E van Dyk, MJT Reinders, LFA Wessels (2013), A scale-space method for detecting recurrent DNA copy number changes with analytical false discovery rate control, In Nucleic Acids Research Volume 41 p.1-14.

CN Klijn, MJ Koudijs, J Kool, J ten Hoeve, M Boer, J de Moes, W Akhtar, M van Miltenburg, A Vendel-Zwaagstra, MJT Reinders, DJ Adams, M. van Lohuizen, J Hilkens, LFA Wessels, J Jonkers (2013), Analysis of tumor heterogeneity and cancer gene networks using deep sequencing of MMTV-induced mouse mammary tumors, In PLoS ONE Volume 8 p.1-10.

Ahmed Mahfouz, Mark N. Ziats, Owen M. Rennert, Boudewijn Lelieveldt, Marcel Reinders (2013), Co-expression Network Analysis of the Developing Human Brain Implicates Synaptogenesis and Mitochondrial Function as Central Mechanisms in Autism.

T Gehrmann, M Loog, MJT Reinders, D de Ridder (2013), Conditional random fields for protein function prediction, A Ngom, E Formenti, J-K Hao, X-M Zhao, T van Laarhoven (Eds.), In Pattern Recognition in Bioinformatics - Proceedings 8th IAPR International Conference PRIB 2013 p.184-195, Springer.

Alexey Gritsenko, Frank Koopman, Marcel Reinders, Jean Marc Daran, Dick de Ridder (2013), Data-driven codon optimization in Saccharomyces cerevisiae.

S Babaei, M Hulsman, MJT Reinders, J de Ridder (2013), Detecting recurrent gene mutation in interaction network context using multi-scale graph diffusion, In BMC Bioinformatics Volume 14:29 p.1-12.

RJP van Berlo, W Winterbach, MJL de Groot, A Bender, PJT Verheijen, MJT Reinders, D de Ridder (2013), Efficient calculation of compound similarity based on maximum common subgraphs and its application to prediction of gene transcript levels, In International Journal of Bioinformatics Research and Applications Volume 9 p.407-432.

JF Nijkamp, M Pop, MJT Reinders, D de Ridder (2013), Exploring variation aware contig graphs for (comparative) metagenomics using MARYGOLD, In Bioinformatics Volume 29 p.2826-2834.

E Taskesen, R Hoogeboezem, R Delwel, MJT Reinders (2013), Hypergeometric analysis of tiling-array and sequence data: detection and interpretation of peaks, In Advances and Applications in Bioinformatics and Chemistry Volume 6 p.55-62.

M Hulsman, JJ Bot, AP de Vries, MJT Reinders (2013), Ibidas: querying flexible data structures to explore heterogeneous bioinformatics data, CJO Baker, G Butler, I Jurisca (Eds.), In Proceedings 9th International Conference on Data Integration in Life Sciences p.23-37, Springer.