PUBLICATIONS

 


Demotic Script from the Ptolemy Dynasty. Hermitage Museum



Publications are provided for viewing purposes only. In order to respect journal copyright I request that these not be printed or disseminated without prior permission of the copyright holder (That would be the journal). In response to requests, I now include papers and chapters that are published, in press, and submitted.


PDFs are available for many of the publications, but sometimes the most recent are absent with incomplete references awaiting the final published version (or request it from me as a LaTeX pdf).


Brush, E, Krakauer, D.C., Flack, D.C. A family of measures for computing power on social networks under uncertainty.  (2011) PDF


Krakauer, D.C. Darwinian demons, evolutionary complexity and information maximization. Chaos. (2011) PDF


Daniels, B. C. Krakauer, D.C. Flack. J.C.  Predictive sparse coding of conflict through derivation of functional subgroups. (2011) PDF


DeDeo, S., Krakauer, D.C. Dynamics and information processing in contrasting self similar networks. (2011) PDF


Foti, N., Hughes, J.M., Krakauer, D.C., Rockmore, D.  Evolution of literature: quantitative patterns of stylistic influence (2011) PDF


Flack, J. C, Erwin, D. Elliot, T, and  Krakauer, D.C. Construction of Slow Variables Required for the Emergence of Aggregates: a New Approach to the the Origins of Levels in Evolution. IN: Evolution Cooperation and Complexity. MIT Press. PDF (2011)


Krakauer, D.C., Flack, J.C., Page, K. A The Immuno-Dynamics of Conflict Intervention in Social Systems.  In Press PLoS ONE. (2011) PDF


Krakauer, D.C. The Star Gazer and the Flesh Eater. Elements of a theory of Metahistory. Cliodynamics: The Journal of Theoretical and Mathematical History. 2. 82-105 (2011) PDF


Krakauer, D.C. Pomeranz, L. Gaddis, J.L.  An inquiry into History, Big History & Metahistory. Cliodynamics: The Journal of Theoretical and Mathematical History. 2. 1-5  (2011) PDF


Krakauer, D.C. Complexity and the ultimate meaning of health and disease. In: Philosophical Studies in Medicine and Health. Ed. Stephen M. Modell. University of Toronto Press. In Press (2011) PDF


Dedeo, S., Krakauer, D.C., Flack, J.C. Evidence of Strategic Periodicity in collective conflict dynamics. Proc. Roy. Soc. Interface. 16, doi: 10.1098/rsif.2010.0687  (2011) PDF


Krakauer, D.C.,  Prohaska, S. J., West, G.B., Flack, J.C., Erwin, D. Fontana, W., Collins, J., Laubichler, M, Stadler, P.  The Challenges and Scope of Theoretical Biology.  J. Theor. Biol., 276, 269-276 (2011) PDF


Krakauer, D.C., Flack, J.C. Better living through physics. Nature, 467, 661 (2010) PDF

See full comment here: PDF


Krakauer, D.C., Flack, J.C., DeDeo, S., Farmer, D.,  Rockmore, D. Intelligent data analysis of intelligent systems. IDA 2010, LNCS 6065, pp. 8–17, Springer-Verlag Berlin Heidelberg (2010) PDF


Prohaska, S.J.,  Stadler, P.F. , Krakauer, D.C. Innovation in Gene Regulation: The case of Chromatin Computation. J. theor. Biol.   265(1) , 27-44 (2010) PDF


Dedeo, S., Krakauer, D.C., Flack, J.C., Inductive Game Theory & the Dynamics of Conflict.  Plos. Comp. Biol. 6(5): e1000782. doi:10.1371/journal.pcbi.1000782  (2010) PDF


Krakauer, D.C. Flack, J.C., Ay, N. Probabilistic design principles for robust, multimodal communication networks. In: Modeling Perception with Artificial Neural Networks. Eds. G. Ruxton and C. Tosh. Cambridge University Press. UK. 255-268 (2010)  PDF


Stadler, P.F., Prohaska, S.J.,  Forst, C.V., Krakauer, D.C. Defining Genes. A Computational Framework. Theory in the Biosciences. 128( 3) 1431- (2009) PDF


Flack, J.C., Krakauer, D.C. The evolution and construction of moral systems. In: Games, Groups and the Global Good. Ed. Simon Levin. Springer Verlag.  117-142  (2009) PDF


Krakauer, D.C. Evolution, Complexity and Metahistoricism. Nouvelles perspectives en sciences sociales. 4. 53-67 (2009). PDF (this is a draft of the paper in English)


