<div dir="ltr"><div class="gmail_quote"><div lang="NL" link="blue" vlink="purple"><div class="m_8471939308632178219WordSection1"><p class="MsoNormal" style="margin-bottom:12.0pt"><b><span lang="EN-US">BioSB Course Comparative Genomics: from evolution to function (3<sup>rd</sup> edition) <br></span></b><u><span lang="EN-US"><br>Date:</span></u><span lang="EN-US"> November 21-25, 2016<br><u>Location</u>: CMBI, Radboudumc, Nijmegen, the Netherlands<br><u>Course coordinators:</u> Berend Snel (UU), Martijn Huynen (Radboudumc), Jaap Heringa (VU), Celia van Gelder (BioSB)<br><u>Course website</u>: <a href="http://biosb.nl/education/course-portfolio/course-comparative-genomics/" target="_blank"><span style="color:windowtext">http://biosb.nl/<wbr>education/course-portfolio/<wbr>course-comparative-genomics/</span></a> <br><u>Registration:</u> <a href="http://biosb.nl/education/course-portfolio/enrollment-comparative-genomics-from-evolution-to-function-course-2016/" target="_blank"><span style="color:windowtext">http://biosb.nl/<wbr>education/course-portfolio/<wbr>enrollment-comparative-<wbr>genomics-from-evolution-to-<wbr>function-course-2016/</span></a> <br><u>More information</u>: <a href="mailto:education@biosb.nl" target="_blank"><span style="color:windowtext">education@biosb.<wbr>nl</span></a><u></u><u></u></span></p><p class="MsoNormal" style="margin-bottom:12.0pt"><b><span lang="EN-US">Course description<br></span></b><span lang="EN-US"><br>Comparative genomics between species and between types of data facilitates the understanding of what these data really reflect about the underlying biological 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 these methods sometimes fail (or misdetect) as a consequence of a variety of biological /evolutionary causes, and in which situations which method is most appropriate. The first two days of the course provide a basis for the course with the aim to move “beyond blast” in terms of the most 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 and of RNA structures</span><u></u><u></u></p><p class="MsoNormal" style="margin-bottom:12.0pt"><b><span lang="EN-US">Target audience</span></b><u></u><u></u></p><p class="MsoNormal" style="margin-bottom:12.0pt"><span lang="EN-US">The course is intended for PhD students and master students in bioinformatics or geneticists and experimental biologists with a strong interest in evolution of the eukaryotes. It is especially relevant to students who want to compare various types of genomics data between species. Participants are expected to have some hands on experience with tools like blast, constructing multiple sequence alignments and phylogenetic trees, and in addition to have some familiarity with concepts such as orthology, synteny and protein domains.</span><u></u><u></u></p><p class="MsoNormal" style="margin-bottom:12.0pt"><b><span lang="EN-US">Programme</span></b><u></u><u></u></p><p class="MsoNormal" style="margin-bottom:18.0pt;vertical-align:baseline;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><u><span lang="EN-US">Monday November 21: Distant homology and protein domains (lecturer Jaap Heringa)</span></u><span lang="EN-US"><br>Topics & Tools: Divergent and convergent evolution, (multiple) sequence alignment, psiblast, jackhmmer, hhsearch, pfam, homology and function, undetected orthology from failure to detect homology, paralogs and function specificity prediction</span><u></u><u></u></p><p class="MsoNormal" style="margin-bottom:18.0pt;vertical-align:baseline;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><u><span lang="EN-US">Tuesday Nov 22: Small scale orthology and large scale databases (lecturers Martijn Huynen, Berend Snel)<br></span></u>Topics & Tools: tree reconciliation, relation between homology and orthology, ensembl compara, COGs, inparalogs vs outparalogs, fusion and fission<u></u><u></u></p><p class="MsoNormal" style="margin-bottom:18.0pt;vertical-align:baseline;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><u><span lang="EN-US">Wednesday Nov 23: Comparative Interactomics (lecturers Jaap Heringa, Martijn Huynen/John van Dam)</span></u><span lang="EN-US"><br>Topics & Tools: network alignment, phylogenetic profiles, biogrid, cytoscape, Bayesian data integration, neofunctionalization vs subfunctionalization</span><u></u><u></u></p><p class="MsoNormal" style="margin-bottom:18.0pt;vertical-align:baseline;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><u><span lang="EN-US">Thursday Nov 24 : Genome duplications (lecturer Berend Snel)</span></u><span lang="EN-US"><br>Topics & Tools: yeast gene order browser, synteny, consequences of genome duplications, timing of duplications, ensembl biomart</span><u></u><u></u></p><p class="MsoNormal" style="margin-bottom:18.0pt;vertical-align:baseline;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><u><span lang="EN-US">Friday Nov 25: Finding functional elements in DNA and RNA sequences, Biased gene conversion (lecturer Martijn Huynen)</span></u><span lang="EN-US"><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.</span><u></u><u></u></p><p class="MsoNormal"><b><span lang="EN-US">BioSB Education Programme</span></b><u></u><u></u></p><p class="MsoNormal" style="margin-bottom:12.0pt"><span lang="EN-US">This course is part of the Education Programme of BioSB, the Netherlands Bioinformatics and Systems Biology research school, which offers training and education for in bioinformatics and systems biology. <br>More information about BioSB can be found at </span><a href="http://www.biosb.nl/" target="_blank"><span lang="EN-US" style="color:windowtext">www.biosb.nl</span></a><span lang="EN-US">. </span><u></u><u></u></p><p class="MsoNormal"><b><span lang="EN-US">More information</span></b><u></u><u></u></p><p class="MsoNormal"><span lang="EN-US">For more information about the course you can contact Celia van Gelder at <u><a href="mailto:education@biosb.nl" target="_blank"><span style="color:windowtext">education@biosb.nl</span></a></u>. </span><u></u><u></u></p><div><p class="MsoNormal"><u></u> <u></u></p></div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><div><p class="MsoNormal"><u></u> <u></u></p></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><p><a name="UNIQUE_ID_SafeHtmlFilter_UNIQUE_ID_SafeHtmlFilter__MailAutoSig"><span style="font-size:10.5pt;font-family:"Arial","sans-serif"">Dr.
Celia W.G. van Gelder<br>
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<p><span lang="EN-US" style="font-size:10.5pt;font-family:"Arial","sans-serif"">Programme Manager Learning
DTL/ELIXIR-NL Training<br>
Education Manager BioSB<br>
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<p><span lang="EN-US" style="font-size:10.5pt;font-family:"Arial","sans-serif"">tel. +31613375327<br><span style="font-family:Arial,sans-serif;font-size:10.5pt">e-mail: </span><a href="mailto:celia.van.gelder@dtls.nl" style="font-family:Arial,sans-serif;font-size:10.5pt" target="_blank">celia.van.gelder@dtls.nl</a><br><span lang="EN-US" style="font-size:10.5pt;font-family:Arial,sans-serif">websites: </span><a href="http://www.dtls.nl/" style="font-family:arial,sans-serif;font-size:12.8px" target="_blank"><span lang="EN-US" style="font-size:10.5pt;font-family:"Arial","sans-serif"">www.dtls.nl</span></a><span lang="EN-US" style="font-size:10.5pt;font-family:Arial,sans-serif">, </span><span lang="EN-US" style="font-family:Arial,sans-serif;font-size:10.5pt"><a href="http://www.biosb.nl/" style="font-family:arial,sans-serif;font-size:12.8px" target="_blank">www.biosb.nl</a><br><span style="font-size:10.5pt">skype: celia.van.gelder</span><br></span></span></p>
<p><span style="font-family:Arial,sans-serif;font-size:10.5pt">Postal address:<br></span><span style="color:black;font-family:Arial,sans-serif;font-size:10pt">DTL<br></span><span style="color:black;font-family:Arial,sans-serif;font-size:10pt">PO Box 19245<br></span><span style="color:black;font-family:Arial,sans-serif;font-size:10pt">3501 DE Utrecht</span><span style="color:black;font-family:Arial,sans-serif;font-size:10pt"><br></span></p>
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