[67] Leo van Iersel, Mark Jones, Mathias Weller. When Three Trees Go to War. hal-04013152 (2023).
[66] Elise Deen, Leo van Iersel, Remie Janssen, Mark Jones, Yukihiro Murakami and Norbert Zeh. A Near-Linear Kernel for Two-Parsimony Distance. arXiv:2211.00378 (2022).
[65] Leo van Iersel, Vincent Moulton and Yukihiro Murakami. Polynomial invariants for cactuses. arXiv:2209.12525 (2022).
[64] Mark Jones, Mathias Weller and Leo van Iersel. Embedding phylogenetic trees in networks of low treewidth, ESA 2022. 10.4230/LIPIcs.ESA.2022.69. arXiv:2207.00574
[63] Giulia Bernardini, Leo van Iersel, Esther Julien and Leen Stougie. Reconstructing Phylogenetic Networks via Cherry Picking and Machine Learning, WABI 2022. 10.4230/LIPIcs.WABI.2022.16
[62] Leo van Iersel, Remie Janssen, Mark Jones and Yukihiro Murakami. Orchard Networks are Trees with Additional Horizontal Arcs. Bulletin of Mathematical Biology, 84:76 (2022).
[61] Katharina T. Huber, Leo van Iersel, Remie Janssen, Mark Jones, Vincent Moulton and Yukihiro Murakami. Level-2 networks from shortest and longest distances. Discrete Applied Mathematics 306:138-165 (2022). (arXiv)
[60] Sander Borst, Leo van Iersel, Mark Jones and Steven Kelk. New FPT algorithms for finding the temporal hybridization number for sets of phylogenetic trees. Algorithmica, 84:2050–2087 (2022).
[59] Leo van Iersel, Remie Janssen, Mark Jones, Yukihiro Murakami and Norbert Zeh. A Practical Fixed-Parameter Algorithm for Constructing Tree-Child Networks from Multiple Binary Trees. Algorithmica, 84: 917–960 (2022). (arXiv).
[58] Leo van Iersel, Sjors Kole, Vincent Moulton and Leonie Nipius. An algorithm for reconstructing level-2 phylogenetic networks from trinets. Information Processing Letters, 178:106300 (2022). (arXiv).
[57] Rosanne Wallin, Leo van Iersel, Steven Kelk and Leen Stougie. Applicability of several rooted phylogenetic network algorithms for representing the evolutionary history of SARS-CoV-2. BMC Ecology and Evolution, 21:220 (2021).
[56] Leo van Iersel, Remie Janssen, Mark Jones, Yukihiro Murakami and Norbert Zeh. A Unifying Characterization of Tree-based Networks and Orchard Networks using Cherry Covers. Advances in Applied Mathematics, 129:102222 (2021). (arXiv)
[55] Elizabeth Gross, Leo van Iersel, Remie Janssen, Mark Jones, Colby Long and Yukihiro Murakami. Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes. Journal of Mathematical Biology, 83:32 (2021). (arXiv)
[54] Leo van Iersel, Vincent Moulton and Yukihiro Murakami. Reconstructibility of unrooted level-k phylogenetic networks from distances. Advances in Applied Mathematics, 120:102075 (2020). (arXiv).
[53] Mark Jones, Philippe Gambette, Leo van Iersel, Remie Janssen, Steven Kelk, Fabio Pardi and Celine Scornavacca. Cutting an alignment with Ockham’s razor. arXiv:1910.11041 [q-bio.PE] (2019).
[52] Katharina T. Huber, Leo van Iersel, Remie Janssen, Mark Jones, Vincent Moulton, Yukihiro Murakami and Charles Semple. Orienting undirected phylogenetic networks. arXiv:1906.07430 [cs.DS] (2019).
