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Charles Ofria, Ph.D. - Publications

Affiliations: 
2002- Computer Science and Engineering Michigan State University, East Lansing, MI 
Area:
Artificial Life, Evolution
Website:
http://www.cse.msu.edu/~ofria/

90 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Lehman J, Clune J, Misevic D. The Surprising Creativity of Digital Evolution: A Collection of Anecdotes from the Evolutionary Computation and Artificial Life Research Communities. Artificial Life. 1-33. PMID 32271631 DOI: 10.1162/Artl_A_00319  0.44
2020 Dolson E, Lalejini A, Jorgensen S, Ofria C. Interpreting the Tape of Life: Ancestry-Based Analyses Provide Insights and Intuition about Evolutionary Dynamics. Artificial Life. 1-22. PMID 32027535 DOI: 10.1162/artl_a_00313  0.92
2019 Vostinar AE, Goldsby HJ, Ofria C. Suicidal selection: Programmed cell death can evolve in unicellular organisms due solely to kin selection. Ecology and Evolution. 9: 9129-9136. PMID 31463010 DOI: 10.1002/Ece3.5460  1
2019 Canino-Koning R, Wiser MJ, Ofria C. Fluctuating environments select for short-term phenotypic variation leading to long-term exploration. Plos Computational Biology. 15: e1006445. PMID 31002665 DOI: 10.1371/Journal.Pcbi.1006445  1
2019 Dolson EL, Vostinar AE, Wiser MJ, Ofria C. The MODES Toolbox: Measurements of Open-Ended Dynamics in Evolving Systems. Artificial Life. 25: 50-73. PMID 30933626 DOI: 10.1162/Artl_A_00280  1
2019 Vostinar AE, Ofria C. Spatial Structure Can Decrease Symbiotic Cooperation. Artificial Life. 1-21. PMID 30681912 DOI: 10.1162/artl_a_00273  0.92
2017 Fortuna MA, Zaman L, Ofria C, Wagner A. The genotype-phenotype map of an evolving digital organism. Plos Computational Biology. 13: e1005414. PMID 28241039 DOI: 10.1371/Journal.Pcbi.1005414  1
2016 Taylor T, Bedau M, Channon A, Ackley D, Banzhaf W, Beslon G, Dolson E, Froese T, Hickinbotham S, Ikegami T, McMullin B, Packard N, Rasmussen S, Virgo N, Agmon E, ... ... Ofria C, et al. Open-Ended Evolution: Perspectives from the OEE Workshop in York. Artificial Life. 408-423. PMID 27472417 DOI: 10.1162/ARTL_a_00210  1
2016 Taylor T, Auerbach JE, Bongard J, Clune J, Hickinbotham S, Ofria C, Oka M, Risi S, Stanley KO, Yosinski J. WebAL Comes of Age: A Review of the First 21 Years of Artificial Life on the Web. Artificial Life. 364-407. PMID 27472416 DOI: 10.1162/Artl_A_00211  1
2016 Ofria C, Wiser M, Dolson E. The Effects of Evolution and Spatial Structure on Diversity in Biological Reserves Artificial Life. 434-441. DOI: 10.7551/978-0-262-33936-0-Ch071  0.92
2016 Ofria C, Wiser MJ, Canino-Koning R. The Evolution of Evolvability: Changing Environments Promote Rapid Adaptation in Digital Organisms Artificial Life. 268-275. DOI: 10.7551/978-0-262-33936-0-Ch047  1
2015 Ostrowski EA, Ofria C, Lenski RE. Genetically integrated traits and rugged adaptive landscapes in digital organisms. Bmc Evolutionary Biology. 15: 83. PMID 25963618 DOI: 10.1186/S12862-015-0361-X  1
2015 Dolson E, Vostinar A, Ofria C. What’s holding artificial life back from open-ended evolution? The Winnower. DOI: 10.15200/Winn.152418.86598  0.92
2014 Zaman L, Meyer JR, Devangam S, Bryson DM, Lenski RE, Ofria C. Coevolution drives the emergence of complex traits and promotes evolvability. Plos Biology. 12: e1002023. PMID 25514332 DOI: 10.1371/Journal.Pbio.1002023  1
