Publications of the Systems Biology group

  • 2013 Rossell S, Huynen MA, Notebaart RA.
    Inferring metabolic States in uncharacterized environments using gene-expression measurements.
    PLoS Comput Biol, Mar;9(3):e1002988. doi: 10.1371/journal.pcbi.1002988. Details

  • 2013 Lu X, Kensche PR, Huynen MA, Notebaart RA.
    Genome evolution predicts genetic interactions in protein complexes and reveals cancer drug targets.
    Nat Commun, Jul 11;4:2124. doi: 10.1038/ncomms3124. Details

  • 2013 Ljosa V, Caie PD, Ter Horst R, Sokolnicki KL, Jenkins EL, Daya S, Roberts ME, Jones TR, Singh S, Genovesio A, Clemons PA, Carragher NO, Carpenter AE.
    Comparison of methods for image-based profiling of cellular morphological responses to small-molecule treatment.
    J Biomol Screen, Dec;18(10):1321-1329. doi: 10.1177/1087057113503553. Details

  • 2012 Balsa E, Marco R, Perales-Clemente E, Szklarczyk R, Calvo E, Landázuri MO, Enríquez JA.
    NDUFA4 Is a Subunit of Complex IV of the Mammalian Electron Transport Chain.
    Cell Metab, Sep 5;16(3):378-386. Details

  • 2012 Dessimoz C, Gabaldón T, Roos DS, Sonnhammer EL, Herrero J; Quest for Orthologs Consortium.
    Toward community standards in the quest for orthologs.
    Bioinformatics, Mar 15;28(6):900-904. Details

  • 2011 Papp B, Notebaart RA, Pál C.
    Systems-biology approaches for predicting genomic evolution.
    Nat Rev Genet, Aug 2;12(9):591-602. Details

  • 2011 Papp B, Szappanos B, Notebaart RA.
    Use of genome-scale metabolic models in evolutionary systems biology.
    Methods Mol Biol, 759(3):483-497. Details

  • 2011 Rossell S, Solem C, Jensen PR, Heijnen JJ.
    Towards a quantitative prediction of the fluxome from the proteome.
    Metab Eng, May;13(3):253-262. Details

  • 2011 van Eunen K, Rossell S, Bouwman J, Westerhoff HV, Bakker BM.
    Quantitative analysis of flux regulation through hierarchical regulation analysis.
    Methods Enzymol, 500:571-595. Details

  • 2009 Papp B, Teusink B, Notebaart RA.
    A critical view of metabolic network adaptations.
    HFSP J, Feb;3(1):24-35. Details

  • 2009 Verouden MPH, Notebaart RA, Westerhuis JA, van der Werf MJ, Teusink B, Smilde AK.
    Multi-way analysis of flux distributions across multiple conditions.
    J. Chemometrics, 23(7-8):406-420. Details

  • 2009 Teusink B, Wiersma A, Jacobs L, Notebaart RA, Smid EJ.
    Understanding the adaptive growth strategy of Lactobacillus plantarum by in silico optimisation.
    PLoS Comput Biol, Jun;5(6):e1000410. Details

  • 2009 Notebaart RA, Kensche PR, Huynen MA, Dutilh BE.
    Asymmetric relationships between proteins shape genome evolution.
    Genome Biol, Feb 12;10(2):R19. Details

  • 2008 Notebaart RA, Teusink B, Siezen RJ, Papp B.
    Co-regulation of metabolic genes is better explained by flux coupling than by network distance.
    PLoS Comput Biol, 4(1):e26 Details

  • 2006 Wessels E, Notebaart RA, Duijsings D, Lanke K, Vergeer B, Melchers WJ, van Kuppeveld FJ.
    Structure-function analysis of the coxsackievirus protein 3A: identification of residues important for dimerization, viral rna replication, and transport inhibition.
    J Biol Chem, Sep 22;281(38):28232-28243. Details

  • 2005 Wessels E, Duijsings D, Notebaart RA, Melchers WJ, van Kuppeveld FJ.
    A proline-rich region in the coxsackievirus 3A protein is required for the protein to inhibit endoplasmic reticulum-to-golgi transport.
    J Virol, Apr;79(8):5163-5173. Details