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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">NBIC/BioSB Course Comparative Genomics: from evolution to function (2nd edition)<span style="color:#1F497D">
</span>– Registration open!<br>
</span></b><u><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:#1F497D"><br>
</span></u><u><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">Date:</span></u><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif""> June 2 – June 6, 2014<br>
<u>Location</u>: VU University, Amsterdam, the Netherlands<br>
<u>Course coordinators:</u> Berend Snel (UU), Martijn Huynen (Radboudumc), Jaap Heringa (VU), Celia van Gelder (NBIC/BioSB,
<a href="mailto:education@biosb.nl">education@biosb.nl</a>)<br>
<u>Course website</u>: <a href="http://biosb.nl/comparative-genomics-2014/">http://biosb.nl/comparative-genomics-2014/</a>
<br>
<u>Registration:</u> </span><span lang="EN-US" style="color:#1F497D"><a href="http://biosb.nl/education/enrollment-comparative-genomics/">http://biosb.nl/education/enrollment-comparative-genomics/</a></span><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif""><br>
<u>More information</u>: <a href="mailto:education@biosb.nl">education@biosb.nl</a><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">Course description<br>
</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif""><br>
Comparative genomics between species and between types of data facilitates the understanding of what these data really reflect about the underlying processes. Comparative genomics therewith relies on a solid understanding of basic elements of Bioinformatics
like homology and orthology. Moreover it is important to know the assumptions and heuristics of bioinformatic methods for comparative genomics and hence we aim to let participants develop an understanding of why they fail (or misdetect) as a consequence of
a variety of biological /evolutionary causes. <o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">The first two days of the course provide a basis for the course with the aim to move "beyond blast" in terms of more sensitive
homology searches, domain level analysis of protein evolution as well as more fine grained definitions of relatedness as can be obtained from the proper interpretation of gene trees (i.e. various levels of orthology).This foundation is used to discuss in the
three following days in more detail three topics: (1) the study of functional and evolutionary consequence of (genome) duplications, (2) the evolution of interactions and complexes and (3) the prediction and evolution of genomic regulatory elements.
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">Target audience<o:p></o:p></span></b></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">The course is intended for PhD students and master students in bioinformatics, especially those interested in evolution and/or
those who want to compare various genomics data between species. Participants are expected to have some hands on experience with blast, constructing multiple sequence alignments and phylogenetic trees, and in addition to have some familiarity with concepts
such as orthology, synteny and protein domains.<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">Programme<o:p></o:p></span></b></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><u><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">Monday June 2:</span></u><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif""> Distant homology
and protein domains (lecturer Jaap Heringa) <br>
Topics & Tools: Divergent and convergent evolution, (multiple) sequence alignment, psiblast, hhsearch, pfam, homology and function, undetected orthology from failure to detect homology, paralogs and function specificity prediction<br>
<br>
<u>Tuesday June 3:</u> Comparative Interactomics (lecturers Jaap Heringa, Martijn Huynen/John van Dam)
<br>
Topics & Tools: network alignment, phylogenetic profiles, biogrid, cytoscape, Bayesian data integration, neofunctionalization vs subfunctionalization
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><u><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">Wednesday June 4:</span></u><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif""> Small scale orthology
and large scale databases (lecturers Martijn Huynen, Berend Snel) <br>
Topics & Tools: tree reconciliation, relation between homology and orthology, ensembl compara, COGs, inparalogs vs outparalogs, fusion and fission
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><u><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">Thursday June 5</span></u><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">: Genome duplications
(lecturer Berend Snel) <br>
Topics & Tools: yeast gene order browser, synteny, consequences of genome duplications, timing of duplications, ensembl biomart
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><u><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">Friday June 6:</span></u><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif""> Finding functional
elements in DNA and RNA sequences, Biased gene conversion (lecturer Martijn Huynen)
<br>
Topics & Tools: phylogenetic footprinting, (phylogeny aware) gibbs sampling, RNA secondary structure prediction based on sequences and on experimental data, biased gene conversion & positive selection.<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">BioSB Course Programme</span></b><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">The course portfolios of NBIC (bioinformatics) and NCSB (systems biology) will be integrated and continued in the Netherlands Bioinformatics and Systems Biology
Research School (BioSB). <br>
The Education Portfolio of BioSB can be found at <a href="http://biosb.nl/education/course-portfolio/">
<span style="color:windowtext">http://biosb.nl/education/course-portfolio/</span></a>.
</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif""><br>
<b>More information</b></span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Helvetica","sans-serif"">For more information about the course you can contact Celia van Gelder at
<u><a href="mailto:education@biosb.nl">education@biosb.nl</a></u>. </span><span lang="EN-US" style="font-size:12.0pt;font-family:"Times New Roman","serif""><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Consolas">Dr. Celia W.G. van Gelder<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas">Coordinator Education CMBI<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas">Projectleader Education NBIC<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas">tel. +31-(0)24-3666120<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas">e-mail:
</span><span style="font-size:10.5pt;font-family:Consolas"><a href="mailto:C.vanGelder@umcn.nl"><span lang="EN-US">Celia.vanGelder@radboudumc.nl</span></a></span><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas">websites:
</span><span style="font-size:10.5pt;font-family:Consolas"><a href="http://www.cmbi.ru.nl/"><span lang="EN-US">www.cmbi.ru.nl</span></a></span><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas">,
</span><span style="font-size:10.5pt;font-family:Consolas"><a href="http://www.nbic.nl/"><span lang="EN-US">www.nbic.nl</span></a></span><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas">Postal address:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas">CMBI 260<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.5pt;font-family:Consolas">Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p><span style="font-size:10.0pt;font-family:"Arial","sans-serif"">Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629.<br>
The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.<o:p></o:p></span></p>
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<p style="font-size:13px;font-family:arial;">Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629.<br>
The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.<br>
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