Daniel Ashlock

Position

Associate Professor of Mathematics,
Faculty, Bioinformatics and Computational Biology Program,
Faculty, Ecology and Evolutionary Biology Program,
Chair, Complex Adaptive Systems Program,
Member of the Graduate Faculty.

Personal Data

Born: December 14, 1961,
Wife: Wendy,
Children: Charlotte, Peter, Richard.

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.

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Professional Experience

Consultant, Proctor and Gamble Corporation, 1998-
Consultant, Electric Power Research Institute, 1995-1996
Iowa State University, Associate Professor of Mathematics 1996-
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

• Combinatorics: graph theory, algebraic combinatorics, coding theory, computational and experimental techniques.
• Evolutionary computation: representation, application, modeling. Includes genetic algorithms and genetic programming.
• Bioinformatics: high throughput techniques, data mining, theory.
• Computational biology: modeling of evolution, speciation, and ecologies.

Recent Teaching

Students

Masters Students

Doctoral Students

Curriculum Development

1. (1991)Development of "sports day" a competitive problem working technique that enhances student attendance, student-instructor dialogue, and student retention of information. The "sports day" rules are available at href="http://www.math.iastate.edu/danwell/sdrules.txt".
2. (1994)Developed Math 378, Optimization and Modeling with Artificial Life. This course has run 5 times. I maintain a homepage for this course with extensive lecture notes.
3. (1998)Developed CS/Math/Genetics 594, with Jim Cornette, Drena Dobbs, David Fernandez-Baca, and Patrick Schnable. This course has run twice, I was the primary instructor for the first offering, Volker Brendel has taken over the course.
4. (1999)Formed the Complex Adaptive Systems graduate minor, with Veronica Dark, Vasant Honavar, John Mayfield, Bill Robinson, Gerald Sheble, and Leigh Tesfatsion. I had primary responsibility for taking the program through the approval process.
5. (1999)Aided in forming the Bioinformatics and Computational Biology graduate major, with Drena Dobbs, Patrick Schnable, Dan Voytas, and many others.
6. (1999)Developed CS/Math/Genetics 592, with Drena Dobbs. This course has run once. I maintain a homepage for this course with lecture notes.
7. (In Progress)Development of Math 394x, Introduction to Bioinformatics, for undergraduates. Anticipated first run of the course, Spring 2001.
8. (In Progress)Development of Survey of Complex Adaptive Systems, introductory graduate course for the complex adaptive systems program.

