Photographer: onbekend

dr. T.M. (Timo) Breit


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

MAD + RB&AB

I am heading the genome technology and bioinformatics expertise centre of the FNWI named "MAD:Dutch Genomics Service & Support Provider)" and the research group "RNA Biology and Applied Bioinformatics (RB&AB)" .  The group consists of about 10 multidiciplinary experts in the fields of microarray, next-generation sequencing, bioinformatics and informatics. For detailed information see our websites: www.dutchgenomics.nl and www.RNAbiology.nl.

Service: The MAD is a genomics technology centre with two Affymetrix Genechip® platforms and IonProton next-generation sequencing platform. 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 genomics experiment design;
  2. Support en execution of genomics experiments;
  3. Comprehensive genomics 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, next-generations sequencing or bioinformatics partner for your project, please contact me (t.m.breit -at- uva.nl).
 

With respect to RB&AB: RNA is increasingly recognized to have more functions than just being a “messenger” between DNA and proteins. New forms of RNA and RNA functions are continuously discovered, such as small regulatory microRNAs. Our research aims to understand transcriptome dynamics plus the role of RNA as a carrier of genetic information. As such, we have a keen interest in so-called ‘non-coding RNA’, ‘maternal RNA’ as well as ‘cell-free RNA’. We apply an multidisciplinary omics approach that includes a large bioinformatics component. Therefore, our research also includes applied bioinformatics with emphasis on ‘design-for-experimentation’ and development of algorithms to optimally utilize next-generation RNA sequencing data. The RNA Biology & Applied Bioinformatics research group (RB&AB) is part of the University of Amsterdam.

Research lines RNA Biology:

 

 

2017

2016

2015

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] 

2013

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] 
  • 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] 
  • 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

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] 
  • 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] 
  • 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] 
  • 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] 

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] 
  • 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] 
  • 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] 

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] 
  • 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] 
  • 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] 
  • 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] 
  • 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] 
  • 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] 
  • 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] 
  • 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] 

Talk / presentation

  • Breit, T.M. (invited speaker) (9-11-2016): Muskusratten opsporen met DNA; Oftewel CSI in de Polder, Hoogheemraadschap Hollands Noorderkwartier.
  • Breit, T.M. (invited speaker) (12-4-2016): Genomics Life-Sciences, RNA Biology & Applied Bioinformatics (SILS, FNWI).
  • Breit, T.M. (invited speaker) (4-4-2016): 4 plant breeding projects, Virtual Lab for Plant Breeding (VLPB).
  • Breit, T.M. (invited speaker) (31-3-2016): Genomische technieken binnen handbereik., RNA Biology & Applied Bioinformatics (SILS, FNWI).

2017

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.
  • Universiteit Leiden*
    Expert adviseur
  • Vereniging VLPB
    Bestuurslid

edit contact information edit tabs