Articles and chapters
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.
The third technical report below was reworked as an article. After a strenuous and intermittently very dormant submission process started in 2000 it was belatedly published as Graph clustering via a discrete uncoupling process in Siam Journal on Matrix Analysis and Applications 30—1, p121—141, 2008.
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.