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
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 framework for orthology assignment from gene rearrangement data
RCG'05 Proceedings of the 2005 international conference on Comparative Genomics
A network flow approach to the minimum common integer partition problem
Theoretical Computer Science
Comparing Genomes with Duplications: A Computational Complexity Point of View
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Better approximations for the minimum common integer partition problem
APPROX'06/RANDOM'06 Proceedings of the 9th international conference on Approximation Algorithms for Combinatorial Optimization Problems, and 10th international conference on Randomization and Computation
Inferring positional homologs with common intervals of sequences
RCG'06 Proceedings of the RECOMB 2006 international conference on Comparative Genomics
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The assignment of orthologous genes between a pair of genomes is a fundamental and challenging problem in comparative genomics, since many computational methods for solving various biological problems critically rely on bona fide orthologs as input. While it is usually done using sequence similarity search, we recently proposed a new combinatorial approach that combines sequence similarity and genome rearrangement. This paper continues the development of the approach and unites genome rearrangement events and (post-speciation) duplication events in a single framework under the parsimony principle. In this framework, orthologous genes are assumed to correspond to each other in the most parsimonious evolutionary scenario involving both genome rearrangement and (post-speciation) gene duplication. Besides several original algorithmic contributions, the enhanced method allows for the detection of inparalogs. Following this approach, we have implemented a high-throughput system for ortholog assignment on a genome scale, called MSOAR, and applied it to the genomes of human and mouse. As the result will show, MSOAR is able to find 99 more true orthologs than the INPARANOID program did. We have also compared MSOAR with the iterated exemplar algorithm on simulated data and found that MSOAR performed very well in terms of assignment accuracy. These test results indiate that our approach is very promising for genome-wide ortholog assignment.