PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships C Than, D Ruths, L Nakhleh BMC bioinformatics 9, 1-16, 2008 | 487 | 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 | 296 | 2005 |
Inferring phylogenetic networks using PhyloNet D Wen, Y Yu, J Zhu, L Nakhleh Systematic biology 67 (4), 735-740, 2018 | 274 | 2018 |
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 | 263 | 2014 |
Reconstructing reticulate evolution in species: theory and practice L Nakhleh, T Warnow, CR Linder Proceedings of the eighth annual international conference on Research in …, 2004 | 245 | 2004 |
The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection Y Yu, JH Degnan, L Nakhleh PLoS genetics 8 (4), e1002660, 2012 | 238 | 2012 |
Computational approaches to species phylogeny inference and gene tree reconciliation L Nakhleh Trends in ecology & evolution 28 (12), 719-728, 2013 | 232 | 2013 |
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 | 231 | 2004 |
Species tree inference by minimizing deep coalescences C Than, L Nakhleh PLoS computational biology 5 (9), e1000501, 2009 | 226 | 2009 |
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 | 215 | 2011 |
Identification of three distinct phylogenetic groups of CAX cation/proton antiporters T Shigaki, I Rees, L Nakhleh, KD Hirschi Journal of Molecular Evolution 63, 815-825, 2006 | 212 | 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 | 195 | 2013 |
A maximum pseudo-likelihood approach for phylogenetic networks Y Yu, L Nakhleh BMC genomics 16, 1-10, 2015 | 194 | 2015 |
Irrational exuberance for resolved species trees MW Hahn, L Nakhleh Evolution 70 (1), 7-17, 2016 | 186 | 2016 |
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 | 176 | 2016 |
Current progress and open challenges for applying deep learning across the biosciences N Sapoval, A Aghazadeh, MG Nute, DA Antunes, A Balaji, R Baraniuk, ... Nature Communications 13 (1), 1728, 2022 | 170 | 2022 |
SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models H Zafar, A Tzen, N Navin, K Chen, L Nakhleh Genome biology 18, 1-20, 2017 | 157 | 2017 |
Evolutionary phylogenetic networks: models and issues L Nakhleh Problem solving handbook in computational biology and bioinformatics, 125-158, 2010 | 151 | 2010 |
Maximum likelihood of phylogenetic networks G Jin, L Nakhleh, S Snir, T Tuller Bioinformatics 22 (21), 2604-2611, 2006 | 145 | 2006 |
Coestimating reticulate phylogenies and gene trees from multilocus sequence data D Wen, L Nakhleh Systematic biology 67 (3), 439-457, 2018 | 140 | 2018 |