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1

The evolutionary origin of complex features

Lenski, Richard E., Ofria, Charles, Pennock, Robert T., Adami, Christoph

Journal:

Year:

2003

Language:

english

File:

PDF, 285 KB

english, 2003

2

Understanding Evolutionary Potential in Virtual CPU Instruction Set Architectures

Bryson, David M., Ofria, Charles, Fernando, Chrisantha

Journal:

Year:

2013

Language:

english

File:

PDF, 454 KB

english, 2013

3

[Genetic and Evolutionary Computation] Evolution in Action: Past, Present and Future (A Festschrift in Honor of Erik D. Goodman) ||

Banzhaf, Wolfgang, Cheng, Betty H.C., Deb, Kalyanmoy, Holekamp, Kay E., Lenski, Richard E., Ofria, Charles, Pennock, Robert T., Punch, William F., Whittaker, Danielle J.

Year:

2020

File:

PDF, 24.14 MB

2020

4

The MODES Toolbox: Measurements of Open-Ended Dynamics in Evolving Systems

Dolson, Emily L., Vostinar, Anya E., Wiser, Michael J., Ofria, Charles

Journal:

Artificial Life

Year:

2019

File:

PDF, 1.78 MB

2019

5

Avida: A Software Platform for Research in Computational Evolutionary Biology

Ofria, Charles, Wilke, Claus O.

Journal:

Artificial Life

Year:

2004

Language:

english

File:

PDF, 201 KB

english, 2004

6

WebAL Comes of Age: A Review of the First 21 Years of Artificial Life on the Web

Taylor, Tim, Auerbach, Joshua E., Bongard, Josh, Clune, Jeff, Hickinbotham, Simon, Ofria, Charles, Oka, Mizuki, Risi, Sebastian, Stanley, Kenneth O., Yosinski, Jason

Journal:

Artificial Life

Year:

2016

Language:

english

File:

PDF, 2.79 MB

english, 2016

7

Selective pressures for accurate altruism targeting: evidence from digital evolution for difficult-to-test aspects of inclusive fitness theory

Jeff Clune, Heather J. Goldsby, Charles Ofria and Robert T. Pennock

Journal:

Proceedings Biological Sciences

Year:

2011

Language:

english

File:

PDF, 1.82 MB

english, 2011

8

10.1038/23245

Lenski, Richard E., Ofria, Charles, Collier, Travis C., Adami, Christoph

Journal:

Year:

1999

Language:

english

File:

PDF, 143 KB

english, 1999

9

The Evolutionary Origin of Associative Learning

Pontes, Anselmo, Mobley, Robert B., Ofria, Charles, Adami, Christoph, Dyer, Fred C.

Journal:

American Naturalist

Year:

2019

Language:

english

File:

PDF, 5.17 MB

english, 2019

10

Ecological Specialization and Adaptive Decay in Digital Organisms.

Ostrowski, Elizabeth A., Ofria, Charles, Lenski, Richard E.

Journal:

American Naturalist

Year:

2007

Language:

english

File:

PDF, 992 KB

english, 2007

11

Toward Open-Ended Fraternal Transitions in Individuality

Moreno, Matthew Andres, Ofria, Charles

Journal:

Artificial Life

Year:

2019

Language:

english

File:

PDF, 4.52 MB

english, 2019

12

Natural Selection Fails to Optimize Mutation Rates for Long-Term Adaptation on Rugged Fitness Landscapes

Clune, Jeff, Misevic, Dusan, Ofria, Charles, Lenski, Richard E., Elena, Santiago F., Sanjuán, Rafael, Hurst, Laurence D.

Journal:

PLoS Computational Biology

Year:

2008

Language:

english

File:

PDF, 285 KB

english, 2008

13

Ontogeny Tends to Recapitulate Phylogeny in Digital Organisms.

Jeff Clune, Robert T. Pennock, Charles Ofria, and Richard E. Lenski

Journal:

American Naturalist

Year:

2012

Language:

english

File:

PDF, 324 KB

english, 2012

14

The genotype-phenotype map of an evolving digital organism

Fortuna, Miguel A., Zaman, Luis, Ofria, Charles, Wagner, Andreas, Wilke, Claus O.