[51] Leo van Iersel, Mark Jones and Steven Kelk. A third strike against perfect phylogeny. Systematic Biology, 68(5):814–827 (2019). (arXiv)
[50] Janosch Döcker, Leo van Iersel, Steven Kelk, Simone Linz. Deciding the existence of a cherry-picking sequence is hard on two trees. Discrete Applied Mathematics, 260: 131-143 (2019). (arXiv)
[49] Yukihiro Murakami, Leo van Iersel, Remie Janssen, Mark Jones and Vincent Moulton. Reconstructing Tree-Child Networks from Reticulate-Edge-Deleted Subnetworks. Bulletin of Mathematical Biology, 81(10):3823–3863 (2019). (arXiv)
[48] Péter L. Erdős, Leo van Iersel and Mark Jones. Not all phylogenetic networks are leaf-reconstructible. Journal of Mathematical Biology, 79(5):1623–1638 (2019). (arXiv)
[47] Steven Kelk, Fabio Pardi, Celine Scornavacca and Leo van Iersel. Finding a most parsimonious or likely tree in a network with respect to an alignment. Journal of Mathematical Biology, 78(1-2):527 – 547 (2019). (arXiv)
[46] Leo van Iersel, Remie Janssen, Mark Jones, Yukihiro Murakami and Norbert Zeh. Polynomial-Time Algorithms for Phylogenetic Inference Problems involving duplication and reticulation. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 17(1): 14 – 26 (2020). Preliminary version in AlCoB 2018, LNBI 10849: 37–49 (2018). (arXiv)
[45] Teun Janssen, Céline Swennenhuis, Abdoul Bitar, Thomas Bosman, Dion Gijswijt, Leo van Iersel, Stèphane Dauzére-Pérès and Claude Yugma. Parallel Machine Scheduling with a Single Resource per Job. arXiv:1809.05009 [cs.DM] (2018).
[44] Leo van Iersel and Vincent Moulton. Leaf-reconstructibility of phylogenetic networks. SIAM Journal on Discrete Mathematics 32(3): 2047–2066 (2018). (arXiv) (PDF)
[43] Remie Janssen, Mark Jones, Péter L. Erdős, Leo van Iersel, Celine Scornavacca. Exploring the tiers of rooted phylogenetic network space using tail moves. Bulletin of Mathematical Biology, 80 (8): 2177–2208 (2018).
[42] Leo van Iersel, Mark Jones and Celine Scornavacca. Improved maximum parsimony models for phylogenetic networks. Systematic Biology, 67(3):518-542 (2018) (free-access link) (preprint).
[41] Laura Jetten and Leo van Iersel. Nonbinary tree-based phylogenetic networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 14(1):205 – 217 (2018). (arXiv)
[40] 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, 80 (11): 2993–3022 (2018).
[39] Martijn van Ee, Leo van Iersel, Teun Janssen and Rene Sitters. A Priori TSP in the Scenario Model. Discrete Applied Mathematics, 250:313-341 (2018). (postprint) Preliminary version in WAOA2016, LNCS 10138: 183-196 (2017).
[38] Philippe Gambette, Leo van Iersel, Mark Jones, Manuel Lafond, Fabio Pardi and Celine Scornavacca. Rearrangement moves on rooted phylogenetic networks. PLoS Computational Biology, 13(8):e1005611 (2017).
[37] 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).
[36] 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).
[35] Katharina Huber, Leo van Iersel, Vincent Moulton, Celine Scornavacca and Taoyang Wu. Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets. Algorithmica, 77 (1): 173-200 (2017). (arXiv)
[34] 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)
[33] 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)
[32] 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)
[31] Leo van Iersel, Steven Kelk and Celine Scornavacca, Kernelizations for the hybridization number problem on multiple nonbinary trees. Journal of Computer and System Sciences, 82(6): 1075–1089 (2016). (arXiv) Preliminary version in WG 2014. LNCS 8747, 299-311 (2014). Software: Treeduce.
[30] Steven Kelk, Leo van Iersel, Celine Scornavacca and Mathias Weller. Phylogenetic incongruence through the lens of Monadic Second Order logic. Journal of Graph Algorithms and Applications, 20(2): 189-215 (2016).
[29] Leo van Iersel, Steven Kelk, Nela Lekic and Simone Linz. Satisfying ternary permutation constraints by multiple linear orders or phylogenetic trees. Theoretical Computer Science, 609 (1): 1-21 (2016). (arXiv)
[28] Leo van Iersel. Hoe zijn ze verwant? Nieuw Archief voor Wiskunde, 5/16 (3): 174-178 (2015).
[27] 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)
[26] 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).
[25] 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).
[24] Leo van Iersel, Celine Scornavacca and Steven Kelk. Exact Reconciliation of undated trees. arXiv:1410.7004 [q-bio.PE] (2014).
[23] 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).
[22] 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)
[21] 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.
[20] 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).
[19] 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).
[18] 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).
[17] 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.
[16] 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)
[15] 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)
[14] 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)
[13] 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)
[12] 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)
[11] Leo van Iersel and Steven Kelk, When Two Trees Go to War, Journal of Theoretical Biology, 269, pp. 245-255 (2011). (arXiv)
[10] 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).
[9] 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.
[8] 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)
[7] 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).
[6] 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).
[5] 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).
[4] 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.
[3] 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.
[2] 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. (arXiv)
[1] 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).
Leo van Iersel 