Professor of Mathematics

521 MacNaughton Building

Department of Mathematics and Statistics

University of Guelph, 50 Stone Road East

Guelph, Ontario, Canada N1G 2W1

VOX: 519-824-8166 x 53453

FAX: 519-837-0221 dashlock@uoguelph.ca

**Education**

B.S., University of Kansas, 1984, Mathematics, with Honors,

B.S., University of Kansas, 1984, Computer Science, with Honors and Distinction,

Ph.D., California Institute of Technology, 1990, Mathematics.

**Professional Experience**

Chief of Innovation, Ashlock and McGuinness Inc., 2016-

University of Guelph, Professor of Mathematics 2007-

University of Guelph, Associate Professor of Mathematics 2004-2007

Iowa State University, Associate Professor of Mathematics 1996-2004

Iowa State University, Assistant Professor of Mathematics 1990-1996

California Institute of Technology, Graduate Teaching Assistant 1985-1990

University of Kansas, Undergraduate Teaching Assistant 1979-1985

SoftCole Educational Software, Software Developer, 1981-1984

**Research Interests**
(E-prints)

Bioinformatics and computational biology

Evolutionary computation

Games and automatic content generation

Modeling of biological systems

Mathematics Education

Graph theory and combinatorics

Management of Large Data Sets

- Outstanding Teacher, Iowa State College of Liberal Arts and Sciences, 1998.
- Study in a Second Discipline (one semester release), Molecular Biology, Spring 2000.
- Vinograd Award for Excellence in Graduate Teaching in Mathematics, Spring 2003.
- Award for mid-career achievement in research, Iowa State University College of Liberal Arts and Sciences, 2004.
- Bioinformatics chair, University of Guelph, Department of Mathematics and Statistics, 2004.
- Senior Member of the IEEE, 2006.
- Best Theoretical Paper, Artificial Neural Networks in
Engineering conference, for
*D. Ashlock, A. J. Shuttleworth, and K.M. Bryden*,**Induction of Virtual Sensors with Function Stacks**, In Intelligent Engineering Systems Through Artificial Neural Networks, 19, PP 27-34, 2009. - Best Paper, CEC 2011, D. Ashlock, E. Shiller, and C. Lee
*Comparison of Evolved Epidemic Networks with Diffusion Characters*, Proceedings of IEEE Congress on Evolutionary Computation, PP 781-788, 2011. - Best undergraduate research advisor, 2019, College of Engineering and Physical Sciences, University of Guelph.

*Creating real-time data driven music using context sensitive grammars and fractal algorithms*, with Kris Bryden and Mark Bryden, 2007.

- A. Saunders, D. Ashlock, S. Graether,
*Testing the Rogue Taxa Hypothesis for Clustering Instability*, Journal of Theoretical Biology, 472, PP 36-45, 2019. - E. Y. Kim and D. Ashlock,
*Testing a Protocol for Characterizing Game Playing Agents Trained via Evolution on a New Game*, IEEE Transactions on Games, early electronic access, 2019. - A.C. Riley, D. Ashlock, and S.P. Graether,
*Evolution of the modular, disordered stress proteins known as dehydrins*, PLOS One, 2019,

https://doi.org/10.1371/journal.pone.0211813 - A. Goren, D. Ashlock, and I. J. Tetlow,
*Starch formation inside plastids of higher plants*, Protoplasma, 255(6), PP 1855-1876, 2018. - D. Ashlock and A. McEachern,
*Edit Games*, Game & Puzzle Design, vol. 3, no. 2, 2017, PP 47-55. - M. Timmins and D. Ashlock,
*Network Induction for Epidemic Profiles with a Novel Representation*, Biosystems 162, PP 205-214, 2017. - D. Ashlock and A. McEachern,
*CliqeR: a Graph Theory Game*, Game and Puzzle Design, PP 42-50, 2017. - D. Ashlock and C. McGuinness,
*Graph-Based Search for Game Design*, Game and Puzzle Design, 2(2), PP 68-75, 2016. - D. Ashlock,
*Graph Theory in Game and Puzzle Design*, Game and Puzzle Design, 2(1), PP 62-70, 2016. - E. Y. Kim and D. Ashlock,
*Changing Resources Available to Game Playing Agents: Another Relevant Design Factor in Agent Experiments*, IEEE Transactions on Computational Intelligence and AI in Games, 9(4), PP 321 - 332, 2016. - D. Ashlock and J. Schonfeld,
*Deriving Card Games from Mathematical Games*, in Game and Puzzle Design, 1(2), PP 55-63, 2015. - D. Ashlock and C. Lee,
*Influence Maps and New Versions of Risk*, in Game and Puzzle Design, 1(1), PP 38-43, 2015. - J. D. Phillips, R. A. Gwiazdowski, D. Ashlock, R. Hanner,
*An exploration of sufficient sampling effort to describe intraspecific DNA barcode haplotype diversity: examples from the ray-finned fishes (Chordata: Actinopterygii)*in DNA Barcodes, Volume 3, PP 66-73, 2015. - D. Ashlock and A. McEachern,
*Evolutionary Nonlinear Projection*, IEEE Transactions on Evolutionary Computation, 19(6), PP 857-869, 2015. - D. Ashlock, J. Brown, and P. Hingston,
*Multiple Opponent Optimization of Prisoner's Dilemma Playing Agents*, in IEEE Transactions on Computational Intelligence and Artificial Intelligence in Games, pages 53-65, 2015. - J. A. Huges Hughes, S. Houghten, D. Ashlock,
*Recentering and restarting a genetic algorithm using a generative representation for an ordered gene problem*, International journal of hybrid intelligent systems, 11(4), PP257-271, 2014. - P. Johnson, D. Ashlock, K. M. Bryden,
*A Novel Engineering Tool for Creative Design of Fluid Systems Engineering with Computers*, Engineering with Computers, Volume 30(1), PP 15-29, 2014. - A. McEachern, D. Ashlock, and J. Shonfeld,
*Sequence classification with side effect machines evolved via ring optimization*, Biosystems, Volume 113(1), PP9-27, 2013. - D. Ashlock, S. McNicholas,
*Fitness Landscapes of Evolved Cellular Automata*, IEEE Transaction on Evolutionary Computation, volume 17(2), PP 198-212, 2013. - D. Ashlock, C. Lee,
*Agent-Case Embeddings for the Analysis of Evolved Systems*, IEEE Transaction on Evolutionary Computation, volume 17(2), PP 227-240, 2013. - D. Ashlock, S. K. Houghten, J. A. Brown, and J. Orth,
*On the Synthesis of DNA Error Correcting Codes*, Biosystems(110), pages 1-8, 2012. - D. Ashlock, C. Lee, and C. McGuinness,
*Search-Based Procedural Generation of Maze-Like Levels*, IEEE Transactions on Computational Intelligence and AI in Games, 3(3), PP 260-273, 2011. - D. Ashlock, C. Lee, and C. McGuinness,
*Simultaneous Dual Level Creation for Games*, IEEE Computational Intelligence Magazine, 6(2), PP 26-37, 2011. (Invited Publication). - D. Ashlock, E. Clare, T. vonKonigslow, and W. Ashlock,
*Evolution and instability in ring species complexes: an in silico approach to the study of speciation,*Journal of Theoretical Biology, 264(4), 1202-1213, 2010. - E.Y. Kim, S.Y. Kim, D. Ashlock, D. Nam,
*MULTI-K: accurate classification of microarray subtypes using ensemble k-means clustering*, BMC Bioinformatics, 10(260), PP1-12, doi:10.1186/1471-2105-10-260, 2009. - D. Ashlock, E.Y. Kim, and W. Ashlock,
*Fingerprint Analysis of the Noisy Prisoner's Dilemma Using a Finite State Representation*, IEEE Transactions on Computational Intelligence and AI in Games, 1(2), 157-167, 2009. - D. S. Skibbe, X. Wang, L. A. Borsuk, D. A. Ashlock, D. Nettleton,
and P. S. Schnable,
*Floret-specific differences in gene expression and support for the hypothesis that tapetal degeneration of Zea mays L. occurs via programmed cell death,*Journal of Genetic and Genomics 35, PP 603-616, 2008. - D. Ashlock and E.Y. Kim,
*Fingerprinting: Visualization and Analysis of Prisoner's Dilemma Strategies*, IEEE Transactions on Evolutionary Computation, 12(5), 647-659, 2008. - D. Ashlock and B. Jamieson,
*Evolutionary computation to search Mandelbrot sets for aesthetic images*Journal of Mathematics and Art 1(3), PP 147-158, 2008. - S. J. Emrich, L. Li, T. J. Wen, M. D. Yandeau-Nelson, Y. Fu,
L. Guo, H. H. Chou, S. Aluru, D. A. Ashlock, P. S. Schnable,
*Nearly Identical Paralogs(NIPs): implications for maize(Zea Mays L.) genome evolution*, Genetics 175(1), PP 429-439, 2006. - A. L. Kaleita, B. L. Steward, R. P. Ewing, D. A. Ashlock,
M. E. Westgate, J. L. Hatfield,
*Novel Analysis Of Hyperspectral Reflectance Data for Detecting Onset of Pollen Shed in Maize*, in Transactions of the American Society of Agricultural and Biological Engineers, Vol. 49(6): 1947-1954, 2006. - Y. Fu, T.J. Wen, Y.I. Ronin, H.D. Chen, L. Guo, D. Mester,
Y. Yang, M. Lee, A. B. Korol, D. A. Ashlock, P. Schnable,
*Genetic Dissection of Intermated Recombinant Inbred Lines Using a New Genetic Map of Maize*, in Genetics, 174:1671-1638, 2006 - D. Ashlock, E.Y. Kim, N. Leahy,
*Understanding Representational Sensitivity in the Iterated Prisoner's Dilemma with Fingerprints*, in the Transactions on Systems, Man, and Cybernetics--Part C: Applications and Reviews, 36(4):464-475, 2006. - K.M. Bryden, D. Ashlock, S. Corns, S. Willson,
*Graph Based Evolutionary Algorithms*in the IEEE Transactions on Evolutionary Computation, 10(5):550-567,2005. - Ding J, K Viswanathan, D Berleant, E Wurtele, D Ashlock, J.
Dickerson, A Fulmer, PS Schnable
*PathBinderH: a tool for sentence-focused, plant taxonomy-sensitive access to the biological literature*, Bioinformatics, 21:2560-2, 2005. - S. J. Kirstukas, K. M. Bryden, and D. A. Ashlock,
*A Hybrid Evolutionary Strategy for the Analytical Solution of Differential Equations*, in the International Journal of General Systems Design, 34(3), 279-299(2005). - Hong Yao, Ling Guo, Yan Fu, Lisa A. Borsuk, Tsui-Jung Wen, David
S. Skibbe, Xiangqin Cui1, Brian E. Scheffler, Jun Cao1, Scott
J. Emrich, Daniel A. Ashlock, and Patrick S. Schnable,
*Evaluation of five ab initio gene prediction programs for the discovery of maize genes*, in Plant Molecular Biology, Volume 57, Issue 3, Feb 2005, Pages 445 - 460 - Scott J. Emrich, Srinivas Aluru, Yan Fu, Tsui-Jung Wen, Mahesh
Narayanan, Ling Guo, Daniel Ashlock, Patrick S. Schnable,
*A Strategy for Assembling the Maize (Zea mays L.) Genome*, in BioInformatics Vol.20 no.2: 140-147, 2004. - Timothy J. Close, Steve I. Wanamaker, Rico A. Caldo, Stacy
M. Turner, Daniel A. Ashlock, Julie A. Dickerson, Rod A. Wing, Gary
J. Muehlbauer, Andris Kleinhofs and Roger P. Wise,
*A New Resource for Cereal Genomics: 22K Barley GeneChip Comes of Age*, in Plant Physiology Vol. 134:960-968, 2004. - F. Qiu, L. Guo, T.J. Wen, D.A. Ashlock, P.S. Schnable,
*DNA Sequence-based Bar-codes for Tracking the Origins of ESTs from a maize cDNA Library Constructed using Multiple mRNA Sources*, in Plant Physiology, 133: 475-481, 2003. - Zhiqiang Chen, Ron M. Nelson, Daniel Ashlock,
*Comparison of Methods for Predicting Monthly Post Retrofit Energy Use in Buildings*in the Transactions of ASHRAE, Volume 109, Part 2, 2003, Pages KC-03-2-3-1 to KC-03-2-3-10, 2003. - Daniel Ashlock and James B. Goldin III,
*Chaos Automata: Iterated Function Systems with Memory*, in Physica D. 181: 274-285, 2003. - Kenneth M. Bryden, Daniel A. Ashlock, Douglas S. McCorkle, and
Gregory L. Urban,
*Optimization of heat transfer utilizing graph based evolutionary algorithms*, in the International Journal of Heat and Fluid Flow Volume 24, Issue 2: 267-277, 2003. - Xiangqin Cui, An-Pin Hsia, Feng Liu, Daniel A. Ashlock, Roger
P. Wise, Patrick Schnable,
*Alternative Transcription Initiation Sites and Polyadenylation Sites Are Recruited During Mu Supression at the rf2a Locus of Maize*, in Genetics, Volume 163: 685-698, 2003. - Dietrich C, F Cui, M Packila, D Ashlock, B Nikolau, PS Schnable,
*Maize Mu transposons are targeted to the 5' UTR of the gl8a gene and sequences flanking Mu target site duplications throughout the genome exhibit non-random nucleotide composition*, in Genetics, 160: 697-716, 2002. - G.L. Urban, K. M. Bryden, and D. A. Ashlock,
*Engineering Optimization of an Improved Plancha Stove*, in Energy for Sustainable Development, Vol. VI, No. 2: 9-19, 2001. - Richter, Charles W., Jr., Gerald Sheble, and Daniel Ashlock,
*Comprehensive Bidding Strategies with Genetic Programming/Finite State Automata*, in -PWRS-0-10-1998, IEEE Transactions on Power Systems, Vol. 14, no. 4:1207-1212, 1999. - Kenneth R. Driessel, Irvin Hentzel, and Daniel Ashlock,
*On Matrix Structures Invariant under Toda-like Isospectral Flows*, in Linear Algebra and its Applications 254:29-48, 1997. - E Ann Stanley, Daniel Ashlock, Leigh Tesfatsion, and Mark Smucker,
*Preferential Partner Selection in an Evolutionary Study of Prisoner's Dilemma*, in Biosystems 37: 99-125, 1996 - Daniel Ashlock and David Schweizer,
*Graphical Construction of Cubic Cages*, in Congressus Numerantium 112: 213-221, 1995. - Daniel Ashlock and Jenette Tilliotson,
*Minimal Superpermutations*, Congressus Numerantium 93: 91-98, 1993. - Daniel Ashlock,
*Permutation Polynomials on Abelian Group Rings*, in Journal of Pure and Applied Algebra 86:1-5, 1993. - Daniel Ashlock, The Costas Invariant for Graphs, Congress Numerantium 90:7-14, 1992
- Daniel Ashlock,
*Compositional Attractors and Enumeration of Permutation Polynomials Over Finite Fields*, Journal of Pure and Applied Algebra 81: 1-9, 1992.

