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In Press
Gehrmann, T., M. Loog, M. J. T. Reinders, and D. de Ridder, "Conditional random fields for protein function prediction", Pattern Recognition in Bioinformatics 2013, Nice, France, In Press.
van Berlo, R. J. P., W. Winterbach, M. J. L. de Groot, A. Bender, P. J. T. Verheijen, M. J. T. Reinders, and D. de Ridder, "Efficient calculation of compound similarity based on maximum common subgraphs and its application to prediction of gene transcript levels", International Journal of Bioinformatics Research & Applications, In Press. Abstract
Berkhout, J., E. Bosdriesz, E. I. Nikerel, D. Molenaar, D. de Ridder, B. Teusink, and F. Bruggeman, "How biochemical constraints of cellular growth shape evolutionary adaptations in metabolism", Genetics, In Press.
Winterbach, W., P. Van Mieghem, M. J. T. Reinders, H. Wang, and D. de Ridder, "Local topological signatures for network-based prediction of biological function", Pattern Recognition in Bioinformatics 2013, Nice, France, In Press.
de Ridder, D., J. de Ridder, and M. J. T. Reinders, "Pattern recognition in bioinformatics", Briefings in Bioinformatics, In Press.
Gritsenko, A. A., M. J. T. Reinders, and D. de Ridder, "Using predictive models to engineer biology: a case study in codon optimization", Pattern Recognition in Bioinformatics 2013, Nice, France, In Press.
2013
Unadkat, H. V., R. R. Rewagad, M. Hulsman, G. F. B. Hulshof, R. K. Truckenmüller, D. F. Stamatialis, M. J. T. Reinders, J. C. T. Eijkel, A. van den Berg, C. A. van Blitterswijk, et al., "A modular versatile chip carrier for high-throughput screening of cell-biomaterial interactions", J R Soc Interface, vol. 10, issue 78, pp. 20120753, 2013 Jan 6. Abstract
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
Wessels, L. F. A., M. H. van Vliet, H. M. Horlings, M. J. van den vijver, and M. J. T. Reinders, "Integration of Clinical and Gene Expression Data Has a Synergetic Effect on Predicting Breast Cancer Outcome", PLOS ONE, vol. 7, issue 7, July 11, 2012.
Meuleman, W., D. Peric-Hupkes, J. Kind, J. - B. Beaudry, L. Pagie, M. Kellis, M. J. T. Reinders, L. F. A. Wessels, and B. van Steensel, "Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence", Genome Res, 2012 Nov 2. Abstract
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
Alves, H., J. van Ginkel, N. Groen, M. Hulsman, A. Mentink, M. J. T. Reinders, C. A. van Blitterswijk, and J. de Boer, "A mesenchymal stromal cell gene signature for donor age", PLoS One, vol. 7, issue 8, pp. e42908, 2012. Abstract
Blokzijl, F., Recurrently altered sub-network analysis of SNP data using multi-scale graph diffusion, , Delft, Delft University of Technology, pp. 12+94, 11-2012.
van den Berg, B., M. J. T. Reinders, M. Hulsman, L. Wu, H. J. Pel, J. A. Roubos, and D. de Ridder, "Exploring sequence characteristics related to high-level production of secreted proteins in Aspergillus niger", PLoS ONE, vol. 7, issue 10, 10/2012. Abstract
Gehrmann, T., "Conditional random fields for protein function prediction", Pattern Recognition & Bioinformatics Group, Dept. of Intelligent Systems, Faculty of Electrical Engineering, Mathematics & Computer Science, Delft, Delft University of Technology, 2012.
Nijkamp, J. F., M. A. van den Broek, J. - M. A. Geertman, M. J. T. Reinders, J. - M. G. Daran, and D. de Ridder, "De novo detection of copy number variation by co-assembly", Bioinformatics, vol. 28, issue 24, pp. 3195-3202, 2012. Abstract
Nijkamp, J. F., M. A. van den Broek, E. Datema, S. de Kok, L. Bosman, M. A. H. Luttik, P. A. S. Daran-Lapujade, W. Vongsangnak, J. Nielsen, W. H. M. Heijne, et al., "De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology", Microbial Cell Factories, vol. 11, issue 36, 2012. Abstract
Winterbach, W., D. de Ridder, H. Wang, M. J. T. Reinders, and P. Van Mieghem, "Do greedy assortativity optimization algorithms produce good results?", The European Physical Journal B, vol. 85, issue 5, 2012. Abstract
Gritsenko, A. A., J. F. Nijkamp, M. J. T. Reinders, and D. de Ridder, "GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies", Bioinformatics, vol. 28, issue 11, pp. 1429-1437, 2012. Abstract
de Kok, S., J. F. Nijkamp, B. Oud, F. Roque, D. de Ridder, J. - M. G. Daran, J. T. Pronk, and A. J. A. van Maris, "Laboratory evolution of new lactate transporter genes in a jen1Δ mutant of Saccharomyces cerevisiae and their identification as ADY2 alleles by whole-genome resequencing and transcriptome analysis", FEMS Yeast Research, vol. 12, issue 3, pp. 359-374, 2012. Abstract
Sinha, S., M. J. T. Reinders, and W. F. J. Verhaegh, Prior Biological Knowledge and Epigenetic Information Enhances Prediction Accuracy of Bayesian Wnt Pathway, , Delft, TU Delft, 2012.
Nikerel, E. I., J. Berkhout, F. Hu, B. Teusink, M. J. T. Reinders, and D. de Ridder, "Understanding regulation of metabolism through feasibility analysis", PLoS ONE, vol. 7, issue 7, 2012. Abstract
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
Meenhuis, A., P. A. van Veelen, H. de Looper, N. van Boxtel, I. J. van den Berge, S. M. Sun, E. Taskesen, P. Stern, A. H. de Ru, A. J. van Adrichem, et al., "MiR-17/20/93/106 promote hematopoietic cell expansion by targeting sequestosome 1-regulated pathways in mice.", Blood, 2011 May 31. Abstract
Rácz, E., E. P. Prens, D. Kurek, M. Kant, D. de Ridder, S. Mourits, E. M. Baerveldt, Z. Ozgur, W. F. J. van IJcken, J. D. Laman, et al., "Effective treatment of psoriasis with narrow-band UVB phototherapy is linked to suppression of the IFN and Th17 pathways", The Journal of Investigative Dermatology, 2011 Mar 17. Abstract