Prediction of gene function and regulation

General info

Date from - to

01 Nov 2005 - 01 Jan 2010

Project leader(s)

Dr. Cajo J.F. ter Braak

Participant(s)

Dr. Roeland van Ham

Prof. dr. Edwin Cuppen

Theme

Integrative bioinformatics

Abstract

To predict the function and regulation of genes, evidence from various data sources has to be pieced together. The challenge is to do this on a genome-wide scale and with significant sensitivity and specificity. The project distinguishes 3 work packages.
WP 1 builds on a probabilistic framework for gene function prediction, based on Saccharomyces cerevisiae. This framework is being expanded to more complex plant genomes. WP 2 studies the role of alternative splicing in gene functionalisation in plants, as well as evaluates its impact on computational methods of gene function prediction. WP 3 focuses on animal species. Genomes are explored for functional elements and genetic variations, concentrating on non-protein coding genomic elements (e.g. promoter elements, but also microRNA-coding sequences).

Publications

• Distribution and functional impact of DNA copy number variation in the rat
• PDB_REDO: automated re-refinement of X-ray structure models in the PDB
• Limitations and possibilities of small RNA digital gene expression profiling
• A genome-wide SNP panel for mapping and association studies in the rat
• SNP and haplotype mapping for genetic analysis in the rat
• Comparative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome