Items where Author is "Wu, Taoyang"

Article

Choi, Kwok Pui, Kaur, Gursharn, Thompson, Ariadne and Wu, Taoyang (2024) Distributions of 4-subtree patterns for uniform random unrooted phylogenetic trees. Journal of Theoretical Biology, 584. ISSN 0022-5193

Moulton, Vincent and Wu, Taoyang (2023) Planar rooted phylogenetic networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 20 (2). pp. 1289-1297. ISSN 1545-5963

Tansley, Connor, Houghton, James, Rose, Althea M. E., Witek, Bartosz, Payet, Rocky D., Wu, Taoyang and Miller, J. Benjamin (2023) CIPK-B is essential for salt stress signalling in Marchantia polymorpha. New Phytologist, 237 (6). pp. 2210-2223. ISSN 0028-646X

Kaur, Gursharn, Choi, Kwok Pui and Wu, Taoyang (2023) Distributions of cherries and pitchforks for the Ford model. Theoretical Population Biology, 149. pp. 27-38. ISSN 0040-5809

Francis, Andrew, Huber, Katharina T., Moulton, Vincent and Wu, Taoyang (2023) Encoding and ordering X-cactuses. Advances in Applied Mathematics, 142. ISSN 0196-8858

Moulton, Vincent and Wu, Taoyang (2022) Posets and spaces of k-noncrossing RNA structures. SIAM Journal on Discrete Mathematics, 36 (3). pp. 1586-1611. ISSN 0895-4801

Xu, Junlin, Cui, Lingyu, Zhuang, Jujuan, Meng, Yajie, Bing, Pingping, He, Binsheng, Tian, Geng, Pui, Choi Kwok, Wu, Taoyang, Wang, Bing and Yang, Jialiang (2022) Evaluating the performance of dropout imputation and clustering methods for single-cell RNA sequencing data. Computers in Biology and Medicine, 146. ISSN 0010-4825

Tatman, Ben, Mock, Thomas, Wu, Taoyang and van Oosterhout, Cock (2021) Significance of differential allelic expression (DAE) in phenotypic plasticity and evolutionary potential of microbial eukaryotes. Quantitative Biology, 9 (4). pp. 400-410. ISSN 2095-4689

Yuan, Kai, Ni, Xumin, Liu, Chang, Pan, Yuwen, Deng, Lian, Zhang, Rui, Gao, Yang, Ge, Xueling, Liu, Jiaojiao, Ma, Xixian, Lou, Haiyi, Wu, Taoyang and Xu, Shuhua (2021) Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0. Nature Communications, 12. ISSN 2041-1723

Choi, Kwok Pui, Kaur, Gursharn and Wu, Taoyang (2021) On asymptotic joint distributions of cherries and pitchforks for random phylogenetic trees. Journal of Mathematical Biology, 83 (4). ISSN 0303-6812

Huang, Guohua, Yang, Jialiang, Chen, Lei and Wu, Taoyang (2021) Editorial: Applications of metagenomics in studying human cancer. Frontiers in Genetics, 12. ISSN 1664-8021

Greenman, Christopher, Wu, Taoyang and Penso Dolfin, Luca (2020) The complexity of genome rearrangement combinatorics under the infinite sites model. Journal of Theoretical Biology, 501. ISSN 0022-5193

Choi, Kwok Pui, Thompson, Ariadne and Wu, Taoyang (2020) On cherry and pitchfork distributions of random rooted and unrooted phylogenetic trees. Theoretical Population Biology, 132. pp. 92-104. ISSN 0040-5809

Janssen, Remie, Jones, Mark, Kelk, Steven, Stamoulis, Georgios and Wu, Taoyang (2019) Treewidth of display graphs: bounds, brambles and applications. Journal of Graph Algorithms and Applications, 23 (4). pp. 715-743. ISSN 1526-1719

Huber, Katharina, Moulton, Vincent and Wu, Taoyang (2019) Hierarchies from lowest stable ancestors in nonbinary phylogenetic networks. Journal of Classification, 36 (2). pp. 200-231. ISSN 0176-4268

Huber, Katharina T., Moulton, Vincent, Semple, Charles and Wu, Taoyang (2018) Quarnet inference rules for level-1 networks. Bulletin of Mathematical Biology, 80 (8). 2137–2153. ISSN 0092-8240

Yang, Jialiang, Liao, Bo, Ye, Jianqiang and Wu, Taoyang (2018) Special Issue on “Computational Tools for Investigating Pathogen, Pathogen-Host Interaction, and Infectious Disease”. Canadian Journal of Infectious Diseases and Medical Microbiology, 2018. ISSN 1712-9532

Kelk, Steven, Stamoulis, Georgios and Wu, Taoyang (2018) Treewidth distance on phylogenetic trees. Theoretical Computer Science, 731. pp. 99-117. ISSN 0304-3975

Moulton, Vincent, Spillner, Andreas and Wu, Taoyang (2018) UPGMA and the normalized equidistant minimum evolution problem. Theoretical Computer Science, 721. pp. 1-15. ISSN 0304-3975

