Dr. Christoph Adami

Professor
Microbiology and Molecular Genetics
Physics and Astronomy
Michigan State University

Contact Information
Biomedical Physical Sciences
567 Wilson Road, 2228E
East Lansing, MI 48824
E-mail: adami@nullmsu.edu
Tel.: (517) 884-5068

Calendar: http://bit.ly/CA-calendar
Google Scholar: http://scholar.google.com/citations?user=VXM7wUMAAAAJ&hl=en
Wikipedia: http://en.wikipedia.org/wiki/Chris_Adami
News site at College of Natural Sciences

Biography

Dr. Adami is Professor for Microbiology and Molecular Genetics & Physics and Astronomy at Michigan State University in East Lansing, Michigan. As a computational biologist, Dr. Adami’s main focus is Darwinian evolution, which he studies theoretically, experimentally, and computationally, at different levels of organization (from simple molecules to brains). He has pioneered the application of methods from information theory to the study of evolution, and designed the “Avida” system that launched the use of digital life (mutating and adapting computer viruses living in a controlled computer environment) as a tool for investigating basic questions in evolutionary biology. He was also a Principal Scientist at the Jet Propulsion Laboratory where he conducted research into the foundations of quantum mechanics and quantum information theory. Dr. Adami earned a BS in physics and mathematics and a Diplom in theoretical physics from the University of Bonn (Germany) and MA and PhD degrees in physics from the State University of New York at Stony Brook. He wrote the textbook “Introduction to Artificial Life” (Springer, 1998) and is the recipient of NASA’s Exceptional Achievement Medal. He was elected a Fellow of the American Association for the Advancement of Science (AAAS) in 2011 and a Fellow of the American Physical Society in 2017. He received the Lifetime Achievement Award from the International Society for Artificial Life (ISAL) in 2019.

Publications

2023

172. C. Adami, The Evolution of Biological Information: How Evolution Creates Complexity, from Viruses to Brains. Princeton University Press (2023).

171. C. Adami, On the Origin of Quantum Uncertainty. [arXiv]. In review.

170. A. Tehrani-Saleh, D. McAuley, and C. Adami, Mechanism of Perceived Event Duration in Artificial Brains Suggests Extended Model of Attentional Entrainment. [BioRxiv] in review.

169. A. Hintze and C. Adami, Detecting Information Relays In Deep Neural Networks. Entropy 25 (2023) 401. [Journal]

2022

168. A. Hintze and C. Adami. Neuroevolution Gives Rise to More Focused Information Transfer Compared to Backpropagation in Recurrent Neural Networks. Neural Computing & Applications 34 (2022) 022-08125. [Journal]

167. C. Adami, Making Artificial Brains: Components, Topology, and Optimization. Artificial Life 28 (2022) 157-166. [Journal].

166. C. Bohm, D. Kirkpatrick, V. Cao, and C. Adami, Information Fragmentation, Encryption and Data Flow in Complex Biological Networks, Entropy 24 (2022) 735. [Journal].

165. Nitash C G and C. Adami, Emergence of Functional Information From Multivariate Correlations. Phil. Trans. Roy. Society A 380 (2022) 20210250. [Journal].

2021

164. C. Adami, A Brief History of Artificial Intelligence Research. Artificial Life 27 (2021) 131-137.

163. C. Adami, Escape from the Prisoner’s Dilemma. Inference 6 (2021) DOI: 10.37282/991819.21.47

162. Nitash C G and C. Adami, Information-Theoretic Characterization of the Complete Genotype-Phenotype Map of a Complex Pre-Biotic World. Phys. Life Rev. 38 (2021) 111-114.

161. A. Tehrani-Saleh and C. Adami, Psychophysical Tests Reveal that Evolved Artificial Brains Perceive Time Like Humans. Proc. Artificial Life 2021, J. Cejkova, S. Holler, L. Soros, & O. Witkowski, eds. (MIT Press, 2021), pp. 57-59.

2020

160. A. Hintze and C. Adami, Cryptic Information Transfer in Differently-Trained Neural Networks. Proc. of 7th Intl. Conf. on Soft Computing & Machine Intelligence (ISCMI 2020), pp. 115-120.

159. J.R. Glick and C. Adami, Markovian and non-Markovian Quantum Measurements. Found. Phys. 50 (2020) 1008-1055. [Article] [PDF].

