Linz Publications of Simone Linz     Order by:   Type | Year
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2020
1
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Simone Linz and Charles Semple. Caterpillars on three and four leaves are sufficient to reconstruct binary normal networks. In JOMB, 2020.
Keywords: explicit network, from rooted trees, from triplets, normal network, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: https://arxiv.org/abs/2002.00483, to appear.
       

2
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Katharina Huber, Simone Linz and Vincent Moulton. Weakly displaying trees in temporal tree-child network. 2020.
Keywords: cherry-picking, from rooted trees, phylogenetic network, phylogeny, reconstruction, rigidly displaying, time consistent network, tree-child network, weakly displaying.
Note: https://arxiv.org/abs/2004.02634.
       

2019
3
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Simone Linz and Charles Semple. Attaching leaves and picking cherries to characterise the hybridisation number for a set of phylogenies. In AAM, Vol. 105:102-129, 2019.
Keywords: agreement forest, cherry-picking, explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction, tree-child network.
Note: https://doi.org/10.1016/j.aam.2019.01.004.
       

4
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Janosch Döcker, Leo van Iersel, Steven Kelk and Simone Linz. Deciding the existence of a cherry-picking sequence is hard on two trees. In DAM, Vol. 260:131-143, 2019.
Keywords: cherry-picking, explicit network, hybridization, minimum number, NP complete, phylogenetic network, phylogeny, reconstruction, temporal-hybridization number, time consistent network, tree-child network.
Note: https://arxiv.org/abs/1712.02965.
       

5
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Jonathan Klawitter and Simone Linz. On the Subnet Prune and Regraft Distance. In ELJC, Vol. 26(2):P2.3.1-23, 2019.
Keywords: agreement forest, explicit network, phylogenetic network, phylogeny, reticulation-visible network, SPR distance, tree-based network, tree-child network.
Note: https://arxiv.org/abs/1805.07839.
       

6
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Janosch Döcker, Simone Linz and Charles Semple. Displaying trees across two phylogenetic networks. In TCS, Vol. 796:129-146, 2019.
Keywords: display set, explicit network, normal network, phylogenetic network, phylogeny, time consistent network, tree-child network.
Note: https://arxiv.org/abs/1901.06612.
       

2018
7
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Daniel H. Huson and Simone Linz. Autumn Algorithm - Computation of Hybridization Networks for Realistic Phylogenetic Trees. In TCBB, Vol. 15:398-410, 2018.
Keywords: explicit network, from rooted trees, phylogenetic network, phylogeny, Program Dendroscope, reconstruction.
Note: https://simonelinz.files.wordpress.com/2016/06/hl16.pdf.
       

8
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Janosch Döcker and Simone Linz. On the existence of a cherry-picking sequence. In TCS, Vol. 714:36-50, 2018.
Keywords: cherry-picking, explicit network, from rooted trees, NP complete, phylogenetic network, phylogeny, reconstruction, temporal-hybridization number, time consistent network, tree-child network.
Note: https://arxiv.org/abs/1712.04127.
       

2017
9
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Christopher Bryant, Mareike Fischer, Simone Linz and Charles Semple. On the Quirks of Maximum Parsimony and Likelihood on Phylogenetic Networks. In JTB, Vol. 417:100-108, 2017.
Keywords: explicit network, from sequences, likelihood, parsimony, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/1505.06898.
       

10
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Magnus Bordewich, Simone Linz and Charles Semple. Lost in space? Generalising subtree prune and regraft to spaces of phylogenetic networks. In JTB, Vol. 423:1-12, 2017.
Keywords: distance between networks, explicit network, phylogenetic network, phylogeny, reticulation-visible network, SPR distance, tree-based network, tree-child network.
Note: https://simonelinz.files.wordpress.com/2017/04/bls171.pdf.
       

2016
11
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Katharina Huber, Simone Linz, Vincent Moulton and Taoyang Wu. Spaces of phylogenetic networks from generalized nearest-neighbor interchange operations. In JOMB, Vol. 72(2):699-725, 2016.
Keywords: bound, distance between networks, from network, LST distance, phylogenetic network, phylogeny.
       

2014
12
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Paul Cordue, Simone Linz and Charles Semple. Phylogenetic Networks that Display a Tree Twice. In BMB, Vol. 76(10):2664-2679, 2014.
Keywords: from rooted trees, normal network, phylogenetic network, phylogeny, reconstruction, tree-child network.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/CLS14.pdf.
       
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2013
13
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Leo van Iersel and Simone Linz. A quadratic kernel for computing the hybridization number of multiple trees. In IPL, Vol. 113:318-323, 2013.
Keywords: explicit network, FPT, from rooted trees, kernelization, minimum number, phylogenetic network, phylogeny, Program Clustistic, Program MaafB, Program PIRN, reconstruction.
Note: http://arxiv.org/abs/1203.4067, poster.
       
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14
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Peter J. Humphries, Simone Linz and Charles Semple. On the complexity of computing the temporal hybridization number for two phylogenies. In DAM, Vol. 161:871-880, 2013.
Keywords: agreement forest, APX hard, characterization, from rooted trees, hybridization, NP complete, phylogenetic network, phylogeny, reconstruction, time consistent network.
Note: http://ab.inf.uni-tuebingen.de/people/linz/publications/TAFapx.pdf.
       
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15
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Simone Linz, Katherine St. John and Charles Semple. Counting trees in a phylogenetic network is #P-complete. In SICOMP, Vol. 42(4):1768-1776, 2013.
Keywords: counting, from network, phylogenetic network, phylogeny.
Note: http://ab.inf.uni-tuebingen.de/people/linz/publications/counting.pdf.
       

16
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Simone Linz. Reticulation. In Brenner's Encyclopedia of Genetics (Second Edition), 2013.
Keywords: phylogenetic network, phylogeny, survey.
       

17
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Peter J. Humphries, Simone Linz and Charles Semple. Cherry picking: a characterization of the temporal hybridization number for a set of phylogenies. In BMB, Vol. 75(10):1879-1890, 2013.
Keywords: characterization, cherry-picking, from rooted trees, hybridization, NP complete, phylogenetic network, phylogeny, reconstruction, time consistent network.
Note: http://ab.inf.uni-tuebingen.de/people/linz/publications/CPSpaper.pdf.
       
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18
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Steven Kelk, Simone Linz and David A. Morrison. Fighting network space: it is time for an SQL-type language to filter phylogenetic networks. 2013.
Keywords: database, explicit network, from network, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/1310.6844.
       

2012
19
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Celine Scornavacca, Simone Linz and Benjamin Albrecht. A fi rst step towards computing all hybridization networks for two rooted binary phylogenetic trees. In JCB, Vol. 19:1227-1242, 2012.
Keywords: agreement forest, explicit network, FPT, from rooted trees, phylogenetic network, phylogeny, Program Dendroscope, Program Hybroscale, reconstruction.
Note: http://arxiv.org/abs/1109.3268.
       
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20
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Steven Kelk, Leo van Iersel, Nela Lekic, Simone Linz, Celine Scornavacca and Leen Stougie. Cycle killer... qu'est-ce que c'est? On the comparative approximability of hybridization number and directed feedback vertex set. In SIDMA, Vol. 26(4):1635-1656, 2012.
Keywords: agreement forest, approximation, explicit network, from rooted trees, minimum number, phylogenetic network, phylogeny, Program CycleKiller, reconstruction.
Note: http://arxiv.org/abs/1112.5359, about the title.
       
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2011
21
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Josh Voorkamp né Collins, Simone Linz and Charles Semple. Quantifying hybridization in realistic time. In JCB, Vol. 18(10):1305-1318, 2011.
Keywords: explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, software.
Note: http://wwwcsif.cs.ucdavis.edu/~linzs/CLS10_interleave.pdf, software available at http://www.math.canterbury.ac.nz/~c.semple/software.shtml.
       
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2010
22
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Simone Linz, Charles Semple and Tanja Stadler. Analyzing and reconstructing reticulation networks under timing constraints. In JOMB, Vol. 61(5):715-737, 2010.
Keywords: explicit network, from rooted trees, hybridization, lateral gene transfer, NP complete, phylogenetic network, phylogeny, reconstruction, time consistent network.
Note: http://dx.doi.org/10.1007/s00285-009-0319-y..
       
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2009
23
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Simone Linz and Charles Semple. Hybridization in non-binary trees. In TCBB, Vol. 6(1):30-45, 2009.
Keywords: agreement forest, FPT, from rooted trees, hybridization, phylogenetic network, phylogeny, reconstruction.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/LS08.pdf, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw03/1220/linz/.
       

2008
24
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Simone Linz. Reticulation in evolution. PhD thesis, Heinrich-Heine-University, Düsseldorf, Germany, 2008.
Keywords: agreement forest, FPT, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, SPR distance, statistical model.
Note: http://docserv.uni-duesseldorf.de/servlets/DocumentServlet?id=8505.
       

2007
25
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Magnus Bordewich, Simone Linz, Katherine St. John and Charles Semple. A reduction algorithm for computing the hybridization number of two trees. In EBIO, Vol. 3:86-98, 2007.
Keywords: agreement forest, FPT, from rooted trees, hybridization, phylogenetic network, phylogeny, Program HybridNumber.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BLSS07.pdf.