Publications

Books

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

Journal Articles

  1. K.T. Huber, S. Linz, V. Moulton, C. Semple, Phylogenetic trees defined by at most three characters, submitted.
  2. N. Brettell, S. Jowett, J. Oxley, C. Semple, G. Whittle, What is a 4-connected matroid?, submitted.
  3. M. Bordewich, C. Semple, Quantifying the difference between phylogenetic diversity and diversity indices, Journal of Mathematical Biology, in press.
  4. E. Hogan, C. Semple, The excluded minors for the intersection of bicircular and lattice path matroids, European Journal of Combinatorics 118 (2024) 103923, 14 pp.
  5. K.T. Huber, L. van Iersel, R. Janssen, M. Jones, V. Moulton, Y. Murakami, C. Semple, Orienting undirected phylogenetic networks, Journal of Computer and System Sciences 140 (2024) 103480, 25 pp.
  6. J. Doecker, S. Linz, C. Semple, Hypercubes and Hamilton cycles of display sets of rooted phylogenetic networks, Advances in Applied Mathematics 152 (2024) 102595, 31 pp.
  7. N. Brettell, J. Oxley, C. Semple, G. Whittle, Excluded minors are almost fragile II: Essential elements, Journal of Combinatorial Theory, Series B 163 (2023) 272-307.
  8. N. Brettell, J. Oxley, C. Semple, G. Whittle, The excluded minors for 2- and 3-regular matroids, Journal of Combinatorial Theory, Series B 163 (2023) 133-218.
  9. N. Brettell, C. Semple, G. Toft, Cyclic matroids, SIAM Journal on Discrete Mathematics 37 (2023) 1212-1236.
  10. G. Drummond, C. Semple, A splitter theorem for elastic elements in 3-connected matroids, Electronic Journal of Combinatorics 30 (2023) #P2.12, 20 pp.
  11. K. Manson, C. Semple, M. Steel, Counting and optimising maximum phylogenetic diversity sets, Journal of Mathematical Biology 85 (2022) 11, 23 pp.
  12. M. Bordewich, C. Semple, K. Wicke, On the complexity of optimising variants of phylogenetic diversity on phylogenetic networks, Theoretical Computer Science 917 (2022) 66-80.
  13. S. Linz, C. Semple, Non-essential arcs in phylogenetic networks, Journal of Computer and System Sciences 128 (2022) 1-17.
  14. M. Bordewich, S. Linz, M. Owen, K. St John, C. Semple, K. Wicke, On the maximum agreement subtree conjecture for balanced trees, SIAM Journal on Discrete Mathematics 36 (2022) 336-354.
  15. C. Semple, G. Toft, Trinets encode orchard phylogenetic networks, Journal of Mathematical Biology 83 (2021) 28, 20 pp.
  16. G. Drummond, Z. Gershkoff, S. Jowett, C. Semple, J. Singh, Elastic elements in 3-connected matroids, Electronic Journal of Combinatorics 28 (2021) #P2.39, 15 pp.
  17. A. Bai, P.L. Erdos, C. Semple, M. Steel, Defining phylogenetic networks using ancestral profiles, Mathematical Biosciences 332 (2021) 108537, 7 pp.
  18. J. Doecker, S. Linz, C. Semple, Display sets of normal and tree-child networks, Electronic Journal of Combinatorics 28 (2021) #P1.8, 21 pp.
  19. S. Linz, C. Semple, Caterpillars on three and four leaves are sufficient to reconstruct binary normal networks, Journal of Mathematical Biology 81 (2020) 961-980.
  20. T. Fife, D. Mayhew, J. Oxley, C. Semple, The unbreakable frame matroids, SIAM Journal on Discrete Mathematics 34 (2020) 1522-1537.
  21. J. Doecker, B. Dorn, S. Linz, C. Semple, Placing quantified variants of 3-SAT and Not-All-Equal 3-SAT in the polynomial hierarchy, Theoretical Computer Science 822 (2020) 72-91.
  22. N. Brettell, B. Clark, J. Oxley, C. Semple, G. Whittle, Excluded minors are almost fragile, Journal of Combinatorial Theory, Series B 140 (2020) 263-322.
  23. J. Doecker, S. Linz, C. Semple, Displaying trees across two phylogenetic networks, Theoretical Computer Science 796 (2019) 129-146.
  24. N. Brettell, D. Chun, T. Fife, C. Semple, Matroids with a cyclic arrangement of circuits and cocircuits, European Journal of Combinatorics 81 (2019) 195-209.
  25. J. Oxley, C. Semple, G. Whittle, A splitter theorem for 3-connected 2-polymatroids, Electronic Journal of Combinatorics 26 (2019) #P2.37, 95 pp.
  26. P.L. Erdos, C. Semple, M. Steel, A class of phylogenetic networks reconstructable from ancestral profiles, Mathematical Biosciences 313 (2019) 33-40.
  27. J.C. Pons, C. Semple, M. Steel, Tree-based networks: Characterisations, metrics, and support trees, Journal of Mathematical Biology 78 (2019) 899-918.