- D. Ashlock and C. Salge,
*The Riddle of Togelby*, to appear in the proceedings of the IEEE 2019 Conference on Games. - D. Ashlock, A. Saunders, and E.Y. Kim,
*Prisoner's Dilemma Agents with Phenotypic Plasticity*, to appear in the proceedings of the IEEE 2019 Conference on Games. - D. Ashlock and C. Salge,
*Automatic Generation of Level Maps with the Do What's Possible Representation*, to appear in the proceedings of the IEEE 2019 Conference on Games. - M. Kreitzer, D. Ashlock, and R. Pereira,
*Automatic Generation of Diverse Cavern Maps with Morphing Cellular Automata*, to appear in the proceedings of the IEEE 2019 Conference on Games. - D. Ashlock, W. Ashlock, and J. Montgomery,
*Implementing Phenotypic Plasticity with an Adaptive Generative Representation*, in IEEE 2019 Conference on Bioinformatics and Computational Biology, PP. 173-180, 2019. - M. Dube, S. Houghten, and D. Ashlock,
*Pandemic: A Graph Evolution Story*, in Proceedings of the IEEE 2019 Conference on Bioinformatics and Computational Biology, PP 157-164, 2019. - D. Ashlock, S. Gillis, A. Saunders, and A. Riley,
*Large Block Matching Characters for Dehydrin Classification*, in Proceedings of the IEEE 2019 Conference on Bioinformatics and Computational Biology, PP 199-206, 2019. - R. Brown and D. Ashlock,
*Parameter Tuning of a Peak Fitting Algorithm with an Evolved Experimental Design*, in Proceedings of the 2019 IEEE Congress on Evolutionary Computation, PP. 2379-2386, 2019. - Michael Dube, Sheridan Houghten, and D. Ashlock,
*Representation for Evolution of Epidemic Models*, to appear in the proceedings of the 2019 IEEE Congress on Evolutionary Computation, PP 2371-2378, 2019. - J. Gilbert and D. Ashlock,
*A Greedy, Generative, Lattice Representation for Point Packing*, to appear in the proceedings of the 2019 IEEE Congress on Evolutionary Computation, PP 3182-3189, 2019. - D. Ashlock and J. Mongomery,
*Applying an Adaptive Generative Representation to the Investigation of Affordances in Puzzles*, to appear in the proceedings of the 2019 IEEE Congress on Evolutionary Computation, PP. 762-769, 2019. - D. Ashlock, A Saunders, J. Marshall and D. Calder,
*Modelling Standard Work with Simple Virtual Agents*, to appear in the proceedings of the 2019 IEEE Congress on Evolutionary Computation, PP 2999-3006, 2019. - M. S. Nobile, P. Cazzaniga and D. Ashlock,
*Dilation Functions in Global Optimization*, to appear in the proceedings of the 2019 IEEE Congress on Evolutionary Computation, 2301-2308, 2019. - D. Ashlock and E.Y. Kim and D. Perez-Lebana,
*Toward General Mathematical Game Playing Agents*, Proceedings of the 2018 IEEE Conference on Computational Intelligence in Games, PP 110-116, 2018. - D. Ashlock and C. Kolthof,
*Evolving Number Sentence Morphing Puzzles*, Proceedings of the 2018 IEEE Conference on Computational Intelligence in Games, PP 102-109, 2018. - D. Ashlock and J. A. Brown and L. Sulancva,
*Exploiting Fertility to Enable Automatic Content Generation to Ameliorate User Fatigue in Interactive Evolutionary Computation**, in the Proceedings of the 2018 Congress on Evolutionary Computation, PP 1392-1398, 2018.* *G. W. Greenwood and D. Ashlock,**On the Evolution of Fairness in*, in the Proceedings of the 2018 Congress on Evolutionary Computation, PP 17-22, 2018.*N*-player Ultimatum Games*D. Ashlock and E. Y. Kim,**Two Population Studies of Evolving Game-Playing Agents*in the Proceedings of the 2018 Congress on Evolutionary Computation, PP 23-29, 2018.*M. Stoodley, D. Ashlock, M. Graether,**Data driven point packing for fast clustering*in the Proceedings of the 2018 IEEE Conference on Computational Intelligence in Bioiformatics and Computational Biology, Pages 1-8, 2018.*A Saunders, D. Ashlock, S. Houghten,**Heirarchical clustering and tree stability*in the Proceedings of the 2018 IEEE Conference on Computational Intelligence in Bioiformatics and Computational Biology, Pages 1-8, 2018.*M. Dube, S. Houghten, and D. Ashlock,**Parameter selection for modeling of epidemic networks*, in the Proceedings of the 2018 IEEE Conference on Computational Intelligence in Bioiformatics and Computational Biology, Pages 1-8, 2018.*J. A. Brown and D. Ashlock**Using Multiple Worlds for Multiple Agent Roles in Games*, in Proceedings of the 2017 IEEE Conference on Computational Intelligence in Games, Pages 1-8, 2017.*D. Ashlock, D. P. Lebana, and A. Saunders**General Video Game Playing Escapes the No Free Lunch Theorem*, in Proceedings of the 2017 IEEE Conference on Computational Intelligence in Games, Pages 1-8, 2017.*D. Ashlock and S. Houghten,**Hybridization and Ring Optimization for Larger Sets of Embeddable Biomarkers*, in the Proceedings of the 2017 IEEE Conference on Computational Intelligence in Bioiformatics and Computational Biology, Pages 1-8, 2017.*G. A. Ruz, D. Ashlock, T. Ledger, and E. Goles**Inferring bistable lac operon Boolean regulatory networks using evolutionary computation*, in the Proceedings of the 2017 IEEE Conference on Computational Intelligence in Bioiformatics and Computational Biology, Pages 1-8, 2017.*D. Ashlock and G. A. Ruz,**A Novel Representation for Boolean Networks Designed to Enhance Heritability and Scalability*, in the Proceedings of the 2017 IEEE Conference on Computational Intelligence in Bioiformatics and Computational Biology, Pages 1-8, 2017.*D. Ashlock, S. Gillis, and W. Ashlock**Infinite String Block Matching Features for DNA Classification*, in the Proceedings of the 2017 IEEE Conference on Computational Intelligence in Bioiformatics and Computational Biology, Pages 1-8, 2017.*D. Ashlock and W. Ashlock,**A Note On Population Size Inspired By The Extinction Of Mammoths*, in the Proceedings of the 2017 IEEE Conference on Computational Intelligence in Bioiformatics and Computational Biology, Pages 1-8, 2017.*D. Ashlock and G. Greenwood,**Modeling Undependable Subsidies with Three-player Generalized Divide the Dollar*, in Proceedings of the 2017 IEEE Congress on Evolutionary Computation, PP 1335-1342, 2017.*D. Ashlock and A. McEachern,**Evolutionary Design of FRAX Decks*, in Proccedings of the 2017 IEEE Congress on Evolutionary Computation, PP 994-951, 2017.*J. Montgomery and D. Ashlock,**Applying the Biased Form of the Adaptive Generative Representation*, in Proccedings of the 2017 IEEE Congress on Evolutionary Computation, PP 1079-1086, 2017.*D. Ashlock and L. Bickley,**Rescalable, replayable maps generated with evolved cellular automata*, Acta Physica Polonica (B), Proceedings Supplement, 9(1), PP 13-14, 2016.*D. Ashlock and S. Graether,**Conway Crossover to Create Hyperdimensional Point Packings, with Applications*in Proceedings of the IEEE 2016 Congress on Evolutionary Computation, PP 1570-1577, 2016.*D. Ashlock and G. Greenwood,**Generalized Divide the Dollar*in Proceedings of the IEEE 2016 Congress on Evolutionary Computation, PP 343-350, 2016.*D. Ashlock and E. Y. Kim,**The Impact of Elite Fraction and Population Size on Evolved Iterated Prisoner's Dilemma Agents*in Proceedings of the IEEE 2016 Congress on Evolutionary Computation, PP 364-371, 2016.*D. Ashlock and L. Taylor,**Evolving Polyomino Puzzles*in Proceedings of the IEEE 2016 Congress on Evolutionary Computation, PP 327-334, 2016.*D. Ashlock and J. Montgomery,**An Adaptive Generative Representation for Evolutionary Computation*in Proceedings of the IEEE 2016 Congress on Evolutionary Computation, PP 1578-1585, 2016.*D. Ashlock and S. Gillis, A. McEachern and J. Tsang ,**The Do What's Possible Representation*in Proceedings of the IEEE 2016 Congress on Evolutionary Computation, PP 1586-1593, 2016.*D. Ashlock and M. Timmins,**Adding Local Edge Mobility to Graph Evolution*in Proceedings of the IEEE 2016 Congress on Evolutionary Computation, PP 1594-1601, 2016.*D. Ashlock and J. Brown,**Evolutionary Partitioning Regression with Function Stacks*in Proceedings of the IEEE 2016 Congress on Evolutionary Computation, PP 1469-1476, 2016.*J. Gilbert and D. Ashlock,**Evolvable Warps for Data Normalization*in Proceedings of the IEEE 2016 Congress on Evolutionary Computation, PP 1562-1569, 2016.*J. Tsang and D. Ashlock,**The Impact of Obstruction on a Model of Competitive Exclusion in Plants*Proccedings of the 2015 IEEE Symposium Series on Computational Intelligence, pages 1110-1117, 2015.*D. Ashlock,**Evolvable Fashion Based Cellular Automata for Generating Cavern Systems*, in Proceedings of the 2015 IEEE Conference on Computatational Intelligence in Games, pages 306-313, 2015.*D. Ashlock and S. Houghten,**Lexicode Crossover for Embeddable Biomarkers*, in Proccedings of the 2015 IEEE Conference on Computational Intelligence in Bioioinformatics and Comutational Biology, PP 1-7, 2015.*M. Page and D. Ashlock,**Stress and Productivity Performance in the Workforce Modelled with Binary Decision Automata*, in Proceedings of the 2015 IEEE Conference on Computational Intelligence in Bioioinformatics and Comutational Biology, PP 1-8, 2015.*L. Barlow and D. Ashlock,**Varying Decision Inputs in Prisoner's Dilemma*, in Proceedings of the 2015 IEEE Conference on Computational Intelligence in Bioioinformatics and Comutational Biology, PP 1-8, 2015.*D. Ashlock, C. McGuinness and J. O'Neill,**Interactive Evolution Instead of Default Parameters*, in Proceedings of the 2015 IEEE Conference on Computational Intelligence in Bioioinformatics and Comutational Biology, PP 1-8, 2015.*D. Ashlock and M. Timmins,**A Comparison of Incremental Community Assembly with Evolutionary Community Selection*, in Proceedings of the 2015 IEEE Conference on Computational Intelligence in Bioioinformatics and Comutational Biology, PP 1-8, 2015.*D. Ashlock, S. Gillis, J. Garner, and G. Fogel,**Evolving DNA Classifiers with Extinction Based Ring Optimization*, in Proceedings of the 2015 IEEE Conference on Computational Intelligence in Bioioinformatics and Comutational Biology, PP 1-8, 2015.*D. Ashlock, C. McGuinness, and W. Ashlock**Chaos Automata for Sequence Visualization*, in Proceedings of the the 2015 IEEE Conference on Computational Intelligence in Bioioinformatics and Comutational Biology, PP 1-8, 2015.*D. Ashlock and J. Tsang,**Evolving Fractal Art with a Directed Acyclic Graph Genetic Programming Representation*, Proceedings of the 2015 Congress on Evolutionary Computation, PP 2137-2144, 2015.*J. Garner and D. Ashlock**Evolution of 2D Apoptotic Cellular Automata*, Proceedings of the 2015 Congress on Evolutionary Computation, PP 2160-2167, 2015.*J. Schonfeld and D. Ashlock**Flow of Control in Linear Genetic Programming*, Proceedings of the 2015 Congress on Evolutionary Computation, PP 1175-1182, 2015.*D. Ashlock, S. Gillis, and G. Fogel**Ring Optimization with Extinction*, Proceedings of the 2015 Congress on Evolutionary Computation, PP 1311-1318, 2015.*D. Ashlock and L. Barlow**A Class of Representations for Evolving Graphs*, Proceedings of the 2015 Congress on Evolutionary Computation, PP 1295-1302, 2015.*D. Ashlock, P. Hingston, and C. McGuinness**Evolving Point Packing in the Plane*, Proceedings of the Australasian Conference on Artificial Live and Computational Intelligence, PP. 297-309, 2015.*D. Ashlock and J. Gilbert,**A Discrete Representation for Real Optimization with Unique Search Properties*, Proceedings of the IEEE Symposium on the Foundations of Computational Intelligence, PP 54-61, 2014.*D. Ashlock, J. Schonfeld, L. Barlow and C. Lee,**Test Problems and Representations for Graph Evolution*, Proccedings of the IEEE Symposium on the Foundations of Computational Intelligence, PP 38-45, 2014.*W. Ashlock, J. Tsang, and D. Ashlock,**The Evolution of Exploitation*, Proceedings of the IEEE Symposium on the Foundations of Computational Intelligence, PP 135-142, 2014.*D. Ashlock and C. McGuinness,**Automatic Generation of Fantasy Role-playing Modules,*Proceedings of the IEEE Conference on Computatiational Inteligence in Games, PP 60-67, 2014.*W. Ashlock and D. Ashlock,**Shaped Prisoner's Dilemma Automata,*Proceedings of the IEEE Conference on Computatiational Inteligence in Games, PP 76-83, 2014.*J.Hughes, S.Houghten and D.Ashlock,**Recentering, Reanchoring and Restarting an Evolutionary Algorithm*, 5th World Congress on Nature and Biologically Inspired Computing, p.76-83, 2013.*D. Ashlock and A. Goren,**Agent-based Modelling of Resource Flow in Plant Networks*, in Proceedings of the 2013 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, PP 1-8, 2014*D. Ashlock and E. Y. Kim,**Using Associators To Generate Ensemble Biclustering From Multiple Evolved Biclusterings*, in Proceedings of the 2013 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, PP 1-8, 2014*A. McEachern and D. Ashlock,**Shape Control of Side Effect Machines for DNA Classification*in Proceedings of the 2013 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, PP 1-8, 2014*J. Hughes, S. Houghten, G. Mallen-Fullerton and D. Ashlock**Recentering and Restarting Genetic Algorithms Variations for DNA Fragment Assembly*in Proceedings of the 2013 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, PP 1-8, 2014.*D. Ashlock and C. McGuinness,**Landscape Automata for Search Based Procedural Content Generation*, in Proceedings of the 2013 IEEE Conference on Computational Intelligence in Games, PP 9-16, 2013.*D. Ashlock and J. Gilbert,**Creativity and Competitiveness in Polyomino-Developing Game Playing Agents*in Proceedings of the 2013 IEEE Conference on Computational Intelligence in Games, PP 249-256, 2013.*L. A. Barlow and D. Ashlock,**The Impact of Connection Topology and Agent Size on Cooperation in the Iterated Prisoner's Dilemma*in Proceedings of the 2013 IEEE Conference on Computational Intelligence in Games, PP 299-306, 2013.*H. James, S. Houghten, and D. Ashlock,**Recentering, reanchoring & restarting an evolutionary algorithm,*in Proceedings of the 2013 World Congress on Nature and Biologically Inspired Computing (NaBIC), PP 76-83, 2013.*M. Page and D. Ashlock,**Binary Decision Automata Modelling Stress in the Workplace*, Proceedings of the 2013 Congress on Evolutionary Computation, PP 3331-3338, 2013.*D. Ashlock and C. Pugh,**Evolutionary Cellular Automata Bonsai*, Proceedings of the 2013 Congress on Evolutionary Computation, PP 325-332, 2013.*D. Ashlock, N. Krisk, and G. Fogel,**Functions for the Analysis of Exploration and Exploitation*, Proceedings of the 2013 Congress on Evolutionary Computation, PP 2020-2027, 2013.*A. McEachern and D. Ashlock,**Woven String Kernels for DNA Sequence Classification*Proceedings of the 2013 Congress on Evolutionary Computation, PP 1578-1585, 2013.*J. Hughes, J. Brown, S. Houghten and D. Ashlock,**Edit Metric Decoding: Representation Strikes Back*, Proceedings of the 2013 Congress on Evolutionary Computation, PP 229-236, 2013.*D. Ashlock and E. Shiller,**Evolving a social fabric to fit an epidemic profile*, Proceedings of the 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, PP 363-370, 2012.*D. Ashlock and E. Wild,**A model of competitive exclusion in plants*, Proceedings of the 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, PP 206-213, 2012.*D. Ashlock and E. Y. Kim,**The Impact of Varying Resources Available to Iterated Prisoner's Dilemma Agents*Proceedings of FOCI 2013, PP 60-67.*D. Ashlock and M. Page,**An Agent Based Model of Stress in the Workplace*Proceedings of EAIS 2013, PP 114-121.*D. Ashlock and E. Knowles,**Deck-Based Prisoner's Dilemma*, Proceedings of the IEEE 2012 Conference on Computational Intelligence in Games, PP 17-24, 2012.*D. Ashlock, W. Ashlock, S. Samothrakis, S. Lucas, and C. Lee**From Competition to Cooperation: Co-evolution In A Rewards Continuum*, proceedings of the IEEE 2012 Conference on Computational Intelligence in Games, PP 33-40, 2012.*D. Ashlock and W. Ashlock,**Impact of Regulatory Genes on Optimization Behavior*, Proceedings of the 2012 IEEE Congress on Evolutionary Computation, PP 3372-3379, 2012.*D. Ashlock and S. McNicholas,**Single Parent Generalization of Cellular Automata Rules*, Proceedings of the 2012 IEEE Congress on Evolutionary Computation, PP 179-186, 2012.*G. Greenwood and D. Ashlock,**Evolutionary Games and the Study of Cooperation: Why Has So Little Progress Been Made?*, Proceedings of the 2012 IEEE Congress on Evolutionary Computation, PP 680-687, 2012.*D. Ashlock and S. Nguyen,**Financial Control of the Evolution of Autonomous NPCs*, Proceedings of IEEE Congress on Evolutionary Computation, PP 823-835, 2011.*D. Ashlock, C. Kuusela, and M. Cojocaru**Shopkeeper Strategies in the Iterated Prisoner's Dilemma*,, Proceedings of IEEE Congress on Evolutionary Computation, PP 1063-1070, 2011.*D. Ashlock and C. McGuinness**Decomposing the Level Generation Problem with Tiles*, Proceedings of IEEE Congress on Evolutionary Computation, PP 849-856, 2011.*D. Ashlock and J. Brown**Fitness Functions for Searching the Mandelbrot Set*, Proceedings of IEEE Congress on Evolutionary Computation, PP 1108-1115, 2011.*D. Ashlock, J. Schonfeld and P. McNicholas**Translation Tables: A Genetic Code in an Evolutionary Algorithm*, Proceedings of IEEE Congress on Evolutionary Computation, PP 2685-2692, 2011.*J. Brown, D. Ashlock, S. Houghten and J. Orth**Autogeneration of Fractal Photographic Mosaic Images*, Proceedings of IEEE Congress on Evolutionary Computation, PP 1116-1123, 2011.*D. Ashlock, E. Shiller, and C. Lee**Comparison of Evolved Epidemic Networks with Diffusion Characters*, Proceedings of IEEE Congress on Evolutionary Computation, PP 781-788, 2011.*J. Brown and D. Ashlock,**Domination in Iterated Prisoner's Dilemma*, Proceedigns of CCECE 2011, PP 1125-1128, 2011.*D. Ashlock and E. Shiller**Fitting Contact Networks to Epidemic Behavior with an Evolutionary Algorithm*, Proceedings of CIBCB 2011, PP 1-8, 2011.*D. Ashlock and A. McEachern**A Simulation of Bacterial Communities*, Proceedings of CIBCB 2011, PP 1-8, 2011.*W. Ashlock and D. Ashlock**Designing Artificial Organisms For Use In Biological Simulations*, Proceedings of CIBCB 2011, PP 1-8, 2011.*A. Ashlock, C. Kuusela, N. Rogers,**Hormonal systems for prisoners dilemma agents*, Proceedings of CIG 2011, PP 63-70, 2011.*C. McGuinness and D. Ashlock,**Incorporating required structure into tiles*, Proceedings of CIG 2011, PP 16-23, 2011.*D. A. Ashlock, J. A. Brown, and S. M. Corns,**K-models Clustering, a Generalization of K-means Clustering*, Intelligent Engineering Systems Through Artificial Neural Networks(20), PP 485-492, 2010.*J. A. Brown and D. A. Ashlock,**Using Evolvable Regressors to Partition Data*, Intelligent Engineering Systems Through Artificial Neural Networks(20), PP 187-194, 2010.*D. Ashlock,**Automatic Generation of Game Elements via Evolution*, Proceedings of the 2010 IEEE Conference on Computational Intelligence in Games, 289-296, 2010.*D. Ashlock and E.Y. Kim,**Prisoner's Dilemma: the Payoff Values Matter*, Proceedings of the 2010 IEEE Conference on Computational Intelligence in Games, PP 219-226, 2010.*D. Ashlock and J. Schonfeld,**Evolution for Automatic Assessment of the Difficulty of Sokoban Boards*, Proceedings of the 2010 IEEE Congress on Evolutionary Computation, PP 2179-2186, 2010.*W. Ashlock and D. Ashlock,**Virtual retroviruses in grid walkers: effects on genome organization,*Proceedings of the 2010 IEEE Congress on Evolutionary Computation, PP 4616-4623, 2010.*D. Ashlock and A. McEachern,**Nearest Neighbor Training of Side Effect Machines for Sequence Classification*, in Proceedings of the 2010 IEEE Symposium on Bioinformatics and Computational Biology, PP 111-118, 2010.*D. Ashlock and J. Schonfeld,**Classifying Cytochrome C Oxidase Subunit 1 by Translation Initiation Mechanism using Side Effect Machines*, in Proceedings of the 2010 IEEE Symposium on Bioinformatics and Computational Biology, 262-268, 2010.*J. Brown, S. Hougthen and D. Ashlock,**Side Effect Machines for Quaternary Edit Metric Decoding*, to in the Proceedings of the 2010 IEEE Symposium on Bioinformatics and Computational Biology, PP 103-110, 2010.*J. A. Brown, S. K. Houghten, D. A. Ashlock,**Edit Metric Decoding: A New Hope*in Proceedings of the 2nd Canadian Conference on Computer Science and Software Engineering, PP 233-242, 2009.*D. Ashlock, T. vonKonigslow, and J. Schonfeld,**Breaking a Hierarchical Clustering Algorithm with an Evolutionary Algorithm*, In Intelligent Engineering Systems Through Artificial Neural Networks, 19, PP 197-204, 2009.*D. Ashlock, A. J. Shuttleworth, and K.M. Bryden,**Induction of Virtual Sensors with Function Stacks*, In Intelligent Engineering Systems Through Artificial Neural Networks, 19, PP 27-34, 2009.*D. Ashlock, K.M. Bryden, and S. Gent,**Multiscale Feature Location with a Fractal Representation*,In Intelligent Engineering Systems Through Artificial Neural Networks, 19, PP 173-180, 2009.*D. Ashlock, K.M. Bryden, and D. McCorkle,**Logic Function Induction with the Blender Algorithm using Function Stacks*,In Intelligent Engineering Systems Through Artificial Neural Networks, 19, PP 189-196, 2009.*D. Ashlock and A. McEachern,**Ring Optimization of Side Effect Machines*, In Intelligent Engineering Systems Through Artificial Neural Networks, 19, PP 165-172, 2009.*D. Ashlock, K.M. Bryden, and S. M. Corns,**Taxonomy of a Diverse Collection of String Optimization Problems*, In Intelligent Engineering Systems Through Artificial Neural Networks, 19, PP 181-188, 2009.*D. Ashlock and N. Rogers,**The Imapact of Long Term Memory in the Iterated Prisoner's Dilemma*, In Intelligent Engineering Systems Through Artificial Neural Networks, 19, PP 245-252, 2009.*D. Ashlock, J. Schonfeld, J. Humphrey,**Robustness in Evolved Grid Structures*in Proceedings of the 2009 Congress on Evolutionary Computation, PP 1343-1350, 2009.- D. Ashlock and J. Tsang,
*Evolved Art via Control of Cellular Automata*in Proceedings of the 2009 Congress on Evolutionary Computation, PP 3338-3344, 2009. - D. Ashlock and T. VonKonigslow,
*Diagnostic Character Location within the Cryptic Skipper Butterfly Species Complex with an Evolutionary Algorithm*, in Proceedings of the 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, PP 92-99, 2009. - D. Ashlock and W. Ashlock,
*Simulation of the Impact of Retroviruses on Genome Organization of an Artificial Organism*, in Proceedings of the 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, PP 140-147, 2009. - D. Ashlock and C. Lee,
*Using Diffusion Characters for the Taxonomy of Self-Organizing Social Networks*, in Proceedings of the 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, PP 60-67, 2009. - D. Ashlock and S. Houghten,
*Title: DNA Error Correcting Codes: No Crossover,*in Proceedings of the 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, PP 38-45, 2009. - D. Ashlock, T. VonKonigslow, E. Clare and W. Ashlock,
*Transience in the Simulation of Ring Species*, Proccedings of the 2008 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, PP 256-263, 2008. - D. Ashlock and C. Lee,
*Characterization of Extremal Epidemic Networks with Diffusion Characters*Proccedings of the 2008 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, PP 264-271, 2008. - D. Ashlock and N. Rogers,
*A Model of Emotion in the Prisoner's Dilemma*Proceedings of the 2008 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, PP 272-279, 2008. - D. Ashlock and E. Warner,
*Classifying Synthetic and Biological DNA Sequences with Side Effect Machines*Proceedings of the 2008 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, PP 22-29, 2008. - D. A. Ashlock, K. M. Bryden, and S. Corns
*Small Population Effects and Hybridization*, in Proceedings of the 2008 Congress on Evolutionary Computation, PP 2642-2648, 2008. - D. A. Ashlock and E. Warner,
*The Geometry of Tartarus Fitness Cases*, in Proceedings of the 2008 Congress on Evolutionary Computation, PP 1309-1316, 2008. - D. A. Ashlock and F. Jafargholi,
*Behavioral Regimes in the Evolution of Extremal Epidemic Graphs*, in Proceedings of the 2008 Congress on Evolutionary Computation, PP 660-667, 2008. - D. A. Ashlock and T. von Konigslow,
*Evolution of Artifical Ring Species*, in Proceedings of the 2008 Congress on Evolutionary Computation, PP 653-659, 2008. - D. Ashlock and E. Warner,
*Side Effect Machines for Sequence Classification*, in Proceedings of the Canadian Conference on Electrical & Computer Engineering 2008, PP 1453-1456, 2008. - C. Lee and D. Ashlock,
*Diffusion Characters: Breaking the Spectral Barrier*, in Proceedings of the Canadian Conference on Electrical & Computer Engineering 2008, PP 847-850, 2008. - D. A. Ashlock and J. Schonfeld,
*A Fractal Representation for Real Optimization*, in Proceedings of the 2007 Congress on Evolutionary Computation, PP 87-94, 2007. - D. A. Ashlock and E.Y. Kim,
*Fingerprint Analysis of the Noisy Prisoner's Dilemma*, in Proceedings of the 2007 Congress on Evolutionary Computation, PP 4073-4080, 2007. - D. Ashlock and B. Jamieson,
*Evolutionary Exploration of Generalized Julia Sets*in the Proceedings of the 2007 IEEE Symposium on Computational Intelligence in Signal Processing, PP 163-170, 2007. - D. Ashlock,
*Cooperation in Prisoner's Dilemma on Graphs*in the Proceedings of the 2007 IEEE Symposium on Computational Intelligence in Games, PP 48-55, 2007. - D. Ashlock and F. Jafargholi,
*Evolving Extremal Epidemic Networks*in the Proceedings of the 2007 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, PP 338-345. - D. Ashlock and L. Guo,
*Evolutionary Parameter Setting of Multi-clustering*in the Proceedings of the 2007 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, PP 25-31, 2007. - S. M. Corns, H. S. Hurd, D. Ashlock and K.M. Bryden,
*Evolutionary Optimization of an Antibiotic Feed Regimen Applied to Multiple Bacteria*, in Intelligent Engineering Systems Through Artificial Neural Networks, Vol 16, PP. 255-260, 2007. - D. Ashlock and K.M. Bryden,
*Function Stacks, GBEAs, and Crossover for the Parity Problem*, in Intelligent Engineering Systems Through Artificial Neural Networks, Vol 16, PP 109-118, 2007. - S. M. Corns, K.M. Bryden, and D.A. Ashlock
*Takeover Times in Graph Based Evolutionary Algorithms*, in Intelligent Engineering Systems Through Artificial Neural Networks, Vol 16, PP 119-124. - D. Ashlock, K.M. Bryden, and N. G. Johnson,
*Evolvable Threaded Controllers for a Multi-agent Grid Robot Task*, in Intelligent Engineering Systems Through Artificial Neural Networks, Vol 16, PP 137-142, 2007. - D. Ashlock and K.M. Bryden,
*Breeding Schedules Improve Grid Robot Performance*, in Intelligent Engineering Systems Through Artificial Neural Networks, Vol 16, PP 143-148, 2007. - D. Ashlock, K.M. Bryden, and A. Toole
*Obstructed Tartarus: Generalizing a Grid Robot Task*, in Intelligent Engineering Systems Through Artificial Neural Networks, Vol 16, PP 149-154, 2007. - B. Karthikeyan. D. Ashlock, and K.M. Bryden,
*A New Image Quality Metric for Evolver, Weighted Voronoi Image Segments*, in Intelligent Engineering Systems Through Artificial Neural Networks, Vol 16, PP. 433-438, 2007. - S. Corns, S. Hurd, D. Ashlock and K. M. Bryden,
*Developing Antibiotic Regimens Using Graph Based Evolutionary Algorithms*in Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, PP. 476-481, 2006. - J. Schonfeld and D. Ashlock,
*Filtration and Depth Annotation Improve Non-linear Projection for RNA Motif Discovery*, in Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, PP 352-359, 2006. - D. Ashlock, K. Cottenie, L. Carson, K.M. Bryden, and S. Corns,
*An Evolutionary Algorithm for the Selection of Geographically Informatics Species*, in Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, PP 279-285, 2006. - D. Ashlock, W. Ashlock and G. Umphrey,
*An Exploration of Differential Utility in Iterated Prisoner's Dilemma*, in Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, PP 271-278, 2006. - D. Ashlock,
*Evolutionary Exploration of the Mandelbrot Set*in the Proceedings of the 2006 Congress On Evolutionary Computation, pages 7432-7439, 2006. - J. Schonfeld and D. Ashlock,
*Evaluating Distance Measures for RNA Motif Search*, in the Proceedings of the 2006 Congress On Evolutionary Computation, pages 8095-8102, 2006. - N. Johnson, B. Karthikeyan, D. Ashlock and K. Bryden,
*AMoEBA Image Segmentation: Modeling of Individual Voronoi Tessellations*, in the Proceedings of the 2006 Congress On Evolutionary Computation, pages 7480-7486, 2006. - S. Corns, D. Ashlock, D. McCorkle and K. Bryden
*Improving Design Diversity Using Graph Based Evolutionary Algorithms*, in the Proceedings of the 2006 Congress On Evolutionary Computation, pages 1037-1043, 2006. - S. Gent, D. Ashlock, A. Willms and K. Bryden,
*Generalized Thermal Agents with Multiple Boundary Conditions and Three-Dimensional Thermal Agents*, in the Proceedings of the 2006 Congress On Evolutionary Computation, pages 10935-10942, 2006. - W. Ashlock and D. Ashlock,
*Changes in Prisoner's Dilemma Strategies Over Evolutionary Time With Different Population Sizes*, in the Proceedings of the 2006 Congress On Evolutionary Computation, pages 1001-1008, 2006. - D. Ashlock, K. Bryden, S. Corns and J. Schonfeld
*An Updated Taxonomy of Evolutionary Computation Problems using Graph-based Evolutionary Algorithms*, in the Proceedings of the 2006 Congress On Evolutionary Computation, pages 403-410, 2006. - D. Ashlock, T. Manikas and K. Ashenayi,
*Evolving A Diverse Collection of Robot Path Planning Problems*, in the Proceedings of the 2006 Congress On Evolutionary Computation, pages 6728-6735, 2006. - D. Ashlock, K. Bryden and S. Gent,
*Simultaneous Evolution of Bracketed L-system Rules and Interpretation*, in the Proceedings of the 2006 Congress On Evolutionary Computation, pages 7403-7410, 2006. - D. Ashlock, B. Karthikeyan and K. Bryden
*Non-photorealistic Rendering of Images as Evolutionary Stained Glass*, in the Proceedings of the 2006 Congress On Evolutionary Computation, pages 7440-7447, 2006. - D. Ashlock,
*Training Function Stacks to Play Iterated Prisoner's Dilemma*in the Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Games, pages 111-118, 2006. - D. Ashlock,
*Grid-Robot Drivers: an Evolutionary Multi-agent Virtual Robotics Task*, in the Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Games, pages 19-26, 2006. - S. Suram, D. S. McCorkle, D. A. Ashlock, K. M. Bryden,
*Modeling Tracking Behavior with Virtual Autonomous Agents,*in Proceedings of the Seventh International Conference in Adaptive Computing in Design and Manufacture, 121-127, 2006. - D. A. Ashlock, J. Schoenfeld, E. Kim, and K. M. Bryden,
*Fitness Webs for Analysis of Braitenberg Vehicles*, in Proceedings of the Seventh International Conference in Adaptive Computing in Design and Manufacture, 109-119, 2006. - D. A. Ashlock, S. P. Gent, and K. M. Bryden,
*Thermal Agents: Learning Harder Thermal Profiles,*Proceedings of the Seventh International Conference in Adaptive Computing in Design and Manufacture, 53-60, 2006. - D. A. Ashlock, A. Willms, S. P. Gent, and K. M. Bryden,
*Rapid Training of Thermal Agents with Gradient Single Parents,*Proceedings of the Seventh International Conference in Adaptive Computing in Design and Manufacture, 191-198, 2006. - B. Karthikeyan, K. M. Bryden, D. A. Ashlock,
*Interactive Engineering Decision Making Using Image Segmentation and Quality Assessment,*Proceedings of the Seventh International Conference in Adaptive Computing in Design and Manufacture, pp. 279-283, 2006. - D. A. Ashlock and J. Schonfeld,
*Depth Annotation of RNA Folds for Secondary Structure Motif Search*, Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, pages 38-45, 2005. - D. A. Ashlock and S. Houghten,
*A Novel Variation Operator for More Rapid Evolution of DNA Error Correcting Codes*, Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, pages 53-60, 2005. - D. A. Ashlock, R. Swanson, and P. S. Schnable,
*Selection of Genetically Diverse Recombinant Inbreds with and Ordered Gene Evolutionary Algorithm*, Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, pages 237-242, 2005. - D. A. Ashlock, K. M. Bryden, and S. P. Gent,
*Evolving L-systems to Locate Edit Metric Codes*, in Smart Engineering System Design: Neural Networks, Fuzzy, Evolutionary Programming, and Artificial Life, edited by C. H. Dagli et al., ASME Press, 15:201-209 , 2005. - D. A. Ashlock and K. M. Bryden,
*Non-Local Adaptation in Bidding Agents*, in Smart Engineering System Design: Neural Networks, Evolutionary Programming, and Artificial Life, edited by C. H. Dagli et al., ASME Press, 15:193-199 , 2005. - S. M. Corns, K. M. Bryden, and D. A. Ashlock,
*The Impact of Novel Connection Topologies on Graph Based Evolutionary Algorithms*, in Smart Engineering System Design: Neural Networks, Evolutionary Programming, and Artificial Life, edited by C. H. Dagli et al., ASME Press, 15:201-209 , 2005. - K. M. Bryden, D. A. Ashlock, and B. Karthikeyan.
*Low-Impact Image Segmentation by Balanced Weighted Voronoi Tessellations*, in Smart Engineering System Design: Neural Networks, Evolutionary Programming, and Artificial Life, edited by C. H. Dagli et al., ASME Press, 15:533-541 , 2005. - D. A. Ashlock, K. M. Bryden, and S. P. Gent.
*Creating Spatially Constrained Virtual Plants Using L-Systems*, in Smart Engineering System Design: Neural Networks, Evolutionary Programming, and Artificial Life, edited by C. H. Dagli et al., ASME Press, 15:185-192 , 2005. - D. A. Ashlock, E.Y. Kim, and L. Guo.
*Multi-clustering: avoiding the natural shape of underlying metrics*, in Smart Engineering System Design: Neural Networks, Evolutionary Programming, and Artificial Life, edited by C. H. Dagli et al., ASME Press, 15:453-461 , 2005. - S. Corns, K. Bryden, D. Ashlock and D. Muth
*On the Effects of Representation on Evolving Grid Robot*, Proceedings of the 2005 Congress on Evolutionary Computation, pages 1135-1140, 2005. - D. Ashlock, K. M. Bryden, and S. Corns,
*Graph Based Evolutionary Algorithms Enhance the Location of Steiner Systems,*Proceedings of the 2005 Congress on Evolutionary Computation, Vol. 2, pages 1861-1866, 2005. - Daniel Ashlock, Kenneth M. Bryden, Wendy Ashlock, and Stephen
P. Gent,
*Rapid Training of Thermal Agents with Single Parent Genetic Programming,*Proceedings of the 2005 Congress on Evolutionary Computation,Vol. 3, pages 2122-2129, 2005. - Wendy Ashlock and Daniel Ashlock,
*Single Parent Genetic Programming*, Proceedings of the 2005 Congress on Evolutionary Computation, Vol 2, pages 1172-1179, 2005. - Daniel Ashlock and Adam Sherk,
*Non-local Adaptation of Artificial Predators and Prey*, Proceedings of the 2005 Congress on Evolutionary Computation, Vol. 1, pages 41-48, 2005. - Daniel Ashlock and Justin Schonfeld,
*Nonlinear Projection for the Display of High Dimensional Distance Data,*Proceedings of the 2005 Congress on Evolutionary Computation, Vol. 3, pages 2776-2783, 2005. - Daniel Ashlock, Stephen P. Gent, and Kenneth M. Bryden,
*Evolution of L-systems for Compact Virtual Landscape Generation,*Proceedings of the 2005 Congress on Evolutionary Computation, Vol. 3, pages 2760-2767, 2005. - Daniel Ashlock and Eun-Youn Kim,
*Techniques for Analysis of Evolved Prisoner's Dilemma Strategies with Fingerprints.*, Proceedings of the 2005 Congress on Evolutionary Computation, Vol 3, pages 2613-2620, 2005. - Justin Schonfeld and Daniel Ashlock,
*A Study of Evolutionary Robustness in Stochastically Tiled Polyominos.*Proceedings of the 2005 Genetic and Evolutionary Computation Conference, pages 19-26. - Daniel Ashlock and Eun-Youn Kim,
*The Impact of Cellular Representation on Finite State Agents for Prisoner's Dilemma*, Proceedings of the 2005 Genetic and Evolutionary Computation Conference, pages 59-66, 2005. - D. A. Ashlock, K. M. Bryden, S. Corns, P. S. Schnable and T.J. Wen,
*Training Finite State Classifiers to Improve PCR Primer Design*, Proceedings of the 10th Annual AIAA/ISSMO Multidisciplinary Analysis and Optimization Conference, Albany, NY, 2004. - Daniel A. Ashlock, Kenneth M. Bryden, and Douglas McCorkle,
*Multi-deme Planned Tournament Selection*, in Intelligent Engineering Systems Through Artificial Neural Networks, Vol 14:217-221, 2004. - Peter G. Anderson and Daniel A. Ashlock,
*Advances in Ordered Greed*, in Intelligent Engineering Systems Through Artificial Neural Networks, Vol 14:223-228, 2004. - Dan Ashlock, Kenneth M. Bryden, Steven Corns, and Stephen J. Willson,
*A Taxonomy of Evolutionary Computation Problems*, in Intelligent Engineering Systems Through Artificial Neural Networks, Vol 14:235-240, 2004. - Steven J. Kirstukas, Kenneth M. Bryden, and Daniel A. Ashlock,
*A Genetic Programming Technique for Solving Systems of Differential Equations*, in Intelligent Engineering Systems Through Artificial Neural Networks, Vol 14:241-246, 2004. - Aaron N. Bryden, Kris A. Bryden, and Daniel A. Ashlock,
*Presenting a large audience interactive multimedia performance driven by a circular Lindenmayer system*, in Intelligent Engineering Systems Through Artificial Neural Networks, Vol 14:253-258, 2004. - Dan Ashlock, Kenneth M. Bryden, and Stephen Patrick Gent,
*Evolutionary Control of Bracked L-system Interpretation*, in Intelligent Engineering Systems Through Artificial Neural Networks, Vol 14:271-276, 2004. - Brian L. Steward, Robert P. Ewing, Daniel A. Ashlock, Amy
L. Kaleita, and Steve M. Shaner,
*Range Operator Enhanced Genetic Algorithms fir Hyperspectral Analysis*, in Intelligent Engineering Systems Through Artificial Neural Networks, Vol 14:295-300, 2004. - Peter E. Johnson, Kenneth M. Bryden, and Daniel A. Ashlock,
*Using Evolutionary Data Segregation Techniques to Reduce the Computation Time Needed to Design Piping Flow using CFD*, in Intelligent Engineering Systems Through Artificial Neural Networks, Vol 14:433-438, 2004. - D. A. Ashlock, S. J. Emrich, K. M. Bryden, S.M. Corns, T.J. Wen,
and P. S. Schnable,
*A Comparison of Evolved Finite State Classifiers and Interpolated Markov Models for Improving PCR Primer Design*,in the Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB '04): 190-197, 2004. - Dan Ashlock and Kenneth M. Bryden,
*Evolutionary Control of L-system Interpretation*, in Proceedings of the 2004 Congress on Evolutionary Computation, Vol 2:2273-2279, 2004. - Sunil Suram, Kenneth M. Bryden, and Daniel Ashlock,
*Quantitative Trait Loci base Solution of an Inverse Radiation Heat Transfer Problem*, in Proceedings of the 2004 Congress on Evolutionary Computation, Vol 1:427-432, 2004. - Daniel Ashlock, Stephen Willson and Nicole Leahy,
*Coevolution and Tartarus*, in Proceedings of the 2004 Congress on Evolutionary Computation, Vol 2:1618-1624, 2004. - Daniel Ashlock, Eun-youn Kim and Warren vonRoeschlaub,
*Fingerprints: Enabling Visualization and Automatic Analysis of Strategies for Two Player Games*, in Proceedings of the 2004 Congress on Evolutionary Computation, Vol 1:381-387, 2004. - Daniel Ashlock, Kenneth Bryden and Steven Corns,
*On Taxonomy of Evolutionary Computation Problems*, in Proceedings of the 2004 Congress on Evolutionary Computation, Vol 2:1713-1719, 2004. - Dan Ashlock and Brad Powers,
*The Effect of Tag Recognition on Non-Local Adaptation*, in Proceedings of the 2004 Congress on Evolutionary Computation, Vol2:2045-2051. - Daniel Ashlock and James Lathrop,
*Program Induction: Building a Wall*, in Proceedings of the 2004 Congress on Evolutionary Computation, Vol 2:1844-1850, 2004. - Dan Ashlock and Jessica Oftelie,
*Simulation of Floral Specialization in Bees*, in Proceedings of the 2004 Congress on Evolutionary Computation, Vol 2:1859-1864. - Justin Schonfeld and Dan Ashlock,
*Comparison of Robustness of Solutions Located by Evolutionary Computation and Other Search Algorithms*, in Proceedings of the 2004 Congress on Evolutionary Computation, Vol 1:250-257, 2004. - Kenneth Bryden, Daniel Ashlock and Douglas McCorkle,
*An Application of Graph Based Evolutionary Algorithms for Diversity Preservation*, in Proceedings of the 2004 Congress on Evolutionary Computation, Vol 1:419-426. - Dan Ashlock and Nicole Leahy,
*A Representational Study of Game Theoretic Simulations, in SMCia/03: Proceedings of the 2003 IEEE Conference on Soft Computing in Industrial Applications*:67-72, 2003. - Dan Ashlock, Dean C. Adams, David Doty,
*Morphometric Grayscale Texture Analysis using Foot Patterns*, in Proceedings of the 2003 Congress on Evolutionary Computation:1575-1581, 2003. - Dan Ashlock, Elizabeth Blankenship, Jonathan D. Gandrud,
*A Note on General Adaptation in Populations of Painting Robots*, in Proceedings of the 2003 Congress on Evolutionary Computation: 46-53, 2003. - Dan Ashlock and Kenneth M. Bryden,
*Thermal Agents: An Application of Genetic Programming to Virtual Engineering*, in Proceedings of the 2003 Congress on Evolutionary Computation: 1340-1347, 2003. - Douglas S. McCorkle, Kenneth M. Bryden, Daniel
A. Ashlock
*Planned Tournament Selection*, Proceedings of ANNIE: 385-390, 2003. - Balu Karthikeyan, Kenneth M. Bryden, Daniel A. Ashlock,
*Visualizing Information Flow in Evolving Graph-based Population*, Proceedings of ANNIE:299-305, 2003. - Peter E. Johnson, Kenneth M. Bryden, Daniel A. Ashlock,
*Solution of a 2-D Inverse Heat Conduction Problem Using Evolutionary Data Segregation Techniques*, Proceedings of ANNIE:315-320, 2003. - Steven M. Corns, Kenneth M. Bryden, Daniel A. Ashlock,
*Rate of Information Transfer in Graph Based Evolutionary Algorithms*, Proceedings of ANNIE:261-266, 2003. - Kenneth M. Bryden and Daniel A. Ashlock,
*Thermal Agents: Learning Thermal Profiles for Rapid Design*, Proceedings of ANNIE:939-945, 2003. - Steven M. Corns, Kenneth M. Bryden, Daniel A. Ashlock,
*Evolutionary Optimization Using Graph Based Evolutionary Algorithms*, proceedings of IMECE, 2003. - Peter E. Johnson, Kenneth M. Bryden, Daniel A. Ashlock,
*Inverse Solution of a Heat Conduction Problem Using Evolutionary Data Segregation Techniques*, proceedings of IMECE, 2003. - Kris Bryden, Kevin Meinert, Dan Ashlock and Kenneth Bryden,
*Transforming Data into Music Using Fractal Algorithms*, in Intelligent Engineering Systems Through Artificial Neural Networks: 665-670, 2002. - Steve Kirstukas, Kenneth Bryden and Daniel A. Ashlock,
*Evolving Solutions of Differential Equations Utilizing Analytical Derivatives*, in Intelligent Engineering Systems Through Artificial Neural Networks:275-280, 2002. - Dan Ashlock, Kenneth Bryden, Peter Johnson and Douglas McCorkle,
*Improving Data Segregation with a Graph Based Evolutionary Algorithm*, in Intelligent Engineering Systems Through Artificial Neural Networks:417-422, 2002. - Dan Ashlock, Andrew Wittrock, and Tsui-Jung Wen,
*Training Finite State Classifiers to Improve PCR Primer Design*, in Proceedings of the 2002 Congress on Evolutionary Computation:13-18, 2002. - Dan Ashlock, Ling Guo, and Fang Qiu,
*Greedy Closure Genetic Algorithms*,in Proceedings of the 2002 Congress on Evolutionary Computation:1296-1301, 2002. - P. Johnson, M. Bryden, D. Ashlock, and E. Vasquez,
*Evolving Cooperative Partial Functions for Data Summary and Interpolation*, in Intelligent Engineering Systems through Artificial Neural Networks:405-410, 2001. - Daniel Ashlock and Jennifer Freeman,
*A Pure Finite State Baseline for Tartarus*, in Proceedings of the 2000 Congress on Evolutionary Computation:1223-1230, 2000. - Daniel Ashlock and James B. Golden III,
*Iterated Function Systems Fractals for the Detection and Display of DNA Reading Frame*, in Proceedings of the 2000 Congress on Evolutionary Computation:1160-1167, 2000. - Daniel Ashlock,
*Data Crawlers for Optical Character Recognition*, in Proceedings of the 2000 Congress on Evolutionary Computation:706-713, 2000. - 21. Kenneth Bryden, Carolina Cruz-Neira, Jeff Doran, Daniel
Ashlock, and Shaohau Liu,
*Interactive Design of Fluid Systems in a Virtual Environment*, in Proceedings of the 4th International Immersive Projection Technology Workshop, Ames Iowa, June 19-20:CD- ROM, 2000. - J. L Davidson, R. Thompson, and D. Ashlock,
*Protein Structure Matching by Genetic Algorithm*, in Proceedings of the 2000 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, Las Vegas:225-231, 2000. - Daniel Ashlock and Jennifer L. Davidson,
*Texture Synthesis with Tandem Genetic Algorithms using Nonparametric Partially Ordered Markov Models*, om Proceedings of the 1999 Congress on Evolutionary Computation:1157-1163, 1999. - Daniel Ashlock, Mark Smucker, and John Walker,
*Graph Based Genetic Algorithms*, in Proceedings of the 1999 Congress on Evolutionary Computation:1362-1368, 1999. - Daniel Ashlock and John Mayfield,
*Acquisition of General Adaptive Features by Evolution*in EP VII, Proceedings of the Seventh Annual Conference on Evolutionary Programming:75-84, 1998. - Daniel Ashlock and James Lathrop,
*A Fully Characterized Test Suite for Genetic Programming*, in EP VII, Proceedings of the Seventh Annual Conference on Evolutionary Programming:537-546, 1998. - C. Richter, G. Sheble, and D. Ashlock,
*Effects of Tree Size and State Number on GP-Automata Bidding Strategies*, in Genetic Programming 1998, Proceedings of the Second Annual Conference on Genetic Programming:329-337, 1998. - D. Ashlock and M. Joenks,
*ISAc Lists: A Different Program Induction Method*, in Genetic Programming 1998, Proceedings of the Second Annual Conference on Genetic Programming:18-26, 1998. - D. Ashlock and J. Davidson,
*Lexicodes in the Space of Foot Patterns for Image Classification*, in Proceedings of the 1998 IEEE Southwest Symposium on Image Analysis and Interpretation, Tucson, AZ: 97-102, 1998. - Daniel Ashlock,
*GP-Automata for Dividing the Dollar*, in Genetic Programming 1997, Proceedings of the Second Annual Conference on Genetic Programming:18-26, 1997. - Charles Richter and Daniel Ashlock,
*The Effect of Splitting Populations on Bidding Strategies*, in Genetic Programming 1997, Proceedings of the Second Annual Conference on Genetic Programming:27-34, 1997. - D. Ashlock, D. Zheng, and J. L. Davidson,
*Genetic Algorithms for Automatic Texture Classification*, om Statistical and Stochastic Methods in Image Processing II, (F. Preteux, C. Cougherty, J. Davidson, eds.), Proceedings of SPIE, Vol. 3167:140-151, 1997. - Daniel Ashlock, John Walker, and James Oliver,
*Evolution of Ultrasimple Virtual Robots*, Proceedings of the 1996 IEEE International Joint Symposia on Intelligence and Systems. - Xia Hau, Jennifer Davidson, and Daniel Ashlock,
*A comparison of genetic algorithm, regression, and Newton's method for parameter estimation of texture models*, Proceedings of the IEEE Southwest Symposium on Image Analysis and Interpretation, San Antonio, TX:201-206, 1996. - C. Engbretson, J. L. Davidson, and D. Ashlock,
*Genetic Algorithms for Texture Model Identification and Synthesis*, in Statistical and Stochastic Methods in Image Processing, (E. Dougherty, F. Preteux, J. Davidson, eds.), Proceedings of SPIE 2823:20-31, 1996. - Jennifer Davidson, Xia Hau, and Daniel Ashlock,
*Texture Analysis Using Genetic Algorithms and Partially Ordered Markov Models*, in the Proceedings of the International Society for Optical Engineering (SPIE) Conference on Neural, Morphological, and Stochastic Methods in Image and Signal, 2568:197-208, 1995. - E. A. Stanley, Daniel Ashlock, and Mark Smucker,
*Iterated Prisoner's Dilemma with Choice and Refusal of Partners: Evolutionary Results*, om Advances in Artificial Life : Third European Conference on Artificial Life:1995. - D. Ashlock, E. A. Stanley, L. Tesfatsion,
*Iterated Prisoner's Dilemma with Choice and Refusal*, in Alife III, ed. Christopher Langton:131-176, 1994.

