Dr. M.J. (Martijs) Jonker
Faculteit der Natuurwetenschappen, Wiskunde en Informatica
Swammerdam Institute for Life Sciences
Bezoekadres
- Science Park 904
- Kamernummer: C2.201
Postadres
- Postbus 1212
1000 BE Amsterdam
Contactgegevens
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Publicaties
2021
- Hammoudi, V., Beerens, B., Jonker, M. J., Helderman, T. A., Vlachakis, G., Giesbers, M., Kwaaitaal, M., & van den Burg, H. A. (2021). The protein modifier SUMO is critical for integrity of the Arabidopsis shoot apex at warm ambient temperatures. Journal of Experimental Botany. https://doi.org/10.1093/jxb/erab262
2020
Swarge, B., Abhyankar, W., Jonker, M., Hoefsloot, H., Kramer, G., Setlow, P., Brul, S., & de Koning, L. J. (2020). Integrative Analysis of Proteome and Transcriptome Dynamics during Bacillus subtilis Spore Revival. mSphere, 5(4), [e00463-20]. https://doi.org/10.1128/mSphere.00463-20 [details]- van der Kloet, F. M., Buurmans, J., Jonker, M. J., Smilde, A. K., & Westerhuis, J. A. (2020). Increased comparability between RNA-Seq and microarray data by utilization of gene sets. PLoS Computational Biology, 16(9), [e1008295]. https://doi.org/10.1371/journal.pcbi.1008295 [details]
2019
- Gray, D. A., Dugar, G., Gamba, P., Strahl, H., Jonker, M. J., & Hamoen, L. W. (2019). Extreme slow growth as alternative strategy to survive deep starvation in bacteria. Nature Communications, 10, [890]. https://doi.org/10.1038/s41467-019-08719-8 [details]
- Hoeksema, M., Jonker, M. J., Brul, S., & Ter Kuile, B. H. (2019). Effects of a previously selected antibiotic resistance on mutations acquired during development of a second resistance in Escherichia coli. BMC Genomics, 20, [284]. https://doi.org/10.1186/s12864-019-5648-7 [details]
- Opperhuizen, A-L., Foppen, E., Jonker, M., Wackers, P., van Faassen, M., van Weeghel, M., van Kerkhof, L., Fliers, E., & Kalsbeek, A. (2019). Effects of Light-at-Night on the Rat Liver - A Role for the Autonomic Nervous System. Frontiers in Neuroscience, 13, [647]. https://doi.org/10.3389/fnins.2019.00647 [details]
2018
- Bohorquez, L. C., Surdova, K., Jonker, M. J., & Hamoen, L. W. (2018). The Conserved DNA Binding Protein WhiA Influences Chromosome Segregation in Bacillus subtilis. Journal of Bacteriology, 200(8), [e00633-17]. https://doi.org/10.1128/JB.00633-17 [details]
- Hammoudi, V., Fokkens, L., Beerens, B., Vlachakis, G., Chatterjee, S., Arroyo-Mateos, M., ... van den Burg, H. A. (2018). The Arabidopsis SUMO E3 ligase SIZ1 mediates the temperature dependent trade-off between plant immunity and growth. PLOS Genetics, 14(1), [e1007157]. https://doi.org/10.1371/journal.pgen.1007157 [details]
- Hoeksema, M., Jonker, M. J., Bel, K., Brul, S., & Ter Kuile, B. H. (2018). Genome rearrangements in Escherichia coli during de novo acquisition of resistance to a single antibiotic or two antibiotics successively. BMC Genomics, 19, [973]. https://doi.org/10.1186/s12864-018-5353-y [details]
- Locati, M. D., Pagano, J. F. B., Abdullah, F., Ensink, W. A., van Olst, M., van Leeuwen, S., ... Breit, T. M. (2018). Identifying small RNAs derived from maternal- and somatic-type rRNAs in zebrafish development. Genome, 61(5), 371-378. https://doi.org/10.1139/gen-2017-0202 [details]
2017
- Gao, Y., Wenzel, M., Jonker, M. J., & Hamoen, L. W. (2017). Free SepF interferes with recruitment of late cell division proteins. Scientific Reports, 7, [16928]. https://doi.org/10.1038/s41598-017-17155-x [details]
- Locati, M. D., Pagano, J. F. B., Ensink, W. A., van Olst, M., van Leeuwen, S., Nehrdich, U., ... Breit, T. M. (2017). Linking Maternal and Somatic 5S rRNA types with Different Sequence-Specific Non-LTR Retrotransposons. RNA, 23(4), 446-456. https://doi.org/10.1261/rna.059642.116 [details]
- Locati, M. D., Pagano, J. F. B., Girard, G., Ensink, W. A., van Olst, M., van Leeuwen, S., ... Breit, T. M. (2017). Expression of distinct maternal and somatic 5.8S, 18S, and 28S rRNA types during zebrafish development. RNA, 23(8), 1188-1199. https://doi.org/10.1261/rna.061515.117 [details]
