Publications list            
Showing 31 - 60 (705 total)
31
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Paul Bastide, Claudia Solís-Lemus, Ricardo Kriebel, Kenneth William Sparks and Cécile Ané. Phylogenetic Comparative Methods on Phylogenetic Networks with Reticulations. In SB, 2018.  
Keywords: ancestral trait reconstruction, from network, likelihood, Program PhyloNetworks SNaQ, software, statistical model, statistical test.
Note: https://doi.org/10.1101/194050, to appear.
       

32
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James H. Degnan. Modeling Hybridization Under the Network Multispecies Coalescent. In SB, 2018.  
Keywords: distance between networks, phylogenetic network, phylogeny, reconstruction, survey.
Note: to appear.
       

33
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Leo van Iersel, Mark Jones and Celine Scornavacca. Improved maximum parsimony models for phylogenetic networks. In SB, Vol. 67(3):518-542, 2018.  
Keywords: explicit network, FPT, from sequences, NP complete, parsimony, phylogenetic network, phylogeny, reconstruction.
Note: https://leovaniersel.files.wordpress.com/2017/12/improved_parsimony_networks.pdf.
       

34
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Elizabeth Gross and Colby Long. Distinguishing Phylogenetic Networks. In SIAM Journal on Applied Algebra and Geometry, Vol. 2(1):72-93, 2018.  
Keywords: phylogenetic network, phylogeny, semidirected network, statistical model, uniqueness.
Note: https://arxiv.org/abs/1706.03060.
       

35
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Leo van Iersel and Vincent Moulton. Leaf-reconstructibility of phylogenetic networks. In SIAM Journal on Discrete Mathematics, Vol. 32(3):2047-2066, 2018.  
Keywords: explicit network, from network, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: https://arxiv.org/abs/1701.08982.
       

36
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Laura Jetten and Leo van Iersel. Nonbinary tree-based phylogenetic networks. In TCBB, Vol. 15(1):205-217, 2018.  
Keywords: characterization, explicit network, phylogenetic network, phylogeny, tree-based network.
Note: http://arxiv.org/abs/1601.04974.
       

37
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Daniel H. Huson and Simone Linz. Autumn Algorithm - Computation of Hybridization Networks for Realistic Phylogenetic Trees. In TCBB, Vol. 15:398-410, 2018.  
Keywords: explicit network, from rooted trees, phylogenetic network, phylogeny, Program Dendroscope, reconstruction.
Note: https://simonelinz.files.wordpress.com/2016/06/hl16.pdf.
       

38
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Janosch Döcker and Simone Linz. On the existence of a cherry-picking sequence. In TCS, Vol. 714:36-50, 2018.  
Keywords: cherry-picking, explicit network, from rooted trees, NP complete, phylogenetic network, phylogeny, reconstruction, temporal-hybridization number, time consistent network, tree child network.
Note: https://arxiv.org/abs/1712.04127.
       

39
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Joan Carles Pons, Charles Semple and Mike Steel. Nonbinary tree-based networks: characterisations, metrics, and support trees. 2017.  
Keywords: characterization, explicit network, from network, phylogenetic network, phylogeny, time consistent network, tree-based network.
Note: https://arxiv.org/abs/1710.07836.
       

40
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Jonathan Klawitter. The SNPR neighbourhood of tree-child networks. 2017.  
Keywords: distance between networks, phylogenetic network, phylogeny, SPR distance, tree child network.
Note: https://arxiv.org/abs/1707.09579
       

41
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Simone Linz and Charles Semple. Attaching leaves and picking cherries to characterise the hybridisation number for a set of phylogenies. 2017.  
Keywords: agreement forest, cherry-picking, explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction, tree child network.
Note: https://arxiv.org/abs/1712.04131.
       

42
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Janosch Döcker, Leo van Iersel, Steven Kelk and Simone Linz. Deciding the existence of a cherry-picking sequence is hard on two trees. 2017.  
Keywords: cherry-picking, explicit network, hybridization, minimum number, NP complete, phylogenetic network, phylogeny, reconstruction, temporal-hybridization number, time consistent network, tree child network.
Note: https://arxiv.org/abs/1712.02965.
       

43
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Hussein A. Hejase. Scalable Phylogenetic Analysis and Functional Interpretation of Genomes with Complex Evolutionary Histories. PhD thesis, Michigan State University, 2017.  
Keywords: explicit network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program FastNet, reconstruction.
Note: https://dx.doi.org/10.25335/M5T855.
       

44
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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.
       

45
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Celine Scornavacca. Occam's razor in phylogenetic network reconstruction. Phyloseminar #71, 2017.  
Keywords: explicit network, from rooted trees, parsimony, phylogenetic network, phylogeny, reconstruction.
Note: https://www.youtube.com/watch?v=W6tEVulgQu8.
       

46
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Cécile Ané. From reconstructing to using phylogenetic networks. Phyloseminar #72, 2017.  
Keywords: explicit network, from sequences, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, semidirected network.
Note: https://www.youtube.com/watch?v=PF4j_JOQP0c.
       

