Eukaryotic bioinformatics

Cancer is a widespread cause of death and hence much research efforts concentrate on improving prognosis and therapy of diverse cancer types. Since shedding light on the landscape of molecular dysregulation leading to cancer cell growth and progression will help to characterize preclinical cellular models of cancers. With continuing technical improvements and decreasing costs of Next Generation Sequencing (NGS) technologies at hand as well as immortalized tumor cell lines as model systems for cancer research the eukaryotic bioinformatics group develops bioinformatic pipelines for molecular characterization for tumorigenesis, discovery of oncogenes and tumor suppressor genes or biomarkers.

Online tools

The Eukaroytic bioinformatics group offers a free accessible online tool:

Research activities

In close collaboration with the Human and Animal Cell Lines department projects in following areas are performed for the molecular characterization of human tumorgenesis:

  • Genetic aberrations to tumour progression: Recurrent chromosomal aberrations are well described for specific cancer types such as 11q23 abnormalities in diffuse large B-cell lymphoma (DLBCL). Additional to these large scale genetic events even single nucleotide variants (SNV), small insertions and deletions (InDels) influence disease outcome. In order to identify these key genetic alterations and to drive tumor diagnosis hereby, whole exome sequencing (WES) and whole genome sequencing (WGS) data are being analyzed.
  • Therapeutic targets via expression profiling: Gene expression profiling is a well-established method to capture the abnormal cell behavior. Besides identifying differentially expressed genes, mRNA sequencing (mRNA-seq) harbors the ability to detect fusion genes and alternative spliced transcripts and hence delivers potential  drug targets to control abnormal gene expression.
  • Epigenetic factors regulating gene expression: The architecture of cellular processes in humans is diverse and complex: cofactors and transcription factors either activate or inhibit gene expression by directly or indirectly binding to DNA, fine-tuning of mRNA expression is silenced via miRNAs by direct binding to their target mRNA, and DNA-methyltransferases catalyze methylation of human DNA, which itself regulate gene expression. Since understanding the molecular dysregulation of such processes in cancer cells will lead to disentangle tumor progression, ChIP-seq, miRNA-seq and methylation arrays serve as basis for epigenetic studies.