158. D.K. Sydykova, T. LaBar, C. Adami, and C.O. Wilke, Moderate Amounts of Epistasis Are Not Evolutionarily Stable in Small Populations. J. Mol. Evol. 88 (2020) 435-444. [Journal] [PDF] [Commentary]

157. A. Tehrani-Saleh and C. Adami, Can Transfer Entropy Infer Information Flow in Neuronal Circuits for Cognitive Processing? Entropy 22 (2020) 385. [Journal] [PDF].

156. J. Lehmann, et al. The Surprising Creativity of Digital Evolution: A Collection of Anecdotes from the Evolutionary Computation and Artificial Life Research Communities. Artificial Life 26 (2020) 274-306. [arXiv] [Journal]

155. T. LaBar and C. Adami, Genome Size and the Extinction of Small Populations. [BioRxiv], in “Evolution in Action – Past, Present, and Future: A Festschrift in Honor of Erik D. Goodman” (Springer-Verlag, 2020. pp. 167-183.[Book] [PDF]

154. A.C. Pontes, R.B. Mobley, C. Ofria, C. Adami, and F.C. Dyer, The Evolutionary Origin of Associative Learning. Am. Nat. 195 (2020) E1-E19. [Abstract]

2019

153. A. Hintze, J.A. Edlund, R.S. Olson, D. B. Knoester, J. Schossau, L. Albantakis, A. Tehrani-Saleh, P. Kvam, L. Sheneman, H. Goldsby, C. Bohm, and C. Adami, Markov Brains: A Technical Introduction [arXiv]

152. J. Franklin, T. LaBar, and C. Adami, Mapping the Peaks: Local Fitness Landscapes of the Fittest and the Flattest. Artificial Life 25 250-262 (2019).[BioRxiv] [PDF]

2018

151. A. Tehrani-Saleh, T. LaBar, and C. Adami, Evolution Leads to a Diversity of Motion-Detection Neuronal Circuits In: Proceedings Artificial Life 2017 (MIT Press, 2018). T. Ikegami, N. Virgo, O. Witkowski, M. Oka, R. Suzuki and H. Iizuka eds., pp. 625-632.[Article] [PDF].

150. A. Hintze, D. Kirkpatrick, and C. Adami, The Structure of Evolved Representations Across Different Substrates for Artificial Intelligence. In: Proceedings Artificial Life 2017 (MIT Press, 2018). T. Ikegami, N. Virgo, O. Witkowski, M. Oka, R. Suzuki and H. Iizuka, eds., pp.388-395. [Article] [PDF].

149. C. Adami and A. Hintze, Thermodynamics of Evolutionary Games. Phys. Rev. E 97 (2018) 062136 [Journal] [PDF]

2017

148. Nitash C G., T. LaBar, A. Hintze, and C. Adami, Origin of Life in a Digital Microcosm. Phil. Trans. Royal Soc. A 357 (2017) 20160350. [Article] [PDF]

147. T. LaBar and C. Adami, Evolution of Drift Robustness in Small Populations. Nature Communications 8 (2017) 1012 [Article] [PDF] [Press Release]

146. 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] [PDF].

145. C. Adami and T. LaBar, From Entropy to Information: Biased Typewriters and the Origin of Life. In: From Matter to Life: Information and Causality (Cambridge University Press, 2017). S.I. Walker, P.C.W. Davies, and G. Ellis, eds., pp. 130-154. [PDF][arXiv]

144. 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] [PDF]

143. J.R. Glick and C. Adami, Quantum Information Theory of the Bell-State Quantum Eraser, Phys. Rev. A 95 (2017) 012105. [Article] [PDF]

2016

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

141. 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] [PDF].

140. R.S Olson, J.H Moore, and C Adami, Evolution of Active Categorical Image Classification via Saccadic Eye Movement. Lecture Notes in Computer Science 9921 (2016) 581-590. [PDF]

139. 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]

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

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

136. 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]

135. 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].

