Publications

Leo van Iersel, Mark Jones and Celine Scornavacca. Improved maximum parsimony models for phylogenetic networks. Systematic Biology, in press.

Janosch Döcker, Leo van Iersel, Steven Kelk, Simone Linz. Deciding the existence of a cherry-picking sequence is hard on two trees. arXiv:1712.02965 [q-bio.PE] (2017).

Remie Janssen, Mark Jones, Péter L. Erdős, Leo van Iersel and Celine Scornavacca. Exploring the tiers of rooted phylogenetic network space using tail moves.  arXiv:1708.07656 [math.CO] (2017).

Philippe Gambette, Leo van Iersel, Mark Jones, Manuel Lafond, Fabio Pardi and Celine Scornavacca. Rearrangement moves on rooted phylogenetic networksPLoS Computational Biology, 13(8):e1005611 (2017).

Péter L. Erdős, Stephen G. Hartke, Leo van Iersel and István Miklós. Graph realizations constrained by skeleton graphs. The Electronic Journal of Combinatorics, 24 (2), \#P2.47 (2017).

Leo van Iersel, Steven Kelk, Georgios Stamoulis, Leen Stougie and Olivier Boes. On unrooted and root-uncertain variants of several well-known phylogenetic network problems. Algorithmica, DOI: 10.1007/s00453-017-0366-5 (2017).

Leo van Iersel and Vincent Moulton. Leaf-reconstructibility of phylogenetic networks, arXiv:1701.08982 [math.CO] (2017).

Leo van Iersel, Vincent Moulton, Eveline de Swart and Taoyang Wu. Binets: fundamental building blocks for phylogenetic networks. Bulletin of Mathematical Biology, 79 (5): 1135–1154 (2017).

Laura Jetten and Leo van Iersel. Nonbinary tree-based phylogenetic networksIEEE/ACM Transactions on Computational Biology and Bioinformatics. DOI:10.1109/TCBB.2016.2615918 (2016). (arXiv).

Martijn van Ee, Leo van Iersel, Teun Janssen and Rene Sitters. A Priori TSP in the Scenario Model. WAOA2016, LNCS 10138, DOI: 10.1007/978-3-319-51741-4_15.

Philippe Gambette, Leo van Iersel, Steven Kelk, Fabio Pardi and Celine Scornavacca. Do branch lengths help to locate a tree in a phylogenetic network? Bulletin of Mathematical Biology, 78 (9): 1773–1795 (2016). (arXiv).

Leo van Iersel, Steven Kelk, Nela Lekic, Chris Whidden and Norbert Zeh, Hybridization Number on Three Rooted Binary Trees is EPT, SIAM Journal on Discrete Mathematics, 30(3): 1607–1631 (2016). (arXiv) (PDF)

James Oldman, Taoyang Wu, Leo van Iersel and Vincent Moulton. TriLoNet: Piecing together small networks to reconstruct reticulate evolutionary histories. Molecular Biology and Evolution, 33 (8): 2151-2162 (2016). (postprint)

Leo van Iersel, Steven Kelk and Celine Scornavacca, Kernelizations for the hybridization number problem on multiple nonbinary treesJournal of Computer and System Sciences, 82(6): 1075–1089 (2016). (arXivPreliminary version in WG 2014. LNCS 8747, 299-311 (2014). Software: Treeduce.

Steven Kelk, Leo van Iersel, Celine Scornavacca and Mathias Weller. Phylogenetic incongruence through the lens of Monadic Second Order logicJournal of Graph Algorithms and Applications, 20(2): 189-215 (2016).

Leo van Iersel, Steven Kelk, Nela Lekic and Simone Linz. Satisfying ternary permutation constraints by multiple linear orders or phylogenetic treesTheoretical Computer Science, 609 (1): 1-21 (2016). (arXiv)

Leo van Iersel. Hoe zijn ze verwant? Nieuw Archief voor Wiskunde, 5/16 (3): 174-178 (2015).

Katharina Huber, Leo van Iersel, Vincent Moulton, Celine Scornavacca and Taoyang Wu. Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets. Algorithmica. DOI: 10.1007/s00453-015-0069-8 (2015). (arXiv)

Mareike Fischer, Leo van Iersel, Steven Kelk and Celine Scornavacca. On Computing the Maximum Parsimony Score of a Phylogenetic Network. SIAM Journal on Discrete Mathematics, 29 (1): 559-585 (2015). (arXiv)

Katharina Huber, Leo van Iersel, Vincent Moulton and Taoyang Wu. How much information is needed to infer reticulate evolutionary histories? Systematic Biology, 64 (1): 102-111 (2015).

Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau and Alexander Schoenhuth, WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads. Journal of Computational Biology, 22 (6): 498-509 (2015). Preliminary version in proc. of RECOMB 2014. LNCS 8394, pp. 237-249 (2014).

Leo van Iersel, Celine Scornavacca and Steven Kelk. Exact Reconciliation of undated trees. arXiv:1410.7004 [q-bio.PE] (2014).

Celine Scornavacca, Leo van Iersel, Steven Kelk and David Bryant. The agreement problem for unrooted phylogenetic trees is FPT. Journal of Graph Algorithms and Applications, 18(3), pp. 385-392 (2014).

Leo van Iersel and Vincent Moulton, Trinets encode tree-child and level-2 phylogenetic networks, Journal of Mathematical Biology, 68(7), pp. 1707-1729 (2014). (arXiv)

Leo van Iersel, Steven Kelk, Nela Lekic and Celine Scornavacca, A practical approximation algorithm for solving massive instances of hybridization number for binary and nonbinary trees. BMC Bioinformatics 15:127 (2014). Preliminary version in proc. of WABI 2012, LNCS 7534, pp. 430-440.

