User profiles for L. Nakhleh
Luay NakhlehProfessor of Computer Science, Rice University Verified email at rice.edu Cited by 8417 |
[HTML][HTML] Current progress and open challenges for applying deep learning across the biosciences
Deep Learning (DL) has recently enabled unprecedented advances in one of the grand
challenges in computational biology: the half-century-old problem of protein structure prediction. …
challenges in computational biology: the half-century-old problem of protein structure prediction. …
Computational approaches to species phylogeny inference and gene tree reconciliation
L Nakhleh - Trends in ecology & evolution, 2013 - cell.com
An intricate relation exists between gene trees and species phylogenies, due to evolutionary
processes that act on the genes within and across the branches of the species phylogeny. …
processes that act on the genes within and across the branches of the species phylogeny. …
Networks: expanding evolutionary thinking
Networks allow the investigation of evolutionary relationships that do not fit a tree model.
They are becoming a leading tool for describing the evolutionary relationships between …
They are becoming a leading tool for describing the evolutionary relationships between …
[HTML][HTML] PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships
… Then, T is a phylogenetic tree over χ if there is a bijection between χ and L(T). Henceforth, …
such that there is a bijection between χ and the set L(N) of the network's leaves (see Figure 2). …
such that there is a bijection between χ and the set L(N) of the network's leaves (see Figure 2). …
Inferring phylogenetic networks using PhyloNet
PhyloNet was released in 2008 as a software package for representing and analyzing
phylogenetic networks. At the time of its release, the main functionalities in PhyloNet consisted of …
phylogenetic networks. At the time of its release, the main functionalities in PhyloNet consisted of …
Perfect phylogenetic networks: A new methodology for reconstructing the evolutionary history of natural languages
… perfect phylogenetic networks was written by Luay Nakhleh but used ea code (for … L of
languages described by set C of qualitative characters, f estimate the optimal genetic tree T for L. …
languages described by set C of qualitative characters, f estimate the optimal genetic tree T for L. …
Maximum likelihood inference of reticulate evolutionary histories
… We use the phylogenetic network model given by Nakhleh (2). A phylogenetic X -network, or
X -… Ψ to generate ℓ datasets, from which we infer ℓ phylogenetic networks Ψ 1 , … , Ψ ℓ . We …
X -… Ψ to generate ℓ datasets, from which we infer ℓ phylogenetic networks Ψ 1 , … , Ψ ℓ . We …
Identification of three distinct phylogenetic groups of CAX cation/proton antiporters
Ca 2+ /cation antiporter (CaCA) proteins are integral membrane proteins that transport Ca 2+
or other cations using the H + or Na + gradient generated by primary transporters. The CAX …
or other cations using the H + or Na + gradient generated by primary transporters. The CAX …
[HTML][HTML] The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection
Gene tree topologies have proven a powerful data source for various tasks, including
species tree inference and species delimitation. Consequently, methods for computing …
species tree inference and species delimitation. Consequently, methods for computing …
[HTML][HTML] Species tree inference by minimizing deep coalescences
In a 1997 seminal paper, W. Maddison proposed minimizing deep coalescences, or MDC,
as an optimization criterion for inferring the species tree from a set of incongruent gene trees, …
as an optimization criterion for inferring the species tree from a set of incongruent gene trees, …