Publications

2017


Nitash C G., T. LaBar, A. Hintze, and C. Adami, Origin of Life in a Digital Microcosm. To appear in Phil. Trans. Royal Soc. A (2017).

T. Pinto, L. Cai, C. Wang, and X. Tan, CNT-based sensor arrays for local strain measurements in soft pneumatic actuators, submitted to International Journal of Intelligent Robotics and Applications.

T. LaBar and C. Adami, Evolution of Drift Robustness in Small Populations of Digital Organisms, to appear. [bioRxiv]

S. D. Chapman, C. Adami, C.O. Wilke, and Dukka B. Kc, The Evolution of Logic Circuits for the Purpose of Protein Contact Map Prediction. PeerJ 5 (2017) e3139. [Article]

B. Patra, Y. Kon, G. Yadav, A. Sevold, J. Frumkin, R.R. Vallabhajosyula, A. Hintze, B. Østman, J. Schossau, A. Bhan, B. Marzolf, J. Tamashiro, A. Kaur, N. Baliga, E. Grayhack, C. Adami, D. Galas, A. Raval, E. Phizicky, A. Ray. A Genome-wide Dosage-Rescue Network Reveals Genetic Robustness. Nucleic Acids Research 45 (2017) 255-270. [Article]

T. LaBar and C. Adami, From Entropy to Information: Biased Typewriters and the Origin of Life. In: “From Matter to Life: Information and Causality “, (S.I. Walker, P.C.W. Davies, and G. Ellis, eds.) Cambridge University Press (2016), pp. 130-154. [arXiv]

2016


A. Gupta and C. Adami, Shared Information Between Residues is Sufficient to Detect Epistasis in a Protein. PLoS Genetics 12 (2016) e1006471. [Article][PDF]

R. S. Olson, J. H. Moore, and C. Adami, Evolution of Active Categorical Image Classification via Saccadic Eye Movement. In Proc. “Parallel Problem Solving in Nature” Conference. Lecture Notes in Computer Science 9921 (2016) 581-590. [PDF]

C. Adami, J. Schossau, and A. Hintze, The Reasonable Effectiveness of Agent-based Simulations in Evolutionary Game Theory. Physics of Life Reviews 19 (2016) 38-42. [Article][PDF]

C. Adami, J. Schossau, and A. Hintze, Evolutionary Game Theory Using Agent-based Methods. Physics of Life Reviews 19 (2016) 1-26. [Article]

T. LaBar, A. Hintze, and C. Adami, Evolvability Tradeoffs in Emergent Digital Replicators. Artificial Life 22 (2016) 483-498. [Abstract] [PDF]

T. LaBar and C. Adami, Different Evolutionary Paths to Complexity for Small and Large Populations of Digital Organisms. PLoS Comp. Biol. 12 (2016) 1005066. [Article].

A. Tehrani-Saleh and C. Adami, Flies as Ship Captains? Digital Evolution Unravels Selective Pressures to Avoid Collision in Drosophila. In: Proceedings Artificial Life 15 (C. Gershenson, T. Froese, J.M. Sisqueiros, W. Aguilar, E.J. Izquierdo, H. Sayama, eds.) MIT Press (Cambridge, MA, 2016), pp. 554-561. [Article] [PDF]

R.S Olson, A. Hintze, F.C. Dyer, J.H. Moore, C. Adami, Exploring the Coevolution of Predator and Prey Morphology and Behavior. In: Proceedings Artificial Life 15 (C. Gershenson, T. Froese, J.M. Sisqueiros, W. Aguilar, E.J. Izquierdo, H. Sayama, eds.) MIT Press (Cambridge, MA, 2016), pp. 250-258. [Article] [PDF].

