Who is Who in Phylogenetic Networks

Publications of Louxin Zhang     Order by:   Type | Year

Associated keywords

bound characterization cluster-containment counting distance-between-networks dynamic-programming enumeration evaluation explicit-network exponential-algorithm from-clusters from-distances from-network from-rooted-trees from-sequences from-species-tree galled-network galled-tree generation genetically-stable-network labeling nearly-stable-network NNI-moves normal-network NP-complete parsimony perfect phylogenetic-network phylogeny polynomial Program-icelu-PhyloNetwork quasi-reticulation-visible-network recombination reconstruction reticulation-visible-network SAT software stable-child-network survey time-consistent-network tree-containment tree-based-network tree-child-network

Article (Journal)

1 Gabriel Cardona and Louxin Zhang. Counting and Enumerating Tree-Child Networks and Their Subclasses. In JCSS, Vol. 114:84-104, 2020. Keywords: counting, enumeration, explicit network, galled network, galled tree, normal network, phylogenetic network, phylogeny, tree-child network.         2 Andreas Gunawan, Jeyaram Rathin and Louxin Zhang. Counting and enumerating galled networks. In DAM, Vol. 283:644-654, 2020. Keywords: counting, enumeration, explicit network, galled network, phylogenetic network, phylogeny. Note: https://arxiv.org/abs/1812.08569.         3 Andreas Gunawan, Hongwei Yan and Louxin Zhang. Compression of Phylogenetic Networks and Algorithm for the Tree Containment Problem. In JCB, Vol. 25(3), 2019. Keywords: explicit network, phylogenetic network, phylogeny, polynomial, quasi-reticulation-visible network, reticulation-visible network, tree containment, tree-child network. Note: https://arxiv.org/abs/1806.07625.         4 Louxin Zhang. Generating normal networks via leaf insertion and nearest neighbor interchange. In BMC Bioinformatics, Vol. 20(642):1-9, 2019. Keywords: enumeration, explicit network, generation, NNI moves, phylogenetic network, phylogeny. Note: https://link.springer.com/content/pdf/10.1186/s12859-019-3209-3.pdf.         5 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/.         6 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.         7 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.         8 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.         9 Cam Thach Nguyen, Nguyen Bao Nguyen, Wing-Kin Sung and Louxin Zhang. Reconstructing Recombination Network from Sequence Data: The Small Parsimony Problem. In TCBB, Vol. 4(3):394-402, 2007. Keywords: explicit network, from sequences, labeling, NP complete, parsimony, phylogenetic network, phylogeny. Note: http://www.cs.washington.edu/homes/ncthach/Papers/TCBB2007.pdf.

InProceedings

10 Louxin Zhang. Recent Progresses in the Combinatorial and Algorithmic Study of Rooted Phylogenetic Networks. In WALCOM20, Vol. 12049:22-27 of LNCS, Springer, 2020. Keywords: cluster containment, galled network, galled tree, nearly-stable network, phylogenetic network, phylogeny, polynomial, reticulation-visible network, survey, time consistent network, tree containment, tree-based network, tree-child network.         11 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.         12 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.         13 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 .         14 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.         15 Philippe Gambette, Andreas Gunawan, Anthony Labarre, Stéphane Vialette and Louxin Zhang. Locating a Tree in A Phylogenetic Network in Quadratic Time. In RECOMB15, Vol. 9029:96-107 of LNCS, Springer, 2015. Keywords: evaluation, explicit network, from network, from rooted trees, genetically stable network, nearly-stable network, phylogenetic network, phylogeny, polynomial, tree containment. Note: https://hal.archives-ouvertes.fr/hal-01116231/en.         16 Louxin Zhang, Yen Kaow Ng, Taoyang Wu and Yu Zheng. Network model and efficient method for detecting relative duplications or horizontal gene transfers. In ICCABS11, Pages 214-219, 2011. Keywords: dynamic programming, explicit network, from network, from rooted trees, from species tree, phylogenetic network, phylogeny, polynomial, reconstruction.         Toggle abstract "Background: Horizontal gene transfer and gene duplication are two significant forces behind genome evolution. As more and more well-supported examples of HGTs are being revealed, there is a growing awareness that HGT is more widespread than previously thought, occurring often not only within bacteria, but also between species remotely related such as bacteria and plants or plants and animals. Although a substantial number of genomic sequences are known, HGT inference remains challenging. Parsimony-based inferences of HGT events are typically NP-hard under the framework of gene tree and species tree comparison; it is even more timeconsuming if the maximum likelihood approach is used. The fact that gene tree and species tree incongruence can be further confounded by gene duplication and gene loss events motivates us to incorporate considerations for these events into our inference of HGT events. Similarly, it will be beneficial if known HGT events are considered in the inference of gene duplications and gene losses. © 2011 IEEE." 17 Lusheng Wang, Kaizhong Zhang and Louxin Zhang. Perfect phylogenetic networks with recombination. In SAC01, Pages 46-50, 2001. Keywords: from sequences, galled tree, NP complete, perfect, phylogenetic network, phylogeny, polynomial, recombination, reconstruction. Note: http://dx.doi.org/10.1145/372202.372271.

InBook

18 Louxin Zhang. Clusters, Trees, and Phylogenetic Network Classes. In Tandy Warnow editor, Bioinformatics and Phylogenetics. Seminal Contributions of Bernard Moret, Vol. 29:277-315 of Computational Biology, Springer, 2019. Keywords: cluster containment, explicit network, phylogenetic network, phylogeny, polynomial, tree containment.         19 Guillaume Bourque and Louxin Zhang. Models and Methods in Comparative Genomics. In Chau-Wen Tseng editor, Advances in Computers, Special Volume: Computational Biology, Vol. 68, Elsevier, 2006. Keywords: from distances, from rooted trees, from sequences, galled tree, phylogenetic network, phylogeny, survey. Note: http://www.math.nus.edu.sg/~matzlx/papers/CompGen_ZLX.pdf.

Misc

20 Michael Fuchs, Guan-Ru Yu and Louxin Zhang. On the Asymptotic Growth of the Number of Tree-Child Networks. 2020. Keywords: counting, explicit network, phylogenetic network, phylogeny, tree-child network. Note: https://arxiv.org/abs/2003.08049.         21 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.