Journal:

PLoS Computational Biology

Year:

2017

Language:

english

File:

PDF, 1.51 MB

english, 2017

15

Selective pressures on genomes in molecular evolution

Charles Ofria, Christoph Adami, Travis C. Collier

Journal:

Journal of Theoretical Biology

Year:

2003

Language:

english

File:

PDF, 175 KB

english, 2003

16

[IEEE 2009 IEEE Congress on Evolutionary Computation (CEC) - Trondheim, Norway (2009.05.18-2009.05.21)] 2009 IEEE Congress on Evolutionary Computation - Evolving coordinated quadruped gaits with the HyperNEAT generative encoding

Clune, Jeff, Beckmann, Benjamin E., Ofria, Charles, Pennock, Robert T.

Year:

2009

Language:

english

File:

PDF, 962 KB

english, 2009

17

[IEEE First International Conference on Self-Adaptive and Self-Organizing Systems (SASO 2007) - Cambridge, MA, USA (2007.07.9-2007.07.11)] First International Conference on Self-Adaptive and Self-Organizing Systems (SASO 2007) - Evolution of Cooperative Information Gathering in Self-Replicating Digital Organisms

Beckmann, Benjamin E., McKinley, Philip K., Knoester, David B., Ofria, Charles

Year:

2007

Language:

english

File:

PDF, 1.74 MB

english, 2007

18

[IEEE International Workshop on Software Technologies for Ultra-Large-Scale Systems (ULS '07) - Minneapolis, MN, USA (2007.05.20-2007.05.26)] International Workshop on Software Technologies for Ultra-Large-Scale Systems (ULS '07) - Applying Digital Evolution to the Development of Self-Adaptive ULS Systems

McKinley, Philip K., Cheng, Betty H. C., Ofria, Charles A.

Year:

2007

Language:

english

File:

PDF, 153 KB

english, 2007

19

10.1038/35085569

Wilke, Claus O., Wang, Jia Lan, Ofria, Charles, Lenski, Richard E., Adami, Christoph

Journal:

Year:

2001

Language:

english

File:

PDF, 260 KB

english, 2001

20

[ACM Press the 11th Annual conference - Montreal, Québec, Canada (2009.07.08-2009.07.12)] Proceedings of the 11th Annual conference on Genetic and evolutionary computation - GECCO '09 - Problem decomposition using indirect reciprocity in evolved populations

Goldsby, Heather J., Goings, Sherri, Clune, Jeff, Ofria, Charles

Year:

2009

Language:

english

File:

PDF, 798 KB

english, 2009

21

The Evolutionary Origin of Somatic Cells under the Dirty Work Hypothesis

Goldsby, Heather J., Knoester, David B., Ofria, Charles, Kerr, Benjamin, Keller, Laurent

Journal:

Year:

2014

Language:

english

File:

PDF, 1.03 MB

english, 2014

22

Sexual Reproduction Reshapes the Genetic Architecture of Digital Organisms

Dusan Misevic, Charles Ofria and Richard E. Lenski

Journal:

Proceedings Biological Sciences

Year:

2006

Language:

english

File:

PDF, 1.87 MB

english, 2006

23

Effects of Population Size and Mutation Rate on the Evolution of Mutational Robustness

Santiago F. Elena, Claus O. Wilke, Charles Ofria and Richard E. Lenski

Journal:

Year:

2007

Language:

english

File:

PDF, 1.38 MB

english, 2007

24

[IEEE 2008 International Conference on Autonomic Computing (ICAC) - Chicago, IL, USA (2008.06.2-2008.06.6)] 2008 International Conference on Autonomic Computing - Autonomic Software Development Methodology Based on Darwinian Evolution

Beckmann, Benjamin E., Grabowski, Laura M., McKinley, Philip K., Ofria, Charles

Year:

2008

Language:

english

File:

PDF, 1.36 MB

english, 2008

25

[ACM Press Proceeding of the fifteenth annual conference companion - Amsterdam, The Netherlands (2013.07.06-2013.07.10)] Proceeding of the fifteenth annual conference companion on Genetic and evolutionary computation conference companion - GECCO '13 Companion - Natural selection fails to optimize mutation rates for long-term adaptation on rugged fitness landscapes

Clune, Jeff, Misevic, Dusan, Ofria, Charles, Lenski, Richard E., Elena, Santiago, Sanjuán, Rafael

Year:

2013

Language:

english

File:

PDF, 878 KB

english, 2013

26

Fluctuating environments select for short-term phenotypic variation leading to long-term exploration

Canino-Koning, Rosangela, Wiser, Michael J., Ofria, Charles, Keller, Laurent

Journal:

PLoS Computational Biology

Year:

2019

File:

