We have published a paper describing PathVisio in 2008. Please make use of the following reference when citing PathVisio:

van Iersel MP, Kelder T, Pico AR, Hanspers K, Coort S, Conklin BR, and Evelo C. Presenting and exploring biological pathways with PathVisio. BMC Bioinformatics 2008 Sep 25; 9 399. doi:10.1186/1471-2105-9-399 pmid:18817533.

Free full text copy available at  http://www.biomedcentral.com/1471-2105/9/399