Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals
STOC '95 Proceedings of the twenty-seventh annual ACM symposium on Theory of computing
Reconstructing an ancestral genome using minimum segments duplications and reversals
Journal of Computer and System Sciences - Computational biology 2002
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
The Median Problem for Breakpoints in Comparative Genomics
COCOON '97 Proceedings of the Third Annual International Conference on Computing and Combinatorics
Phylogenetic Reconstruction from Arbitrary Gene-Order Data
BIBE '04 Proceedings of the 4th IEEE Symposium on Bioinformatics and Bioengineering
Genomic distances under deletions and insertions
Theoretical Computer Science - Special papers from: COCOON 2003
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
Inferring positional homologs with common intervals of sequences
RCG'06 Proceedings of the RECOMB 2006 international conference on Comparative Genomics
A parsimony approach to genome-wide ortholog assignment
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
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Gene rearrangements have been used successfully in phylogenetic reconstruction and comparative genomics, but usually under the assumption that all genomes have the same gene content and that no gene is duplicated. While these assumptions allow one to work with organellar genomes, they are too restrictive for nuclear genomes. The main challenge in handling more realistic data is how to deal with gene families, specifically, how to identify orthologs. While searching for orthologies is a common task in computational biology, it is usually done using sequence data. Sankoff first addressed the problem in 1999, introducing the notion of exemplar, but his approach uses an NP-hard optimization step to discard all but one member (the exemplar) of each gene family, losing much valuable information in the process. We approach the problem using all available data in the gene orders and gene families, provide an optimization framework in which to phrase the problem, and present some preliminary theoretical results.