Who is Who in Phylogenetic Networks

Publications of Year 2018

Article (Journal)

1 Andrew R. Francis, Charles Semple and Mike Steel. New characterisations of tree-based networks and proximity measures. In Advances in Applied Mathematics, Vol. 93:93-107, 2018. Keywords: characterization, explicit network, phylogenetic network, phylogeny, time consistent network, tree-based network. Note: https://arxiv.org/abs/1611.04225.         2 Leo van Iersel, Steven Kelk, Giorgios Stamoulis, Leen Stougie and Olivier Boes. On unrooted and root-uncertain variants of several well-known phylogenetic network problems. In ALG, Vol. 80(11):2993-3022, 2018. Keywords: explicit network, FPT, from network, from unrooted trees, NP complete, phylogenetic network, phylogeny, reconstruction, tree containment. Note: https://hal.inria.fr/hal-01599716.         3 Magnus Bordewich, Charles Semple and Nihan Tokac. Constructing tree-child networks from distance matrices. In Algorithmica, Vol. 80(8):2240-2259, 2018. Keywords: compressed network, explicit network, from distances, phylogenetic network, phylogeny, polynomial, reconstruction, tree-child network, uniqueness. Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BSN17.pdf.         4 Hongwei Yan, Andreas Gunawan and Louxin Zhang. S-Cluster++: a fast program for solving the cluster containment problem for phylogenetic networks. In BIO, Vol. 34(17):i680–i686, 2018. Keywords: cluster containment, explicit network, phylogenetic network, phylogeny, SAT. Note: http://dx.doi.org/10.1093/bioinformatics/bty594.         5 Sarah Bastkowski, Daniel Mapleson, Andreas Spillner, Taoyang Wu, Monika Balvociute and Vincent Moulton. SPECTRE: a Suite of PhylogEnetiC Tools for Reticulate Evolution. In BIO, Vol. 34(6):1057-1058, 2018. Keywords: abstract network, NeighborNet, phylogenetic network, phylogeny, Program FlatNJ, Program QNet, Program SplitsTree, reconstruction, software, split network. Note: https://doi.org/10.1101/169177.         6 Katharina Huber, Vincent Moulton, Charles Semple and Taoyang Wu. Quarnet inference rules for level-1 networks. In BMB, Vol. 80:2137-2153, 2018. Keywords: explicit network, from quarnets, from subnetworks, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction. Note: https://arxiv.org/abs/1711.06720.         7 Andrew R. Francis, Katharina Huber and Vincent Moulton. Tree-based unrooted phylogenetic networks. In BMB, Vol. 80(2):404-416, 2018. Keywords: characterization, explicit network, NP complete, phylogenetic network, phylogeny, tree containment, tree-based network, unrooted tree-based network. Note: https://arxiv.org/abs/1704.02062.         8 Remie Janssen, Mark Jones, Péter L. Erdös, Leo van Iersel and Celine Scornavacca. Exploring the tiers of rooted phylogenetic network space using tail moves. In BMB, Vol. 80(8):2177-2208, 2018. Keywords: distance between networks, explicit network, from network, NNI moves, orientation, phylogenetic network, phylogeny, SPR distance. Note: https://arxiv.org/abs/1708.07656.         9 Charles Semple and Jack Simpson. When is a phylogenetic network simply an amalgamation of two trees? In BMB, Vol. 80(9):2338-2348, 2018. Keywords: characterization, phylogenetic network, phylogeny, reticulation-visible network, stack-free network, tree-based network. Note: http://www.math.canterbury.ac.nz/~c.semple/papers/SS18.pdf.         10 Philippe Gambette, Andreas Gunawan, Anthony Labarre, Stéphane Vialette and Louxin Zhang. Solving the Tree Containment Problem in Linear Time for Nearly Stable Phylogenetic Networks. In DAM, Vol. 246:62-79, 2018. Keywords: explicit network, from network, from rooted trees, nearly-stable network, phylogenetic network, phylogeny, polynomial, tree containment. Note: https://hal-upec-upem.archives-ouvertes.fr/hal-01575001/en/.         11 Magnus Bordewich and Charles Semple. A universal tree-based network with the minimum number of reticulations. In DAM, Vol. 250:357-362, 2018. Keywords: explicit network, phylogenetic network, phylogeny, tree-based network. Note: https://arxiv.org/abs/1707.08274.         