dhr. dr. M.J. (Martijs) Jonker

  • Faculteit der Natuurwetenschappen, Wiskunde en Informatica
  • Bezoekadres
    Science Park A
    Science Park 904  Amsterdam
    Kamernummer: C2.272
  • Postadres:
    Postbus  94215
    1090 GE  Amsterdam
  • M.J.Jonker@uva.nl
    T: 0205257939


  • Bruning, O., Rodenburg, W., Wackers, P. F. K., van Oostrom, C., Jonker, M. J., Dekker, R. J., ... Breit, T. M. (2016). Confounding Factors in the Transcriptome Analysis of an In-Vivo Exposure Experiment. PLoS One, 11(1), [e0145252]. DOI: 10.1371/journal.pone.0145252 [details / files]
  • Feng, Y., Jonker, M. J., Moustakas, I., Brul, S., & ter Kuile, B. H. (2016). Dynamics of mutations during development of resistance by Pseudomonas aeruginosa against five antibiotics. Antimicrobial Agents and Chemotherapy, 60(7), 4229-4236. DOI: 10.1128/AAC.00434-16 [details]
  • Mantikou, E., Jonker, M. J., Wong, K. M., van Montfoort, A. P. A., de Jong, M., Breit, T. M., ... Mastenbroek, S. (2016). Factors affecting the gene expression of in vitro cultured human preimplantation embryos. Human Reproduction, 31(2), 298-311. DOI: 10.1093/humrep/dev306 [details]


  • Bruning, O., Rauwerda, H., Dekker, R. J., de Leeuw, W. C., Wackers, P. F. K., Ensink, W. A., ... Breit, T. M. (2015). Valuable lessons-learned in transcriptomics experimentation. Transcription, 6(3), 51-55. DOI: 10.1080/21541264.2015.1064195 [details] [PDF]
  • Händel, N., Otte, S., Jonker, M. J., Brul, S., & ter Kuile, B. H. (2015). Factors that affect transfer of the IncI1 β-lactam resistance plasmid pESBL-283 between E. coli strains. PLoS One, 10(4), e0123039. DOI: 10.1371/journal.pone.0123039 [details] [PDF]
  • Schaap, M. M., Wackers, P. F. K., Zwart, E. P., Huijskens, I., Jonker, M. J., Hendriks, G., ... Luijten, M. (2015). A novel toxicogenomics-based approach to categorize (non-)genotoxic carcinogens. Archives of toxicology = Archiv für Toxikologie, 89(12), 2413-2427. DOI: 10.1007/s00204-014-1368-6 [details]
  • Gamba, P., Jonker, M. J., & Hamoen, L. W. (2015). A Novel Feedback Loop That Controls Bimodal Expression of Genetic Competence. PLOS Genetics, 11(6), e1005047. DOI: 10.1371/journal.pgen.1005047 [details] [PDF]
  • Kleijkers, S. H. M., Eijssen, L. M. T., Coonen, E., Derhaag, J. G., Mantikou, E., Jonker, M. J., ... van Montfoort, A. P. A. (2015). Differences in gene expression profiles between human preimplantation embryos cultured in two different IVF culture media. Human Reproduction, 30(10), 2303-2311. DOI: 10.1093/humrep/dev179 [details]
  • Locati, M. D., Terpstra, I., de Leeuw, W. C., Kuzak, M., Rauwerda, H., Ensink, W. A., ... Dekker, R. J. (2015). Improving small RNA-seq by using a synthetic spike-in set for size-range quality control together with a set for data normalization. Nucleic Acids Research, 43(14), [e89]. DOI: 10.1093/nar/gkv303 [details / files]


  • Tulinski, P., Duim, B., Wittink, F. R., Jonker, M. J., Breit, T. M., van Putten, J. P., ... Fluit, A. C. (2014). Staphylococcus aureus ST398 gene expression profiling during ex vivo colonization of porcine nasal epithelium. BMC Genomics, 15, 915. DOI: 10.1186/1471-2164-15-915 [details] [PDF]


