Research:

My research is about i) evolutionary systems biology of metabolism to study adaptations of microorganisms (e.g., E. coli) and ii) systems-level understanding of mitochondria phenotypes in health and disease.

Both topics have a strong association between computational and experimental systems biology approaches. We, for example, use human and mouse tissues to construct mathematical models of human metabolism, including metabolomics, proteomics and transcriptomics, to predict and experimentally characterize the effects of genetic disorders at systems-level with the final aim to design therapeutic interventions. Mathematical modeling includes large-scale stoichiometric and smaller-scale dynamic (kinetic) modeling.

Please find more information on Postdoc positions here.

Education and positions:

2009 - Tenure post-doctoral research at the Center for Molecular and Biomolecular Informatics (CMBI) and Center for Systems Biology and Bioenergetics (CSBB), Radboud University Nijmegen, The Netherlands.

2009 - Doctoral degree (Ph.D) in bioinformatics and systems biology at the Center for Molecular and Biomolecular Informatics, Radboud University Nijmegen, The Netherlands.

2005 - Master of Science in Bioinformatics at the Radboud University Nijmegen, The Netherlands

Grants:

2010 - NWO/ZonMW - Centre for Systems Biology Research (as member of CSBB)

2009 - NWO - VENI

2009 - NWO - Horizon Breakthrough

Open positions:

We support applications of ambitious and motivated post-docs who want to work in computational systems biology within our new CSBB (Centre of Systems Biology and Bioenergetics). A strong background in bioinformatics, computer science, and/or cell biology (biochemistry) science will be needed. Please send me your CV, list of publications and two reference letters.

Publications:

Papp B., Szappanos B., Notebaart R.A. (2010), Use of genome-scale metabolic models in evolutionary systems biology, Methods Mol Biol, in press

Notebaart R.A.*, Kensche P.R.*, Huynen M.A., Dutilh B.E. (2009), Asymmetric relationships between proteins shape genome evolution, Genome Biol., 10:R19 Pubmed, PDF, *contributed equally

Papp B., Teusink B., Notebaart R.A. (2009), A critical view of metabolic network adaptations, HFSP J, 3(1), 24-35 Pubmed, PDF

Teusink B., Wiersma A., Jacobs L., Notebaart R.A., Smid E.J. (2009), Understanding the adaptive growth strategy of L. plantarum on glycerol by in silico optimisation, PLoS Comput Biol, Pubmed, PDF

Verouden M.P.H.,Notebaart R.A., Westerhuis J.A., van der Werf M.J., Teusink B., Smilde A.K. (2009), Multi-way analysis of flux distributions across multiple conditions, J. Chemometrics, PDF 

Notebaart R.A., Teusink B., Siezen R.J., Papp B. (2008), Co-regulation of metabolic genes is better explained by flux coupling than by network distance, PLoS Comput Biol, 4, e26, Pubmed, PDF

Wessels E., Notebaart R.A., Duijsings D., Lanke K., Vergeer B., Melchers W.J., van Kuppeveld F.J. (2006), Structure-function analysis of the coxsackievirus protein 3A: Identification of residues important for dimerization, viral RNA replication, and transport inhibition, J. Biol. Chem. 281, 28232-28243. Pubmed, PDF

Notebaart R.A., van Enckevort F.J.H., Francke C., Siezen R.J., Teusink B. (2006), Accelerating the reconstruction of genome-scale metabolic networks, BMC Bioinformatics, 7, 296. Pubmed, PDF

Notebaart R.A., Huynen M.A., Teusink B., Siezen R.J., Snel B. (2005), Correlation between sequence conservation and the genomic context after gene duplication, Nucleic Acids Res. 33, 6164-6171. Pubmed, PDF

Wessels E., Duijsings D., Notebaart R.A., Melchers W.J.G., van Kuppeveld F.J.M. (2005), A Proline-Rich Region in the Coxsackievirus 3A Protein Is Required for the Protein To Inhibit Endoplasmic Reticulum-to-Golgi Transport, J. Virol. 79, 5163-5173. Pubmed, PDF

Collaborators:

Balázs Papp: Biological Research Centre (BRC), Szeged, Hungary and Cambridge Systems Biology Centre, University of Cambridge, UK

Csaba Pál: Biological Research Centre (BRC), Szeged, Hungary

Balint Kintses: Department of Biochemistry, University of Cambridge, UK

Lars Keld Nielsen: Systems and Synthetic Biology, The University of Queensland

Ying-Mei Qi: Systems and Synthetic Biology, The University of Queensland

Seminar:

Systems biology / Modeling large biological networks, click here