Publications

2012

• K.I. Roschmann, A.M. van Kuijen, S. Luiten, M.J. Jonker, T.M. Breit, W.J. Fokkens, A. Petersen & C.M. van Drunen (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), 413-21.
• J.V. Chikhovskaya, M.J. Jonker, A. Meissner, T.M. Breit, S. Repping & A.M.M. van Pelt (2012). Human testis-derived embryonic stem cell-like cells are not pluripotent, but possess potential of mesenchymal progenitors. Human Reproduction, 27(1), 210-221.
• M. Marinkovic, W.C. de Leeuw, M. de Jong, W. Admiraal, T.M. Breit, M.H.S. Kraak & M.J. Jonker (2012). Sequencing the Chironomus riparius transcriptome to compare the sensitivity of gene expression and life-cycle endpoints to toxicant exposure. In 6th SETAC World Congress/SETAC Europe 22nd Annual Meeting, Berlin, Germany, May 2012.

2011

• X. Yuan, M.J. Jonker, J. de Wilde, A. Verhoef, F.R.A. Wittink, J. van Benthem, J.G. Bessems, B.C. Hakkert, R.V. Kuiper, H. van Steeg, T.M. Breit & M. Luijten (2011). Finding maximal transcriptome differences between reprotoxic and non-reprotoxic phthalate responses in rat testis. J Appl Toxicol, 31(5), 421-430.
• K.I.L. Röschmann, S. Luiten, M.J. Jonker, T.M. Breit, W.J. Fokkens, A. Petersen & C.M. van Drunen (2011). Timothy grass pollen extract-induced gene expression and signalling pathways in airway epithelial cells. Clinical and Experimental Allergy, 41(6), 830-841.
• J.L.A. Pennings, W. Rodenburg, S. Imholz, M.P.H. Koster, C.T.M. van Oostrom, T.M. Breit, P.C.J.I. Schielen & A. de Vries (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.
• T.B.M. Hakvoort, P.D. Moerland, R. Frijters, A. Sokolović, W.T. Labruyère, J.L.M. Vermeulen, E. Ver Loren van Themaat, T.M. Breit, F.R.A. Wittink, A.H.C. van Kampen, A.J. Verhoeven, W.H. Lamers & M. Sokolović (2011). Interorgan coordination of the murine adaptive response to fasting. The Journal of Biological Chemistry, 286(18), 16332-16343.
• O. Bruning, W Rodenburg, Teodora Radonic, A.H. Zwinderman, A de Vries, T.M. Breit & H.M. de Jong (2011). RNA isolation for transcriptomics of human and mouse small skin biopsies. BMC Research Notes, 4(1), 438.
• J.P.M. Melis, E.M. Hoogervorst, C.T.M. van Oostrom, E. Zwart, T.M. Breit, J.L.A. Pennings, A de Vries & H. van Steeg (2011). Genotoxic exposure: novel cause of selection for a functional DeltaN-p53 isoform. Oncogene, 30(15), 1764-1772.
• J.P.M. Melis, E.M. Hoogervorst, C.T.M. van Oostrom, E. Zwart, T.M. Breit, J.L.A. Pennings, A. de Vries & H. van Steeg (2011). Genotoxic exposure: novel cause of selection for a functional ΔN-p53 isoform. Oncogene, 30(15), 1764-1772.
• C. de Bekker, O. Bruning, M.J. Jonker, T.M. Breit & H.A.B. Wösten (2011). Single cell transcriptomics of neighboring hyphae of Aspergillus niger. Genome Biology, 12(8), R71.

