MS2011-01: Cell Screening Analysis: CeScA

posted Mar 23, 2011, 4:09 AM by Marco Spruit   [ updated Nov 22, 2011, 4:40 AM ]
The UMC Utrecht has a pressing need for a 'process method' to help guide its various cell analysis processes by directing the users to the right data mining technique for each specific medical problem based on large amounts of generated data from medical devices. Help solve cancer by structuring the relevant subset of available data parameters, deducing requirements and a generic process flow through expert interviews, and prototyping the applicability of various data mining techniques! You will combine information technology capabilities from a people's perspective to help strenghten societal welfare. A PhD follow-up is explicitly possible upon successful completion. Below is a description from our biomedical colleagues at the UMCU:

Bioinformatics Techniques for the Analysis of High Content Data

The Cell Screening Center (CSC) is a center within the Cell Biology Department at UMC Utrecht that specializes in automated high throughput screening experiments. Examples of such experiments include small molecule compound screens against cellular and biochemical targets, and siRNA knock-down screens. The center aims to be a center of excellence in the area of high content screening (HCS). HCS makes use of automated microscopy and advanced image analysis techniques to generate multi-parameter data from morphological cellular assays. 

In collaboration with Prof. dr. Sjaak Brinkkemper and Dr. Marco Spruit at the University of Utrecht Department of Information & Computing Sciences, we can offer a 6 or 9 month Master’s student rotation on the development and implementation of bioinformatics techniques for the analysis of high content multiparameter data. The goal is to use data mining techniques (such as clustering) to compare biological profiles generated by large numbers of reagents. This will allow us to gain insights into the mechanism of action of small molecule compounds or the interaction of genes. These techniques will be applied in the areas of neuroscience, cancer drug discovery & stem cell biology. 
The CSC already has example datasets from previous screens that can be used to validate techniques and we are in the process of generating new datasets. The project will be carried out in a highly collaborative dynamic environment where the student will be working with biologists and an organic chemist as well as our IT personnel.

It turns out there this type of research even already has its own rather prestigious conference:

Type: external (UMCU) and suitable for non-Dutch students as well
Contact: Marco
Requirements: affinity with medical informatics, method engineering, and data mining techniques. Coding abilities are desirable.