Publications
(including PDFs, when possible):

70. Fortuna MA, Zaman L, Wagner AP, and Ofria C (2013) Evolving Digital Ecological Networks, PLoS Computational Biology (in press) 69. Chandler CH, Ofria C, and Dworkin I (2012) Runaway Sexual Selection Leads to Good Genes, Evolution. [PDF]

68. Goldsby H, Dornhaus A, Kerr B, and Ofria C (2012) Task Switching Costs Promote the Evolution of Division of Labor and Shifts in Individuality, Proc. Natl. Acad. Sci. USA, 109(34):13686-13691. [PDF]

67. Clune J, Pennock RT, Ofria C, and Lenski RE (2012) Ontogeny Tends to Recapitulate Phylogeny in Digital Organisms, The American Naturalist, 180:E54-E63. [PDF]

66. Goings S, Goldsby HJ, Cheng BHC, and Ofria C (2012) An Ecology-based Evolutionary Algorithm to Evolve Solutions to Complex Problems, Proceedings of the 13th International Conference for Artificial Life, East Lansing, MI. [PDF]

65. Bryson DM, and Ofria C (2012) Digital Evolution Demonstrates Surprising Robustness to Poor Design Decisions, Proceedings of the 13th International Conference for Artificial Life, East Lansing, MI. [PDF]

64. Goldsby H, Serra N, Dyer F, Kerr B, and Ofria C (2012) The Evolution of Temporal Polyethism, Proceedings of the 13th International Conference for Artificial Life, East Lansing, MI. [PDF]

63. Zaman L, Ofria C, and Lenski RE (2012) Finger-painting Fitness Landscapes: An Interactive Tool for Exploring Complex Evolutionary Dynamics, Proceedings of the 13th International Conference for Artificial Life, East Lansing, MI. [PDF]

62. Walker B and Ofria C (2012) Evolutionary Potential is Maximized at Intermediate Diversity Levels, Proceedings of the 13th International Conference for Artificial Life, East Lansing, MI. [PDF]

61. Yedid G, Stredwick J, Ofria C, and Agapow (2012) A Comparison of the Effects of Random and Selective Mass Extinctions on Erosion of Evolutionary History in Communities of Digital Organisms. PLoS ONE. [PDF]

60. Grabowski LM, Bryson DM, Dyer FC, Pennock RT, and Ofria C (2011) Clever Creatures: Case Studies of Evolved Digital Organisms. Proceedings of the Proceedings of the 2011 European Conference on Artificial Life. [PDF]

59. Connelly BD, Zaman L, Ofria C, and McKinley PK (2011). Modeling the Evolutionary Dynamics of Plasmids in Spatial Populations. Proceedings of the 2011 Genetic and Evolutionary Computation Conference. [PDF]

58. Zaman L, Devangam S, and Ofria C (2011). Rapid Host-Parasite Co-Evolution Drives the Production and Maintenance of Diversity in Digital Organisms. Proceedings of the 2011 Genetic and Evolutionary Computation Conference. [PDF]

57. Clune J, Stanley KO, Pennock RT, and Ofria C (2011). On the Performance of Indirect Encoding Across the Continuum of Regularity, IEEE Transactions on Evolutionary Computation, 15(3):346-367. [PDF]

56. Clune J, Goldsby HJ, Ofria C, and Pennock RT (2011). Selective Pressures for Accurate Altruism Targeting: Empirical Support for Difficult-to-Test Aspects of Inclusive Fitness Theory, Proceedings of the Royal Society of London, 278(1706):666-674. [PDF]

55. Strelioff CC, Ofria C, and Lenski RE (2010). Evolutionary Dynamics, epistatic interactions, and Biological Information. Journal of Theoretical Biology, 266(4):584-594. [PDF]

54. Connelly BD, Zaman L, Ofria C, and McKinley PK (2010). Social Structure and the Maintenance of Biodiversity, The Proceedings of the 12th International Conference on Artificial Life, Odense, Denmark.[PDF]

53. Grabowski LM, Bryson DM, Dyer F, Pennock RT, Ofria C (2010). Early Evolution of Memory Usage in Digital Organisms, The Proceedings of the 12th International Conference on Artificial Life, Odense, Denmark. [PDF]

52. Clune J, Beckmann BE, McKinley PK, and Ofria C (2010). Investigating Whether HyperNEAT Produces Modular Neural Networks. The Proceedings of the 2010 Genetic and Evolutionary Computation Conference. Pages 634-642. [PDF]