134. 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]

133. N. Chaumont and C. Adami, Evolution of Sustained Foraging in 3D Environments with Physics. Genetic Programming and Evolvable Machines 17 (2016) 359-390.[Article] [PDF]

132. A. Gupta, T. LaBar, M. Miyagi, and C. Adami, Evolution of Genome Size in Asexual Populations of Digital Organisms. Scientific Reports 6 (2016) 25786. [Article][PDF]

131. 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] [PDF] [Press Release]

130. K. Brádler and C. Adami, One-shot Decoupling and Page Curves from a Dynamical Model for Black Hole Evaporation. Physical Review Letters 116 (2016) 101301. [Journal] [PDF] [Press Release]

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

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

2015

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

126. 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 science 2 (2015) 150135. [Journal] [PDF]

125. K. Brádler and C. Adami, Black Holes as Bosonic Gaussian Channels. Physical Review D 92 (2015) 025030 [Journal]. [PDF]

124. 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. [Proceedings] [PDF]

123. 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]

122. C. Adami, Information-theoretic Considerations Concerning the Origin of Life. Origins of Life and Evolution of Biospheres 45 (2015) 309-317. [Journal] [PDF]

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

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

119. C. Adami and G. Ver Steeg. Black Holes Are Almost Optimal Quantum Cloners. J. Phys. A 48 (2015) 23FT01. [Journal] [PDF] [Press Release]

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

2014

117. 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][PDF] [Press Release]

116. 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] [PDF]

115. B. Østman, R. Lin, and C. Adami. Trade-offs Drive Resource Specialization and the Gradual Establishment of Ecotypes. BMC Evol. Biol. 14 (2014) 113. [Journal] [PDF][Press Release]

114. K. Brádler and C. Adami. The Capacity of Black Holes to Transmit Quantum Information. J. High Energy Phys. 1405 (2014) 095. [Journal] [PDF]

113. C. Adami and G. Ver Steeg, Classical Information Transmission Capacity of Quantum Black Holes. Class. Quantum Grav. 31 (2014) 075015. [Journal][PDF] [Press Release]

2013

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

111. 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]

110. 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]

109. 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

108. 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. [SpringerLink] [PDF]

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

106. 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: 20130305 (2013) [Journal] [PDF] [Press Release] BibTeX

105. L. Marstaller, A. Hintze, and C. Adami, The Evolution of Representation in Simple Cognitive Networks. Neural Computation 25 (2013) 2079-2107. [Journal] [PDF]

2012

104. C. Adami. Boldly Going Beyond Mathematics. Science 338 (2012) 1421-1422.[Journal] [PDF]

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

102. 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].

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

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

99. 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

98. 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]

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

96. 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]

95. 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]

94. 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]

93. 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]

2010

92. D. Iliopoulos, A. Hintze, and C. Adami. Critical Dynamics in the Evolution of Stochastic Strategies for the Iterated Prisoner’s Dilemma. PLoS Comp. Biol. 6 (2010) e1000948. [Journal] [PDF] [Supp.PDF]

91. B. Østman, A. Hintze, and C. Adami. Critical Properties of Complex Fitness Landscapes. Proc. 12th Intern. Conference on Artificial Life, H. Fellerman et al, eds. (MIT Press, 2010), pp. 126-132. [PDF]

90. A. Hintze and C. Adami. Darwinian Evolution of Cooperation via Punishment in the “Public Goods” Game. Proc. 12th Intern. Conference on Artificial Life, H. Fellerman et al, eds. (MIT Press, 2010) pp. 445-450. [PDF]

89. A. Hintze and C. Adami. Modularity and Anti-Modularity in Networks with Arbitrary Degree Distribution. Biology Direct 5 (2010) 32. [PDF]

88. L. Marstaller, C. Adami, and A. Hintze. Measuring Representation. In: W. Christensen, E. Schier, & J. Sutton (Eds.), ASCS09: Proceedings of the 9th Conference of the Australasian Society for Cognitive Science (pp. 232-237). Sydney, Australia: Macquarie Centre for Cognitive Science (2010). [Abstract] [PDF]

2009

87. C. Adami. Biological Complexity and Biochemical Information. In: Encyclopedia of Complexity and Systems Science, R. Meyers, ed., Springer Verlag (2009), pp 489-511. [PDF]

86. D. Iliopoulos, C. Adami, and P. Szor. Darwin Inside the Machines: Malware Evolution and the Consequences for Computer Security (2009). Proceedings of the 18th Virus Bulletin International Conference (Ottawa), H. Martin ed., pp. 187-194. [PDF]

2008

85. C. Adami. The Logic of Science. The New Atlantis 19 (Winter 2008) 3-5. [Journal] [PDF]

84. A. Hintze and C. Adami. Evolution of Complex Modular Biological Networks. PLoS Comp. Biol. 4 (2008) e23. [Journal] [PDF]

2007

83. C. Adami. Who Watches the Watcher? Science 316 (2007) 1125-1126. [Journal] [PDF]

82. N. Chaumont, R. Egli, and C. Adami. Evolving Virtual Creatures and Catapults. Artificial Life 13 (2007) 139-157. [PDF]

