Please cite this publication if you are using PathVisio 3.0.0+ in your research:

PathVisio 3: An Extendable Pathway Analysis Toolbox.
Martina Kutmon, Martijn P. van Iersel, Anwesha Bohler, Thomas Kelder, Nuno Nunes, Alexander R. Pico, Chris T. Evelo
PLoS Comput Biol 11(2): e1004085 (2015).
doi: 10.1371/journal.pcbi.1004085

If you are using the WikiPathways pathway collections, please also cite the latest WikiPathways publications:

WikiPathways: connecting communities.
Martens M, Ammar A, Riutta A, Waagmeester A, Slenter DN, Hanspers K, Miller RA, Digles D, Lopes EN, Ehrhart F, Dupuis LJ, Winckers LA, Coort SL, Willighagen EL, Evelo CT, Pico AR, Kutmon M.
Nucleic Acids Res. 49(D1):D613-D621 (2021).
doi: 10.1093/nar/gkaa1024

If you are using an older app version of PathVisio, please cite this publication in your research:

Presenting and exploring biological pathways with PathVisio.
Martijn P van Iersel, Thomas Kelder, Alexander R Pico, Kristina Hanspers, Susan Coort, Bruce R Conklin, Chris Evelo
BMC Bioinformatics volume 9, Article number: 399 (2008)
doi: 10.1186/1471-2105-9-399