Research and Technologies

Mission

Major diseases such as cancer, cardiovascular, neurodegenerative and metabolic disorders are known to be multifactorial, involving many genes, causes and variants. To extend our understanding of the interplay of functions and regulatory networks in the course of disease, we aim to quantitatively characterize disease relevant events where genes, transcripts, signals, and metabolites interact. Collecting and analysing genome-wide quantitative data will allow developing diagnostic and therapeutic concepts as well as predictive models for modern biomedicine. Recent research has particularly highlighted that cells employ multiple sophisticated levels of gene regulation, which include the organization of chromosomes in the nucleus, epigenetic gene regulation, transcription, post-transcriptional gene regulation and post-translational modifications.

The grand challenge and Scientific Mission of the “Berlin Institute for Medical Systems Biology” (BIMSB) is to integrate these levels of gene regulatory control into comprehensive and predictive models that elucidate their functioning in health and disease, which is by its nature a truly inter disciplinary endeavour.

Research at the BIMSB is focused on the understanding several levels of gene regulatory networks, in particular transcriptional and post-transcriptional processes and their integration with major cellular regulatory mechanisms, such as protein-protein and protein-nucleic acid interaction networks, signal transduction pathways, post-translational modifications, metabolic feedback, both, in health and disease states. BIMSB researchers apply quantitative experimental and theoretical approaches to model systems suitable for multi-level high-throughput analyses. Model organisms such as Drosophila, nematodes and flatworms, fish and cell culture are employed as they are particularly amenable to systems wide investigations. Major research projects address basic cell biology, developmental biology, regeneration, stem cell biology, immunology, genetic variability as well as health questions including cancer, obesity, metabolism, cardiovascular and neurological diseases.

A list of publications can be found here.

 

Technologies

BIMSB research is based on successfully established  bioinformatics-, genomics-, proteomics and metabolomics platforms, offering services, expertise and technology development, state-of-the-art instrumentation, software and training opportunities to BIMSB and MDC scientists. These resources and technologies are complemented by the MDC core facilities at campus, including advanced light and electron microscopy, cytometry and a transgenic core facility.

 

The BIMSB Technology Platforms currently offer:

Genomics (Sascha Sauer)
With machines from Pacific Biosciences, Illumina (2 HiSeq 2500, 2 HiSeq 2000), Roche (454)

Proteomics & Metabolomics (Stefan Kempa)
With the following instruments: LTQ-Orbitrap Velos, GCxGC-ToF mass spectrometer, one triple Quad mass spectrometer, qTrap mass spectrometer

Bioinformatics (Altuna Akalin)
Using the high performance Cluster of the MDC with continuously increasing capacities (recently 1000CPU core cluster and two 1TB high-memory nodes).
The bioinformatics platform maintains and develops the internal UCSC browser, the (dorina.mdc-berlin.de), circbase (circrna.org), elegans (http://elegans.mdc-berlin.de/) databases.

Light Microscopy (Andrew Woehler)

 

The technology platforms allow the application of sophisticated, novel and specialized methodologies such as PAR-CLIP (photoactivatable- ribonucleoside- enhanced- crosslinking and immunoprecipitation),  eFACS (fluorescence-activated cell sorting of embryos), SILAC and pulsed SILAC (stable isotope labeling by amino acids in culture cells), different sequencing protocols, and metabolic profiling. Capacities and technologies are constantly extending according to the general expansion of the BIMSB.

 

POST-TRANSCRIPTIONAL REGULATORY NETWORKS
(Copyright MDC)