Nature 409: 860--921. Moret, B., Wang, L., Warnow, T., and Wyman, S. 2001. New approaches for reconstructing phylogenies from gene order data.  Home/Search Document Details and Download
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Inversion Medians Outperform Breakpoint Medians in.. - Moret, Siepel, Tang, Liu (2002) (1 citation) Self-citation (Moret) (Correct)
.... Pevzner [9] has shown that inversion distance can be computed in linear time [1] a development that has allowed us to base the reconstruction process on the inversion score of a tree rather than on its breakpoint score, with significant resulting improvements in the accuracy of reconstructions [13]. Other recent results have shown that the inversion median of three genomes can be obtained quickly for a reasonable range of instances [5, 23, 24] in spite of the NP hardness of the problem) These developments have enabled us to extend GRAPPA by replacing the breakpoint median routine with an ....
....algorithm is applied to the labels at the leaves of such a tree, it should infer an evolutionary history resembling the model tree. 3. 3 Labelling internal nodes One of the major advantages of median based phylogeny reconstruction over alternative methods (such as the encoding methods of [13, 26]) is that it estimates the configurations of ancestral genomes as well as the topology of the tree. The approach proposed by Sankoff and Blanchette to estimate ancestral genomes is iterative, using a local optimization strategy. It is applied in turn to each plausible tree topology; in the end, ....
B. Moret, L.-S. Wang, T. Warnow, and S. Wyman. New approaches for reconstructing phylogenies from gene-order data. In Proc. 9th Int'l Conf. on Intelligent Systems for Mol. Biol. ISMB 2001, volume 17 of Bioinformatics, pages S165--S173, 2001.
Finding an Optimal Inversion Median: Experimental Results - Siepel, Moret (2001) Self-citation (Moret) (Correct)
....by reversals [2,12] and a linear time algorithm for computing inversion distances [1] Note that signed permutations correspond to genomes for which the direction of transcription of each gene is known as well as the ordering of the genes. Much recent work on rearrangement based phylogeny [ 5,6,14,15,18] stems from an algorithm by Sankoff and Blanchette [ 17] that iterates over a prospective tree, repeatedly finds medians of the three permutations adjacent to each internal vertex, and uses them to improve the tree until convergence occurs. This method finds locally optimal trees and ....
B.M.E. Moret, L.-S. Wang, T. Warnow, and S.K. Wyman. New approaches for reconstructing phylogenies from gene-order data. In Proceedings 9th International Conference on Intelligent Systems for Molecular Biology ISMB-2001, 2001. to appear in Bioinformatics.
Inversion Medians Outperform Breakpoint Medians in.. - Moret, Siepel, Tang, Liu (2002) (1 citation) Self-citation (Moret) (Correct)
.... Pevzner [9] has shown that inversion distance can be computed in linear time [1] a development that has allowed us to base the reconstruction process on the inversion score of a tree rather than on its breakpoint score, with significant resulting improvements in the accuracy of reconstructions [13]. Other recent results have shown that the inversion median of three genomes can be obtained quickly for a reasonable range of instances [5,23,24] in spite of the NP hardness of the problem) These developments have enabled us to extend GRAPPA by replacing the breakpoint median routine with an ....
....algorithm is applied to the labels at the leaves of such a tree, it should infer an evolutionary history resembling the model tree. 3. 3 Labeling Internal Nodes One of the major advantages of median based phylogeny reconstruction over alternative methods (such as the encoding methods of [13,26]) is that it estimates the configurations of ancestral genomes as well as the topology of the tree. The approach proposed by Sanko# and Blanchette to estimate ancestral genomes is iterative, using a local optimization strategy. It is applied in turn to each plausible tree topology; in the end, the ....
B. Moret, L.-S. Wang, T. Warnow, and S. Wyman. New approaches for reconstructing phylogenies from gene-order data. In Proc. 9th Int'l Conf. on Intelligent Systems for Mol. Biol. ISMB 2001, volume 17 of Bioinformatics, pages S165--S173, 2001.
Fast Phylogenetic Methods for the Analysis of.. - Wang, Jansen.. (2002) Self-citation (Moret Wang Warnow) (Correct)
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B.M.E. Moret, L.-S. Wang, T. Warnow, and S. Wyman. New approaches for reconstructing phylogenies from gene order data. In Proc. 9th Intl. Conf. on Intel. Sys. for Mol. Bio. ISMB
Exact-IEBP: A New Technique For Estimating Evolutionary Distances.. - Wang (2001) Self-citation (Wang) (Correct)
....bound. The method can be applied to any dataset of genomes with equal gene content, and for any relative probabilities of rearrangement event classes. Moreover, the method is robust when the assumptions about the model parameters are wrong. EDE. In the EDE (Empirically Derived Estimator) method [10] we estimate the true evolutionary distance by inverting the expected inversion distance. We estimate the expected inversion distance by a nonlinear regression on simulation data. The evolutionary model in the simulation is inversion only, but NJ using EDE distance has very good accuracy even when ....
.... the following ve distance estimators on circular genomes: 1) BP, the breakpoint distance between two genomes, 2) INV [2] the minimum number of inversions needed to transform one genome into another, 3) IEBP [21] an approximation to the Exact IEBP method with fast running time, 4) EDE [10], an estimation of the true evolutionary distance based on the INV distance, and (5) Exact IEBP, our new method. Software. We use PAUP 4.0 [19] to compute the neighbor joining method and the false negative rates between two trees (which will be de ned 0 100 200 300 0 50 100 150 200 250 ....
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B.M.E. Moret, L.-S. Wang, T. Warnow, and S. Wyman. New approaches for reconstructing phylogenies from gene order data. In Proc. 9th Intl. Conf. on Intel. Sys. for Mol. Bio. ISMB
Finding an Optimal Inversion Median: Experimental Results - Siepel, Moret (2001) Self-citation (Moret) (Correct)
....by reversals [2, 12] and a linear time algorithm for computing inversion distances [1] Note that signed permutations correspond to genomes for which the direction of transcription of each gene is known as well as the ordering of the genes. Much recent work on rearrangement based phylogeny [5, 6, 14, 15, 18] stems from an algorithm by Sankoff and Blanchette [17] that iterates over a prospective tree, repeatedly finds medians of the three permutations adjacent to each internal vertex, and uses them to improve the tree until convergence occurs. This method finds locally optimal trees and simultaneously ....
B. Moret, L.-S. Wang, T. Warnow, and S. Wyman. New approaches for reconstructing phylogenies from gene-order data. In Proceedings 9th International Conference on Intelligent Systems for Molecular Biology ISMB-2001, 2001. to appear in Bioinformatics.
Genome-Scale Evolution: Reconstructing Gene - Orders In The (Correct)
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Nature 409: 860--921. Moret, B., Wang, L., Warnow, T., and Wyman, S. 2001. New approaches for reconstructing phylogenies from gene order data.
Construction of Phylogenetic Trees on parallel - Clusters Fr Ed (2001) (Correct)
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B. Moret, L.-S. Wang, T. Warnow, and S. Wyman. New approaches for reconstructing phylogenies from gene order data. In Intelligent Systems for Molecular Biology (ISMB'01), Copenhagen, Denmark, 22-25 july 2001.
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