Publications

Publications can be downloaded from Scribd, members can obtain citation and other information on these publications from CiteULike.

Late breaking publications can be found HERE.

Selected Publications by Category

Ecosystems

  • Atamas, S. and J. Bell, Degeneracy-Driven Self-Structuring Dynamics in Selective Repertoires. Bulletin of Mathematical Biology, 2009. 71(6): p. 1349-1365.
  • Levin, S. and J. Lubchenco, Resilience, robustness, and marine ecosystem-based management. Bioscience, 2008. 58(1): p. 27-32.

Multidisciplinary 

  • Csermely, P., Weak links: Stabilizers of complex systems from proteins to social networks. 2006: Springer Verlag.
  • Whitacre, J.M. and A. Bender, Networked buffering: a basic mechanism for distributed robustness in complex adaptive systems. Theoretical Biology and Medical Modelling 2010. 7(20).

History and Philosophy

  • Mason, P.H., Degeneracy at Multiple Levels of Complexity. Biological Theory, 2010. 5(3): p. 277-288.

Systems Biology

  • Solé, R.V., R. Ferrer-Cancho, J.M. Montoya, and S. Valverde, Selection, tinkering, and emergence in complex networks. Complexity, 2002. 8(1): p. 20-33.
  • Csermely, P., Strong links are important, but weak links stabilize them. Trends in Biochemical Sciences, 2004. 29(7): p. 331-334.
  • Tieri, P., A. Grignolio, A. Zaikin, M. Mishto, D. Remondini, G.C. Castellani, and C. Franceschi, Network, degeneracy and bow tie integrating paradigms and architectures to grasp the complexity of the immune system. Theor Biol Med Model, 2010. 7: p. 32.

Evolution

  • Edelman, G.M. and J.A. Gally, Degeneracy and complexity in biological systems. Proceedings of the National Academy of Sciences, USA, 2001. 98(24): p. 13763-13768.
  • Whitacre, J.M., Degeneracy: a link between evolvability, robustness and complexity in biological systems. Theoretical Biology and Medical Modelling, 2010. 7(6).
  • Whitacre, J. and A. Bender, Degeneracy: a design principle for achieving robustness and evolvability. Journal of Theoretical Biology, 2010. 263(1): p. 143-53.

Immunology

  • Cohn, M., Degeneracy, mimicry and crossreactivity in immune recognition. Molecular immunology, 2005. 42(5): p. 651-655.
  • Cohen, I.R., U. Hershberg, and S. Solomon, Antigen-receptor degeneracy and immunological paradigms. Molecular immunology, 2004. 40(14-15): p. 993-996.
  • Tieri, P., G.C. Castellani, D. Remondini, S. Valensin, J. Loroni, S. Salvioli, and C. Franceschi, Capturing degeneracy of the immune system. In Silico Immunology. Springer, 2007.

Artificial Life, Computational Intelligence

  • Andrews, P.S. and J. Timmis, A Computational Model of Degeneracy in a Lymph Node. Lecture Notes in Computer Science, 2006. 4163: p. 164.
  • Mendao, M., J. Timmis, P.S. Andrews, and M. Davies. The Immune System in Pieces: Computational Lessons from Degeneracy in the Immune System. in Foundations of Computational Intelligence (FOCI). 2007.
  • Whitacre, J.M. and A. Bender. Degenerate neutrality creates evolvable fitness landscapes. in WorldComp-2009. 2009. Las Vegas, Nevada, USA.
  • Whitacre, J.M., P. Rohlfshagen, X. Yao, and A. Bender. The role of degenerate robustness in the evolvability of multi-agent systems in dynamic environments. in PPSN XI. 2010. Krakow, Poland.
  • Macia, J. and R. Solé, Distributed robustness in cellular networks: insights from synthetic evolved circuits. Royal Society Interface, 2009 6: p. 393-400.

Systems Engineering

  • Whitacre, J. M., Rohlfshagen, P., Bender, A, and  Yao, X.  “Evolutionary Mechanics: new engineering principles for the emergence of flexibility in a dynamic and uncertain world,” Journal of Natural Computing (in press)  http://www.box.net/shared/l56kcd62uk
  • Sussman, G., Building Robust Systems an essay. 2007, Citeseer.

Ontogenesis

  • Kupiec, J.J., On the lack of specificity of proteins and its consequences for a theory of biological organization. Progress in biophysics and molecular biology, 2010. 102(1): p. 45-52.

Neuroscience

  • Price, C. and K. Friston, Degeneracy and cognitive anatomy. Trends in Cognitive Sciences, 2002. 6(10): p. 416-421.
  • Tononi, G., O. Sporns, and G.M. Edelman, Measures of degeneracy and redundancy in biological networks. Proceedings of the National Academy of Sciences, USA, 1999. 96(6): p. 3257-3262.
  • Sporns, O., G. Tononi, and G. Edelman, Connectivity and complexity: the relationship between neuroanatomy and brain dynamics. Neural Networks, 2000. 13(8-9): p. 909-922.

Oncology

  • Tian, T., S. Olson, J.M. Whitacre, and A. Harding, The origins of cancer robustness and evolvability. Integrative Biology, 2011. 3: p. 17-30.

Peer Review

  • Lehky, S., Peer Evaluation and Selection Systems: Adaptation and Maladaptation of Individuals and Groups through Peer Review. 2011: BioBitField Press.
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