81. R. Conduit, C. Adami, H. Lipson, V. Zykov, and J. Bongard. To Sleep, Perchance To Dream. Science 315 (2007) 1219-1220. [PDF]

2006

80. C. Adami. What Do Robots Dream Of? Science 314 (2006) 1093-1094. [PDF]

79. R. Forster, C. Adami, and C.O. Wilke. Selection for Mutational Robustness in Finite Populations. J. theor. Biology 243 (2006) 181-190. [PDF]

78. C. Adami. Three Weeks with Hans Bethe. In: Hans Bethe and His Physics, G.E. Brown and C.-H. Lee, eds., World Scientific (Singapore, 2006), pp. 45-111. [PDF]

77. N. Chaumont, R. Egli, and C. Adami. Evolution of Virtual Catapults. In: Proc. 10th Conference on Artificial Life, L.M. Rocha, L.S. Yeager, M.A. Bedau, D. Floreano, R.L. Goldstone, and A.Vespignani, eds., (MIT Press, 2006) pp. 262-268. [PDF]

76. C. Adami. Reducible Complexity. Science 312 (2006) 61-63. [PDF]

75. C. Adami. Digital Genetics: Unraveling the Genetic Basis of Evolution. Nature Reviews Genetics 7 (2006) 109-118. [PDF]

2005

74. D.A. Drummond, J.D. Bloom, C.O. Wilke, C. Adami, and F.H. Arnold. Why Highly Expressed Proteins Evolve Slowly. Proc. Natl. Acad. Sci. USA 102 (2005) 14338-14343. [PDF]

73. D.R. Mitchell, C. Adami, W. Lue, and C.P. Williams. A Random Matrix Model of Adiabatic Quantum Computation. Phys. Rev. A 71 (2005) 052324. [PDF]

72. R.J. Terrile, C. Adami, H. Aghazarian, S.N. Chau, V.T. Dang, M.I. Ferguson, W. Fink, T.L. Huntsberger, G. Klimeck, M.A. Kordon, S. Lee, P. von Allmen, and J. Xu. Evolutionary Computation Technologies for Space Systems. Proc. IEEE Aerospace Conference (2005) pp. 4284-4295. [Article][PDF]

71. J.D. Bloom, J.J. Silberg, C.O. Wilke, D.A. Drummond, C. Adami, and F.H. Arnold. Thermodynamic Prediction of Protein Neutrality. Proc. Natl. Acad. Sci. 102 (2005) 606-611. [PDF]

2004

70. A.N. Hampton and C. Adami. Evolution of Robust Developmental Neural Networks. In: Proc. of Artificial Life IX, Boston, MA, Sep 12-15, 2004. J. Pollack, M.A. Bedau, P. Husbands, T. Ikegami, and R. Watson, eds., pp 438-443. [PDF]

69. J.D. Bloom and C. Adami. Evolutionary Rate Depends on Number of Protein-Protein Interactions Independently of Gene Expression Level: Response. BMC Evol. Biol. 4 (2004) 14. [PDF]

68. S.S. Chow, C.O. Wilke, R.E. Lenski, C. Ofria, and C. Adami. Adaptive Radiation from Resource Competition in Digital Organisms. Science 305 (2004) 83-85. [PDF]

67. H. Lee, U.H. Yurtsever, P. Kok, G.H. Hockney, C. Adami, S.L. Braunstein, and J.P. Dowling. Towards Photostatistics From Photon-Number Discriminating Detectors. J. Mod. Optics 51 (2004) 1517-1528. [PDF]

66. C. Adami. Information Theory in Molecular Biology. Physics of Life Reviews 1 (2004) 3-22. [PDF]

65. J.D. Bloom, C.O. Wilke, C. Adami, and F.H. Arnold. Stability and Evolvability of Function in a Model Protein. Biophys. Jour. 86 (2004) 2758-2764. [PDF]

64. P.R.A.Campos, C.O. Wilke, and C. Adami. Modeling Stochastic Clonal Interference. In: Modelling in Molecular Biology (Springer Series in Natural Computing, 2004). G. Ciobanu and G. Rozenberg, eds., pp. 21-39. [PDF]

63. D. A. Wagenaar and C. Adami. Influence of Chance, History, and Adaptation on Digital Evolution. Artif. Life 10 (2004) 181-190. [PDF]

