Parallel analysis of gene activity of single cells in miniaturized formats


Interim Heads: Tatiana Borodina (NGS Unit) & Thomas Conrad (Single Cell Unit)


The main focus of the Scientific Genomics Platforms lies on functional genome research using sophisticated next generation sequencing methodologies.

The department is located at the Max Delbrück Center for Molecular Medicine (MDC) in Berlin-Buch are funded by the Berlin Institute for Medical Systems Biology (BIMSB) and the Berlin Institute of Health (BIH ).

In the associated Laboratory of Functional Genomics, Nutrigenomics and Systems Biology, we aim to explore fundamental biological phenomena and to pursue innovative approaches for translating new insights to eventually help the patient.

The Scientific Genomics Platforms invite all researchers from the MDC, Charité and elsewhere to collaborate on cutting-edge functional genomics-oriented projects. Therefore, we establish and develop procedures to provide access to newest technologies, particularly highly parallel sequencing. Moreover, the team supports collaborators in data analyses.

Current key activities of the platforms comprise basic research-oriented functional genomics research projects (e.g. RNA-based regulatory mechanisms and epigenetic phenomena), as well as medically relevant projects (e.g. decoding of genetic or gene-regulatory mechanisms with relevance in disease-associated processes, for example in cancer and metabolic diseases). Furthermore, we establish methods and provide services to cater large-scale projects in the field of gene panel, exome- or whole genome sequencing.

A particular focus of the Scientific Genomics Platforms consists of application of large-scale single-cell genomics analyses for which we have established unique, scalable technologies.

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Technology Support

Dear Colleague,

Please contact me directly via phone or e-mail ( if you need whatever kind of support in high-throughput genomics experiments in the course of your systems medical or systems biological research.

We furthermore offer diverse collaborations, in particular to support research-intensive projects in the fields of functional genomics, single-cell analysis and integrated biological data analysis.

Kind regards,
Sascha Sauer




Single Cell

Hitherto, nucleic acids  are commonly analysed by using pooled cell populations. However, cell-to-cell variation detected by single-cell measurements can reveal deeper insights into the interplay of gene regulatory circuits and allows to determine the degree of biological plasticity and flexibility to react to environmental changes. Eventually, single-cell analysis approaches provide an unique opportunity to discover exclusive characteristics of a diseased cell state. 

We recently started analysing quantitatively cellular stress-related signaling at the level of individual immune and cancer cells. We established methods to measure gene expression of gene sets in hundreds of individual cells by single-cell quantitative reverse transcription PCR. Furthermore, we applied powerful FACS-, microfluidics- and microdroplet-based single-cell RNA-seq workflows to decipher pathway modules in the context of cell-environment interactions on a transcriptome-wide scale. This approach allowed us to discover new gene-gene interactions during stress response. Eventually our data sets provided us with information to quantify the balancing of a cell between determinacy and flexibility to cope with environmental changes.

Recently, we further expanded our single-cell research activities towards analysing clinical tumor samples, including (simultaneous) detection of transcriptome, DNA methylation and genomic information. This way, we could decipher so far unexplored mechanisms of tumor development and discover novel treatment options to more efficiently targeting individual tumors.


Many physiological processes are controlled by complex molecular mechanisms. This includes daily environmental factors such as nutrition. In order to prevent health decline and prolong the quality of life we aim to identify causal connections between environmental factors and disease, to increase the acceptance of emerging strategies for preventive medicine.

Recently, our research group has been exploring health implications of the interaction between nutrition and genomics or the so-called “nutrigenomics”. For example, the regulation of genes plays an important role in various molecular processes of metabolic disorders such as insulin resistance or atherosclerosis.

One emphasis of our research lies in analysing genome-wide and on the level of individual cells the modulation of gene expression to endow cells with resilience to respond to environmental changes.

A second emphasis of our research concerns the analysis and optimisation of natural products to interact with gene regulatory pathways. For example, we recently discovered a so far largely unexplored class of natural products, the amorfrutins that we isolated from the roots of liquorice. These metabolic efficient molecules interact selectively with the nuclear receptor PPARgamma to exert beneficial metabolic and anti-inflammatory effects. Furthermore, we recently presented a new paradigm of the mode of action of the famous, widely consumed natural product resveratrol from red wine.