User profiles for L. Nakhleh

Luay Nakhleh

Professor 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

…, RAL Elworth, B Kille, A Kyrillidis, L Nakhleh… - Nature …, 2022 - nature.com
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. …

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. …

Networks: expanding evolutionary thinking

…, DA Morrison, L Nakhleh, M Steel, L Stougie… - Trends in Genetics, 2013 - cell.com
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 …

[HTML][HTML] PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

C Than, D Ruths, L Nakhleh - BMC bioinformatics, 2008 - Springer
… 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). …

Inferring phylogenetic networks using PhyloNet

D Wen, Y Yu, J Zhu, L Nakhleh - Systematic biology, 2018 - academic.oup.com
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 …

Perfect phylogenetic networks: A new methodology for reconstructing the evolutionary history of natural languages

L Nakhleh, D Ringe, T Warnow - Language, 2005 - JSTOR
… 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. …

Maximum likelihood inference of reticulate evolutionary histories

Y Yu, J Dong, KJ Liu, L Nakhleh - Proceedings of the …, 2014 - National Acad Sciences
… We use the phylogenetic network model given by Nakhleh (2). A phylogenetic X -network, or
X -… Ψ to generate datasets, from which we infer phylogenetic networks Ψ 1 , … , Ψ . We …

Identification of three distinct phylogenetic groups of CAX cation/proton antiporters

T Shigaki, I Rees, L Nakhleh, KD Hirschi - Journal of Molecular Evolution, 2006 - Springer
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 …

[HTML][HTML] The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection

Y Yu, JH Degnan, L Nakhleh - PLoS genetics, 2012 - journals.plos.org
Gene tree topologies have proven a powerful data source for various tasks, including
species tree inference and species delimitation. Consequently, methods for computing …

[HTML][HTML] Species tree inference by minimizing deep coalescences

C Than, L Nakhleh - PLoS computational biology, 2009 - journals.plos.org
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, …