62. J.A. Edlund and C. Adami. Evolution of Robustness in Digital Organisms. Artif. Life 10 (2004) 167-179. [PDF]

61. J.S. White and C. Adami. Bifurcation into Functional Niches in Adaptation. Artif. Life 10 (2004) 135-144. [PDF]

60. C. Adami and C.O. Wilke. Experiments in Digital Evolution (Editors’ Introduction). Artif. Life 10 (2004) 117-122. [PDF]

2003

59. J.D. Bloom and C. Adami. Apparent Dependence of Protein Evolutionary Rate on Number of Interactions is Linked to Biases in Protein-Protein Interactions Data Sets. BMC Evol. Biol. 3 (2003) 21. [PDF]

58. R.M. Gingrich, A.J. Bergou, and C. Adami. Entangled Light in Moving Frames. Phys. Rev. A 68 (2003) 042102. [PDF]

57. C. Ofria, C. Adami, and T. C. Collier. Selective Pressures on Genomes in Molecular Evolution. J. theor. Biology 222 (2003) 477-483. [PDF]

56. R.E. Lenski, C. Ofria, R.T. Pennock, and C. Adami. The Evolutionary Origin of Complex Features. Nature 423 (2003) 139-144. [PDF]

55. C. Adami. Sequence Complexity in Darwinian Evolution. Complexity (Wiley) 8 (2003) 49-56. [PDF]

54. C. Kamp, C.O. Wilke, C. Adami, and S. Bornholdt. Viral Evolution Under the Pressure of an Adaptive Immune System: Optimal Mutation Rates for Viral Escape. Complexity (Wiley) 8 (2003) 28-33. [PDF]

53. C.O. Wilke, R.E. Lenski, and C. Adami. Compensatory Mutations Cause Excess of Antagonistic Epistasis in RNA Secondary Folding. BMC Evol. Biol. 3 (2003) 3. [PDF]

52. C.O. Wilke and C. Adami. Evolution of Mutational Robustness. Mut. Research 522 (2003) 3-11. [PDF]

2002

51. R.M. Gingrich and C. Adami. Quantum Entanglement of Moving Bodies. Phys. Rev. Lett. 89 (2002) 270402. [PDF]

50. C. Adami. What is Complexity? BioEssays 24 (2002) 1085-1094. [PDF]

49. C. O. Wilke and C. Adami. The Biology of Digital Organisms. Trends in Ecology and Evolution 17 (2002) 528-532. [PDF]

48. C. Ofria, T.C. Collier, and C. Adami. Design of Evolvable Computer Languages. IEEE Transactions on Evolutionary Computation 6 (2002) 420-424. [PDF]

47. C. Adami and J. Chu. Critical and Near-Critical Branching Processes. Phys. Rev. E 66 (2002) 011907. [PDF]

46. C. Adami. Ab Initio Modeling of Ecosystems with Artificial Life. Natural Resource Modeling 15 (2002) 133-146. [PDF]

45. C. Adami. Simulations of Evolution. In: Encyclopedia of Evolution, M. Pagel, S. Frank, C. Godfray, B. K. Hall, K. Hawkes, D. M. Hillis, A. Kodric-Brown, R. E. Lenski, and A. Pomiankowski, eds., (Oxford University Press, New York, 2002), pp. 1064-1066.

44.P.R.A. Campos, C. O.Wilke, and C. Adami. Optimal Adaptive Performance and Delocalization in NK Landscapes. Physica A 304 (2002) 495-506. [PDF]

2001

43. C. Adami and J.P. Dowling. Quantum Computation—The Ultimate Frontier. Proc. AMOS 2001 Tech. Conf., Sept. 10-14, Wailea, Maui, Hawaii. P. Kervin, L. Bragg, and S. Ryan, eds. Maui (2002) pp. 462-467. [PDF]

42. C. O. Wilke, J.L. Wang, C. Ofria, R. E. Lenski, and C. Adami. Evolution of Digital Organisms at High Mutation Rate Leads To Survival of the Flattest. Nature 412 (2001) 331-333. [PDF]

41. C. O. Wilke and C. Adami. Interaction Between Directional Epistasis and Average Mutational Effects. Proc. Royal Society London B 268 (2001) 1469. [PDF]

40. C. Adami and S.E. Koonin. Complex Langevin Equation and the Many-Fermion Problem. Phys. Rev. C 63 (2001) 034319. [PDF]

