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Department of Microbiology and Systems Biology TNO

Contact Details

TNO

Utrechtseweg 48, 3704HE, Zeist

www.tno.nl

dr. J. Bouwman

0031 (0)6 11700518

Hotel Description

TNO is internationally acclaimed for finding innovative solutions for diverse challenges in nutrition, health, toxicogenomics and biotechnology. Related to the objectives of DTL, TNO couples dedicated expertise in data processing, data basing infrastructure, statistics, machine learning, network biology and systems modeling to proficiency in systems biology of health and (metabolic ) disease, and toxicogenomics. Through collaboration with other TNO groups we combine a broad collection of state-of-the-art analytical platforms and statistical approaches with an extensive collection of in vitro and in vivo models of health and disease. We work within multiple industrial and (inter)national consortia/projects where we contribute as an applied research institute, to translate research findings to applications. In addition, we often provide services or consultancy to organisations or companies. Our organisation is acclaimed for our professionalism and excellent project management. Our key technical capabilities (related to DTL objectives) are:
• Full studies for nutrition, toxicogenomics and pharma applications: from study design, execution to biological interpretation;
• Metabolomics platforms (e.g. endocannabinoids, oxylipids, bile acids) including biological interpretation;
• Microbiome analysis;
• Data warehousing for (pre)clinical omics, phenotypic studies and n=1 studies;
• Complex statistical analysis of heterogeneous datasets;
• Network biology, mechanistic interpretation and prioritisation of cross-omics data;
• Biological systems modelling.

Systems biology
Public
  • Biomedical & health
  • Agri & Food
  • Mechanism of action investigations (particularly in Type-2 Diabetes, CVD, OA, fibrosis): analysis of nutritional effect, pharmaceutical drug effects, disease etiology elucidation, identification of novel candidate drug targets
  • Discovery, prioritization and validation of diagnostic, prognostic, and predictive biomarkers for assessment of: efficacy, safety, patient stratification, on risk and responders, patient motivation, predictive toxicology
  • Metabolomics analytical platforms with specialities such as endocannabinoids, bile acids, eicosanoids: analysis of microbiome composition, drug repurposing, repositioning
  • Metabolic health and disease
  • Systems toxicology
  • Nutrigenomics
  • Biotechnology
  • Microbiology

Expertise and Track Record

We offer state of the art technology, highly educated personnel in many areas combined with excellent project management. We are very strong in designing tailor-made projects to solve specific research questions from the industry.

• Netherlands Metabolomics centre
o Consultancy on interpretation of metabolomics data in at least 8 NMC projects
o Given support on the usage of the Phenotype database
• EU project NU-AGE
o Given support on the usage of the Phenotype database
• EU project EURRECA
o Consultancy on interpretation of omics data

• Participation in >30 EU FP6 and FP7 projects as RTD, as coordinator or work package leader. We are valued because of our professional project focus, experience in translating findings to clinical, commercial applications, our expertise in data handling and biological network analysis, and our biological and mechanistic knowledge.

  • Pellis L, van Erk MJ, van Ommen B, Bakker GC, Hendriks HF, Cnubben NH, Kleemann R, van Someren EP, Bobeldijk I, Rubingh CM, Wopereis S. Plasma metabolomics and proteomics profiling after a postprandial challenge reveal subtle diet effects on human metabolic status. Metabolomics. 2012 Apr;8(2):347-359
  • Bouwman J, Vogels JT, Wopereis S, Rubingh CM, Bijlsma S, Ommen Bv., Visualization and identification of health space, based on personalized molecular phenotype and treatment response to relevant underlying biological processes. BMC Med Genomics. 2012
  • Van Schalkwijk DB, van Ommen B, Freidig AP, van der Greef J, de Graaf AA.Diagnostic markers based on a computational model of lipoprotein metabolism.J Clin Bioinforma. 2011 Oct 26;1(1):29
  • Crielaard W, Zaura E, Schuller AA, Huse SM, Montijn RC, Keijser BJ. Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health. BMC Med Genomics. 2011 Mar 4;4:22
  • Van der Greef J, van Wietmarschen H, van Ommen B, Verheij E (2013). Looking back into the future: 30 years of metabolomics at TNO. Mass Spectrom Rev. doi: 10.1002/mas.21370
  • Van Ommen B, El-Sohemy A,Hesketh J and 16 others -The micronutrient genomics project: creating a community driven knowledge base for micronutrient research – Genes and Nutrition, 2009, 5 (3) 189-203 DOI 10.1007/s12263-010-0192-8
  • Van Ommen B, Bouwman J and 16 others , Challenges of molecular nutrition research 6: The Nutritional Phenotype database to store, share and evaluate nutritional systems biology studies. Genes and Nutrition 5 (2010), 189- 203 - DOI 10.1007/s12263-010-0167-9

TNO is participant in:
Netherlands:
DTL – founding member, DISC CT memeber
TI Coast– project partner
NuGO organisation –Director
NMC (Netherlands Metabolomics Centre) – Founding member, steering group member, data support platform – Principle Investigator
NTC (Netherlands Toxicogenomics Centre) – partner
TIFN (Top Institute Food and Nutrition) – project partner
CTMM (Center for Translational Molecular Medicine) – project partner
TI Pharma – project partner

Europe:
EU FP6 and FP7 – project coordinator or project partner in a variety of projects (eg EURRECA, NuGO, Bioclaims, Nutritech, Food4me, NU-AGE, CARTARDIS, MISSION-T2D)
EU coordination activity – project partner (eg Cosmos, EURO-DISH (via NuGO))
IMI – project partner
EuropaBio Personalized Medicine Topic Group – steering committee member

Hotel Characteristics

  • 6
  • 2
  • 3

20

  • servers including servers for heavy calculation work

ISO 9001

Phenotype database (www.dbnp.org)