PDF, 3.42 MB

2019

27

[ACM Press the Genetic and Evolutionary Computation Conference Companion - Kyoto, Japan (2018.07.15-2018.07.19)] Proceedings of the Genetic and Evolutionary Computation Conference Companion on - GECCO '18 - Digital investigations on the evolution of prokaryote photosynthesis regulation

Pontes, Anselmo C., Ofria, Charles

Year:

2018

Language:

english

File:

PDF, 342 KB

english, 2018

28

[ACM Press the Genetic and Evolutionary Computation Conference Companion - Kyoto, Japan (2018.07.15-2018.07.19)] Proceedings of the Genetic and Evolutionary Computation Conference Companion on - GECCO '18 - Visualizing the tape of life

Dolson, Emily, Ofria, Charles

Year:

2018

Language:

english

File:

PDF, 1.25 MB

english, 2018

29

Evolutionary dynamics, epistatic interactions, and biological information

Christopher C. Strelioff, Richard E. Lenski, Charles Ofria

Journal:

Journal of Theoretical Biology

Year:

2010

Language:

english

File:

PDF, 651 KB

english, 2010

30

Coevolution Drives the Emergence of Complex Traits and Promotes Evolvability

Zaman, Luis, Meyer, Justin R., Devangam, Suhas, Bryson, David M., Lenski, Richard E., Ofria, Charles, Keller, Laurent

Journal:

Year:

2014

Language:

english

File:

PDF, 1.10 MB

english, 2014

31

[ACM Press the 13th annual conference - Dublin, Ireland (2011.07.12-2011.07.16)] Proceedings of the 13th annual conference on Genetic and evolutionary computation - GECCO '11 - Rapid host-parasite coevolution drives the production and maintenance of diversity in digital organisms

Zaman, Luis, Devangam, Suhas, Ofria, Charles

Year:

2011

Language:

english

File:

PDF, 1.18 MB

english, 2011

32

[ACM Press the 2016 - Denver, Colorado, USA (2016.07.20-2016.07.24)] Proceedings of the 2016 on Genetic and Evolutionary Computation Conference Companion - GECCO '16 Companion - What Factors Drive the Evolution of Mutualism?

Vostinar, Anya E., Zaman, Luis, Ofria, Charles

Year:

2016

Language:

english

File:

PDF, 931 KB

english, 2016

33

[ACM Press the Genetic and Evolutionary Computation Conference Companion - Kyoto, Japan (2018.07.15-2018.07.19)] Proceedings of the Genetic and Evolutionary Computation Conference Companion on - GECCO '18 - Ecological theory provides insights about evolutionary computation

Dolson, Emily, Ofria, Charles

Year:

2018

Language:

english

File:

PDF, 634 KB

english, 2018

34

[MIT Press The 2019 Conference on Artificial Life - Newcastle, United Kingdom (2019.07.29-2019.08.02)] The 2019 Conference on Artificial Life - On Sexual Selection in the Presence of Multiple Costly Displays

Bohm, Clifford, Ackles, Acacia L., Ofria, Charles, Hintze, Arend

Year:

2019

File:

PDF, 4.63 MB

2019

35

Using Avida to Test the Effects of Natural Selection on Phylogenetic Reconstruction Methods

Hagstrom, George I., Hang, Dehua H., Ofria, Charles, Torng, Eric

Journal:

Artificial Life

Year:

2004

Language:

english

File:

PDF, 83 KB

english, 2004

36

[ACM Press the 2014 conference - Vancouver, BC, Canada (2014.07.12-2014.07.16)] Proceedings of the 2014 conference on Genetic and evolutionary computation - GECCO '14 - There and back again

Bryson, David M., Wagner, Aaron P., Ofria, Charles

Year:

2014

Language:

english

File:

PDF, 2.23 MB

english, 2014

37

[ACM Press the Genetic and Evolutionary Computation Conference Companion - Prague, Czech Republic (2019.07.13-2019.07.17)] Proceedings of the Genetic and Evolutionary Computation Conference Companion on - GECCO '19 - Tag-accessed memory for genetic programming

Lalejini, Alexander, Ofria, Charles

Year:

2019

Language:

english

File:

PDF, 931 KB

english, 2019

38

A Comparison of the Effects of Random and Selective Mass Extinctions on Erosion of Evolutionary History in Communities of Digital Organisms

Yedid, Gabriel, Stredwick, Jason, Ofria, Charles A., Agapow, Paul-Michael, Poon, Art F. Y.

