Publications

Journal publications

[53] Choi, K.P., Kaur, G., Thompson, A., and Wu, T. (2024)  Distributions of 4-subtree patterns for uniform random unrooted phylogenetic trees. Journal of Theoretical Biology, in press.  

[52] Tansley, C., Houghton, J., Rose, A.M.E, Witek, B., Payet, R.D., Wu, T., and Miller J.B.  (2023) CIPK-B is essential for salt stress signalling in Marchantia polymorpha. New Phytologist, 237: 2210-2223. www.biorxiv.org/10.1101/2022.08.22.504506v1

[51]  Francis, A.,  Huber, K.T., Moulton, V., and Wu, T.  (2023) Encoding and ordering X-cactuses. Advance in Applied Mathematics, 142:102414. arxiv.org/abs/2109.03183 

[50] Moulton, V. and Wu, T.  (2023) Planar rooted phylogenetic networks.  IEEE/ACM Transactions on Computational Biology and Bioinformatics, 20:1289-1297. arxiv.org/abs/2203.10156

[49] Kaur, G., Choi, K.P., and Wu, T.  (2023) Distributions of cherries and pitchforks for the Ford model. Theoretical Population Biology, 149: 27-38. arxiv.org/abs/2110.02850 

[48] Xu, J., Cui, L., Zhuang, Z., Meng, Y., Bing, P., He, B., Tian, G., Choi, K.P., Wu, T.,  Wang, B., and Yang, J. (2022)  Evaluating the performance of dropout imputation and clustering methods for single-cell RNA sequencing.  Computers in Biology and Medicine, 146:105697.

[47] Moulton, V. and Wu, T. (2022)  Posets and spaces of k-noncrossing RNA structures.  SIAM J. Discrete Mathematics, 36(3):1586-1611. arxiv.org/abs/2204.05934

[46] Yuan, K., Ni,  X.,  Liu C.,  Pan Y.,  Deng,  L., Zhang, R.,  Gao. Y.,  Ge,  X.,  Liu J.,  Ma, X., Lou, H., Wu, T., and Xu, S. (2021) Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0. Nature Communications, 12:6232.  Link

[45]  Choi, K.P., Kaur, G., and Wu, T. (2021) On asymptotic joint distributions of cherries and pitchforks for random phylogenetic trees. Journal of Mathematical Biology, 83:40. Link arXiv:2101.07488

[44] Tatman, B., Mock, T.,  Wu, T., and van Oosterhout, C.  (2021)  Significance of differential allelic expression (DAE) in phenotypic plasticity and evolutionary potential of microbial eukaryotes.  Quantitative Biology,  9(4):400-410.  Link

[43] Greenman, C., Penso-Dolfin, L., and Wu, T. (2020)  The complexity of genome rearrangement combinatorics under the infinite sites model.  Journal of Theoretical Biology,  501:110335. Link

[42] Choi, K.P., Thompson, A., and Wu, T. (2020) On cherry and pitchfork distributions of random rooted and unrooted phylogenetic trees.  Theoretical Population Biology, 132: 92-104. arXiv:2002.12643

[41] Janssen, R., Jones, M., Kelk, S.,  Stamoulis, G., and Wu, T. (2019)  Treewidth of display graphs: bounds, brambles and applications.  Journal of Graph Algorithms and Applications, 23(4): 715-743.  PDF  arXiv:1809.00907

[40] Huber, K.T., Moulton, V., and Wu, T. (2019) Hierarchies from lowest stable ancestors in nonbinary phylogenetic networks. Journal of Classification, 36: 200-231.

[39] Huber, K.T., Moulton, V., Semple, C., and Wu, T. (2018) Quarnet inference rules for level-1 networks. Bulletin of Mathematical Biology,  80: 2137-2153. arXiv:1711.06720

[38] Kelk, S.,  Stamoulis, G., and Wu, T. (2018) Treewidth distance on phylogenetic trees. Theoretical Computer Science, 731: 99-117. arXiv:1703.10840

[37] Francis, A.,  Huber, K.T., Moulton, V., and Wu, T. (2018) Bounds for phylogenetic network space metrics. Journal of Mathematical Biology, 76: 1229-1248.  arXiv:1702.05609

[36] Moulton, V., Spillner, A., and Wu, T. (2018) UPGMA and the normalized equidistant minimum evolution problem.  Theoretical Computer Science, 721: 1-15.   arXiv:1704.00479

[35] Bastkowski, S., Mapleson, D.,  Spillner, A., Wu, T., Balvociute, M.,  and  Moulton, V. (2018) SPECTRE: a Suite of PhylogEnetiC Tools for Reticulate Evolution. Bioinformatics, 34: 1056-1057.

