| 2010 | CIBCB | Classifying Cytochrome c Oxidase subunit 1 by translation initiation mechanism using side effect machines. | Justin Schonfeld, Dan Ashlock |
| 2008 | CIBCB | Transience in the simulation of ring species. | Dan Ashlock, Taika von Konigslow, Elizabeth Clare, Wendy Ashlock |
| 2008 | CIBCB | Characterization of extremal epidemic networks with diffusion characters. | Dan Ashlock, Colin Lee |
| 2008 | CIBCB | A model of emotion in the prisoner's dilemma. | Dan Ashlock, Nicholas Rogers |
| 2008 | CIBCB | Classifying synthetic and biological DNA sequences with side effect machines. | Dan Ashlock, Elizabeth Warner |
| 2007 | CIBCB | Evolutionary Parameter Setting of Multi-clustering. | Dan Ashlock, Ling Guo |
| 2007 | CIBCB | Evolving Extremal Epidemic Networks. | Dan Ashlock, Fatemeh Jafargholi |
| 2006 | CIBCB | An Exploration of Differential Utility in Iterated Prisoner's Dilemma. | Dan Ashlock, Wendy Ashlock, Gary Umphry |
| 2006 | CIBCB | An Evolutionary Algorithm for the Selection of Geographically Informative Species. | Dan Ashlock, Karl Cottenie, Lindsey Carson, Kenneth Mark Bryden, Steven M. Corns |
| 2006 | CIBCB | Developing Antibiotic Regimens Using Evolutionary Algorithms. | Steven M. Corns, H. Scott Hurd, Dan Ashlock, Kenneth Mark Bryden |
| 2006 | CIBCB | Filtration and Depth Annotation Improve Non-linear Projection for RNA Motif Discovery. | Justin Schonfeld, Dan Ashlock |
| 2005 | CEC | Single parent genetic programming. | Wendy Ashlock, Dan Ashlock |
| 2005 | CEC | Techniques for analysis of evolved prisoner's dilemma strategies with fingerprints. | Dan Ashlock, Eun-Youn Kim |
| 2005 | CEC | Nonlinear projection for the display of high dimensional distance data. | Dan Ashlock, Justin Schonfeld |
| 2004 | CEC | Evolutionary control of Lsystem interpretation. | Dan Ashlock, Kenneth M. Bryden |
| 2004 | CEC | On taxonomy of evolutionary computation problems. | Dan Ashlock, Kenneth M. Bryden, Steven M. Corns |
| 2004 | CEC | Fingerprints: enabling visualization and automatic analysis of strategies for two player games. | Dan Ashlock, Eun-Youn Kim, Warren K. von Roeschlaub |
| 2004 | CEC | Program induction: building a wall. | Dan Ashlock, James I. Lathrop |
| 2004 | CEC | Simulation of floral specialization in bees. | Dan Ashlock, Jessica Oftelie |
| 2004 | CEC | The effect of tag recognition on non-local adaptation. | Dan Ashlock, Brad Powers |
| 2004 | CEC | Coevolution and Tartarus. | Dan Ashlock, Stephen J. Willson, Nicole P. Leahy |
| 2003 | CEC | Morphometric grayscale texture analysis using foot patterns. | Dan Ashlock, Dean C. Adams, David Doty |
| 2003 | CEC | A note on general adaptation in populations of painting robots. | Dan Ashlock, Elizabeth Blankenship, Jonathan Gandrud |
| 2002 | CEC | Training finite state machines to improve PCR primer design. | Dan Ashlock, Andrew Wittrock, Tsui-Jung Wen |
| 2000 | CEC | Data crawlers for simple optical character recognition. | Dan Ashlock |
| 2000 | CEC | A pure finite state baseline for Tartarus. | Dan Ashlock, J. Freeman |
| 2000 | CEC | Iterated function system fractals for the detection and display of DNA reading frame. | Dan Ashlock, James B. Golden III |
| 1999 | CEC | Graph based genetic algorithms. | Dan Ashlock, Mark D. Smucker, John Walker |