  • Jonker, M. J., Melis, J. P. M., Kuiper, R. V., van der Hoeven, T. V., Wackers, P. F. K., Robinson, J., ... van Steeg, H. (2013). Life spanning murine gene expression profiles in relation to chronological and pathological aging in multiple organs. Aging Cell, 12(5), 901-909. DOI: 10.1111/acel.12118 [details / files]
  • Melis, J. P., Jonker, M. J., Vijg, J., Hoeijmakers, J. H., Breit, T. M., & van Steeg, H. (2013). Aging on a different scale - chronological versus pathology-related aging. Aging, 5(10), 782-788. [details] [PDF]
  • Surdova, K., Gamba, P., Claessen, D., Siersma, T., Jonker, M. J., Errington, J., & Hamoen, L. W. (2013). The Conserved DNA-Binding Protein WhiA Is Involved in Cell Division in Bacillus subtilis. Journal of Bacteriology, 195(24), 5450-5460. DOI: 10.1128/JB.00507-13 [details / files]


  • Doroszuk, A., Jonker, M. J., Pul, N., Breit, T. M., & Zwaan, B. J. (2012). Transcriptome analysis of a long-lived natural Drosophila variant: a prominent role of stress- and reproduction-genes in lifespan extension. BMC Genomics, 13(1), [167]. DOI: 10.1186/1471-2164-13-167 [details] [PDF]
  • Marinković, M., de Bruijn, K., Asselman, M., Bogaert, M., Jonker, M. J., Kraak, M. H. S., & Admiraal, W. (2012). Response of the nonbiting midge Chironomus riparius to multigeneration toxicant exposure. Environmental Science and Technology, 46(21), 12105-12111. DOI: 10.1021/es300421r [details]
  • Marinković, M., de Leeuw, W. C., Ensink, W. A., de Jong, M., Breit, T. M., Admiraal, W., ... Jonker, M. J. (2012). Gene expression patterns and life cycle responses of toxicant-exposed chironomids. Environmental Science and Technology, 46(22), 12679-12686. DOI: 10.1021/es3033617 [details]
  • Marinković, M., de Leeuw, W. C., de Jong, M., Kraak, M. H. S., Admiraal, W., Breit, T. M., & Jonker, M. J. (2012). Combining next-generation sequencing and microarray technology into a transcriptomics approach for the non-model organism Chironomus riparius. PLoS One, 7(10), e48096. DOI: 10.1371/journal.pone.0048096 [details] [PDF]
  • Schaap, M. M., Zwart, E. P., Wackers, P. F. K., Huijskens, I., van de Water, B., Breit, T. M., ... Luijten, M. (2012). Dissecting modes of action of non-genotoxic carcinogens in primary mouse hepatocytes. Archives of toxicology = Archiv für Toxikologie, 86(11), 1717-1727. DOI: 10.1007/s00204-012-0883-6 [details]
  • Chikhovskaya, J. V., Jonker, M. J., Meissner, A., Breit, T. M., Repping, S., & van Pelt, A. M. M. (2012). Human testis-derived embryonic stem cell-like cells are not pluripotent, but possess potential of mesenchymal progenitors. Human Reproduction, 27(1), 210-221. DOI: 10.1093/humrep/der383 [details]
  • Röschmann, K. I. L., van Kuijen, A. M., Luiten, S., Jonker, M. J., Breit, T. M., Fokkens, W. J., ... van Drunen, C. M. (2012). Comparison of Timothy grass pollen extract- and single major allergen-induced gene expression and mediator release in airway epithelial cells: a meta-analysis. Clinical and Experimental Allergy, 42(10), 1479-1490. DOI: 10.1111/j.1365-2222.2012.04033.x [details]
  • Röschmann, K. I. L., van Kuijen, A. M., Luiten, S., Jonker, M. J., Breit, T. M., Fokkens, W. J., ... van Drunen, C. M. (2012). Purified Timothy grass pollen major allergen Phl p 1 may contribute to the modulation of allergic responses through a pleiotropic induction of cytokines and chemokines from airway epithelial cells. Clinical and experimental immunology, 167(3), 413-421. DOI: 10.1111/j.1365-2249.2011.04522.x [details]


