An Efficient Genetic Algorithm for Job Shop Scheduling Problems
Proceedings of the 6th International Conference on Genetic Algorithms
Algorithmic Graph Theory and Perfect Graphs (Annals of Discrete Mathematics, Vol 57)
Algorithmic Graph Theory and Perfect Graphs (Annals of Discrete Mathematics, Vol 57)
Journal of Computer and System Sciences
Proceedings of the sixth annual international conference on Computational biology
Algorithms for Finding Gene Clusters
WABI '01 Proceedings of the First International Workshop on Algorithms in Bioinformatics
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
RCIS: A Common Interval Searching Algorithm for Amino Acid Sequences
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
An algorithmic view of gene teams
Theoretical Computer Science
Information Processing Letters
Fast algorithms for identifying maximal common connected sets of interval graphs
Discrete Applied Mathematics
Perfect Sorting by Reversals Is Not Always Difficult
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Journal of Discrete Algorithms
Hierarchical alignment graph for gene teams finding on whole genomes
Proceedings of the 2007 ACM symposium on Applied computing
Evolution under Reversals: Parsimony and Conservation of Common Intervals
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
New algorithms for text fingerprinting
Journal of Discrete Algorithms
Permu-pattern: discovery of mutable permutation patterns with proximity constraint
Proceedings of the 14th ACM SIGKDD international conference on Knowledge discovery and data mining
Solving the Preserving Reversal Median Problem
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
SPIRE '08 Proceedings of the 15th International Symposium on String Processing and Information Retrieval
Improved Algorithms for the Gene Team Problem
COCOA '09 Proceedings of the 3rd International Conference on Combinatorial Optimization and Applications
Information Processing Letters
On the similarity of sets of permutations and its applications to genome comparison
COCOON'03 Proceedings of the 9th annual international conference on Computing and combinatorics
A fast and exact algorithm for the perfect reversal median problem
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
Computation of median gene clusters
RECOMB'08 Proceedings of the 12th annual international conference on Research in computational molecular biology
EMNLP '10 Proceedings of the 2010 Conference on Empirical Methods in Natural Language Processing
Ultra-perfect sorting scenarios
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
A PTAS for the square tiling problem
SPIRE'10 Proceedings of the 17th international conference on String processing and information retrieval
Proceedings of the 17th ACM SIGKDD international conference on Knowledge discovery and data mining
Algorithms for computing bidirectional best hit r-window gene clusters
FAW-AAIM'11 Proceedings of the 5th joint international frontiers in algorithmics, and 7th international conference on Algorithmic aspects in information and management
Individual gene cluster statistics in noisy maps
RCG'05 Proceedings of the 2005 international conference on Comparative Genomics
Gapped permutation patterns for comparative genomics
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
A parallel algorithm for solving the reversal median problem
PPAM'05 Proceedings of the 6th international conference on Parallel Processing and Applied Mathematics
Computing common intervals of K permutations, with applications to modular decomposition of graphs
ESA'05 Proceedings of the 13th annual European conference on Algorithms
COCOON'05 Proceedings of the 11th annual international conference on Computing and Combinatorics
A New Efficient Algorithm for the Gene-Team Problem on General Sequences
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Output-Sensitive Algorithms for Finding the Nested Common Intervals of Two General Sequences
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Revisiting t. uno and m. yagiura's algorithm
ISAAC'05 Proceedings of the 16th international conference on Algorithms and Computation
Using PQ trees for comparative genomics
CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
Algebraic operations on PQ trees and modular decomposition trees
WG'05 Proceedings of the 31st international conference on Graph-Theoretic Concepts in Computer Science
Perfect sorting by reversals is not always difficult
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
Conservation of combinatorial structures in evolution scenarios
RCG'04 Proceedings of the 2004 RECOMB international conference on Comparative Genomics
The statistical significance of max-gap clusters
RCG'04 Proceedings of the 2004 RECOMB international conference on Comparative Genomics
Software note: Gene teams: a new formalization of gene clusters for comparative genomics
Computational Biology and Chemistry
Consecutive ones property and PQ-trees for multisets: Hardness of counting their orderings
Information and Computation
Preserving inversion phylogeny reconstruction
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
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Given k permutations of n elements, a k-tuple of intervals of these permutations consisting of the same set of elements is called a common interval. We present an algorithm that finds in a family of k permutations of n elements all K common intervals in optimal O(nk+K) time and O(n) additional space.This extends a result by Uno and Yagiura (Algorithmica 26, 290-309, 2000) who present an algorithm to find all K common intervals of k = 2 permutations in optimal O(n+K) time and O(n) space. To achieve our result, we introduce the set of irreducible intervals, a generating subset of the set of all common intervals of k permutations.