Projects
April 12, 2023 2023-04-13 22:52Projects
Overview
The Center for Bioinformatics participates in the Graduate School for Computer Science and the Cluster of Excellence (MMCI) and plays a central role in many projects, for example:
- Blueprint
- CHAIN
- DEEP project
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DFG project
“Infection Biology and Epidemiology of Staphylococci and Staphylococcal Diseases in sub-Saharan Africa” - BioMarker Detection (supported by Siemens)
- DZIF (German Center for Infection Research)
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Graduate School 1276
Structure formation and transport in complex systems - PREDEMICS
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SFB 1027, project C3
Stochastic switching during cell differentiation/reprogramming
Many more and newer projects are presented in detail on the websites of the respective research groups.
Blueprint
This largest EU project in the life sciences ever (2011-2016, 40M € budget, 30M € EU funding) represents the European contribution to IHEC. The project focuses on the cells and diseases of the blood. Jörn Walter and Thomas Lengauer are partners in BLUEPRINT covering the topics DNA methylation and software tools and analyzing methylation data as well as intergative analysis of heterogeneous epigenetics data, respectively.
CHAIN
This EU Integrating Project (2009-2014) is concerned with bringing advanced HIV resistance analysis technology to the clinic. MPI Informatics (Thomas Lengauer) is partner of the project in their role as partner of the EuResist Consortium. The work in this project partly covers the activities of MPI Informatics in furthering their very successful bioinformatical technology for interpreting clinical and virological data on HIV drug resistance. Several of the software offers on the geno2pheno Server offering the resistance analysis methods for free have
found entry into clinical practice.
DEEP
This five-year prgram (2012-2017) which is being funded by the German Science Minsirty with roughly 20 M€ represents the German contribution to the International Human Epigenome Consoritum (IHEC). The project comprises the measurement and biological interpretation of about 70 reference epigenomes from (mostly) human and mouse. The focus is on metabolic and immunological diseases. The Center provides the coordinator off DEEP (Jörn Walter, Genetics and Epigenetics, UdS) and the coordinator of the data analysis effort in the project (Thomas Lengauer, MPI Informatics).
DZIF
In this project, the CBI Saar acts as an outpost of the DZIF site Bonn-Köln with an own budget. Research at the Bonn-Cologne partner site addresses the following topics:
- Infection & immunity research
- Anti-microbial effector mechanisms
- Translational infectious disease research (target identification, gene therapy, drug research)
- Clinical trials and research
- Epidemiology of infection and resistance development, infection control
Graduate School 1276
The research group of Prof. Helms uses computer simulations to investigate the dynamics and energetics of single and interacting proteins, as well as their interactions with cell membranes. Besides the usual atomistic molcular dynamics simulations, we develop model systems with medium-resolution potentials. These potentials can either be generated using individual amino acids or even whole proteins. To simulate protein-protein interactions as well as interactions of proteins and membranes, the participants are first modeled as rigid bodies. Subsequently, their Brownian movement subject to external forces is simulated.
PREDEMICS
This EU projekt (2011-2016) performs research on four viruses that bear epidemic risk for humanity, namely influenza, rabies virus, flaviviruses and Hepatitis E virus. MPI Informatics (Thomas Lengauer) contributes to the development of software for sharing and analyzing the respective viral sequence data.
SFB 1027 - Project C3
Gene expression in all biological cells is tightly regulated by the binding of transcription factors and by epigenetic modifications of the DNA. Importantly, gene expression and cell differentiation or cell reprogramming are triggered by suitable stimuli in a stochastic manner. Here, atomistic biomolecular simulations and coarse-grained Brownian dynamics simulations will be used to study the binding processes governing gene expression in the E.coli pap operon that is being studied experimentally in project C1. A second part of the project involves stochastic dynamics simulations to model state transitions of the gene-regulatory network centered on the pluripotency factors Oct4, Nanog and Sox2. In collaboration with project C2, we will characterize how dynamic changes of transcription factor concentrations and DNA methylation levels affect cell differentiation during the development of the early mouse embryo until the 32-cell stage.
