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Integrative biological simulation praxis: Considerations from physics, philosophy, and data/model curation practices.

Sarma GP, Faundez V.

Cell Logist. 2017 Nov 29;7(4):e1392400. doi: 10.1080/21592799.2017.1392400. eCollection 2017.


Atmospheric escape from the TRAPPIST-1 planets and implications for habitability.

Dong C, Jin M, Lingam M, Airapetian VS, Ma Y, van der Holst B.

Proc Natl Acad Sci U S A. 2018 Jan 9;115(2):260-265. doi: 10.1073/pnas.1708010115. Epub 2017 Dec 28.


Origin of life in a digital microcosm.

C G N, LaBar T, Hintze A, Adami C.

Philos Trans A Math Phys Eng Sci. 2017 Dec 28;375(2109). pii: 20160350. doi: 10.1098/rsta.2016.0350.


A probabilistic framework for identifying biosignatures using Pathway Complexity.

Marshall SM, Murray ARG, Cronin L.

Philos Trans A Math Phys Eng Sci. 2017 Dec 28;375(2109). pii: 20160342. doi: 10.1098/rsta.2016.0342.


Information theory, evolutionary innovations and evolvability.

Wagner A.

Philos Trans R Soc Lond B Biol Sci. 2017 Dec 5;372(1735). pii: 20160416. doi: 10.1098/rstb.2016.0416.


Evolution of drift robustness in small populations.

LaBar T, Adami C.

Nat Commun. 2017 Oct 18;8(1):1012. doi: 10.1038/s41467-017-01003-7.


Biomolecular information gained through in vitro evolution.

Aita T, Husimi Y.

Biophys Rev. 2010 Feb;2(1):1-11. doi: 10.1007/s12551-009-0021-8. Epub 2009 Dec 15. Review.


How evolution learns to generalise: Using the principles of learning theory to understand the evolution of developmental organisation.

Kouvaris K, Clune J, Kounios L, Brede M, Watson RA.

PLoS Comput Biol. 2017 Apr 6;13(4):e1005358. doi: 10.1371/journal.pcbi.1005358. eCollection 2017 Apr.


Different Evolutionary Paths to Complexity for Small and Large Populations of Digital Organisms.

LaBar T, Adami C.

PLoS Comput Biol. 2016 Dec 6;12(12):e1005066. doi: 10.1371/journal.pcbi.1005066. eCollection 2016 Dec.


Evolution of Genome Size in Asexual Digital Organisms.

Gupta A, LaBar T, Miyagi M, Adami C.

Sci Rep. 2016 May 16;6:25786. doi: 10.1038/srep25786.


The meaning of biological information.

Koonin EV.

Philos Trans A Math Phys Eng Sci. 2016 Mar 13;374(2063). pii: 20150065. doi: 10.1098/rsta.2015.0065.


Evolution of integrated causal structures in animats exposed to environments of increasing complexity.

Albantakis L, Hintze A, Koch C, Adami C, Tononi G.

PLoS Comput Biol. 2014 Dec 18;10(12):e1003966. doi: 10.1371/journal.pcbi.1003966. eCollection 2014 Dec.


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.


Drake's rule as a consequence of approaching channel capacity.

Shadrin AA, Parkhomchuk DV.

Naturwissenschaften. 2014 Nov;101(11):939-54. doi: 10.1007/s00114-014-1235-6. Epub 2014 Sep 17.


Hypothesizing the body's genius to trigger and self-organize its healing: 25 years using a standardized neurophysics therapy.

Ross SN, Ware K.

Front Physiol. 2013 Nov 19;4:334. doi: 10.3389/fphys.2013.00334. eCollection 2013.


Systematic analysis of compositional order of proteins reveals new characteristics of biological functions and a universal correlate of macroevolution.

Persi E, Horn D.

PLoS Comput Biol. 2013;9(11):e1003346. doi: 10.1371/journal.pcbi.1003346. Epub 2013 Nov 21.


The minimal complexity of adapting agents increases with fitness.

Joshi NJ, Tononi G, Koch C.

PLoS Comput Biol. 2013;9(7):e1003111. doi: 10.1371/journal.pcbi.1003111. Epub 2013 Jul 11.


Fusion of locomotor maneuvers, and improving sensory capabilities, give rise to the flexible homing strikes of juvenile zebrafish.

Westphal RE, O'Malley DM.

Front Neural Circuits. 2013 Jun 7;7:108. doi: 10.3389/fncir.2013.00108. eCollection 2013.


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.

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