Leo van Iersel, Steven Kelk, Nela Lekic and Leen Stougie, Approximation algorithms for nonbinary agreement forests, SIAM Journal on Discrete Mathematics, 28(1), pp. 49-66 (2014). (arXiv).

Eric Bapteste, Leo van Iersel, Axel Janke, Scot Kelchner, Steven Kelk, James O. McInerney, David A. Morrison, Luay Nakhleh, Mike Steel, Leen Stougie and James Whitfield, Networks: expanding evolutionary thinking. Trends in Genetics, 29 (8), pp. 439–441 (2013).

Kantarawee Khayhan et al., Geographically Structured Populations of Cryptococcus neoformans Variety grubii in Asia Correlate with HIV Status and Show a Clonal Population Structure. PLoS ONE, 8(9): e72222. doi:10.1371/journal.pone.0072222 (2013).

Ferry Hagen et al., Ancient dispersal of the human fungal pathogen Cryptococcus gattii from the Amazon rainforest, PLoS ONE 8(8): e71148. doi:10.1371/journal.pone.0071148 (2013). Press release.

Leo van Iersel and Simone Linz, A quadratic kernel for computing the hybridization number of multiple trees, Information Processing Letters 113 (9), pp. 318–323 (2013). (arXiv)

Leo van Iersel, Book Review: Basic Phylogenetic Combinatorics. — Andreas Dress, Katharina T. Huber, Jacobus Koolen, Vincent Moulton and Andreas Spillner. Systematic Biology 62 (2), pp. 346–348 (2013). (free-access link)

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, SIAM Journal on Discrete Mathematics, 26(4), pp. 1635–1656 (2012). (arXiv)

Steven Kelk, Celine Scornavacca and Leo van Iersel, On the elusiveness of clusters, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9 (2), pp. 517-534 (2012). (arXiv)

Gregory Gutin, Leo van Iersel, Matthias Mnich and Anders Yeo, Every Ternary Permutation Constraint Satisfaction Problem Parameterized Above Average Has a Kernel with a Quadratic Number of Variables, Journal of Computer and System Sciences, 78, pp. 151-163 (2012). Preliminary version in proc. of ESA 2010, LNCS 6346, pp. 326-337. (arXiv)

Leo van Iersel and Steven Kelk, When Two Trees Go to War, Journal of Theoretical Biology, 269, pp. 245-255 (2011). (arXiv)

Katharina Huber, Leo van Iersel, Steven Kelk and Radoslaw Suchecki, A Practical Algorithm for Reconstructing Level-1 Phylogenetic Networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8 (3), pp. 635-649 (2011).

Leo van Iersel and Steven Kelk, Constructing the Simplest Possible Phylogenetic Network from Triplets, Algorithmica, 60, pp. 207-235 (2011). Preliminary verion in proc. of ISAAC 2008, LNCS 5369, pp. 472-483.

Leo van Iersel, Charles Semple and Mike Steel, Locating a Tree in a Phylogenetic Network, Information Processing Letters, 110 (23), pp. 1037-1043 (2010). (arXiv)

Leo van Iersel, Charles Semple and Mike Steel, Quantifying the Extent of Lateral Gene Transfer Required to Avert a ‘Genome of Eden’, Bulletin of Mathematical Biology, 72(7), pp. 1783-1798 (2010).

Leo van Iersel, Steven Kelk, Regula Rupp and Daniel Huson, Phylogenetic Networks Do not Need to Be Complex: Using Fewer Reticulations to Represent Conflicting Clusters, Bioinformatics, 26, pp. i124-i131 (2010) (proceedings of ISMB 2010).

Leo van Iersel, Steven Kelk and Matthias Mnich, Uniqueness, Intractability and Exact Algorithms: Reflections on Level-k Phylogenetic Networks, Journal of Bioinformatics and Computational Biology, 7 (4), pp. 597-623 (2009).

Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie, Ferry Hagen and Teun Boekhout, Constructing Level-2 Phylogenetic Networks from Triplets, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6 (4), pp. 667-681 (2009). Preliminary version in proc. of RECOMB 2008, LNBI 4955, pp. 450-462.

Leo van Iersel, Judith Keijsper, Steven Kelk and Leen Stougie, Shorelines of Islands of Tractability: Algorithms for Parsimony and Minimum Perfect Phylogeny Haplotyping Problems, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 5 (2), pp. 301-312 (2008). Preliminary version in proc. of WABI 2006, LNCS 4175, pp. 80-91.

Cor Hurkens, Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie and John Tromp, Prefix reversals on binary and ternary strings, SIAM Journal on Discrete Mathematics, 21 (3), pp. 592-611 (2007). Preliminary version in proc. of AB 2007, LNCS 4545, pp. 292-306.

Rudi Cilibrasi, Leo van Iersel, Steven Kelk and John Tromp, The Complexity of the Single Individual SNP Haplotyping Problem, Algorithmica, 49 (1), pp. 13-36 (2007). Preliminary version in proc. of WABI 2005, LNCS 3692, pp. 128-139.

Short Notes

Leo van Iersel, Steven Kelk, Nela Lekic and Leen Stougie, A short note on exponential-time algorithms for hybridization number, arXiv:1312.1255 [q-bio.PE] (2013).

Thesis

Leo van Iersel, Algorithms, Haplotypes and Phylogenetic Networks, Ph.D. Thesis, Eindhoven University of Technology, 2009 (pdf for viewing, pdf for printing).

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