JOURNAL PUBLICATIONS

On the gradual evolution of complexity and the sudden emergence of complex features.
Ofria C, Huang W and Torng E
(to appear in Artificial Life)

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

Specialization in digital organisms
Ostrowski E, Ofria C, and Lenski RE
The American Naturalist 169:E1-E20 (2007).

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

Sexual reproduction reshapes the genetic architecture of digital organisms
Misevic D, Ofria C, and Lenski RE
to appear in Proceedings of the Royal Society of London: Biological Sciences 273:457-464 (2006).
Paper / Supporting Info

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

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

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

Evolution and Detection of Genetic Robustness
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
Evolution, 57:1959-1972 (2003).
Paper

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

Selective Pressures on Genomes in Molecular Evolution
Ofria C, Adami C, and Collier TC
J. theor. Biology 222:477-483 (2003).
Abstract / Paper

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

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

Evolution of Biological Complexity
Adami C, Ofria C and Collier TC
Proc. Natl. Acad. Sci. USA 97:4463-4468 (2000)
Abstract    Full Paper

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

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

CONFERENCE PUBLICATIONS

Digitally Evolving Models for Dynamically Adaptive Systems
Goldsby HJ, Knoester DB, Cheng BHC, McKinley PK, and Ofria C
(to appear at SEAMS workshop, 2007)

Evolution of Cooperative Information Gathering in Self-Replicating Digital Organisms
Beckmann BE, McKinley PK, Knoester DB, and Ofria C
(to appear at SASO 2007)

Using Group Selection to Evolve Leadership in Populations of Self-Replicating Digital Organisms
Knoester DB, McKinley PK, and Ofria C
(to appear at GECCO 2007)

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

Measuring Biological Complexity in Digital Organisms
Huang W, Ofria C, and Torng E
Proceedings of the Ninth International Conference on Artificial Life (p. 315-321), Boston MA, Sept 12-15 (2004).
Paper

Kin Selection: The Rise and Fall of Kin-Cheaters
Goings S, Clune J, Ofria C, and Pennock R
Proceedings of the Ninth International Conference on Artificial Life (p. 303-308), Boston MA, Sept 12-15 (2004).
Paper

Sexual reproduction and Muller's ratchet in digital organisms
Misevic D, Lenski RE, and Ofria C
Proceedings of the Ninth International Conference on Artificial Life (p. 340-345), Boston MA, Sept 12-15 (2004).
Paper

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

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

Evolution of Genetic Organization in Digital Organisms
Ofria C and Adami C
Proc. of DIMACS workshop Evolution as Computation, Jan 11-12 Princeton, NJ, Landweber L and Winfree E, eds (Springer, 1999) p. 167
Abstract    Full Paper

NON-REFEREED PUBLICATIONS

Avida: Evolution Experiments with Self-Replicating Computer Programs
Ofria C and Wilke CO
Published in Artificial Life Models in Software by Adamatzky A and Komosinski M (Eds.)
Springer Verlag, London, 2005, pages 3-35.

The Avida Technical Manual
Ofria C, Brown CT, and Adami C
Published in Introduction to Artificial Life by Christoph Adami
Telos Springer Verlag, New York 1998, pages 297-350.
Abstract    Full Paper: HTML or PostScript.

The Avida Artificial Life Platform
Ofria C, Wilke C, Collier TC, Adami C, Brown CT, Adler D, Hsu GK
Included on CD with Introduction to Artificial Life by Christoph Adami
Telos Springer Verlag, New York 1998
Webpage

Evolution of genetic codes
Ph.D. Thesis
The California Institue of Technology (1999)
Abstract