Publications

Peer-reviewed publications.

  1. J. Döcker and S. Linz. On the existence of a cherry-picking sequence, submitted.
  2. S. Linz and C. Semple. Attaching leaves and picking cherries to characterise the hybridisation number for a set of phylogenies, submitted.
  3. M. Bordewich, S. Linz, and C. Semple (2017). Lost in space? Generalising subtree prune and regraft to spaces of phylogenetic networks. Journal of Theoretical Biology, 423:1-12
  4.  C. Bryant, M. Fischer, S. Linz, and C. Semple (2017). On the quirks of maximum parsimony and likelihood on phylogenetic networks.  Journal of Theoretical Biology, 417:100-108.
  5. D. H. Huson and S. Linz. Autumn algorithm: computation of hybridization networks for realistic phylogenetic trees. Accepted for publication in IEEE/ACM Transactions on Computational Biology and Bioinformatics.
  6. K. T. Huber, S. Linz, V. Moulton, and T. Wu (2016). Spaces of phylogenetic networks from generalized nearest-neighbor interchange operations. Journal of Mathematical Biology72:699-725.
  7. L. van Iersel, S. Kelk, N. Lekić, and S. Linz (2016). Satisfying ternary permutation constraints by multiple linear orders or phylogenetic trees. Theoretical Computer Science, 609:1-21.
  8. P. Cordue, S. Linz, and C. Semple (2014). Phylogenetic networks that display a tree twice. Bulletin of Mathematical Biology, 76:2664-2679.
  9. M. Syvanen, B. Ericksen, S. Linz, and J. Ducore (2014). Quartet partitioning reveals hybrid origins of the Vertebrate. In Evolutionary Biology: Genome Evolution, Speciation, Coevolution and Origin of Life. Ed.: Pierre Pontarotti. Springer, pp. 191-205.
  10. S. Linz, K. St. John, and C. Semple (2013). Optimizing tree and character compatibility across several phylogenetic trees. Theoretical Computer Science, 513:129-136.
  11. P. J. Humphries, S. Linz, and C. Semple (2013). Cherry picking: a characterization of the temporal hybridization number for a set of phylogenies. Bulletin of Mathematical Biology, 75:1879-1890.
  12. S. Linz, K. St. John, and C. Semple (2013). Counting trees in a phylogenetic network is #P-complete. SIAM Journal on Computing, 42:1768-1776.
  13. S. Linz. Reticulation. In Brenner’s Encyclopedia of Genetics. Eds.: Stanley Maloy and Kelly Hughes. Academic Press, pp. 196-198, 2013, (invited).
  14. P. J. Humphries, S. Linz, and C. Semple (2013). On the complexity of computing the temporal hybridization number for two phylogenies. Discrete Applied Mathematics, 161:871-880.
  15. M. Steel, S. Linz, D. H. Huson, and M. J. Sanderson (2013). Identifying a species tree subject to random lateral gene transfer. Journal of Theoretical Biology, 322:81-93.
  16. L. van Iersel and S. Linz (2013). A quadratic kernel for computing the hybridization number of multiple trees. Information Processing Letters, 113:318-323.
  17. S. Kelk, L. van Iersel, N. Lekić, S. Linz, C. Scornavacca, and L. Stougie (2012). Cycle killer… qu’est-ce que c’est? On the comparative approximability of hybridization number and directed feedback vertex set. SIAM Journal on Discrete Mathematics, 26:1635–1656.
  18. C. Scornavacca, S. Linz, and B. Albrecht (2012). A first step toward computing all hybridization networks for two rooted binary phylogenetic trees. Journal of Computational Biology, 19:1227-1242.
  19. M. L. Bonet, S. Linz, and K. St. John (2012). The complexity of finding multiple solutions to Betweenness and Quartet Compatibility. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9:273-285.
  20. J. Collins, S. Linz, and C. Semple (2011). Quantifying hybridization in realistic time. Journal of Computational Biology, 18:1305-1318.
  21. S. Linz and C. Semple (2011). A cluster reduction for computing the subtree distance between phylogenies. Annals of Combinatorics, 15:465-484.
  22. S. Linz. (2010). On Hill et al’s conjecture for calculating the subtree prune and regraft distance between phylogenies. BMC Evolutionary Biology, 10:334.
  23. S. Linz, C. Semple, and T. Stadler (2010). Analyzing and reconstructing reticulation networks under timing constraints. Journal of Mathematical Biology, 61:715-735.
  24. S. Linz and C. Semple (2009). Hybridization in nonbinary trees. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6:30-45.
  25. M. Bordewich, S. Linz, K. St. John, and C. Semple (2007). A reduction algorithm for computing the hybridization number of two trees. Evolutionary Bioinformatics, 3:86-98.
  26. S. Linz, A. Radtke, and A. von Haeseler (2007). A likelihood framework to measure horizontal gene transfer. Molecular Biology and Evolution 24:1312-1319.
  27. R. Münch, K. Hiller, H. Barg, D. Heldt, S. Linz, E. Wingender, and D. Jahn (2003). PRODORIC: prokaryotic database of gene regulation. Nucleic Acids Research, 31:266-269.

Theses.

  1. S. Linz (2008). Reticulation in Evolution. PhD thesis. Heinrich Heine University, Düsseldorf, Germany.
  2. S. Linz (2004). Proteomvergleich und Analyse molekularer Netzwerke in Prokaryoten. MSc thesis. Heinrich Heine University, Düsseldorf, Germany.

Other unpublished items.

  1. S. Kelk, S. Linz, and D. A. Morrison (2013). Fighting network space: it is time for an SQL-type language to filter phylogenetic networks.
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