Faculty of Science
J. Rauwerda
drs. J. (Han) Rauwerda
Swammerdam Institute for Life Sciences University of Amsterdam


POSTBUS 94215
1090 GE Amsterdam

Telephone
0205257201

http://home.medewerker.uva.nl/j.rauwerda/
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Integrative Bioinformatics Research in the e-BioScience Laboratory

I am working in the Integrative Bioinformatics unit on the VL-e and BioAssist projects. Currently my main focus is on setting up an  e-BioScience Laboratory (e-BioLab). In the e-BioLab, scientist should be able to experiment with and present different views on their complex multi-dimensional datasets in a multidisciplinary approach. The idea is to make the domain interaction interactive with a (5x4) tiled display for easy representation and tools and methods to enable multidisciplinary (remote) collaboration. At this point we have ensured substantial technical support from different collaborators (SARA, IvI, NIKHEF , UT ) and biological use cases (SILS, AMC, RIVM, Unilever) to set-up and test the usability of the e-BioLab concept. The concept of an e-BioLab initself will be a topic of research.Basedon ourcurrent knowledge and examples worldwide, we will create a prototype e-BioLab that will be tested and improved over time. Services that realize ideas put forward in research into the e-BioLab concept and that specifically can be used in the multimodal architecture of the e-BioLab have yet to be build.  The plans for an e-BioLab are primarily drawn up from the viewpoint of e-BioSciences, since we will create the lab to enable interaction of the life sciences domain with the VL-e. However, we foresee that the newly build e-BioLab software will be re-usable in many other scientific disciplines, such as geo sciences and particle physics.

Publications:

  1. 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
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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
  8. 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.
  9. 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.
  10. Rauwerda H, de Leeuw W, Jonker M, Breit T: Salvaging Affymetrix probes after probe-level re-annotation. BMC Res Notes 2008, 1:66.
  11. 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.
  12. 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.
  13. 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 eChallenges 2007, The Hague 2007.
  14. 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
  15. 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.
  16. 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
  17. 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.
  18. 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.
  19.  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.
  20. 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
  21. 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