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<small><font face="Helvetica, Arial, sans-serif"><b>NBIC PhD course
Algorithms for Biological Networks</b><br>
<br>
<br>
</font></small><small><font face="Helvetica, Arial, sans-serif"><u>Date:</u>
16-20 January 2012<br>
</font></small><small><font face="Helvetica, Arial, sans-serif"><u>Course
coordinator</u>: Dick de Ridder</font></small><br>
<small><font face="Helvetica, Arial, sans-serif"> <u>Location:</u>
Delft University of Technology, Delft, the Netherlands<br>
<u>Website: </u><a moz-do-not-send="true"
class="moz-txt-link-freetext"
href="http://www.nbic.nl/education/nbic-phd-school/course-schedule/algorithms-for-biological-networks/">http://www.nbic.nl/education/nbic-phd-school/course-schedule/algorithms-for-biological-networks/</a><u>
</u><br>
</font></small><small><font face="Helvetica, Arial, sans-serif"><u>Registration:</u>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://www.nbic.nl/education/nbic-phd-school/enrolment/">http://www.nbic.nl/education/nbic-phd-school/enrolment/</a></font></small><br>
<br>
<div class="moz-text-html" lang="x-western">
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<p class="MsoNormal" style=""><b style=""><span style="font-size:
10pt; font-family:
"Helvetica","sans-serif";" lang="EN-US">Target
audience</span><i style=""><span style="font-size: 10pt;
font-family:
"Helvetica","sans-serif";"
lang="EN-US"><o:p></o:p></span></i></b></p>
The course is aimed at PhD students with a background in
bioinformatics, computer science or a related field; a working
knowledge of basic statistics and linear algebra is assumed. The
NBIC Technology Track course"Pattern recognition" and the ASCI
course "Advanced pattern recognition" (a1) discuss many of the
tools used in this course, but it is not required to have followed
these. Prior knowledge of molecular biology is a bonus, but also
not strictly required. <span style="font-size: 10pt; font-family:
"Helvetica","sans-serif";" lang="EN-US"></span><span
style="font-size: 10pt; font-family: "Trebuchet
MS","sans-serif";" lang="EN-US"><span style=""><i><br>
</i><br>
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<p class="MsoNormal" style=""><b style=""><span style="font-size:
10pt; font-family:
"Helvetica","sans-serif";" lang="EN-US">Course
Description </span><i style=""><span style="font-size:
10pt; font-family:
"Helvetica","sans-serif";"
lang="EN-US"><o:p></o:p></span></i></b></p>
In this course, we will first give a brief overview of molecular
biology, the advent of high-throughput measurement techniques and
large databases containing biological knowledge, and the
importance of networks to model all this. We will highlight a
number of peculiar features of biological networks. Next, a number
of basic network models (linear, Boolean, Bayesian) will be
discussed, as well as methods of inferring these from observed
measurement data. A number of alternative network models more
suited for high-level simulation of cellular behaviour will also
be introduced. Building on the network inference methods, a number
of ways of integrating various data sources and databases to
refine biological networks will be discussed, with specific
attention to the use of sequence information to refine
transcription regulation networks. Finally, we will give some
examples of algorithms exploiting the networks found to learn
about biology, specifically for inspecting protein interaction
networks and for finding active subnetworks.<br>
<br>
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font-family: "Helvetica","sans-serif";"
lang="EN-US"><o:p> <b>Course topics<br>
</b></o:p></span>
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<p class="MsoNormal"><span
style="mso-ansi-language:EN-US;mso-bidi-font-weight: bold"
lang="EN-US">1. Monday 16-1-2012</span><span
style="mso-ansi-language:EN-US" lang="EN-US"> <span
style="mso-bidi-font-weight:bold">Networks in biology</span>
<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="mso-ansi-language:EN-US;mso-bidi-font-weight: bold"
lang="EN-US">2. Tuesday 17-1-2012</span><span
