Stijn van Dongen, Graph Clustering by Flow Simulation. PhD thesis, University of Utrecht, May 2000.
Download a gzipped PDF of the thesis (3.5Mb, unpacked 4.5Mb). The University of Utrecht publishes the thesis as well. They host a PDF of each separate chapter, plus the whole shebang in one piece as well. The PS file is unfortunately only useful if you have Lucida fonts installed on your system. Few people have them, so I withhold the PS source - mail me if you are interested. The thesis was written in LaTeX, and I did the utmost to avoid that dreary default LaTeX look.
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 first 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. 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, pages 281—295 (2012). PMID 22144159.
The meat of the thesis [constists of / was cut into] three parts which can be found at CWI's report repository. The references and CWI links are:
Stijn van Dongen. A stochastic uncoupling process for graphs. Technical Report INS-R0011, National Research Institute for Mathematics and Computer Science in the Netherlands, Amsterdam, May 2000. Download.
Stijn van Dongen. Performance criteria for graph clustering and Markov cluster experiments. Technical Report INS-R0012, National Research Institute for Mathematics and Computer Science in the Netherlands, Amsterdam, May 2000. Download.