Articles and chapters
If you use MCL, please cite
van Dongen, Stijn, Graph clustering via a discrete uncoupling process, Siam Journal on Matrix Analysis and Applications 30-1, p121-141, 2008. ( https://doi.org/10.1137/040608635 ). This was published after a strenuous and intermittently very dormant submission process started in 2000. It is a reworking of the third technical report listed below.
The MCL algorithm has been successfully applied in the field of protein family detection. I co-authored a paper with Anton Enright and Christos Ouzounis. It was published as Enright A.J., Van Dongen S., Ouzounis C.A. An efficient algorithm for large-scale detection of protein families, Nucleic Acids Research 30(7):1575-1584 (2002). It is appropriate to additionally cite this paper when applying MCL to biological data.
This book chapter coauthored by Cei-Abreu-Goodger contains two worked examples detailing the application of mcl to protein sequence clustering and gene expression clustering: Using MCL to extract clusters from networks, in Bacterial Molecular Networks: Methods and Protocols, Methods in Molecular Biology, Vol 804, p281—295 (2012). PMID 22144159.
Stijn van Dongen, Graph Clustering by Flow Simulation. PhD thesis, University of Utrecht, May 2000.
Download a gzipped PDF of the thesis The University of Utrecht publishes the thesis as well.