Genomatix

BLUEPRINT - A BLUEPRINT of Haematopoietic Epigenomes

The BLUEPRINT consortium has been formed with the aim of generating at least 100 reference epigenomes and studying them to advance and exploit knowledge of the underlying biological processes and mechanisms in health and disease. It is funded by the European Commission as a high impact project within its seventh framework program (FP7).

Genomatix' contributions will be next generation sequencing data analysis and the development of an intuitive GUI to make the project's results easily accessible to researchers within and outside the consortium.

Project web site: http://www.blueprint-epigenome.eu/

European Commission project web site: http://cordis.europa.eu/fetch?CALLER=FP7_PROJ_EN&ACTION=D&RCN=99677

Prostate Cancer Prognostic Marker Discovery by Next Generation Sequencing -
Cooperation to further progress in prostate disease research.

Genomatix and the CPDR (the Center for Prostrate Disease Research of the Uniformed Services University of theHealth Sciences and the Henry M. Jackson Foundation) have entered into a Cooperative Research and Development Agreement (CRADA) to extend their collaborative endeavors in prostate disease research. The aim of the joint research will be to differentiate patients with favorable versus poor prognosis at the time of diagnosis and primary treatment using definitive genetic markers.

CPDR web site: http://www.cpdr.org/

USUHS web site: http://www.usuhs.mil/

m4 - Personalized Medicine

Within the Munich excellence cluster, various biotechnology companies and academic groups work together under the guiding concept of Personalised Medicine on about 30 research projects, developing new drugs and technologies.

Genomatix works on the development of integrated prognostic, diagnostic and therapeutic approaches in personalized medicine by integral network analysis.

Project web site: http://www.m4.de/en/personalized-medicine/m4-projects/details/PM13.html

SYNERGY - ERASysBio+

The major objectives of SYNERGY (funded by the European Commission) are to characterize the roles of nuclear receptors (NRs), RNA polymerase II and histone marks in tumor and normal cells. The determination of NR binding (via ChIP-Seq) and gene expression (via RNA-Seq) and placement of these datasets in context with DNA methylation and histone marks at multiple time points will provide unique temporal datasets that can be used to design and implement computational methods to identify genes regulated by NRs, infer the mechanisms of NR-triggered gene regulation, and identify pathways, biological processes and gene regulatory networks that the NR-responsive genes are involved in.

Among Genomatix' tasks within the project are high throughput mapping of the generated NGS reads and the analysis of gene networks of NR-responsive genes.

Project web site: http://www.erasysbio.net/index.php?index=271

European Commission project web site: http://cordis.europa.eu/fetch?CALLER=FP7_PROJ_EN&ACTION=D&RCN=93038

MEDSYS - Medical Systems Biology

Within the Medical Systems Biology network MedSys (funded by the German Federal Ministry of Education and Research), Genomatix is a partner in Drug-iPS, a consortium to elucidate the development of pluripotent stem cells derived from human somatic cells. Pluripotency and self-renewal are under tight control by specific molecular networks, Genomatix brings the expertise to focus on the transcriptional control of the pertinent genes.

The Genomatix PathwaySystem (GePS is) especially suited to examine differences between regular stem cells and their differentiation patterns in comparison to reprogrammed cells. Based on the reconstruction of relevant regulatory networks, the team was able to arrive at the identification of differences in derived network topologies between those two cell types.

Network description (in German): http://www.ptj.de/lw_resource/datapool/_items/item_1721/medsys.d.web.pdf