Finished Projects

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SYSCOL

Systems Biology of Colorectal Cancer
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A collaborative project funded by the European Union Seventh Framework Programme ( FP7/2007-2013 ) under grant agreement no. 258236, research area HEALTH.2010.2.1.2-1, Tackling Human Diseases through Systems Biology Approaches.

Coordinator:
The project is coordinated by Prof. Jussi Taipale, Karolinska Institute, Uppsala, Sweden. The 11 participants of the consortium are from 8 European countries, from Israel and the United States.

Contract period: January 1st, 2011 – December 31st, 2015

Contract no. 258236.

Summary:
SYSCOL is a systems biological project that aims at developing a quantitative and comprehensive model of colorectal tumorigenesis, one of the most common cancers in both males and females.

GeneXPlain contributes to the project by developing an integrative tool platform for bioinformatic and systems biological software and databases.

Further information:

Homepage of SYSCOL.
Press release of the Karolinska Institute
Project description on the CORDIS server of the European Commission

Jussi Taipale’s collection of Positional Weight Matrices, the most comprehensive experimental set available to date (Jolma et al., Cell 153: 327-338, 2013; PMID 23332764), has been consistently linked to E. Wingender’s transcription factor classification.

Publications:

Wingender, E., Schoeps, T., Haubrock, M., Dönitz, J. (2015) TFClass: a classification of human transcription factors and their rodent orthologs. Nucleic Acids Res., in press. doi: 10.1093/nar/gku1064. Link
Wingender, E. (2013) Criteria for an updated classification of human transcription factor DNA-binding domains. J. Bioinform. Comput. Biol. 11, 1340007. doi: 10.1142/S0219720013400076. Link

Wingender, E., Schoeps, T., Dönitz, J. (2013) TFClass: An expandable hierarchical classification of human transcription factors. Nucleic Acids Res. 41, D165-D170. doi: 10.1093/nar/gks1123. Link

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GERONTOSHIELD

GERONTOSHIELD – Systems biology-driven approach to unravel and revert the mechanisms responsible for poor immune responses in the elderly
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A collaborative project funded by the German Federal Ministry of Education and Research (BMBF) in the funding program “Systems Biology for Health in the Old Age – GerontoSys2”

Coordinator:
The project is coordinated by Prof. Dr. Carlos Guzmán, Helmholtz Centre for Infection Research (HZI) in Braunschweig, Germany. The 6 participants of the consortium are from Braunschweig, Jena, Martinsried, Regensburg, Tübingen, and Wolfenbüttel.

  • Contract period: February 1st, 2011 – January 31st, 2014
  • Grant no.: FKZ0315890B
  • Summary:

The strategic objective of the GERONTOSHIELD project is to draw on a Systems Biology-driven approach to understand the molecular processes affected during immunosenescence, in order to derive (i) global mathematical models describing the involved processes, (ii) a holistic model for flu infections in young and elderly, and (iii) strategies to overcome these processes to establish immune interventions tailored for the elderly.

Further information:
Homepage of GERONTOSHIELD
Press release of the Helmholtz Centre for Infection Research (HZI; in German)
Press release of the Helmholtz Centre for Infection Research (HZI; in English)

Publications:
Wingender, E. (2013) Criteria for an updated classification of human transcription factor DNA-binding domains. J. Bioinform. Comput. Biol. 11, 1340007. doi: 10.1142/S0219720013400076. Link
Wingender, E., Schoeps, T., Dönitz, J. (2013) TFClass: An expandable hierarchical classification of human transcription factors. Nucleic Acids Res. 41, D165-D170. doi: 10.1093/nar/gks1123. Link

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TEMPUS

TEMPUS project “Rehaut”
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A collaborative educational & training project financially supported by TEMPUS program of the European Union, phase TEMPUS IV, under grant agreement no. 511426-TEMPUS-1-2010-1-RU-TEMPUS-JPCR.

Coordinator:
The project is coordinated by Prof. Alexander Kuznetsov, D. Mendeleyev University of Chemical Technology of Russia, Moscow. The participants of the consortium are from 3 EU member states, from Russia and Belorus.

Contract period: October 15th, 2010 – October 14th, 2013

Summary:
The project aims at harmonizing, standardizing and developing further the European BSc and MSc biotechnology curricula and their applicability to biotechnology education in Belorus and Russia. It is geneXplain’s contribution to reinforce the industrial view in this project, in particular with regard to the inclusion of the methods of computational biology.

Further information:News about the project from the National TEMPUS Office of Belorus.
Rehaut Tempus project page (in Russian)

EPIMETAB

EPIMETAB   Epigenetic mechanisms underlying predisposition to metabolic syndrome-associated diseases
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A collaborative project funded by the German Federal Ministry of Education and Research (BMBF) in a Joint Transnational Call 2011 for “Integrated Research on Genomics and Pathophysiology of the Metabolic Syndrome and the Diseases arising from it”
Coordinator:
The project is coordinated by Prof. Dr. Pierre Fafournoux, Institut National de la Recherche Agronomique in Saint Genès Champanelle, France. The 4 participants of the consortium are from France (Saint Genès Champanelle and Paris), Spain (Barcelona), and Germany (Wolfenbüttel).
Contract period: April 1st, 2012 – March 31st, 2015
Summary:
The project aims at gaining a better insight on the etiology of different disease conditions such as obesity or type-2 diabetes by investigating the intertwining of genetic, epigenetic and environmental factors. This innovative project is expected to pave the way to new preventive and therapeutic approaches at the individual level and for ameliorating the quality of life at the general population level.
GeneXplain contributes to the project its expertise in promoter analysis and its platform, which will be adapted to the specific needs of the project partners. At the end, a novel integrative view on the regulatory network comprising genetic and epigenetics influences will be provided.
Further information: Project summary (pdf; 8kB)
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