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Items: 36

1.

The genotype-phenotype map of an evolving digital organism.

Fortuna MA, Zaman L, Ofria C, Wagner A.

PLoS Comput Biol. 2017 Feb 27;13(2):e1005414. doi: 10.1371/journal.pcbi.1005414. eCollection 2017 Feb.

2.

Open-Ended Evolution: Perspectives from the OEE Workshop in York.

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, Clark E, McGregor S, Ofria C, Ropella G, Spector L, Stanley KO, Stanton A, Timperley C, Vostinar A, Wiser M.

Artif Life. 2016 Summer;22(3):408-23. doi: 10.1162/ARTL_a_00210. Epub 2016 Jul 29.

PMID:
27472417
3.

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

Taylor T, Auerbach JE, Bongard J, Clune J, Hickinbotham S, Ofria C, Oka M, Risi S, Stanley KO, Yosinski J.

Artif Life. 2016 Summer;22(3):364-407. doi: 10.1162/ARTL_a_00211. Epub 2016 Jul 29. Review.

PMID:
27472416
4.

Genetically integrated traits and rugged adaptive landscapes in digital organisms.

Ostrowski EA, Ofria C, Lenski RE.

BMC Evol Biol. 2015 May 12;15:83. doi: 10.1186/s12862-015-0361-x.

5.

Coevolution drives the emergence of complex traits and promotes evolvability.

Zaman L, Meyer JR, Devangam S, Bryson DM, Lenski RE, Ofria C.

PLoS Biol. 2014 Dec 16;12(12):e1002023. doi: 10.1371/journal.pbio.1002023. eCollection 2014 Dec.

6.

The effect of conflicting pressures on the evolution of division of labor.

Goldsby HJ, Knoester DB, Kerr B, Ofria C.

PLoS One. 2014 Aug 5;9(8):e102713. doi: 10.1371/journal.pone.0102713. eCollection 2014.

7.

The evolutionary origin of somatic cells under the dirty work hypothesis.

Goldsby HJ, Knoester DB, Ofria C, Kerr B.

PLoS Biol. 2014 May 13;12(5):e1001858. doi: 10.1371/journal.pbio.1001858. eCollection 2014 May.

8.

Understanding evolutionary potential in virtual CPU instruction set architectures.

Bryson DM, Ofria C.

PLoS One. 2013 Dec 23;8(12):e83242. doi: 10.1371/journal.pone.0083242. eCollection 2013.

9.

Experiments on the role of deleterious mutations as stepping stones in adaptive evolution.

Covert AW 3rd, Lenski RE, Wilke CO, Ofria C.

Proc Natl Acad Sci U S A. 2013 Aug 20;110(34):E3171-8. doi: 10.1073/pnas.1313424110. Epub 2013 Aug 5.

10.

A case study of the de novo evolution of a complex odometric behavior in digital organisms.

Grabowski LM, Bryson DM, Dyer FC, Pennock RT, Ofria C.

PLoS One. 2013;8(4):e60466. doi: 10.1371/journal.pone.0060466. Epub 2013 Apr 8.

11.

Evolving digital ecological networks.

Fortuna MA, Zaman L, Wagner AP, Ofria C.

PLoS Comput Biol. 2013;9(3):e1002928. doi: 10.1371/journal.pcbi.1002928. Epub 2013 Mar 7.

12.

Runaway sexual selection leads to good genes.

Chandler CH, Ofria C, Dworkin I.

Evolution. 2013 Jan;67(1):110-9. doi: 10.1111/j.1558-5646.2012.01750.x. Epub 2012 Aug 22.

PMID:
23289565
13.

Task-switching costs promote the evolution of division of labor and shifts in individuality.

Goldsby HJ, Dornhaus A, Kerr B, Ofria C.

Proc Natl Acad Sci U S A. 2012 Aug 21;109(34):13686-91. doi: 10.1073/pnas.1202233109. Epub 2012 Aug 7.

14.

Ontogeny tends to recapitulate phylogeny in digital organisms.

Clune J, Pennock RT, Ofria C, Lenski RE.

Am Nat. 2012 Sep;180(3):E54-63. doi: 10.1086/666984. Epub 2012 Jul 16.

PMID:
22854085
15.

A comparison of the effects of random and selective mass extinctions on erosion of evolutionary history in communities of digital organisms.

Yedid G, Stredwick J, Ofria CA, Agapow PM.

PLoS One. 2012;7(5):e37233. doi: 10.1371/journal.pone.0037233. Epub 2012 May 31.

16.

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

Clune J, Goldsby HJ, Ofria C, Pennock RT.

