Key algorithms (Qcut and HQcut):

[1] Ruan J and Zhang W. "Identifying network communities with a high resolution", Physical Review E, 2008, 77:016104.

Included algorithms (MCL and MCODE):

[2] Dongen SV. "Graph clustering via a discrete uncoupling process", SIAM Journal on Matrix Analysis and Applications, 2008, 30:121-141.

[3] Bader GD and Hogue C. "An automated method for finding molecular complexes in large protein interaction networks", BMC Bioinformatics, 2003, 4:2.

Modularity-based community finding:

[4] Newman M. "Modularity and community structure in networks", PNAS, 2006, 103:8577-8582.