Important Related Papers

This page includes papers that are significant to degeneracy research but do not necessarily focus on degeneracy or use this terminology.  If you would like to contribute, please add a comment that provides a reference for the paper and a brief description of why this paper is relevant.  Some examples are given below.

Description: This paper reports evidence that degeneracy is pervasive and potentially of great relevance to regulatory interactions in signalling networks. I have added this paper because I feel that this link between degeneracy and distributed control is underappreciated.

van Wageningen, S., P. Kemmeren, P. Lijnzaad, T. Margaritis, J.J. Benschop, I.J. de Castro, D. van Leenen, M.J.A. Groot Koerkamp, C.W. Ko, and A.J. Miles, Functional Overlap and Regulatory Links Shape Genetic Interactions between Signaling Pathways. Cell, 2010. 143(6): p. 991-1004.

Description: Degeneracy in biological networks results in overlapping community structures that are not fully separable and have been historically difficult to analyze. This paper introduces an interesting tool for revealing and analyzing partially overlapping community structures within networks.

Palla, G., I. Derényi, I. Farkas, and T. Vicsek, Uncovering the overlapping community structure of complex networks in nature and society. Nature, 2005. 435(7043): p. 814-818.

Description: Degeneracy amongst ensembles of models could be useful for sheding light into the compensatory mechanisms and degeneracy within biological networks

Marder, E. and A.L. Taylor, Multiple models to capture the variability in biological neurons and networks. Nature Neuroscience, 2011. 14(2): p. 133-138. (Link)

Description: This paper documents evidence supporting an interesting and potentially prevalent pathway (the IAD model) by which degenerate and promiscuous gene products can confer new adaptive traits. The IAD model basically claims that selection acts on weak promiscuous activities present in existing proteins.

Soo, V.W.C., P. Hanson-Manful, and W.M. Patrick, Artificial gene amplification reveals an abundance of promiscuous resistance determinants in Escherichia coli. Proceedings of the National Academy of Sciences, 2011. 108(4): p. 1484. http://www.pnas.org/content/108/4/1484.full Commentary can also be found HERE

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