- D. Ashlock,
*Exploring Representation in Evolutionary Level Design*, Morgan and Claypool. This is a research monograph on using evolutionary computation to design levels for video games. - E.Y. Kim and D. Ashlock,
*On the Design of Game-Playing Agents*, Morgan and Claypool. This is a research monograph on techniques for designing agents to play mathematical games. - D. Ashlock,
*Fast Start Calculus for Physics*, Ashlock and McGuinness Consulting. This is a first-year calculus text written in support of the IPS 1500-1510 course, 480 pages. Currently in its third edition. - D. Ashlock, C. McGuinness and W. Ashlock,
*Representation in Evolutionary Computation*Chapter in Invited Speakers Book for the 2012 Congress on Evolutionary Computation. - D. Ashlock,
*Optimization and Modeling with Evolutionary Computation*, Springer-Verlag, 2006. This text is an undergraduate introduction to evolutionary computation. - D. Ashlock,
*Application of Evolutionary Computation to Bioinformatics*, Chapter 2 in*Genome Exploitation: Data Mining the Genome*, J. Perry, R. Shoemaker, J. W. Snape eds, PP 13-30, Springer, 2005. - D. Ashlock and J. W. Goldin III,
*Evolutionary Computation and Fractal Visualization of Sequence Data*, Chapter 11, in Evolutionary Computation in Bioinformatics, Gary B. Fogel and David W. Corne eds., Morgan Kauffman, 2002.*Invited Publication.* - J.A. Dickerson, D. Berleant, Z. Cox, W. Qi, D. Ashlock,
E.S. Wurtele, and A.W. Fulmer,
*Creating and Modeling Metabolic and Regulatory Networks Using Text Mining and Fuzzy Expert Systems*, in Computational Biology and Genome Informatics, edited by Jason T. L. Wang, Cathy H. Wu, Paul Wang, World Scientific Publishing:Singapore:207-238, 2003.*Invited Publication* - D. Ashlock,
*Finding Designs with Genetic Algorithms*, Chapter 4 in Computational and Constructive Design Theory, edited by Wal Wallis:1996.*Invited Publication*

