Luay Nakhleh

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Tandy WarnowGrainger Distinguished Chair in Engineering, UIUCVerified email at illinois.edu
Derek RuthsAssociate Professor of Computer Science, McGill UniversityVerified email at mcgill.ca
Cuong Van ThanAxonVerified email at rice.edu
Nicholas NavinMD Anderson Cancer CenterVerified email at mdanderson.org
C. Randal LinderUniversity of Texas at AustinVerified email at austin.utexas.edu
Bernard M.E. MoretISCB Fellow, Professor emeritus, Computer & Communication Sciences, EPFLVerified email at epfl.ch
Sagi SnirUniversity of HaifaVerified email at research.haifa.ac.il
Tamir Tuller (תמיר טולר)Tel Aviv UniversityVerified email at post.tau.ac.il
Jiafan ZhuPhD in Computer Science, Rice UniversityVerified email at rice.edu
Matthew W. HahnDistinguished Professor of Biology and Computer Science, Indiana UniversityVerified email at indiana.edu
Hideki InnanGraduate University for Advanced StudiesVerified email at soken.ac.jp
Usman RoshanAssociate Professor, Department of Computer Science, New Jersey Institute of TechnologyVerified email at njit.edu
James H. DegnanDept. of Mathematics and Statistics, University of New MexicoVerified email at unm.edu
Wanding ZhouUniversity of Pennyslvania, Children's Hospital of PhiladelphiaVerified email at email.chop.edu
Peng DuRice UniversityVerified email at rice.edu
Kevin J. LiuAssociate Professor, Department of Computer Science and Engineering, Michigan State UniversityVerified email at msu.edu
Xian MalloryFlorida State UniversityVerified email at fsu.edu
Katherine St. JohnCity University of New YorkVerified email at hunter.cuny.edu
Ruth E. TimmeActing Director, GenomeTrakr & Computational Science Staff, US Food and Drug AdministrationVerified email at fda.hhs.gov
Li-San WangUniversity of PennsylvaniaVerified email at upenn.edu

Luay Nakhleh

Professor of Computer Science and Dean of Engineering and Computing, Rice University

Verified email at rice.edu - Homepage

Computational biology Bioinformatics Phylogenomics


Title Sort by citations Sort by year Sort by title	Cited by Cited by	Year
PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships C Than, D Ruths, L Nakhleh BMC bioinformatics 9, 1-16, 2008	513	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	302	2005
Inferring phylogenetic networks using PhyloNet D Wen, Y Yu, J Zhu, L Nakhleh Systematic biology 67 (4), 735-740, 2018	301	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	269	2014
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	247	2012
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	246	2004
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	245	2022
Computational approaches to species phylogeny inference and gene tree reconciliation L Nakhleh Trends in ecology & evolution 28 (12), 719-728, 2013	240	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	233	2004
Species tree inference by minimizing deep coalescences C Than, L Nakhleh PLoS computational biology 5 (9), e1000501, 2009	227	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	221	2011
A maximum pseudo-likelihood approach for phylogenetic networks Y Yu, L Nakhleh BMC genomics 16, 1-10, 2015	217	2015
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	215	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	206	2013
Irrational exuberance for resolved species trees MW Hahn, L Nakhleh Evolution 70 (1), 7-17, 2016	199	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	181	2016
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	167	2017
Coestimating reticulate phylogenies and gene trees from multilocus sequence data D Wen, L Nakhleh Systematic biology 67 (3), 439-457, 2018	155	2018
Evolutionary phylogenetic networks: models and issues L Nakhleh Problem solving handbook in computational biology and bioinformatics, 125-158, 2010	155	2010
Maximum likelihood of phylogenetic networks G Jin, L Nakhleh, S Snir, T Tuller Bioinformatics 22 (21), 2604-2611, 2006	146	2006

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