The focus of the research in the bioinformatics group is on methods for the analysis functional genomics data and on analysis of biological sequences and structures and for structure prediction. Below we describe the most important areas in some more detail:
- Integrative bioinformatics:
We are working on development of methods for supporting integration of heterogenous tools and databases using grid technologies specifically the technology of web services and for composing such services into analysis workflows/pipelines. We are part of an EU funded Network of Excellence (EMBRACEgrid) related to this. In context of an eVITA funded project (eSysbio) we are working to develop a virtual workspace for supporting systems biology research that will utilize web services and workflows in automating and documenting bioinformatics analyses performed as part of systems biology research projects
- Analysis of sequences from ultra high-throughput sequencing platforms:
Novel sequencing platforms (such as 454 and Solexa) are producing large amounts of relatively short sequence reads that pose new challenges in data analysis and interpretation. We are working on development and application of methods in context of meta-genomics and genomics projects.
- Microarray Data Analysis:
We are working on development and application of methods for the analysis of microarray gene expression data. On the methods side we work on a number of different problems. Some of these are prediction problems problems including class prediction and feature subset selection as well as imputation of missing values. Other problems are utilisation of microarrays to study alternative splicing and oligonucleotide design. In addition we work on development and implementation of standards for representation of microarray data. The software tool J-Express for analysis of microarray data was initially developed in the group and is now commercialised through the company MolMine. We contribute to a number of bio-medical research projects utilising microarrays for gene expression analyses. This work is closely linked with the Norwegian Microarray Consortium, and the Alvis Brazma group at the European Bioinformatics Institute.
- Proteomics Data Analysis:
We work on development of methods for the analysis and publishing of proteomics data, focusing on data from mass spectrometry based instruments. We develope tools for easy publishing of proteomic data in public available databases, and tools for searching in these. The work is collaborated with people at University of Gent and EBI. Further a framework for quantitative analyses of protein samples is under development, based on existing tools as XCMS, Mascot, KEGG and GO.
- Structure Motif Discovery:
Based on our experience in methods for sequence motif discovery, we develop new methods for the discovery of motifs in protein strucutures. A method named SPratt has been developed that is able to analyse one or several protein structures to find recurrring patterns (motifs) of local packing of residues. This work is done in close collaboration with Willie Taylor (National Institute of Medical Research, London and CBU, University of Bergen).
- Protein Structure Prediction:
We are developing new methods for the prediction of the structures of proteins from their sequences. This work focuses on use of structural patterns for the evaluation of strucutural models and for use of threading based approaches for model generation. This work is done in close collaboration with Willie Taylor (National Institute of Medical Research, London and CBU, University of Bergen).