Simone Linz
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Position | Marie Curie Fellow |
| Address | Currently, visiting the Department of Mathematics and Statistics at the University of Canterbury, New Zealand. |
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| linz@informatik.uni-tuebingen.de |
Research Interests.
Publications.
D. H. Huson and S. Linz. Computing minimum hybridization networks from real phylogenetic trees, submitted.
L. van Iersel and S. Linz. A quadratic kernel for computing the hybridization number of multiple trees, submitted.
P. J. Humphries, S. Linz, and C. Semple. On the complexity of computing the temporal hybridization number for two phylogenies, submitted.
S. Kelk, L. van Iersel, N. Lekić, S. Linz, C. Scornavacca, and L. Stougie. Cycle killer... qu'est-ce que c'est? On the comparative approximability of hybridization number and directed feedback vertex set, submitted.
C. Scornavacca, S. Linz, and B. Albrecht. A first step towards computing all hybridization networks for two rooted binary phylogenetic trees, submitted.
M. Syvanen, B. Erickson, S. Linz, and J. Ducore. Hybrid origins of the Vertebrate, submitted.
S. Linz. Reticulation. In Brenner's Encyclopedia of Genetics. Eds: Stanley Maloy and Kelly Hughes. Elsevier, in press (invited).
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.
J. Collins, S. Linz, and C. Semple (2011). Quantifying hybridization in realistic time. Journal of Computational Biology, 18:1305-1318.
S. Linz and C. Semple (2011). A cluster reduction for computing the subtree distance between phylogenies. Annals of Combinatorics, 15:465-484.
S. Linz. (2010). On Hill et al's conjecture for calculating the subtree prune and regraft distance between phylogenies. BMC Evolutionary Biology, 10:334.
S. Linz, C. Semple, and T. Stadler (2010). Analyzing and reconstructing reticulation networks under timing constraints. Journal of Mathematical Biology, 61:715-735.
S. Linz and C. Semple (2009). Hybridization in nonbinary trees. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6:30-45.
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.
S. Linz, A. Radtke, and A. von Haeseler (2007). A likelihood framework to measure horizontal gene transfer. Molecular Biology and Evolution, 24:1312-1319.
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.
Reticulation in Evolution (2008). PhD thesis. Heinrich Heine University, Düsseldorf, Germany.
Supervised by Prof. Charles Semple and Prof. Arndt von Haeseler.
Proteomvergleich und Analyse molekularer Netzwerke in Prokaryoten (2004). MSc thesis. Heinrich Heine University, Düsseldorf, Germany.
Supervised by Prof. Dieter Jahn and Prof. William Martin.
Software.
HybridInterleave. A Java program for an exact calculation of the minimum number of hybridization events to explain two rooted binary phylogenetic trees on the same taxa set in realistic time. HybridInterleave is a fixed-parameter algorithm that is based on interleaving.
A software package to simulate and estimate horizontal gene transfer.