2010

• K. Boer, P.B. Crino, J.A. Gorter, M. Nellist, F.E. Jansen, W.G.M. Spliet, P.C. van Rijen, F.R.A. Wittink, T.M. Breit, D. Troost, W.J. Wadman & E. Aronica (2010). Gene expression analysis of tuberous sclerosis complex cortical tubers reveals increased expression of adhesion and inflammatory factors. Brain pathology, 20(4), 704-719.
• O. Bruning, X. Yuan, W. Rodenburg, W. Bruins, C.T. van Oostrom, H. Rauwerda, F.R.A. Wittink, M.J. Jonker, A. de Vries & T.M. Breit (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.
• N.J.P. ten Broeke-Smits, T.E. Pronk, I. Jongerius, O. Bruning, F.R. Wittink, T.M. Breit, J.A.G. van Strijp, A.C. Fluit & C.H.E. Boel (2010). Operon structure of Staphylococcus aureus. Nucleic Acids Research, 38(10), 3263-3274.
• I. Wassink, M. Ooms, P. Neerincx, G. van der Veer, H. Rauwerda, J.A.M. Leunissen, T.M. Breit, A. Nijholt & P. van der Vet (2010). e-BioFlow: improving practical use of workflow systems in bioinformatics. In S. Khuri, L. Lhotská & N. Pisanti (Eds.), Information Technology in Bio- and Medical Informatics (ITBAM 2010) Vol. 6266. Lecture Notes in Computer Science (pp. 1-15). Berlin: Springer.
• O.W. Stockhammer, H. Rauwerda, F.R. Wittink, T.M. Breit, A.H. Meijer & H.P. Spaink (2010). Transcriptome analysis of Traf6 function in the innate immune response of zebrafish embryos. MOL IMMUNOL, 48(1-3), 179-190.
• M. de Jong, H. Rauwerda, O. Bruning, J. Verkooijen, H.P. Spaink & T.M. Breit (2010). RNA isolation method for single embryo transcriptome analysis in zebrafish. BMC Research Notes, 3(1), 73.
• J. Brunner, F.R.A. Wittink, M.J. Jonker, M. de Jong, T.M. Breit, M.L. Laine, J.J. de Soet & W. Crielaard (2010). The core genome of the anaerobic oral pathogenic bacterium Porphyromonas gingivalis. BMC Microbiology, 10, 252.
• H. Rauwerda, M. de Jong, W.C. de Leeuw, H.P. Spaink & T.M. Breit (2010). Integrating heterogeneous sequence information for transcriptome-wide microarray design; a Zebrafish example. BMC Research Notes, 3, 192.

2009

• W. Fikkert, P. van der Vet, H. Rauwerda, T. Breit & A. Nijholt (2009). Gestures to intuitively control large displays. 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 (Lecture notes in artificial intelligence, 5085) (pp. 199-204). Berlin: Springer.
• P.B.T. Neerincx, H. Rauwerda, H. Nie, M.A.M. Groenen, T.M. Breit & J.A.M. Leunissen (2009). OligoRAP – an Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity. In D.-J. de Koning (Ed.), EADGENE and SABRE Post-analyses Workshop: Proceedings Vol. 3. BMC Proceedings (pp. S4). London: BioMed Central.
• I. Wassink, H. Rauwerda, P.B.T. Neerincx, P.E. van der Vet, T.M. Breit, J.A.M. Leunissen & A. Nijholt (2009). Using R in Taverna: RShell v1.2. BMC Research Notes, 2, 138.
• I. Wassink, P.E. van der Vet, K. Wolstencroft, P.B.T. Neerincx, M. Roos, H. Rauwerda & T.M. Breit (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.
• S.J.C.M. Oomes, M.J. Jonker, F.R.A. Wittink, J.O. Hehenkamp, T.M. Breit & S. Brul (2009). The effect of calcium on the transcriptome of sporulating B. subtilis cells. International Journal of Food Microbiology, 133(3), 234-242.
• M.J. Jonker, O. Bruning, M. van Iterson, M.M. Schaap, T.V. van der Hoeven, H. Vrieling, R.B. Beems, A. de Vries, H. van Steeg, T.M. Breit & M. Luijten (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.
• W. Fikkert, P. van der Vet, H. Rauwerda, T. Breit & A. Nijholt (2009). Gestures to intuitively control large displays. In M.S. 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 Vol. 5085. Lecture Notes in Computer Science (pp. 199-204). Berlin: Springer.
• G.A. Garinis, L.M. Uittenboogaard, H. Stachelscheid, M. Fousteri, W. van IJcken, T.M. Breit, H. van Steeg, L.H.F. Mullenders, G.T.J. van der Horst, J.C. Brüning, C.M. Niessen, J.H.J. Hoeijmakers & B. Schumacher (2009). Persistent transcription-blocking DNA lesions trigger somatic growth attenuation associated with longevity. Nature Cell Biology, 11(5), 604-615.
• W.C. de Leeuw, H. Rauwerda, M.A. Inda, O. Bruning & T.M. Breit (2009). SigWinR; the SigWin-detector updated and ported to R. BMC Research Notes, 2(1), 205.

