## Publications

### Books

- Semple, C. and Steel, M. (2003).
*Phylogenetics*. Oxford University Press. Errata.

### Journal Articles

- Francis, A., Semple, C., and Steel, M. New characterisations of tree-based networks and proximity measures.
*Advances in Applied Mathematics*, in press. - Bordewich, M., Semple, C., and Tokac, N. Constructing tree-child networks from distance matrices.
*Algorithmica*, in press. - Bordewich, M., Linz, S., and Semple, C. (2017). Lost in space? Generalising subtree prune and regraft to spaces of phylogenetic networks.
*Journal of Theoretical Biology*, 423, 1-12. - Bryant, C., Fischer, M., Linz, S., and Semple, C. (2017). On the quirks of maximum parsimony and likelihood on phylogenetic networks.
*Journal of Theoretical Biology*, 417, 100-108. - Semple, C. (2017). Size of a phylogenetic network.
*Discrete Applied Mathematics*, 217, 362-367. - Bordewich, M. and Semple, C. (2016). Determining phylogenetic networks from inter-taxa distances.
*Journal of Mathematical Biology*, 73, 283-303. - Bordewich, M. and Semple, C. (2016). Reticulation-visible networks.
*Advances in Applied Mathematics*, 78, 114-141. - Oxley, J., Semple, C., and Whittle, G. (2016). A Wheels-and-Whirls Theorem for 3-connected 2-polymatroids.
*SIAM Journal on Discrete Mathematics*, 30, 493-524. - Oxley, J., Semple, C., and Whittle, G. (2016). Determining a binary matroid from its small circuits.
*Electronic Journal of Combinatorics*, P1.26. - Semple, C. (2016). Phylogenetic networks with every embedded phylogenetic tree a base tree.
*Bulletin of Mathematical Biology*, 78, 132-137. - Bordewich, M. and Semple, C. (2015). Defining a phylogenetic tree with the minimum number of
*r*-state characters.*SIAM Journal on Discrete Mathematics*, 29, 835-853. - McDiarmid, C., Semple, C., and Welsh, D. (2015). Counting phylogenetic networks.
*Annals of Combinatorics*, 19, 205-224. - Brettell, N. and Semple, C. (2015). An algorithm for constructing a
*k*-tree for a*k*-connected matroid.*Annals of Combinatorics*, 19, 29-78. - Semple, C., Welsh, D., and Whittle, G. (2015). Special issue in honour of James Oxley.
*Annals of Combinatorics*, 19, 1-5. - Cordue, P., Linz, S., and Semple, C. (2014). Phylogenetic networks that display a tree twice.
*Bulletin of Mathematical Biology*, 76, 2664-2679. - Huber, K. T., Moulton, V., Semple, C., and Wu, T. (2014). Representing partitions on trees.
*SIAM Journal on Discrete Mathematics*, 28, 1152-1172. - Brettell, N. and Semple, C. (2014). A splitter theorem relative to a fixed basis.
*Annals of Combinatorics*, 18, 1-20. - Linz, S., St John, K., and Semple, C. (2013). Optimizing tree and character compatibility across several phylogenetic trees.
*Theoretical Computer Science*, 513, 129-136. - Humphries, P. J., Linz, S., and Semple, C. (2013). Cherry picking: A characterization of the temporal hybridization number for a set of phylogenies.
*Bulletin of Mathematical Biology*, 75, 1879-1890. - Linz, S., St John, K., and Semple, C. (2013). Counting trees in a phylogenetic network is #P-complete.
*SIAM Journal on Computing*, 42, 1768-1776. - Humphries, P. J., Linz, S., and Semple, C. (2013). On the complexity of computing the temporal hybridization number for two phylogenies.
*Discrete Applied Mathematics*, 161, 871-880. - Berry, V., Bininda-Emonds, O. R. P., and Semple, C. (2013). Amalgamating source trees with different taxonomic levels.
*Systematic Biology*, 62, 231-249. - Oxley, J. and Semple, C. (2013). Constructing a 3-tree for a 3-connected matroid.
*Advances in Applied Mathematics*, 50, 176-200. - Lowrance, L., Oxley, J., Semple, C., and Welsh, D. (2013). On properties of almost all matroids.
*Advances in Applied Mathematics*, 50, 115-124. - Mayhew, D., Oxley, J., and Semple, C. (2013). Special issue in honor of Geoff Whittle.
*Advances in Applied Mathematics*, 50, 1-5. - Dietrich, M., McCartin, C., and Semple, C. (2012). Bounding the maximum size of a minimal definitive set of quartets.
*Information Processing Letters*, 112, 651-655. - Oxley, J., Semple, C., and Whittle, G. (2012). An upgraded Wheels-and-Whirls Theorem for 3-connected matroids.
