SIAM Journal on Discrete Mathematics
Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals
Journal of the ACM (JACM)
A Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals
SIAM Journal on Computing
An algorithm to enumerate all sorting reversals
Proceedings of the sixth annual international conference on Computational biology
Efficient algorithms for multichromosomal genome rearrangements
Journal of Computer and System Sciences - Computational biology 2002
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Finding All Common Intervals of k Permutations
CPM '01 Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching
Efficient Bounds for Oriented Chromosome Inversion Distance
CPM '94 Proceedings of the 5th Annual Symposium on Combinatorial Pattern Matching
Transforming men into mice (polynomial algorithm for genomic distance problem)
FOCS '95 Proceedings of the 36th Annual Symposium on Foundations of Computer Science
Information Processing Letters
Genome Rearrangement Based on Reversals that Preserve Conserved Intervals
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Exemplar Longest Common Subsequence
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Comparing Genomes with Duplications: A Computational Complexity Point of View
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Permu-pattern: discovery of mutable permutation patterns with proximity constraint
Proceedings of the 14th ACM SIGKDD international conference on Knowledge discovery and data mining
HP Distance Via Double Cut and Join Distance
CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
Hurdles Hardly Have to Be Heeded
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
Comparing Bacterial Genomes by Searching Their Common Intervals
BICoB '09 Proceedings of the 1st International Conference on Bioinformatics and Computational Biology
Approximability and Fixed-Parameter Tractability for the Exemplar Genomic Distance Problems
TAMC '09 Proceedings of the 6th Annual Conference on Theory and Applications of Models of Computation
Sorting Signed Permutations by Inversions in O(nlogn) Time
RECOMB 2'09 Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology
A new linear time algorithm to compute the genomic distance via the double cut and join distance
Theoretical Computer Science
Pseudo Boolean Programming for Partially Ordered Genomes
RECOMB-CG '09 Proceedings of the International Workshop on Comparative Genomics
Information Processing Letters
Genes order and phylogenetic reconstruction: application to γ-proteobacteria
RCG'05 Proceedings of the 2005 international conference on Comparative Genomics
Maximizing synteny blocks to identify ancestral homologs
RCG'05 Proceedings of the 2005 international conference on Comparative Genomics
A unifying view of genome rearrangements
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
The approximability of the exemplar breakpoint distance problem
AAIM'06 Proceedings of the Second international conference on Algorithmic Aspects in Information and Management
The reversal median problem, common intervals, and mitochondrial gene orders
CompLife'06 Proceedings of the Second international conference on Computational Life Sciences
Conserved interval distance computation between non-trivial genomes
COCOON'05 Proceedings of the 11th annual international conference on Computing and Combinatorics
Lower bounds on the approximation of the exemplar conserved interval distance problem of genomes
COCOON'06 Proceedings of the 12th annual international conference on Computing and Combinatorics
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
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
RCG'06 Proceedings of the RECOMB 2006 international conference on Comparative Genomics
A PQ framework for reconstructions of common ancestors and phylogeny
RCG'06 Proceedings of the RECOMB 2006 international conference on Comparative Genomics
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The comparison of genomes with the same gene content relies on our ability to compare permutations, either by measuring how much they differ, or by measuring how much they are alike. With the notable exception of the breakpoint distance, which is based on the concept of conserved adjacencies, measures of distance do not generalize easily to sets of more than two permutations. In this paper, we present a basic unifying notion, conserved intervals, as a powerful generalization of adjacencies, and as a key feature of genome rearrangement theories. We also show that sets of conserved intervals have elegant nesting and chaining properties that allow the development of compact graphic representations, and linear time algorithms to manipulate them.