1988-2000

39. M.A. Bedau, C. Adami, J.S. McCaskill, N.H. Packard, S. Rasmussen, D.G. Green, T. Ikegami, K. Kaneko, and T.S. Ray. Open Problems in Artificial Life. Artificial Life 6 (2000) 363-376. [PDF]

38. D. Wagenaar and C. Adami. Influence of Chance, History and Adaptation on Evolution in Digitalia. In: Proc. of Artifical Life VII, Portland, OR, Aug. 1-6, 2000. M.A. Bedau, J.S. McCaskill,. N.H. Packard, and S. Rasmussen, eds., MIT Press (2000), p. 216-220. [PDF]

37. J. C. Astor and C. Adami. A Developmental Model for the Evolution of Artificial Neural Networks. Artificial Life 6 (2000) 189-218. [PDF]

36. C. Adami, C. Ofria, and T. C. Collier. Evolution of Biological Complexity. Proc. Nat. Acad. Sci. 97 (2000) 4463-4468. [PDF]

35. C. Adami and N.J. Cerf. Physical Complexity of Symbolic Sequences. Physica D 137 (2000) 62-69. [PDF]

34. J. Chu and C. Adami. A Simple Explanation for Taxon Abundance Patterns. Proc. Nat. Acad. Sci. 96 (1999) 15017-15019. [PDF]

33. R. E. Lenski, C. Ofria,T. C. Collier, and C. Adami. Genome Complexity, Robustness, and Genetic
Interactions in Digital Organisms. Nature 400 (1999) 661-664. [PDF]

32. C. Ofria, C. Adami, T.C. Collier, and G. Hsu. Evolution of Differentiated Expression Patterns in Digital Organisms. Lect. Notes Comput. Sci. 1674 (1999) 129-138. [PDF]

31. N.J. Cerf, R.M. Gingrich, and C. Adami. Reduction Criterion for Separability. Phys. Rev. A 60 (1999) 898. [PDF]

30. N.J. Cerf and C. Adami. Quantum Extension of Conditional Probability. Phys. Rev. A 60 (1999) 893. [PDF]

29. C. Ofria and C. Adami. Evolution of Genetic Organization in Digital Organisms. In: Evolution as Computation, DIMACS Workshop, Princeton, January 1999. L. F. Landweber and E. Winfree, eds., Springer-Verlag, N.Y. (2002) pp. 296-313. [PDF]

28. C. Adami and N.J. Cerf. Prolegomena to a Non-Equilibrium Quantum Statistical Mechanics. Chaos, Solitons & Fractals 10 (1999) 1637-1650 (Special issue on Quantum Computation). [PDF]

27. C. Adami and N.J. Cerf. Quantum Computation with Linear Optics. Lect. Notes in Comp. Sci. 1509 (1999) 391-401. Proc. of QCQC ’98. [PDF]

26. C. Adami and N.J. Cerf. What Information Theory Can Tell us About Quantum Reality. Lect. Notes in Comp. Sci. 1509 (1999) 258-268. Proc. of QCQC ’98. [PDF]

25. J. C. Astor and C. Adami. Development and Evolution of Neural Networks in an Artificial Chemistry. In: Proc. of 3rd German Workshop on Artificial Life. C. Wilke, S. Altmeyer, and T. Martinetz, eds., Verlag Harri Deutsch (1998) pp. 15-29. [PDF]

24. C. Adami, R. Seki and R. Yirdaw. Critical Exponent of Species-Size Distribution in Evolution. In: Proc. of Artificial Life VI Los Angeles, June 27-29, 1998. C. Adami, R. Belew, H. Kitano, and C. Taylor, eds., MIT Press (1998), p. 221-227. [PDF]

23. N. J. Cerf and C. Adami. Information Theory of Quantum Entanglement and Measurement. Physica D 120 (1998) 62-81. [PDF]

22. N.J. Cerf, C. Adami, and P.G. Kwiat. Optical Simulation of Quantum Logic. Phys. Rev. A 57 (1998) R1477-1480. [PDF]

21. C. Adami and N.J. Cerf. von Neumann Capacity of Noisy Quantum Channels. Phys. Rev. A 56 (1997) 3470-3483. [PDF]

20. N.J. Cerf and C. Adami. Entropic Bell Inequalities. Phys. Rev. A 55 (1997) 3371-3374. [PDF]

19. N.J. Cerf and C. Adami. Negative Entropy and Information in Quantum Mechanics. Phys. Rev. Lett. 79 (1997) 5194-5197. [PDF]

18. N.J. Cerf and C. Adami. Negative Entropy in Quantum Information Theory. In: New Developments on Fundamental Problems in Physics. M. Ferrero and A. van der Merwe, eds., Kluwer Academic Publ. (1997) p. 77-84. [PDF]

17. N.J. Cerf and C. Adami. Quantum Information Theory of Entanglement. In: Proc. 4th Workshop on Physics and Computation, Boston Univ. Nov. 22-24, 1996. T. Toffoli, M. Biafore, and J. Leao, eds. (NECSI, 1996), p. 65-71.