  • Marinkovic, M., Verweij, R. A., Nummerdor, G. A., Jonker, M. J., Kraak, M. H. S., & Admiraal, W. (2011). Life cycle responses of the midge Chironomus riparius to compounds with different modes of action. Environmental Science and Technology, 45(4), 1645-1651. DOI: 10.1021/es102904y [details]
  • Röschmann, K. I. L., Luiten, S., Jonker, M. J., Breit, T. M., Fokkens, W. J., Petersen, A., & van Drunen, C. M. (2011). Timothy grass pollen extract-induced gene expression and signalling pathways in airway epithelial cells. Clinical and Experimental Allergy, 41(6), 830-841. DOI: 10.1111/j.1365-2222.2011.03713.x [details]
  • Yuan, X., Jonker, M. J., de Wilde, J., Verhoef, A., Wittink, F. R. A., van Benthem, J., ... Luijten, M. (2011). Finding maximal transcriptome differences between reprotoxic and non-reprotoxic phthalate responses in rat testis. J Appl Toxicol, 31(5), 421-430. DOI: 10.1002/jat.1601 [details]
  • de Bekker, C., Bruning, O., Jonker, M. J., Breit, T. M., & Wösten, H. A. B. (2011). Single cell transcriptomics of neighboring hyphae of Aspergillus niger. Genome Biology, 12(8), R71. DOI: 10.1186/gb-2011-12-8-r71 [details] [PDF]


  • Bruning, O., Yuan, X., Rodenburg, W., Bruins, W., van Oostrom, C. T., Rauwerda, H., ... Breit, T. M. (2010). Serious complications in gene-expression studies with stress perturbation: An example of UV-exposed p53-mutant mouse embryonic fibroblasts. Transcription, 1(3), 159-164. DOI: 10.4161/trns.1.3.13487 [details]
  • Brunner, J., Wittink, F. R. A., Jonker, M. J., de Jong, M., Breit, T. M., Laine, M. L., ... Crielaard, W. (2010). The core genome of the anaerobic oral pathogenic bacterium Porphyromonas gingivalis. BMC Microbiology, 10, 252. DOI: 10.1186/1471-2180-10-252 [details] [PDF]
  • Swain, S., Wren, J. F., Stürzenbaum, S. R., Kille, P., Morgan, A. J., Jager, T., ... Spurgeon, D. J. (2010). Linking toxicant physiological mode of action with induced gene expression changes in Caenorhabditis elegans. BMC Systems Biology, 4, 32. DOI: 10.1186/1752-0509-4-32 [details] [PDF]


  • Jonker, M. J., Bruning, O., van Iterson, M., Schaap, M. M., van der Hoeven, T. V., Vrieling, H., ... Luijten, M. (2009). Finding transcriptomics biomarkers for in vivo identification of (non-)genotoxic carcinogens using wild-type and Xpa/p53 mutant mouse models. Carcinogenesis, 30(10), 1805-1812. DOI: 10.1093/carcin/bgp190 [details]
  • Oomes, S. J. C. M., Jonker, M. J., Wittink, F. R. A., Hehenkamp, J. O., Breit, T. M., & Brul, S. (2009). The effect of calcium on the transcriptome of sporulating B. subtilis cells. International Journal of Food Microbiology, 133(3), 234-242. DOI: 10.1016/j.ijfoodmicro.2009.05.019 [details]


