The paper itself contains a full list of references and citations -- here we wanted to call out a few good examples with annotations.
Yuri Lazebnik's original paper that was our inspiration -- the pdf is available from Cell
Lazebnik, Y. (2002). Can a biologist fix a radio? - Or, what I learned while studying apoptosis. Cancer Cell, 2(3), 179–182. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/15627398
None of this work would have been possible without the original work done by the Visual 6502 team in acquiring the 6502 connectome. They had a great talk on their efforts at Siggraph 2010 (slides). They even have a 6502 simulator directly in the browser.
James, G., Silverman, B., & Silverman, B. (2010). Visualizing a classic CPU in action. In ACM SIGGRAPH 2010 Talks on - SIGGRAPH ’10 (p. 1). New York, New York, USA: ACM Press. doi: 10.1145/1837026.1837061