16. C. Adami and N.J. Cerf. Complexity, Computation, and Measurement. In: Proc. 4th Workshop on Physics and Computation, Boston Univ. Nov. 22-24, 1996. T. Toffoli, M. Biafore, and J. Leao, eds. (NECSI, 1996), p. 7-11. [PDF]

15. J. Chu and C. Adami. Propagation of Information in Populations of Self-Replicating Code. In: Proc. of Artificial Life V, Nara (Japan), May 16-18, 1996. C.G. Langton and T. Shimohara, eds., MIT Press (1997) p. 462-469. [PDF]

14. C. Adami, C.T. Brown and M.R. Haggerty. Abundance Distributions in Artificial Life and Stochastic Models: “Age and Area” revisited. Lect. Notes in Artif. Intell. 929 (1995) 503-514. [PDF]

13. C. Adami. Self-Organized Criticality in Living Systems. Phys. Lett. A 203 (1995) 29-32. [PDF]

12. C. Adami. Learning and Complexity in Genetic Auto-Adaptive Systems. Physica D 80 (1995) 154-170. [PDF]

11. C. Adami and C.T. Brown. Evolutionary Learning in the 2D Artificial Life System `Avida’. In: Proc. of Artificial Life IV. MIT July 6-8, 1994 R. Brooks and P. Maes, eds., MIT Press (1994) pp. 377-381. [arXiv][PDF]

10. C. Adami. On Modeling Life. Artificial Life 1 (1994) 429. [PDF]. Also in: Proc. of “Artificial Life IV”; MIT July 6-8, 1994, R. Brooks and P. Maes, eds., MIT Press (1994) p.269-274.

9. C. Adami. Matter Under Extreme Conditions. Phys. Rep. 234 (1993) 1-71 (with G.E. Brown) [PDF]

8. C. Adami, E.G. Drukarev and B.L. Ioffe. Isospin Breaking in QCD Sum Rules for Baryons. Phys. Rev. D 48 (1993) 2304-2312 [PDF], Erratum D 52 (1995) 4254 [PDF]

7. C. Adami and G. E. Brown. Order of the QCD Transition and QCD Sum Rules. Phys. Rev. D 46 (1992) 478-481 [PDF]

6. C. Adami and I. Zahed. Finite-temperature QCD Sum Rules for the Nucleon. Phys. Rev. D 45 (1992) 4312-4322 [PDF]

5. C. Adami and G. E. Brown. Isospin Breaking in Nuclear Physics: The Nolen-Schiffer Effect. Z. f. Phys. A 340 (1991) 93-100 [PDF]

4. C. Adami, T. Hatsuda and I. Zahed. QCD Sum Rules at Low Temperatures. Phys. Rev. D 43 (1991) 921-932 [PDF]

3. C. Adami, M. Prakash and I. Zahed. Charmonium Disintegration by Field-Ionization. Phys. Lett. B 217 (1989) 5 [PDF]

2. C. Adami and I. Zahed. The Width of the Delta-Isobar in Chiral Soliton Models. Phys. Lett. B 213 (1988) 373 [PDF]

1. C. Adami and I. Zahed. Soliton Quantization in Chiral Models with Vector Mesons. Phys. Lett. B 215 (1988) 389 [PDF]

Books

1. Introduction to Artificial Life (Springer-Verlag, 1998).
2. Proceedings of Sixth International Conference on Artificial Life (MIT Press, 1998, editor)
3. Proceedings of 13th International Conference on Artificial Life (MIT Press, 2012, editor)

Book Reviews

5. The Engine of Complexity: Evolution as Computation by John E. Mayfield (Columbia University Press, 2013). Quarterly Review of Biology 90 (2015) 90-91. [PDF]

4. Genesis Machines: The New Science of Biocomputing by Martyn Amos (Atlantic Books, 2006). Nature 446 (2007) 263-264. [PDF]

3. Information Theory, Evolution, and the Origin of Life by H. Yockey (Cambridge University Press, Cambridge and New York, 2005). Quarterly Review of Biology 81 (2006) 62. [PDF]

2. Non-Standard Computation by T. Gramß et al. (Wiley-VCH, Weinheim, 1998) Physikalische Blätter (4/1999) 66.

1. Modeling Nature with Cellular Automata using Mathematica by R. Gaylord and K. Nishidate (Springer Verlag, TELOS) SIGSAM Bull. 30/3 (1996) 24.

