Transcriptome Dynamics

My research focusses on transcriptome dynamics in early zebrafish embryogenesis. Surprisingly little is known about the spatio-temporal dynamics of the transcriptome and about the variation of the transcriptome between and within individuals. A deeper understanding of this dynamics is important because with it we expect to be able to understand regulatory relationships within the genome-wide system in much more detail; for example, by choosing a sampling frequency tailored to the process under study we expect to be able to de-confound the sometimes massive transcriptional responses seen in experiments sampled at commonly used sampling intervals. And, we hope to gain a better insight in the way living systems achieve robustness; how similar phenotypical endpoints are reached given the variation between these biological systems. Also regarding robustness and transcriptome dynamics we want to acquire a better understanding on the question if transcriptional responses always unfold via the same route or if alternative routes are available and if so, how these different paths depend on genotype and environmental conditions.

Publications:

1. Rauwerda,H., Pagano,J.F.B., de Leeuw,W.C., Ensink,W., Nehrdich,U., de Jong,M., Jonker,M., Spaink,H.P. and 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.
2. Locati, M. D., Pagano, J. F. B., Ensink, W. A., van Olst, M., van Leeuwen, S., Nehrdich, U., Rauwerda H.,..., 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 
3. Pagano JFB, Rauwerda H, de Leeuw WC, Wackers P, de Jong M, Ensink W, Dekker R, Nehrdich U, Spaink HP, Jonker M, et al. 2016. Transcriptome data on maternal RNA of 24 individual zebrafish eggs from five sibling mothers. Data Br 8: 69–72.
4. Han Rauwerda, Paul Wackers, Johanna F. B. Pagano, Mark de Jong, Wim Ensink, Rob Dekker, Ulrike Nehrdich, Herman P. Spaink, Martijs Jonker, Timo M. Breit, Mother-Specific Signature in the Maternal Transcriptome Composition of Mature, Unfertilized Zebrafish Eggs. PLoS One 11, e0147151 (2016).
5. Locati M, Terpstra I, de Leeuw W, Kuzak, M, Rauwerda H, Ensink W, van Leeuwen S, Nehrdich U, Spaink H, Jonker M, Breit TM, Dekker R, Improving small RNA-seq by using a Synthetic Spike-in Set for Size-Range Quality Control together with a Set for Data Normalization. NAR 2015 Aug 18;43(14):e89 
6. O. Bruning, W. Rodenburg, P.F.K. Wackers, C. van Oostrom, M.J. Jonker, R.J. Dekker, H. Rauwerda, W.A. Ensink, A de Vries & T.M. Breit (2016). Confounding Factors in the Transcriptome Analysis of an In-Vivo Exposure Experiment.  PLoS One, 11 (1):e0145252. doi: 10.1371/journal.pone.0145252
7. Bruning O, Rauwerda H, Dekker RJ, de Leeuw WC, Wackers PFK, Ensink WA, Jonker MJ, Breit TM. Valuable lessons-learned in transcriptomics experimentation. Transcription 2015 May 27;6(3):51-5.
8. Mirabella R, Rauwerda H, Allmann SA, Spyropoulou E, Vries M, Boersma M, Breit TM; Haring M, Schuurink RC. WRKY40 and WRKY6 act downstream of the green leaf volatile E-2-hexenal in Arabidopsis. Plant J. 2015 Sep;83(6):1082-96.
9. Bruning O, Rodenburg W, van Oostrum C, Jonker MJ, de Jong M, Dekker R, Rauwerda J, Ensink W, de Vries A, Breit TM A range finding protocol to support design for transcriptomics experimentation: examples of in-vitro and in-vivo murine UV exposure. Plos One 2014 May 13;9(5) 
10. Aflitos, S., & the 150 Tomato Genome Consortium Exploring genetic variation in the tomato Solanum Lycopersicon clade by whole-genome sequencing. 2014 Plant J. 2014 Oct;80(1):136-48
11. Jonker MJ, de Leeuw Wim, Marinković M, Wittink FRA, Rauwerda H, Bruning O, Ensink WA, Fluit AC, Boel ECH, de Jong M, Timo M. Breit Absence/presence calling in microarray-based CGH experiments with non-model organisms. Nucleic Acids Res. 2014;42(11)
12. Collaborative e-Science experiments: from scientific workflow to knowledge sharing, Adam Belloum, Marcia A Inda, Dmitry Vasunin, Vladimir Korkhov, Zhiming Zhao, Han Rauwerda , T.M. Breit, Marian Bubak, IEEE Internet Computing   IC-2010-07-009, 2011
13. Serious complications in gene-expression studies with stress perturbation: an example with UV-exposed p53-mutant mouse embryonic fibroblasts,Oskar Bruning, Xiaolian Yuan, Wendy Rodenburg, Wendy Bruins, Conny T. van Oostrom, Han Rauwerda , Floyd R.A. Wittink, Martijs J. Jonker, Annemieke de Vries, and Timo M. Breit, Transcriptome, in press.
14. Oliver W. Stockhammer, Han Rauwerda , Floyd R. Wittink, Timo M. Breit, Annemarie H. Meijer, Herman P. Spaink,Transcriptome analysis of Traf6 function in the innate immune response of zebrafish embryos, Molecular Immunology, in press.
