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<body class='hmmessage'><P class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: justify"><FONT face="Times New Roman"><SPAN class=sensecontent1><B style="mso-bidi-font-weight: normal"><U><SPAN lang=EN-US style="FONT-SIZE: 14pt; COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'"></SPAN></U></B></SPAN></FONT> </P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: justify"><FONT face="Times New Roman"><SPAN class=sensecontent1><B style="mso-bidi-font-weight: normal"><U><SPAN lang=EN-US style="FONT-SIZE: 14pt; COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'"></SPAN></U></B></SPAN></FONT> </P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: justify"><FONT face="Times New Roman"><SPAN class=sensecontent1><B style="mso-bidi-font-weight: normal"><U><SPAN lang=EN-US style="FONT-SIZE: 14pt; COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'">Internship v</SPAN></U></B></SPAN><B style="mso-bidi-font-weight: normal"><U><SPAN lang=EN-US style="FONT-SIZE: 14pt; COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'">acancy : Evaluation of Pathway Analysis tools for Cancer related Biomarker discovery data.<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></SPAN></U></B></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: center" align=center><SPAN lang=EN-US style="COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: justify"><FONT size=3><FONT face="Times New Roman"><SPAN lang=EN-US style="COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'">Visualization of biological data is one of the best aids for scientists to gain knowledge about complex biological issues. Cancer is a very complex disease, encompassing a broad range of genes and proteins. Mass spectrometry techniques generate large volumes of protein data. This data is a combination<SPAN style="mso-spacerun: yes"> </SPAN>of the abundance and identification of a large number of proteins/peptides. To visualize this data in a biological context (e.g. the interaction with other proteins, DNA, RNA and small molecules), a number bioinformatics efforts have been made.<I> Cytoscape </I>(</SPAN><SPAN lang=EN-US style="COLOR: navy; FONT-FAMILY: 'Garamond Antiqua'"><A href="http://www.cytoscape.org/"><SPAN style="COLOR: navy"><U>http://www.cytoscape.org</U></SPAN></A></SPAN><SPAN lang=EN-US style="COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'">) is a bioinformatics software platform for <I><SPAN style="mso-bidi-font-weight: bold">visualizing</SPAN></I> molecular interaction networks and <I><SPAN style="mso-bidi-font-weight: bold">integrating </SPAN></I>these interactions with gene and protein expression profiles.<o:p></o:p></SPAN></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: justify"><SPAN lang=EN-US style="COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'"><FONT size=3><FONT face="Times New Roman">We are seeking a highly motivated individual for the exploration of pathway analysis using <SPAN style="mso-spacerun: yes"> </SPAN>cytoscape software. Goal of the project is to explore the usability of Cytoscape and its plug-inn’s and apply this knowledge to different sets of cancer related data. Initial efforts will be made with a proof-of-principle strategy using known data-sets. Different pathway databases will be explored using these data-sets. This experience will be further exploited to gain biological knowledge into in-house produced datasets originating from colon and breast carcinomas or proximal fluids, using normal tissues as a reference. The project falls into a Systems Biology approach to determine biomarkers for the early detection and diagnostics of cancer.<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: justify"><SPAN lang=EN-US style="COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'"><FONT face="Times New Roman" size=3>Also </FONT><A name=FUNC_ENRICHMENT_PLUGINS><SPAN style="mso-bidi-font-weight: bold"><FONT face="Times New Roman" color=#333333 size=3>functional enrichment </FONT></SPAN></A><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-bidi-font-weight: bold">analysis</SPAN> of the protein profiles in a pathway analysis context will be done. For this reason, we will implement the BiNGO plug-inn (</FONT></FONT></SPAN><SPAN lang=EN-US style="COLOR: navy; FONT-FAMILY: 'Garamond Antiqua'"><A href="http://www.psb.ugent.be/cbd/papers/BiNGO"><SPAN style="COLOR: navy"><U><FONT face="Times New Roman" size=3>http://www.psb.ugent.be/cbd/papers/BiNGO</FONT></U></SPAN></A></SPAN><SPAN lang=EN-US style="COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'"><FONT size=3><FONT face="Times New Roman">).<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: justify"><SPAN lang=EN-US style="COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'"><FONT size=3><FONT face="Times New Roman">A second(ary) goal is to compare the results generated in the cytoscape environment to other pathway and gene-set enrichment analysis tools.