Krakauer, D.C., Page, K. and Erwin. D. Diversity, Dilemmas and Monopolies of Niche Construction. Am. Nat.   173(1) 26- 40. (2009). PDF


Krakauer, D.C. & Zanotto de A, P. Viral Individuality & Limitations of the Life Concept. pp 513-536  Protocells: Bridging Non-living and Living Matter. Edited by Steen Rasmussen, Mark A. Bedau, Liaohai Chen, David Deamer, David C. Krakauer, Norman H. Packard and Peter F. Stadler. MIT Press (2009) PDF


Borenstein, E. and Krakauer, D.C. An End to Endless Forms:  Epistasis,, phenotype distribution bias and non-uniform evolution. PloS. Comp. Biol. 4. 1-13. e1000202. (2008). PDF. Nature Reviews Summary of publication: PDF


Bershad, A.K., Fuentes, M.A, Krakauer, D.C. Developmental autonomy and somatic niche construction during cellular division and differentiation. J. theor. Biol. 254. 408-416. (2008). PDF


de A. Zanotto, P., Krakauer, D.C. Complete genome viral phylogenies suggests the concerted evolution of regulatory cores and accessory satellites . PloS One. 3. 1-17. e3500 (2008) PDF


Krakauer, D.C (July 2008) Genetic Redundancy. In: Encyclopedia of  Life Sciences (ELS). John Wiley & Sons, Ltd: Chichester. pp 1-6. (2008) PDF


Fuentes, M. Krakauer, D.C The evolution of developmental patterning under genetic duplication constraints. Proceedings of the Royal Society. Interface.  5:237-245 (2008) PDF


Ay, N., Flack. J.C. & Krakauer, D.C. Robustness and Complexity Co-constructed in Multi-modal Signaling Networks. Philosophical Transactions of the Royal Society. London. 362, 441-447.  (2007) PDF


Krishnamurthy, S., Smith, E.D, Krakauer, D.C. and Fontana, W. The stochastic behavior of a molecular switching circuit with  feedback. 2:13-25 Biology Direct.  (2007) PDF


Kai W. Wucherpfennig, Paul Allen, Franco Celada, Irun Cohen, Rob deBoer, Herman Eisen,   K. Christopher Garcia, Byron Goldstein, Ralph Greenspan, David Hafler, Philip Hodgkin, Erik Huseby, David C. Krakauer, David Nemazee, Alan Perelson,  Clemencia Pinilla, Roland Strong and Eli Sercarz.  Polyspecificity of T cell receptor recognition. Seminars in Immunology. 19(4) 216-224. (2007) PDF


Ay, N. & Krakauer, D.C. Geometric Robustness Theory and Biological Networks. Theory in the Biosciences.125(2), 93-121. (2007) PDF


Lillo, F. and Krakauer, D.C. A statistical analysis of the three-fold evolution of genomic

compression through frame overlaps in prokaryotes. Biology Direct. doi:10.1186/1745-6150-2-22A. (2007)   PDF


Flack, J.C. & Krakauer, D.C. Encoding power in communication networks. American Naturalist. 163(3), 87-102  (2006) PDF


Krakauer, D.C. Sasaki, A. The Greater than two-fold cost of Integration for Retroviruses Proceedings of the Royal Society. London. B. 273(1590):1159-63. (2006). PDF

 

Flack, J.C., Girvan, M.C., de Waal, F.B.M, & Krakauer, D.C. Policing stabilizes construction of social niches in primates. Nature, 439, 426-429.  (2006)  PDF

 

Flack, J.C., Krakauer, D.C., & de Waal, F.B.M. Social Structure, Robustness, and Policing Cost in a Cognitively Sophisticated Species. Am. Nat. Vol. 165, pp. E126-E139 (2005) PDF


Krakauer, D.C. Robustness in Biological Systems: a provisional taxonomy. In: Complex Systems Science in Biomedicine. Kluwer. (2005)  PDF


Krakauer, D.C. & Plotkin, J. Principles and parameters of molecular robustness. In: E. Jen (ed.) Robust design: a repertoire for Biology, Ecology and Engineering, Oxford University Press. (2005) PDF


Flack, J.C., Krakauer, D.C., & de Waal, F.B.M. Robustness mechanisms in primate societies: a perturbation study. Proceedings of the Royal Society, London. B. 272, 1091-1099 (2004)  PDF

 

Erwin, D. and Krakauer, D.C. Insights into Innovation. Science 304: 1117-1119 (2004)  PDF


Rasmussen, S.,Chen, L., Deamer, D., Krakauer, D.C, Packard, N.H., Stadler. P.H. and Bedau, M.A. Transitions from nonliving to living matter . Science (2004) 303: 963-965  PDF


