Photographer: onbekend

dr. T.M. (Timo) Breit


  • Faculty of Science
    SILS
  • Visiting address
    Science Park A
    Science Park 904  Amsterdam
    Room number: C2.273
  • Postal address:
    Postbus  94215
    1090 GE  Amsterdam
  • T.M.Breit@uva.nl
    T: 0205257058

MAD & IBU

I am heading the genome technology and bioinformatics expertise centre of the FNWI named "The MicroArray Department (MAD)" and the bioinformatics research group "Integrative Bioinformatics Unit (IBU)" .  The group consists of about 14 multidiciplinary experts in the fields of microarray, next-generation sequencing and bioinformatics. For detailed information see our website: www.micro-array.nl

Service: The MAD is a microarray technology centre with NimbleGen, Affymetrix Genechip®, and Agilent platforms. We operate as platform for R&D, as well as service center. As  Genomics Service Provider, we offer tailor-made services in the field of gene expression, DNA analysis and related bioinformatics. Our expertise includes:

  1. consultancy about experiment design;
  2. use of microarrays as Affymetrix, Agilent and NimbleGen ServiceProvider;
  3. high-quality microarray experiments;
  4. comprehensive transcriptomics data analysis by expert bioinformaticians.
The MAD comprises a wet-lab and a dry-lab. The wet-lab takes care of all genomics technology services. The dry-lab acts as a bioinformatics support group for all genomics data analyses.   Research: The MAD acts not only as a service provider but also as a partner in scientific projects. These projects range from toxicogenomics (genomic analysis and in vivo imaging of stress in aging-related disease funded by IOP -EMC, LUMC, LACDR, RIVM), food safety (Unilever) and mechanistic studies (e.g. Biofilm -ACTA-) and biomarkers (RIVM). The MAD is always in for collaboration or participation in projects concerning genomics technology or analysis. If you need an expert microarray, next0generations sequencing or bioinformatics partner for your project, please contact Dr Timo Breit (t.m.breit@uva.nl) or Dr Mark de Jong (h.m.dejong@uva.nl).

Both wet-lab and dry-lab have their own research program. While the wet-lab focuses on technology research (e.g. design of new arrays) and implementation of high and up-to-date QC standards, the dry-lab concentrates on the evaluation and implementation of tools for genomics data analysis.
The Integrative Bioinformatics Unit (IBU) emerged in 2003 from the MAD. IBU's main research effort is aimed at evaluating the possibilities for computer-assisted experimental biology research by building an e-BioScience problem solving environment (eBioPSE). The focus is on development of a comprehensive microarray data analysis eBioPSE for biological problem-solving and phenomenon discovery by means of data integration and computational experimentation.

The most important IBU long-term goals:

  1. Develop a problem-solving environment for microarray data analysis;
  2. Enhance life-sciences design-for-experimentation.
  3. Research on in-silico experimentation approach with genomics data and knowledge models.

There are numerous methods and tools to analyze microarray experiments and many more are being developed continuously. Each method and tool has its own use and merits. We are trying to keep track of what has been and is being developed worldwide. We aim to create a comprehensive suite of microarray data analysis tools by drawing up an inventory, evaluation, and selection of valuable methods and tools. The total microarray data analysis environment will be built by introducing methods and tools to it, embedded in workflows. This will enhance the re-usability of data, methods, and tools dramatically.

We participate in severallarge integrated national projects: "BioRange", "BioAssist", BiG Grid, and "Virtual Lab for Plant Breeding (VLPB)". BioRange is a nation-wide NBIC bioinformatics research project; BioAssist is a nation-wide NBIC bioinformatics support program; BiGGrid is a nation-wide e-science infrastructure program;  and VLPB is the Dutch e-science project concerned with ICT infrastructure and methods, meant to support applications from plant breeding.

2017

  • 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. DOI: 10.1261/rna.061515.117 [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. DOI: 10.1261/rna.059642.116 [details / files]

2016

  • 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. DOI: 10.1016/j.dib.2016.04.045 [details / files]
  • 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]. DOI: 10.1371/journal.pone.0147151 [details / files]
  • 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]
  • 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]

2015

  • Mirabella, R., Rauwerda, H., Allmann, S., Scala, A., Spyropoulou, E. A., de Vries, M., ... Schuurink, R. C. (2015). WRKY40 and WRKY6 act downstream of the green leaf volatile E-2-hexenal in Arabidopsis. Plant Journal, 83(6), 1082-1096. DOI: 10.1111/tpj.12953 [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]
  • 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]
  • 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]
  • Mantikou, E., Bruning, O., Mastenbroek, S., Repping, S., Breit, T. M., & de Jong, M. (2015). Evaluation of ribonucleic acid amplification protocols for human oocyte transcriptome analysis. Fertility and Sterility, 105(2), 511-519.e4. DOI: 10.1016/j.fertnstert.2015.10.025 [details]

