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2011
Smith, L. - L., J. Yeung, B. B. Zeisig, N. Popov, I. Huijbers, J. Barnes, A. J. Wilson, E. Taskesen, R. Delwel, J. Gil, et al., "Functional Crosstalk between Bmi1 and MLL/Hoxa9 Axis in Establishment of Normal Hematopoietic and Leukemic Stem Cells.", Cell stem cell, vol. 8, issue 6, pp. 649-62, 2011 Jun 3. Abstract
Taskesen, E., L. Bullinger, A. Corbacioglu, M. A. Sanders, C. A. J. Erpelinck, B. J. Wouters, S. C. van der Poel-van de Luytgaarde, F. Damm, J. Krauter, A. Ganser, et al., "Prognostic impact, concurrent genetic mutations, and gene expression features of AML with CEBPA mutations in a cohort of 1182 cytogenetically normal AML patients: further evidence for CEBPA double mutant AML as a distinctive disease entity.", Blood, vol. 117, issue 8, pp. 2469-75, 2011 Feb 24. Abstract
Lazova, M. D., T. Ahmed, D. Bellomo, R. Stocker, and T. S. Shimizu, "Response rescaling in bacterial chemotaxis", Proceedings of the National Academy of Sciences of the United States of America, vol. 108, issue 33, pp. 13870-5, 2011 Aug 16. Abstract
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
van den Akker, E. B., B. Verbruggen, B. T. Heijmans, M. Beekman, J. N. S. Kok, P. E. Slagboom, and M. J. T. Reinders, "Integrating protein-protein interaction networks with gene-gene co-expression networks improves gene signatures for classifying breast cancer metastasis", J Integr Bioinform, vol. 8, issue 2, pp. 188, 2011. Abstract
Sinha, S., and G. J. ter Horst, "Bounded Multivariate Surfaces On Monovariate Internal Functions", IEEE International Conference on Image Processing, Brussels, Belgium, 09/2011. Abstract
Gritsenko, A. A., Scaffolding of next-generation sequencing assemblies using diverse information sources, , vol. M.Sc., Delft, Delft University of Technology, pp. 26+29, 08/2011.
Sinnige, R., A dynamical game between organisms competing for resources, , Delft, Delft University of Technology, pp. 48, 07/2011.
Sontrop, H. M. J., W. F. J. Verhaegh, M. J. T. Reinders, and P. D. Moerland, "An Evaluation Protocol for Subtype-Specific Breast Cancer Event Prediction", PLoS ONE, vol. 6, no. 7: Public Library of Science, pp. e21681, 07, 2011.
Unadkat, H. V., M. Hulsman, K. Cornelissen, B. J. Papenburg, R. K. Truckenmüller, G. F. Post, M. Uetz, M. J. T. Reinders, D. F. Stamatialis, C. A. van Blitterswijk, et al., "An algorithm-based topographical biomaterials library to instruct cell fate", Proceedings of the National Academy of National Sciences, vol. 108, issue 40, 04/10/2011.
Helbig, A. O., P. A. S. Daran-Lapujade, A. J. A. van Maris, E. A. F. de Hulster, D. de Ridder, J. T. Pronk, A. J. R. Heck, and M. Slijper, "The diversity of protein turnover and abundance under nitrogen-limited steady-state condition in Saccharomyces cerevisiae", Molecular Biosystems, vol. 7, issue 12, pp. 3316-3326 , 2011. Abstract
Rácz, E., D. Kurek, M. Kant, E. M. Baerveldt, E. Florencia, S. Mourits, D. de Ridder, J. D. Laman, L. van der Fits, and E. P. Prens, "GATA3 expression is decreased in psoriasis and during epidermal regeneration; induction by narrow-band UVB and IL-4", PLoS ONE, vol. 6, issue 5, pp. e19806, 2011. Abstract
Nodland, S., M. A. Berkowska, A. A. Bajer, N. Shah, D. de Ridder, J. J. M. van Dongen, T. W. Lebien, and M. C. van Zelm, "IL-7R expression and IL-7 signaling confer a distinct phenotype on developing human B-lineage cells", Blood, 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.
Winterbach, W., H. Wang, M. J. T. Reinders, P. Van Mieghem, and D. de Ridder, "Metabolic network destruction: relating topology to robustness", Nano Communication Networks, vol. 2, issue 2-3, pp. 88-98, 2011. Abstract
Rácz, E., E. P. Prens, M. Kant, E. Florencia, N. G. Jaspers, J. D. Laman, D. de Ridder, and L. van der Fits, "Narrow-band UVB inhibits innate cytosolic dsRNA receptors in psoriatic skin and keratinocytes", British Journal of Dermatology, vol. 164, issue 4, pp. 838-847, 2011. Abstract
Loog, M., L. F. A. Wessels, M. J. T. Reinders, and D. de Ridder, "Pattern Recognition in Bioinformatics (PRIB2011)", Lecture Notes in Computer Science, vol. 7036, Heidelberg, Springer-Verlag, pp. 342, 2011.
van Berlo, R. J. P., D. de Ridder, J. - M. G. Daran, P. A. S. Daran-Lapujade, B. Teusink, and M. J. T. Reinders, "Predicting metabolic fluxes using gene expression differences as constraints", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, issue 1, pp. 206-216, 2011. Abstract
Sinha, S., M. J. T. Reinders, and W. F. J. Verhaegh, Reproducibility of Parameter Learning In A Bayesian Network For Predicting Wnt Pathway Activation, , Delft, TU Delft, 2011.
2010
Verbruggen, B., "Predicting breast cancer outcome using subnetworks of genes based on gene expression and PPI data", Delft Bioinformatics Lab, Delft, Delft University Technoly, pp. 32 (56 suplement), 24/08/2010.
Varela, I., C. N. Klijn, P. J. Stephens, L. J. Mudie, L. Stebbings, D. Galappaththige, H. van der Gulden, E. Schut, S. Klarenbeek, P. J. Campbell, et al., "Somatic structural rearrangements in genetically engineered mouse mammary tumors.", Genome biology, vol. 11, issue 10, pp. R100, 2010 Oct 13. Abstract
Peric-Hupkes, D., W. Meuleman, L. Pagie, S. W. M. Bruggeman, I. Solovei, W. Brugman, S. Gräf, P. Flicek, R. M. Kerkhoven, M. van Lohuizen, et al., "Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation.", Molecular cell, vol. 38, issue 4, pp. 603-13, 2010 May 28. Abstract
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