*Vector Space Techniques for Gene Sequence Analysis*, Pioneer Hi-Bred International,**$40,000**,(01/01/99-12/31/01).- Extraction of Gene Regulation Patterns From Expression Data,
Pioneer Hi-Bred International,
**$11,264.00**, (8/23/99-6/30/00). - Visualization of Gene Expression Data, Pioneer Hi-Bred
International,
**$20,000**,(01/01/00-12/31/00). - Bioinformatics Tools for Extraction and Modeling of Signal
Transduction Networks, Proctor and Gamble Corporation,
**$220,000**, (9/15/00-12/31/02). - An Integrate Database for Barley Genomics, United States
Department of Agriculture,
**$50,000**(8/15/02-8/14/03). - Family Math Night, NSF,
**$21,802**(9/1/99-6/30/03). - Bioinformatics and Representation, NSERC,
**$63,000**(9/1/05-8/31/07). - Adaptive computation for Biological Modeling, NSERC,
**$113,450**(8/31/08-8/31/12). - Developing and Integrated Course in Mathematics and the
Physical Sciences, Guelph Learning Enhancement Fund,
**$100,000**(6/1/09-6/1/10). - Automatic Design, Evolutionary Computation, Computational
Intelligence, Product Design, Self-inking stamps, Inteligence
Augmentation, NSERC Engage grant with TCI Stamps,
**$22,869**, (6/1/11-3/31/12). - Adaptive Planning for Smart Manufacturing, NSERC Engage grant with
Polycon Corporation,
**$19,339**, (1/1/12-9/31/12). - Develop a Software Platform using a Smartphone Interface and a
Cloud-Based Application to Enable Consumers to Design Personalized or
Monogrammed Merchandise via an In-Store Kiosk, FedDev Grant with
InStamp Corporation,
**$48,000**(6/1/12-3/10/13).