Rasmussen, Bedau, M.A., S.,Chen L., Deamer, D., Krakauer, D.C, Packard, N.H., Stadler. P.H.Living and Non living Matter: A Response. Science 305: 41-42

(2004)

 

Krakauer, D.C. An Inordinate Fondness for Bacteria. Heredity 93:116-118 (2004)


Krakauer, D.C. & Komarova, N. Levels of selection in positive strand virus dynamics. Journal of Evolutionary Biology , 16, 64-73 (2003)  PDF


Krakauer, D.C. Genetic Redundancy. Evolution and Comparative Genomics. Encyclopedia of the Human Genome. Nature Publishing Group. Macmillan Publishers (2003)


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 and detection of genetic robustness.  Evolution. 57(9): 1959-72 (2003)  PDF

 

Krakauer, D.C. & Page, K & Sealfon, S. Module dynamics of the GnRH signal transduction network. J. theor, Biol. 218, 457-470  (2002)  PDF

 

Krakauer, D.C. Evolutionary principles of genomic compression Comments on theor. Biol. 7, 215-236,  (2002) PDF

 

Krakauer, D.C., Sasaki, A.  Noisy Clues to the Origin of Life. Proc. R. Soc. Lond. B. 269, 2423-2428  (2002)  PDF

 

Krakauer, D.C, Jansen, V. Red Queen Dynamics and the Evolution of protein translation. J. theor, Biol. 218, 97-109 (2002)  PDF

 

Krakauer, D.C, From physics to phenomenology. Levels of selection and levels of description. Novartis Found. Symp. Foundation 247, 42-52, (2002)  PDF

 

Krakauer, D.C. Genetic redundancy.  Encyclopedia of Evolution. Ed. Mark Pagel. Oxford University Press, Oxford (2002)

 

Krakauer, D.C. & Nowak, M.A Quasispecies. Encyclopedia of Evolution. Ed. Mark Pagel. Oxford University Press, Oxford (2002)

 

Krakauer, D.C, Jansen, V. and Nowak, M.A. Red queen dynamics and the evolution of translational redundancy and degeneracy. Biological Evolution and Statistical Physics. Eds. Laessig. M. and Valleriani, A Springer Verlag. (2002)  PDF

 

Krakauer, D.C. Coevolution of virus and host cell death signals. Adaptive Dynamics of Infectious Diseases. Eds: U. Dieckmann, J. A. J. Metz, M. W. Sabelis, K. Sigmund. CUP. Cambridge. (2002)  PDF


Krakauer, D.C. & Plotkin, J. Redundancy, antiredundancy and the robustness of genomes PNAS 99, 1405-1409 (2002)  PDF

 

Wodarz, D & Krakauer D.C Genetic instability, somatic progression and angiogenesis (Oncology  Reports 8, 1195-1201 2001) PDF


Krakauer, D.C. & Nowak, M.A. Genetic redundancy. Eds. Brenner, S. and Miller, J.  Encyclopedia of Genetics. Academic Press pp 845-846 (2001) PDF


Krakauer, D.C. Kin imitation for a private sign system. ( J. theor. Biol 213, 145-157. 2001)   PDF                      


Krakauer, D.C. Evolving cell death in the virus infected nervous system. TINS. 23, 617. (2000) PDF

 

Wahl, L. & Krakauer, D. C. Models of experimental evolution: The role of genetic chance and selective necessity. Genetics. 156. (2000)  PDF


Payne, R.J.H. & Krakauer, D. C. Disruptive sexual selection. TREE. 15. 419-420. (2000) PDF


Wodarz, D. & Krakauer, D.C. Defining CTL-induced pathology: Implications for HIV. Virology 274. 94-104. (2000)  PDF


Stumpf, M. & Krakauer, D.C. Mapping the parameters of prion induced neuropathology. Proc. Natl. Acad. Sci. USA. 97. 10573-10577. (2000)  PDF


Krakauer, D.C. & Nowak, M.A. Fragile Dominion. Notices of the AMS 47: 564-568 (2000)


Krakauer, D.C. & Mira, A. Mitochondria and the death of oocytes. Nature 403: 501 (2000) PDF


Krakauer, D.C. Stability and evolution of overlapping genes. Evolution 54: 731-739 (2000) PDF


Grassly, N.,  von Haesler, A. & Krakauer, D.C. Error, population structure and the origin of diverse  sign systems. J. theor. Biol. 206. 369-378. (2000) PDF