2008

• B. Schumacher, I. van der Pluijm, M.J. Moorhouse, T. Kosteas, A.R. Robinson, Y. Suh, T.M. Breit, H. van Steeg, L.J. Niedernhofer, W. van IJcken, A. Bartke, S.R. Spindler, J.H.J. Hoeijmakers, G.T.J. van der Horst & G.A. Garinis (2008). Delayed and accelerated aging share common longevity assurance mechanisms. PLOS Genetics, 4(8), e1000161.
• K.A. Baken, J.L.A. Pennings, M.J. Jonker, M.M. Schaap, A. de Vries, H. van Steeg, T.M. Breit & H. van Loveren (2008). Overlapping gene expression profiles of model compounds provide opportunities for immunotoxicity screening. Toxicology and Applied Pharmacology, 226(1), 46-59.
• S.B.I. Luppens, D. Kara, L. Bandounas, M.J. Jonker, F.R.A. Wittink, O. Bruning, T.M. Breit, J.M. ten Cate & W. Crielaard (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.
• S. Polstra, T.E. Pronk, A.D. Pimentel & T.M. Breit (2008). Towards design space exploration for biological systems. Journal of Computers, 3(2), 1-9.
• A.B. Vroling, M.J. Jonker, S. Luiten, T.M. Breit, W.J. Fokkens & C.M. van Drunen (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.
• M.A. Inda, M.F. van Batenburg, M. Roos, A.S.Z. Belloum, D. Vasunin, A. Wibisono, A.H.C. van Kampen & T.M. Breit (2008). SigWin-detector: A Grid-enabled workflow for discovering enriched windows of genomic features related to DNA sequences. BMC Research Notes, 1, 63.
• O. Bruning, W. Bruins, M.J. Jonker, E. Zwart, T.V. van der Hoeven, J.L.A. Pennings, H. Rauwerda, A. de Vries & T.M. Breit (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.
• A.B. Vroling, M.J. Jonker, T.M. Breit, W.J. Fokkens & C.M. van Drunen (2008). Comparison of expression profiles induced by dust mite in airway epithelia reveals a common pathway. Allergy, 63(4), 461-467.
• M.G.A. Smit van Dixhoorn, R. Munir, G. Sussman, R. Stad, M. de Haan, T. van der Hoeven, H. Rauwerda, T.M. Breit, G.G. Thallinger & A.A. Wadee (2008). Gene expression profiling of suppressor mechanisms in tuberculosis. MOL IMMUNOL, 45(6), 1573-1586.
• W.C. de Leeuw, H. Rauwerda, M.J. Jonker & T.M. Breit (2008). Salvaging Affymetrix probes after probe-level re-annotation. BMC Research Notes, 1, 66.
• E. Aronica, K. Boer, A. Becker, S. Redeker, P.C. van Rijen, F. Wittink, T. Breit, W.G.M. Spliet, W.J. Wadman, F.H. Lopes da Silva, D. Troost & J.A. Gorter (2008). Gene expression profile analysis of epilepsy-associated gangliogliomas. Neuroscience, 151(1), 272-292.

2011

• A.S.Z. Belloum, M. A. Inda, D. Vasunin, V. Korkhov, Z. Zhao, H. Rauwerda, T. Breit, M.T. Bubak & B. Hertzberger (2011). Collaborative e-Science Experiments and Scientific Workflows. IEEE Internet Computing, 15(4), 39-47.