Computational methods for functional genomics

We develop computational methods and software for the analysis of primary experimental data as well as for the systematic higher-level analysis of functional relationships between genes and gene products. We are working together with various experimental groups, of which we get data for analysis. The methods and software developed are made subsequently available via publications, teaching, as web applications, or as packages for the statistical software R within the Bioconductor project.

Our main aim is to develop methods that after primary statistical data analysis allow a more detailed functional analysis and understanding of the data. For this we employ gene ontology, pattern and pathway analysis. We aim to construct functional gene networks that allow intuitive visualization of data and enable Systems Biology approaches.

Collaborating Groups and Projects

• Gene Expression Group (microarray data analysis and network reconstruction)
• Functional Profiling Group (analysis of high-throghput cellular assay FACS and RNAi screening data and pathway overrepresentation analysis)
• Proteomics Group (robust estimation of protein expression and phosphorilation levels from quantitative microspot immunoassays on protein microarrays)
• Integratiove Cell Biology Group (modelling of boolean networks)

Collaborating Groups and Projects

• Gene Expression Group (microarray data analysis and network reconstruction)
• Functional Profiling Group (analysis of high-throghput cellular assay FACS and RNAi screening data and pathway overrepresentation analysis)
• Proteomics Group (robust estimation of protein expression and phosphorilation levels from quantitative microspot immunoassays on protein microarrays)
• Integratiove Cell Biology Group (modelling of boolean networks)

The group is involved in organizing the established Practical Microarray Analysis courses and developing tools for the Bioconductor platform. Further, the group is active in several different projects.

Activities

• The Bioconductor project
• NGFN SMP Bioinformatics
• Workshops on Practical Microarray Analysis and Good Statistical Practice
• Systems Biology of Cancer

A number of different tools were developed within the group that are publically available. Many of those are available via Bioconductor or via CRAN.

Software and Projects

• 3of5 Complex Pattern Search
• GOstat: Gene Set Enrichment Analysis
• MCRestimate: Microarray Classification Analysis

• Dr. Tim Beißbarth


• Dr. Holger Fröhlich


• Christian Bender


• Marc Johannes


• Jitao Zhang

• Dr. Wolfgang Huber


• Dr. Achim Tresch


• Dr. Florian Hahne


• Dr. Markus Ruschhaupt


• Andreas Buness


• Jörg Kunert