Hoffmann Research Group

Additional Projects

Joint Project „de.NBI – Partner: de.STAIR“

Bioinformatics Services for Structured Analysis and Integration of RNA-Seq experiments (de.STAIR)

BMBF project 031L016A

Website: http://destair.bioinf.uni-leipzig.de

Research focuses on RNA-Seq analysis, to develop best practices and user-friendly workflows for processing and integrating gene expression data as well as to provide assistance for experiment design, analysis and interpretation. The variety of RNA-Seq study designs and characteristic properties of studied organisms greatly affect bioinformatics analysis. As part of the RNA Bioinformatics center (RBC), which supports all RNA-related research within de.NBI, de.STAIR summarizes the expertise of three participating laboratories to develop and maintain an flexible RNA-Seq analysis workbench for different RNA-Seq protocols, to be used locally or in a cloud environment as provided by the open source Galaxy platform for biomedical research. In addition, de.STAIR provides workshops, training programs and screencasts for experts and non-experts to lower the barriers to RNA-Seq data analysis.

Figure 6: Conceptualization of the de.STAIR project’s recommendation system. The figure shows how the use of our guided and modularized workflows allow end users to achieve their goals by actively choosing a trajectory path that optimizes their analysis. A recommendation system is responsible for the interactive guidance of the trajectory, leaving the user the choice of which tool to operate with. Such a system lets researchers carry out their analyses while providing the benefits of using a modularized workflow instead of developing data analysis pipelines from scratch.

Mapping the indirect p53 gene regulatory network

Research focuses on dissecting gene regulatory networks that control the cell cycle and functions of the tumor suppressor p53. For example, the transcription factor p53 serves as a central suppressor of tumor progression. It controls cell proliferation and apoptosis by regulating a plethora of target genes. However, it is not clear how p53 regulates many of its target genes, what factors besides p53 itself are necessary for up or downregulation and what their regulation contributes to a normal or cancer cell. Our incomplete picture of the molecular basis of p53-dependent gene regulation remains a critical gap to our overall understanding of tumor suppression.

Figure 7: Mechanisms involving direct target gene activation by p53 and indirect repression through p53-p21-DREAM/RB are supported by genome-wide data.

Contact

Prof. Dr. Dr. Steve Hoffmann

Steve Hoffmann
Group Leader
+49 3641 656810
steve.hoffmann@leibniz-fli.de

 

Patricia Möckel
Secretary
+49 3641 65-6240
patricia.moeckel@leibniz-fli.de


Team

Name Phone Email Position
Steve Hoffmann +49 3641 656810 steve.hoffmann@leibniz-fli.de Group Leader
Martin Fischer +49 3641 656876 martin.fischer@leibniz-fli.de Postdoc
Konstantin Riege +49 3641 656875 konstantin.riege@leibniz-fli.de Scientist
Lion Müller +49 3641 656053/6875 lion.mueller@leibniz-fli.de Master Student