Computational Biology Group > Teaching > Student Projects

The group for computational biology and bioinformatics at the Institute for Medical Genetics at the Charité offers challenging internships, bachelor and masterthesis for interested students of Computer Sciences and Bioinformatics.   


Next Generation Sequencing
Sequencing techniques of the second generation are revolutionizing genetics. These high through-put techniques generate several orders of magnitude more sequencing data and challenge bioinformaticians. We use a Genome Analyzer II for genome wide mutation screening.
We will sketch three projects, that could be dealt within the scope of asoftware internship or "Berufspraktikum" of 8 weeks:
  • After a sequencing run the raw data consists of millions of short sequence reads that have to be aligned to a reference sequence before further analysis. After the alignment, one is interested how well the genomic region of interest is covered by short reads. The goal of this software internship is the development of a automatized pipeline, that computes the coverage of the target region an further meaningful statistics of a sequencing run.
  • High-throughput sequencing is used to detect homozygous and heterozygous variants in a target region of several megabases of a sample sequence. This step of the data analysis is called "variant calling". The goal of this software internship is to analyze the performance of several theoretically different approaches for variant detection 
  • In our NGS screening datasets we detect variants in the order of several thousands. These calls have to be further classified. Public databases have to be queried for existing entries. New mutations may be preanalyzed with bioinformatics predictin tools. The goal of this software internship is refine the batch analysis of our called variants. 
All software projects deal with topics that are also of high interest to the research community. Commited students my be able to publish their work in scientific journals. For the projects described above interested students should contact Peter Nick Robinson and Peter Krawitz. Ideally, the student should already have good programming skills in Perl, Java, C++ or comparable programming languages.
Human Phenotype Ontology

The Human Phenotype Ontology project requires new interfaces for exploring, visualising and improve the ontology. The student should develop Java-servlets for these tasks.

Disease Gene Prediction
Possible projects are:
  • Improve the user-interface of the GeneWanderer by making it more interactive (GWT)
  • New algorithmic ideas could be tested to improve the performance of Disease Gene Prediction