51. Goldsby HJ, Knoester DB, and Ofria C (2010). Evolution of Division of Labor in Genetically Homogenous Groups. The Proceedings of the 2010 Genetic and Evolutionary Computation Conference. [PDF]

50. Misevic D, Ofria C, and Lenski RE (2010). Experiments with Digital Organisms on the Origin and Maintenance of Sex in Changing Environments. Journal of Heredity. 101(supp 1):S46-54. doi:10.1093/jhered/esq017. [PDF]

49. Clune J, Beckmann BE, Pennock RT, and Ofria C (2009). HybrID: A Hybridization of Indirect and Direct Encodings for Evolutionary Computation. Proceedings of the European Conference on Artificial Life (ECAL), 2009. Budapest, Hungary. [PDF]

48. Goldsby H, Knoester DB, Clune J, McKinley PK, Ofria C (2009). The Evolution of Division of Labor. Proceedings of the European Conference on Artificial Life (ECAL), 2009. Budapest, Hungary. [PDF]

47. Clune J, Pennock R, and Ofria C (2009). The Sensitivity of HyperNEAT to Different Geometric Representations of a Problem. Proceedings of the 2009 Genetic and Evolutionary Computation Conference. [PDF]

46. Goldsby H, Goings S, Clune J, and Ofria C (2009). Problem Decomposition Using Indirect Reciprocity in Evolved Populations. Proceedings of the 2009 Genetic and Evolutionary Computation Conference. [PDF]

45. Clune J, Beckmann B, Ofria C, and Pennock R (2009). Evolving coordinated quadruped gaits using the HyperNEAT generative encoding. Proceedings of the IEEE Congress on Evolutionary Computations, Special Session on Evolutionary Robotics. [PDF]

44. Goings S and Ofria C (2009). Ecological Approaches to Diversity Maintenance in Evolutionary Algorithms. Proceedings of the IEEE Symposium on Artificial Life.

43. Beckmann B, Grabowski L, McKinley P, and Ofria C (2009). Applying Digital Evolution to the Design of Self-Adaptive Software. Proceedings of the IEEE Symposium on Artificial Life. [PDF]

42. Elsberry W, Grabowski L, Ofria C, and Pennock R (2009). Cockroaches, Drunkards, and Climbers: Evolving Simple Movement Strategies Using Digital Organisms. Proceedings of the IEEE Symposium on Artificial Life. [PDF]

41. Yedid G, Ofria C, and Lenski RE (2009). Selective Press Extinctions, but Not Random Pulse Extinctions, Cause Delayed Ecological Recovery in Communities of Digital Organisms, The American Naturalist. 173(4):E139-E154.

40. Clune J, Misevic D, Ofria C, Lenski RE, Elena SF, and Sanjuan R (2008). Natural Selection Fails to Optimize Mutation Rates for Long-Term Adaptation on Rugged Fitness Landscapes, PLoS Computational Biology, 4(9): e1000187. doi:10.1371/journal.pcbi.1000187 [PDF]

39. Yedid G, Ofria C, and Lenski RE (2008). Historical and Contingent Factors Affect Re-Evolution of a Complex Feature Lost During Mass Extinction in Communities of Digital Organisms, Journal of Evolutionary Biology, 21(5):1335-1357.

38. Ofria C, Huang W and Torng E. (2008). On the Gradual Evolution of Complexity and the Sudden Emergence of Complex Features. Artificial Life, 14(3) 255-263. doi:10.1162/artl.2008.14.3.14302 [PDF]

37. Clune J, Ofria C, and Pennock RT (2008). How Generative Encodings Fare on Less Regular Problems, Proceedings of the ACM Genetic and Evolutionary Computation Conference (GECCO-2008), Atlanta GA, July 2008, Pages 867-868. (abstract) http://doi.acm.org/10.1145/1389095.1389263 [PDF]

36. Grabowski LM, Elsberry WR, Pennock RT, and Ofria C. (2008) On the Evolution of Motility and Intelligent Tactic Response, Proceedings of the ACM Genetic and Evolutionary Computation Conference (GECCO-2008), Atlanta GA, July 2008, Pages 209-216. http://doi.acm.org/10.1145/1389095.1389129 [PDF]

