[BBC] internship vacancy Evaluation of Pathway Analysis tools for Cancer related Biomarker discovery

[marc warmoes]

Internship vacancy : Evaluation of Pathway Analysis tools for Cancer related Biomarker discovery data.
 
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  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. Cytoscape (http://www.cytoscape.org) is a bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene and protein expression profiles.
We are seeking a highly motivated individual for the exploration of pathway analysis using  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.
Also functional enrichment analysis of the protein profiles in a pathway analysis context will be done. For this reason, we will implement the BiNGO plug-inn (http://www.psb.ugent.be/cbd/papers/BiNGO).
A second(ary) goal is to compare the results generated in the cytoscape environment to other pathway and gene-set enrichment analysis tools.
The research can lead into the writing of a publication of the results.
 
Interested individuals should contact:
 
Dr. Connie R. JimenezHead OncoProteomics Laboratory, CCA 1-60Dept. Medical OncologyVUmc-Cancer Center AmsterdamDe Boelelaan 11171081 HV AmsterdamThe NetherlandsPhone: +31(0)20-4442340Email: c.jimenez at vumc.nl
 
Or
 
Marc O. Warmoes, Msc
Dept. Medical Oncology, OPL
Tel +32(0)20-44-43845
Mobile: +32(0)628785335
Mail : m.warmoes at vumc.nl
 
More information on the OncoProteomics Laboratory(OPL) can be found on our website: http://www.oncoproteomics.nl/
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