Nakhleh Publications of Luay Nakhleh     Order by:   Type | Year
Associated keywords
2019
1
photophoto
R. A. Leo Elworth, Huw A. Ogilvie, Jiafan Zhu and Luay Nakhleh. Advances in Computational Methods for Phylogenetic Networks in the Presence of Hybridization. In Tandy Warnow editor, Bioinformatics and Phylogenetics. Seminal Contributions of Bernard Moret, Vol. 29 of Computational Biology, Springer, 2019.
Keywords: explicit network, phylogenetic network, phylogeny, Program Dendroscope, Program PhyloNet, Program PhyloNetworks SNaQ, Program PIRN, Program SplitsTree, reconstruction, survey.
Note: https://bioinfocs.rice.edu/sites/g/files/bxs266/f/ElworthZhuOgilvieNakhleh.pdf
       

2018
2
photophotophoto
Dingqiao Wen, Yun Yu, Jiafan Zhu and Luay Nakhleh. Inferring Phylogenetic Networks Using PhyloNet. In SB, Vol. 67(4):735-740, 2018.
Keywords: bayesian, likelihood, parsimony, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, software.
       

3
photophotophoto
Jiafan Zhu, Dingqiao Wen, Yun Yu, Heidi M. Meudt and Luay Nakhleh. Bayesian inference of phylogenetic networks from bi-allelic genetic markers. In PLoS Computational Biology, Vol. 14(1):e1005932.1-32, 2018.
Keywords: bayesian, explicit network, from multistate characters, phylogenetic network, phylogeny, Program PhyloNet.
Note: https://doi.org/10.1371/journal.pcbi.1005932.
       

4
photophoto
Dingqiao Wen and Luay Nakhleh. Coestimating Reticulate Phylogenies and Gene Trees from Multilocus Sequence Data. In SB, Vol. 67(3):439-457, 2018.
Keywords: bayesian, explicit network, from sequences, incomplete lineage sorting, phylogenetic network, phylogeny, Program PhyloNet, reconstruction.
Note: https://doi.org/10.1093/sysbio/syx085.
       

2017
5
photo
Luay Nakhleh. Phylogenetic Networks: From Displayed Trees to a Distribution of Gene Trees. Phyloseminar #70, 2017.
Keywords: bayesian, coalescent, explicit network, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, statistical model.
Note: https://www.youtube.com/watch?v=dkQsvLUUDcQ.
       

2016
6
photophotophoto
Dingqiao Wen, Yun Yu and Luay Nakhleh. Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent. In PLoS Genetics, Vol. 12(5):e1006006, 2016.
Keywords: bayesian, coalescent, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, software.
       

7
photophoto
Jiafan Zhu, Yun Yu and Luay Nakhleh. In the Light of Deep Coalescence: Revisiting Trees Within Networks. In RECOMB-CG16, Vol. 17(suppl. 14):415.271-282 of BMCB, 2016.
Keywords: branch length, evaluation, explicit network, incomplete lineage sorting, phylogenetic network, phylogeny, statistical model, tree-based network, weakly displaying.
Note: http://arxiv.org/abs/1606.07350.
       

2015
8
photophoto
Yun Yu and Luay Nakhleh. A Distance-Based Method for Inferring Phylogenetic Networks in the Presence of Incomplete Lineage Sorting. In ISBRA15, Vol. 9096:378-389 of LNCS, springer, 2015.
Keywords: bootstrap, explicit network, from distances, heuristic, incomplete lineage sorting, phylogenetic network, phylogeny, reconstruction.
Note: http://bioinfo.cs.rice.edu/sites/bioinfo.cs.rice.edu/files/YuNakhleh-ISBRA15.pdf.
       

9
photophoto
Yun Yu and Luay Nakhleh. A maximum pseudo-likelihood approach for phylogenetic networks. In RECOMB-CG15, Vol. 16(Suppl 10)(S10):1-10 of BMC Genomics, BioMed Central, 2015.
Keywords: explicit network, from rooted trees, hybridization, incomplete lineage sorting, likelihood, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, tripartition distance.
Note: http://dx.doi.org/10.1186/1471-2164-16-S10-S10.
       

2014
10
photophotophotophotophoto
Kevin J. Liu, Jingxuan Dai, Kathy Truong, Ying Song, Michael H. Kohn and Luay Nakhleh. An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes. In PLoS ONE, Vol. 10(6):e1003649, 2014.
Keywords: explicit network, from network, phylogenetic network, phylogeny, Program PhyloNet-HMM.
Note: http://arxiv.org/abs/1310.7989.
       
