Sharon Bruckner

Publications

 

BibTeX bibliography data of my publications

Conference articles

• Sharon Bruckner, Falk Hüffner, Richard M. Karp, Ron Shamir, and Roded Sharan:
  Topology-free querying of protein interaction networks.
  In Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB '09), Tucson, Arizona, USA. May 2009.
  Lecture Notes in Bioinformatics, Springer. [show abstract]

Abstract. 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. 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 combat this problem, we develop a topology-free querying algorithm, which we call Torque. Given a query, represented as a set of proteins, Torque seeks a matching set of proteins that are sequence-similar to the query proteins and span a connected region of the network, while allowing both insertions and deletions. The algorithm uses alternatively dynamic programming and integer linear programming for the search task. We test Torque with queries from yeast, fly, and human, where we compare it to the QNet topology-based approach, and with queries from less studied species, where only topology-free algorithms apply. Torque detects many more matches than QNet, while in both cases giving results that are highly functionally coherent.

 

Journal articles (to appear)

• Sharon Bruckner, Falk Hüffner, Richard M. Karp, Ron Shamir, and Roded Sharan:
  Torque: Topology-free querying of protein interaction networks.
  In Nucleic Acids Research, Web Server Issue
  Under 2nd review, April 2009. [show abstract]

Abstract. Torque is a tool for cross-species querying of protein– protein interaction networks. It aims to answer the following question: given a set of proteins constituting a known complex or a pathway in one species, can a similar complex or pathway be found in the protein network of another species? To this end, Torque seeks a matching set of proteins that are sequence-similar to the query proteins and span a connected region of the target network, while allowing for both insertions and deletions. Unlike existing approaches, Torque does not require knowledge of the interconnections among the query proteins. It can handle large queries of up to 25 proteins.

The Torque web-server is freely available.