[34] Huber, K.T., van Iersel, L., Moulton, V., Scornavacca, C., and Wu, T. (2017) Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets. Algorithmica, 77: 173-200. PDF.   arXiv:1411.6804

[33] Moulton, V., Oldman, J., and Wu, T. (2017) A cubic-time algorithm for computing the trinet distance between level-1 networks.  Information Processing Letters, 123: 36-41.  arXiv:1703.05097

[32] van Iersel, L., Moulton, V., de Swart, E., and Wu, T. (2017) Binets: fundamental building blocks for phylogenetic networks. Bulletin of Mathematical Biology, 79: 1135-1154. pdf arXiv:1701.08995

[31] Mock, T et al. (2017)   Evolutionary genomics of a cold-adapted diatom: Fragilariopsis cylindrus.  Nature, 541:536-540.  Link

[30] Oldman, J*., Wu, T*., van Iersel, L., and  Moulton, V. (2016) TriLoNet: Piecing together small networks to reconstruct reticulate evolutionary histories. (* indicates equal contribution.)  Molecular Biology and Evolution, 33: 2151-2162. software  Link

[29] Kelk, S., Fischer, M., Moulton, V., and Wu, T. (2016) Reduction rules for the maximum parsimony distance on phylogenetic tree.  Theoretical Computer Sciences, 646: 1-15. arXiv:1512.07459

[28] Huber, K.T., Moulton, V., Steel, M., and Wu, T. (2016) Folding and unfolding phylogenetic trees and networks. Journal of Mathematical Biology, 73: 1761-1780. DOI arXiv:1506.0443814

[27] Wu, T. and Choi, K.P. (2016) On joint subtree distributions under two evolutionary models.  Theoretical Population Biology, 108: 13-23. Link arXiv:1508.031394

[26] Huber, K.T., Moulton, V., and Wu, T. (2016) Transforming phylogenetic networks: Moving beyond tree space. Journal of Theoretical Biology, 404: 30-39.  arXiv:1601.01788  Link

[25] Bastkowski, S., Moulton, V.,  Spillner, A. and Wu. T. (2016) The minimum evolution problem is hard: A link between tree inference and graph clustering problems.  Bioinformatics, 32(4): 518-522. Link

[24] Huber, K.T., Linz, S., Moulton, V., and Wu, T. (2016) Space of phylogenetic networks from generalized nearest-neighbor interchange operations.  Journal of Mathematical Biology, 72(3): 699-725. Link:

[23] Huber, K.T., van Iersel, L., Moulton, V., and Wu, T. (2015) How much information is needed to infer reticulate evolutionary histories? Systematic Biology, 64: 102-111. pdf

[22] Zhu, S., Than, C.,  and Wu, T. (2015)  Clades and clans: a comparison study of two evolutionary models. Journal of Mathematical Biology, 71: 99-124. Link  arXiv:1407.3880  

[21] Herrmann, S.,  Koolen, J.,  Lesser, A.,  Moulton, V., and Wu, T. (2015) Optimal realisations of two-dimensional, totally-decomposable metrics.  Discrete Mathematics, 338: 1289-1299.   arXiv:1108.0290 

[20] Penso-Dolfin, L., Wu, T., and Greenman, C. (2015) The combinatorics of tandem duplication. Discrete Applied Mathematics, 194: 1-22.

[19] Moulton, V. and Wu, T. (2015) A parsimony-based metric for phylogenetic trees. Advance in Applied Mathematics, 66: 22-45. Link

[18] Bastkowski, S., Moulton, V.,  Spillner, A. and Wu. T. (2015) Neighborhoods of trees in circular ordering.  Bulletin of Mathematical Biology, 77: 46-70.   Erratum  Link

[17] Huber, K.T., Moulton, V., Semple, C., and Wu, T. (2014) Representing partitions on trees. SIAM J. Discrete Mathematics, 28(3): 1152-1172. arXiv:1405.2225

[16] Wade, A.S.I,  Barov, B.,  Burfield, I.J.,  Gregory, R.D.,  Norris, K., Wu, T., and Butler S.J. (2014) A niche-based framework to assess current monitoring of European forest birds and guide indicator species' selection. PLoS One, 9(5): e97217  pdf software

[15] Li, S.,  Choi, K.P.,  Wu, T., and Zhang, L.X. (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: 1412-1421.   arXiv:1203.2430  (An extended abstract appeared in Proc. ISBRA'12, LNBI 7292, 165-176).