R. S. Olson, D. B. Knoester, and C. Adami, Evolution of Swarming Behavior is Shaped By How Predators Attack. Artificial Life 22 (2016) 299-318. [Journal][PDF]

N. Chaumont and C. Adami, Evolution of Sustained Foraging in Three-Dimensional Environments with Physics. Genetic Programming and Evolvable Machines 17 (2016) 359-390. [Article]

A. Gupta, T. LaBar, M. Miyagi, and C. Adami, Evolution of Genome Size in Asexual Digital Organisms. Sci. Rep. 6 (2016) 25786. [Article]

A. Gupta and C. Adami, Strong Selection Significantly Increases Epistatic Interactions in the Long-Term Evolution of a Protein. PLoS Genetics 12 (2016) e1005960. [Article] [Press Release]

C. Adami, What is Information? Phil. Trans. Roy. Soc. A 374 (2016) 20150230. [Article]

J. Schossau, C. Adami, and A. Hintze, Information-theoretic Neuro-correlates Boost Evolution of Cognitive Systems. Entropy 18 (2016) 6. [Article]

2015


A. Gupta, C.T. Brown, Y. Zheng, and C. Adami, Differentially-Expressed Pseudogenes in HIV-1 Infection. Viruses 7 (2015) 5191-5205 [Journal] [PDF].

P. Kvam, J. Cesario, J. Schossau, H. Eisthen, and A. Hintze, Computational Evolution of Decision-Making Strategies. In: D.C. Noelle, R. Dale, A.S. Warlaumont, J. Yoshimi, T. Matlock, C.D. Jennings, & P.P. Maglio (eds.), Proceedings of the 37th Annual Conference of the Cognitive Science Society (pp. 1225-1230). Austin, TX: Cognitive Science Society. [PDF]

A. Hintze, N. Phillips, and R. Hertwig, The Janus Face of Darwinian Competition. Scientific Reports 5 (2015) 13662 [Article] [Press Release].

R.S. Olson*, P.B. Haley*, F.C. Dyer, and C. Adami, Exploring the Evolution of a Trade-off Between Vigilance and Foraging in Group-living Organisms. Royal Society open sci. 2 (2015) 150135. [Article] [PDF] (*: Joint first authors.)

T. LaBar, C. Adami, and A. Hintze, Does Self-Replication Imply Evolvability? Proc. of European Conference on Artificial Life 2015 (P. Andrews, L. Caves, R. Doursat, S. Hickinbotham, F. Polack, S. Stepney, T. Taylor & J. Timmis, eds.) MIT Press (Cambridge, MA, 2015) pp. 596-602. [Article][PDF]

C. Adami, Information-theoretic Considerations Concerning the Origin of Life. Origins of Life and Evolution of Biospheres 45 (2015) 9439. [Article] [PDF] .

J. Clifford and C. Adami, Discovery and Information-theoretic Characterization of Transcription Factor Binding Sites that Act Cooperatively. Physical Biology 12 (2015) 056004. [Journal] [PDF]

A. Hintze and C. Adami, Punishment in Public Goods Games Leads to Meta-Stable Phase Transitions and Hysteresis. Physical Biology 12 (2015) 046005. [Journal]

C. Adami, Robots with Instincts. Nature 521 (2015) 426-427. [Journal] [PDF]

A. Hintze, R. S. Olson, C. Adami, and R. Hertwig. Risk Sensitivity as an Evolutionary Adaptation. Sci. Rep. 5 (2015) 8242. [Journal] [Press Release]

M. Vital, B. Chai, B. Østman, J. Cole, K. T. Konstantinidis, and J. M. Tiedje. Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification. The ISME Journal 9 (2015) 1130–1140. [Journal]

2014


H.J. Goldsby, D.B. Knoester, B. Kerr, and C. Ofria. The Effect of Conflicting Pressures on the Evolution of Division of Labor. PLoS ONE 9 (2014) e102713. [Journal]

L. Albantakis, A. Hintze, C. Koch, C. Adami, and G. Tononi, Evolution of Integrated Causal Structures in Animats Exposed to Environments of Increasing Complexity. PLoS Comp. Biol. 10 (2014) e1003966 [Journal].

A. E. Johnson, E. Strauss, R. Pickett, C. Adami, I. Dworkin, and H. J. Goldsby. More Bang For Your Buck: Quorum-Sensing Capabilities Improve the Efficacy of Suicidal Altruism. Proceedings of Artificial Life 14 (H. Sayama, J. Rieffel, S. Risi, R. Doursat and H. Lipson, eds.) MIT Press, Cambridge, MA (2014) pp. 25-32. [Proceedings]

D. Higgins, T. Padilla, and A. Hintze. Defining Literary Data: An Information Theoretical Approach. Proceedings JADH Conference (2014).

