Publications

2010

• 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.
• 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.
• 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.
• 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.

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.
• 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.
• 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.
• 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.
• 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.

2008

• R. Mirabella, H. Rauwerda, E.A. Struys, C. Jakobs, C. Triantaphylidès, M.A. Haring & R.C. Schuurink (2008). The Arabidopsis her1 mutant implicates GABA in E-2-hexenal responsiveness. Plant Journal, 53(2), 197-213.
• 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.
• 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.

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.