Journal of the ACM (JACM)
Computers and Intractability: A Guide to the Theory of NP-Completeness
Computers and Intractability: A Guide to the Theory of NP-Completeness
Alignment of metabolic pathways
Bioinformatics
Graph algorithms for biological systems analysis
Proceedings of the nineteenth annual ACM-SIAM symposium on Discrete algorithms
Parameterized Algorithms and Hardness Results for Some Graph Motif Problems
CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
Approximating the Number of Network Motifs
WAW '09 Proceedings of the 6th International Workshop on Algorithms and Models for the Web-Graph
GADDI: distance index based subgraph matching in biological networks
Proceedings of the 12th International Conference on Extending Database Technology: Advances in Database Technology
Querying Protein-Protein Interaction Networks
ISBRA '09 Proceedings of the 5th International Symposium on Bioinformatics Research and Applications
Automatic parameter learning for multiple network alignment
RECOMB'08 Proceedings of the 12th annual international conference on Research in computational molecular biology
Quantifying systemic evolutionary changes by color coding confidence-scored PPI networks
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
Counting stars and other small subgraphs in sublinear time
SODA '10 Proceedings of the twenty-first annual ACM-SIAM symposium on Discrete Algorithms
Querying Graphs in Protein-Protein Interactions Networks Using Feedback Vertex Set
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
SAPPER: subgraph indexing and approximate matching in large graphs
Proceedings of the VLDB Endowment
Asymmetric Comparison and Querying of Biological Networks
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
BR-index: an indexing structure for subgraph matching in very large dynamic graphs
SSDBM'11 Proceedings of the 23rd international conference on Scientific and statistical database management
Answering subgraph queries over large graphs
WAIM'11 Proceedings of the 12th international conference on Web-age information management
A novel framework for large scale metabolic network alignments by compression
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Querying KEGG pathways in logic
International Journal of Data Mining and Bioinformatics
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Molecular interaction databases can be used to study the evolution of molecular pathways across species. Querying such pathways is a challenging computational problem, and recent efforts have been limited to simple queries (paths), or simple networks (forests). In this paper, we significantly extend the class of pathways that can be efficiently queried to the case of trees, and graphs of bounded treewidth. Our algorithm allows the identification of non-exact (homeomorphic) matches, exploiting the color coding technique of Alon et al. We implement a tool for tree queries, called QNet, and test its retrieval properties in simulations and on real network data. We show that QNet searches queries with up to 9 proteins in seconds on current networks, and outperforms sequence-based searches.We also use QNet to perform the first large scale cross-species comparison of protein complexes, by querying known yeast complexes against a fly protein interaction network. This comparison points to strong conservation between the two species, and underscores the importance of our tool in mining protein interaction networks.