CSSS 2006 Biological Networks

Lecturer: Andreas Wagner



Resources (an evolving list):

  • Conant, G.C. and A. Wagner. 2003. Convergent evolution in gene circuits. Nature Genetics 34: 264-266. Edwards, J.S. and B.O. Palsson. 2000. The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities. Proceedings of the National Academy of Sciences of the United States of America 97: 5528-5533.
  • Evangelisti, A. and A. Wagner. 2004. Molecular evolution in the transcriptional regulation network of yeast. submitted.
  • Hanlon, S. and J. Lieb. 2004. Progress and challenges in profiling the dynamics of chromatin and transcription factor binding with DNA microarrays Current Opinion in Genetics and Development 14: 697-705.
  • Jeong, H., S.P. Mason, A.-L. Barabasi, and Z.N. Oltvai. 2001. Lethality and centrality in protein networks. Nature 411: 41-42.
  • Lee, T., N. Rinaldi, F. Robert, D. Odom, Z. Bar-Joseph, G. Gerber, N. Hannett, C. Harbison, C. Thompson, I. Simon, J. Zeitlinger, E. Jennings, H. Murray, D. Gordon, B. Ren, J. Wyrick, J. Tagne, T. Volkert, E. Fraenkel, D. Gifford, and R. Young. 2002. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799-804.
  • Maslov, S. and K. Sneppen. 2002. Specificity and stability in topology of protein networks. Science 296: 910-913.
  • Milo, R., S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, and U. Alon. 2002. Network motifs: Simple building blocks of complex networks. SCIENCE 298: 824-827.
  • Ptacek, J., G. Devgan, G. Michaud, H. Zhu, X. Zhu, J. Fasolo, H. Guo, G. Jona, A. Breitkreutz, R. Sopko, R. McCartney, M. Schmidt, N. Rachidi, S. Lee, A. Mah, L. Meng, M. Stark, D. Stern, C. De Virgilio, M. Tyers, B. Andrews, M. Gerstein, B. Schweitzer, P. Predki, and M. Snyder. 2005. Global analysis of protein phosphorylation in yeast. NATURE 438: 679-684.
  • Wagner, A. 2001. The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Molecular Biology and Evolution. 18: 1283-1292.
  • Wagner, A. 2003. How the global structure of protein interaction networks evolves. Proceedings of the Royal Society of London Series B. 270: 457-466.
  • Wagner, A. and J. Wright. 2005. Compactness and cycles in signal transduction and transcriptional regulation networks: a signature of natural selection? Advances in Complex Systems 7: 419-432.
  • Watts, D.J. and S.H. Strogatz. 1998. Collective dynamics of small-world networks. Nature 393: 440-442. Background