all of the superior alleles. The current observation showed that the hybrid-like lines could indeed be created for rosette diameter in <em>Arabidopsis</em>. Their results thus rejected this early criticism against dominant complementation theory for heterosis. But the trait in the current study may be controlled by relative few segregating genetic variants. For more complex traits, like grain yield, hybrid mimics may be hard or almost impossible to obtain.</p>
+<p>In general, during R-I lab <a href="http://www.rilab.org/jclub.html">journal club</a> discussion, most of us liked the paper. It was well written with explicit figures. The authors selected rosette diameter as a trait of interest. With the selection intensity of 4-10%, they were able to create F4-F6 hybrid mimics, which provided evidence to argue against early criticism about the complementation of deleterious alleles in explaining heterosis. The early idea was that if the complementation hypothesis were true, it should be possible to create a hybrid-like inbred line with all of the superior alleles. The current observation showed that the hybrid-like lines could indeed be created for rosette diameter in <em>Arabidopsis</em>. Their results thus rejected this early criticism against dominant complementation theory for heterosis. But the trait in the current study may be controlled by relative few segregating genetic variants. For more complex traits, like grain yield, hybrid mimics may be hard or almost impossible to obtain.</p>
 <p>The authors referred to their selection method as “recurrent selection”. However, I do not think it is the same recurrent selection we use in plant breeding. In plant breeding, the inbred parents were <a href="https://dl.sciencesocieties.org/publications/aj/abstracts/37/2/AJ0370020134">selected recurrently</a> from the interbreeding plants according to their combining abilities. I think in the current study, what the authors did was just “selection”. This potential terminology issue would not affect their analysis.</p>
 <p>I liked the way the authors used to present gene expression profiles in <strong>Fig.4</strong> and <strong>Fig.5</strong>. We all understand that RNA-seq data are difficult to present. The authors came up with this very smart strategy to compare expression among different lines. In panel B of <strong>Fig.4</strong>, one of the F4 lines looks very similar to the hybrid. However, it may not that obvious for other lines, especially with only one negative control. The analysis would have been more silid with a statistical comparison of quantitative differences. (I know I have been too picky about this. :( ) We found that the scales for <strong>Fig.4</strong> and <strong>Fig.5</strong> are different. We were wondering why in one study the scales changed from -5 to 5, but in the other, from -50 to 50. And, the criterion they used for detecting DEG were less stringent than normally used (FC &gt;= 1.3 and P-value &lt; 0.05 in this study, normally FC &gt; 2 and FDR &lt; 0.05).</p>
 <p>In <strong>Fig.6</strong>, we expected the authors to conduct a genetic scanning to confirm whether there were heterozygosity regions shared among lines. Unfortunately, they failed to deliver this message. It would be interesting to see, in the future, the dissection of the genetic architecture of this trait and the genetic explanations of heterosis for these very interesting hybrid mimics.</p>

blogs/02102015.md

@@ -6,7 +6,7 @@ output:
 
 [Wang *et. al.*, 2015](http://www.pnas.org/content/112/35/E4959.long) created a set of F4-F6 pure breeding lines, called hybrid mimics, which exhibit hybrid vigor similar to F1 hybrids in *Arabidopsis*. The authors compared the differentially expressed genes in F1 hybrid and the hybrid mimics and found similar expression pattern between them. The authors proposed that the altered expression could be a consequence of trans-regulation of genes or epigenetic modifications.
 
-In general, during R-I lab [R.E.H.A.B.](http://www.rilab.org/rehab.html) discussion, most of us liked the paper. It was well written with explicit figures. The authors selected rosette diameter as a trait of interest. With the selection intensity of 4-10%, they were able to create F4-F6 hybrid mimics, which provided evidence to argue against early criticism about the complementation of deleterious alleles in explaining heterosis. The early idea was that if the complementation hypothesis were true, it should be possible to create a hybrid-like inbred line with all of the superior alleles. The current observation showed that the hybrid-like lines could indeed be created for rosette diameter in *Arabidopsis*. Their results thus rejected this early criticism against dominant complementation theory for heterosis. But the trait in the current study may be controlled by relative few segregating genetic variants. For more complex traits, like grain yield, hybrid mimics may be hard or almost impossible to obtain.
+In general, during R-I lab [journal club](http://www.rilab.org/jclub.html) discussion, most of us liked the paper. It was well written with explicit figures. The authors selected rosette diameter as a trait of interest. With the selection intensity of 4-10%, they were able to create F4-F6 hybrid mimics, which provided evidence to argue against early criticism about the complementation of deleterious alleles in explaining heterosis. The early idea was that if the complementation hypothesis were true, it should be possible to create a hybrid-like inbred line with all of the superior alleles. The current observation showed that the hybrid-like lines could indeed be created for rosette diameter in *Arabidopsis*. Their results thus rejected this early criticism against dominant complementation theory for heterosis. But the trait in the current study may be controlled by relative few segregating genetic variants. For more complex traits, like grain yield, hybrid mimics may be hard or almost impossible to obtain.
 
