Scientific publications

Maastricht University

  • Kienhuis AS, Wortelboer HM, Hoflack JC, Kleinjans JCS, van Ommen B, van Delft JHM, and Stierum RH. Comparison of coumarin-induced toxicity in sandwich-cultured rat hepatocytes in vitro versus rats in vivo following a toxicogenomics approach. Drug Metabolism and Biotransformation 2006; 34:2083-90.
  • Staal YCM, van Herwijnen MHM, van Schooten FJ, van Delft JHM Modulation of gene expression and DNA adduct formation in HepG2 cells by polycyclic aromatic hydrocarbons with different carcinogenic potencies. Carcinogenesis, 2006;27(3):646-55.
  • Breikers G, van Breda SG, Bouwman FG, van Herwijnen MH, Renes J, Mariman EC, Kleinjans JC, van Delft JH. Potential protein markers for nutritional health effects on colorectal cancer in the mouse as revealed by proteomics analysis. Proteomics. 2006 May;6(9):2844-52
  • Bons JAP, Wodzig WKWH, van Dieijen-Visser MP. Protein profiling as a diagnosic tool in clinical chemistry: a review. Clin Chem. Lab. Med. 2005;43(12):1281-1290
  • van Delft JHM, van Agen E, van Breda SGJ, Herwijnen MH, Staal YCM, Kleinjans JCS Discrimination of genotoxic from non-genotoxic carcinogens by gene expression profiling. Carcinogenesis 2004;25:165-76.

Leiden University

  • Van de Water, B., G.J. Mulder, and J.L. Stevens. (1999) Dephosphorylation of focal adhesion kinase (FAK) and loss of focal contacts precede caspase-mediated cleavage of FAK during apoptosis in renal epithelial cells. J. Biol. Chem. 274: 13328-13337.
  • Van de Water, B., R.B. Tijdens, A. Verbrugge, M. Huigsloot, A.A. Dihal, J.L. Stevens, S. Jaken and G.J. Mulder. (2000) Cleavage of the actin-capping protein ?-adducin at DDSD633A by caspase-3 is preceded by its phosphorylation on serine-726 in cisplatin-induced apoptosis of renal epithelial cells. J. Biol. Chem. 275: 25805-25813.
  • Van de Water, B., F. Houtepen, M. Huigsloot and R.B. Tijdens. (2001) Suppression of chemical-induced apoptosis but not necrosis of renal proximal tubular epithelial (LLC-PK1) cells by focal adhesion kinase (FAK). Role of FAK in maintaining focal adhesion organization after acute renal cell injury. J. Biol. Chem. 276: 36183-36193.
  • Huigsloot, M., R.B. Tijdens, G.J. Mulder, and B. van de Water. (2002) Differential regulation of doxorubicin-induced mitochondrial dysfunction and apoptosis by Bcl-2 in mammary (MTLn3) cells. J. Biol. Chem. 277: 35869-35879.
  • de Graauw M, Tijdens I, Cramer R, Corless S, Timms JF, van de Water B. (2005) Heat shock protein 27 is the major differentially phosphorylated protein involved in renal epithelial cellular stress response and controls focal adhesion organization and apoptosis. J Biol Chem. 280: 29885-98.

Leiden University Medical Centre

  • Boerma M, van der Wees CG, Vrieling H, Svensson JP, Wondergem J, van der Laarse A, Mullenders LH, van Zeeland AA. Microarray analysis of gene expression profiles of cardiac myocytes and fibroblasts after mechanical stress, ionising or ultraviolet radiation. BMC Genomics. 2005, 6,6.
  • Svensson JP, de Menezes RX, Turesson I, Giphart-Gassler M, Vrieling H. Dissecting systems-wide data using mixture models: application to identify affected cellular processes. BMC Bioinformatics. 2005,14,177.
  • van Haaften G, Romeijn R, Pothof J, Koole W, Mullenders LH, Pastink A, Plasterk RH, Tijsterman M. Identification of conserved pathways of DNA-damage response and radiation protection by genome-wide RNAi. Curr Biol. 2006, 16, 1344-50.
  • Svensson JP, Stalpers LJ, Esveldt-van Lange RE, Franken NA, Haveman J, Klein B, Turesson I, Vrieling H, Giphart-Gassler M. Analysis of gene expression using gene sets discriminates cancer patients with and without late radiation toxicity. PLoS Med. 2006, 3, 422. Comment in PLoS Med. 2006, 3, 440.
  • Kruse JJ, Svensson JP, Huigsloot M, Giphart-Gassler M, Schoonen WG, Polman JE, Jean Horbach G, van de Water B, Vrieling H. A portrait of cisplatin-induced transcriptional changes in mouse embryonic stem cells reveals a dominant p53-like response. Mutat Res. 2007, 617, 58-70.

