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Jeroen de Ridder

In Press
de Ridder, D., J. de Ridder, and M. J. T. Reinders, "Pattern recognition in bioinformatics", Briefings in Bioinformatics, In Press.
2013
Babaei, S., M. Hulsman, M. J. T. Reinders, and J. de Ridder, "Detecting recurrent gene mutation in interaction network context using multi-scale graph diffusion.", BMC Bioinformatics, vol. 14, issue 1, pp. 29, 2013 Jan 23. Abstract
2012
Pérez-Mancera, P. A., A. G. Rust, L. van der Weyden, G. Kristiansen, A. Li, A. L. Sarver, K. A. T. Silverstein, R. Grützmann, D. Aust, P. Rümmele, et al., "The deubiquitinase USP9X suppresses pancreatic ductal adenocarcinoma.", Nature, vol. 486, issue 7402, pp. 266-270, 2012. Abstract
2011
de Jong, J., J. de Ridder, L. van der Weyden, N. Sun, M. J. G. van Uitert, A. Berns, M. van Lohuizen, J. Jonkers, D. J. Adams, and L. F. A. Wessels, "Computational identification of insertional mutagenesis targets for cancer gene discovery.", Nucleic acids research, vol. 39, issue 15, pp. e105, 2011 Aug. Abstract
March, N. H., A. G. Rust, N. A. Wright, J. J. ten Hoeve, J. de Ridder, M. Eldridge, L. van der Weyden, A. Berns, J. Gadiot, A. G. Uren, et al., "Insertional mutagenesis identifies multiple networks of cooperating genes driving intestinal tumorigenesis.", Nature genetics, vol. 43, issue 12, pp. 1202-9, 2011. Abstract
Babaei, S., E. B. van den Akker, J. de Ridder, and M. J. T. Reinders, "Integrating Protein Family Sequence Similarities with Gene Expression to Find Signature Gene Networks in Breast Cancer Metastasis", Pattern Recognition in Bioinformatics: Springer, pp. 247–259, 2011.
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
Kool, J., A. G. Uren, C. P. Martins, D. Sie, J. de Ridder, G. Turner, M. J. G. van Uitert, K. Matentzoglu, W. Lagcher, P. Krimpenfort, et al., "Insertional mutagenesis in mice deficient for p15Ink4b, p16Ink4a, p21Cip1, and p27Kip1 reveals cancer gene interactions and correlations with tumor phenotypes.", Cancer research, vol. 70, issue 2, pp. 520-31, 2010 Jan 15. Abstract
Taskesen, E., R. Beekman, J. de Ridder, B. J. Wouters, J. K. Peeters, I. P. Touw, M. J. T. Reinders, and R. Delwel, "HAT: hypergeometric analysis of tiling-arrays with application to promoter-GeneChip data.", BMC bioinformatics, vol. 11, pp. 275, 2010. Abstract
Mattison, J., J. Kool, A. G. Uren, J. de Ridder, L. F. A. Wessels, J. Jonkers, G. R. Bignell, A. Butler, A. G. Rust, M. Brosch, et al., "Novel candidate cancer genes identified by a large-scale cross-species comparative oncogenomics approach", Cancer Research, vol. 70, no. 3, pp. 883–895, 2010. Abstract
2009
Abeel, T., J. de Ridder, and L. Peixoto, "Highlights from the 5th International Society for Computational Biology Student Council Symposium at the 17th Annual International Conference on Intelligent Systems for Molecular Biology and the 8th European Conference on Computational Biology", BMC Bioinformatics, vol. 10(Suppl 13):I1, October, 2009. Abstract
Nierop, J., "An in silico tumor growth simulation model for study of cancer hallmark acquisition", M.Sc. Thesis: Delft University of Technology, pp. 33 pages (13 pages suplement), august 31, 2009.  Download: Nier09a.pdf (1.95 MB)
2008
Uren, A. G., J. Kool, K. Matentzoglu, J. de Ridder, J. Mattison, M. J. G. van Uitert, W. Lagcher, D. Sie, E. Tanger, T. Cox, et al., "Large-Scale Mutagenesis in p19ARF- and p53-Deficient Mice Identifies Cancer Genes and Their Collaborative Networks", Cell, vol. 133, pp. 727-741, May, 2008. Abstract
de Ridder, J., M. J. T. Reinders, and L. F. A. Wessels, "Inference of logic networks from insertion and expression data", Proceedings of the Fourteenth annual conference of the Advanced School for Computing and Imaging, June, 2008.
Klijn, C. N., H. Holstege, J. de Ridder, X. Liu, M. J. T. Reinders, J. Jonkers, and L. F. A. Wessels, "Identification of cancer genes using a statistical framework for multi-experiment analysis of non-discretized array CGH data", Nucl. Acids Res., vol. 36, no. 6, pp. 2106-, 2008.
2007
Verver, O., "Prioritization of Candidate Disease Genes using Microarray Data and Functional Relations", M.Sc. Thesis: Delft University of Technology, pp. 12 pages (29 pages supplement), July 13 2007.  Download: Verv07a.pdf (618.6 KB)
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
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.
2006
Shao, L., J. Lin, G. Saikalis, J. McCune, and J. de Ridder, "An electronic throttle simulation model with automatic parameter tuning", SAE 2005 Transactions Journal of Passenger Cars – Electronic and Electrical Systems, vol. 2005, pp. 383-387, March, 2006.
de Ridder, J., A. G. Uren, J. Kool, M. J. T. Reinders, and L. F. A. Wessels, "Detecting Statistically Significant Common Insertion Sites in Retroviral Insertional Mutagenesis Screens", PLoS Computational Biology, vol. 2, no. 12, pp. 166, 2006.
2005
de Ridder, J., Statistical analysis of common insertion sites in retroviral insertional mutagenesis screens, , Delft University of Technology, pp. 27, 2005.