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
Compression-based fixed-parameter algorithms for feedback vertex set and edge bipartization
Journal of Computer and System Sciences
A quadratic kernel for feedback vertex set
SODA '09 Proceedings of the twentieth Annual ACM-SIAM Symposium on Discrete Algorithms
QNet: a tool for querying protein interaction networks
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
A cubic kernel for feedback vertex set
STACS'07 Proceedings of the 24th annual conference on Theoretical aspects of computer science
Parameterized Complexity
Dividing protein interaction networks for modular network comparative analysis
Pattern Recognition Letters
Querying Graphs in Protein-Protein Interactions Networks Using Feedback Vertex Set
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
NABEECO: biological network alignment with bee colony optimization algorithm
Proceedings of the 15th annual conference companion on Genetic and evolutionary computation
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Recent techniques increase the amount of our knowledge of interactions between proteins. To filter, interpret and organize this data, many authors have provided tools for querying patterns in the shape of paths or trees in Protein-Protein Interaction networks. In this paper, we propose an exact algorithm for querying graphs pattern based on dynamic programming and color-coding. We provide an implementation which has been validated on real data.