style="mso-ansi-language: EN-US" lang="EN-US"> <span
style="mso-bidi-font-weight:bold">Network inference</span> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-ansi-language:EN-US"
lang="EN-US"><span style="mso-spacerun:yes"> </span><span
style="mso-bidi-font-weight:bold">3. Wednesday 18-1-2012</span>
<span style="mso-bidi-font-weight:bold">Network enhancement<o:p></o:p></span></span></p>
<p class="MsoNormal"><span style="mso-ansi-language:EN-US"
lang="EN-US"><span style="mso-spacerun:yes"> </span><span
style="mso-bidi-font-weight:bold">4. Thursday 19-1-2012</span>
<span style="mso-bidi-font-weight:bold">Network validation and
execution</span> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-ansi-language:EN-US"
lang="EN-US"><span style="mso-spacerun:yes"> </span><span
style="mso-bidi-font-weight:bold">5. Friday 20-1-2012</span>
<span style="mso-bidi-font-weight:bold">Network mining</span><o:p></o:p></span></p>
<i><span style="font-size: 10pt; line-height: 115%; font-family:
"Helvetica","sans-serif";" lang="EN-US"></span></i>
<i><br>
</i>
<p class="MsoNormal" style=""><big><big><span style="font-size:
10pt; font-family:
"Helvetica","sans-serif";"
lang="EN-US"><big>More information about the course
programme can be found on:</big> </span></big><small><font
face="Helvetica, Arial, sans-serif"><a
moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://www.nbic.nl/education/nbic-phd-school/course-schedule/algorithms-for-biological-networks/">http://www.nbic.nl/education/nbic-phd-school/course-schedule/algorithms-for-biological-networks/</a></font></small><span
style="font-size: 10pt; font-family:
"Helvetica","sans-serif";" lang="EN-US">
<br>
.</span><span style="font-size: 10pt; font-family:
"Helvetica","sans-serif";" lang="EN-US"><o:p></o:p></span></big><br>
</p>
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<p class="MsoNormal" style=""><b style=""><span style="font-size:
10pt; font-family:
"Helvetica","sans-serif";" lang="EN-US">NBIC
PhD School</span><i style=""><span style="font-size: 10pt;
font-family:
"Helvetica","sans-serif";"
lang="EN-US"><o:p></o:p></span></i></b></p>
<p class="MsoNormal" style=""><span style="font-size: 10pt;
font-family: "Helvetica","sans-serif";"
lang="EN-US">This course is part of the Education Programme of
the NBIC PhD School. The NBIC PhD School offers training and
education for PhD students in bioinformatics. <br>
More information about the NBIC PhD School can also be found
on <a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://www.nbic.nl">http://www.nbic.nl</a> =>
Education => NBIC PhD School.<span style=""> </span><o:p></o:p></span></p>
<p class="MsoNormal" style=""><span style="font-size: 10pt;
font-family: "Helvetica","sans-serif";"
lang="EN-US"><span style=""> </span><o:p></o:p></span></p>
<p class="MsoNormal" style=""><b style=""><span style="font-size:
10pt; font-family:
"Helvetica","sans-serif";" lang="EN-US">More
information</span><i style=""><span style="font-size: 10pt;
font-family:
"Helvetica","sans-serif";"
lang="EN-US"><o:p></o:p></span></i></b></p>
<p class="MsoNormal" style=""><span style="font-size: 10pt;
font-family: "Helvetica","sans-serif";"
lang="EN-US">For more information about the course you can
contact Celia van Gelder (NBIC Education) at <a
moz-do-not-send="true" class="moz-txt-link-abbreviated"
href="mailto:celia.van.gelder@nbic.nl">education@nbic.nl</a>.<span
style=""> </span></span></p>
</div>
<pre class="moz-signature" cols="72">--
Dr. Celia W.G. van Gelder
Coordinator Education CMBI
Projectleader Education NBIC
tel. +31-(0)24-3666120
e-mail: <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:C.vanGelder@cmbi.ru.nl">C.vanGelder@cmbi.ru.nl</a>
websites: <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="http://www.cmbi.ru.nl">www.cmbi.ru.nl</a>, <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="http://www.nbic.nl">www.nbic.nl</a>
Postal address:
CMBI 260
Radboud University Nijmegen-Medical Centre /NCMLS
PO Box 9101, 6500 HB Nijmegen
The Netherlands
</pre>
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