*Journal of Combinatorial Theory, Series B*, 102, 610-637. - Bordewich, M. and Semple, C. (2012). Budgeted Nature Reserve Selection with diversity feature loss and arbitrary split systems.
*Journal of Mathematical Biology*, 64, 69-85. - Collins, J., Linz, S., and Semple, C. (2011). Quantifying hybridization in realistic time.
*Journal of Computational Biology*, 18, 1305-1318. - Linz, S. and Semple, C. (2011). A cluster reduction for computing the subtree distance between phylogenies.
*Annals of Combinatorics*,15, 465-484. - Oxley, J., Semple, C., and Whittle, G. (2011). Exposing 3-separations in 3-connected matroids.
*Advances in Applied Mathematics*, 47, 463-508. - Faller, B., Semple, C., and Welsh, D. (2011). Optimizing phylogenetic diversity with ecological constraints.
*Annals of Combinatorics*, 15, 255-266. - van Iersel, L., Semple, C., and Steel, M. (2010). Quantifying the extent of lateral gene transfer required to avert a `Genome of Eden'.
*Bulletin of Mathematical Biology*, 72, 1783-1798. - van Iersel, L., Semple, C., and Steel, M. (2010). Locating a tree in a phylogenetic network.
*Information Processing Letters*, 110, 1037-1043. - Linz, S., Semple, C., and Stadler, T. (2010). Analyzing and reconstructing reticulation networks under timing constraints.
*Journal of Mathematical Biology*, 61, 715-737. - Bordewich, M., Semple, C., and Spillner, A. (2009). Optimizing phylogenetic diversity across two trees.
*Applied Mathematics Letters*, 22, 638-641. - Humphries, P. J. and Semple, C. (2009). Note on the hybridization number and subtree distance in phylogenetics.
*Applied Mathematics Letters*, 22, 611-615. - Grunewald, S., Huber, K. T., Moulton, V., Semple, C., Spillner, A. (2009). Characterizing weak compatibility in terms of weighted quartets.
*Advances in Applied Mathematics*, 42, 329-341. - Linz, S. and Semple, C. (2009). Hybridization in non-binary
trees.
*IEEE/ACM Transactions on Computational Biology and Bioinformatics*, 6, 30-45. - Bordewich, M., Rodrigo, A. G., and Semple, C. (2008). Selecting taxa to save or sequence: desirable criteria and a greedy solution.
*Systematic Biology*, 57, 825-834. - Grunewald, S., Humphries, P. J., and Semple, C. (2008). Quartet compatibility and the quartet graph.
*Electronic Journal of Combinatorics*, 15, R103. - Bordewich, M., McCartin, C., and Semple, C. (2008). A 3-approximation algorithm for the subtree distance between phylogenies.
*Journal of Discrete Algorithms*, 6, 458-471. - Bordewich, M. and Semple, C. (2008). Nature reserve selection problem: a tight approximation algorithm.
*IEEE/ACM Transactions on Computational Biology and Bioinformatics*, 5, 275-280. - Oxley, J., Semple, C., and Whittle, G. (2008). A chain theorem for matroids.
*Journal of Combinatorial Theory, Series B*, 98, 447-483. - Oxley, J., Semple, C., and Whittle, G. (2008). Maintaining 3-connectivity relative to a fixed basis.
*Advances in Applied Mathematics*, 41, 1-9. - Semple, C. and Welsh, D. (2008). Negative correlation in graphs and matroids.
*Combinatorics, Probability and Computing*, 17, 423-435. - Grunewald, S., Huber, K. T., Moulton, V., and Semple, C. (2008). Encoding phylogenetic trees in terms of weighted quartets.
*Journal of Mathematical Biology*, 56, 465-477. - Oxley, J., Semple, C., and Whittle, G. (2008). Wild triangles in 3-connected matroids.
*Journal of Combinatorial Theory, Series B*, 98, 291-323. - Bordewich, M. and Semple, C. (2007). Computing the hybridization number of two phylogenetic trees is fixed-parameter tractable.
*IEEE/ACM Transactions on Computational Biology and Bioinformatics*, 4, 458-466. - Bordewich, M., Linz, S., St. John, K., and Semple, C. (2007). A reduction algorithm for computing the hybridization number of two trees.
*Evolutionary Bioinformatics*, 3, 86-98. - Moulton, V., Semple, C., and Steel, M. (2007). Optimizing phylogenetic diversity under constraints.
*Journal of Theoretical Biology*, 246, 186-194. - Bordewich, M. and Semple, C. (2007). Computing the minimum number of hybridization events for a consistent evolutionary history.
*Discrete Applied Mathematics*, 155, 914-928. - Oxley, J., Semple, C., and Whittle, G. (2007). The structure of the 3-separations of 3-connected matroids II.