Journal:

Year:

2012

Language:

english

File:

PDF, 827 KB

english, 2012

39

[ACM Press the Genetic and Evolutionary Computation Conference - Kyoto, Japan (2018.07.15-2018.07.19)] Proceedings of the Genetic and Evolutionary Computation Conference on - GECCO '18 - Evolving event-driven programs with SignalGP

Lalejini, Alexander, Ofria, Charles

Year:

2018

Language:

english

File:

PDF, 945 KB

english, 2018

40

Selective Press Extinctions, but Not Random Pulse Extinctions, Cause Delayed Ecological Recovery in Communities of Digital Organisms.

Yedid, Gabriel, Ofria, Charles A., Lenski, Richard E.

Journal:

American Naturalist

Year:

2009

Language:

english

File:

PDF, 661 KB

english, 2009

41

[IEEE 2009 IEEE Symposium on Artificial Life (ALife) - Nashville, TN, USA (2009.03.3-2009.04.2)] 2009 IEEE Symposium on Artificial Life - Applying digital evolution to the design of self-adaptive software

Beckmann, Benjamin E., Grabowski, Laura M., McKinley, Philip K., Ofria, Charles

Year:

2009

Language:

english

File:

PDF, 2.67 MB

english, 2009

42

[ACM Press the 12th annual conference - Portland, Oregon, USA (2010.07.07-2010.07.11)] Proceedings of the 12th annual conference on Genetic and evolutionary computation - GECCO '10 - Evolution of division of labor in genetically homogenous groups

Goldsby, Heather J., Knoester, David B., Ofria, Charles

Year:

2010

Language:

english

File:

PDF, 770 KB

english, 2010

43

[ACM Press the Genetic and Evolutionary Computation Conference Companion - Kyoto, Japan (2018.07.15-2018.07.19)] Proceedings of the Genetic and Evolutionary Computation Conference Companion on - GECCO '18 - Visualizing the tape of life

Dolson, Emily, Ofria, Charles

Year:

2018

File:

PDF, 1.25 MB

2018

44

Interpreting the Tape of Life: Ancestry-Based Analyses Provide Insights and Intuition about Evolutionary Dynamics

Dolson, Emily, Lalejini, Alexander, Jorgensen, Steven, Ofria, Charles

Journal:

Artificial Life

Year:

2020

Language:

english

File:

PDF, 1.49 MB

english, 2020

45

Genetically integrated traits and rugged adaptive landscapes in digital organisms

Ostrowski, Elizabeth A, Ofria, Charles, Lenski, Richard E

Journal:

BMC Evolutionary Biology

Year:

2015

Language:

english

File:

PDF, 931 KB

english, 2015

46

Balancing Robustness and Evolvability

Lenski, Richard E., Barrick, Jeffrey E., Ofria, Charles

Journal:

Year:

2006

Language:

english

File:

PDF, 218 KB

english, 2006

47

[ACM Press the 10th annual conference - Atlanta, GA, USA (2008.07.12-2008.07.16)] Proceedings of the 10th annual conference on Genetic and evolutionary computation - GECCO '08 - How generative encodings fare on less regular problems

Clune, Jeff, Ofria, Charles, Pennock, Robert T.

Year:

2008

Language:

english

File:

PDF, 510 KB

english, 2008

48

[ACM Press the 10th annual conference - Atlanta, GA, USA (2008.07.12-2008.07.16)] Proceedings of the 10th annual conference on Genetic and evolutionary computation - GECCO '08 - Selection for group-level efficiency leads to self-regulation of population size

Beckmann, Benjamin E., McKinley, Philip K., Ofria, Charles

Year:

2008

Language:

english

File:

PDF, 3.18 MB

english, 2008

49

[ACM Press the 13th annual conference - Dublin, Ireland (2011.07.12-2011.07.16)] Proceedings of the 13th annual conference on Genetic and evolutionary computation - GECCO '11 - Modeling the evolutionary dynamics of plasmids in spatial populations

Connelly, Brian D., Zaman, Luis, McKinley, Philip K., Ofria, Charles

Year:

2011

Language:

english

File:

PDF, 17.44 MB

english, 2011

50

[ACM Press the 10th annual conference - Atlanta, GA, USA (2008.07.12-2008.07.16)] Proceedings of the 10th annual conference on Genetic and evolutionary computation - GECCO '08 - Cooperative network construction using digital germlines

Knoester, David B., McKinley, Philip K., Ofria, Charles

Year:

2008

Language:

english

File:

PDF, 773 KB

english, 2008

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