2014 Goldsby HJ, Knoester DB, Kerr B, Ofria C. The effect of conflicting pressures on the evolution of division of labor. Plos One. 9: e102713. PMID 25093399 DOI: 10.1371/Journal.Pone.0102713  1
2014 Goldsby HJ, Knoester DB, Ofria C, Kerr B. The evolutionary origin of somatic cells under the dirty work hypothesis. Plos Biology. 12: e1001858. PMID 24823361 DOI: 10.1371/Journal.Pbio.1001858  1
2014 Bryson DM, Wagner AP, Ofria C. There and back again: Gene-processing hardware for the evolution and robotic deployment of robust navigation strategies Gecco 2014 - Proceedings of the 2014 Genetic and Evolutionary Computation Conference. 689-696. DOI: 10.1145/2576768.2598363  1
2014 Johnson AE, Goldsby HJ, Goings S, Ofria C. The evolution of kin inclusivity levels Gecco 2014 - Proceedings of the 2014 Genetic and Evolutionary Computation Conference. 177-184. DOI: 10.1145/2576768.2598283  1
2013 Bryson DM, Ofria C. Understanding evolutionary potential in virtual CPU instruction set architectures. Plos One. 8: e83242. PMID 24376669 DOI: 10.1371/Journal.Pone.0083242  1
2013 Covert AW, Lenski RE, Wilke CO, Ofria C. Experiments on the role of deleterious mutations as stepping stones in adaptive evolution. Proceedings of the National Academy of Sciences of the United States of America. 110: E3171-8. PMID 23918358 DOI: 10.1073/Pnas.1313424110  1
2013 Grabowski LM, Bryson DM, Dyer FC, Pennock RT, Ofria C. A case study of the de novo evolution of a complex odometric behavior in digital organisms. Plos One. 8: e60466. PMID 23577113 DOI: 10.1371/Journal.Pone.0060466  1
2013 Fortuna MA, Zaman L, Wagner AP, Ofria C. Evolving digital ecological networks. Plos Computational Biology. 9: e1002928. PMID 23533370 DOI: 10.1371/Journal.Pcbi.1002928  1
2013 Chandler CH, Ofria C, Dworkin I. Runaway sexual selection leads to good genes. Evolution; International Journal of Organic Evolution. 67: 110-9. PMID 23289565 DOI: 10.1111/j.1558-5646.2012.01750.x  1
2013 Taghizadeh M, Micinski K, Biswas S, Ofria C, Torng E. Distributed cooperative caching in social wireless networks Ieee Transactions On Mobile Computing. 12: 1037-1053. DOI: 10.1109/Tmc.2012.66  1
2012 Goldsby HJ, Dornhaus A, Kerr B, Ofria C. Task-switching costs promote the evolution of division of labor and shifts in individuality. Proceedings of the National Academy of Sciences of the United States of America. 109: 13686-91. PMID 22872867 DOI: 10.1073/Pnas.1202233109  1
2012 Clune J, Pennock RT, Ofria C, Lenski RE. Ontogeny tends to recapitulate phylogeny in digital organisms. The American Naturalist. 180: E54-63. PMID 22854085 DOI: 10.1086/666984  1
2012 Yedid G, Stredwick J, Ofria CA, Agapow PM. A comparison of the effects of random and selective mass extinctions on erosion of evolutionary history in communities of digital organisms. Plos One. 7: e37233. PMID 22693570 DOI: 10.1371/Journal.Pone.0037233  1
2012 Zaman L, Ofria C, Lenski RE. Finger-painting fitness landscapes: An interactive tool for exploring complex evolutionary dynamics Artificial Life 13: Proceedings of the 13th International Conference On the Simulation and Synthesis of Living Systems, Alife 2012. 499-505. DOI: 10.7551/978-0-262-31050-5-Ch065  1
2012 Goldsby HJ, Serra N, Dyer F, Kerr B, Ofria C. The evolution of temporal polyethism Artificial Life 13: Proceedings of the 13th International Conference On the Simulation and Synthesis of Living Systems, Alife 2012. 178-185. DOI: 10.7551/978-0-262-31050-5-Ch025  1
