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
Formulations and hardness of multiple sorting by reversals
RECOMB '99 Proceedings of the third annual international conference on Computational molecular biology
The Median Problem for Breakpoints in Comparative Genomics
COCOON '97 Proceedings of the Third Annual International Conference on Computing and Combinatorics
INFORMS Journal on Computing
Stochastic Local Search: Foundations & Applications
Stochastic Local Search: Foundations & Applications
Genome Rearrangement Based on Reversals that Preserve Conserved Intervals
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Progressive Tree Neighborhood Applied to the Maximum Parsimony Problem
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A population-based local search for solving a bi-objective vehicle routing problem
EvoCOP'07 Proceedings of the 7th European conference on Evolutionary computation in combinatorial optimization
Swarming along the evolutionary branches sheds light on genome rearrangement scenarios
Proceedings of the 11th Annual conference on Genetic and evolutionary computation
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We present a novel population-based local search algorithm for the median genome problem. The primary result of this article is that this probabilistic approach significantly improves the performance of ancestral genome reconstruction compared to existing methods, making it possible to tackle problems where the contemporary genomes may contain many hundreds of markers. Moreover, our method is not limited to triples of genomes, and thus solves the median genome problem in its generality. We show that in real application cases the computational results are highly robust, suggesting that we can interpret the computed median genomes as candidates carrying the semantics of ancestral architectures.