Who is Who in Phylogenetic Networks

Publications list	Showing 121 - 150 (752 total)

121 Monika Balvociute, David Bryant and Andreas Spillner. When can splits be drawn in the plane? In SIAM Journal on Discrete Mathematics, Vol. 31(2):839-856, 2017. Keywords: abstract network, characterization, flat, phylogenetic network, planar, split, split network. Note: http://arxiv.org/abs/1509.06104v1.         122 Julia Matsieva, Steven Kelk, Celine Scornavacca, Chris Whidden and Dan Gusfield. A Resolution of the Static Formulation Question for the Problem of Computing the History Bound. In TCBB, Vol. 14(2):404-417, 2017. Keywords: ARG, explicit network, from sequences, minimum number, phylogenetic network, phylogeny.         123 Misagh Kordi and Mukul S. Bansal. On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees. In TCBB, Vol. 14(3):587-599, 2017. Keywords: duplication, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction. Note: http://compbio.engr.uconn.edu/papers/Kordi_DTLreconciliationPreprint2015.pdf.         124 Jonathan Mitchell. Distinguishing Convergence on Phylogenetic Networks. PhD thesis, University of Tasmania, Australia, 2016. Keywords: phylogenetic network, phylogeny, statistical model. Note: http://arxiv.org/abs/1606.07160.         125 Hussein A. Hejase and Kevin J. Liu. A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation. Vol. 17(422):1-12, 2016. Keywords: abstract network, evaluation, from sequences, phylogenetic network, phylogeny, Program PhyloNet, Program PhyloNetworks SNaQ, reconstruction, simulation, unicyclic network. Note: http://dx.doi.org/10.1186/s12859-016-1277-1.         126 Benjamin Albrecht. Computing Hybridization Networks Using Agreement Forests. PhD thesis, Ludwig-Maximilians-Universität München, 2016. Note: https://edoc.ub.uni-muenchen.de/19444/.         127 Nihan Tokac. Efficiency of Algorithms in Phylogenetics. PhD thesis, Durham University, U.K., 2016. Keywords: explicit network, from distances, phylogenetic network, phylogeny, reconstruction, tree-child network. Note: http://etheses.dur.ac.uk/11768/.         128 Kristina Wicke. Extending the concept of phylogenetic diversity and its measures from trees to networks. Master's thesis, Ernst-Moritz-Arndt-Universität Greifswald, 2016. Keywords: diversity, explicit network, from network, normal network, phylogenetic network, phylogeny. Note: https://math-inf.uni-greifswald.de/fileadmin/uni-greifswald/fakultaet/mnf/mathinf/wicke/MasterThesis_KristinaWicke.pdf.         129 Pei Wu. Quartet weights in phylogenetic network reconstruction. PhD thesis, University of Chinese Academy of Sciences, 2016. Keywords: abstract network, from distances, from quartets, phylogenetic network, phylogeny, reconstruction, split, split network. Note: https://www.researchgate.net/publication/324475948_Quartet_weights_in_phylogenetic_network_reconstruction.         130 Monika Balvociute. Flat Embeddings of Genetic and Distance Data. PhD thesis, University of Otago, 2016. Keywords: abstract network, flat, phylogenetic network, phylogeny, planar, Program FlatNJ, Program SplitsTree, split, split network. Note: http://hdl.handle.net/10523/6286.         131 Dingqiao Wen. Bayesian Inference of Phylogenetic Networks. Master's thesis, Rice University, Texas, 2016. Keywords: bayesian, explicit network, phylogenetic network, phylogeny, Program PhyloNet, reconstruction. Note: https://scholarship.rice.edu/bitstream/handle/1911/96515/WEN-DOCUMENT-2016.pdf?sequence=1&isAllowed=y.         132 Nikita Alexeev and Max A. Alekseyev. Combinatorial Scoring of Phylogenetic Networks. In COCOON16, Vol. 9797:560-572 of LNCS, Springer, 2016. Keywords: cactus graph, counting, explicit network, galled tree, phylogenetic network, phylogeny. Note: http://arxiv.org/abs/1602.02841.         133 Andreas Gunawan, Bingxin Lu and Louxin Zhang. A program for verification of phylogenetic network models. In ECCB16, Vol. 32(17):i503-i510 of BIO, 2016. Keywords: exponential algorithm, from network, from rooted trees, phylogenetic network, phylogeny, software, tree containment. Note: http://dx.doi.org/10.1093/bioinformatics/btw467.         134 Ioannis G. Tollis and Konstantinos G. Kakoulis. Algorithms for Visualizing Phylogenetic Networks. In GD16, Vol. 9801:183-195 of LNCS, springer, 2016. Keywords: explicit network, galled network, galled tree, NP complete, planar, visualization. Note: http://arxiv.org/abs/1609.00755.         135 Philippe Gambette, Andreas Gunawan, Anthony Labarre, Stéphane Vialette and Louxin Zhang. Solving the Tree Containment Problem for Genetically Stable Networks in Quadratic Time. In IWOCA15, Vol. 9538:197-208 of LNCS, springer, 2016. Keywords: explicit network, from network, from rooted trees, genetically stable network, phylogenetic network, phylogeny, polynomial, tree containment. Note: https://hal-upec-upem.archives-ouvertes.fr/hal-01226035 .         