  28. S. Linz, C. Semple, Attaching leaves and picking cherries to characterise the hybridisation number for a set of phylogenies, Advances in Applied Mathematics 105 (2019) 102-129.
  29. J. Oxley, S. Pfeil, C. Semple, G. Whittle, Matroids with many small circuits and cocircuits, Advances in Applied Mathematics 105 (2019) 1-24.
  30. M. Bordewich, C. Semple, A universal tree-based network with the minimum number of reticulations, Discrete Applied Mathematics 250 (2018) 357-362.
  31. M. Bordewich, K.T. Huber, V. Moulton, C. Semple, Recovering normal networks from shortest inter-taxa distance information, Journal of Mathematical Biology 77 (2018) 571-594.
  32. M. Bordewich, I.M. Deutschmann, M. Fischer, E. Kasbohm, C. Semple, M. Steel, On the information content of discrete phylogenetic characters, Journal of Mathematical Biology 77 (2018) 527-544.
  33. C. Semple, J. Simpson, When is a phylogenetic network simply an amalgamation of two trees?, Bulletin of Mathematical Biology 80 (2018) 2338-2348.
  34. K.T. Huber, V. Moulton, C. Semple, T. Wu, Quarnet inference rules for level-1 networks, Bulletin of Mathematical Biology 80 (2018) 2137-2153.
  35. M. Bordewich, C. Semple, N. Tokac, Constructing tree-child networks from distance matrices, Algorithmica 80 (2018) 2240-2259.
  36. A. Francis, C. Semple, M. Steel, New characterisations of tree-based networks and proximity measures, Advances in Applied Mathematics 93 (2018) 93-107.
  37. M. Bordewich, S. Linz, C. Semple, Lost in space? Generalising subtree prune and regraft to spaces of phylogenetic networks, Journal of Theoretical Biology 423 (2017) 1-12.
  38. C. Bryant, M. Fischer, S. Linz, C. Semple, On the quirks of maximum parsimony and likelihood on phylogenetic networks, Journal of Theoretical Biology 417 (2017) 100-108.
  39. C. Semple, Size of a phylogenetic network, Discrete Applied Mathematics 217 (2017) 362-367.
  40. M. Bordewich, C. Semple, Determining phylogenetic networks from inter-taxa distances, Journal of Mathematical Biology 73 (2016) 283-303.
  41. M. Bordewich, C. Semple, Reticulation-visible networks, Advances in Applied Mathematics 78 (2016) 114-141.
  42. J. Oxley, C. Semple, G. Whittle, A Wheels-and-Whirls Theorem for 3-connected 2-polymatroids, SIAM Journal on Discrete Mathematics 30 (2016) 493-524.
  43. J. Oxley, C. Semple, G. Whittle, Determining a binary matroid from its small circuits, Electronic Journal of Combinatorics (2016) #P1.26, 7 pp.
  44. C. Semple, Phylogenetic networks with every embedded phylogenetic tree a base tree, Bulletin of Mathematical Biology 78 (2016) 132-137.
  45. M. Bordewich, C. Semple, Defining a phylogenetic tree with the minimum number of r-state characters, SIAM Journal on Discrete Mathematics 29 (2015) 835-853.
  46. C. McDiarmid, C. Semple, D. Welsh, Counting phylogenetic networks, Annals of Combinatorics 19 (2015) 205-224.
  47. N. Brettell, C. Semple, An algorithm for constructing a k-tree for a k-connected matroid, Annals of Combinatorics 19 (2015) 29-78.
  48. C. Semple, D. Welsh, G. Whittle, Special issue in honour of James Oxley, Annals of Combinatorics 19 (2015) 1-5.
  49. P. Cordue, S. Linz, C. Semple, Phylogenetic networks that display a tree twice, Bulletin of Mathematical Biology 76 (2014) 2664-2679.
  50. K.T. Huber, V. Moulton, C. Semple, T. Wu, Representing partitions on trees, SIAM Journal on Discrete Mathematics 28 (2014) 1152-1172.
  51. N. Brettell, C. Semple, A splitter theorem relative to a fixed basis, Annals of Combinatorics 18 (2014) 1-20.
  52. S. Linz, K. St John, C. Semple, Optimizing tree and character compatibility across several phylogenetic trees, Theoretical Computer Science 513 (2013) 129-136.
  53. P.J. Humphries, S. Linz, C. Semple, Cherry picking: A characterization of the temporal hybridization number for a set of phylogenies, Bulletin of Mathematical Biology 75 (2013) 1879-1890.
  54. S. Linz, K. St John, C. Semple, Counting trees in a phylogenetic network is #P-complete, SIAM Journal on Computing 42 (2013) 1768-1776.
  55. P.J. Humphries, S. Linz, C. Semple, On the complexity of computing the temporal hybridization number for two phylogenies, Discrete Applied Mathematics 161 (2013) 871-880.
  56. V. Berry, O.R.P. Bininda-Emonds, C. Semple, Amalgamating source trees with different taxonomic levels, Systematic Biology 62 (2013) 231-249.
  57. J. Oxley, C. Semple, Constructing a 3-tree for a 3-connected matroid, Advances in Applied Mathematics 50 (2013) 176-200.