Francis, Andrew, Huber, Katharina T., Moulton, Vincent and Wu, Taoyang (2018) Bounds for phylogenetic network space metrics. Journal of Mathematical Biology, 76 (5). 1229–1248. ISSN 0303-6812

Bastkowski, Sarah, Mapleson, Daniel, Spillner, Andreas, Wu, Taoyang, Balvočiūtė, Monika and Moulton, Vincent (2018) SPECTRE: a Suite of PhylogEnetiC Tools for Reticulate Evolution. Bioinformatics, 34 (6). 1056–1057. ISSN 1367-4803

Moulton, Vincent, Oldman, James and Wu, Taoyang (2017) A cubic-time algorithm for computing the trinet distance between level-1 networks. Information Processing Letters, 123. 36–41. ISSN 0020-0190

Van Iersel, Leo, Moulton, Vincent, de Swart, Eveline and Wu, Taoyang (2017) Binets: fundamental building blocks for phylogenetic networks. Bulletin of Mathematical Biology, 79 (5). 1135–1154. ISSN 0092-8240

Mock, Thomas, Otillar, Robert P., Strauss, Jan, McMullan, Mark, Paajanen, Pirita, Schmutz, Jeremy, Salamov, Asaf, Sanges, Remo, Toseland, Andrew, Ward, Ben J., Allen, Andrew E., Dupont, Christopher L., Frickenhaus, Stephan, Maumus, Florian, Veluchamy, Alaguraj, Wu, Taoyang, Barry, Kerrie W., Falciatore, Angela, Ferrante, Maria I., Fortunato, Antonio E., Glöckner, Gernot, Gruber, Ansgar, Hipkin, Rachel, Janech, Michael G., Kroth, Peter G., Leese, Florian, Lindquist, Erika A., Lyon, Barbara R., Martin, Joel, Mayer, Christoph, Parker, Micaela, Quesneville, Hadi, Raymond, James A., Uhlig, Christiane, Valas, Ruben E., Valentin, Klaus U., Worden, Alexandra Z., Armbrust, E. Virginia, Clark, Matthew D., Bowler, Chris, Green, Beverley R., Moulton, Vincent, van Oosterhout, Cock and Grigoriev, Igor V. (2017) Evolutionary genomics of a cold-adapted diatom: Fragilariopsis cylindrus. Nature, 541. 536–540. ISSN 0028-0836

Huber, Katharina, van Iersel, Leo, Moulton, Vincent, Scornavacca, Celine and Wu, Taoyang (2017) Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets. Algorithmica, 77 (1). pp. 173-200. ISSN 0178-4617

Huber, Katharina, Moulton, Vincent, Steel, Mike and Wu, Taoyang (2016) Folding and unfolding phylogenetic trees and networks. Journal of Mathematical Biology, 73 (6). 1761–1780. ISSN 0303-6812

Kelk, Steven, Fischer, Mareike, Moulton, Vincent and Wu, Taoyang (2016) Reduction rules for the maximum parsimony distance on phylogenetic trees. Theoretical Computer Science, 646. pp. 1-15. ISSN 0304-3975

Huber, Katharina, Moulton, Vincent and Wu, Taoyang (2016) Transforming phylogenetic networks: Moving beyond tree space. Journal of Theoretical Biology, 404. pp. 30-39. ISSN 0022-5193

Oldman, James, Wu, Taoyang, van Iersel, Leo and Moulton, Vincent (2016) TriLoNet: Piecing together small networks to reconstruct reticulate evolutionary histories. Molecular Biology and Evolution, 33 (8). pp. 2151-2162. ISSN 0737-4038

Wu, Taoyang and Choi, Kwok Pui (2016) On joint subtree distributions under two evolutionary models. Theoretical Population Biology, 108. pp. 13-23. ISSN 1096-0325

Bastkowski, Sarah, Moulton, Vincent, Spillner, Andreas and Wu, Taoyang (2016) The minimum evolution problem is hard:A link between tree inference and graph clustering problems. Bioinformatics, 32 (4). pp. 518-522. ISSN 1367-4803

Huber, Katharina T., Linz, Simone, Moulton, Vincent and Wu, Taoyang (2016) Spaces of phylogenetic networks from generalized nearest-neighbor interchange operations. Journal of Mathematical Biology, 72 (3). pp. 699-725. ISSN 0303-6812

Penso-Dolfin, L., Wu, T. and Greenman, C. (2015) The combinatorics of tandem duplication. Discrete Applied Mathematics, 194. 1–22. ISSN 0166-218X

Herrmann, Sven, Koolen, Jack H., Lesser, Alice, Moulton, Vincent and Wu, Taoyang (2015) Optimal realisations of two-dimensional, totally split-decomposable metrics. Discrete Mathematics, 338 (8). 1289–1299. ISSN 0012-365X

Moulton, Vincent and Wu, Taoyang (2015) A parsimony-based metric for phylogenetic trees. Advances in Applied Mathematics, 66. 22–45. ISSN 0196-8858

