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., 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, 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., 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., 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, 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, 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, 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., 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., 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., 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
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