Krakauer, D.C. & Nowak, M.A. Evolutionary preservation of redundant duplicated genes. Seminars in Cell and Developmental Biology 10: 555-559 (1999)  PDF


Nowak, M.A & Krakauer, D.C. The evolution of language. Proc. Natl. Acad. Sci. USA 96: 8028-8033 (1999)  PDF


Nowak, M.A , Plotkin, J. & Krakauer, D.C. The Evolutionary Language Game. J. theor. Biol 200, 147-162 (1999)  PDF


Nowak, M.A, Krakauer, D.C., and Dress, A. An error limit for the evolution of language. Proc. Roy. Soc. Lond. B. 2131-2136 (1999)  PDF


Krakauer, D.C. & Nowak, M.A. CTL pathogenesis in HIV: bystander effects and latent infection. Proc. Roy. Soc 266: 1069-1075 (1999) PDF


Krakauer D.C. & Mira, A. Mutation, mitochondria and germ cell death. Nature 400: 125-126 (1999)  PDF


Collett, M., Despland, E., Simpson, S.J. & Krakauer, D.C. The spatial scales of locust swarms. Proc. Natl. Acad. Sci. USA 95:13052-13055. (1998)  PDF


Krakauer, D.C., Zanotto, P. & Pagel, M. Prion’s Progress: patterns and rates of molecular evolution in relation to spongiform disease. J. Mol. Evol: 47: 133-145 (1998)  PDF


Nowak, M., Krakauer, D.C., Klug, A. & May, R. Prion infection dynamics. Integrative Biology 1:3-15 (1998)  PDF


Ostrowski, M., Krakauer, D.C., Nowak, M. & Fauci, A. The effect of immune activation on the dynamics of HIV replication on the distribution of viral quasispecies. J. Virol 72:7772-7784  PDF

 

Payne, R.J.H & Krakauer, D.C. The paradoxical dynamics of prion disease latency. J. theor. Biol. 191: 345-352 (1998)  PDF


Payne, R.J.H & Krakauer D.C. The spatial dynamics of prion infection. Proc. Roy. Soc. Lond B 265:2341-2346 (1998)  PDF


Krakauer, D.C. & Payne, R.J.H. The evolution of virus induced apoptosis. Proc. Roy. Soc. Lond B 264:1757-1762 (1997) PDF


Pagel, M. & Krakauer, D.C. Is the propagation of prion molecules in different hosts an example of Lamarckian inheritance? A reply. TREE. 12: 194 (1997)


Krakauer, D.C. The evolutionary imperative and the origin of the prion pathogen. Nutrition 13:692-694 (1997)


Payne, R.J.H & Krakauer, D.C.  Sexual selection, space and speciation. Evolution 51:1-9 (1997)  PDF              


Krakauer, D.C. & Pagel, M. The geneology of a toxic protein and the case of BSE. Social Biology & Human Affairs 61: 45-54 (1996)


Pagel, M. & Krakauer, D.C. Prions and the new molecular phenetics. TREE 11: 487-488 (1996) PDF


Krakauer, D.C. -- contributing author. Report of a WHO Consultation on Clinical and Neuropathological Characteristics of the New Variant of CJD and other Human and Animal Transmissible Spongiform Encephalopathies. (1996)


Krakauer, D.C. , Pagel, M. Zanotto, P., & Southwood, T.R.E.   Phylogenesis of prion protein. Nature 380: 675 (1996) PDF


Krakauer, D.C. & Pagel, M. Selection by somatic signals. Phil.Trans. Roy Soc 351: 647-658 (1996) PDF

 

Krakauer, D.C. & Pagel, M. Spatial structure & the evolution of honest cost-free signals. Proc. Roy. Soc. Lond. B 260: 365-372 (1995) PDF


Krakauer, D.C. & Johnstone, R. The Evolution og Exploitation and Honesty animal communication. Phil.Trans. Roy Soc 348: 355-361 (1995) PDF


Krakauer, D.C. Prey confuse predators by exploiting perceptual bottlenecks. Behav Ecol & Socio 36: 421-429 (1995) PDF


Krakauer, D.C. , & Houston, A. I. An Evolutionary perspective on Hebb's reverberatory representations. Behavioural & Brain Sciences 18: 636-637 (1995)


Krakauer, D.C. & Rodriguez-Girones, M. Searching & learning in a random environment. J .theor.Biol 177: 417-429 (1995) PDF


Krakauer, D.C. Simple connectionist models of spatial learning in bees. J. theor Biol 172:149-160 (1995) PDF

“Unprovided with original learning, unformed in the habits of thinking,unskilled in the arts of composition, I resolved to write a book.”


Edward Gibbon