  58. L. Lowrance, J. Oxley, C. Semple, D. Welsh, On properties of almost all matroids, Advances in Applied Mathematics 50 (2013) 115-124.
  59. D. Mayhew, J. Oxley, C. Semple, Special issue in honor of Geoff Whittle, Advances in Applied Mathematics 50 (2013) 1-5.
  60. M. Dietrich, C. McCartin, C. Semple, Bounding the maximum size of a minimal definitive set of quartets, Information Processing Letters 112 (2012) 651-655.
  61. J. Oxley, C. Semple, G. Whittle, An upgraded Wheels-and-Whirls Theorem for 3-connected matroids, Journal of Combinatorial Theory, Series B 102 (2012) 610-637.
  62. M. Bordewich, C. Semple, Budgeted Nature Reserve Selection with diversity feature loss and arbitrary split systems, Journal of Mathematical Biology 64 (2012) 69-85.
  63. J. Collins, S. Linz, C. Semple, Quantifying hybridization in realistic time, Journal of Computational Biology 18 (2011) 1305-1318.
  64. S. Linz, C. Semple, A cluster reduction for computing the subtree distance between phylogenies, Annals of Combinatorics 15 (2011) 465-484.
  65. J. Oxley, C. Semple, G. Whittle, Exposing 3-separations in 3-connected matroids, Advances in Applied Mathematics 47 (2011) 463-508.
  66. B. Faller, C. Semple, D. Welsh, Optimizing phylogenetic diversity with ecological constraints., Annals of Combinatorics 15 (2011) 255-266.
  67. L. van Iersel, C. Semple, M. Steel, Quantifying the extent of lateral gene transfer required to avert a `Genome of Eden', Bulletin of Mathematical Biology 72 (2010) 1783-1798.
  68. L. van Iersel, C. Semple, M. Steel, Locating a tree in a phylogenetic network, Information Processing Letters 110 (2010) 1037-1043.
  69. S. Linz, C. Semple, T. Stadler, Analyzing and reconstructing reticulation networks under timing constraints, Journal of Mathematical Biology 61 (2010) 715-737.
  70. M. Bordewich, C. Semple, A. Spillner, Optimizing phylogenetic diversity across two trees, Applied Mathematics Letters 22 (2009) 638-641.
  71. P.J. Humphries, C. Semple, Note on the hybridization number and subtree distance in phylogenetics, Applied Mathematics Letters 22 (2009) 611-615.
  72. S. Grunewald, K.T. Huber, V. Moulton, C. Semple, A. Spillner, Characterizing weak compatibility in terms of weighted quartets, Advances in Applied Mathematics 42 (2009) 329-341.
  73. S. Linz, C. Semple, Hybridization in non-binary trees, IEEE/ACM Transactions on Computational Biology and Bioinformatics 6 (2009) 30-45.
  74. M. Bordewich, A.G. Rodrigo, C. Semple, Selecting taxa to save or sequence: desirable criteria and a greedy solution, Systematic Biology 57 (2008) 825-834.
  75. S. Grunewald, P.J. Humphries, C. Semple, Quartet compatibility and the quartet graph, Electronic Journal of Combinatorics 15 (2008) #R103, 27 pp.
  76. M. Bordewich, C. McCartin, C. Semple, A 3-approximation algorithm for the subtree distance between phylogenies, Journal of Discrete Algorithms 6 (2008) 458-471.
  77. M. Bordewich, C. Semple, Nature reserve selection problem: a tight approximation algorithm, IEEE/ACM Transactions on Computational Biology and Bioinformatics 5 (2008) 275-280.
  78. J. Oxley, C. Semple, G. Whittle, A chain theorem for matroids, Journal of Combinatorial Theory, Series B 98 (2008) 447-483.
  79. J. Oxley, C. Semple, G. Whittle, Maintaining 3-connectivity relative to a fixed basis, Advances in Applied Mathematics 41 (2008) 1-9.
  80. C. Semple, D. Welsh, Negative correlation in graphs and matroids, Combinatorics, Probability and Computing 17 (2008) 423-435.
  81. S. Grunewald, K.T. Huber, V. Moulton, C. Semple, Encoding phylogenetic trees in terms of weighted quartets, Journal of Mathematical Biology 56 (2008) 465-477.
  82. J. Oxley, C. Semple, G. Whittle, Wild triangles in 3-connected matroids, Journal of Combinatorial Theory, Series B 98 (2008) 291-323.
  83. M. Bordewich, C. Semple, Computing the hybridization number of two phylogenetic trees is fixed-parameter tractable, IEEE/ACM Transactions on Computational Biology and Bioinformatics 4 (2007) 458-466.
  84. M. Bordewich, S. Linz, K. St. John, C. Semple, A reduction algorithm for computing the hybridization number of two trees, Evolutionary Bioinformatics 3 (2007) 86-98.
  85. V. Moulton, C. Semple, M. Steel, Optimizing phylogenetic diversity under constraints, Journal of Theoretical Biology 246 (2007) 186-194.
