Research

My research is about i) evolutionary systems biology to study how organisms adapt to changing environments by using mechanistic models of the cell and genome evolution techniques, and ii) systems-level understanding of genetic disorders.

Both topics have strong association between computational and experimental systems biology approaches. We, for example, use human and mouse tissues to construct mathematical models of human metabolism with 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. Click here for more information.

Education and Positions

2009 - Assistent professor (Tenure Post-doc) at the Centre for Molecular and Biomolecular Informatics (CMBI) and Centre for Systems Biology and Bioenergetics (CSBB), Radboud University Nijmegen, The Netherlands.
2009 - Doctoral degree (Ph.D) in bioinformatics and systems biology at the Centre 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

Publications

Papp B., Notebaart R.A. , Pal C. (2011), Systems-biology approaches for predicting genomic evolution, Nature Rev. Genet., 12(9):591-602, Pubmed, PDF

Papp B., Szappanos B., Notebaart R.A. (2011), Use of genome-scale metabolic models in evolutionary systems biology, Methods Mol. Biol., 759:483-97, Pubmed, PDF

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, DOI: 10.1002/cem.1238, 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

Open positions

We support applications of motivated PhD students and Post-docs who want to work in evolutionary systems biology within our new CSBB (Centre for Systems Biology and Bioenergetics). A strong background in bioinformatics / computer science / cell biology (biochemistry) is needed. Please send me your CV, list of publications and two reference letters.