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Jan J. Bot

2011
Bot, J. J., and M. J. T. Reinders, "CytoscapeRPC: a plugin to create, modify and query Cytoscape networks from scripting languages", Bioinformatics (Oxford, England), vol. 27, issue 17, pp. 2451-2, 2011 Sep 1. Abstract
2010
de Ridder, J., A. Gerrits, J. J. Bot, G. de Haan, M. J. T. Reinders, and L. F. A. Wessels, "Inferring combinatorial association logic networks in multimodal genome-wide screens.", Bioinformatics (Oxford, England), vol. 26, issue 12, pp. i149-57, 2010 Jun 15. Abstract
Klijn, C. N., J. J. Bot, D. J. Adams, M. J. T. Reinders, L. F. A. Wessels, and J. Jonkers, "Identification of networks of co-occurring, tumor-related DNA copy number changes using a genome-wide scoring approach.", PLoS computational biology, vol. 6, issue 1, pp. e1000631, 2010 Jan. Abstract
2009
Kouteren, P., "Ibidas: to serve and to protect", M.Sc. Thesis: Delft University of Technology, pp. 32 pages, November 9, 2009.  Download: Kout09a.pdf (1.01 MB)
Li, Y., J. J. Bot, M. J. T. Reinders, and D. de Ridder, "A pathway approach to align regulatory-metabolic networks", 8th Annual International Conference on Computational Systems Bioinformatics, vol. 8: Life Sciences Society, pp. 177-188, August, 2009. Abstract  Download: 055Li.pdf (566.24 KB)
2008
Bot, J. J., Multi-Marker Analysis Pipeline for GWA SNP Studies: a Comparison of Methods and Datasets, , vol. M.Sc.: Delft University of Technology, pp. 14 pages (5 pages suplement), March 10, 2008.  Download: Bot08a.pdf (1.28 MB)
2007
de Ridder, J., J. Kool, A. G. Uren, J. J. Bot, L. F. A. Wessels, and M. J. T. Reinders, "Co-occurrence analysis of insertional mutagenesis data reveals cooperating oncogenes.", Bioinformatics, vol. 23, no. 13, pp. i133-41, July, 2007. Abstract
Bot, J. J., "Text-mining in the Life-Sciences, an Exploration", Research Assignment, 2007.  Download: Research Assignment Jan Bot.pdf (176.85 KB)
de Ridder, J., J. Kool, A. G. Uren, J. J. Bot, L. F. A. Wessels, and M. J. T. Reinders, "Discovering cooperating oncogenes by statistical co-occurrence analysis.", Proceedings of the Thirteenth annual conference of the Advanced School for Computing and Imaging, 2007.