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Publications

Journal Articles

1. Compositional Attractors and Enumeration of Permutation Polynomials Over Finite Fields, Journal of Pure and Applied Algebra 81 (1992)1-9.
2. The Costas Invariant for Graphs, Congress Numerantium 90 (1992) 7-14.
3. Permutation Polynomials on Abelian Group Rings, Journal of Pure and Applied Algebra 86 (1993) 1-5.
4. Minimal Superpermutations, (with J. Tillotson), Congressus Numerantium 93(1993), 91-98.
5. Graphical Construction of Cubic Cages, (with D. Schweizer), Congressus Numerantium 112(1995), 213-221.
6. Preferential Partner Selection in an Evolutionary Study of Prisoner's Dilemma, (with E. Ann Stanley, L. Tesfatsion, Mark Smucker), Biosystems 37 (1996) 99-125.
7. On Matrix Structures Invariant under Toda-like Isospectral Flows, (with Kenneth R. Driessel and Irvin Hentzel), Linear Algebra and its Applications 254 (1997) 29-48.
8. Richter, Charles W., Jr., Gerald Sheble, and Daniel Ashlock. Comprehensive Bidding Strategies with Genetic Programming/Finite State Automata, PE-030-PWRS-0-10-1998, IEEE Transactions on Power Systems, Vol. 14, no. 4, November 1999, pp. 1207-1212.
9. 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., Genetics, 160, (2002), 697-716.
10. G.L. Urban, K. M. Bryden, and D. A. Ashlock, Engineering Optimization of an Improved Plancha Stove,, (2001), Energy for Sustainable Development, Vol. VI, No. 2, 9-19.
11. 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 MaizeGenetics Volume 163, February 2003, Pages 685-698.
12. Kenneth M. Bryden, Daniel A. Ashlock, Douglas S. McCorkle, and Gregory L. Urban Optimization of heat transfer utilizing graph based evolutionary algorithms International Journal of Heat and Fluid Flow Volume 24, Issue 2, April 2003, Pages 267-277.
13. Daniel Ashlock and James B. Goldin III, Chaos Automata: Iterated Function Systems with Memory, Physica D. 181(2003), 274-285.
14. 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, 2003, Plant Physiology, 133: 475-481.
15. Zhiqiang Chen, Ron M. Nelson, Daniel Ashlock, Comparison of Methods for Predicting Montly Post Retrofit Energy Use in Buildings(2003) to appear in the Transactions of ASHRAE, Volume 109, Part 2.
16. S. J. Kirstukas, K. M. Bryden, and D. A. Ashlock,A Hybrid Evolutionary Strategy for the Analytical Solution of Differential Equations. (2003) International Journal of Smart Engineering System Design, accepted for publication.
17. Emrich, S. J., Aluru, S., Fu, Y., Wen, T., Narayanan, M., Guo, L., Ashlock, D. A., and P.S. Schnable. A Strategy for Assembling the Maize (Zea mays L.) Genome}, (2004) Bioinformatics, 20(2):140-147.

