Bioinformatics platform of the Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine (MDC)

Berlin, Germany

General information

The Berlin Institute for Medical Systems Biology Bioinformatics (BIMSB) platform is a research group at the MDC-Berlin, headed by Dr. Altuna Akalin. The platform creates and maintains bioinformatics tools and databases, and studies biology using available or in-house computational techniques.



The platform has a broad research interest in gene regulation, specifically transcriptional regulation and association of transcriptional regulation with epigenomics. The team is aiming  to use data intensive computational methods to uncover patterns in gene regulation relating to cell differentiation and complex diseases. The platform regularly organizes computional genomics training and summer schools including theoretical lectures followed by practical sessions where participants directly apply what they have learned.


Technologies offered for the Open Call

- Computational analysis:
   Determination of cancer sample type identity from molecular signatures such as gene expression,
   SNPs and copy number variation. The approach applicable for subtype detection and survival
   estimation. Currently applicable to cancer setting.
- Support for proper data processing
- Reproducible pipelines for RNA-seq, ChIP-seq and BS-seq analysis



BIMSB computational pipeline for the prediction of sample type identity

Additional resources offered for the Open Call

- Application in single-cell analysis or for non-cancer samples
- Databases, webapps, software and how-tos maintained by the platform are listed on the
   resources page


Access modalities

Virtual access.
In case of non cancer samples, it should be discussed prior to application which scientific questions aimed to be answered with this approach.


Scientific and technical requirements

For cancer samples, the following combinations of datasets are accepted:
- RNA-seq
- SNPs (Exome-seq or WGS)
- SNPs + CNVs (CNVs from sequencing or arrayCGH)
- RNA-seq + SNPs
- RNA-seq + SNPs + CNVs
For non-cancer samples:
- RNA-seq
The provided data have to be processed properly. These aspects should be discussed prior application.



Scientific contact: Altuna Akalin
Technical contact: Bren Osberg