Items where Author is "Wu, Taoyang"

Article

Winder, Johanna C. ORCID: https://orcid.org/0000-0002-7509-772X, Poulton, Simon, Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001, Mock, Thomas ORCID: https://orcid.org/0000-0001-9604-0362 and van Oosterhout, Cock ORCID: https://orcid.org/0000-0002-5653-738X (2025) Environmental adaptations in metagenomes revealed by deep learning. BMC Biology, 23. ISSN 1741-7007

Choi, Kwok Pui, Kaur, Gursharn, Thompson, Ariadne and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2024) Distributions of 4-subtree patterns for uniform random unrooted phylogenetic trees. Journal of Theoretical Biology, 584. ISSN 0022-5193

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (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 ORCID: https://orcid.org/0000-0002-2663-2001 and Miller, J. Benjamin ORCID: https://orcid.org/0000-0003-0882-033X (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 ORCID: https://orcid.org/0000-0002-2663-2001 (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. ORCID: https://orcid.org/0000-0002-6368-7511, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2023) Encoding and ordering X-cactuses. Advances in Applied Mathematics, 142. ISSN 0196-8858

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (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 ORCID: https://orcid.org/0000-0002-2663-2001, 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 ORCID: https://orcid.org/0000-0001-9604-0362, Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 and van Oosterhout, Cock ORCID: https://orcid.org/0000-0002-5653-738X (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 ORCID: https://orcid.org/0000-0002-2663-2001 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 ORCID: https://orcid.org/0000-0002-2663-2001 (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 ORCID: https://orcid.org/0000-0002-2663-2001 (2021) Editorial: Applications of metagenomics in studying human cancer. Frontiers in Genetics, 12. ISSN 1664-8021

Greenman, Christopher, Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 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 ORCID: https://orcid.org/0000-0002-2663-2001 (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 ORCID: https://orcid.org/0000-0002-2663-2001 (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 ORCID: https://orcid.org/0000-0002-6368-7511, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2019) Hierarchies from lowest stable ancestors in nonbinary phylogenetic networks. Journal of Classification, 36 (2). pp. 200-231. ISSN 0176-4268

Huber, Katharina T. ORCID: https://orcid.org/0000-0002-6368-7511, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Semple, Charles and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (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 ORCID: https://orcid.org/0000-0002-2663-2001 (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 ORCID: https://orcid.org/0000-0002-2663-2001 (2018) Treewidth distance on phylogenetic trees. Theoretical Computer Science, 731. pp. 99-117. ISSN 0304-3975

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Spillner, Andreas and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2018) UPGMA and the normalized equidistant minimum evolution problem. Theoretical Computer Science, 721. pp. 1-15. ISSN 0304-3975

Francis, Andrew, Huber, Katharina T. ORCID: https://orcid.org/0000-0002-6368-7511, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (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 ORCID: https://orcid.org/0000-0002-2663-2001, Balvočiūtė, Monika and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2018) SPECTRE: a Suite of PhylogEnetiC Tools for Reticulate Evolution. Bioinformatics, 34 (6). 1056–1057. ISSN 1367-4803

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Oldman, James and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (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 ORCID: https://orcid.org/0000-0001-9371-6435, de Swart, Eveline and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2017) Binets: fundamental building blocks for phylogenetic networks. Bulletin of Mathematical Biology, 79 (5). 1135–1154. ISSN 0092-8240

Mock, Thomas ORCID: https://orcid.org/0000-0001-9604-0362, 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 ORCID: https://orcid.org/0000-0002-2663-2001, 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 ORCID: https://orcid.org/0000-0001-9371-6435, van Oosterhout, Cock ORCID: https://orcid.org/0000-0002-5653-738X and Grigoriev, Igor V. (2017) Evolutionary genomics of a cold-adapted diatom: Fragilariopsis cylindrus. Nature, 541. 536–540. ISSN 0028-0836

Huber, Katharina ORCID: https://orcid.org/0000-0002-6368-7511, van Iersel, Leo, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Scornavacca, Celine and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2017) Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets. Algorithmica, 77 (1). pp. 173-200. ISSN 0178-4617

