O(n2.5) time algorithms for the subgraph homeomorphism problem on trees
Journal of Algorithms
Introduction to algorithms
A compression algorithm for DNA sequences and its applications in genome comparison
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
Introduction to the Theory of Computation
Introduction to the Theory of Computation
A Multiple Alignment Algorithm for Metabolic Pathway Analysis Using Enzyme Hierarchy
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
Comparison of metabolic pathways using constraint graph drawing
APBC '03 Proceedings of the First Asia-Pacific bioinformatics conference on Bioinformatics 2003 - Volume 19
Alignment of metabolic pathways
Bioinformatics
An Introduction to Kolmogorov Complexity and Its Applications
An Introduction to Kolmogorov Complexity and Its Applications
ICALP'05 Proceedings of the 32nd international conference on Automata, Languages and Programming
Information theoretic approaches to whole genome phylogenies
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
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We describe a new approach for comparing cellular-biological networks, and finding conserved regions in two or more such networks. We use the length of describing one network, given the description of the other one, as a distance measure. We employ these distances as inputs for generating phylogenetic trees. Our algorithms are fast enough for generating phylogenetic tree of more than two hundreds metabolic networks that appear in KEGG. Using KEGG's metabolic networks as our starting point, we got trees that are not perfect, but are surprisingly good. We also found conserved regions among more than a dozen metabolic networks, and among two protein interaction networks. These conserved regions seem biologically relevant, proving the viability of our approach.