Research

I use systems biology and bioinformatics to understand the underlying principles of how micro-organisms adapt to changing environments in the context of food and health.


All topics include bioinformatics as well as computational and experimental systems biology approaches. We use biological network models of bacterial metabolism together with comparative genomics, functional genomics and adaptive evolution to investigate the molecular trajectories of environmental adaptation, such as the evolution of underground enzyme activities.


Education and Positions

2016 - Associate Professor Food Microbiology, Wageningen University and Research, The Netherlands.
2009 - 2016 Staff Member at the Centre for Molecular and Biomolecular Informatics (CMBI) and Centre for Systems Biology and Bioenergetics (CSBB), Radboud university medical center, The Netherlands.2009 - Doctoral degree (Ph.D) in bioinformatics and computational 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

 

 

 

 

 

 

Publications

Arts R.J., Novakovic B., ter Horst R., Carvalho A., ......, Clish C., Notebaart R.A., Joosten L.A., Stunnenberg H.G., Xavier R.J., Netea M.G.
Glutaminolysis and Fumarate Accumulation Integrate Immunometabolic and Epigenetic Programs in Trained Immunity 
Cell Metabolism, pii: S1550-4131(16)30539-3, 2016

ter Horst R., Jaeger M., Smeekens S.P., Oosting M., ......, Wijmenga C., Notebaart R.A., Joosten L.A., Netea M.G.
Host and Environmental Factors Influencing Individual Human Cytokine Responses 
Cell, 167(4):1111-1124, 2016

Netea M.G., ..., Notebaart R.A., ..., Wijmenga C.
Understanding human immune function using the resources from the Human Functional Genomics Project 
Nature Medicine, 22(8):831-3, 2016

Szappanos B., Fritzemeier J., Csörgő B., Lázár V., Lu X., Fekete G., Bálint B., Herczeg R., Nagy I., Notebaart R.A., Lercher MJ., Pál C, Papp B.
Adaptive evolution of complex innovations through stepwise metabolic niche expansion 
Nature Communications, 11607(7), 2016

Megchelenbrink W., Katzir R., Lu X., Ruppin E., Notebaart R.A.
Synthetic dosage lethality in the human metabolic network is highly predictive of tumor growth and cancer patient survival 
Proceedings of the National Academy of Sciences of the USA (PNAS), 112(39):12217-22, 2015

Lu X., Megchelenbrink W., Notebaart R.A., Huynen M.A.
Predicting human genetic interactions from cancer genome evolution
PLoS ONE, DOI: 10.1371/journal.pone.0125795, 2015

Alam M.T., Manjeri G.R., Rodenburg R.J., Smeitink J.A.M., Notebaart R.A., Huynen M., Willems P.H.G.M., Koopman W.J.H.
Skeletal muscle mitochondria from NDUFS4-/- mice display normal pyruvate oxidation and ATP producion
Biochimica et Biophysica Acta (BBA), 1847(6-7):526-33, 2015

Megchelenbrink W., Rossell S., Huynen M.A., Notebaart R.A., Marchiori E.
Estimating metabolic fluxes using a maximum network flexibility paradigm
PLoS ONE, 10(10):e0139665. doi: 10.1371/journal.pone.0139665, 2015

Notebaart R.A., Szappanos B., Kintses B., Pál F., Györkei Á., Bogos B., Lázár V., Spohn R., Csörgő B., Wagner A., Ruppin E., Pal C., Papp B.
Network-level architecture and the evolutionary potential of underground metabolism
Proceedings of the National Academy of Sciences of the USA (PNAS), 111(32):11762-7, 2014

Lu X., Kensche P.R., Huynen M.A., Notebaart R.A.
Genome evolution predicts genetic interactions in protein complexes and reveals cancer drug targets
Nature Communications, 2124(4), 2013

Rossell S., Huynen M.A., Notebaart R.A.
Inferring metabolic states in uncharacterized environments using gene-expression measurements
PLoS Computational Biology, 9(3): e1002988, 2013

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

Papp B., Szappanos B., Notebaart R.A.
Use of genome-scale metabolic models in evolutionary systems biology
Methods Molecular Biology, 759:483-97, 2011

Notebaart R.A., Kensche P.R., Huynen M.A., Dutilh B.E.
Asymmetric relationships between proteins shape genome evolution
Genome Biology, 10:R19, 2009

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

Teusink B., Wiersma A., Jacobs L., Notebaart R.A., Smid E.J.
Understanding the adaptive growth strategy of L. plantarum on glycerol by in silico optimisation
PLoS Computational Biology, 5(6):e1000410., 2009

Verouden M.P.H., Notebaart R.A., Westerhuis J.A., van der Werf M.J., Teusink B., Smilde A.K.
Multi-way analysis of flux distributions across multiple conditions
Journal of Chemometrics, DOI: 10.1002/cem.1238, 2009

Notebaart R.A., Teusink B., Siezen R.J., Papp B.
Co-regulation of metabolic genes is better explained by flux coupling than by network distance
PLoS Computational Biology, 4, e26, 2008

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

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

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

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

 

Collaborators

Balázs Papp, Csaba Pál: Biological Research Centre (BRC), Szeged, Hungary (Microbial Evolutionary Systems Biology)
Frank Holstege: Academic Biomedical Center (ABC), University Medical Center Utrecht, The Netherlands (Yeast Functional Genomics)
Eytan Ruppin: School of Computer Sciences & School of Medicine, Tel Aviv University, Israel (Cancer Research)
Werner Koopman, Peter Willems, Martijn Huijnen, Jan Smeitink, Frans Russel: Radboud University Medical Center, Nijmegen, The Netherlands (Mitochondrial Disorder Research)
Mihai Netea, Leo Joosten: Radboud University Medical Center, Nijmegen, The Netherlands (Experimental Infectious Diseases - Internal Medicine)