Principal Investigator (PI): Dr Jacob Odeberg

Personnel: Malin Andersen, Jorge Andrade, Kristina Holmberg, Torbjörn Öst

Description:

Common genetic variation in gene regulation and its link to complex disease. A combined bioinformatic and molecular genetic approach is pursued to identify and characterise the roles of individual genetic variations in gene regulation and gene function on a molecular level, and includes a collaboration with groups at CGB (1)(2) and CMM, Karolinska Institutet (within the Applied Bioinformatics Network). The aim is to further understand the complex elements of transcriptional regulation, and to identify functional candidate polymorphisms for subsequent association studies. Tools for prediction and selection of functional candidate SNPs in gene regulatory regions have been developed (The Raven resource). An important focus is cardiovascular disease and thrombosis, and the work includes identification of regulatory mechanisms candidate genes and gene variations by combining gene expression analysis, ChIP-chip analysis and genotyping in clinical patient materials. A high throughput DNA typing facility has been built up around the Pyrosequencing technology, and functions as a resource centre for genotyping projects.

GRID-based computing for bioinformatic applications.The use of remote resources by distributing and parallelizing the execution of standard bioinformatics tasks in a Grid implementation is an economical and time efficient alternative compared with acquiring and setting up computational hardware in house. We are developing Grid enabled procedures for computationally and data intensive bioinformatics tasks in dynamic Grid environments. This is particulary attractive for computationally demanding re-processing of constantly evolving genome and proteome databases, to work with the most up-to-date information .