An algebraic view of the relation between largest common subtrees and smallest common supertrees
Theoretical Computer Science
GOSAP: Gene Ontology-Based Semantic Alignment of Biological Pathways
International Journal of Bioinformatics Research and Applications
Approximate labelled subtree homeomorphism
Journal of Discrete Algorithms
An Introduction to Metabolic Networks and Their Structural Analysis
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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
Topology-Free Querying of Protein Interaction Networks
RECOMB 2'09 Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology
QNet: a tool for querying protein interaction networks
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
Pairwise global alignment of protein interaction networks by matching neighborhood topology
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
Automatic parameter learning for multiple network alignment
RECOMB'08 Proceedings of the 12th annual international conference on Research in computational molecular biology
Protein-to-protein interactions: Technologies, databases, and algorithms
ACM Computing Surveys (CSUR)
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)
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)
Have your spaghetti and eat it too: evolutionary algorithmics and post-evolutionary analysis
Genetic Programming and Evolvable Machines
Algorithmic aspects of heterogeneous biological networks comparison
COCOA'11 Proceedings of the 5th international conference on Combinatorial optimization and applications
A method for querying conserved subnetwork in a large-scale biomolecular network
HPCA'09 Proceedings of the Second international conference on High Performance Computing and Applications
Identification of conserved protein complexes by module alignment
International Journal of Data Mining and Bioinformatics
A novel framework for large scale metabolic network alignments by compression
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Topology aware coloring of gene regulatory networks
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
SubMAP: aligning metabolic pathways with subnetwork mappings
RECOMB'10 Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology
Biological networks: comparison, conservation, and evolutionary trees
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
Survey: Computational challenges in systems biology
Computer Science Review
Probabilistic Biological Network Alignment
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Motivation: Several genome-scale efforts are underway to reconstruct metabolic networks for a variety of organisms. As the resulting data accumulates, the need for analysis tools increases. A notable requirement is a pathway alignment finder that enables both the detection of conserved metabolic pathways among different species as well as divergent metabolic pathways within a species. When comparing two pathways, the tool should be powerful enough to take into account both the pathway topology as well as the nodes' labels (e.g. the enzymes they denote), and allow flexibility by matching similar---rather than identical---pathways. Results: MetaPathwayHunter is a pathway alignment tool that, given a query pathway and a collection of pathways, finds and reports all approximate occurrences of the query in the collection, ranked by similarity and statistical significance. It is based on a novel, efficient graph matching algorithm that extends the functionality of known techniques. The program also supports a visualization interface with which the alignment of two homologous pathways can be graphically displayed. We employed this tool to study the similarities and differences in the metabolic networks of the bacterium Escherichia coli and the yeast Saccharomyces cerevisiae, as represented in highly curated databases. We reaffirmed that most known metabolic pathways common to both the species are conserved. Furthermore, we discovered a few intriguing relationships between pathways that provide insight into the evolution of metabolic pathways. We conclude with a description of biologically meaningful meta-queries, demonstrating the power and flexibility of our new tool in the analysis of metabolic pathways. Availability: Code and data upon request. Contact: pinter@cs.technion.ac.il