- Rauwerda, H., Pagano, J. F. B., de Leeuw, W. C., Ensink, W., Nehrdich, U., de Jong, M., Jonker, M., Spaink, H. P., & Breit, T. M. (2017). Transcriptome dynamics in early zebrafish embryogenesis determined by high-resolution time course analysis of 180 successive, individual zebrafish embryos. BMC Genomics, 18, [287]. https://doi.org/10.1186/s12864-017-3672-z [details]
- Smith, R. L., Tan, J. M. E., Jonker, M. J., Jongejan, A., Buissink, T., Veldhuijzen, S., ... van der Spek, H. (2017). Beyond the polymerase-γ theory: Production of ROS as a mode of NRTI-induced mitochondrial toxicity. PLoS ONE, 12(11), [e0187424]. https://doi.org/10.1371/journal.pone.0187424 [details]
2016
- 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]. https://doi.org/10.1371/journal.pone.0145252 [details]
- 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. https://doi.org/10.1128/AAC.00434-16 [details]
- Fluit, A. C., Jansen, M. D., Bosch, T., Jansen, W. T. M., Schouls, L., Jonker, M. J., & Boel, C. H. E. (2016). rRNA Operon Copy Number Can Explain the Distinct Epidemiology of Hospital-Associated Methicillin-Resistant Staphylococcus aureus. Antimicrobial Agents and Chemotherapy, 60(12), 7313-7320. https://doi.org/10.1128/AAC.01613-16 [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. https://doi.org/10.1093/humrep/dev306 [details]
- Pagano, J. F. B., Rauwerda, H., de Leeuw, W. C., Wackers, P., de Jong, M., Ensink, W., ... Breit, T. M. (2016). Transcriptome data on maternal RNA of 24 individual zebrafish eggs from five sibling mothers. Data in Brief, 8, 69-72. https://doi.org/10.1016/j.dib.2016.04.045 [details]
- Rauwerda, H., Wackers, P., Pagano, J. F. B., de Jong, M., Ensink, W., Dekker, R., ... Breit, T. M. (2016). Mother-Specific Signature in the Maternal Transcriptome Composition of Mature, Unfertilized Zebrafish Eggs. PLoS ONE, 11(1), [e0147151]. https://doi.org/10.1371/journal.pone.0147151 [details]
2015
- 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. https://doi.org/10.1080/21541264.2015.1064195 [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. https://doi.org/10.1371/journal.pgen.1005047 [details]
- 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. https://doi.org/10.1371/journal.pone.0123039 [details]
- 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. https://doi.org/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]. https://doi.org/10.1093/nar/gkv303 [details]
- 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. https://doi.org/10.1007/s00204-014-1368-6 [details]
2014
- 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. https://doi.org/10.1186/1471-2164-15-915 [details]
2013
- 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. https://doi.org/10.1111/acel.12118 [details]
- 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]
- 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. https://doi.org/10.1128/JB.00507-13 [details]
2012
- 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. https://doi.org/10.1093/humrep/der383 [details]
- 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]. https://doi.org/10.1186/1471-2164-13-167 [details]
- 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. https://doi.org/10.1021/es300421r [details]
- Marinković, M., de Leeuw, W. C., Ensink, W. A., de Jong, M., Breit, T. M., Admiraal, W., Kraak, M. H. S., & Jonker, M. J. (2012). Gene expression patterns and life cycle responses of toxicant-exposed chironomids. Environmental Science and Technology, 46(22), 12679-12686. https://doi.org/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. https://doi.org/10.1371/journal.pone.0048096 [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. https://doi.org/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. https://doi.org/10.1111/j.1365-2249.2011.04522.x [details]
- 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. https://doi.org/10.1007/s00204-012-0883-6 [details]
