SIAM Journal on Discrete Mathematics
Nonoverlapping local alignments (weighted independent sets of axis-parallel rectangles)
Discrete Applied Mathematics - Special volume on computational molecular biology
Tree adjoining grammars for RNA structure prediction
Theoretical Computer Science - Special issue: Genome informatics
Approximating discrete collections via local improvements
Proceedings of the sixth annual ACM-SIAM symposium on Discrete algorithms
Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots
Discrete Applied Mathematics - Special volume on combinatorial molecular biology
Simple approximation algorithm for nonoverlapping local alignments
SODA '02 Proceedings of the thirteenth annual ACM-SIAM symposium on Discrete algorithms
A d/2 approximation for maximum weight independent set in d-claw free graphs
Nordic Journal of Computing
On the computational complexity of 2-interval pattern matching problems
Theoretical Computer Science
SIAM Journal on Computing
An O(v|v| c |E|) algoithm for finding maximum matching in general graphs
SFCS '80 Proceedings of the 21st Annual Symposium on Foundations of Computer Science
Approximating the 2-interval pattern problem
Theoretical Computer Science
Delta: a toolset for the structural analysis of biological sequences on a 3D triangular lattice
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
Approximating the 2-interval pattern problem
ESA'05 Proceedings of the 13th annual European conference on Algorithms
On Recovering Syntenic Blocks from Comparative Maps
COCOA 2008 Proceedings of the 2nd international conference on Combinatorial Optimization and Applications
On the Tractability of Maximal Strip Recovery
TAMC '09 Proceedings of the 6th Annual Conference on Theory and Applications of Models of Computation
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We study three closely related problems motivated by the prediction of RNA secondary structures with arbitrary pseudoknots: the Maximum Base Pair Stackingsproblem proposed by Ieong et al. [19] , the Maximum Stacking Base Pairsproblem proposed by Lyngsø [22], and the 2-Interval Patternproblem proposed by Vialette [36] . For Maximum Base Pair Stackingsand Maximum Stacking Base Pairs, we present improved approximation algorithms that can incorporate covariance information from comparative analysis as explicit input of candidate base pairs. For 2-Interval Pattern, we present improved approximation algorithms on unitary and near-unitary input, and propose a new variant called Length-Weighted Balanced 2-Interval Pattern, which is natural in the nearest-neighbor energy model that emphasizes base pair stacking.