Publications

Books

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


Journal Articles

  1. Francis, A., Semple, C., and Steel, M. New characterisations of tree-based networks and proximity measures. Advances in Applied Mathematics, in press.
  2. Bordewich, M., Semple, C., and Tokac, N. Constructing tree-child networks from distance matrices. Algorithmica, in press.
  3. 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.
  4. 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.
  5. Semple, C. (2017). Size of a phylogenetic network. Discrete Applied Mathematics, 217, 362-367.
  6. Bordewich, M. and Semple, C. (2016). Determining phylogenetic networks from inter-taxa distances. Journal of Mathematical Biology, 73, 283-303.
  7. Bordewich, M. and Semple, C. (2016). Reticulation-visible networks. Advances in Applied Mathematics, 78, 114-141.
  8. 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.
  9. Oxley, J., Semple, C., and Whittle, G. (2016). Determining a binary matroid from its small circuits. Electronic Journal of Combinatorics, P1.26.
  10. Semple, C. (2016). Phylogenetic networks with every embedded phylogenetic tree a base tree. Bulletin of Mathematical Biology, 78, 132-137.
  11. 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.
  12. McDiarmid, C., Semple, C., and Welsh, D. (2015). Counting phylogenetic networks. Annals of Combinatorics, 19, 205-224.
  13. Brettell, N. and Semple, C. (2015). An algorithm for constructing a k-tree for a k-connected matroid. Annals of Combinatorics, 19, 29-78.
  14. Semple, C., Welsh, D., and Whittle, G. (2015). Special issue in honour of James Oxley. Annals of Combinatorics, 19, 1-5.
  15. Cordue, P., Linz, S., and Semple, C. (2014). Phylogenetic networks that display a tree twice. Bulletin of Mathematical Biology, 76, 2664-2679.
  16. Huber, K. T., Moulton, V., Semple, C., and Wu, T. (2014). Representing partitions on trees. SIAM Journal on Discrete Mathematics, 28, 1152-1172.
  17. Brettell, N. and Semple, C. (2014). A splitter theorem relative to a fixed basis. Annals of Combinatorics, 18, 1-20.
  18. Linz, S., St John, K., and Semple, C. (2013). Optimizing tree and character compatibility across several phylogenetic trees. Theoretical Computer Science, 513, 129-136.
  19. 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.
  20. 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.
  21. 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.
  22. Berry, V., Bininda-Emonds, O. R. P., and Semple, C. (2013). Amalgamating source trees with different taxonomic levels. Systematic Biology, 62, 231-249.
  23. Oxley, J. and Semple, C. (2013). Constructing a 3-tree for a 3-connected matroid. Advances in Applied Mathematics, 50, 176-200.
  24. Lowrance, L., Oxley, J., Semple, C., and Welsh, D. (2013). On properties of almost all matroids. Advances in Applied Mathematics, 50, 115-124.
  25. Mayhew, D., Oxley, J., and Semple, C. (2013). Special issue in honor of Geoff Whittle. Advances in Applied Mathematics, 50, 1-5.
  26. 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.
  27. 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.
  28. 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.
  29. Collins, J., Linz, S., and Semple, C. (2011). Quantifying hybridization in realistic time. Journal of Computational Biology, 18, 1305-1318.
  30. Linz, S. and Semple, C. (2011). A cluster reduction for computing the subtree distance between phylogenies. Annals of Combinatorics,15, 465-484.
  31. Oxley, J., Semple, C., and Whittle, G. (2011). Exposing 3-separations in 3-connected matroids. Advances in Applied Mathematics, 47, 463-508.
  32. Faller, B., Semple, C., and Welsh, D. (2011). Optimizing phylogenetic diversity with ecological constraints. Annals of Combinatorics, 15, 255-266.
  33. 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.
  34. van Iersel, L., Semple, C., and Steel, M. (2010). Locating a tree in a phylogenetic network. Information Processing Letters, 110, 1037-1043.
  35. Linz, S., Semple, C., and Stadler, T. (2010). Analyzing and reconstructing reticulation networks under timing constraints. Journal of Mathematical Biology, 61, 715-737.
  36. Bordewich, M., Semple, C., and Spillner, A. (2009). Optimizing phylogenetic diversity across two trees. Applied Mathematics Letters, 22, 638-641.
  37. Humphries, P. J. and Semple, C. (2009). Note on the hybridization number and subtree distance in phylogenetics. Applied Mathematics Letters, 22, 611-615.
  38. 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.
  39. Linz, S. and Semple, C. (2009). Hybridization in non-binary trees. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6, 30-45.
  40. 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.
  41. Grunewald, S., Humphries, P. J., and Semple, C. (2008). Quartet compatibility and the quartet graph. Electronic Journal of Combinatorics, 15, R103.
  42. 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.
  43. 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.
