Reconstructing the pre-doubling genome
RECOMB '99 Proceedings of the third annual international conference on Computational molecular biology
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
Genome Rearrangements and Sorting by Reversals
SIAM Journal on Computing
A Very Elementary Presentation of the Hannenhalli-Pevzner Theory
CPM '01 Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching
CPM '98 Proceedings of the 9th Annual Symposium on Combinatorial Pattern Matching
The Reconstruction of Doubled Genomes
SIAM Journal on Computing
Whole Genome Duplications and Contracted Breakpoint Graphs
SIAM Journal on Computing
Maximizing synteny blocks to identify ancestral homologs
RCG'05 Proceedings of the 2005 international conference on Comparative Genomics
A framework for orthology assignment from gene rearrangement data
RCG'05 Proceedings of the 2005 international conference on Comparative Genomics
Whole genome duplications, multi-break rearrangements, and genome halving problem
SODA '07 Proceedings of the eighteenth annual ACM-SIAM symposium on Discrete algorithms
Multichromosomal Genome Median and Halving Problems
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
HCV quasispecies assembly using network flows
ISBRA'08 Proceedings of the 4th international conference on Bioinformatics research and applications
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
WABI'10 Proceedings of the 10th international conference on Algorithms in bioinformatics
Advances on genome duplication distances
RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
On minimal Sturmian partial words
Discrete Applied Mathematics
Binary de bruijn partial words with one hole
TAMC'10 Proceedings of the 7th annual conference on Theory and Applications of Models of Computation
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Breakpoint graph analysis is a key algorithmic technique in studies of genome rearrangements. However, breakpoint graphs are defined only for genomes without duplicated genes, thus limiting their applications in rearrangement analysis. We discuss a connection between the breakpoint graphs and de Bruijn graphs that leads to a generalization of the notion of breakpoint graph for genomes with duplicated genes. We further use the generalized breakpoint graphs to study the Genome Halving Problem (first introduced and solved by Nadia El-Mabrouk and David Sankoff). The El-Mabrouk-Sankoff algorithm is rather complex, and, in this paper, we present an alternative approach that is based on generalized breakpoint graphs. The generalized breakpoint graphs make the El-Mabrouk-Sankoff result more transparent and promise to be useful in future studies of genome rearrangements.