15. Rauwerda, H. , deJong, M.,de Leeuw, W. C., Spaink, H. P., Breit, T. M., Integrating heterogeneous sequence information for transcriptome-wide microarray design; a Zebrafish example, BMC Research Notes 2010, 3(1):192, July 2010.
16. Ingo Wassink, Matthijs Ooms, Pieter Neerincx, Gerrit van der Veer, Han Rauwerda , Jack A.M. Leunissen, Timo M. Breit, Anton Nijholt, Paul van der Vet, e-BioFlow: Improving Practical Use of Workflow Systems in Bioinformatics, International Conference on Information Technology in Bio- and Medical Informatics ITBAM´10, August 30 - September 3, 2010 Bilbao, Spain.
17. Mark de Jong, Han Rauwerda , Oskar Bruning, Jurgo Verkooijen, Herman P. Spaink and Timo M. Breit, RNA isolation method for single embryo transcriptome analysis in zebrafish, BMC Research Notes 2010, 3:73, 16 March2010.
18. Han Rauwerda , Ingo Wassink, Pieter B.T. Neerincx, Paul E. van der Vet, Timo M. Breit, Jack A.M. Leunissen and Anton Nijholt, Using R in Taverna: RShell v1.2, BMC Research Notes , 2:138, 16 July 2009
19. Neerincx P, Rauwerda H , Nie H, Groenen M, Breit T, Leunissen J: OligoRAP - an Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity. BMC Proceedings 2009, 3:S4.
20. W. Fikkert, P. van der Vet, H. Rauwerda, T. Breit and A. Nijholt, Gestures to Intuitively Control Large Displays, in: Advances in Gesture-Based Human-Computer Interaction and Simulation, M. Sales Dias, S. Gibet, M. Wanderley (eds.) , revised selected papers, pp. 199-205, Springer Berlin / Heidelberg, Lecture Notes inComputer Science, vol 5085/2009, ISBN 978-3-540-92864-5, 2009.
21. Rauwerda H , de Leeuw W, Jonker M, Breit T: Salvaging Affymetrix probes after probe-level re-annotation. BMC Res Notes 2008, 1:66.
22. Ingo Wassink, Han Rauwerda , Paul van der Vet, Timo Breit, and Anton Nijholt, E-BioFlow: Different Perspectives on ScientificWorkflows, Bioinformatics Research and Development, BIRD 2008 , 07-09 Jul 2008 , Vienna, Austria . pp. 243-257 . Communications in Computer and Information Science 13 ( XXI ). Springer Verlag . ISSN 1865-0929 ISBN 978-3-540-70598-7.
23. Bruins W, Bruning O, Jonker MJ, Zwart E, van der Hoeven TV, Pennings JL, Rauwerda H , de Vries A, Breit TM. 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 embryonicfibroblasts. Mol Cell Biol . 2008 Mar; 28 ( 6 ): 1974-87 .
24. Han Rauwerda , Wim C. de Leeuw, Jorrit Adriaanse , Maurice Bouwhuis, Paul van der Vet , Timo M. Breit, The Role of e-BioLabs in a Life Sciences Collaborative Working Environment, Proceedings of eChallenges2007 , The Hague 2007.
25. Smit van Dixhoorn, M.G., Munir, R., Sussman, G., Stad, R., de Haan, M., van der Hoeven, T., Rauwerda, H ., Breit, T.M., Thallinger, G.G. and Wadee, A.A. Gene expression profiling of suppressor mechanisms in tuberculosis,MolImmunol. 2007
26. Mirabella, R, Rauwerda, H , Struys, E. A, Jakobs, C, Triantaphylides, C, Haring, M. A.Schuurink, R. C, The Arabidopsis her1 mutant implicates GABA in E-2-hexenal responsiveness, Plant J, 2007.
27. J.A. Gorter, E.A. van Vliet, H. Rauwerda , T.M. Breit, R.Stad, L.van Schaik, E. Vreugdenhil, S. Redeker, E. Hendriksen, E. Aronica, F.H. Lopes da Silva, W.J. Wadman. Dynamic changes of proteases and protease inhibitors revealed by micorarray analysis in CA3 and entorhinal cortex during epileptogenesis in the rat, Epilepsia , 2007
28. B. J. Keijser, A. Ter Beek, H. Rauwerda , F. Schuren, R. Montijn, H. van der Spek, and S. Brul, Analysis of Temporal Gene Expression during Bacillus subtilis Spore Germination and Outgrowth, J Bacteriol , vol.189, pp. 3624-34, 2007.
29. Rauwerda H , Roos M, Hertzberger BO, Breit TM: The promise of a virtual lab in drug discovery. Drug Discov Today 2006, 11(5-6):228-236.
30.  J.A. Gorter, E. A. van Vliet, E. Aronica, T. Breit, H. Rauwerda , F. H. Lopes da Silva, and W. J. Wadman, Potential new antiepileptogenic targets indicated by microarray analysis in a rat model fortemporal lobe epilepsy, J Neurosci , vol. 26, pp. 11083-110, 2006.
31. van der Vet, P.E., Kulyk, O., Wassink, I., Fikkert, F.W., Rauwerda, H., van Dijk, E.M.A.G., van der Veer, G., Breit, T., Nijholt, A.: Smart Environments for Collaborative Design, Implementation,and Interpretation of Scientific Experiments, In: Proceedings of the  International Workshop on AI for Human Computing Hyderabad, India, T. Huang, A. Nijholt, M. Pantic and A. Pentland (eds.), Twentieth International Joint Conference on Artificial Intelligence (2007), 79-86
32. Rauwerda, H. , G.J. Roerink & Z. Su ; Estimation of evaporative fractions by the use of vegetation and soil component temperatures determined by means of dual-looking remote sensing; Alterra Report, 2002