Refereed Conference Proceedings

1. Iterated Prisoner's Dilemma with Choice and Refusal, (with E. A. Stanley and L. Tesfatsion), in Alife III, ed. Christopher Langton (1994), PP131-176.
2. Texture Analysis Using Genetic Algorithms and Partially Ordered Markov Models, (with Jennifer Davidson and Xia Hua), in the Proceedings of the International Society for Optical Engineering (SPIE) Conference on Neural, Morphological, and Stochastic Methods in Image and Signal, 2568 (1995) PP197-208.
3. Iterated Prisoner's Dilemma with Choice and Refusal of Partners: Evolutionary Results, (with E. Ann Stanley and Mark D. Smucker), Advances in Artificial Life : Third European Conference on Artificial Life (1995).
4. Evolution of Ultrasimple Virtual Robots (with John Walker and James Oliver), Proceedings of the 1996 IEEE International Joint Symposia on Intelligence and Systems.
5. A comparison of genetic algorithm, regression, and Newton's method for parameter estimation of texture models, (with Jennifer Davidson and Xau Hua, Proceedings of the IEEE Southwest Symposium on Image Analysis and Interpretation, San Antonio, TX, (1996) 201-206.
6. Genetic Algorithms for Texture Model Identification and Synthesis, (with C. Engbretson and J. L. Davidson), Statistical and Stochastic Methods in Image Processing, (E. Dougherty, F. Preteux, J. Davidson, eds.), Proceedings of SPIE 2823 (1996), PP 20-31.
7. GP-Automata for Dividing the Dollar, Genetic Programming 1997, Proceedings of the Second Annual Conference on Genetic Programming, (1997), PP 18-26.
8. The Effect of Splitting Populations on Bidding Strategies, (with Charles Richter), Genetic Programming 1997, Proceedings of the Second Annual Conference on Genetic Programming, (1997), PP 27-34.
9. Genetic Algorithms for Automatic Texture Classification, (with Jennifer Davidson and D. Zheng), Statistical and Stochastic Methods in Image Processing II, (F. Preteux, C. Cougherty, J. Davidson, eds.), Proceedings of SPIE, Vol. 3167, (1997), PP 140-151.
10. Aquisition of General Adaptive Features by Evolution, (with John Mayfield), EP VII, Proceedings of the Seventh Annual Conference on Evolutionary Programming, (1998), PP75-84
11. A Full Characterized Test Suite for Genetic Programming, (with James Lathrop) Proceedings of the Seventh Annual Conference on Evolutionary Programming, (1998), PP 537-546.
12. Effects of Tree Size and State Number on GP-Automata Bidding Strategies, (with Charles Richter and Gerald Shebele), Genetic Programming 1998, Proceedings of the Second Annual Conference on Genetic Programming, (1998), 329-337.
13. ISAc Lists: A Different Program Induction Method, (with Mark Joenks), Genetic Programming 1998, Proceedings of the Second Annual Conference on Genetic Programming, (1998), 18-26.
14. Lexicodes in the Space of Foot Patterns for Image Classification, (with J. Davidson), Proceedings of the 1998 IEEE Southwest Symposium on Image Analysis and Interpretation, Tucson, AZ, (1998) 97-102.
15. Lexicodes of Foot Patterns for Object Recognition, (with J. Davidson and V. Kumar), Mathematical Modeling and Estimation Techniques for Computer Vision, Proceedings of SPIE, 3457, San Diego (1998), 97-102.
16. Texture Synthesis with Tandem Genetic Algorithms using Nonparametric Partially Ordered Markov Models, (with Jennifer Davidson), Proceedings of the 1999 Congress on Evolutionary Computation, (1999), PP 1157-1163.
17. Graph Based Genetic Algorithms, (with Mark Smucker and John Walker), Proceedings of the 1999 Congress on Evolutionary Computation, (1999), PP 1362-1368.
18. A Pure Finite State Baseline for Tartarus, (with Jennifer Freeman), Proceedings of the 2000 Congress on Evolutionary Computation, (2000), PP 1223-1230.
19. Iterated Function Systems Fractals for the Detection and Display of DNA Reading Frame, (with Jim Golden), Proceedings of the 2000 Congress on Evolutionary Computation, (2000), PP 1160-1167.
20. Data Crawlers for Optical Character Recognition, Proceedings of the 2000 Congress on Evolutionary Computation, (2000), PP 706-713.
21. Interactive Design of Fluid Systems in a Virtual Environment, (with Kenneth Bryden, Carolina Cruz-Neira, Jef Doran, and Shaohau Liu), Proceedings of the 4th International Immersive Projection Technology Workshop, Ames Iowa, June 19-20, 2000.
22. Protein Structure Matching by Genetic Algorithm (with J. Davidson and R. Thompson), 2000 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, Las Vegas, pp. 225-231 (2000)
23. 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, (2001), PP. 405-410.