  • Bruning, O., Bruins, W., Jonker, M. J., Zwart, E., van der Hoeven, T. V., Pennings, J. L. A., ... Breit, T. M. (2008). The absence of Ser389 phosphorylation in p53 affects the basal gene expression level of many p53-dependent genes and alters the biphasic response to UV exposure in mouse embryonic fibroblasts. Molecular and Cellular Biology, 28(6), 1974-1987. DOI: 10.1128/MCB.01610-07 [details] [PDF]
  • Luppens, S. B. I., Kara, D., Bandounas, L., Jonker, M. J., Wittink, F. R. A., Bruning, O., ... Crielaard, W. (2008). Effect of Veillonella parvula on the antimicrobial resistance and gene expression of Streptococcus mutans grown in a dual-species biofilm. Oral Microbiology and Immunology, 23(3), 183-189. DOI: 10.1111/j.1399-302X.2007.00409.x [details]
  • Vroling, A. B., Jonker, M. J., Luiten, S., Breit, T. M., Fokkens, W. J., & van Drunen, C. M. (2008). Primary nasal epithelium exposed to house dust mite extract shows activated expression in allergic individuals. American Journal of Respiratory Cell and Molecular Biology, 38(3), 293-299. DOI: 10.1165/rcmb.2007-0278OC [details]
  • Vroling, A. B., Jonker, M. J., Breit, T. M., Fokkens, W. J., & van Drunen, C. M. (2008). Comparison of expression profiles induced by dust mite in airway epithelia reveals a common pathway. Allergy, 63(4), 461-467. DOI: 10.1111/j.1398-9995.2007.01621.x [details]
  • de Leeuw, W. C., Rauwerda, H., Jonker, M. J., & Breit, T. M. (2008). Salvaging Affymetrix probes after probe-level re-annotation. BMC Research Notes, 1, 66. DOI: 10.1186/1756-0500-1-66 [details] [PDF]
  • Baken, K. A., Pennings, J. L. A., Jonker, M. J., Schaap, M. M., de Vries, A., van Steeg, H., ... van Loveren, H. (2008). Overlapping gene expression profiles of model compounds provide opportunities for immunotoxicity screening. Toxicology and Applied Pharmacology, 226(1), 46-59. DOI: 10.1016/j.taap.2007.08.026 [details]
  • Owen, J., Hedley, B. A., Svendsen, C., Wren, J., Jonker, M. J., Hankard, P. K., ... Kille, P. (2008). Transcriptome profiling of developmental and xenobiotic responses in a keystone soil animal, the oligochaete annelid Lumbricus rubellus. BMC Genomics, 9, 266. DOI: 10.1186/1471-2164-9-266 [details] [PDF]
  • Svendsen, C., Owen, J., Kille, P., Wren, J., Jonker, M. J., Headley, B. A., ... Spurgeon, D. J. (2008). Comparative transcriptomic responses to chronic cadmium, fluoranthene, and atrazine exposure in Lumbricus rubellus. Environmental Science and Technology, 42(11), 4208-4214. DOI: 10.1021/es702745d [details]


  • Bruning, O., Rodenburg, W., van Oostrom, C. T., Jonker, M. J., de Jong, M., Dekker, R. J., ... Breit, T. M. (2014). A range finding protocol to support design for transcriptomics experimentation: examples of in-vitro and in-vivo murine UV exposure. PLoS One, 9(5), e97089. DOI: 10.1371/journal.pone.0097089 [details] [PDF]
  • Jonker, M. J., de Leeuw, W. C., Marinković, M., Wittink, F. R. A., Rauwerda, H., Bruning, O., ... Breit, T. M. (2014). Absence/presence calling in microarray-based CGH experiments with non-model organisms. Nucleic Acids Research, 42(11), e94. DOI: 10.1093/nar/gku343 [details / files]
  • Melis, J. P. M., Derks, K. W. J., Pronk, T. E., Wackers, P., Schaap, M. M., Zwart, E., ... Luijten, M. (2014). In vivo murine hepatic microRNA and mRNA expression signatures predicting the (non-)genotoxic carcinogenic potential of chemicals. Archives of toxicology = Archiv für Toxikologie, 88(4), 1023-1034. DOI: 10.1007/s00204-013-1189-z [details]
  • van Dycke, K. C., Nijman, R. M., Wackers, P. F. K., Jonker, M. J., Rodenburg, W., van Oostrom, C. T. M., ... van der Horst, G. T. J. (2014). A day and night difference in the response of the hepatic transcriptome to cyclophosphamide treatment. Archives of toxicology = Archiv für Toxikologie, 89(2), 221-231. DOI: 10.1007/s00204-014-1257-z [details]


  • Jonker, M. J., Gerhardt, A., Backhaus, T., & van Gestel, C. A. M. (2010). Test Design, mixture characterization, and data evaluation. In C. A. M. van Gestel, M. J. Jonker, J. E. Kammenga, R. Laskowski, & C. Svendsen (Eds.), Mixture toxicity: linking approaches from ecology and human toxicology. (pp. 121-155-4). CRC Press. DOI: 10.1201/b10292-5 [details]
This list of publications is extracted from the UvA-Current Research Information System. Questions? Ask the library or the Pure staff of your faculty / institute. Log in to Pure to edit your publications.
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