  86. M. Bordewich, C. Semple, Computing the minimum number of hybridization events for a consistent evolutionary history, Discrete Applied Mathematics 155 (2007) 914-928.
  87. J. Oxley, C. Semple, G. Whittle, The structure of the 3-separations of 3-connected matroids II, European Journal of Combinatorics 28 (2007) 1239-1261.
  88. R. Hall, J. Oxley, C. Semple, The structure of 3-connected matroids of path-width three , European Journal of Combinatorics 28 (2007) 964-989.
  89. M. Bordewich, C. Semple, M. Steel, Identifying X-trees with few characters, Electronic Journal of Combinatorics 13 (2006) #R83, 11 pp.
  90. V. Berry, C. Semple, Fast computation of supertrees for compatible phylogenies with nested taxa, Systematic Biology 55 (2006) 270-288.
  91. M. Bordewich, G. Evans, C. Semple, Extending the limits of supertree methods, Annals of Combinatorics 10 (2006) 31-51.
  92. M. Baroni, C. Semple, M. Steel, Hybrids in real time, Systematic Biology 55 (2006) 46-56.
  93. C. Semple, M. Steel, Unicyclic networks: compatibility and enumeration, IEEE/ACM Transactions on Computational Biology and Bioinformatics 3 (2006) 84-91.
  94. P. Daniel, C. Semple, A class of general supertree methods for nested taxa, SIAM Journal on Discrete Mathematics 19 (2005) 463-480.
  95. M. Bordewich, K.T. Huber, C. Semple, Identifying phylogenetic trees, Discrete Mathematics 300 (2005) 30-43.
  96. M. Baroni, S. Grunewald, V. Moulton, C. Semple, Bounding the number of hybridisation events for a consistent evolutionary history, Journal of Mathematical Biology 51 (2005) 171-182.
  97. R. Hall, J. Oxley, C. Semple, The structure of equivalent 3-separations in a 3-connected matroid, Advances in Applied Mathematics 35 (2005) 123-181.
  98. K.T. Huber, V. Moulton, C. Semple, M. Steel, Recovering a phylogenetic tree using pairwise closure operations, Applied Mathematics Letters 18 (2005) 361-366.
  99. M. Bordewich, C. Semple, On the computational complexity of the rooted subtree prune and regraft distance, Annals of Combintorics 8 (2004) 409-423.
  100. M. Baroni, C. Semple, M. Steel, A framework for representing reticulate evolution, Annals of Combinatorics 8 (2004) 391-408.
  101. J. Oxley, C. Semple, G. Whittle, The structure of the 3-separations of 3-connected matroids, Journal of Combinatorial Theory, Series B 92 (2004) 257-293.
  102. C. Semple, P. Daniel, W. Hordijk, R.D.M. Page, M. Steel, Supertree algorithms for ancestral divergence dates and nested taxa, Bioinformatics 20 (2004) 2355-2360.
  103. K.T. Huber, V. Moulton, C. Semple, Replacing cliques by stars in quasi-median graphs, Discrete Applied Mathematics 143 (2004) 194-203.
  104. M. Bordewich, C. Semple, J. Talbot, Counting consistent phylogenetic trees is #P-complete, Advances in Applied Mathematics 33 (2004) 416-430.
  105. C. Semple, M. Steel, Cyclic permutations and evolutionary trees, Advances in Applied Mathematics 32 (2004) 669-680.
  106. R. Hall, J. Oxley, C. Semple, G. Whittle, Fork-decompositions of matriods, Advances in Applied Mathematics 32 (2004) 523-575.
  107. C. Semple, Reconstructing minimal rooted trees, Discrete Applied Mathematics 127 (2003) 489-503.
  108. R. Hall, J. Oxley, C. Semple, G. Whittle, On matroids of branch-width three, Journal of Combinatorial Theory, Series B 86 (2002) 148-171.
  109. C. Semple, M. Steel, A characterization for a set of partial partitions to define an X-tree, Discrete Mathematics 247 (2002) 169-186.
  110. C. Semple, M. Steel, Tree reconstruction from multi-state characters, Advances in Applied Mathematics 28 (2002) 169-184.
  111. J. Oxley, C. Semple, D. Vertigan, G. Whittle, Infinite antichains of matroids with character set {p}, Discrete Mathematics 242 (2002) 175-185.
  112. C. Semple, M. Steel, A supertree method for rooted trees, Discrete Applied Mathematics 105 (2000) 147-158.
  113. J. Oxley, C. Semple, D. Vertigan, Generalized delta-wye exchange and k-regular matroids, Journal of Combinatorial Theory, Series B 79 (2000) 1-65.
  114. C. Semple, On maximum-sized k-regular matroids, Graphs and Combinatorics 15 (1999) 441-462.
  115. C. Semple, M. Steel, Tree representations of non-symetric group-valued proximities, Advances in Applied Mathematics 23 (1999) 300-321.
  116. C. Semple, G. Whittle, Partial fields and matroid representation, Advances in Applied Mathematics 17 (1996) 184-208.

