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
Efficient algorithms for multichromosomal genome rearrangements
Journal of Computer and System Sciences - Computational biology 2002
Genome Rearrangement by Reversals and Insertions/Deletions of Contiguous Segments
COM '00 Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching
A Very Elementary Presentation of the Hannenhalli-Pevzner Theory
CPM '01 Proceedings of the 12th 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
Genomic distances under deletions and insertions
Theoretical Computer Science - Special papers from: COCOON 2003
Assignment of Orthologous Genes via Genome Rearrangement
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A simpler 1.5-approximation algorithm for sorting by transpositions
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
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
Conserved interval distance computation between non-trivial genomes
COCOON'05 Proceedings of the 11th annual international conference on Computing and Combinatorics
Colored de Bruijn Graphs and the Genome Halving Problem
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Whole genome duplications, multi-break rearrangements, and genome halving problem
SODA '07 Proceedings of the eighteenth annual ACM-SIAM symposium on Discrete algorithms
Comparing Genomes with Duplications: A Computational Complexity Point of View
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Fundamenta Informaticae
RECOMB-CG'07 Proceedings of the 2007 international conference on Comparative genomics
Decoding synteny blocks and large-scale duplications in mammalian and plant genomes
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
Inferring positional homologs with common intervals of sequences
RCG'06 Proceedings of the RECOMB 2006 international conference on Comparative Genomics
How pseudo-boolean programming can help genome rearrangement distance computation
RCG'06 Proceedings of the RECOMB 2006 international conference on Comparative Genomics
Fundamenta Informaticae
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Most genome rearrangement studies are based on the assumption that the compared genomes contain unique gene copies. This is clearly unsuitable for species with duplicated genes or when local alignment tools provide many ambiguous hits for the same gene. In this paper, we compare different measures of order conservation to select, among a gene family, the pair of copies in two genomes that best reflects the common ancestor. Specifically, we present algorithms to identify ancestral homologs, or exemplars [1] , by maximizing synteny blocks between genomes. Using simulated data, we validate our approach and show the merits of using a conservative approach when making such assignments.