<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: justify"><SPAN lang=EN-US style="COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'"><FONT size=3><FONT face="Times New Roman">The research can lead into the writing of a publication of the results.<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: center" align=center><SPAN lang=EN-US style="COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'"><FONT size=3><FONT face="Times New Roman">Interested individuals should contact:<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'; mso-bidi-font-family: Arial"><FONT face="Times New Roman" size=3>Dr. Connie R. Jimenez<BR>Head OncoProteomics Laboratory, CCA 1-60<BR><?xml:namespace prefix = st1 ns = "urn:schemas-microsoft-com:office:smarttags" /><st1:PlaceType w:st="on">Dept.</st1:PlaceType> <st1:PlaceName w:st="on">Medical</st1:PlaceName> <st1:PlaceName w:st="on">Oncology</st1:PlaceName><BR><st1:PlaceName w:st="on">VUmc-Cancer</st1:PlaceName> <st1:PlaceType w:st="on">Center</st1:PlaceType> <st1:City w:st="on">Amsterdam</st1:City><BR>De Boelelaan 1117<BR>1081 HV <st1:City w:st="on">Amsterdam</st1:City><BR>The <st1:place w:st="on"><st1:country-region w:st="on">Netherlands</st1:country-region></st1:place><BR>Phone: +31(0)20-4442340<BR>Email: </FONT><A href="mailto:c.jimenez@vumc.nl"><U><FONT size=3><FONT face="Times New Roman"><SPAN style="COLOR: navy">c.jimenez@vumc.n</SPAN><SPAN style="COLOR: #333333">l</SPAN></FONT></FONT></U></A><o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'; mso-bidi-font-family: Arial"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'; mso-bidi-font-family: Arial"><FONT size=3><FONT face="Times New Roman">Or<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'; mso-bidi-font-family: Arial"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'; mso-bidi-font-family: Arial; mso-no-proof: yes"><FONT size=3><FONT face="Times New Roman">Marc O. Warmoes, Msc<o:p></o:p></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman"><SPAN lang=EN-US style="COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'; mso-bidi-font-family: Arial">Dept. Medical Oncology, OPL</SPAN><SPAN lang=EN-US style="COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'; mso-no-proof: yes"><o:p></o:p></SPAN></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman"><SPAN lang=EN-US style="COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'; mso-bidi-font-family: Arial; mso-no-proof: yes">Tel +32(0)20-44-43845</SPAN><SPAN lang=EN-US style="COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'; mso-no-proof: yes"><o:p></o:p></SPAN></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman"><st1:City w:st="on"><st1:place w:st="on"><SPAN lang=EN-US style="COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'; mso-bidi-font-family: Arial; mso-no-proof: yes">Mobile</SPAN></st1:place></st1:City><SPAN lang=EN-US style="COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'; mso-bidi-font-family: Arial; mso-no-proof: yes">: +32(0)628785335</SPAN><SPAN lang=EN-US style="COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'; mso-no-proof: yes"><o:p></o:p></SPAN></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman"><SPAN lang=EN-US style="COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'; mso-bidi-font-family: Arial; mso-no-proof: yes">Mail : </SPAN><SPAN lang=EN-US style="COLOR: navy; FONT-FAMILY: 'Garamond Antiqua'; mso-bidi-font-family: Arial; mso-no-proof: yes"><A title=mailto:m.warmoes@vumc.nl href="mailto:m.warmoes@vumc.nl"><SPAN style="COLOR: navy"><U>m.warmoes@vumc.nl</U></SPAN></A></SPAN><SPAN lang=EN-US style="COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'; mso-no-proof: yes"><o:p></o:p></SPAN></FONT></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-US style="COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'; mso-bidi-font-family: Arial"><o:p><FONT face="Times New Roman" size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT size=3><FONT face="Times New Roman"><SPAN lang=EN-US style="COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'; mso-bidi-font-family: Arial">More information on the OncoProteomics Laboratory(OPL) can be found on our website: </SPAN><SPAN lang=EN-US style="COLOR: navy; FONT-FAMILY: 'Garamond Antiqua'; mso-bidi-font-family: Arial"><A href="http://www.oncoproteomics.nl/"><SPAN style="COLOR: navy"><U>http://www.oncoproteomics.nl/</U></SPAN></A></SPAN></FONT></FONT><SPAN lang=EN-US style="COLOR: #333333; FONT-FAMILY: 'Garamond Antiqua'; mso-bidi-font-family: Arial"><o:p></o:p></SPAN></P><br /><hr />Update vandaag nog in één klik je hele online leven! <a href='http://get.live.com' target='_new'>Windows Live </a></body>
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