 The authors referred to their selection method as "recurrent selection". However, I do not think it is the same recurrent selection we use in plant breeding. In plant breeding, the inbred parents were [selected recurrently](https://dl.sciencesocieties.org/publications/aj/abstracts/37/2/AJ0370020134) from the interbreeding plants according to their combining abilities. I think in the current study, what the authors did was just "selection". This potential terminology issue would not affect their analysis.
 

blogs/09052014.html

@@ -20,7 +20,7 @@
   </head>
   <body>
   <p><a href="research.html#adaptation"> <img src="http://www.rilab.org/images/teosinte.jpg" style="width: 150px;"></a> <a href="research.html#experimental"> <img src="http://www.rilab.org/images/corn.jpg" style="width: 150px;"></a> <a href="research.html#csomes"> <img src="http://www.rilab.org/images/csomes.jpg" style="width: 150px;"></a></p>
-  <h4 id="home-people-research-publications-lab-docs-r.e.h.a.b.-news-press"><a href="index.html">Home</a> || <a href="people.html">People</a> || <a href="research.html">Research</a> || <a href="pubs.html">Publications</a> || <a href="https://github.com/RILAB/lab-docs">Lab Docs</a> || <a href="rehab.html">R.E.H.A.B.</a> || <a href="news.html">News</a> || <a href="press.html">Press</a></h4>
+  <h4 id="home-people-research-publications-lab-docs-r.e.h.a.b.-news-press"><a href="index.html">Home</a> || <a href="people.html">People</a> || <a href="research.html">Research</a> || <a href="pubs.html">Publications</a> || <a href="https://github.com/RILAB/lab-docs">Lab Docs</a> || <a href="jclub.html">journal club</a> || <a href="news.html">News</a> || <a href="press.html">Press</a></h4>
   </body>
   </html>
 </head>

blogs/13062014.html

@@ -169,7 +169,7 @@
         <li><a href="research.html">Research</a></li>
         <li><a href="pubs.html">Publications</a></li>
         <li><a href="https://github.com/RILAB/lab-docs">Lab Docs</a></li>
-        <li><a href="rehab.html">R.E.H.A.B</a></li>
+        <li><a href="jclub.html">journal club</a></li>
         <li><a href="news.html">News</a></li>
         <li><a href="press.html">Press</a></li>
     </div><!--/.nav-collapse -->

blogs/16052014.html

@@ -169,7 +169,7 @@
         <li><a href="research.html">Research</a></li>
         <li><a href="pubs.html">Publications</a></li>
         <li><a href="https://github.com/RILAB/lab-docs">Lab Docs</a></li>
-        <li><a href="rehab.html">R.E.H.A.B</a></li>
+        <li><a href="jclub.html">journal club</a></li>
         <li><a href="news.html">News</a></li>
         <li><a href="press.html">Press</a></li>
     </div><!--/.nav-collapse -->

blogs/18072014.html

@@ -169,7 +169,7 @@
         <li><a href="research.html">Research</a></li>
         <li><a href="pubs.html">Publications</a></li>
         <li><a href="https://github.com/RILAB/lab-docs">Lab Docs</a></li>
-        <li><a href="rehab.html">R.E.H.A.B</a></li>
+        <li><a href="jclub.html">journal club</a></li>
         <li><a href="news.html">News</a></li>
         <li><a href="press.html">Press</a></li>
     </div><!--/.nav-collapse -->

