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Publications

  1. Rauwerda H, de Jong M, de Leeuw WC, Spaink HP, Breit TM Integrating heterogeneous sequence information for transcriptome-wide microarray design; a Zebrafish example BMC Res Notes. 2010 Jul 13;3:192


  2. Bosnacki D, Pronk TE, de Vink EP. In Silico Modelling and Analysis of Ribosome Kinetics and aa-tRNA Competition. Lecture Notes in Bioinformatics: Transactions on Computational System Biology XI. Priami C, Back R-J, Petre I (eds.) Springer Verlag. 2009, pages 69-89
  3. de Leeuw WC, Rauwerda H, Inda MA, Bruning O, Breit TM. SigWinR; the SigWin-detector updated and ported to R. BMC Res Notes 2009 Oct 6;2(1):205
  4. Pronk TE, During HJ, Schieving F, Werger MJA Diversity by Temporal Oscillations in Plant Communities with a Differential Timing of Reproduction In: Game Theory: Strategies, Equilibria, and Theorems. Ingrid N. Haugen and Anna S. Nilsen (editors) 2009 pp. 297-317
  5. H Rauwerda, I Wassink, PBT Neerincx, PE van der Vet, TM Breit, JAM Leunissen and A Nijholt Using R in Taverna: RShell v1.2 BMC Res Notes 2009 Jul 16;2:138
  6. PBT Neerincx, H Rauwerda, H Nie, MAM Groenen, TM Breit, JAM Leunissen OligoRAP - an Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity. BMC Proc. 2009 Jul 16;3 Suppl 4:S4
  7. I. Wassink, K. Wolstencroft, M. Roos, P.B.T. Neerincx, P. van der Vet, H. Rauwerda, T. Breit Analysing scientific workflows: why workflows not only connect web services. Workshop on Scientific Workflows SWF2009 2009 accepted
  8. 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 in Computer Science2009 accepted
  9. Wassink I, Rauwerda H, van der Vet P, Breit TM, Nijholt A. E-BioFlow: Different Perspectives on Scientific Workows. Communications in Computer and Information Science 2009 Accepted


  10. de Leeuw WC, Rauwerda H, Jonker MJ, Breit TM. Salvaging Affymetrix probes after probe-level re-annotation. BMC Res Notes 2008 Aug 19;1:66-71 Suppl.Information
  11. Inda MA, van Batenburg MF, Roos M, Belloum AS, Vasunin D, Wibisono A, van Kampen AH, Breit TM. SigWin-detector: a Grid-enabled workflow for discovering enriched windows of genomic features related to DNA sequences. BMC Res. Notes 2008 Aug 8;1:63-73
  12. D. Bosnacki, T.E. Pronk, E.P. de Vink, In Silico Modelling and Analysis of Ribosome Kinetics and aa-tRNA Competition. Proc. of COMPMOD 2008, Workshop on Computational Models for Cell Processes, satelite event of FM 2008, Turku, Finland, R.-J. Back and I. Petre (eds.), Turku Centre for Computer Science 2008 pages 23-38
  13. Wassink I, Rauwerda H, van der Vet P, Breit TM, Nijholt A. E-BioFlow: Different Perspectives on Scientific Workflows. Bioinformatics Research and Development, BIRD 2008, Vienna, Austria. Communications in Computer and Information Science 13 (XXI). Springer Verlag. ISSN 1865-0929 ISBN 978-3-540-70598-7 07-09 Jul 2008 pp. 243-257
  14. Pronk TE, Polstra S., Pimentel AD, Breit TM. Towards Design Space Exploration for Biological Systems. Journal of Computers 2008 3;1-9


