Combinatorial optimization: algorithms and complexity
Combinatorial optimization: algorithms and complexity
Separators for sphere-packings and nearest neighbor graphs
Journal of the ACM (JACM)
On the approximation of protein threading
Theoretical Computer Science - Special issue: Genome informatics
The anatomy of a large-scale hypertextual Web search engine
WWW7 Proceedings of the seventh international conference on World Wide Web 7
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Algorithmic Aspects of Protein Structure Similarity
FOCS '99 Proceedings of the 40th Annual Symposium on Foundations of Computer Science
Tree Decomposition Based Fast Search of RNA Structures Including Pseudoknots in Genomes
CSB '05 Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference
A Tree-Decomposition Approach to Protein Structure Prediction
CSB '05 Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference
Fast and accurate algorithms for protein side-chain packing
Journal of the ACM (JACM)
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
Rapid ab initio RNA folding including pseudoknots via graph tree decomposition
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
AAIM'06 Proceedings of the Second international conference on Algorithmic Aspects in Information and Management
Rapid protein side-chain packing via tree decomposition
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
Integrated protein interaction networks for 11 microbes
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
A parameterized algorithm for protein structure alignment
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
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The post-genomic era has witnessed an explosion in the quality, quantity and variety of biological data---sequence, structure, and networks. However, when building computational models on these data, some abstractions recur often. In particular, graph-based computational models are a powerful, flexible and efficient way of modeling many biological systems. Graph models are used in systems biology where the goal is to understand relationships among biological entities, and in structural bioinformatics where a graph is used to represent the amino acid (or atom) interaction relationships in a protein or the secondary structure base-pairing relationships in RNA. For many of these problems, we can develop algorithms that explore the fact that certain key parameters have complexity dependent on the treewidth of the system, which is typically very small for a variety of biological systems. When treewidth is large, we can still use spectral methods to find biologically sound solutions in an efficient manner.