2012 Goings S, Goldsby H, Cheng BHC, Ofria C. An ecology-based evolutionary algorithm to evolve solutions to complex problems Artificial Life 13: Proceedings of the 13th International Conference On the Simulation and Synthesis of Living Systems, Alife 2012. 171-177. DOI: 10.7551/978-0-262-31050-5-Ch024  1
2012 Walker BL, Ofria C. Evolutionary potential is maximized at intermediate diversity levels Artificial Life 13: Proceedings of the 13th International Conference On the Simulation and Synthesis of Living Systems, Alife 2012. 116-120. DOI: 10.7551/978-0-262-31050-5-Ch017  1
2012 Bryson DM, Ofria C. Digital evolution exhibits surprising robustness to poor design decisions Artificial Life 13: Proceedings of the 13th International Conference On the Simulation and Synthesis of Living Systems, Alife 2012. 19-26. DOI: 10.7551/978-0-262-31050-5-Ch003  1
2012 Ofria C, Adami C, Brown A, Bryson DM, Goodman E, James C, Kelsaw T, Lenski R, McKinley P, Pennock RT, Whittaker D. Preface Artificial Life 13: Proceedings of the 13th International Conference On the Simulation and Synthesis of Living Systems, Alife 2012. xv-xx.  1
2011 Clune J, Goldsby HJ, Ofria C, Pennock RT. Selective pressures for accurate altruism targeting: evidence from digital evolution for difficult-to-test aspects of inclusive fitness theory. Proceedings. Biological Sciences / the Royal Society. 278: 666-74. PMID 20843843 DOI: 10.1098/Rspb.2010.1557  1
2011 Connelly BD, Zaman L, McKinley PK, Ofria C. Modeling the evolutionary dynamics of plasmids in spatial populations Genetic and Evolutionary Computation Conference, Gecco'11. 227-233. DOI: 10.1145/2001576.2001608  1
2011 Zaman L, Devangam S, Ofria C. Rapid host-parasite coevolution drives the production and maintenance of diversity in digital organisms Genetic and Evolutionary Computation Conference, Gecco'11. 219-226. DOI: 10.1145/2001576.2001607  1
2011 Clune J, Stanley KO, Pennock RT, Ofria C. On the performance of indirect encoding across the continuum of regularity Ieee Transactions On Evolutionary Computation. 15: 346-367. DOI: 10.1109/Tevc.2010.2104157  1
2011 Goldsby HJ, Knoester DB, Clune J, McKinley PK, Ofria C. The evolution of division of labor Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5778: 10-18. DOI: 10.1007/978-3-642-21314-4_2  1
2011 Clune J, Beckmann BE, Pennock RT, Ofria C. HybrID: A hybridization of indirect and direct encodings for evolutionary computation Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5778: 134-141. DOI: 10.1007/978-3-642-21314-4_17  1
2010 Strelioff CC, Lenski RE, Ofria C. Evolutionary dynamics, epistatic interactions, and biological information. Journal of Theoretical Biology. 266: 584-94. PMID 20659477 DOI: 10.1016/J.Jtbi.2010.07.025  1
2010 Misevic D, Ofria C, Lenski RE. Experiments with digital organisms on the origin and maintenance of sex in changing environments. The Journal of Heredity. 101: S46-54. PMID 20200140 DOI: 10.1093/Jhered/Esq017  1
2010 Beckmann BE, Clune J, Ofria C. Digital evolution with avida Proceedings of the 12th Annual Genetic and Evolutionary Computation Conference, Gecco '10 - Companion Publication. 2917-2925. DOI: 10.1145/1830761.1830923  1
2010 Clune J, Beckmann BE, McKinley PK, Ofria C. Investigating whether HyperNEAT produces modular neural networks Proceedings of the 12th Annual Genetic and Evolutionary Computation Conference, Gecco '10. 635-642. DOI: 10.1145/1830483.1830598  1
