SYSCOL
Systems Biology of Colorectal Cancer
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.
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., Dönitz, J. (2013) TFClass: An expandable hierarchical classification of human transcription factors. Nucleic Acids Res. 41, D165-D170. doi: 10.1093/nar/gks1123. Link
GERONTOSHIELD
GERONTOSHIELD – Systems biology-driven approach to unravel and revert the mechanisms responsible for poor immune responses in the elderly
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.
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
TEMPUS
TEMPUS project “Rehaut”
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.
EPIMETAB
EPIMETAB Epigenetic mechanisms underlying predisposition to metabolic syndrome-associated diseases
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.
ExITox
ExITox – Explain Inhalation Toxicity
Coordinator:
The project was coordinated by Dr. Sylvia Escher, Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM) in Hannover, Germany. The 6 participants of the consortium are from Hannover, Freiburg, Göttingen, and Wolfenbüttel.
Contract period: November 1st, 2013 – October 31st, 2015, extended until January 31st, 2016
Grant no.: 031 A269 D
Summary:
This project aims at developing an integrated testing strategy (ITS) for the human health risk assessment of repeated dose toxicity after inhalation exposure for the replacement of de novo animal testing. In the pilot phase chemicals with different mode of action will be selected and tested with human precision cut lung slices (PCLS) and human pulmonary cell cultures in order to identify route specific biomarkers. Genome wide transcriptome analyses will be conducted in these models and evaluated using bioinformatics methods. These results will be complemented with data mining results and QSAR predictions. Further, structurally related chemicals will be tested in addition to investigate the possibility of the test system to support read across. The outcome of this pilot project will be a proposal for an integrated testing strategy for respiratory toxicity. Further validation e.g. testing of a broader spectrum of chemicals is foreseen in a follow up project. The proposed ITS, the developed methodologies on data sharing and data integration are not limited to the evaluation of transcriptome data but allow to integrate proteome and metabolome data in a follow up project.
It is geneXplain’s task to analyze transcriptome data of the partners and contribute to the specification of new biomarkers.
Homepage of the project at Fraunhofer ITEM
Fraunhofer-Datenbank RepDose
Research Database at Albert Ludwigs University Freiburg (in German)
Publications:
Koschmann, J., Bhar, A., Stegmaier,P., Kel, A. E. and Wingender, E. (2015) “Upstream Analysis”: An integrated promoter-pathway analysis approach to causal interpretation of microarray data. Microarrays 4, 270-286. doi:10.3390/microarrays4020270. Link
Niehof, M., Hildebrandt, T., Danov, O., Arndt, K., Koschmann, J., Dahlmann, F., Hansen, T. and Sewald, K. (2017) RNA isolation from precision-cut lung slices (PCLS) from different species. BMC Res. Notes 10, 121. doi: 10.1186/s13104-017-2447-6. Link
The project continues with ExITox-II.
Mediomics
Mediomics – Systems biology modeling of diseases through integration of multiple “-omics” data
Coordinator:
Dr. Alexander Kel, geneXplain GmbH. The 3 partners are University Regensburg and University Medical Center Göttingen from Germany and biosoft.ru from Russia.
Funding period: December 1st, 2013 – August 31st, 2016 (with extension)
Summary:
The main goal of the project is to push ahead the idea of a systems-biological software platform that integrates different high-throughput (‘omics’) data to generate models for certain chronic diseases. A particular focus of the project will be given onto the inclusion of gene regulatory processes into the modeling, which is still largely neglected by present systems biological modeling approaches.
Project page at the University Medical Center Göttingen