GeneMCL in microarray analysis. - B. Samuel Lattimore; Stijn van Dongen; M. James C. Crabbe (Comput. Biol. Chem., 2005)

miRBase: microRNA sequences, targets and gene nomenclature. - Sam Griffiths-Jones; Russell J. Grocock; Stijn van Dongen; Alex Bateman; Anton J. Enright (Nucleic Acids Res., 2006)

Construction, Visualisation, and Clustering of Transcription Networks from Microarray Expression Data. - Tom C. Freeman; Leon Goldovsky; Markus Brosch; Stijn van Dongen; Pierre Mazière; Russell J. Grocock; Shiri Freilich; Janet M. Thornton; Anton J. Enright (PLoS Comput. Biol., 2007)

miRBase: tools for microRNA genomics. - Sam Griffiths-Jones; Harpreet Kaur Saini; Stijn van Dongen; Anton J. Enright (Nucleic Acids Res., 2008)

Graph Clustering Via a Discrete Uncoupling Process. - Stijn van Dongen (SIAM J. Matrix Anal. Appl., 2008)

Metric distances derived from cosine similarity and Pearson and Spearman correlations - Stijn van Dongen; Anton J. Enright (CoRR, 2012)