blogs/20062014.html

@@ -169,7 +169,7 @@
         <li><a href="research.html">Research</a></li>
         <li><a href="pubs.html">Publications</a></li>
         <li><a href="https://github.com/RILAB/lab-docs">Lab Docs</a></li>
-        <li><a href="rehab.html">R.E.H.A.B</a></li>
+        <li><a href="jclub.html">journal club</a></li>
         <li><a href="news.html">News</a></li>
         <li><a href="press.html">Press</a></li>
     </div><!--/.nav-collapse -->
@@ -195,7 +195,7 @@ <h4>Part I: Divergence Hitchhiking</h4>
 <div id="part-ii-evolution-of-genome-architecture" class="section level4">
 <h4>Part II: Evolution of genome architecture</h4>
 <p>After providing a compelling argument for why divergence hitchhiking is unlikely to explain genomic islands of divergence, Yeaman investigates the evolution of genome architecture, or mutations that rearrange the genome, as a potential explanation. This analysis begins with an elegant simplified model, and then expands to include a simulation approach with fewer assumptions. The model estimates the time required for a population to evolve a clustered architecture, which depends on the genome size, population size, migration rate, rearrangement rate, and length of completely linked genomic segments. Yeaman emphasizes that the model, or heuristic, is only an approximation that should not be expected to give exact values. He uses the model to demonstrate that clustering can occur in a relatively short time, given the right model parameters. It is difficult to judge how realistic these parameters are, however, especially the values for the rearrangement rate. Still, Yeaman has more or less proven that under certain scenarios, genome architecture can evolve as a result of divergent selection, and that this can lead to genomic islands of divergence.</p>
-<p>Without going into great depth, the simulations that Yeaman performs agree with the model, and allow additional insights. For instance, the simulations demonstrate that even when environments fluctuate in time and space (and therefore so does selection), genome architecture may still evolve. Among my fellow R.E.H.A.B. participants, the biggest complaint with the simulations is that they are based on a cut-and-paste method to approximate genomic rearrangements. Whether or not this reasonably reflects how genome architecture actually evolves is left to speculation. In fact, Yeaman describes six known mechanisms for modifications of genome architecture – four of which are at least somewhat approximated by cut-and-paste – but highlights that the relative abundance of each mechanism in nature is unknown. When gene duplication was simulated (rather than cut-and-paste), gene deletion also had to be included for genome architecture to evolve.</p>
+<p>Without going into great depth, the simulations that Yeaman performs agree with the model, and allow additional insights. For instance, the simulations demonstrate that even when environments fluctuate in time and space (and therefore so does selection), genome architecture may still evolve. Among my fellow journal club participants, the biggest complaint with the simulations is that they are based on a cut-and-paste method to approximate genomic rearrangements. Whether or not this reasonably reflects how genome architecture actually evolves is left to speculation. In fact, Yeaman describes six known mechanisms for modifications of genome architecture – four of which are at least somewhat approximated by cut-and-paste – but highlights that the relative abundance of each mechanism in nature is unknown. When gene duplication was simulated (rather than cut-and-paste), gene deletion also had to be included for genome architecture to evolve.</p>
 </div>
 <div id="part-iii-discussion-and-implications" class="section level4">
 <h4>Part III: Discussion and Implications</h4>

blogs/20062014.md

@@ -14,7 +14,7 @@ Based on these results, Yeaman asserts that divergence hitchhiking is unlikely t
 
 After providing a compelling argument for why divergence hitchhiking is unlikely to explain genomic islands of divergence, Yeaman investigates the evolution of genome architecture, or mutations that rearrange the genome, as a potential explanation. This analysis begins with an elegant simplified model, and then expands to include a simulation approach with fewer assumptions. The model estimates the time required for a population to evolve a clustered architecture, which depends on the genome size, population size, migration rate, rearrangement rate, and length of completely linked genomic segments. Yeaman emphasizes that the model, or heuristic, is only an approximation that should not be expected to give exact values. He uses the model to demonstrate that clustering can occur in a relatively short time, given the right model parameters. It is difficult to judge how realistic these parameters are, however, especially the values for the rearrangement rate. Still, Yeaman has more or less proven that under certain scenarios, genome architecture can evolve as a result of divergent selection, and that this can lead to genomic islands of divergence.
 
-Without going into great depth, the simulations that Yeaman performs agree with the model, and allow additional insights. For instance, the simulations demonstrate that even when environments fluctuate in time and space (and therefore so does selection), genome architecture may still evolve. Among my fellow R.E.H.A.B. participants, the biggest complaint with the simulations is that they are based on a cut-and-paste method to approximate genomic rearrangements. Whether or not this reasonably reflects how genome architecture actually evolves is left to speculation. In fact, Yeaman describes six known mechanisms for modifications of genome architecture -- four of which are at least somewhat approximated by cut-and-paste -- but highlights that the relative abundance of each mechanism in nature is unknown. When gene duplication was simulated (rather than cut-and-paste), gene deletion also had to be included for genome architecture to evolve.
+Without going into great depth, the simulations that Yeaman performs agree with the model, and allow additional insights. For instance, the simulations demonstrate that even when environments fluctuate in time and space (and therefore so does selection), genome architecture may still evolve. Among my fellow journal club participants, the biggest complaint with the simulations is that they are based on a cut-and-paste method to approximate genomic rearrangements. Whether or not this reasonably reflects how genome architecture actually evolves is left to speculation. In fact, Yeaman describes six known mechanisms for modifications of genome architecture -- four of which are at least somewhat approximated by cut-and-paste -- but highlights that the relative abundance of each mechanism in nature is unknown. When gene duplication was simulated (rather than cut-and-paste), gene deletion also had to be included for genome architecture to evolve.
 
 #### Part III: Discussion and Implications