*Comparison of Methods for Verification of Energy Improvements*, Iowa Energy Center,**$120,000**(6/1/98-5/30/01), PI is Ron Nelson of the ISU Mechanical Engineering Department. Renewed for an additional year, amount includes renewal.- Investigation of Interactive Design of Fluids and Heat Transfer
Systems within a Virtual Environment, IPRT Research Seed-Funding
Program,
**$126,421.00**(7/1/98-6/30/00) , PI is Mark Bryden of the ISU Mechanical Engineering Department. There is one other co-PI. - An Integrated Field Stream Bioinformatics Data System ,
National Institutes of Health,
**$169,540**, (08/15/99-05/15/01), PI is Michael K. Bergman of Visualmetrics Corporation. There are four other co-PIs. - High-Throughput Mapping Tools for Maize Genomics , National
Science Foundation
**$2,947,701**, (09/01/99-08/31/02), PI is Patrick Schnable of the Iowa State Agronomy Department. There are five other co-PIs. - Computational Analysis for Combining Genomic (EST) Sequences and
Expression Profiles, Pioneer Hi-Bred International,
**$20,000**, (01/01/00-12/31/00), PI is Xun Gu of the Iowa State Zoology and Genetic Department. - Algorithms for Resource Allocation under Dynamic Constraints,
Rockwell Collins,
**$159,797.13**, (05/01/00-06/01/01), PI is Eric Bartlett of the Electrical and Computer Engineering Department. - Content Preserving Data Synthesis to Support Rapid Design
CyclesJohn Deere Corporation,
**$45,000**(1/1/03-12/31/04), PI is Kenneth Mark Bryden of the Mechanical Engineering Department. - Statistical, Computational, and Genetic Analysis of HIV
NIH,
**$979,194**(7/1/03-6/30/07), PI is Karin Dorman of the ISU Statistics department. - VCA - A High-Density Genetic Map of Maize Transcripts, NSF,
**$3,255,928**(10/1/03-9/30/06), PI is Patrick Schnable of the ISU Agronomy Deprtment.

