Journal of the ACM (JACM)
The Parameterized Complexity of Counting Problems
SIAM Journal on Computing
Parameterized Complexity Theory (Texts in Theoretical Computer Science. An EATCS Series)
Parameterized Complexity Theory (Texts in Theoretical Computer Science. An EATCS Series)
Motif Search in Graphs: Application to Metabolic Networks
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Fourier meets möbius: fast subset convolution
Proceedings of the thirty-ninth annual ACM symposium on Theory of computing
Parameterized Algorithms and Hardness Results for Some Graph Motif Problems
CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
Faster Algebraic Algorithms for Path and Packing Problems
ICALP '08 Proceedings of the 35th international colloquium on Automata, Languages and Programming, Part I
Finding paths of length k in O∗(2k) time
Information Processing Letters
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
Annotating fragmentation patterns
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
Sharp tractability borderlines for finding connected motifs in vertex-colored graphs
ICALP'07 Proceedings of the 34th international conference on Automata, Languages and Programming
Finding approximate and constrained motifs in graphs
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
On the parameterized complexity of the repetition free longest common subsequence problem
Information Processing Letters
Finding maximum colorful subtrees in practice
RECOMB'12 Proceedings of the 16th Annual international conference on Research in Computational Molecular Biology
Constrained multilinear detection for faster functional motif discovery
Information Processing Letters
RANGI: A Fast List-Colored Graph Motif Finding Algorithm
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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The problems studied in this article originate from the GRAPH MOTIF problem introduced by Lacroix et al. [17] in the context of biological networks. The problem is to decide if a vertex-colored graph has a connected subgraph whose colors equal a given multiset of colors M. Using an algebraic framework recently introduced by Koutis et al. [15,16], we obtain new FPT algorithms for GRAPH MOTIF and variants, with improved running times. We also obtain results on the counting versions of this problem, showing that the counting problem is FPT if M is a set, but becomes #W[1]-hard if M is a multiset with two colors.