Wageningen University

  • Blankvoort, B.M., de Groene, E.M., van Meeteren-Kreikamp, A.P., Witkamp, R.F., Rodenburg, R.J. and Aarts, J.M. (2001). Development of an androgen reporter gene assay (AR-LUX) utilizing a human cell line with an endogenously regulated androgen receptor. Analytical biochemistry 298, 93-102.
  • Boerboom, A.-M.J.F., Vermeulen, M., van der Woude, H., Bremer, B.I., Lee-Hilz, Y.Y., Kampman, E., van Bladeren, P.J., Rietjens, I.M.C.M. and Aarts, J.M.M.J.G. (2006). Newly constructed stable reporter cell lines for mechanistic studies on electrophile-responsive element-mediated gene expression reveal a role for flavonoid planarity. Biochemical Pharmacology 72, 217-226.
  • De Boer, V.C.J., van Schothorst, E.M., Dihal, A.A., van der Woude, H., Arts, I.C.W., Rietjens, I.M.C.M., Hollman, P.C.H., Keijer, J. (2007). Chronic quercetin exposure affects fatty acid catabolism in rat lung.Cellular and Molecular Life Sciences (in press).
  • van Beelen, V.A., Aarts, J.M.M.J.G., Reus, A., Mooibroek, H., Sijtsma, L., Bosch, D., Rietjens, I.M.C.M. and Alink, G.M. (2006). Differential induction of electrophile-responsive element-regulated genes by n - 3 and n - 6 polyunsaturated fatty acids. FEBS Letters 580, 4587-4590.
  • van Erk, M.J., Roepman, P., van der Lende, T.R., Stierum, R.H., Aarts, J.M.M.J.G., van Bladeren, P.J. and van Ommen, B. (2005). Integrated assessment by multiple gene expression analysis of quercetin bioactivity on anticancer-related mechanisms in colon cancer cells in vitro. European Journal of Nutrition 44, 143-156.

Erasmus Medical Centre

  • van der Horst, G.T.J., Muijtjens, M., Kobayashi, K., Takano, R., Kanno, S., Takao, M., de Wit, J., Verkerk, A., Eker, A.P.M., van Leenen, D., Buijs, R., Bootsma, D., Hoeijmakers, J.H.J., and Yasui, A. (1999) Mammalian blue-light photoreceptor homologs CRY1 and CRY2 are essential for maintenance of circadian rhythms. Nature 398:627-630. Addressed in Nature 398 "News and Views" section, pg. 557-558 and Science 284 "News" section pg. 421-422.
  • Yagita, K., Tamanini, F., van der Horst, G.T.J., and Okamura, H. (2001) Molecular mechanism of the biological clock in cultured fibroblasts. Science 292:278-281.
  • Garinis, G.A., Mitchell, J.R., Moorhouse, M.J., Jans, J.J., Brand, K., Smid, M.,van der Spek, P.J., Hoeijmakers, J.H.J., and van der Horst, G.T.J. (2004) Photolyase transgenic cells reveal CPD lesion-dependent transcriptional responses upon UV exposure. EMBO J., 24:3952-3962.
  • van der Pluijm, I.,Garinis, G.A., Brandt, R., Gorgels, T.G.M.F., Diderich, K.E.M., Mitchell, J.R., van Steeg, H., van Oostrom, C., Beems, R.B., Niedernhofer, L.J., Friedberg, E.C., Tanaka, K., Hoeijmakers, J.H.J., and van der Horst, G.T.J. (2006) Premature aging mice link impaired genome maintenance with IGF1/GH suppression. PLoS Biol. 5:e2.
  • Niedernhofer, L.J., Garinis, G.A., Raams, A., Lalai, A., Robinson, A., Appeldoorn, E., Odijk, H., Oostendorp, R., Ahmad, A., van Leeuwen, Theil, A.F., Vermeulen, W., van der Horst, G.T.J., Meinecke, P., Kleijer, W.J., Vijg, J., Jaspers, N.G.J., and Hoeijmakers, J.H.J. (2006) A novel progeroid syndrome reveals genotoxic stress suppresses the somatotroph axis. Nature 444:1038-1043.