35. Knoester DB, McKinley PK, and Ofria C. (2008) Cooperative Network Construction Using Digital Germlines, Proceedings of the ACM Genetic and Evolutionary Computation Conference (GECCO-2008), Atlanta GA, July 2008, Pages 217-224. [PDF]

34. Beckmann B, McKinley PK, and Ofria C. (2008) Selection for Group-Level Efficiency Leads to Self-Regulation of Population Size, Proceedings of the ACM Genetic and Evolutionary Computation Conference (GECCO-2008), Atlanta GA, July 2008, Pages 185-192. [PDF]

33. Beckmann B, Grabowski L, McKinley PK, and Ofria C. (2008) Autonomic Software Development Methodology Based on Darwinian Evolution, Proceedings of the 5th IEEE International Conference on Autonomic Computing, Chicago IL, June 2008. Page 203. (abstract) [PDF]

32. Goldsby HC, Cheng BHC, McKinley PK, Knoester DB, and Ofria C. (2008) Digital Evolution of Behavioral Models for Autonomic Systems, Proceedings of the 5th IEEE International Conference on Autonomic Computing, Chicago IL, June 2008. Pages 86-96 (Best paper award). [PDF]

31. McKinley PK, Cheng BHC, Ofria C, Knoester DB, Beckmann B, and Goldsby HC. (2008) Harnessing Digital Evolution, IEEE Computer, 41(1):54-63. [PDF]

30. Clune J, Ofria C, and Pennock RT. (2007) Investigating the Emergence of Phenotypic Plasticity in Evolving Digital Organisms, Lecture Notes in Computer Science (Proceedings of the 2007 European Conference on Artificial Life), 4648:74-83. [PDF]

29. Beckmann B, McKinley PK, and Ofria C. (2007b) Evolution of an Adaptive Sleep Response in Digital Organisms, Lecture Notes in Computer Science (Proceedings of the 2007 European Conference on Artificial Life), 4648:233-242. [PDF]

28. Knoester DB, McKinley PK, Beckmann B, and Ofria C. (2007b) Directed Evolution of Communication and Cooperation in Digital Organisms, Lecture Notes in Computer Science (Proceedings of the 2007 European Conference on Artificial Life), 4648:384-394. [PDF]

27. Beckmann BE, McKinley PK, Knoester DB, and Ofria C. (2007a) Evolution of Cooperative Information Gathering in Self-Replicating Digital Organisms. Proceedings of the First IEEE International Conference on Self-Adaptive and Self-Organizing Systems (SASO), Boston, Massachusetts, July 2007. Pages 65-76. [PDF]

26. Knoester DB, McKinley PK, and Ofria C. (2007a) Using Group Selection to Evolve Leadership in Populations of Self-Replicating Digital Organisms, Proceedings of the 2007 Genetic and Evolutionary Computation Conference, London, England, July 2007. Pages 293-300. [PDF]

25. Hang D, Torng E, Ofria C, and Schmidt TM. (2007) The Effect of Natural Selection on the Performance of Maximum Parsimony. BMC Evolutionary Biology, 7:94. [PDF]

24. McKinley PK, Cheng BHC, and Ofria C. (2007) Applying Digital Evolution to the Design of Self-Adaptive ULS Systems (position paper), in Proceedings of the Workshop Software Engineering for Adaptive and Self-Managing Systems, with ICSE 2007, Minneapolis, Minnesota, May 2007. [PDF]

23. Goldsby HJ, Knoester DB, Cheng BHC, McKinley PK, and Ofria C. (2007) Digitally Evolving Models for Dynamically Adaptive Systems, in Proceedings of the Workshop Software Engineering for Adaptive and Self-Managing Systems, with ICSE 2007, Minneapolis, Minnesota, May 2007. [PDF]

22. Elena SF, Wilke CO, Ofria C, and Lenski RE. (2007) Effects of population size and mutation rate on the evolution of mutational robustness. Evolution 61(3):666-674. [PDF]

21. Ostrowski E, Ofria C, and Lenski RE (2007). Ecological specialization and adaptive decay in digital organisms, The American Naturalist 169:E1-E20. [PDF]

20. Lenski RE, Barrick JE, Ofria C (2006). Balancing Robustness and Evolvability, PLoS Biology 4(12):e428. [PDF]

19. Rupp M, Torng E, and Ofria C (2006). The evolution of novel body types under differing selective pressures in digital organisms, Proceedings of the Tenth International Conference on Artificial Life (p268-274), Bloomington IN.

