Luay Nakhleh
Luay Nakhleh
Professor of Computer Science, Rice University
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PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships
C Than, D Ruths, L Nakhleh
BMC bioinformatics 9 (1), 1-16, 2008
Perfect phylogenetic networks: A new methodology for reconstructing the evolutionary history of natural languages
L Nakhleh, DA Ringe, T Warnow
Language 81 (2), 382-420, 2005
Reconstructing reticulate evolution in species—theory and practice
L Nakhleh, T Warnow, CR Linder, KS John
Journal of Computational Biology 12 (6), 796-811, 2005
Phylogenetic networks: modeling, reconstructibility, and accuracy
BME Moret, L Nakhleh, T Warnow, CR Linder, A Tholse, A Padolina, ...
IEEE/ACM Transactions on Computational Biology and Bioinformatics 1 (1), 13-23, 2004
Species tree inference by minimizing deep coalescences
C Than, L Nakhleh
PLoS Comput Biol 5 (9), e1000501, 2009
Computational approaches to species phylogeny inference and gene tree reconciliation
L Nakhleh
Trends in ecology & evolution 28 (12), 719-728, 2013
Maximum likelihood inference of reticulate evolutionary histories
Y Yu, J Dong, KJ Liu, L Nakhleh
Proceedings of the National Academy of Sciences 111 (46), 16448-16453, 2014
Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting
Y Yu, C Than, JH Degnan, L Nakhleh
Systematic Biology 60 (2), 138-149, 2011
The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection
Y Yu, JH Degnan, L Nakhleh
PLoS Genet 8 (4), e1002660, 2012
Identification of three distinct phylogenetic groups of CAX cation/proton antiporters
T Shigaki, I Rees, L Nakhleh, KD Hirschi
Journal of Molecular Evolution 63 (6), 815-825, 2006
Networks: expanding evolutionary thinking
E Bapteste, L van Iersel, A Janke, S Kelchner, S Kelk, JO McInerney, ...
Trends in Genetics 29 (8), 439-441, 2013
Irrational exuberance for resolved species trees
MW Hahn, L Nakhleh
Evolution 70 (1), 7-17, 2016
Evolutionary phylogenetic networks: models and issues
L Nakhleh
Problem solving handbook in computational biology and bioinformatics, 125-158, 2010
Maximum likelihood of phylogenetic networks
G Jin, L Nakhleh, S Snir, T Tuller
Bioinformatics 22 (21), 2604-2611, 2006
A comparison of phylogenetic reconstruction methods on an Indo‐European dataset
L Nakhleh, T Warnow, D Ringe, SN Evans
Transactions of the Philological Society 103 (2), 171-192, 2005
The signaling petri net-based simulator: a non-parametric strategy for characterizing the dynamics of cell-specific signaling networks
D Ruths, M Muller, JT Tseng, L Nakhleh, PT Ram
PLoS Comput Biol 4 (2), e1000005, 2008
Inferring phylogenetic networks using PhyloNet
D Wen, Y Yu, J Zhu, L Nakhleh
Systematic biology 67 (4), 735-740, 2018
A maximum pseudo-likelihood approach for phylogenetic networks
Y Yu, L Nakhleh
BMC genomics 16 (10), 1-10, 2015
Monovar: single-nucleotide variant detection in single cells
H Zafar, Y Wang, L Nakhleh, N Navin, K Chen
Nature methods 13 (6), 505-507, 2016
Confounding factors in HGT detection: statistical error, coalescent effects, and multiple solutions
C Than, D Ruths, H Innan, L Nakhleh
Journal of computational biology 14 (4), 517-535, 2007
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