24. Dan Ashlock, Andrew Wittrock, and Tsui-Jung Wen, (2001) Training Finite State Classifiers to Improve PCR Primer Design, Proceedings of the 2002 Congress on Evolutionary Computation, PP 13-18.
25. Dan Ashlock, Ling Guo, and Fang Qiu, (2001), Greedy Closure Genetic Algorithms Proceedings of the 2002 Congress on Evolutionary Computation, PP 1296-1301
26. Kris Bryden, Kevin Meinert, Dan Ashlock and Kenneth Bryden, Transforming Data into Music Using Fractal Algorithms, in Intelligent Engineering Systems Through Artificial Neural Networks, PP 665-670.
27. Steve Kirstukas, Kenneth Bryden and Daniel A. Ashlock, Evolving Solutions of Differential Equations Utilizing Analytical Derivatives, in Intelligent Engineering Systems Through Artificial Neural Networks, PP 275-280.
28. 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, PP 417-422.
29. Steven M. Corns, Kenneth M. Bryden, Daniel A. Ashlock, Evolutionary Optimization Using Graph Based Evolutionary Algorithms to appear in the proceddings of IMECE 2003.
30. Peter E. Johnson, Kenneth M. Bryden, Daniel A. Ashlock, Inverse Solution of a Heat Conduction Problem Using Evolutionary Data Segregation Techniques, Proceddings of IMECE 2003.
31. Douglas S. McCorkle, Kenneth M. Bryden, Daniel A. Ashlock, Planned Tournament Selection, Intelligent Engineering Systems Through Artificial Neural Networks, Vol. 13,(2003) PP. 385-390.
32. Balu Karthikeyan, Kenneth M. Bryden, Daniel A. AshlockVisualizing Information Flow in Evolving Graph-based Population Intelligent Engineering Systems Through Artificial Neural Networks, Vol. 13,(2003) PP. 299-305.
33. Peter E. Johnson, Kenneth M. Bryden, Daniel A. AshlockSolution of a 2-D Inverse Heat Conduction Problem Using Evolutionary Data Segregation Techniques, Intelligent Engineering Systems Through Artificial Neural Networks, Vol. 13,(2003) PP. 315-320.
34. Steven M. Corns, Kenneth M. Bryden, Daniel A. Ashlock Rate of Information Transfer in Graph Based Evolutionary Algorithms, Intelligent Engineering Systems Through Artificial Neural Networks, Vol. 13,(2003) PP. 261-266.
35. Kenneth M. Bryden, Daniel A. Ashlock Thermal Agents: Learning Thermal Profiles for Rapid Design, Intelligent Engineering Systems Through Artificial Neural Networks, Vol. 13,(2003) PP. 939-944.
36. Dan Ashlock, Dean C. Adams, David Doty, Morphometric Grayscale Texture Analysis using Foot Patterns Proceedings of the 2003 Congress on Evolutionary Computation, PP. 1575-1581.
37. Dan Ashlock, Elizabeth Blankenship, Jonathan D. Gandrud, A Note on General Adaptation in Populations of Painting Robots, Proceedings of the 2003 Congress on Evolutionary Computation, PP. 46-53.
38. Dan Ashlock and Kenneth M. Bryden, Thermal Agents: An Application of Genetic Programming to Virtual Engineering, Proceedings of the 2003 Congress on Evolutionary Computation, PP. 1340-1347.
39. Dan Ashlock and Kenneth M. Bryden, Evolutionary Control of Lsystem Interpretation, to appear in the proceedings of the 2004 Congress on Evolutionary Computation.
40. Daniel Ashlock, Stephen Willson and Nicole Leahy, Coevolution and Tartarus, to appear in the proceedings of the 2004 Congress on Evolutionary Computation.
41. Daniel Ashlock, Eun-youn Kim and Warren vonRoeschlaub , Fingerprints: Enabling Visualization and Automatic Analysis of Strategies for Two Player Games., to appear in the proceedings of the 2004 Congress on Evolutionary Computation.
42. Daniel Ashlock, Kenneth Bryden and Steven Corns , On Taxonomy of Evolutionary Computation Problems, to appear in the proceedings of the 2004 Congress on Evolutionary Computation.
43. Dan Ashlock and Brad Powers , The Effect of Tag Recognition on Non-Local Adaptation, to appear in the proceedings of the 2004 Congress on Evolutionary Computation.
44. Daniel Ashlock and James Lathrop , Program Induction: Building a Wall, to appear in the proceedings of the 2004 Congress on Evolutionary Computation.
45. Daniel Ashlock and Jessica Oftelie , Simulation of Floral Specialization in Bees, to appear in the proceedings of the 2004 Congress on Evolutionary Computation.
46. Justin Schonfeld and Dan Ashlock , Comparison of Robustness of Solutions Located by Evolutionary Computation and Other Search Algorithms, to appear in the proceedings of the 2004 Congress on Evolutionary Computation.
47. Kenneth Bryden, Daniel Ashlock and Douglas McCorkle , An Application of Graph Based Evolutionary Algorithms for Diversity Preservation, to appear in the proceedings of the 2004 Congress on Evolutionary Computation.