Toggle abstract
11
photophotophoto
Yun Yu, Jianrong Dong, Kevin J. Liu and Luay Nakhleh. Maximum likelihood inference of reticulate evolutionary histories. In PNAS, Vol. 111(46):16448-16453, 2014.
Keywords: explicit network, likelihood, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1073/pnas.1407950111.
       

2013
12
photophotophotophotophotophotophotophotophotophotophoto
Eric Bapteste, Leo van Iersel, Axel Janke, Scott Kelchner, Steven Kelk, James O. McInerney, David A. Morrison, Luay Nakhleh, Mike Steel, Leen Stougie and James B. Whitfield. Networks: expanding evolutionary thinking. In Trends in Genetics, Vol. 29(8):439-441, 2013.
Keywords: abstract network, explicit network, phylogenetic network, phylogeny, reconstruction.
Note: http://bioinf.nuim.ie/wp-content/uploads/2013/06/Bapteste-TiG-2013.pdf.
       
Toggle abstract
13
photophotophoto
Yun Yu, R. Matthew Barnett and Luay Nakhleh. Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting. In Systematic Biology, Vol. 62(5):738-751, 2013.
Keywords: from network, from rooted trees, hybridization, lineage sorting, parsimony, phylogenetic network, phylogeny, Program PhyloNet, reconstruction.
       
Toggle abstract
14
photo
Luay Nakhleh. Computational approaches to species phylogeny inference and gene tree reconciliation. In Trends in Ecology and Evolution, Vol. 28(12):719-728, 2013.
Keywords: from rooted trees, from species tree, phylogenetic network, phylogeny, reconstruction, survey.
Note: http://bioinfo.cs.rice.edu/sites/bioinfo.cs.rice.edu/files/TREE-Nakhleh13.pdf.
       
Toggle abstract
15
photophotophoto
Yun Yu, Nikola Ristic and Luay Nakhleh. Fast algorithms and heuristics for phylogenomics under ILS and hybridization. In RECOMB-CG'13, Vol. 14(Suppl 15):S6 of BMCB, 2013.
Keywords: from network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program PhyloNet, reconstruction.
       

2012
16
photophoto
Yun Yu and Luay Nakhleh. Fast Algorithms for Reconciliation under Hybridization and Incomplete Lineage Sorting. 2012.
Keywords: hybridization, lineage sorting, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, software.
Note: http://arxiv.org/abs/1212.1909.
       

17
photophotophoto
Yun Yu, James H. Degnan and Luay Nakhleh. The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection. In PLoS Genetics, Vol. 8(4):e1002660, 2012.
Keywords: AIC, BIC, explicit network, hybridization, phylogenetic network, phylogeny, statistical model.
Note: http://dx.doi.org/10.1371/journal.pgen.1002660.
       
Toggle abstract
18
photophoto
Hyun Jung Park and Luay Nakhleh. MURPAR: A fast heuristic for inferring parsimonious phylogenetic networks from multiple gene trees. In ISBRA12, Vol. 7292:213-224 of LNCS, springer, 2012.
Keywords: explicit network, from unrooted trees, heuristic, phylogenetic network, phylogeny, reconstruction, software.
Note: https://www.researchgate.net/profile/Hyun_Jung_Park2/publication/262318595_MURPAR_A_Fast_Heuristic_for_Inferring_Parsimonious_Phylogenetic_Networks_from_Multiple_Gene_Trees/links/54b7e7b50cf269d8cbf58cc4.pdf.
       
Toggle abstract
19
photophoto
Hyun Jung Park and Luay Nakhleh. Inference of reticulate evolutionary histories by maximum likelihood: The performance of information criteria. In RECOMB-CG'12, Vol. 13(suppl 19):S12 of BMCB, 2012.
Keywords: AIC, BIC, explicit network, heuristic, likelihood, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: http://www.biomedcentral.com/1471-2105/13/S19/S12.
       

2011
20
photophotophotophoto
Yun Yu, Cuong Than, James H. Degnan and Luay Nakhleh. Coalescent Histories on Phylogenetic Networks and Detection of Hybridization Despite Incomplete Lineage Sorting. In Systematic Biology, Vol. 60(2):138-149, 2011.
Keywords: coalescent, hybridization, lineage sorting, reconstruction, statistical model.
Note: http://www.cs.rice.edu/~nakhleh/Papers/YuEtAl-SB11.pdf.
       