136 Dan Graur. Reticulate evolution and phylogenetic networks. In Molecular and Genome Evolution, Chapter 6, Sinauer, 2016. Keywords: phylogenetic network, phylogeny, survey. Note: http://www.sinauer.com/media/wysiwyg/samples/Graur_MGE1e_Ch06.pdf.         137 Mike Steel. Introduction to phylogenetic networks. In Phylogeny: Discrete and Random Processes in Evolution, Vol. 89 of CBMS-NSF Regional Conference Series in Applied Mathematics, Chapter 10, SIAM, 2016. Keywords: abstract network, explicit network, phylogenetic network, phylogeny, survey. Note: http://bookstore.siam.org/cb89/.         138 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.         139 Andreas Gunawan, Bhaskar DasGupta and Louxin Zhang. Locating a Tree in a Reticulation-Visible Network in Cubic Time. In RECOMB16, Vol. 9649:266 of LNBI, Springer, 2016. Keywords: cluster containment, explicit network, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulation-visible network, tree containment. Note: http://arxiv.org/abs/1507.02119.         140 Stephen J. Willson. Comparing and simplifying distinct-cluster phylogenetic networks. In ACOM, Vol. 20(4):917-938, 2016. Keywords: distinct-cluster network, explicit network, phylogenetic network, phylogeny. Note: http://arxiv.org/abs/1501.07528.         141 Magnus Bordewich and Charles Semple. Reticulation-visible networks. In Advances in Applied Mathematics, Vol. 78:114-141, 2016. Keywords: explicit network, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, tree containment. Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BS16.pdf.         142 François Chevenet, Jean-Philippe Doyon, Celine Scornavacca, Edwin Jacox, Emmanuelle Jousselin and Vincent Berry. SylvX: a viewer for phylogenetic tree reconciliations. In BIO, Vol. 32(4):608-610, 2016. Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program SylvX, software, visualization. Note: https://www.researchgate.net/profile/Emmanuelle_Jousselin/publication/283446016_SylvX_a_viewer_for_phylogenetic_tree_reconciliations/links/5642146108aec448fa621efa.pdf.         143 Edwin Jacox, Cédric Chauve, Gergely J. Szöllösi, Yann Ponty and Celine Scornavacca. EcceTERA: comprehensive gene tree-species tree reconciliation using parsimony. In BIO, Vol. 32(13):2056-2058, 2016. Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, parsimony, phylogenetic network, phylogeny, polynomial, Program ecceTERA. Note: https://doi.org/10.1093/bioinformatics/btw105.         144 Philippe Gambette, Leo van Iersel, Steven Kelk, Fabio Pardi and Celine Scornavacca. Do branch lengths help to locate a tree in a phylogenetic network? In BMB, Vol. 78(9):1773-1795, 2016. Keywords: branch length, explicit network, FPT, from network, from rooted trees, NP complete, phylogenetic network, phylogeny, pseudo-polynomial, time consistent network, tree containment, tree sibling network. Note: http://arxiv.org/abs/1607.06285.         145 Charles Semple. Phylogenetic Networks with Every Embedded Phylogenetic Tree a Base Tree. In BMB, Vol. 78(1):132-137, 2016. Keywords: characterization, explicit network, phylogenetic network, phylogeny, tree-based network, tree-child network. Note: http://www.math.canterbury.ac.nz/~c.semple/papers/S15.pdf.         146 Maria Anaya, Olga Anipchenko-Ulaj, Aisha Ashfaq, Joyce Chiu, Mahedi Kaiser, Max Shoji Ohsawa, Megan Owen, Ella Pavlechko, Katherine St. John, Shivam Suleria, Keith Thompson and Corrine Yap. On Determining if Tree-based Networks Contain Fixed Trees. In BMB, Vol. 78(5):961-969, 2016. Keywords: explicit network, FPT, NP complete, phylogenetic network, phylogeny, tree-based network. Note: http://arxiv.org/abs/1602.02739.         147 Juan Wang. A Metric on the Space of Partly Reduced Phylogenetic Networks. In BMRI, Vol. 2016(7534258):1-9, 2016. Keywords: distance between networks, partly reduced networks, phylogenetic network, phylogeny, polynomial, reduced networks. Note: http://downloads.hindawi.com/journals/bmri/aip/7534258.pdf.         148 Juan Wang, Zhang Zhibin and Yanjuan Li. Constructing phylogenetic networks based on the isomorphism of datasets. In BMRI, Vol. 2016(4236858):1-7, 2016. Keywords: from clusters, phylogenetic network, phylogeny, reconstruction. Note: http://downloads.hindawi.com/journals/bmri/aip/4236858.pdf.         149 Magnus Bordewich and Nihan Tokac. An algorithm for reconstructing ultrametric tree-child networks from inter-taxa distances. In DAM, Vol. 213:47-59, 2016. Keywords: explicit network, from distances, phylogenetic network, phylogeny, reconstruction, tree-child network. Note: http://dx.doi.org/10.1016/j.dam.2016.05.011.         150 Rinku Mathur and Neeru Adlakha. A graph theoretic model for prediction of reticulation events and phylogenetic networks for DNA sequences. In Egyptian Journal of Basic and Applied Sciences, Vol. 3(3):263-271, 2016. Keywords: from sequences, phylogenetic network, phylogeny, Program T REX. Note: http://dx.doi.org/10.1016/j.ejbas.2016.07.004.