Book Chapters

1. Daniel Ashlock, Finding Designs with Genetic Algorithms, Computational and Constructive Design Theory (edited by Wal Wallis) 1996, Chapter 4. Invited Publication
2. 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, pp.207-238, 2003. Invited Publication
3. Dan Ashlock and James W. Goldin III, (2001), Evolutionary Computation and Fractal Visualization of Sequence Data, Chapter 11, Evolutionary Computation in Bioinformatics, Gary B. Fogel and David W. Corne., Morgan Kauffman, 2002. Invited Publication

Books

1. Daniel Ashlock, Optimization and Modeling with Evolutionary Computation, accepted for publication in 2004 by Springer-Verlag.

Submitted:

1. Kenneth M. Bryden, Daniel A. Ashlock, Stever Corns, Graph Based Evolutionary Algorithms, Submitted to IEEE Transactions on Evolutionary Computation.
2. Daniel Ashlock, Steven Corns, Kenneth M Bryden, Tsui-Jung Wen, Training Finite State Classifiers to Improve PCR Primer Design, Submitted to Genetic Programming and Evolvable Hardware.
3. Daniel Ashlock and Nicole Leahy, A Representational Sensitivity Study of Game Theoretic Simulations, submitted to the 2003 IEEE International Workshop on Soft Computing in Industrial Applications.

Unrefereed Publications

1. Sunburn: Exploration of a Model with a Simple Genetic Algorithm, (with John Walker), Proceedings of the First Symposium on Mathematical Modeling in the Undergraduate Curriculum (1993) PP127-149.
2. Optimization and Modeling with Artificial Life, Lecture Notes for Math 378, (228 pages). (1993-1999).
3. Analyzing Social Network Structures in the Iterated Prisoner's Dilemma with Choice and Refusal (with Ann Stanley and Mark Smucker), Technical Report #1259, University of Wisconsin, Department of Computer Science, (1996).
4. Recoloring Groups of Graphs, (with Mark Lewis), ISU Math Dept. Technical Report M97-06 (1997).
5. A GP-Automata Reprise of Astro Tellers Bulldozer Experiment, (with Mike McRoberts), ISU Math Dept. Technical Report AM97-17 (1997).
6. An arithmetic test suite for genetic programming, (with J. Lathrop), ISU Math Dept. Technical Report AM98-01 (1998).
7. Aquisition of General Adaptive Features by Evolution, (with J. Mayfield) ISU Math Dept. Technical Report AM98-04 (1998).
8. ISAc lists, a different program induction model, (with M. Joenks), ISU Math Dept. Technical Report AM98-05 (1998).
9. Direct Incorporation of State Information:GP-Automata, ISU Math Dept. Technical Report AM98-16 (1998).
10. A Gentle Introduction to Bioinformatic Mathematics, Lecture Notes for Bioinformatics and Computational Biology 484, (146 pages), (1999).

Awards

1. Outstanding Teacher, College of Liberal Arts and Sciences, 1998.
2. Study in a Second Discipline (one semester release), Molecular Biology, Spring 2000.

Funding

Principal Investigator

1. Vector Space Techniques for Gene Sequence Analysis, Pioneer Hi-Bred International, $40,000,(01/01/99-12/31/01).
2. Extraction of Gene Regulation Patterns From Expression Data, Pioneer Hi-Bred International, $11,264.00, (8/23/99-6/30/00).
3. Visualization of Gene Expression Data, Pioneer Hi-Bred International, $20,000,(01/01/00-12/31/00).
4. Bioinformatics Tools for Extraction and Modeling of Signal Transduction Networks, Proctor and Gamble Corporation, $220,000, (9/15/00-12/31/02).
5. An Integrate Database for Barley Genomics, United States Department of Agriculture, $50,000 (8/15/02-8/14/03).
6. Family Math Night, NSF, $21,802 (9/1/996/30/03).

Co-principal Investigator

1. 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.
2. 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.
3. 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.
4. 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.
5. 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.
6. 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.
7. 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.
8. 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.
9. 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.

Pending

1. Range operator enhanced genetic programming (ROE-GP) for hyperspectral analysis, NSF, $389,245(8/1/03-7/31/04), PI is Brian L Steward of the ISU Agricultural Engineering Department.

