Cuong Than - Academia.edu (original) (raw)

Papers by Cuong Than

Research paper thumbnail of L.: SPR-based tree reconciliation: Non-binary trees and multiple solutions

Research paper thumbnail of Inference of parsimonious species phylogenies from multi-locus data

Research paper thumbnail of L.: Confounding factors in HGT detection: Statistical error, coalescent effects, and multiple solutions

Research paper thumbnail of Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer

Lecture Notes in Computer Science, 2008

Research paper thumbnail of Species Tree Inference by Minimizing Deep Coalescences

PLoS Computational Biology, 2009

Research paper thumbnail of SPR-Based Tree Reconciliation: Non-Binary Trees and Multiple Solutions

Proceedings of the 6th Asia-Pacific Bioinformatics Conference, 2007

Research paper thumbnail of Identifiability Issues in Phylogeny-Based Detection of Horizontal Gene Transfer

Lecture Notes in Computer Science, 2006

Research paper thumbnail of Seeing the trees and their branches in the network is hard

Theoretical Computer Science, 2008

Research paper thumbnail of Coalescent Histories on Phylogenetic Networks and Detection of Hybridization Despite Incomplete Lineage Sorting

Research paper thumbnail of Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions

Journal of Computational Biology, 2007

Research paper thumbnail of Consistency Properties of Species Tree Inference by Minimizing Deep Coalescences

Journal of Computational Biology, 2011

Research paper thumbnail of Mathematical Properties of the Deep Coalescence Cost

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2000

In the minimizing-deep-coalescences (MDC) approach for species tree inference, a tree that has th... more In the minimizing-deep-coalescences (MDC) approach for species tree inference, a tree that has the minimal deep coalescence cost for reconciling a collection of gene trees is taken as an estimate of the species tree topology. The MDC method possesses the desirable Pareto property, and in practice it is quite accurate and computationally efficient. Here, in order to better understand the MDC method, we investigate some properties of the deep coalescence cost. We prove that the unit neighborhood of either a rooted species tree or a rooted gene tree under the deep coalescence cost is exactly the same as the tree's unit neighborhood under the rooted nearest-neighbor interchange (NNI) distance. Next, for a fixed species tree, we obtain the maximum deep coalescence cost across all gene trees as well as the number of gene trees that achieve the maximum cost. We also study corresponding problems for a fixed gene tree.

Research paper thumbnail of PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

Research paper thumbnail of Efficient inference of bacterial strain trees from genome-scale multilocus data

Research paper thumbnail of Clades and clans: a comparison study of two evolutionary models

Journal of mathematical biology

Research paper thumbnail of L.: SPR-based tree reconciliation: Non-binary trees and multiple solutions

Research paper thumbnail of Inference of parsimonious species phylogenies from multi-locus data

Research paper thumbnail of L.: Confounding factors in HGT detection: Statistical error, coalescent effects, and multiple solutions

Research paper thumbnail of Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer

Lecture Notes in Computer Science, 2008

Research paper thumbnail of Species Tree Inference by Minimizing Deep Coalescences

PLoS Computational Biology, 2009

Research paper thumbnail of SPR-Based Tree Reconciliation: Non-Binary Trees and Multiple Solutions

Proceedings of the 6th Asia-Pacific Bioinformatics Conference, 2007

Research paper thumbnail of Identifiability Issues in Phylogeny-Based Detection of Horizontal Gene Transfer

Lecture Notes in Computer Science, 2006

Research paper thumbnail of Seeing the trees and their branches in the network is hard

Theoretical Computer Science, 2008

Research paper thumbnail of Coalescent Histories on Phylogenetic Networks and Detection of Hybridization Despite Incomplete Lineage Sorting

Research paper thumbnail of Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions

Journal of Computational Biology, 2007

Research paper thumbnail of Consistency Properties of Species Tree Inference by Minimizing Deep Coalescences

Journal of Computational Biology, 2011

Research paper thumbnail of Mathematical Properties of the Deep Coalescence Cost

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2000

In the minimizing-deep-coalescences (MDC) approach for species tree inference, a tree that has th... more In the minimizing-deep-coalescences (MDC) approach for species tree inference, a tree that has the minimal deep coalescence cost for reconciling a collection of gene trees is taken as an estimate of the species tree topology. The MDC method possesses the desirable Pareto property, and in practice it is quite accurate and computationally efficient. Here, in order to better understand the MDC method, we investigate some properties of the deep coalescence cost. We prove that the unit neighborhood of either a rooted species tree or a rooted gene tree under the deep coalescence cost is exactly the same as the tree's unit neighborhood under the rooted nearest-neighbor interchange (NNI) distance. Next, for a fixed species tree, we obtain the maximum deep coalescence cost across all gene trees as well as the number of gene trees that achieve the maximum cost. We also study corresponding problems for a fixed gene tree.

Research paper thumbnail of PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

Research paper thumbnail of Efficient inference of bacterial strain trees from genome-scale multilocus data

Research paper thumbnail of Clades and clans: a comparison study of two evolutionary models

Journal of mathematical biology