RIKILT - Institute of Food Safety 

  • Nur T, Peijnenburg A, Noteborn, HPJM, Baykus H, Reifen R. (2002). Similar gene expression patterns in vitamin A deficiency and chemically-induced colitis in rats as revealed by DNA microarray technology. J. Nutr. 132:2131-2136.
  • Van der Meer-van Kraaij C, Kramer E, Jonker-Termont D, Katan MB, van der Meer R, Keijer J (2005). Differential gene expression in rat colon by dietary heme and calcium. Carcinogenesis 26:73-9.
  • Nielen MW, Bovee TF, van Engelen MC, Rutgers P, Hamers AR, van Rhijn JH, Hoogenboom LR (2006). Urine testing for designer steroids by liquid chromatography with androgen bioassay detection and electrospray quadrupole time-of-flight mass spectrometry identification. Anal Chem. 78:424-431.
  • Keurentjes JJ, Fu J, de Vos CH, Lommen A, Hall RD, Bino RJ, van der Plas LH, Jansen RC, Vreugdenhil D, Koornneef M. (2006). The genetics of plant metabolism. Nature Genetics 38, 842-849.
  • De Vos CHR, Moco S, Lommen A, Keurentjes JJB, Bino RJ, Hall RD. Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry. Nature Protocols (in press).


  • Ezendam, J., Staedtler, F., Pennings, J., Vandebriel, R. J., Pieters, R., Harleman, J. H., and Vos, J. G. (2004). Toxicogenomics of subchronic hexachlorobenzene exposure in Brown Norway rats. Environ Health Perspect 112, 782-91.
  • Baken KA, Vandebriel RJ, Pennings JLA, Kleinjans JC, Van Loveren H. Toxicogenomics in the assessment of immunotoxicity. Methods 2007, 41, 132-141.
  • Carfi M, Gennari A, Malebra I, Corsini E, Pallardy M, Pieters R, Van Loveren H, Vohr HW, Hartung T, Gribaldo L. In vitro tests to evaluate immunotoxicity: A preliminary study. Toxicol 2007, 229, 11-22.
  • Kooter IM, Pennings J, Fokkens P, Leseman D, Boere J, Gerlofs M, Cassee F, Schalk JA, Orzechowski T, Schaap M, Breit T, Dormans J, van Oostrom C, de Vries A and Van Steeg H. (2006) Ozone induces clear cellular and molecular responses in the mouse lung independently of the transcription-coupled repair status. J Appl Physiol. 2007, 102(3):1185-92.
  • Bruins W, Jonker MJ, Bruning O, Pennings JL, Schaap MM, Hoogervorst EM, Van Steeg H, Breit TM, de Vries A. (2007) Delayed Expression of Apoptotic and Cell Cycle Control Genes in Carcinogen-Exposed Bladders of Mice Lacking p53.S389 Phosphorylation. Carcinogenesis( 2007). In press.


  • Kienhuis AS, Wortelboer HM, Maas WJ, van Herwijnen M, Kleinjans JC, van Delft JH, Stierum RH. A sandwich-cultured rat hepatocyte system with increased metabolic competence evaluated by gene expression profiling. Toxicol In vitro. 2007 Jan 20; [Epub ahead of print].
  • Verwei M, van Burgsteden JA, Krul CA, van de Sandt JJ, Freidig AP. (2006) Prediction of in vivo embryotoxic effect levels with a combination of in vitro studies and PBPK modelling. Toxicol Lett. 2006 Aug 1;165(1):79-87. Epub 2006 Mar 3.
  • Anne S. Kienhuis, Heleen M. Wortelboer, Jean Christoph Hoflack, Jos C. S. Kleinjans, Ben van Ommen, Joost H.M. van Delft, and Rob H. Stierum (2006) Comparison of coumarin-induced toxicity in sandwich-cultured rat hepatocytes in vitro versus rats iv vivo: a toxicogenomics approach. Drug Metab Dispos. 2006 Dec;34(12):2083-90.
  • Heijne WH, Jonker D, Stierum RH, van Ommen B, Groten JP. (2005) Toxicogenomic analysis of gene expression changes in rat liver after a 28-day oral benzene exposure. Mutat Res. 2005, 575(1-2), 85-101.
  • Heijne WH, Slitt AL, Van Bladeren PJ, Groten JP, Klaassen CD, Stierum RH, Van Ommen B. (2004) Bromobenzene-induced hepatotoxicity at the transcriptome level. Toxicol Sci. 2004 Jun;79(2): 411-422.

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