Proc Biol Sci. 2011 Mar 7;278(1706):666-74. doi: 10.1098/rspb.2010.1557. Epub 2010 Sep 15.

17.

Evolutionary dynamics, epistatic interactions, and biological information.

Strelioff CC, Lenski RE, Ofria C.

J Theor Biol. 2010 Oct 21;266(4):584-94. doi: 10.1016/j.jtbi.2010.07.025. Epub 2010 Jul 24.

PMID:
20659477
18.

Experiments with digital organisms on the origin and maintenance of sex in changing environments.

Misevic D, Ofria C, Lenski RE.

J Hered. 2010 Mar-Apr;101 Suppl 1:S46-54. doi: 10.1093/jhered/esq017. Epub 2010 Mar 3.

PMID:
20200140
19.
20.

Natural selection fails to optimize mutation rates for long-term adaptation on rugged fitness landscapes.

Clune J, Misevic D, Ofria C, Lenski RE, Elena SF, Sanjuán R.

PLoS Comput Biol. 2008 Sep 26;4(9):e1000187. doi: 10.1371/journal.pcbi.1000187.

21.

Historical and contingent factors affect re-evolution of a complex feature lost during mass extinction in communities of digital organisms.

Yedid G, Ofria CA, Lenski RE.

J Evol Biol. 2008 Sep;21(5):1335-57. doi: 10.1111/j.1420-9101.2008.01564.x. Epub 2008 Jun 28.

22.

On the gradual evolution of complexity and the sudden emergence of complex features.

Ofria C, Huang W, Torng E.

Artif Life. 2008 Summer;14(3):255-63. doi: 10.1162/artl.2008.14.3.14302.

PMID:
18489251
23.

The effect of natural selection on the performance of maximum parsimony.

Hang D, Torng E, Ofria C, Schmidt TM.

BMC Evol Biol. 2007 Jun 25;7:94.

24.

Effects of population size and mutation rate on the evolution of mutational robustness.

Elena SF, Wilke CO, Ofria C, Lenski RE.

Evolution. 2007 Mar;61(3):666-74.

PMID:
17348929
25.

Balancing robustness and evolvability.

Lenski RE, Barrick JE, Ofria C.

PLoS Biol. 2006 Dec;4(12):e428. No abstract available.

26.

Ecological specialization and adaptive decay in digital organisms.

Ostrowski EA, Ofria C, Lenski RE.

Am Nat. 2007 Jan;169(1):E1-20. Epub 2006 Dec 4.

PMID:
17206577
27.

Sexual reproduction reshapes the genetic architecture of digital organisms.

Misevic D, Ofria C, Lenski RE.

Proc Biol Sci. 2006 Feb 22;273(1585):457-64.

28.

Adaptive radiation from resource competition in digital organisms.

Chow SS, Wilke CO, Ofria C, Lenski RE, Adami C.

Science. 2004 Jul 2;305(5680):84-6.

29.

Avida: a software platform for research in computational evolutionary biology.

Ofria C, Wilke CO.

Artif Life. 2004 Spring;10(2):191-229.

PMID:
15107231
30.

Using Avida to test the effects of natural selection on phylogenetic reconstruction methods.

Hagstrom GI, Hang DH, Ofria C, Torng E.

Artif Life. 2004 Spring;10(2):157-66.

PMID:
15107228
31.

Perspective: Evolution and detection of genetic robustness.

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, Rice SH, von Dassow G, Wagner A, Whitlock MC.

Evolution. 2003 Sep;57(9):1959-72. Review.

PMID:
14575319
32.

Selective pressures on genomes in molecular evolution.

Ofria C, Adami C, Collier TC.

J Theor Biol. 2003 Jun 21;222(4):477-83.

PMID:
12781746
33.

The evolutionary origin of complex features.

Lenski RE, Ofria C, Pennock RT, Adami C.

Nature. 2003 May 8;423(6936):139-44.

PMID:
12736677
34.

Evolution of digital organisms at high mutation rates leads to survival of the flattest.

Wilke CO, Wang JL, Ofria C, Lenski RE, Adami C.

Nature. 2001 Jul 19;412(6844):331-3.

PMID:
11460163
35.

Evolution of biological complexity.

Adami C, Ofria C, Collier TC.

Proc Natl Acad Sci U S A. 2000 Apr 25;97(9):4463-8.

36.

Genome complexity, robustness and genetic interactions in digital organisms.

Lenski RE, Ofria C, Collier TC, Adami C.

Nature. 1999 Aug 12;400(6745):661-4.

PMID:
10458160

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