Toggle abstract
2010
21
photo
Luay Nakhleh. A Metric on the Space of Reduced Phylogenetic Networks. In TCBB, Vol. 7(2), 2010.
Keywords: distance between networks, phylogenetic network, phylogeny.
Note: http://www.cs.rice.edu/~nakhleh/Papers/tcbb-Metric.pdf.
       
Toggle abstract
22
photo
Luay Nakhleh. Evolutionary phylogenetic networks: models and issues. In L. Heath and N. Ramakrishnan editors, The Problem Solving Handbook for Computational Biology and Bioinformatics, Springer, 2010.
Keywords: phylogenetic network, phylogeny, survey.
Note: http://www.cs.rice.edu/~nakhleh/Papers/HeathRamakrishnanBookChapter.pdf.
       

23
photophotophoto
Hyun Jung Park, Guohua Jin and Luay Nakhleh. Bootstrap-based Support of HGT Inferred by Maximum Parsimony. In BMCEB, Vol. 10:131, 2010.
Keywords: bootstrap, explicit network, from sequences, lateral gene transfer, parsimony, phylogenetic network, phylogeny, Program Nepal, reconstruction.
Note: http://dx.doi.org/10.1186/1471-2148-10-131.
       
Toggle abstract
24
photophotophoto
Hyun Jung Park, Guohua Jin and Luay Nakhleh. Algorithmic strategies for estimating the amount of reticulation from a collection of gene trees. In CSB10, 2010.
Keywords: bound, from rooted trees, heuristic, phylogenetic network, phylogeny, reconstruction, SPR distance.
Note: http://www.cs.rice.edu/~nakhleh/Papers/ParkEtAl-CSB2010.pdf.
       

2009
25
photophotophotophoto
Guohua Jin, Luay Nakhleh, Sagi Snir and Tamir Tuller. Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-time Heuristic. In TCBB, Vol. 6(3):495-505, 2009.
Keywords: explicit network, heuristic, parsimony, phylogenetic network, phylogeny, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/tcbb-MP.pdf.
       

26
photophotophoto
Luay Nakhleh, Derek Ruths and Hideki Innan. Gene Trees, Species Trees, and Species Networks. In R. Guerra, D. B. Allison and D. Goldstein editors, Meta-analysis and Combining Information in Genetics and Genomics, 2009.
Keywords: coalescent, explicit network, from rooted trees, from species tree, phylogenetic network, phylogeny, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/GuerraGoldsteinBookChapter.pdf.
       

2008
27
photophotophoto
Iyad A. Kanj, Luay Nakhleh and Ge Xia. The Compatibility of Binary Characters on Phylogenetic Networks: Complexity and Parameterized Algorithms. In ALG, Vol. 51(2):99-128, 2008.
Keywords: perfect, phylogenetic network, phylogeny.
Note: http://www.cs.rice.edu/~nakhleh/Papers/algorithmica.pdf.
       

28
photophoto
Cuong Than and Luay Nakhleh. SPR-based Tree Reconciliation: Non-binary Trees and Multiple Solutions. In APBC08, Pages 251-260, 2008.
Keywords: evaluation, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program LatTrans, Program PhyloNet, reconstruction, SPR distance.
Note: http://www.cs.rice.edu/~nakhleh/Papers/apbc08.pdf.
       

29
photophotophoto
Cuong Than, Derek Ruths and Luay Nakhleh. PhyloNet: A Software Package for Analyzing and Reconstructing Reticulate Evolutionary Relationships. In BMCB, Vol. 9(322), 2008.
Keywords: Program PhyloNet, software.
Note: http://dx.doi.org/10.1186/1471-2105-9-322.
       
Toggle abstract
30
photophotophotophoto
Iyad A. Kanj, Luay Nakhleh, Cuong Than and Ge Xia. Seeing the Trees and Their Branches in the Network is Hard. In TCS, Vol. 401:153-164, 2008.
Keywords: evaluation, from network, from rooted trees, NP complete, phylogenetic network, phylogeny, tree containment.
Note: http://www.cs.rice.edu/~nakhleh/Papers/tcs08.pdf.
       

31
photophotophoto
Cuong Than, Guohua Jin and Luay Nakhleh. Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer. In Proceedings of the Sixth RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG'08), Vol. 5267:113-127 of LNCS, springer, 2008.
Keywords: bootstrap, explicit network, from rooted trees, from sequences, lateral gene transfer, phylogenetic network, phylogeny, Program Nepal, Program PhyloNet, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/recombcg-08.pdf, slides available at http://igm.univ-mlv.fr/RCG08/RCG08slides/Cuong_Than_RCG08.pdf.
       