  44. Oxley, J., Semple, C., and Whittle, G. (2008). A chain theorem for matroids. Journal of Combinatorial Theory, Series B, 98, 447-483.
  45. Oxley, J., Semple, C., and Whittle, G. (2008). Maintaining 3-connectivity relative to a fixed basis. Advances in Applied Mathematics, 41, 1-9.
  46. Semple, C. and Welsh, D. (2008). Negative correlation in graphs and matroids. Combinatorics, Probability and Computing, 17, 423-435.
  47. 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.
  48. Oxley, J., Semple, C., and Whittle, G. (2008). Wild triangles in 3-connected matroids. Journal of Combinatorial Theory, Series B, 98, 291-323.
  49. 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.
  50. 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.
  51. Moulton, V., Semple, C., and Steel, M. (2007). Optimizing phylogenetic diversity under constraints. Journal of Theoretical Biology, 246, 186-194.
  52. Bordewich, M. and Semple, C. (2007). Computing the minimum number of hybridization events for a consistent evolutionary history. Discrete Applied Mathematics, 155, 914-928.
  53. 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.
  54. 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.
  55. Bordewich, M., Semple, C., and Steel, M. (2006). Identifying X-trees with few characters. Electronic Journal of Combinatorics, 13, R83.
  56. Berry, V. and Semple, C. (2006). Fast computation of supertrees for compatible phylogenies with nested taxa. Systematic Biology, 55, 270-288.
  57. Bordewich, M., Evans, G., and Semple, C. (2006). Extending the limits of supertree methods. Annals of Combinatorics, 10, 31-51.
  58. Baroni, M., Semple, C., and Steel, M. (2006). Hybrids in real time. Systematic Biology, 55, 46-56.
  59. Semple, C. and Steel, M. (2006). Unicyclic networks: compatibility and enumeration. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 3, 84-91.
  60. Daniel, P. and Semple, C. (2005). A class of general supertree methods for nested taxa. SIAM Journal on Discrete Mathematics, 19, 463-480.
  61. Bordewich, M., Huber, K. T., and Semple, C. (2005). Identifying phylogenetic trees. Discrete Mathematics, 300, 30-43.
  62. 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.
  63. 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.
  64. 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.
  65. Bordewich, M. and Semple, C. (2004). On the computational complexity of the rooted subtree prune and regraft distance. Annals of Combintorics, 8, 409-423.
  66. Baroni M., Semple, C., and Steel, M. (2004). A framework for representing reticulate evolution. Annals of Combinatorics, 8, 391-408.
  67. 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.
  68. 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.
  69. Huber, K. T., Moulton, V., and Semple, C. (2004). Replacing cliques by stars in quasi-median graphs. Discrete Applied Mathematics, 143, 194-203.
  70. Bordewich, M., Semple, C., and Talbot, J. (2004). Counting consistent phylogenetic trees is #P-complete. Advances in Applied Mathematics, 33, 416-430.
  71. Semple, C., and Steel, M. (2004). Cyclic permutations and evolutionary trees. Advances in Applied Mathematics, 32, 669-680.
  72. Hall, R., Oxley, J., Semple, C. , and Whittle, G. (2004). Fork-decompositions of matriods. Advances in Applied Mathematics, 32, 523-575.
  73. Semple, C. (2003). Reconstructing minimal rooted trees. Discrete Applied Mathematics, 127, 489-503.
  74. 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.
  75. Semple, C. and Steel, M. (2002). A characterization for a set of partial partitions to define an X-tree. Discrete Mathematics, 247, 169-186.
  76. Semple, C. and Steel, M. (2002). Tree reconstruction from multi-state characters. Advances in Applied Mathematics, 28, 169-184.
  77. Oxley, J., Semple, C., Vertigan, D. and Whittle, G. (2002). Infinite antichains of matroids with character set {p}. Discrete Mathematics, 242, 175-185.
  78. Semple, C., and Steel, M. (2000). A supertree method for rooted trees. Discrete Applied Mathematics, 105, 147-158.
  79. 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.
  80. Semple, C. (1999). On maximum-sized k-regular matroids. Graphs and Combinatorics, 15, 441-462.
  81. Semple, C. and Steel, M. (1999). Tree representations of non-symetric group-valued proximities. Advances in Applied Mathematics, 23, 300-321.
  82. Semple, C. and Whittle, G. (1996). Partial fields and matroid representation. Advances in Applied Mathematics, 17, 184-208.

Book Chapters

  1. 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.
  2. 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.
  3. 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.
  4. Semple, C. and Whittle, G. (1996). On representable matroids having neither U2,5- nor U3,5-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

  1. 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.
  2. 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

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

Other Items

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