2014

  • Aflitos, S., Schijlen, E., de Jong, H., de Ridder, D., Smit, S., Finkers, R., ... Peters, S. (2014). Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. Plant Journal, 80(1), 136-148. DOI: 10.1111/tpj.12616 [details]
  • 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]

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. 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]
  • Sasidharan, R., Mustroph, A., Boonman, A., Akman, M., Ammerlaan, A. M. H., Breit, T. M., ... van Tienderen, P. H. (2013). Root transcript profiling of two Rorippa species reveals gene clusters associated with extreme submergence tolerance. Plant Physiology, 163(3), 1277-1292. DOI: 10.1104/pp.113.222588 [details / files]
  • de Knegt, G. J., Bruning, O., ten Kate, M. T., de Jong, M., van Belkum, A., Endtz, H. P., ... de Steenwinkel, J. E. M. (2013). Rifampicin-induced transcriptome response in rifampicin-resistant Mycobacterium tuberculosis. Tuberculosis, 93(1), 96-101. DOI: 10.1016/j.tube.2012.10.013 [details]

2012

  • 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 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]

2011

  • Belloum, A., Inda, M. A., Vasunin, D., Korkhov, V., Zhao, Z., Rauwerda, H., ... Hertzberger, L. O. (2011). Collaborative e-Science Experiments and Scientific Workflows. IEEE Internet Computing, 15(4), 39-47. DOI: 10.1109/MIC.2011.87 [details]
  • Bruning, O., Rodenburg, W., Radonic, T., Zwinderman, A. H., de Vries, A., Breit, T. M., & de Jong, M. (2011). RNA isolation for transcriptomics of human and mouse small skin biopsies. BMC Research Notes, 4(1), 438. DOI: 10.1186/1756-0500-4-438 [details / files]
  • Hakvoort, T. B. M., Moerland, P. D., Frijters, R., Sokolović, A., Labruyère, W. T., Vermeulen, J. L. M., ... Sokolović, M. (2011). Interorgan coordination of the murine adaptive response to fasting. The Journal of Biological Chemistry, 286(18), 16332-16343. DOI: 10.1074/jbc.M110.216986 [details]
  • Melis, J. P. M., Hoogervorst, E. M., van Oostrom, C. T. M., Zwart, E., Breit, T. M., Pennings, J. L. A., ... van Steeg, H. (2011). Genotoxic exposure: novel cause of selection for a functional ΔN-p53 isoform. Oncogene, 30(15), 1764-1772. DOI: 10.1038/onc.2010.552 [details]
  • Pennings, J. L. A., Rodenburg, W., Imholz, S., Koster, M. P. H., van Oostrom, C. T. M., Breit, T. M., ... de Vries, A. (2011). Gene expression profiling in a mouse model identifies fetal liver- and placenta-derived potential biomarkers for Down syndrome screening. PLoS One, 6(4), e18866. DOI: 10.1371/journal.pone.0018866 [details] [PDF]
  • 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]

2010

  • Boer, K., Crino, P. B., Gorter, J. A., Nellist, M., Jansen, F. E., Spliet, W. G. M., ... Aronica, E. M. A. (2010). Gene expression analysis of tuberous sclerosis complex cortical tubers reveals increased expression of adhesion and inflammatory factors. Brain Pathology, 20(4), 704-719. DOI: 10.1111/j.1750-3639.2009.00341.x [details]
  • 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. [252]. DOI: 10.1186/1471-2180-10-252 [details] [PDF]
  • Rauwerda, H., de Jong, M., de Leeuw, W. C., Spaink, H. P., & Breit, T. M. (2010). Integrating heterogeneous sequence information for transcriptome-wide microarray design; a Zebrafish example. BMC Research Notes, 3, 192. DOI: 10.1186/1756-0500-3-192 [details] [PDF]
  • de Jong, M., Rauwerda, H., Bruning, O., Verkooijen, J., Spaink, H. P., & Breit, T. M. (2010). RNA isolation method for single embryo transcriptome analysis in zebrafish. BMC Research Notes, 3(1), 73. DOI: 10.1186/1756-0500-3-73 [details] [PDF]
  • Stockhammer, O. W., Rauwerda, H., Wittink, F. R., Breit, T. M., Meijer, A. H., & Spaink, H. P. (2010). Transcriptome analysis of Traf6 function in the innate immune response of zebrafish embryos. Molecular Immunology, 48(1-3), 179-190. DOI: 10.1016/j.molimm.2010.08.011 [details]
  • Wassink, I., Ooms, M., Neerincx, P., van der Veer, G., Rauwerda, H., Leunissen, J. A. M., ... van der Vet, P. (2010). e-BioFlow: improving practical use of workflow systems in bioinformatics. Lecture Notes in Computer Science, 6266, 1-15. DOI: 10.1007/978-3-642-15020-3_1 [details]
  • ten Broeke-Smits, N. J. P., Pronk, T. E., Jongerius, I., Bruning, O., Wittink, F. R., Breit, T. M., ... Boel, C. H. E. (2010). Operon structure of Staphylococcus aureus. Nucleic Acids Research, 38(10), 3263-3274. DOI: 10.1093/nar/gkq058 [details] [PDF]