2010 Goldsby HJ, Knoester DB, Ofria C. Evolution of division of labor in genetically homogenous groups Proceedings of the 12th Annual Genetic and Evolutionary Computation Conference, Gecco '10. 1357-1364. DOI: 10.1145/1830483.1830507  1
2010 Grabowski LM, Bryson DM, Dyer FC, Ofria C, Pennock RT. Early evolution of memory usage in digital organisms Artificial Life Xii: Proceedings of the 12th International Conference On the Synthesis and Simulation of Living Systems, Alife 2010. 224-231.  1
2010 Connelly BD, Zaman L, Ofria C, McKinley PK. Social structure and the maintenance of biodiversity Artificial Life Xii: Proceedings of the 12th International Conference On the Synthesis and Simulation of Living Systems, Alife 2010. 461-468.  1
2009 Yedid G, Ofria CA, Lenski RE. Selective press extinctions, but not random pulse extinctions, cause delayed ecological recovery in communities of digital organisms. The American Naturalist. 173: E139-54. PMID 19220147 DOI: 10.1086/597228  1
2009 Clune J, Ofria C, Pennock RT. The sensitivity of HyperNEAT to different geometric representations of a problem Proceedings of the 11th Annual Genetic and Evolutionary Computation Conference, Gecco-2009. 675-682. DOI: 10.1145/1569901.1569995  1
2009 Goldsby HJ, Goings S, Clune J, Ofria C. Problem decomposition using indirect reciprocity in evolved populations Proceedings of the 11th Annual Genetic and Evolutionary Computation Conference, Gecco-2009. 105-112. DOI: 10.1145/1569901.1569917  1
2009 Clune J, Beckmann BE, Ofria C, Pennock RT. Evolving coordinated quadruped gaits with the hyperNEAT generative encoding 2009 Ieee Congress On Evolutionary Computation, Cec 2009. 2764-2771. DOI: 10.1109/CEC.2009.4983289  1
2009 Goings S, Ofria C. Ecological approaches to diversity maintenance in evolutionary algorithms 2009 Ieee Symposium On Artificial Life, Alife 2009 - Proceedings. 124-130. DOI: 10.1109/Alife.2009.4937703  1
2009 Beckmann BE, Grabowski LM, McKinley PK, Ofria C. Applying digital evolution to the design of self-adaptive software 2009 Ieee Symposium On Artificial Life, Alife 2009 - Proceedings. 100-107. DOI: 10.1109/Alife.2009.4937700  1
2009 Elsberry WR, Grabowski LM, Ofria C, Pennock RT. Cockroaches, drunkards, and climbers: Modeling the evolution of simple movement strategies using digital organisms 2009 Ieee Symposium On Artificial Life, Alife 2009 - Proceedings. 92-99. DOI: 10.1109/Alife.2009.4937699  1
2009 Ofria C, Bryson DM, Wilke CO. Avida: A software platform for research in computational evolutionary biology Artificial Life Models in Software (Second Edition). 3-35. DOI: 10.1007/978-1-84882-285-6_1  1
2008 Clune J, Misevic D, Ofria C, Lenski RE, Elena SF, Sanjuán R. Natural selection fails to optimize mutation rates for long-term adaptation on rugged fitness landscapes. Plos Computational Biology. 4: e1000187. PMID 18818724 DOI: 10.1371/journal.pcbi.1000187  1
2008 Yedid G, Ofria CA, Lenski RE. 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: 1335-57. PMID 18564346 DOI: 10.1111/J.1420-9101.2008.01564.X  1
2008 Ofria C, Huang W, Torng E. On the gradual evolution of complexity and the sudden emergence of complex features. Artificial Life. 14: 255-63. PMID 18489251 DOI: 10.1162/Artl.2008.14.3.14302  1
