Topology-Free Querying of Protein Interaction Networks

  title={Topology-Free Querying of Protein Interaction Networks},
  author={Sharon Bruckner and Falk H{\"u}ffner and Richard M. Karp and Ron Shamir and Roded Sharan},
  journal={Journal of computational biology : a journal of computational molecular cell biology},
  volume={17 3},
In the network querying problem, one is given a protein complex or pathway of species A and a protein-protein interaction network of species B; the goal is to identify subnetworks of B that are similar to the query in terms of sequence, topology, or both. Existing approaches mostly depend on knowledge of the interaction topology of the query in the network of species A; however, in practice, this topology is often not known. To address this problem, we develop a topology-free querying algorithm… CONTINUE READING


Publications citing this paper.
Showing 1-10 of 63 extracted citations


Publications referenced by this paper.
Showing 1-10 of 46 references

A complexcentric view of protein network evolution

  • H. Yu, P. Braun, M. Yildirim
  • Nucleic Acids Res .
  • 2009

Topology - free querying of protein interaction networks

  • S. Bruckner, F. Hüffner, R. M. Karp
  • Lect . Notes Bioinform .
  • 2009

Fast and accurate alignment of multiple protein networks

  • B. P. Kelley, R. Sharan, +4 authors T. Ideker
  • Lect . Notes Comput . Sci .
  • 2008

Similar Papers

Loading similar papers…