47
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Paul Bastide. Shifted stochastic processes evolving on trees : application to models of adaptive evolution on phylogenies. PhD thesis, Université Paris Saclay, 2017.  
Keywords: ancestral trait reconstruction, bayesian, explicit network, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, statistical model.
Note: https://tel.archives-ouvertes.fr/tel-01629648/en/, slides..
       

48
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Ruzbeh Tusserkani, Hadi Poormohammadi, Azin Azadi and Changiz Eslahchi. Inferring phylogenies from minimal information. In AEEICB17, Pages 202-206, IEEE, 2017.  
Keywords: from triplets, phylogenetic network, phylogeny, Program TripNet, reconstruction.
       

49
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Jesper Jansson, Ramesh Rajaby and Wing-Kin Sung. An Efficient Algorithm for the Rooted Triplet Distance Between Galled Trees. In AlCoB17, Vol. 10252:115-126 of LNCS, Springer, 2017.  
Keywords: distance between networks, from network, phylogenetic network, phylogeny, polynomial, reconstruction, triplet distance.
Note: .
       

50
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Bingxin Lu, Louxin Zhang and Hon Wai Leong. A program to compute the soft Robinson-Foulds distance between phylogenetic networks. In APBC17, Vol. 18(Suppl. 2):111 of BMC Genomics, 2017.  
Keywords: cluster containment, distance between networks, explicit network, exponential algorithm, from network, phylogenetic network, phylogeny, Program icelu-PhyloNetwork.
Note: http://dx.doi.org/10.1186/s12864-017-3500-5.
       

51
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Kuang-Yu Chang, Yun Cui, Siu-Ming Yiu and Wing-Kai Hon. Reconstructing One-Articulated Networks with Distance Matrices. In ISBRA17, Vol. 10330:34-45 of LNCS, Springer, 2017.  
Keywords: explicit network, from distances, k-reticulated, phylogenetic network, phylogeny, reconstruction.
Note: https://link.springer.com/content/pdf/10.1007%2F978-3-319-59575-7.pdf#page=100.
       

52
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Han Lai, Maureen Stolzer and Dannie Durand. Fast Heuristics for Resolving Weakly Supported Branches Using Duplication, Transfers, and Losses. In RECOMB-CG17, Vol. 10562:298-320 of LNCS, Springer, 2017.  
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program Notung, reconstruction.
       

53
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Katharina Huber, Leo van Iersel, Vincent Moulton, Celine Scornavacca and Taoyang Wu. Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets. In ALG, Vol. 77(1):173-200, 2017.  
Keywords: explicit network, FPT, from binets, from subnetworks, from trinets, NP complete, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://arxiv.org/abs/1411.6804.
       

54

Timothy G. Vaughan. IcyTree: rapid browser-based visualization for phylogenetic trees and networks. In BIO, Vol. 33(15):2392-2394, 2017.  
Keywords: ARG, explicit network, from network, phylogenetic network, phylogeny, Program IcyTree, software, visualization.
Note: http://dx.doi.org/10.1093/bioinformatics/btx155.
       

55
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Edwin Jacox, Mathias Weller, Eric Tannier and Celine Scornavacca. Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses. In BIO, Vol. 33(7):980-987, 2017.  
Keywords: duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1093/bioinformatics/btw778.
       

56
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Philippe Gambette, Katharina Huber and Guillaume Scholz. Uprooted Phylogenetic Networks. In BMB, Vol. 79(9):2022-2048, 2017.  
Keywords: circular split system, explicit network, from splits, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction, split network, uniqueness.
Note: http://arxiv.org/abs/1511.08387.
       

57
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Leo van Iersel, Vincent Moulton, Eveline De Swart and Taoyang Wu. Binets: fundamental building blocks for phylogenetic networks. In BMB, Vol. 79(5):1135-1154, 2017.  
Keywords: approximation, explicit network, from binets, from subnetworks, galled tree, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1007/s11538-017-0275-4.
       

58
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Charles Semple. Size of a phylogenetic network. In DAM, Vol. 217(2):362-367, 2017.  
Keywords: compressed network, number of vertices, phylogenetic network, phylogeny, stack-free network.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/S16.pdf.
       

59
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Olga K. Kamneva and Noah A. Rosenberg. Simulation-Based Evaluation of Hybridization Network Reconstruction Methods in the Presence of Incomplete Lineage Sorting. In Evolutionary Bioinformatics, Vol. 13(1176934317691935):1-16, 2017.  
Keywords: evaluation, explicit network, incomplete lineage sorting, simulation.
Note: https://dx.doi.org/10.1177%2F1176934317691935.
       

60
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Andreas Gunawan, Bhaskar DasGupta and Louxin Zhang. A decomposition theorem and two algorithms for reticulation-visible networks. In Information and Computation, Vol. 252:161-175, 2017.  
Keywords: cluster containment, explicit network, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulation-visible network, tree containment.
Note: https://www.cs.uic.edu/~dasgupta/resume/publ/papers/Infor_Comput_IC4848_final.pdf.