*European Journal of Combinatorics*, 28, 1239-1261. - Hall, R., Oxley, J., and Semple, C. (2007). The structure of 3-connected matroids of path-width three .
*European Journal of Combinatorics*, 28, 964-989. - Bordewich, M., Semple, C., and Steel, M. (2006). Identifying
*X*-trees with few characters.*Electronic Journal of Combinatorics*, 13, R83. - Berry, V. and Semple, C. (2006). Fast computation of supertrees for compatible phylogenies with nested taxa.
*Systematic Biology*, 55, 270-288. - Bordewich, M., Evans, G., and Semple, C. (2006). Extending the limits of supertree methods.
*Annals of Combinatorics*, 10, 31-51. - Baroni, M., Semple, C., and Steel, M. (2006). Hybrids in real time.
*Systematic Biology*, 55, 46-56. - Semple, C. and Steel, M. (2006). Unicyclic networks: compatibility and enumeration.
*IEEE/ACM Transactions on Computational Biology and Bioinformatics*, 3, 84-91. - Daniel, P. and Semple, C. (2005). A class of general supertree methods for nested taxa.
*SIAM Journal on Discrete Mathematics*, 19, 463-480. - Bordewich, M., Huber, K. T., and Semple, C. (2005). Identifying phylogenetic trees.
*Discrete Mathematics*, 300, 30-43. - Baroni, M., Grunewald, S., Moulton, V., and Semple, C. (2005). Bounding the number of hybridisation events for a consistent evolutionary history.
*Journal of Mathematical Biology*, 51, 171-182. - Hall, R., Oxley, J., and Semple, C. (2005). The structure of equivalent 3-separations in a 3-connected matroid.
*Advances in Applied Mathematics*, 35, 123-181. - Huber, K. T., Moulton, V., Semple, C., and Steel, M. (2005). Recovering a phylogenetic tree using pairwise closure operations.
*Applied Mathematics Letters*, 18, 361-366. - Bordewich, M. and Semple, C. (2004). On the computational complexity of the rooted subtree prune and regraft distance.
*Annals of Combintorics*, 8, 409-423. - Baroni M., Semple, C., and Steel, M. (2004). A framework for representing reticulate evolution.
*Annals of Combinatorics*, 8, 391-408. - Oxley, J., Semple, C., and Whittle, G. (2004). The structure of the 3-separations of 3-connected matroids.
*Journal of Combinatorial Theory, Series B*, 92, 257-293. - Daniel, P., Hordijk, W., Page, R. D. M., Semple, C., and Steel, M. (2004). Supertree algorithms for ancestral divergence dates and nested taxa.
*Bioinformatics*, 20, 2355-2360. - Huber, K. T., Moulton, V., and Semple, C. (2004). Replacing cliques by stars in quasi-median graphs.
*Discrete Applied Mathematics*, 143, 194-203. - Bordewich, M., Semple, C., and Talbot, J. (2004). Counting consistent phylogenetic trees is #P-complete.
*Advances in Applied Mathematics*, 33, 416-430. - Semple, C., and Steel, M. (2004). Cyclic permutations and evolutionary trees.
*Advances in Applied Mathematics*, 32, 669-680. - Hall, R., Oxley, J., Semple, C. , and Whittle, G. (2004). Fork-decompositions of matriods.
*Advances in Applied Mathematics*, 32, 523-575. - Semple, C. (2003). Reconstructing minimal rooted trees.
*Discrete Applied Mathematics*, 127, 489-503. - Hall, R., Oxley, J., Semple, C., and Whittle, G. (2002). On matroids of branch-width three.
*Journal of Combinatorial Theory, Series B*, 86, 148-171. - Semple, C. and Steel, M. (2002). A characterization for a set of partial partitions to define an
*X*-tree.*Discrete Mathematics*, 247, 169-186. - Semple, C. and Steel, M. (2002). Tree reconstruction from multi-state characters.
*Advances in Applied Mathematics*, 28, 169-184. - Oxley, J., Semple, C., Vertigan, D. and Whittle, G. (2002).
Infinite antichains of matroids with character
set {
*p*}.*Discrete Mathematics*, 242, 175-185. - Semple, C., and Steel, M. (2000). A supertree method for rooted trees.
*Discrete Applied Mathematics*, 105, 147-158. - Oxley, J., Semple, C., and Vertigan, D. (2000). Generalized delta-wye exchange and
*k*-regular matroids.*Journal of Combinatorial Theory, Series B*, 79, 1-65. - Semple, C. (1999). On maximum-sized
*k*-regular matroids.*Graphs and Combinatorics*, 15, 441-462. - Semple, C. and Steel, M. (1999). Tree representations of non-symetric group-valued proximities.
*Advances in Applied Mathematics*, 23, 300-321. - Semple, C. and Whittle, G. (1996). Partial fields and matroid representation.
*Advances in Applied Mathematics*, 17, 184-208.

