Who is Who in Phylogenetic Networks

Publications of Year 2016

Article (Journal)

1 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.         2 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.         3 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.         4 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.         5 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.         6 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.         7 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.         8 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.         9 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.         10 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.         11 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.         12 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.         13 Louxin Zhang. On Tree-Based Phylogenetic Networks. In JCB, Vol. 23(7):553-565, 2016. Keywords: characterization, explicit network, phylogenetic network, phylogeny, tree-based network. Note: http://arxiv.org/abs/1509.01663.         14 Leo van Iersel, Steven Kelk and Celine Scornavacca. Kernelizations for the hybridization number problem on multiple nonbinary trees. In JCSS, Vol. 82(6):1075-1089, 2016. Keywords: explicit network, from rooted trees, kernelization, minimum number, phylogenetic network, phylogeny, Program Treeduce, reconstruction. Note: https://arxiv.org/abs/1311.4045v3.         15 Steven Kelk, Leo van Iersel, Celine Scornavacca and Mathias Weller. Phylogenetic incongruence through the lens of Monadic Second Order logic. In JGAA, Vol. 20(2):189-215, 2016. Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, MSOL, phylogenetic network, phylogeny, reconstruction. Note: http://jgaa.info/accepted/2016/KelkIerselScornavaccaWeller2016.20.2.pdf.         16 Katharina Huber, Simone Linz, Vincent Moulton and Taoyang Wu. Spaces of phylogenetic networks from generalized nearest-neighbor interchange operations. In JOMB, Vol. 72(2):699-725, 2016. Keywords: bound, distance between networks, from network, LST distance, phylogenetic network, phylogeny.         17 Vincent Ranwez, Celine Scornavacca, Jean-Philippe Doyon and Vincent Berry. Inferring gene duplications, transfers and losses can be done in a discrete framework. In JOMB, Vol. 72(7):1811-1844, 2016. Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction.         18 Magnus Bordewich and Charles Semple. Determining phylogenetic networks from inter-taxa distances. In JOMB, Vol. 73(2):283-303, 2016. Keywords: from distances, phylogenetic network, phylogeny, reconstruction, reticulation-visible network, time consistent network, tree-child network, uniqueness. Note: http://132.181.26.35/~c.semple/papers/BS15b.pdf.         19 Katharina Huber, Vincent Moulton, Mike Steel and Taoyang Wu. Folding and unfolding phylogenetic trees and networks. In JOMB, Vol. 73(6):1761-1780, 2016. Keywords: compressed network, explicit network, FU-stable network, NP complete, phylogenetic network, phylogeny, tree containment, tree sibling network. Note: http://arxiv.org/abs/1506.04438.         20 Momoko Hayamizu. On the existence of infinitely many universal tree-based networks. In JTB, Vol. 396:204-206, 2016. Keywords: explicit network, phylogenetic network, phylogeny, tree-based network. Note: http://arxiv.org/abs/1512.02402.         21 Katharina Huber, Vincent Moulton and Taoyang Wu. Transforming phylogenetic networks: Moving beyond tree space. In JTB, Vol. 404:30-39, 2016. Keywords: distance between networks, level k phylogenetic network, NNI moves, phylogenetic network, phylogeny. Note: http://arxiv.org/abs/1601.01788.         22 James Oldman, Taoyang Wu, Leo van Iersel and Vincent Moulton. TriLoNet: Piecing together small networks to reconstruct reticulate evolutionary histories. In MBE, Vol. 33(8):2151-2162, 2016. Keywords: explicit network, from subnetworks, from trinets, galled tree, phylogenetic network, phylogeny, Program LEV1ATHAN, Program TriLoNet, reconstruction.         23 Claudia Solís-Lemus and Cécile Ané. Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting. In PLOS Genetics, Vol. 12(3):e1005896, 2016. Keywords: explicit network, from quartets, from unrooted trees, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ. Note: http://arxiv.org/abs/1509.06075v1.         24 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.         25 Juan Wang. A Survey of Methods for Constructing Rooted Phylogenetic Networks. In PLoS ONE, Vol. 11(11):e0165834, 2016. Keywords: evaluation, explicit network, from clusters, phylogenetic network, phylogeny, Program BIMLR, Program Dendroscope, Program LNetwork, reconstruction, survey. Note: http://dx.doi.org/10.1371/journal.pone.0165834.         26 Leo van Iersel, Steven Kelk, Nela Lekic, Chris Whidden and Norbert Zeh. Hybridization Number on Three Rooted Binary Trees is EPT. In SIDMA, Vol. 30(3):1607-1631, 2016. Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction. Note: http://arxiv.org/abs/1402.2136.         27 Sajad Mirzaei and Yufeng Wu. Fast Construction of Near Parsimonious Hybridization Networks for Multiple Phylogenetic Trees. In TCBB, Vol. 13(3):565-570, 2016. Keywords: bound, explicit network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program PIRN, reconstruction, software. Note: http://www.engr.uconn.edu/~ywu/Papers/PIRNs-preprint.pdf.

InProceedings

28 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.         29 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.         30 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.         31 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 .         32 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.         33 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.

InBook

34 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.         35 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/.

MastersThesis

36 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.         37 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.

PhdThesis

38 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.         39 Benjamin Albrecht. Computing Hybridization Networks Using Agreement Forests. PhD thesis, Ludwig-Maximilians-Universität München, 2016. Note: https://edoc.ub.uni-muenchen.de/19444/.         40 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/.         41 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.         42 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.