The prospective resilience of (protein) networks

Python code for calculating the resilience and the prospective resilience in networks. This code accompanies the recent paper:

Resilience and evolvability of protein-protein interaction networks. by Brennan Klein, Ludvig Holmér, Keith M. Smith, Mackenzie M. Johnson, Anshuman Swain, Laura Stolp, Ashley I. Teufel, and April S. Kleppe. (2020).

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Fig. 1: Schematic of network resilience.

Fig. 2: The effect of network density on resilience.

Fig. 3: Different node attachment mechanisms for prospective resilience.

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Analysis Notebooks

1. 01_Intro_Network_Resilience
2. 02_Protein_Network_Resilience
3. 03_Prospective_Resilience

Installation and Usage

In order to use this code, first clone/download the repository. Please feel free to reach out if you find any bugs, have any questions, or if for some reason the code does not run.

Requirements

This code is written in Python 3.x and uses the following packages:

• NetworkX
• Scipy
• Numpy
• And for replicating figures, you will need:
  • matplotlib
  • Pandas

The colormaps in the paper are from https://matplotlib.org/cmocean/ and the named colors are from https://medialab.github.io/iwanthue/.

Citation

If you use these methods and this code in your own research, please cite our paper:

Klein, B., Holmér, L., Smith, K., Johnson, M., Swain, A., Stolp, L., Teufel, A., and Kleppe, A. (2020). Resilience and evolvability of protein-protein interaction networks.

Bibtex:

@article{klein2020presilience,
  title = {Resilience and evolvability of protein-protein interaction networks},
  author = {Klein, Brennan and Holmér, Ludvig and Smith, Keith M. and Johnson, Mackenzie M.
            and Swain, Anshuman and Stolp, Laura and Teufel, Ashley I. and Kleppe, April S.},
  journal = {bioRxiv preprint 10.1101/2020.07.02.184325v1},
  year = {2020}
}

See also:

• Zitnik, M., Sosič, R., Feldman, M.W., and Leskovec, J. (2019). Evolution of resilience in protein interactomes across the tree of life. Proceedings of the National Academy of Sciences. 116, 10, 4426–4433. doi: 10.1073/pnas.1818013116.
  • recent work introducing the network resilience measure used here, showing that the resilience of protein-protein interactomes increases across the tree of life.