Extended Abstracts

1. C. Adami, N. Chaumont, J.A. Edlund, & A Hintze. Topological properties of evolved robot brains. Proceedings of Artificial Life 11 (MIT Press, 2008), S. Bullock et al., eds. p. 742.[PDF]

2. A. Hintze & C. Adami. Information-theoretic measures of network complexity. Proceedings of International Workshop and Conference on Network Science (Norwich, UK, 2008).[PDF]

2. N. Chaumont & C. Adami, Potential and Promise of Open-Ended Evolution in Artificial Life, Proceedings of Artificial Life 12 (MIT Press, 2010), H. Fellerman et al., eds, p. 429.[PDF]

3. R.S. Olson, C. Adami, F. C. Dyer, & A. Hintze, A Bottom-Up Approach to the Evolution of Swarming, Proceedings of Artificial Life 13 (MIT Press, 2012), C. Adami et al., eds. p. 567. [Proceedings][PDF]

4. N. Chaumont & C. Adami, Sustainable Population of Autonomous Foragers in a 3D environment with Physics. Proceedings of Artificial Life 13 (MIT Press, 2012), C. Adami et al., eds. p. 581. [Proceedings][PDF]

5. 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 (MIT Press, 2014), H. Sayama et al., eds, p. 310-311. [PDF][Abstract]

6. P.B. Haley, R.S. Olson, F. C. Dyer, and C. Adami, Evolving an Optimal Group Size in Groups of Prey under Predation. 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. 620. [PDF]

Unpublished

1. C. Adami, The Mind as a Computational System. [arXiv] (University of Bonn, 1985)

2. C. Adami. Hamiltonformalismus des Skyrme-Modells mit omega-Mesonen; BONN-IR-88-36 (Diplom-Thesis, University of Bonn, 1988)

3. C. Adami. Aspects of Matter Under Extreme Conditions; Ph.D. Thesis, SUNY at Stony Brook, 1991

4. N.J. Cerf and C. Adami. Quantum Mechanics of Measurement. quant-ph/9605002. [Arxiv.org].

5. N.J. Cerf and C. Adami. Accessible Information in Quantum Measurement. quant-ph/9611032. [Arxiv.org] [PDF]

6. C. Adami and H.G. Schuster. Driving Molecular Evolution to the Error Threshold. KRL preprint MAP-208 (December 1996).

7. J. Chu and C. Adami. Non-Critical Sandpiles. KRL preprint MAP-243 (December 1998)

8. C. Ofria and T.C. Collier. Robustness and Evolvability of Computer Languages. KRL preprint MAP-250 (January 1999)

9. C. Adami and H.G. Schuster. Optimal Speed of Molecular Evolution. January 2000.

10. C. Adami. Software Bioengineering. January 2002 [PDF]

11. P.R.A. Campos, C.O. Wilke, and C. Adami. A Method to Infer Selective Sweeps from Reduced Diversity at a Linked Microsatellite Locus. December 2002 [PDF] [Supp]

12. C. Adami. The Physics of Information. quant-ph/0405005 [Arxiv.org]

11. U. Beierholm, C. Adami, and C.O. Wilke. Supersaturated Coexistence of Plankton Species is Unstable in Changing Environments. (2004) [PDF]

13. D.B. Knoester, H.J Goldsby, and C. Adami, Leveraging Evolutionary Search to Discover Self-Adaptive and Self-Organizing Cellular Automata. [arXiv]

14. M. Mirmomeni, W.F. Punch, and C. Adami, Is Information a Selectable Trait? [arXiv].

15. J.R. Glick and C. Adami, Quantum Mechanics of Consecutive Measurements. [arXiv]

16. J.R. Glick and C. Adami, Generating Remote Entanglement via Disentangling Operations. [arXiv]

17. C. Adami, Neither Weak Nor Strong Entropic Leggett-Garg Inequalities Can be Violated. [arXiv].

18. C. Adami, Leggett-Garg Inequalities Cannot be Violated in Quantum Measurements. [arXiv].