2007
32
photophotophotophoto
Guohua Jin, Luay Nakhleh, Sagi Snir and Tamir Tuller. Efficient Parsimony-based Methods for Phylogenetic Network Reconstruction. In ECCB06, Vol. 23(2):e123-e128 of BIO, 2007.
Keywords: parsimony, phylogenetic network, phylogeny, Program Nepal, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/eccb06.pdf.
       

33
photophotophotophoto
Iyad A. Kanj, Luay Nakhleh, Cuong Than and Ge Xia. Seeing the Trees and Their Branches in the Network is Hard. In Proceedings of the Tenth Italian Conference on Theoretical Computer Science (ICTCS'07), 2007.
Keywords: evaluation, from network, from rooted trees, NP complete, phylogenetic network, phylogeny, tree containment.
Note: http://www.cs.rice.edu/~nakhleh/Papers/ictcs07.pdf.
       

34
photophotophotophoto
Guohua Jin, Luay Nakhleh, Sagi Snir and Tamir Tuller. Inferring Phylogenetic Networks by the Maximum Parsimony Criterion: A Case Study. In MBE, Vol. 24(1):324-337, 2007.
Keywords: explicit network, parsimony, phylogenetic network, phylogeny, Program Nepal, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/MBE06.pdf.
       

35
photophotophotophoto
Guohua Jin, Luay Nakhleh, Sagi Snir and Tamir Tuller. A New Linear-time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance. In ISBRA07, Vol. 4463:61-72 of LNCS, springer, 2007.
Keywords: approximation, heuristic, parsimony, phylogenetic network, phylogeny, Program Nepal.
Note: http://www.cs.rice.edu/~nakhleh/Papers/isbra07.pdf.
       

36
photophotophotophoto
Cuong Than, Derek Ruths, Hideki Innan and Luay Nakhleh. Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions. In JCB, Vol. 14(4):517-535, 2007.
Keywords: counting, explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, Program LatTrans, Program PhyloNet.
Note: http://www.cs.rice.edu/~nakhleh/Papers/recombcg06-jcb.pdf.
       

2006
37
photophotophoto
Iyad A. Kanj, Luay Nakhleh and Ge Xia. Reconstructing Evolution of Natural Languages: Complexity and Parameterized Algorithms. In COCOON06, Vol. 4112:299-308 of LNCS, springer, 2006.
Note: http://www.cs.rice.edu/~nakhleh/Papers/cocoon06.pdf.
       

38
photophotophotophoto
Guohua Jin, Luay Nakhleh, Sagi Snir and Tamir Tuller. Maximum Likelihood of Phylogenetic Networks. In BIO, Vol. 22(21):2604-2611, 2006.
Keywords: explicit network, likelihood, phylogenetic network, phylogeny, Program Nepal, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/NetworksML06.pdf, supplementary material: http://www.cs.rice.edu/~nakhleh/Papers/Supp-ML.pdf.
       

39
photophotophotophoto
Cuong Than, Derek Ruths, Hideki Innan and Luay Nakhleh. Identifiability Issues in Phylogeny-Based Detection of Horizontal Gene Transfer. In Proceedings of the Fourth RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG'06), Vol. 4205:215-229 of LNCS, springer, 2006.
Keywords: explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, Program LatTrans, Program PhyloNet.
Note: http://www.cs.rice.edu/~nakhleh/Papers/recombcg06-final.pdf.
       

2005
40
photophotophotophoto
Luay Nakhleh, Guohua Jin, Fengmei Zhao and John Mellor-Crummey. Reconstructing Phylogenetic Networks Using Maximum Parsimony. In CSB05, Pages 93-102, 2005.
Keywords: parsimony, phylogenetic network, phylogeny, Program Nepal, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/CSB05.pdf.
       

41
photophoto
Luay Nakhleh and Li-San Wang. Phylogenetic Networks: Properties and Relationship to Trees and Clusters. In TCSB2, Vol. 3680:82-99 of LNCS, springer, 2005.
Keywords: cluster containment, evaluation, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, tree containment, tree-child network.
Note: http://www.cs.rice.edu/~nakhleh/Papers/LNCS_TCSB05.pdf.
       

42
photophoto
Luay Nakhleh and Li-San Wang. Phylogenetic Networks, Trees, and Clusters. In IWBRA05, Vol. 3515:919-926 of LNCS, springer, 2005.
Keywords: cluster containment, evaluation, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, tree containment, tree-child network.
Note: http://www.cs.rice.edu/~nakhleh/Papers/NakhlehWang.pdf.
       