  15. Pronk TE, Pimentel AD, Roos M, Breit TM. Taking the example of computer systems engineering for the analysis of biological cell systems. BioSystems 2007 Nov-Dec;90(3):623-635
  16. van der Vet P, Kulyk O, Wassink I, Fikkert FW, Rauwerda H, van Dijk EMAG, van der Veer G, Breit TM, Nijholt A. Smart environments for collaborative design, implementation and interpretation of scientific experiments. In: Proc. Int. Workshop on AI for Human Computing (T. Huang, A. Nijholt, M. Pantic and A. Pentland, Eds.), Twentieth International Joint Conference on Artificial Intelligence, Hyderabad, India 2007 pp. 79-86
  17. Post LJG, Roos M, Marshall MS, van Driel R, Breit TM. The semantic web Approach applied to integrative bioinformatics experimentation: a biological use case with genomics data. Bioinformatics 2007 Nov 15;23(22):3080-3087
  18. Rauwerda H, de Leeuw WC, Adriaanse J, Bouwhuis M, van der Vet P, Breit TM. The role of e-BioLabs in a life sciences collaborative working environment. The Hague, the Netherlands. Published in Expanding the Knowledge Enconomy: Issues, Applications, Case Studies, vol. 4, P. Cunningham and M. Cunningham, Eds.: IOS, Amsterdam 2007 pp. 866-873
  19. Pronk TE, de Vink E. Bosnacki D, Breit TM. Stochastic modeling of codon bias with PRISM. Proceedings of the 3rd international workshop on Methods and Tools for Coordinating, Distributed and Mobile Systems MTCoord 2007, Paphos, June 4, 2007, I. Linden and C. Talcott (eds.), Computer Science Department, University of Cyprus, Nicosia 2007 15 pages
  20. Korkhov V, Vasunin D, Wibisono A, Belloum A, Inda MA, Roos M, Breit TM. VLAM-G: Interactive dataflow driven workflow engine for Grid enabled resources. Scientific programming 2007 15(3); 173-188
  21. Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H, Doherty D, Forsberg K, Gao Y, Kashyap V, Kinoshita J, Luciano J, Marshall MS, Ogbuji C, Rees J, Stephens S, Wong G, Wu E, Zaccagnini D, Hongsermeier T, Neumann E, Herman I, Cheung KH. Advancing Translational Research with the Semantic Web. BMC Bioinformatics 2007 Vol. 8, suppl.2
  22. Kashyap V, Cheung KH, Doherty D, Samwald M, Marshall MS, Luciano J, Stephens S, Herman I, Hookway R. An ontology based approach for data integration; An application in Biomedical Research. Book Chapter in Cardoso, J., Hepp, M., Lytras, M. (Eds.) "Real-world Applications of Semantic Web Technology and Ontologies". Springer 2007 Hardcover ISBN-10: 0-387-48530-9, ISBN-13: 978-0-387-48530-0
  23. Pronk TE, Polstra S, Pimentel AD, Breit TM. Evaluating the design of biological cells using a computer workbench. Proceedings of the IEEE 40th Annual Simulation Symposium (ANSS) 2007 pages 88-98


  24. Inda MA, Belloum ASZ, Roos M, Vasunin D, de Laat C, Hertzberger LO, Breit TM. Interactive Workflows in a Virtual Laboratory for e-Bioscience: the SigWin-Detector Tool for Gene Expression Analysis. Proceedings of the second IEEE International Conference on e-Science and Grid Computing (e-Science 2006 Amsterdam) 2006 Dec. 19
    http://staff.science.uva.nl/~inda/SigWin-detector.html
  25. Marshall MS, Post L, Roos M, Breit TM. Using semantic web tools to integrate experimental measurement data on our own terms. Conference: International Workshop on Knowledge Systems in Bioinformatics (KSinBIT'06), On the Move to Meaningful Internet Systems Conference 2006 (OTM2006), Montpellier, France
  26. Rauwerda H, Roos M, Hertzberger LO, Breit TM. The promise of a virtual lab in drug discovery. Drug Discov. Today 2006 Mar;11(5-6):228-236. Review


  27. Katrenko S, Marshall MS, Roos M, Adriaans P. Learning Biological Interactions from Medline Abstracts. Conference: Learning Language in Logic (LLL05) Workshop 2005 ICML05, Bonn, Germany


  28. Roos M, Jansen MG, Marshall MS, Breit TM. Future application of ontologies in e-Bioscience. W3C Workshop on Semantic Web for Life Sciences 2004 Position paper


  29. Kaletas EC, Afsarmanesh H, Breit TM, Hertzberger LO, "EXPRESSIVE - A Database for Micro-Array Gene Expression Studies". University of Amsterdam, Informatics Institute, Amsterdam 2001 Technical report CS-2001-02