- Nicole Leahy, Iowa State,
*Pseudophytes, a system for modeling speciation in plants.*, 2004. - Jessie Campbell, Iowa State,
*Enumeration and symmetry of edit metric spaces*, 2005. - Eun-Youn Kim, Iowa State,
*Fingerprinting: Automatic Analysis of Evolved Game Playing Agents*, 2005. - Justin Schonfeld, Iowa State,
*A modular data analysis pipeline for the discovery of novel RNA motifs.*, 2006. - Ling Guo, Iowa State,
*Bioinformatics in maize genome research*, 2007. - Andrew McEachern,
*Woven String Kernals*, 2013. - Joseph Brown,
*Regression and Classification from Extinction*, 2014. - Colin Lee,
*On Diffusion Character Matrices*, 2014. - Andrew McEachern,
*Woven String Kernals*, current. - Cameron McGuinness,
*Monte-Carlo Tree Search: Analysis and Applications*, current. - Sharron McNicholas,
*Topics in Evolutionary Computation and Model-Based Clustering*, 2016. - Amanda Saunders,
*Stability in Heirarchical Clustering*, current. - Matthew Stoodley,
*Point Packing for Analysis of Large Biological Data Sets*, current. - Rachel Brown,
*Peak Finding in NMR Spectra*, Starting Fall 2018.