18. Misevic D, Ofria C, and Lenski RE (2006). Sexual reproduction reshapes the genetic architecture of digital organisms, Proceedings of the Royal Society of London 273:457-464. [PDF, Supplementary Info]

17. Chow S, Wilke CO, Ofria C, Lenski RE, and Adami C (2004). Adaptive Radiation from Resource Competition in Digital Organisms, Science 305:84-86. [PDF]

16. Ofria C and Wilke CO (2004). Avida: A Software Platform for Research in Computational Evolutionary Biology, Journal of Artificial Life, 10:191-229. [PDF]

15. Hagstrom GI, Hang DH, Ofria C, and Torng E (2004). Using Avida to Test the Effects of Natural Selection on Phylogenetic Reconstruction Methods, Journal of Artificial Life, 10:157-166. [PDF]

14. Huang W, Ofria C, and Torng E (2004). Measuring Biological Complexity in Digital Organisms, Proceedings of the Ninth International Conference on Artificial Life (p315-321), Boston MA, Sept 12-15. [PDF]

13. Goings S, Clune J, Ofria C, and Pennock R (2004). Kin Selection: The Rise and Fall of Kin-Cheaters, Proceedings of the Ninth International Conference on Artificial Life (p303-308), Boston MA, Sept 12-15. [PDF]

12. Misevic D, Lenski RE, and Ofria C (2004). Sexual reproduction and Muller's ratchet in digital organisms, Proceedings of the Ninth International Conference on Artificial Life (p340-345), Boston MA, Sept 12-15. [PDF]

11. de Visser JAGM, Hermisson J, Wagner GP, Ancel Meyers L, Bagheri-Chaichian H, Blanchard JL, Chao L, Cheverud JM, Elena SF, Fontana W, Gibson G, Hansen TF, Krakauer D, Lewontin RC, Ofria C, Rice SH, von Dassow G, Wagner A, and Whitlock MC (2003). Evolution and Detection of Genetic Robustness, Evolution, 57:1959-1972. [PDF]

10. Lenski RE, Ofria C, Pennock RT, and Adami C (2003). The Evolutionary Origin of Complex Features, Nature, 423:139-144. [PDF]

9. Ofria C, Adami C, and Collier TC (2003). Selective Pressures on Genomes in Molecular Evolution, J. Theor. Biology 222:477-483. [PDF]

8. Hang D, Ofria C, Schmidt TS, Torng E (2003). The Effect of Natural Selection on Phylogeny Reconstruction Algorithms, Proceedings of the 2003 Genetic and Evolutionary Computation Conference, pp.13-24. [PDF]

7. Ofria C, Adami C, and Collier TC (2002). Design of Evolvable Computer Languages, IEEE Transactions in Evolutionary Computation, 17:528-532. [PDF]

6. Cooper T and Ofria C (2002). Evolution of stable ecosystems in populations of digital organisms, Proceedings of the Eighth International Conference on Artificial Life, pp. 227-232. Dec 9-13, Sydney NSW Australlia, Russell K. Standish, Mark A. Bedau and Hussein A. Abbass (eds.) [PDF]

5. Wilke CO, Wang J, Ofria C, Adami C, and Lenski RE (2001). Evolution of Digital Organisms at High Mutation Rate Leads To Survival of the Flattest, Nature, 412:331-333. [PDF]

4. Adami C, Ofria C and Collier TC (2000). Evolution of Biological Complexity, Proc. Natl. Acad. Sci. USA 97:4463-4468.[PDF]

3. Lenski RE, Ofria C, Collier TC, and Adami C (1999). Genome complexity, robustness and genetic interactions in digital organisms, Nature 400, 661-664. [PDF]

2. Ofria C, Adami C, Collier TC, and Hsu GK (1999). The evolution of differentiated expression patterns in digital organisms, Lect. Notes Artif. Intell. 1674:129-138. [PDF]

1. Ofria C and Adami C (1999). Evolution of Genetic Organization in Digital Organisms Proc. of DIMACS workshop Evolution as Computation, Jan 11-12 Princeton, NJ, Landweber L and Winfree E, eds (Springer) pp. 167-175. [PDF]

Non-reviewed Publications

* Ofria C, Bryson DM, and Wilke CO (2009). Avida: A Software Platform for Research in Computational Evolutionary Biology. [PDF]