Small World and Scale-Free Network Topologies in an Artificial Regulatory Network Model

Small world and scale-free network topologies commonly exist in natural and artificial systems. Many mechanisms for producing these topologies have been presented in the literature. We present an artificial regulatory network model generated by a duplication / divergence process on a randomly generated genetic string and show that networks with small world and scale-free topologies can be produced with some regularity.

[1]  Gavin H. Thomas,et al.  Completing the E. coli proteome: a database of gene products characterised since the completion of the genome sequence , 1999, Bioinform..

[2]  Michalis Faloutsos,et al.  On power-law relationships of the Internet topology , 1999, SIGCOMM '99.

[3]  S. Wuchty Scale-free behavior in protein domain networks. , 2001, Molecular biology and evolution.

[4]  Albert-Laszlo Barabasi,et al.  Deterministic scale-free networks , 2001 .

[5]  Albert,et al.  Emergence of scaling in random networks , 1999, Science.

[6]  E. Davidson Genomic Regulatory Systems , 2001 .

[7]  Jie Wu,et al.  Small Worlds: The Dynamics of Networks between Order and Randomness , 2003 .

[8]  K. H. Wolfe,et al.  Molecular evidence for an ancient duplication of the entire yeast genome , 1997, Nature.

[9]  D. Sankoff,et al.  Comparable rates of gene loss and functional divergence after genome duplications early in vertebrate evolution. , 1997, Genetics.

[10]  R. Solé,et al.  Evolving protein interaction networks through gene duplication. , 2003, Journal of Theoretical Biology.

[11]  D. Watts,et al.  Small Worlds: The Dynamics of Networks between Order and Randomness , 2001 .

[12]  Wolfgang Banzhaf On the Dynamics of an Artificial Regulatory Network , 2003, ECAL.

[13]  L. Hood,et al.  The digital code of DNA , 2003, Nature.

[14]  Hiroaki Kitano,et al.  Foundations of systems biology , 2001 .

[15]  Hawoong Jeong,et al.  Classification of scale-free networks , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[16]  W. Banzhaf Artificial Regulatory Networks and Genetic Programming , 2003 .

[17]  James M. Bower,et al.  Computational modeling of genetic and biochemical networks , 2001 .

[18]  A. Barabasi,et al.  Evolution of the social network of scientific collaborations , 2001, cond-mat/0104162.