Who is Who in Phylogenetic Networks

Publications list	Showing 151 - 180 (752 total)

151 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.         152 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.         153 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.         154 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.         155 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.         156 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.         157 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.         158 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.         159 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.         160 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.         161 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.         162 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.         163 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.         164 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.         165 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.         166 Quan Nguyen. Likelihood-based Phylogenetic Network Inference by Approximate Structural Expectation Maximization. Master's thesis, University of Helsinki, 2015. Keywords: BIC, likelihood, phylogenetic network, phylogeny, Program PhyloDAG, reconstruction, software. Note: http://urn.fi/URN:NBN:fi-fe2015062910525.         167 Maxime Morgado. Propriétés structurelles et relations des classes de réseaux phylogénétiques. Master's thesis, ENS Cachan, 2015. Keywords: compressed network, distinct-cluster network, explicit network, galled network, galled tree, level k phylogenetic network, nested network, normal network, phylogenetic network, phylogeny, regular network, spread, tree containment, tree sibling network, tree-based network, tree-child network, unicyclic network.         168 Dwueng-Chwuan Jhwueng and Brian O'Meara. Trait Evolution on Phylogenetic Networks. 2015. Keywords: explicit network, from network, hybridization, phylogenetic network, phylogeny, Program BMhyd, statistical model. Note: http://dx.doi.org/10.1101/023986.         169 Andreas Gunawan and Louxin Zhang. Bounding the Size of a Network Defined By Visibility Property. 2015. Keywords: bound, explicit network, galled network, nearly-stable network, phylogenetic network, phylogeny, reticulation-visible network, stable-child network. Note: http://arxiv.org/abs/1510.00115.         170 Laura Jetten. Characterising tree-based phylogenetic networks. Bachelor thesis, 2015. Keywords: characterization, explicit network, phylogenetic network, phylogeny, tree-based network. Note: http://resolver.tudelft.nl/uuid:fda2636d-0ed5-4dd2-bacf-8abbbad8994e.         171 Benjamin Albrecht. Computing a Relevant Set of Nonbinary Maximum Acyclic Agreement Forests. 2015. Keywords: agreement forest, explicit network, exponential algorithm, from rooted trees, phylogenetic network, phylogeny, Program Hybroscale, reconstruction, software. Note: http://arxiv.org/abs/1512.05703.         172 Benjamin Albrecht. Fast computation of all maximum acyclic agreement forests for two rooted binary phylogenetic trees. 2015. Keywords: agreement forest, explicit network, from rooted trees, phylogenetic network, phylogeny, Program Hybroscale, reconstruction, software. Note: http://arxiv.org/abs/1512.05656.         173 Nela Lekic. Trees, agreement forests and treewidth: combinatorial algorithms for constructing phylogenetic networks. PhD thesis, Maastricht University, The Netherlands, 2015. Keywords: explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction.         174 Claudia Solís-Lemus. Statistical methods to infer population structure with coalescence and gene flow. PhD thesis, University of Wisconsin-Madison, 2015. Keywords: explicit network, from quartets, from unrooted trees, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, semidirected network. Note: https://www.stat.wisc.edu/~claudia/thesis.pdf.         175 Quan Nguyen and Teemu Roos. Likelihood-based inference of phylogenetic networks from sequence data by PhyloDAG. In AlCoB15, Vol. 9199:126-140 of LNCS, springer, 2015. Keywords: BIC, explicit network, from sequences, likelihood, phylogenetic network, phylogeny, Program PhyloDAG, reconstruction, software. Note: http://www.cs.helsinki.fi/u/ttonteri/pub/alcob2015.pdf.         176 Vladimir Ulyantsev and Mikhail Melnik. Constructing Parsimonious Hybridization Networks from Multiple Phylogenetic Trees Using a SAT-solver. In AlCoB15, Vol. 9199:141-153 of LNCS, springer, 2015. Keywords: explicit network, from rooted trees, from trees, phylogenetic network, phylogeny, Program PIRN, reconstruction. Note: https://www.researchgate.net/profile/Vladimir_Ulyantsev/publication/282816862_Constructing_Parsimonious_Hybridization_Networks_from_Multiple_Phylogenetic_Trees_Using_a_SAT-Solver/links/561d372c08aecade1acb3699/Constructing-Parsimonious-Hybridization-Networks-from-Multiple-Phylogenetic-Trees-Using-a-SAT-Solver.pdf.         177 Dan Gusfield. Persistent Phylogeny: A Galled-Tree and Integer Linear Programming Approach. In BCB15, Pages 443-451, 2015. Keywords: explicit network, from binary characters, galled tree, integer linear programming, phylogenetic network, phylogeny, reconstruction. Note: http://arxiv.org/abs/1506.00678.         178 Misagh Kordi and Mukul S. Bansal. On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees. In ISBRA15, Vol. 9096:187-198 of LNCS, springer, 2015. 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_ISBRA2015.pdf.         179 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.         180 Jittat Fakcharoenphol, Tanee Kumpijit and Attakorn Putwattana. A Faster Algorithm for the Tree Containment Problem for Binary Nearly Stable Phylogenetic Networks. In Proceedings of the The 12th International Joint Conference on Computer Science and Software Engineering (JCSSE'15), Pages 337-342, IEEE, 2015. Keywords: dynamic programming, explicit network, from network, from rooted trees, nearly-stable network, phylogenetic network, phylogeny, polynomial, tree containment.