2008 McKinley P, Cheng BHC, Ofria C, Knoester D, Beckmann B, Goldsby H. Harnessing digital evolution Computer. 41: 54-63. DOI: 10.1109/Mc.2008.17  1
2008 Goldsby HJ, Cheng BHC, McKinley PK, Knoester DB, Ofria CA. Digital evolution of behavioral models for autonomic systems 5th International Conference On Autonomic Computing, Icac 2008. 87-96. DOI: 10.1109/ICAC.2008.26  1
2008 Beckmann BE, Grabowski LM, McKinley PK, Ofria C. Autonomic software development methodology based on Darwinian evolution 5th International Conference On Autonomic Computing, Icac 2008. 203-204. DOI: 10.1109/ICAC.2008.19  1
2008 Clune J, Ofria C, Pennock RT. How a generative encoding fares as problem-regularity decreases Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5199: 358-367. DOI: 10.1007/978-3-540-87700-4_36  1
2008 Knoester DB, McKinley PK, Ofria C. Cooperative network construction using digital germlines Gecco'08: Proceedings of the 10th Annual Conference On Genetic and Evolutionary Computation 2008. 217-224.  1
2008 Beckmann BE, McKinley PK, Ofria C. Selection for group-level efficiency leads to self-regulation of population size Gecco'08: Proceedings of the 10th Annual Conference On Genetic and Evolutionary Computation 2008. 185-192.  1
2008 Clune J, Ofria C, Pennock RT. How generative encodings fare on less regular problems Gecco'08: Proceedings of the 10th Annual Conference On Genetic and Evolutionary Computation 2008. 867-868.  1
2008 Grabowski LM, Elsberry WR, Ofria C, Pennock RT. On the evolution of motility and intelligent tactic response Gecco'08: Proceedings of the 10th Annual Conference On Genetic and Evolutionary Computation 2008. 209-216.  1
2007 Hang D, Torng E, Ofria C, Schmidt TM. The effect of natural selection on the performance of maximum parsimony. Bmc Evolutionary Biology. 7: 94. PMID 17592626 DOI: 10.1186/1471-2148-7-94  1
2007 Elena SF, Wilke CO, Ofria C, Lenski RE. Effects of population size and mutation rate on the evolution of mutational robustness. Evolution; International Journal of Organic Evolution. 61: 666-74. PMID 17348929 DOI: 10.1111/J.1558-5646.2007.00064.X  1
2007 Ostrowski EA, Ofria C, Lenski RE. Ecological specialization and adaptive decay in digital organisms. The American Naturalist. 169: E1-20. PMID 17206577 DOI: 10.1086/510211  1
2007 Knoester DB, McKinley PK, Ofria CA. Using group selection to evolve leadership in populations of self-replicating digital organisms Proceedings of Gecco 2007: Genetic and Evolutionary Computation Conference. 293-300. DOI: 10.1145/1276958.1277016  1
2007 McKinley PK, Cheng BHC, Ofria CA. Applying digital evolution to the development of self-adaptive ULS systems Proceedings - International Conference On Software Engineering. DOI: 10.1109/ULS.2007.1  1
2007 Goldsby HJ, Knoester DB, Cheng BHC, McKinley PK, Ofria CA. Digitally evolving models for dynamically adaptive systems Proceedings - Icse 2007 Workshops: International Workshop On Software Engineering For Adaptive and Self-Managing Systems, Seams 2007. DOI: 10.1109/SEAMS.2007.6  1
2007 Beckmann BE, McKinley PK, Knoester DB, Ofria C. Evolution of cooperative information gathering in self-replicating digital organisms First International Conference On Self-Adaptive and Self-Organizing Systems, Saso 2007. 65-74. DOI: 10.1109/SASO.2007.24  1
2007 Beckmann BE, McKinley PK, Ofria C. Evolution of an adaptive sleep response in digital organisms Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4648: 233-242.  1
