Complexity of finding embeddings in a k-tree
SIAM Journal on Algebraic and Discrete Methods
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
Motif Search in Graphs: Application to Metabolic Networks
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Compression-based fixed-parameter algorithms for feedback vertex set and edge bipartization
Journal of Computer and System Sciences
Parameterized Algorithms and Hardness Results for Some Graph Motif Problems
CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
Fast Alignments of Metabolic Networks
BIBM '08 Proceedings of the 2008 IEEE International Conference on Bioinformatics and Biomedicine
A quadratic kernel for feedback vertex set
SODA '09 Proceedings of the twentieth Annual ACM-SIAM Symposium on Discrete Algorithms
Querying Protein-Protein Interaction Networks
ISBRA '09 Proceedings of the 5th International Symposium on Bioinformatics Research and Applications
Assessing the exceptionality of coloured motifs in networks
EURASIP Journal on Bioinformatics and Systems Biology - Special issue on network structure and biological function: Reconstruction, modelling, and statistical approaches
Topology-Free Querying of Protein Interaction Networks
RECOMB 2'09 Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology
Maximum Motif Problem in Vertex-Colored Graphs
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
QNet: a tool for querying protein interaction networks
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
Sharp tractability borderlines for finding connected motifs in vertex-colored graphs
ICALP'07 Proceedings of the 34th international conference on Automata, Languages and Programming
Combinatorial Optimization on Graphs of Bounded Treewidth
The Computer Journal
Asymmetric Comparison and Querying of Biological Networks
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Mining from protein–protein interactions
Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery
Aggregate nearest neighbor queries in uncertain graphs
World Wide Web
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Recent techniques increase rapidly the amount of our knowledge on interactions between proteins. The interpretation of these new information depends on our ability to retrieve known substructures in the data, the Protein-Protein Interactions (PPIs) networks. In an algorithmic point of view, it is an hard task since it often leads to NP-hard problems. To overcome this difficulty, many authors have provided tools for querying patterns with a restricted topology, i.e., paths or trees in PPI networks. Such restriction leads to the development of fixed parameter tractable (FPT) algorithms, which can be practicable for restricted sizes of queries. Unfortunately, Graph Homomorphism is a W[1]-hard problem, and hence, no FPT algorithm can be found when patterns are in the shape of general graphs. However, Dost et al. [2] gave an algorithm (which is not implemented) to query graphs with a bounded treewidth in PPI networks (the treewidth of the query being involved in the time complexity). In this paper, we propose another algorithm for querying pattern in the shape of graphs, also based on dynamic programming and the color-coding technique. To transform graphs queries into trees without loss of informations, we use feedback vertex set coupled to a node duplication mechanism. Hence, our algorithm is FPT for querying graphs with a bounded size of their feedback vertex set. It gives an alternative to the treewidth parameter, which can be better or worst for a given query. We provide a python implementation which allows us to validate our implementation on real data. Especially, we retrieve some human queries in the shape of graphs into the fly PPI network.