- Kurt Warren von Roeschlaub, Iowa State,
*Fingerprinting Evolved Strategies for the Iterated Prisoner's Dilemma*, 1994. - David Garth, Iowa State,
*Permutation polynomials of matrices over the integers (mod n)*, 1995. - Jennifer Freeman, Iowa State,
*Evolving firing squad automata*, 1996. - John Kosmicke, Iowa State,
*Distance Separating Maps*, 1997. - Scott Krajewski, Iowa State,
*Evolving Bridge Table Designs*, 1997. - Johnathan Schultze-Hewitt, Iowa State,
*Controlling chemical reactions with GP-Automata*, 1997. - Doris Brachter, Iowa State,
*Teaching the Metric System Effectively in Community Coleges*2002. - Jessie Campbell, Iowa State,
*Bounds in Edit Metric Codes*, 2002. - Jessica Oftelie, Iowa State,
*Simulation of Floral Specialization in Bees*, 2004. - Brad Powers, Iowa State,
*The Effect of Tag Recognition on Non-local Adaptation*, 2004. - Douglas Ray, Iowa State,
*Heuristics for locating high girth graphs*, 2004. - Taika Von Konigslow,
*Profile hidden Markov models for DNA barcode assessment*, 2006. - Elizabeth Warner,
*Side effect machines for DNA classification*, 2009. - Nick Rogers,
*Simulation of Emotion in Game Playing Agents*, 2009. - Andrew McEachern,
*Side Effect Machines with Nearest Neighbor Training*, 2010. - Elizabeth Shiller,
*Fitting Contact Networks to Epidemic Profiles*, 2012. - Matt Page,
*An Agent Based Model of Stress in the Workplace*, 2014. - Sarah Brown,
*Modeling Task Assignment in and Industrial Setting*, 2013. - Carolyn Pugh,
*Pareato-monitone Functions for Multicriteria Optimization*, 2014. - Lee Ann Barlow,
*Evoling Networks that Facilitate Cooperation*, 2014. - Thomeas Kielstra,
*Parameters Tuning for Graph Evolution*, current.