12 Kuang-Yu Chang, Yun Cui, Siu-Ming Yiu and Wing-Kai Hon. Reconstructing One-Articulated Networks with Distance Matrices. In JCB, Vol. 25(3):253-269, 2018. Keywords: explicit network, from distances, k-reticulated, phylogenetic network, phylogeny, reconstruction.         13 Jonathan Klawitter. The SNPR neighbourhood of tree-child networks. In JGAA, Vol. 22(2):329-355, 2018. Keywords: distance between networks, phylogenetic network, phylogeny, SPR distance, tree-child network. Note: https://arxiv.org/abs/1707.09579         14 Andrew R. Francis, Katharina Huber, Vincent Moulton and Taoyang Wu. Bounds for phylogenetic network space metrics. In JOMB, Vol. 76(5):1229-1248, 2018. Keywords: bound, distance between networks, from network, NNI distance, NNI moves, phylogenetic network, phylogeny, SPR distance, TBR distance. Note: https://arxiv.org/abs/1702.05609.         15 Magnus Bordewich, Katharina Huber, Vincent Moulton and Charles Semple. Recovering normal networks from shortest inter-taxa distance information. In JOMB, Vol. 77(3):571-594, 2018. Keywords: explicit network, from distances, normal network, phylogenetic network, phylogeny, polynomial, reconstruction, uniqueness. Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BHMS18.pdf.         16 Andrew R. Francis and Vincent Moulton. Identifiability of tree-child phylogenetic networks under a probabilistic recombination-mutation model of evolution. In JTB, Vol. 446:160-167, 2018. Keywords: explicit network, from unrooted trees, phylogenetic network, phylogeny, tree-child network, uniqueness. Note: https://arxiv.org/abs/1712.04223.         17 Kristina Wicke and Mareike Fischer. Phylogenetic diversity and biodiversity indices on phylogenetic networks. In MB, Vol. 298:80-90, 2018. Keywords: diversity, explicit network, from network, normal network, phylogenetic network, phylogeny. Note: https://arxiv.org/abs/1706.05279.         18 Chi Zhang, Huw A. Ogilvie, Alexei J. Drummond and Tanja Stadler. Bayesian Inference of Species Networks from Multilocus Sequence Data. In MBE, Vol. 35(2):504-517, 2018. Keywords: bayesian, explicit network, from sequences, phylogenetic network, phylogeny, reconstruction, statistical model. Note: https://dx.doi.org/10.1093/molbev/msx307.         19 Michael Hendriksen. Tree-based unrooted nonbinary phylogenetic networks. In MBIO, Vol. 302:131-138, 2018. Keywords: characterization, phylogenetic network, phylogeny, tree-based network, unrooted tree-based network.         20 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.         21 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.         22 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, weakly displaying. Note: https://leovaniersel.files.wordpress.com/2017/12/improved_parsimony_networks.pdf.         23 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.         24 James H. Degnan. Modeling Hybridization Under the Network Multispecies Coalescent. In SB, Vol. 67(5):786-799, 2018. Keywords: distance between networks, phylogenetic network, phylogeny, reconstruction, survey. Note: https://academic.oup.com/sysbio/article/67/5/786/5017269.         25 Paul Bastide, Claudia Solís-Lemus, Ricardo Kriebel, Kenneth William Sparks and Cécile Ané. Phylogenetic Comparative Methods on Phylogenetic Networks with Reticulations. In SB, Vol. 67(5):800-820, 2018. Keywords: ancestral trait reconstruction, from network, likelihood, Program PhyloNetworks SNaQ, software, statistical model, statistical test. Note: https://doi.org/10.1101/194050.         26 Elizabeth Gross and Colby Long. Distinguishing Phylogenetic Networks. In SIAM Journal on Applied Algebra and Geometry, Vol. 2(1):72-93, 2018. Keywords: distinguishability, phylogenetic network, phylogeny, semidirected network, statistical model, uniqueness. Note: https://arxiv.org/abs/1706.03060.         27 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.         28 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.         29 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.         30 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.

