Journal of the ACM (JACM)
FANMOD: a tool for fast network motif detection
Bioinformatics
Motif Search in Graphs: Application to Metabolic Networks
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Topology-Free Querying of Protein Interaction Networks
RECOMB 2'09 Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology
Finding and counting vertex-colored subtrees
MFCS'10 Proceedings of the 35th international conference on Mathematical foundations of computer science
Upper and lower bounds for finding connected motifs in vertex-colored graphs
Journal of Computer and System Sciences
Parameterized Algorithmics for Finding Connected Motifs in Biological Networks
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Finding approximate and constrained motifs in graphs
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
Constrained multilinear detection for faster functional motif discovery
Information Processing Letters
Finding dense subgraphs of sparse graphs
IPEC'12 Proceedings of the 7th international conference on Parameterized and Exact Computation
| Hi-index | 0.00 |
Given a multiset of colors as the query and a list-colored graph, i.e., an undirected graph with a set of colors assigned to each of its vertices, in the NP-hard list-colored graph motif problem the goal is to find the largest connected subgraph such that one can select a color from the set of colors assigned to each of its vertices to obtain a subset of the query. This problem was introduced to find functional motifs in biological networks. We present a branch-and-bound algorithm named RANGI for finding and enumerating list-colored graph motifs. As our experimental results show, RANGI's pruning methods and heuristics make it quite fast in practice compared to the algorithms presented in the literature. We also present a parallel version of RANGI that achieves acceptable scalability.