*An Introduction to Genetic Algorithms*, ISU EE General Seminar, Fall 1991.- Artificial Life for Mathematics, ISU Graduate Student Colloquium, Fall 1992.
- Complexity Issues in Genetic Algorithms, ISU Computer Science Department Complexity Theory Seminar, Fall 1992.
- Theory of Genetic Algorithms, ISU EE General Seminar, October 1992.
- Ashlock's Tales, Math Horror Stories, Math Joys, and Interesting
Math Objects, Clinton Community College, Spring
1993. (
**Funded**) - Iterated Prisoner's Dilemma with Choice and Refusal, Los
Alamos National Laboratories, Summer 1993. (
**Funded**) - Iterated Prisoner's Dilemma with Choice and Refusal, Santa Fe
Institute, Santa Fe, New Mexico, Summer 1993. (
**Funded**) - Simulated Annealing, Genetic Algorithms, and Artificial Life Student Chapter, IEEE computer section, Fall 1993.
- GP-Automata for Process Control, ISU Power Systems Colloquium, Spring 1996.
- One Technique for Finding Rules in Data, ISU Computer Science Colloquium, Fall 1997.
- An Introduction to Genetic Algorithms and Data Mining,
Proctor and Gamble Corporation, Dec 15-16, 1997. (
**Funded**) - Greedy Genetic Algorithms, ISU Signal Processing Seminar, Spring 1998.
- Hybridizing Virtual Robots, ISU Graduate Student Colloquium, Fall 1998.
- Rule Induction from Data, ISU IMSE Departmental Colloquium, Fall 1998.
- Vector Space Techniques for Gene Sequence Comparison, Pioneer HiBred Corporation, Spring 1999.
- Data Visualization, Analysis, and Adaptive Computation., Metabolic Networking in Plants Symposium, hosted by the ISU Botany Dept, Summer 1999.
- Short Course on Genetic Algorithms and Related Technologies.,
Proctor and Gamble Corporation, July 13-16, 1999. (
**Funded**) - What is Bioinformatics, to the Biostatistics Colloquium at the
University of Iowa, Spring 2000. (
**Funded**) - Rectophytes, a computational investigation of abstract biological phenomena, Bioinformatics and Computational Biology Student Seminar Series, Iowa State, Sept. 8th 2000.
- Am I doing Bioinformatics?, Joint Iowa/Iowa State Workshop on Bioinformatics, Iowa City, Iowa, Nov 3-4, 2000.
- Gene Expression Chips: Too Much Data, Botany Club, Iowa State, Nov. 24th, 2000.
- Edit Metric Lexicodes for Embedded Genetic Markers, Iowa State Mathematics Colloquium, Nov. 21st, 2000.
- Error Correcting Codes in DNA Brock University Computer
Science Colloquium, January 14th. 2005. (
**Funded**) - Tartarus ExplorationsKent State University, Computer
Science Colloqium, April 26th, 2006. (
**Funded**) - Multiclustering: Avoiding the Underlying MetricCanadian
Statistical Society Meetings, May 27, 2006. (
**Funded**) - Multiclustering: Definition and Applications, IEEE Workshop on Multimedia, Mining, and Knowledge Discovery, University of Waterloo, October 18, 2007.
- The Impact of Representation on the Evolutionary Prisoner's
Dilemma, Keynote Lecture, IEEE Symposium on the Foundations of
Computational Intelligence, April 3rd, 2007. (
**Funded**) - Side Effect Machines for Sequence classification National
Institute of Mathematical Sciences, DeJong, Korea, June 28,
2008. (
**Funded**). - Evolutionary Computation, Ordinary and Graphical, National
Institute of Mathematical Sciences, DeJong, Korea, June 29,
2008. (
**Funded**)

*Enumerating Permutation Polynomials (mod n)*20th Southeastern International Conference on Combinatorics, Graph Theory and Computing, February, 1989.- A Family of Maximal Star-Free k-Hypergraphs 21st Southeastern International Conference on Combinatorics, Graph Theory and Computing, February, 1990.
- The Costas Invariant for Graphs 23rd Southeastern International Conference on Combinatorics, Graph Theory and Computing, February 1992.
- Sunburn: Exploration of a Model with a Simple Genetic Algorithm First Symposium on Mathematical Modeling in the Undergraduate Curriculum, June 1993.
- Minimal Superpermutations 24th Southeastern International Conference on Combinatorics, Graph Theory and Computing, February 1993.
- Prisoner's Dilemma with Choice and Refusal, Third Conference on Artificial Life, July 1993.
- Equidimensional Gray Codes in Cayley Graphs, 25th Southeastern International Conference on Combinatorics, Graph Theory and Computing, March 1994.
- Edge Separating Maps on Graphs 9th Midwestern Conference on Combinatorics Cryptography and Computing, October 1994.
- Matrix Permutation Polynomials over the Integers (mod n) 26th Southeastern International Conference on Combinatorics, Graph Theory and Computing, March 1994.
- Virtual Robotics: Undergraduate Projects Second Symposium on Mathematical Modeling in the Undergraduate Curriculum, June 1995.
- GP-Automata For Dividing the Dollar 1997 Genetic Programming Conference, July 1997.
- A Fully Characterized Test Suite for Genetic Programming , 1998 Conference on Evolutionary Programming, March 1998.
- Mathematical Models with Examples, NCTM 1998 National Meeting, February 1998.
- Acquisition of General Adaptive Features by Evolution , 1998 Conference on Evolutionary Programming, March 1998.
- ISAc lists: a Different Program Induction Technique 1998 Genetic Programming Conference, July 1998.
- Texture Synthesis with Tandem Genetic Algorithms using Nonparametric Partially Ordered Markov Models, 1999 Congress on Evolutionary Computation, July 1999.
- Graph Based Genetic Algorithms 1999 Congress on Evolutionary Computation, July 1999.
- A Pure Finite State Baseline for Tartarus, 2000 Congress on Evolutionary Computation, July 16-19, San Diego Ca.
- Iterated Function System Fractals for the Detection and Display of DNA Reading Frame, 2000 Congress on Evolutionary Computation, July 16-19, San Diego Ca.
- Training Finite Sate Classifiers to Improve PCR Primer Design, WCCI 2002, May 12-17, Honolulu, Hawaii.
- Greedy Closure Genetic Algorithms, WCCI 2002, May 12-17, Honolulu, Hawaii.
- Improving Data Segregation with a Graph Based Evolutionary Algorithm, ANNIE 2002, November 10-13 2002, St. Louis, Missouri.
- Thermal Agents: Learning Thermal Profiles for Rapid DesignANNIE 2003, St. Louis, Missouri, November 2003.
- A Note on General Adaptation in Populations of Painting2003 Congress on Evolutionary Computation, Canberra, Australia, December 2003.
- Thermal Agents: An Application of Genetic Programming to Virtual Engineering2003 Congress on Evolutionary Computation, Canberra, Australia, December 2003.
- Morphometric Grayscale Texture Analysis using Foot Patterns2003 Congress on Evolutionary Computation, Canberra, Australia, December 2003.
- Comparison of Evolved Finite State Classifiers and Interpolated Markov Models for Improving PCR Primer Design, at the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology.
- Evolutionary Control of Bracked L-system Interpretation at ANNIE '04, November 2004.
- Taxonomy of evolutionary computation problems at ANNIE '04, November 2004.
- Evolutionary Control of L-system Interpretation at the 2004 Congress on Evolutionary Computation.
- Coevolution and Tartarus at the 2004 Congress on Evolutionary Computation.
- Program Induction: Building a Wall, at the 2004 Congress on
Evolutionary Computation.
## Service

#### Departmental

- DEO selection committee, 1992.
- Awards committee, 1996-97.
- Endowment and Service committee, 1996-1997.
- Graduate committee, 1997-1999.
- Assistant professor IRT, 1997-1999.
- Development committee, 1999-2004
- Awards Committee 2004-2005
- Information technology committee 2004-2005
- Promotion and Tenure committee 2005-6, 2008-9
- Animal Care committee, alternate, 2007-2008
- Cirriculum committee 2008-
- Search Committees:
- Zoology and genetics bioinformatics position 1997-98.
- Bioinformatics center position 1999-2000
- Mathematics bioinformatics search committee 1999-2000
- Animal science bioinformatics position 1999-2000
- Quantum Information appointment committee 2009

#### Interdisciplinary

- Seminar chairman, complex adaptive systems seminar, 1997-2001
- Complex adaptive systems steering committee, 1998-2001
- Director of graduate education and chair, complex adaptive systems program, 2001-2004
- Web master, Iowa Computational Biology Lab, 1998-1999
- List owner, Iowa Computational Biology Lab listserve.
- Web Master, ISU Maize Genome Project, 1998-2002
- Web Master, Laurence H. Baker Center for Bioinformatics and Biological Statistics, 1999-2000
- Computational Biology and Bioinformatics Program Steering Committee, 1999-2001
- Chair, Workshop and Seminar Committee, Bioinformatics Program, 1999-2000
- Morphogenesis Committee, Laurence H. Baker Center for Bioinformatics and Biological Statistics, 1999-2000

#### College

- Liberal Education Implementation Committee, 1996-1998.
- Faculty Senator at large, Liberal Arts and Sciences, 1999
- Faculty Senator, Mathematics, 2000-2001

#### University

- Information Science and Technology Vision Committee, 1999-
- Plant Sciences Institute Director Search Committee, 1999-
- Genetically Modified Organism Task Force, 1999-
- Faculty Senate Governance Council, 1999-2001
- Baker Center Director Search Committee, 2000-2001
- Faculty Senate Elections Committee, 2000-2001
- Alternate, Animal Care Committee, 2005-
- Joint Faculty Policy Committee, 2005-

#### Professional

- Chair, IEEE Bioinformatics and Bioengineering Technical Committee, 2009- Chair, IEEE Task Force on Ecoinformatics, 2008- Chair, IEEE Task Force on Future Directions in Evolutionary Computation, 2009- Chair, IEEE Task Force on Mathematical Games, 2010-
- Editorial Responsibilities:
- Assocaite Editor IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2009-
- Associate Editor, EEE Tansactions on Computational Intelligence and Artifical Intelligence in Games, 2009-
- Associate Editor, Biosystems 2008-
- Associate Editor,
*IEEE Transactions on Evolutionary Computation*, 1999- - Contributing Editor, with Leigh Tesfatsion, of
*Complexity at Large*in Complexity Magazine, 1998-2004

- Referee for:
- Journal of Combinatorial Theory(A)
- Journal of Design Theory.
- IEEE Tansactions on Computational Intelligence and Artifical Intelligence in Games.
- IEEE Transactions on Evolutionary Computation.
- IEEE Transactions on Systems, Man, and Cybernetics.
- Complexity.
- Computers and Graphic.
- EMBL Bioinformatics Journal.
- Biotechnology Progress.
- Mathematical Biosciences.
- 1996 IEEE Conference on Computational Complexity.
- Journal of Graph Theory.
- Artificial Neural Networks in Engineering conference 2003-2007
- Congress on Evolutionary Computation, 2002, 2004-2007.
- Parallel Problem Solving from Nature conference 2008.
- Genetic and Evolutionary Computation Conference 2002, 2005.
- Addison-Wesley (books).

- Program Committees:
- EvoMuseArt 2010.
- 2000, 2002, 2004, 2005, 2006, 2009, 2010 Congress on Evolutionary Computation.
- 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 IEEE Symposium on Computational Inteligence in Bioinformatics and Computational Biology
- 2006, 2007, 2008, 2009, 2010 Computational Inteligence in Games.
- 2005 Genetic and Evolutionary Computation Conference.
- 2003, 2004, 2005, 2006 Artififical Neural Networks in Engineering Conference.

- Reviewer for Math Reviews 1994-2001
- Student Funding Chair and Contest Chair, 1999 Congress on Evolutionary Computation.
- Organizer of special session of "Evolutionary Computation, the Fossil Record", at the 2000 Congress on Evolutionary Computation.
- Contest Chair 2000, 2004, 2005 Congress on Evolutionary Computation.
- Program Chair, 2005 IEEE Symposium of Bioinformatics and Computational Biology.
- General Chair, 2006 IEEE Symposium on Bioinformatics and Computational Biology.
- Special Session on Evolved Art and Music, 2006 Congress on Evolutionary Computation.
- Chair, Evolved Art Contest, 2006 Congress on Evolutionary Computation.

#### Outreach

- Liason Officee, Department of Mathematics and Statsitcs, University of Guelph, 2008-2010
- Departmental Outreach Coordinator, Department of Mathematics and Statsitcs, University of Guelph, 2008-2010
- Outreach Coordinator, University of Guelph College on Physical and Engineering Sciences, University of Guelph, 2008-2010
- Family Math Night at Edwards Elementary School, 1997, 1998, 1999, 2000, 2001, 2002, 2003. Gilbert Elementary School 2002, 2003.
- Industrial short course on genetic algorithms and related technologies, Proctor and Gamble, July 1999.
- Joint Iowa/Iowa State Bioinformatics Workshop, Co-General Chair, Program Chair, 2000.