[14] Dress, A., Moulton, V., Spillner, A., and Wu, T. (2013)  Obtaining splits from cut sets of tight spans. Discrete Applied Mathematics 161: 1409-1420.

[13] Humphries, P. and Wu, T.  (2013) The neighborhood of tree operations. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10: 721-728.  arXiv:1202.2203

 [12] Li, S.,  Choi, K.P.,  and Wu, T.  (2013) Degree distribution of large networks generated by the partial duplication model. Theoretical Computer Science 476: 94-108.

 [11] Grunewald, S.,  Koolen, J.,  Moulton, V.,  and Wu, T.  (2012) The size of 3-compatible, weakly compatible split systems.  Journal of Applied Mathematics and Computing 40: 249-259.

 [10] Koolen, J.,  Lesser, A.,  Moulton, V., and Wu, T. (2012)  Injective optimal realizations of metrics. Discrete Mathematics 312: 1602-1610. 

 [9] Wu, T. and Zhang L.X. (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):S7  (Also presented at RECOMB CG, 2011)

 [8] Szekely, L, Wang, H. and Wu, T. (2011) The sum of the distances between leaves of a tree and the ‘semi-regular’ property.  Discrete Mathematics 311: 1197-1203.

 [7] Dress, A.,  Moulton. V., Steel, M. and Wu, T. (2010) Species, clusters and the ‘Tree of Life’: A graph-theoretic perspective. Journal of Theoretical Biology 265: 532-542.

 [6] Cameron, P. and Wu, T. (2010) The complexity of the weight problem for permutation groups and matrix groups.  Discrete Mathematics 310: 408-416.

 [5] Dress, A.,  Wu, T., and Xu, X. (2010)  A note on single-linkage equivalence.  Applied Mathematics Letters 23: 432-435.

 [4] Wu, T., Moulton, V and Steel, M. (2009) Refining phylogenetic trees given additional data: An algorithm based on parsimony.  IEEE/ACM Transactions on Computational Biology and Bioinformatics 6: 118-125.

 [3] Dress, A., Moulton, V., Spillner, A. and Wu, T. (2009)  Barriers in metric spaces.  Applied Mathematics Letters 22: 1150-1153.

 [2] Buchheim, C., Cameron, P. and Wu, T. (2009)  On the subgroup distance problem.  Discrete Mathematics 309: 962-968.

 [1] Wu, T., Cameron, P., and Riis, S. (2009) On the guessing number of shift graphs. Journal of Discrete Algorithms 7: 220-226. 

Conference proceedings and book chapters

[7] Mock, T., Hodgkinson, K., Wu, T., Moulton, V., Duncan, A., Oosterhout, C. V., and Pichler, M., (2022)  Structure and Evolution of Diatom Nuclear Genes and Genomes. In The Molecular Life of Diatoms, 111-145, Springer. 

[6]  Zheng, Y., Wu, T., and Zhang, L.X. (2013) A linear-time algorithms for reconciliation of non-binary gene trees and binary species trees. Combinatorial Optimization and Application (COCOA) 2013:  190-201. (see also arXiv:1201.3995 ). 

[5] Li, S., Choi, K.P., Wu, T. and Zhang, L.X. (2012) Reconstruction of network evolutionary history     from extant network topology and duplication history. In: L. Bleris et al. (Eds.): International Symposium on Bioinformatics Research and Application (ISBRA) 2012,  LNBI 7292: 165-176.

[4]  Zhang, L.X.,   Ng, Y.K., Wu, T. and Zheng, Y. (2011) Network model and efficient method for detecting relative duplications or horizontal gene transfers. Proceedings of the 1st International Conference on Computational Advances in Biological and Medical Sciences, 227-232.

[3] Dress, A., Moulton, V., and Wu, T. (2010)  A topological approach to tree (re)-construction. In A. Dress, K-E Biebler, Cieslik D, and  A. Spillner, editors, The Maths of Flu, 59-75, Shaker Verlag, Aachen, Germany 2010. 

[2] Cameron. P., and Wu, T. (2007) The complexity of the weight problem for permutation groups. Electronic Notes in Discrete Mathematics 28 (2007), 109-116.

[1] Cameron. P., and Wu, T. (2007) A new characterization of balanced words. WORDS2007, Proceedings of the 6th International Conference on Words, 63-71.

Others

[2]  Dress, A., Moulton. V., Steel, M. and Wu, T.  On patchworks and hierarchies.  arXiv:1202.2460  

[1] Wu, T.  On regular configurations and disjoint cycles in shift graphs.  arXiv:0710.0125