2007 Clune J, Ofria C, Pennock RT. Investigating the emergence of phenotypic plasticity in evolving digital organisms Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4648: 74-83.  1
2007 Knoester DB, McKinley PK, Beckmann B, Ofria C. Directed evolution of communication and cooperation in digital organisms Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4648: 384-394.  1
2006 Lenski RE, Barrick JE, Ofria C. Balancing robustness and evolvability. Plos Biology. 4: e428. PMID 17238277 DOI: 10.1371/Journal.Pbio.0040428  1
2006 Misevic D, Ofria C, Lenski RE. Sexual reproduction reshapes the genetic architecture of digital organisms. Proceedings. Biological Sciences / the Royal Society. 273: 457-64. PMID 16615213 DOI: 10.1098/Rspb.2005.3338  1
2005 Ofria C, Wilke CO. Avida: Evolution experiments with self-replicating computer programs Artificial Life Models in Software. 3-35. DOI: 10.1007/1-84628-214-4_1  1
2004 Chow SS, Wilke CO, Ofria C, Lenski RE, Adami C. Adaptive radiation from resource competition in digital organisms. Science (New York, N.Y.). 305: 84-6. PMID 15232105 DOI: 10.1126/Science.1096307  1
2004 Ofria C, Wilke CO. Avida: a software platform for research in computational evolutionary biology. Artificial Life. 10: 191-229. PMID 15107231 DOI: 10.1162/106454604773563612  1
2004 Hagstrom GI, Hang DH, Ofria C, Torng E. Using Avida to test the effects of natural selection on phylogenetic reconstruction methods. Artificial Life. 10: 157-66. PMID 15107228 DOI: 10.1162/106454604773563586  1
2003 de Visser JA, 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, et al. Perspective: Evolution and detection of genetic robustness. Evolution; International Journal of Organic Evolution. 57: 1959-72. PMID 14575319 DOI: 10.1554/02-750R  1
2003 Ofria C, Adami C, Collier TC. Selective pressures on genomes in molecular evolution. Journal of Theoretical Biology. 222: 477-83. PMID 12781746 DOI: 10.1016/S0022-5193(03)00062-6  1
2003 Lenski RE, Ofria C, Pennock RT, Adami C. The evolutionary origin of complex features. Nature. 423: 139-44. PMID 12736677 DOI: 10.1038/Nature01568  1
2003 Hang D, Ofria C, Schmidt TM, Torng E. The effect of natural selection on phylogeny reconstruction algorithms Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2723: 13-24.  1
2002 Ofria C, Adami C, Collier TC. Design of evolvable computer languages Ieee Transactions On Evolutionary Computation. 6: 420-424. DOI: 10.1109/Tevc.2002.802442  1
2001 Wilke CO, Wang JL, Ofria C, Lenski RE, Adami C. Evolution of digital organisms at high mutation rates leads to survival of the flattest. Nature. 412: 331-3. PMID 11460163 DOI: 10.1038/35085569  1
2000 Adami C, Ofria C, Collier TC. Evolution of biological complexity. Proceedings of the National Academy of Sciences of the United States of America. 97: 4463-8. PMID 10781045 DOI: 10.1073/Pnas.97.9.4463  1
1999 Lenski RE, Ofria C, Collier TC, Adami C. Genome complexity, robustness and genetic interactions in digital organisms. Nature. 400: 661-4. PMID 10458160 DOI: 10.1038/23245  1
1999 Ofria C, Adami C, Collier TC, Hsu GK. Evolution of differentiated expression patterns in digital organisms Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 1674: 129-138. DOI: 10.1007/3-540-48304-7_19  1
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