Journal of the ACM (JACM)
Analysis of protein-protein interaction networks using random walks
Proceedings of the 5th international workshop on Bioinformatics
Approximating the Number of Network Motifs
WAW '09 Proceedings of the 6th International Workshop on Algorithms and Models for the Web-Graph
Discrete Applied Mathematics
An Efficient Fixed-Parameter Enumeration Algorithm for Weighted Edge Dominating Set
FAW '09 Proceedings of the 3d International Workshop on Frontiers in Algorithmics
RECOMB'06 Proceedings of the joint 2006 satellite conference on Systems biology and computational proteomics
Counting stars and other small subgraphs in sublinear time
SODA '10 Proceedings of the twenty-first annual ACM-SIAM symposium on Discrete Algorithms
Improving the accuracy of signal transduction pathway construction using level-2 neighbours
International Journal of Bioinformatics Research and Applications
On the effective enumerability of NP problems
IWPEC'06 Proceedings of the Second international conference on Parameterized and Exact Computation
Parameterized top-K algorithms
Theoretical Computer Science
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The interpretation of large-scale protein network data depends on our ability to identify significant sub-structures in the data, a computationally intensive task. Here we adapt and extend efficient techniques for finding paths in graphs to the problem of identifying pathways in protein interaction networks. We present linear-time algorithms for finding paths in networks under several biologically-motivated constraints. We apply our methodology to search for protein pathways in the yeast protein-protein interaction network. We demonstrate that our algorithm is capable of reconstructing known signaling pathways and identifying functionally enriched paths in an unsupervised manner. The algorithm is very efficient, computing optimal paths of length 8 within minutes and paths of length 10 in less than two hours.