Book Chapters

  1. C. Semple, Hybridization networks, in: O. Gascuel, M. Steel (Eds.), Reconstructing Evolution: New Mathematical and Computational Advances, Oxford University Press, 2007, pp. 277-314.
  2. P. Daniel, C. Semple, Supertree algorithms for nested taxa, in: O. Bininda-Emonds (Ed.), Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, Computational Biology Series, Kluwer, Dordrecht, 2004, pp. 151-171.
  3. D. Bryant, C. Semple, M. Steel, Supertree methods for ancestral divergence dates and other applications, in: O. Bininda-Edmonds (Ed.), Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, Computational Biology Series, Kluwer, Dordrecht, 2004, pp. 129-150.
  4. C. Semple, G. Whittle, On representable matroids having neither U2,5- nor U3,5-minors, in: J.E. Bonin et al. (Eds.), Matroid Theory, Contemporary Mathematics, 197, American Mathematical Society, Providence, 1996, pp. 377-386.

Refereed Conference Proceedings

  1. C. Semple, M. Steel, Tree reconstruction via a closure operation on partial splits, in: O. Gascuel, M.-F. Sagot (Eds.), Computational Biology: Proceedings of Journées Ouvertes: Biologie, Informatique et Mathématiques, Lecture Notes in Computer Science, 2066, Springer-Verlag, Berlin, 2001, pp. 126-134.
  2. C. Semple, k-regular matroids, in: D.S. Bridges et al. (Eds.), Combinatorics, Complexity, and Logic: Proceedings of DMTCS'96, Discrete Mathematics and Theoretical Computer Science Series, Springer-Verlag, Singapore, 1997, pp. 376-386.

Theses

  1. C. Semple, k-regular matroids, PhD thesis, Victoria University of Wellington, 1998.

Other Items

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