43
photophoto
Derek Ruths and Luay Nakhleh. Recombination and phylogeny: effects and detection. In IJBRA, Pages 202-212, 2005.
Note: http://www.cs.rice.edu/~nakhleh/Papers/IJBRA05.pdf.
       

44
photophotophotophoto
Luay Nakhleh, Tandy Warnow, C. Randal Linder and Katherine St. John. Reconstructing reticulate evolution in species - theory and practice. In JCB, Vol. 12(6):796-811, 2005.
Keywords: from rooted trees, galled tree, phylogenetic network, phylogeny, polynomial, Program SPNet, reconstruction, software.
Note: http://www.cs.rice.edu/~nakhleh/Papers/NWLSjcb.pdf.
       

45
photophotophoto
Luay Nakhleh, Derek Ruths and Li-San Wang. RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer. In COCOON05, Vol. 3595:84-93 of LNCS, springer, 2005.
Keywords: from rooted trees, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program PhyloNet.
Note: http://www.cs.rice.edu/~nakhleh/Papers/COCOON05.pdf.
       

2004
46
photo
Luay Nakhleh. Phylogenetic Networks. PhD thesis, University of Texas at Austin, U.S.A., 2004.
Keywords: distance between networks, evaluation, generation, phylogenetic network, phylogeny, Program SPNet, reconstruction, split, statistical model, tree sibling network.
Note: http://www.library.utexas.edu/etd/d/2004/nakhlehl042/nakhlehl042.pdf.
       

47
photophotophotophotophotophotophotophoto
Bernard M. E. Moret, Luay Nakhleh, Tandy Warnow, C. Randal Linder, Anna Tholse, Anneke Padolina, Jerry Sun and Ruth Timme. Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy. In TCBB, Vol. 1(1):13-23, 2004.
Keywords: distance between networks, evaluation, phylogenetic network, phylogeny, time consistent network, tripartition distance.
Note: http://www.cs.rice.edu/~nakhleh/Papers/tcbb04.pdf.
       

48
photophotophoto
Luay Nakhleh, Tandy Warnow and C. Randal Linder. Reconstructing reticulate evolution in species - theory and practice. In RECOMB04, Pages 337-346, 2004.
Keywords: from rooted trees, galled tree, phylogenetic network, phylogeny, polynomial, Program SPNet, reconstruction, software.
Note: http://www.cs.rice.edu/~nakhleh/Papers/144-nakhleh.pdf.
       

49
photophotophotophoto
C. Randal Linder, Bernard M. E. Moret, Luay Nakhleh and Tandy Warnow. Network (Reticulate) Evolution: Biology, Models, and Algorithms. In PSB04, 2004.
Note: http://www.cs.rice.edu/~nakhleh/Papers/psb04.pdf.
       

2003
50
photophotophotophotophotophoto
Luay Nakhleh, Jerry Sun, Tandy Warnow, C. Randal Linder, Bernard M. E. Moret and Anna Tholse. Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods. In PSB03, 2003.
Keywords: distance between networks, evaluation, phylogenetic network, phylogeny, polynomial, tripartition distance.
Note: http://www.cs.rice.edu/~nakhleh/Papers/psb03.pdf.
       

51
photophotophotophoto
Esra Erdem, Vladimir Lifschitz, Luay Nakhleh and Don Ringe. Reconstructing the evolutionary history of Indo-European languages using answer set programming. In PADL03, Vol. 2562:160-176 of LNCS, springer, 2003.
Note: http://people.sabanciuniv.edu/~esraerdem/papers/padl03.ps.
       

2002
52
photophotophoto
Bernard M. E. Moret, Luay Nakhleh and Tandy Warnow. An error metric for phylogenetic networks. 2002.
Keywords: distance between networks, evaluation, phylogenetic network, phylogeny, tripartition distance.
Note: Technical report TR-02-09, http://www.cs.unm.edu/~treport/tr/03-05/nakhleh.ps.gz.
       

53
photophotophoto
Luay Nakhleh, Don Ringe and Tandy Warnow. Perfect Phylogenetic Networks: A New Methodology for Reconstructing the Evolutionary History of Natural Languages. In Language, Journal of the Linguistic Society of America, Vol. 81(2):382-420, 2002.
Keywords: perfect, phylogenetic network, phylogeny.
Note: http://www.cs.rice.edu/~nakhleh/Papers/81.2nakhleh.pdf.