P.B. Haley, R.S. Olson, F.C. Dyer, and C. Adami. Exploring Conditions that Select for the Evolution of Cooperative Group Foraging. Proceedings of Artificial Life 14 (H. Sayama, J. Rieffel, S. Risi, R. Doursat and H. Lipson, eds.) MIT Press, Cambridge, MA (2014) pp.310-311. [Proceedings]

H.J. Goldsby, D.B. Knoester, C. Ofria, and B. Kerr. The Evolutionary Origin of Somatic Cells under the Dirty Work Hypothesis. PLoS Biology 12 (2014) e1001858. [Journal].

B. Østman, R. Lin, and C. Adami. Tradeoffs Drive Resource Specialization and the Gradual Establishment of Ecotypes. BMC Evol. Biol. 14 (2014) 113 [Journal] [arXiv]

2013


D. B. Knoester, H. J. Goldsby, and P. K. McKinley. Genetic Variation and the Evolution of Consensus in Digital Organisms. IEEE Transactions on Evolutionary Computation 17 (2013) 403-417.

C. Adami. Artificial Evolution. In: “Encyclopaedia of Systems Biology” (W. Dubitzky, O. Wolkenhauer, H. Yokota and K.-H Cho, eds.) Springer Verlag (2013) pp. 39-42. [PDF]

R. S. Olson, M. Mirmomeni, T. Brom, E. Bruger, A. Hintze, D. B. Knoester, and C. Adami. Evolved digital ecosystems: Dynamic steady state, not optimal fixed point. In: “Advances in Artificial Life (ECAL 2013)” (P. Liò, O. Miglino, G. Nicosia, S. Nolfi and M. Pavone, eds.) MIT Press (2013) pp. 126-133. [Proceedings] [PDF] BibTeX

@inproceedings{Olson2013DynamicSteadyState,
author = {Olson, Randal S. and Mirmomeni, Masoud and Brom, Tim and Bruger, Eric and Hintze, Arend and Knoester, David B. and Adami, Christoph},
title = {Evolved digital ecosystems: Dynamic steady state, not optimal fixed point},
booktitle = {Proceedings of the Twelfth European Conference on the Synthesis and Simulation of Living Systems},
series = {ECAL 2013},
year = {2013},
location = {Taormina, Italy},
pages = {126–133},
numpages = {8},
url = {http://dx.doi.org/10.7551/978-0-262-31709-2-ch019},
doi = {10.7551/978-0-262-31709-2-ch019 },
publisher = {MIT Press},
address = {Cambridge, MA, USA}
}

S. D. Chapman, D. B. Knoester, A. Hintze, and C. Adami. Evolution of an artificial visual cortex for image recognition. In: “Advances in Artificial Life (ECAL 2013)” (P. Liò, O. Miglino, G. Nicosia, S. Nolfi and M. Pavone, eds.) MIT Press (2013) pp. 1067-1074. [Proceeedings] [PDF]

R. S. Olson, D. B. Knoester, and C. Adami. Critical Interplay Between Density-dependent Predation and Evolution of the Selfish Herd. Proceedings of GECCO 2013, pp. 247-254. Best paper award in Artificial Life track. [Proceedings] [PDF] BibTeX

@inproceedings{Olson2013SelfishHerd,
author = {Olson, Randal S. and Knoester, David B. and Adami, Christoph},
title = {Critical interplay between density-dependent predation and evolution of the selfish herd},
booktitle = {Proceeding of the fifteenth annual conference on Genetic and evolutionary computation conference},
series = {GECCO ’13},
year = {2013},
location = {Amsterdam, The Netherlands},
pages = {247–254},
numpages = {8},
url = {http://doi.acm.org/10.1145/2463372.2463394},
doi = {10.1145/2463372.2463394},
acmid = {2463394},
publisher = {ACM},
address = {New York, NY, USA}
}

C. Adami and A. Hintze. Evolutionary Instability of Zero-Determinant Strategies Demonstrates That Winning is Not Everything. Nature Communications 4 (2013) 2193. [Journal] [arXiv] [Press release]

