Topological analysis and interactive visualization of biological networks and protein structures. Doncheva, N. T, Assenov, Y., Domingues, F. S, & Albrecht, M. Nature protocols, 7(4):670--685, Nature Publishing Group, 2012.
bibtex   
@article{doncheva2012topological,
  title={Topological analysis and interactive visualization of biological networks and protein structures},
  author={Doncheva, Nadezhda T and Assenov, Yassen and Domingues, Francisco S and Albrecht, Mario},
  journal={Nature protocols},
  volume={7},
  number={4},
  pages={670--685},
  year={2012},
  publisher={Nature Publishing Group}
}

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