2011
- 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. https://doi.org/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. https://doi.org/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. Journal of Applied Toxicology, 31(5), 421-430. https://doi.org/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. https://doi.org/10.1186/gb-2011-12-8-r71 [details]
2010
- 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. https://doi.org/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. [252]. https://doi.org/10.1186/1471-2180-10-252 [details]
- 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. https://doi.org/10.1186/1752-0509-4-32 [details]
2009
- 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. https://doi.org/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. https://doi.org/10.1016/j.ijfoodmicro.2009.05.019 [details]
2008
- 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. https://doi.org/10.1016/j.taap.2007.08.026 [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. https://doi.org/10.1128/MCB.01610-07 [details]
- 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. https://doi.org/10.1111/j.1399-302X.2007.00409.x [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. https://doi.org/10.1186/1471-2164-9-266 [details]
- 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. https://doi.org/10.1021/es702745d [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. https://doi.org/10.1111/j.1398-9995.2007.01621.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. https://doi.org/10.1165/rcmb.2007-0278OC [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. https://doi.org/10.1186/1756-0500-1-66 [details]
2014
- 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. https://doi.org/10.1371/journal.pone.0097089 [details]
- 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. https://doi.org/10.1093/nar/gku343 [details]
- 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. https://doi.org/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. https://doi.org/10.1007/s00204-014-1257-z [details]
2011
- Jonker, M. J., Gerhardt, A., Backhaus, T., & van Gestel, C. A. M. (2011). 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 Ecological and Human Toxicology (pp. 121-155). (Environmental chemistry & toxicology). CRC Press. https://doi.org/10.1201/b10292-5 [details]
- van Gestel, C. A. M., Jonker, M. J., Kammenga, J. E., Laskowski, R., & Svendsen, C. (2011). Mixture Toxicity: Linking Approaches from Ecological and Human Toxicology. (Environmental chemistry & toxicology). Boca Raton: CRC Press. https://doi.org/10.1201/b10292 [details]
2020
- Pagano, J. F. B., Locati, M. D., Ensink, W. A., van Olst, M., van Leeuwen, S., de Leeuw, W. C., Nehrdich, U., Spaink, H. P., Rauwerda, H., Jonker, M. J., Dekker, R. J., & Breit, T. M. (2020). Maternal- and Somatic-type snoRNA Expression and Processing in Zebrafish Development. BioRxiv. https://doi.org/10.1101/858936 [details]
2019
- Pagano, J. F. B., Dekker, R. J., Ensink, W. A., van Olst, M., Bos, A., van Leeuwen, S., de Leeuw, W. C., Nehrdich, U., Spaink, H. P., Rauwerda, H., Jonker, M. J., & Breit, T. M. (2019). An alternative spliceosome defined by distinct snRNAs in early zebrafish embryogenesis. BioRxiv. https://doi.org/10.1101/858944 [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. Log in to Personal Page Publication Selection tool to manage the visibility of your publications on this list. -
Nevenwerkzaamheden
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Millennia Biopharma
Advies met betrekking tot het vinden van transcriptomics biomarkers.
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Millennia Biopharma
Swarge, B., Abhyankar, W., Jonker, M., Hoefsloot, H., Kramer, G., Setlow, P., Brul, S., & de Koning, L. J. (2020). Integrative Analysis of Proteome and Transcriptome Dynamics during Bacillus subtilis Spore Revival. mSphere, 5(4), [e00463-20].