Selected Invited Lectures

1. An Introduction to Genetic Algorithms, ISU EE General Seminar, Fall 1991.
2. Artificial Life for Mathematics, ISU Graduate Student Colloquium, Fall 1992.
3. Complexity Issues in Genetic Algorithms, ISU Computer Science Department Complexity Theory Seminar, Fall 1992.
4. Theory of Genetic Algorithms, ISU EE General Seminar, October 1992.
5. Ashlock's Tales, Math Horror Stories, Math Joys, and Interesting Math Objects, Clinton Community College, Spring 1993. (Funded)
6. Iterated Prisoner's Dilemma with Choice and Refusal, Los Alamos National Laboratories, Summer 1993. (Funded)
7. Iterated Prisoner's Dilemma with Choice and Refusal, Santa Fe Institute, Santa Fe, New Mexico, Summer 1993. (Funded)
8. Simulated Annealing, Genetic Algorithms, and Artificial Life Student Chapter, IEEE computer section, Fall 1993.
9. GP-Automata for Process Control, ISU Power Systems Colloquium, Spring 1996.
10. One Technique for Finding Rules in Data, ISU Computer Science Colloquium, Fall 1997.
11. An Introduction to Genetic Algorithms and Data Mining, Proctor and Gamble Corporation, Dec 15-16, 1997. (Funded)
12. Greedy Genetic Algorithms, ISU Signal Processing Seminar, Spring 1998.
13. Hybridizing Virtual Robots, ISU Graduate Student Colloquium, Fall 1998.
14. Rule Induction from Data, ISU IMSE Departmental Colloquium, Fall 1998.
15. Vector Space Techniques for Gene Sequence Comparison, Pioneer HiBred Corporation, Spring 1999.
16. Data Visualization, Analysis, and Adaptive Computation., Metabolic Networking in Plants Symposium, hosted by the ISU Botany Dept, Summer 1999.
17. Short Course on Genetic Algorithms and Related Technologies., Proctor and Gamble Corporation, July 13-16, 1999. (Funded)
18. What is Bioinformatics, to the Biostatistics Colloqium at the University of Iowa, Spring 2000. (Funded)
19. Rectophytes, a computational investigation of abstract biological phenomena, Bioinformatics and Computational Biology Student Seminar Series, Iowa State, Sept. 8th 2000.
20. Am I doing Bioinformatics?, Joint Iowa/Iowa State Workshop on Bioinformatics, Iowa City, Iowa, Nov 3-4, 2000.
21. Gene Expression Chips: Too Much Data, Botany Club, Iowa State, Nov. 24th, 2000.
22. Edit Metric Lexicodes for Embedded Genetic Markers, Iowa State Mathematics Colloquim, Nov. 21st, 2000.

Contributed Talks

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

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-
• 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

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-
• Web master, Iowa Computational Biology Lab, 1998-1999
• List owner, Iowa Computational Biology Lab listserve.
• Web Master, ISU Maize Genome Project, 1998-
• 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

Professional

• Editorial Responsibilities:
  • Associate Editor, IEEE Transactions on Evolutionary Computation, 1999-
  • Contributing Editor, with Leigh Tesfatsion, of Complexity at Large in Complexity Magazine, 1998-
• Referee for:
  • Journal of Combinatorial Theory(A)
  • Journal of Design Theory.
  • IEEE Transactions on Evolutionary Computation.
  • Complexity.
  • Mathematical Biosciences.
  • 1996 IEEE Conference on Computational Complexity.
  • Journal of Graph Theory.
  • 2002 Congress on Evolutionary Computation.
  • GEKKO 2002.
  • EMBL Bioinformatics Journal.
  • Biotechnology Progress.
  • Addison-Wesley.
• 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 Congress on Evolutionary Computation.

Outreach

• Family Math Night at Edwards Elementary School, 1997, 1998, 1999, 2000, 2001
• 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.