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. DOI: 10.1093/carcin/bgp190 [details]
  • de Leeuw, W. C., Rauwerda, H., Inda, M. A., Bruning, O., & Breit, T. M. (2009). SigWinR; the SigWin-detector updated and ported to R. BMC Research Notes, 2(1), [205]. DOI: 10.1186/1756-0500-2-205 [details / files]
  • Fikkert, W., van der Vet, P., Rauwerda, H., Breit, T., & Nijholt, A. (2009). Gestures to intuitively control large displays: 7th International Gesture Workshop, GW 2007, Lisbon, Portugal, May 23-25, 2007 : revised selected papers. In M. Sales Dias, S. Gibet, M. M. Wanderley, & R. Bastos (Eds.), Gesture-based human-computer interaction and simulation: 7th International Gesture Workshop, GW 2007, Lisbon, Portugal, May 23-25, 2007: Revised selected papers (pp. 199-204). (Lecture Notes in Computer Science; No. 5085), (Lecture notes in artificial intelligence). Berlin: Springer. DOI: 10.1007/978-3-540-92865-2_22 [details]
  • Garinis, G. A., Uittenboogaard, L. M., Stachelscheid, H., Fousteri, M., van IJcken, W., Breit, T. M., ... Schumacher, B. (2009). Persistent transcription-blocking DNA lesions trigger somatic growth attenuation associated with longevity. Nature Cell Biology, 11(5), 604-615. DOI: 10.1038/ncb1866 [details]
  • Neerincx, P. B. T., Rauwerda, H., Nie, H., Groenen, M. A. M., Breit, T. M., & Leunissen, J. A. M. (2009). OligoRAP - an Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity. BMC Proceedings, 3, S4. DOI: 10.1186/1753-6561-3-S4-S4 [details] [PDF]
  • 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]
  • Wassink, I., van der Vet, P. E., Wolstencroft, K., Neerincx, P. B. T., Roos, M., Rauwerda, H., & Breit, T. M. (2009). Analysing scientific workflows: Why workflows not only connect web services. In L. J. Zhang (Ed.), Proceedings 2009 IEEE Congress on Services, SERVICES 2009 (part 1) (pp. 314-321). Los Alamitos, CA: IEEE Computer Society. [details]
  • Wassink, I., Rauwerda, H., Neerincx, P. B. T., van der Vet, P. E., Breit, T. M., Leunissen, J. A. M., & Nijholt, A. (2009). Using R in Taverna: RShell v1.2. BMC Research Notes, 2, 138. DOI: 10.1186/1756-0500-2-138 [details] [PDF]

2008

  • Aronica, E., Boer, K., Becker, A., Redeker, S., van Rijen, P. C., Wittink, F., ... Gorter, J. A. (2008). Gene expression profile analysis of epilepsy-associated gangliogliomas. Neuroscience, 151(1), 272-292. DOI: 10.1016/j.neuroscience.2007.10.036 [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]
  • Inda, M. A., van Batenburg, M. F., Roos, M., Belloum, A. S. Z., Vasunin, D., Wibisono, A., ... Breit, T. M. (2008). SigWin-detector: A Grid-enabled workflow for discovering enriched windows of genomic features related to DNA sequences. BMC Research Notes, 1, 63. DOI: 10.1186/1756-0500-1-63 [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]
  • Polstra, S., Pronk, T. E., Pimentel, A. D., & Breit, T. M. (2008). Towards design space exploration for biological systems. Journal of Computers, 3(2), 1-9. [details] [PDF]
  • 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]
  • Schumacher, B., van der Pluijm, I., Moorhouse, M. J., Kosteas, T., Robinson, A. R., Suh, Y., ... Garinis, G. A. (2008). Delayed and accelerated aging share common longevity assurance mechanisms. PLOS Genetics, 4(8), e1000161. DOI: 10.1371/journal.pgen.1000161 [details] [PDF]
  • Smit van Dixhoorn, M. G. A., Munir, R., Sussman, G., Stad, R., de Haan, M., van der Hoeven, T., ... Wadee, A. A. (2008). Gene expression profiling of suppressor mechanisms in tuberculosis. Molecular Immunology, 45(6), 1573-1586. DOI: 10.1016/j.molimm.2007.10.022 [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. 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]

2017

  • Rauwerda, J. (2017). Transcriptome dynamics in early zebrafish embryogenesis [details / files]
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