InProceedings

31 Kuang-Yu Chang, Wing-Kai Hon and Sharma V. Thankachan. Compact Encoding for Galled-Trees and its Applications. In 2018 Data Compression Conference, Pages 297-306, 2018. Keywords: compression, counting, explicit network, galled tree, phylogenetic network, polynomial.         32 Andreas Gunawan. Solving the Tree Containment Problem for Reticulation-visible Networks in Linear Time. In AlCoB18, Vol. 10849:24-36 of LNCS, Springer, 2018. Keywords: explicit network, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulation-visible network, tree containment. Note: https://arxiv.org/abs/1702.04088.         33 Leo van Iersel, Remie Janssen, Mark Jones, Yukihiro Murakami and Norbert Zeh. Polynomial-Time Algorithms for Phylogenetic Inference Problems. In AlCoB18, Vol. 10849:37-49 of LNCS, Springer, 2018. Keywords: hybridization, minimum number, parental hybridization, phylogenetic network, phylogeny, polynomial, reconstruction, weakly displaying. Note: https://research.tudelft.nl/files/53686721/10.1007_978_3_319_91938_6_4.pdf.         34 Hussein A. Hejase, Natalie VandePol, Gregory A. Bonito and Kevin J. Liu. Fast and accurate statistical inference of phylogenetic networks using large-scale genomic sequence data. In RECOMB-CG18, Vol. 11183:242-259 of LNCS, Springer, 2018. Keywords: explicit network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program FastNet, reconstruction. Note: http://biorxiv.org/content/early/2017/05/01/132795.         35 Mathias Weller. Linear-Time Tree Containment in Phylogenetic Networks. In RECOMB-CG18, Vol. 11183:309-323 of LNCS, Springer, 2018. Keywords: explicit network, from network, from rooted trees, nearly-stable network, phylogenetic network, phylogeny, polynomial, reconstruction, reticulation-visible network, tree containment. Note: https://arxiv.org/abs/1702.06364.         36 Sebastien Roch and Kun-Chieh Wang. Circular Networks from Distorted Metrics. In RECOMB18, Vol. 10812:167-176 of LNCS, Springer, 2018. Keywords: abstract network, circular split system, from distances, NeighborNet, phylogenetic network, phylogeny, reconstruction, split network. Note: https://arxiv.org/abs/1707.05722.

PhdThesis

37 Sajad Mirzaei. Efficient Algorithms for Trees and Networks in Evolutionary Genomics. PhD thesis, University of Connecticut, 2018. Keywords: branch length, explicit network, haplotype network, heuristic, Program PIRN, reconstruction. Note: https://opencommons.uconn.edu/dissertations/1853.         38 Guillaume Scholz. New algorithms and mathematical tools for phylogenetics beyond trees. PhD thesis, University of East Anglia, 2018. Keywords: circular split system, explicit network, explicit network, from splits, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction, split network, uniqueness. Note: https://ueaeprints.uea.ac.uk/id/eprint/66952.         39 Andreas Gunawan. On the tree and cluster containment problems for phylogenetic networks. PhD thesis, National University of Singapore, 2018. Keywords: cluster containment, explicit network, galled network, genetically stable network, nearly-stable network, phylogenetic network, phylogeny, reticulation-visible network, tree containment. Note: https://scholarbank.nus.edu.sg/handle/10635/144270.