B. Østman and C. Adami. Predicting Evolution and Visualizing High-dimensional Fitness Landscapes. In “Recent Advances in the Theory and Application of Fitness Landscapes” (A. Engelbrecht and H. Richter, eds.) Springer Series in Emergence, Complexity, and Computation (2013), pp. 493-510. [Book Chapter]

B. Østman. Effects of Epistasis and Pleiotropy on Fitness Landscapes. In: “Evolutionary Biology: Exobiology and Evolutionary Mechanisms” (P. Pontarotti, ed.). Springer-Verlag, Berlin, Heidelberg (2013) pp. 37-46. [Book Chapter]

R. S. Olson, A. Hintze, F. C. Dyer, D. B. Knoester, C. Adami. Predator Confusion is Sufficient to Evolve Swarming Behavior, Journal of the Royal Society Interface 10 (2013) 20130305. [Journal] [PDF] BibTeX

@article{Olson2013PredatorConfusion,
author = {Olson, Randal S. and Hintze, Arend and Dyer, Fred C. and Knoester, David B. and Adami, Christoph},
doi = {10.1098/rsif.2013.0305},
journal = {Journal of The Royal Society Interface},
month = aug,
number = {85},
pages = {20130305},
title = {{Predator confusion is sufficient to evolve swarming behaviour}},
url = {http://dx.doi.org/10.1098/rsif.2013.0305},
volume = {10},
year = {2013}
}

L. Marstaller, A. Hintze, and C. Adami, The Evolution of Representation in Simple Cognitive Networks. Neural Computation 25 (2013) 2079-2105. [Journal]

2012


C. Adami. Boldly Going Beyond Mathematics. Science 338 (2012) [Journal] [PDF]

C. Adami. Adaptive Walks on the Fitness Landscape of Music. Proc. Natl. Acad. Sci. U.S.A 109 (2012) 11898-11899. [PDF]

J. Qian, T. Ferguson, D. Shinde, A. Ramirez-Borrero, A. Hintze, C. Adami, and A. Niemz. Sequence Dependence of Isothermal DNA Amplification via EXPAR. Nucleic Acids Research 40 (2012) e87 [Journal] [PDF].

C. Adami. The Use of Information Theory in Evolutionary Biology, Annals NY Acad. Sciences 1256 (2012) 49-65. [Journal] [PDF]

C. Adami, J. Schossau, and A. Hintze. Evolution and Stability of Altruist Strategies in Microbial Games. Physical Review E 85 (2012) 011914 [Journal] [PDF]

B. Østman, A. Hintze and C. Adami. Impact of Epistasis and Pleiotropy on Evolutionary Adaptation. Proc. Roy. Soc. 279 (2012) 247-256. [Journal] [PDF]

2011


J. Edlund, N. Chaumont, A. Hintze, C. Koch, G. Tononi, and C. Adami. Integrated Information Increases with Fitness in the Evolution of Animats. PLoS Comp. Biol. 7 (2011) e1002236. [Journal] [PDF]

E.D. Dorn and C. Adami. Robust Monomer Distribution Biosignatures in Evolving Digital Biota. Astrobiology 11 (2011) 959-968. [Journal] [PDF]

C. Adami, J.Qian, M. Rupp, and A. Hintze. Information content of colored motifs in complex networks. Artificial Life 17 (2011) 375-390. [Journal] [PDF]

C. Adami. Toward a Fully Relativistic Theory of Quantum Information. In: From Nuclei to Stars: Festschrift in Honor of Gerald E. Brown, edited by S. Lee (World Scientific, Singapore, 2011). Pp. 71-102. [PDF]

J. Qian, A. Hintze, and C. Adami. Colored Motifs Reveal Computational Building Blocks in the C. elegans Brain. PLoS ONE 6 (2011) e17013. [Journal] [PDF]

E. Dorn, K. H. Nealson, and C. Adami. Monomer Abundance Distribution Patterns as a Universal Biosignature: Examples from Terrestrial and Digital Life. J. Mol. Evol 72 (2011) 283-295. [Abstract] [PDF]

  • Adami Lab Schedule

    April  2017
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