### Book Chapters

- Semple, C. (2007). Hybridization networks. In
*Reconstructing Evolution: New Mathematical and Computational Advances*(eds O. Gascuel and M. Steel), Oxford University Press, pp. 277-314. - Daniel, P. and Semple, C. (2004). Supertree algorithms for nested taxa. In
*Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life*(ed. O. Bininda-Emonds), Computational Biology Series, Kluwer, pp. 151-171. - Bryant, D., Semple, C., and Steel, M. (2004). Supertree methods for ancestral divergence dates and other applications. In
*Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life*(ed. O. Bininda-Edmonds), Computational Biology Series, Kluwer, pp. 129-150. - Semple, C. and Whittle, G. (1996). On representable matroids having neither
*U*_{2,5}- nor*U*_{3,5}-minors. In*Matroid Theory*(eds. J.E. Bonin, J.G. Oxley, and B. Servatius), Contemporary Mathematics, 197, American Mathematical Society, Providence, pp. 377-386.

### Refereed Conference Proceedings

- Semple, C. and Steel, M. (2001). Tree reconstruction via a closure operation on partial splits. In
*Proceedings of Journées Ouvertes: Biologie, Informatique et Mathématiques*(eds. O. Gascuel and M.F. Sagot), Lecture Notes in Computer Science, Springer-Verlag, Berlin, pp. 126-134. - Semple, C. (1996).
*k*-regular matroids. In*Combinatorics, Complexity and Logic*(eds. D.S. Bridges*et al*.), Discrete Mathematics and Theoretical Computer Science Series, Springer-Verlag, Singapore, pp. 376-386.

### Theses

- Semple, C. (1998).
*k*-Regular Matroids. Unpublished PhD thesis, Victoria University of Wellington.

### Other Items

- Semple, C. and Steel, M. (2009). Mathematical aspects of the `Tree of Life'.
*Math Horizons*, 17, Feb 5-9.