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Center for Models of Life
Niels Bohr Institute
University of Copenhagen
Blegdamsvej 17
2100 Copenhagen

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Network measures and comparisons

The relationship between the design and functionality of molecular networks is now a key issue in biology. Comparison of regulatory networks performing similar tasks can give insights into how network architecture is constrained by the functions it directs. This applet illustrates quantitative methods of network comparison based on network architecture and signaling logic.


Ala Trusina, Kim Sneppen, I.B. Dodd, K.E. Shearwin and J.B. Egan.
Functional alignment of regulatory networks: A study of temerate phages
Plos Computational Biology 1 (2005)

Namiko Mitarai, Anna M. C. Andersson, Sandeep Krishna, Szabolcs Semsey, and Kim Sneppen
Efficient degradation and expression prioritization with small RNAs
Phys. biol. 4 (2007)

Jacob Bock Axelsen, Sandeep Krishna, Kim Sneppen
Cost and Capacity of Signaling in the Escherichia coli Protein Reaction Network
J. Stat. Mech. 0 (2008)

Jacob Bock Axelsen, Sebastian Bernhardsson, Kim Sneppen
One Hub-One Process: A Tool Based View on Regulatory Network Topology
BMC Systems Biology 2 (2008)

P. Gerlee, L. Lizana and K. Sneppen
Pathway identification by network pruning in the metabolic network of Escherichia coli
Bioinformatics 25 (2009)

Mikkel Avlund, Ian B. Dodd, Kim Sneppen, and Sandeep Krishna
Minimal gene regulatory circuits that can count like bacteriophage lambda
J Mol Biol. 394 (2009)