Huber, Katharina ORCID: https://orcid.org/0000-0002-6368-7511, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Steel, Mike and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (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 ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2016) Reduction rules for the maximum parsimony distance on phylogenetic trees. Theoretical Computer Science, 646. pp. 1-15. ISSN 0304-3975

Huber, Katharina ORCID: https://orcid.org/0000-0002-6368-7511, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2016) Transforming phylogenetic networks: Moving beyond tree space. Journal of Theoretical Biology, 404. pp. 30-39. ISSN 0022-5193

Oldman, James, Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001, van Iersel, Leo and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (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 ORCID: https://orcid.org/0000-0002-2663-2001 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 ORCID: https://orcid.org/0000-0001-9371-6435, Spillner, Andreas and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (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. ORCID: https://orcid.org/0000-0002-6368-7511, Linz, Simone, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (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. ORCID: https://orcid.org/0000-0002-2663-2001 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 ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2015) Optimal realisations of two-dimensional, totally split-decomposable metrics. Discrete Mathematics, 338 (8). 1289–1299. ISSN 0012-365X

Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2015) A parsimony-based metric for phylogenetic trees. Advances in Applied Mathematics, 66. 22–45. ISSN 0196-8858

Bastkowski, Sarah, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Spillner, Andreas and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2015) Neighborhoods of trees in circular orderings. Bulletin of Mathematical Biology, 77 (1). pp. 46-70. ISSN 0092-8240

Huber, Vincent T. ORCID: https://orcid.org/0000-0002-6368-7511, van Iersel, Leo, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2015) How much information is needed to infer reticulate evolutionary histories? Systematic Biology, 64 (1). pp. 102-111. ISSN 1063-5157

Huber, K. T. ORCID: https://orcid.org/0000-0002-6368-7511, Moulton, V. ORCID: https://orcid.org/0000-0001-9371-6435, Semple, C. and Wu, T. ORCID: https://orcid.org/0000-0002-2663-2001 (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 ORCID: https://orcid.org/0000-0002-2663-2001 (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 ORCID: https://orcid.org/0000-0002-2663-2001 and Butler, Simon ORCID: https://orcid.org/0000-0002-5111-5639 (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 ORCID: https://orcid.org/0000-0002-2663-2001 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 ORCID: https://orcid.org/0000-0001-9371-6435, Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 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 ORCID: https://orcid.org/0000-0002-2663-2001 (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 ORCID: https://orcid.org/0000-0002-2663-2001 (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 ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (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 ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2012) Injective optimal realizations of finite metric spaces. Discrete Mathematics, 312 (10). pp. 1602-1610. ISSN 1872-681X

Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 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 ORCID: https://orcid.org/0000-0002-2663-2001 (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 ORCID: https://orcid.org/0000-0001-9371-6435, Steel, Mike and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (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 ORCID: https://orcid.org/0000-0002-2663-2001 (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 ORCID: https://orcid.org/0000-0002-2663-2001 and Xu, XiaoMing (2010) A note on single-linkage equivalence. Applied Mathematics Letters, 23 (4). pp. 432-435.

Dress, Andreas W. M., Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Spillner, Andreas and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2009) Barriers in metric spaces. Applied Mathematics Letters, 22 (8). pp. 1150-1153.

Buchheim, Christoph, Cameron, Peter J. and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 (2009) On the subgroup distance problem. Discrete Mathematics, 309 (4). pp. 962-968. ISSN 1872-681X

Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001, Cameron, Peter and Riis, Søren (2009) On the guessing number of shift graphs. Journal of Discrete Algorithms, 7 (2). pp. 220-226.

Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 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

Liu, Hexuan, Lu, Bing-Ze, Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001 and Yu, Guan-Ru (2025) Asymptotic Enumeration of Subclasses of Level-2 Phylogenetic Networks. In: EUROCOMB'25. UNSPECIFIED.

Mock, Thomas ORCID: https://orcid.org/0000-0001-9604-0362, Hodgkinson, Kat, Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Duncan, Anthony, Oosterhout, Cock van ORCID: https://orcid.org/0000-0002-5653-738X 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