Bastkowski, Sarah, Moulton, Vincent, Spillner, Andreas and Wu, Taoyang (2015) Neighborhoods of trees in circular orderings. Bulletin of Mathematical Biology, 77 (1). pp. 46-70. ISSN 0092-8240

Huber, Vincent T., van Iersel, Leo, Moulton, Vincent and Wu, Taoyang (2015) How much information is needed to infer reticulate evolutionary histories? Systematic Biology, 64 (1). pp. 102-111. ISSN 1063-5157

Huber, K. T., Moulton, V., Semple, C. and Wu, T. (2014) Representing partitions on trees. SIAM Journal on Discrete Mathematics, 28 (3). pp. 1152-1172. ISSN 0895-4801

Zhu, Sha, Than, Cuong and Wu, Taoyang (2014) Clades and clans: a comparison study of two evolutionary models. Journal of Mathematical Biology, 71 (1). pp. 99-124. ISSN 0303-6812

Wade, Amy S. I., Barov, Boris, Burfield, Ian J., Gregory, Richard D., Norris, Ken, Vorisek, Petr, Wu, Taoyang and Butler, Simon (2014) A niche-based framework to assess current monitoring of European forest birds and guide indicator species' selection. PLoS One, 9 (5). ISSN 1932-6203

Li, Si, Choi, Kwok Pui, Wu, Taoyang and Zhang, Louxin (2013) Maximum likelihood inference of the evolutionary history of a PPI network from the duplication history of its proteins. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10 (6). pp. 1412-1421. ISSN 1545-5963

Dress, A., Moulton, Vincent, Wu, Taoyang and Spillner, A. (2013) Obtaining splits from cut sets of tight spans. Discrete Applied Mathematics, 161 (10-11). pp. 1409-1420. ISSN 0166-218X

Humphries, Peter J. and Wu, Taoyang (2013) On the neighborhoods of trees. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10 (3). pp. 721-728. ISSN 1545-5963

Li, Si, Choi, Kwok Pui and Wu, Taoyang (2013) Degree distribution of large networks generated by the partial duplication model. Theoretical Computer Science, 476. pp. 94-108.

Gruenewald, Stefan, Koolen, Jack H., Moulton, Vincent and Wu, Taoyang (2012) The size of 3-compatible, weakly compatible split systems. Journal of Applied Mathematics and Computing, 40 (1-2). pp. 249-259.

Koolen, Jack H., Lesser, Alice, Moulton, Vincent and Wu, Taoyang (2012) Injective optimal realizations of finite metric spaces. Discrete Mathematics, 312 (10). pp. 1602-1610. ISSN 1872-681X

Wu, Taoyang and Zhang, Louxin (2011) Structural properties of the reconciliation space and their applications in enumerating nearly-optimal reconciliations between a gene tree and a species tree. BMC Bioinformatics, 12 (Suppl 9). ISSN 1471-2105

Székely, LA, Wang, Hua and Wu, Taoyang (2011) The sum of the distances between the leaves of a tree and the ‘semi-regular’ property. Discrete Mathematics, 311 (13). pp. 1197-1203. ISSN 1872-681X

Dress, Andreas, Moulton, Vincent, Steel, Mike and Wu, Taoyang (2010) Species, clusters and the ‘Tree of life’: A graph-theoretic perspective. Journal of Theoretical Biology, 265 (4). pp. 535-542.

Cameron, Peter J. and Wu, Taoyang (2010) The complexity of the weight problem for permutation and matrix groups. Discrete Mathematics, 310 (3). pp. 408-416. ISSN 1872-681X

Dress, Andreas W. M., Wu, Taoyang and Xu, XiaoMing (2010) A note on single-linkage equivalence. Applied Mathematics Letters, 23 (4). pp. 432-435.

Dress, Andreas W. M., Moulton, Vincent, Spillner, Andreas and Wu, Taoyang (2009) Barriers in metric spaces. Applied Mathematics Letters, 22 (8). pp. 1150-1153.

Buchheim, Christoph, Cameron, Peter J. and Wu, Taoyang (2009) On the subgroup distance problem. Discrete Mathematics, 309 (4). pp. 962-968. ISSN 1872-681X

Wu, Taoyang, Cameron, Peter and Riis, Søren (2009) On the guessing number of shift graphs. Journal of Discrete Algorithms, 7 (2). pp. 220-226.

Wu, Taoyang, Moulton, Vincent and Steel, Mike (2009) Refining phylogenetic trees given additional data: An algorithm based on parsimony. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6 (1). pp. 118-125. ISSN 1545-5963

Book Section

Mock, Thomas, Hodgkinson, Kat, Wu, Taoyang, Moulton, Vincent, Duncan, Anthony, Oosterhout, Cock van and Pichler, Monica (2022) Structure and Evolution of Diatom Nuclear Genes and Genomes. In: The Molecular Life of Diatoms. Springer, pp. 111-145. ISBN 9783030924980