CWI

Homepage of Leo van Iersel

Centrum Wiskunde & Informatica
Room M277b
+31(0)20 592 4265


Physical address:
Science Park 123
1098 XG Amsterdam
Netherlands
Postal address:
P.O. Box 94079
1090 GB Amsterdam
Netherlands

Leo van Iersel

After studying applied mathematics at the University of Twente, I obtained my PhD at Eindhoven University of Technology with Leen Stougie, Gerhard Woeginger and Judith Keijsper. After that, I have worked as a postdoc at the University of Canterbury with Mike Steel and Charles Semple and have spent one year teaching in primary and secondary schools in Tanzania and Kenya. I am still involved in several social projects in these countries, which you can find on the right-hand side of this page, on the Cecil Kids website and on facebook. In October 2011, I started a postdoc at CWI in Amsterdam. My main research interest is the design of algorithms for discrete, computational problems, including problems from biology. Also see the websites of some of my main co-authors Steven Kelk, Celine Scornavacca.

Workshops

New papers and preprints

Blog

New software tools. We have developed several methods for constructing phylogenetic networks and related tasks, including:

Cass and various other phylogenetic network methods can be found in the user-friendly software package Dendroscope.

Recommended books. There are two recent books about phylogenetic networks.

 

 

Teaching

2WO12 Optimalisering in Netwerken

2WO11 Optimization in Rn.

Publications

(my google scholar page)

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 Steven Kelk, Kernelizations for the hybridization number problem on multiple nonbinary trees. Workshop on Graph-Theoretic Concepts in Computer Science (WG 2014). To appear. arXiv.

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 Lekić 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.

Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau and Alexander Schoenhuth, WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads. RECOMB 2014. LNCS 8394, pp. 237-249 (2014).

Leo van Iersel, Steven Kelk, Nela Lekić, Chris Whidden and Norbert Zeh, Hybridization Number on Three Trees, arXiv:1402.2136 [cs.DS] (2014).

Leo van Iersel, Steven Kelk, Nela Lekić 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.

Mareike Fischer, Leo van Iersel, Steven Kelk and Celine Scornavacca, On Computing the Maximum Parsimony Score of a Phylogenetic Network, arXiv:1302.2430 [q-bio.PE] (2013).

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 Lekić, 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 Lekić and Leen Stougie, A short note on exponential-time algorithms for hybridization number, arXiv:1312.1255 [q-bio.PE] (2013).

Software

NonbinaryCycleKiller: A practical algorithm for constructing a phylogenetic network from two large (possibly multifurcating) trees. The number of reticulations is very close to the minimum (paper submitted).

ILPEACE: Reconciling a binary gene tree with a binary undated species tree (paper submitted).

MPNet: Computing the Maximum Parsimony score of a phylogenetic NETwork, see the paper.

MAF: Maximum Agreement Forests for nonbinary trees, see the paper.

CycleKiller: A practical algorithm for constructing a phylogenetic network from two large bifurcating trees. The number of reticulations is very close to the minimum, see the paper.

Cass: Integrated into Dendroscope. Combines any set of phylogenetic trees into a phylogenetic network representing all clusters of all input trees. CASS uses significanly fewer reticulations than other methods. Paper. User Guide.

LEV1ATHAN: A Practical Algorithm for Reconstructing Level-1 Phylogenetic Networks. Combines any set of phylogenetic trees into a level-1 phylogenetic network (a galled tree) that is consistent with a large number of the triplet topologies of the input trees. Paper. Download.

SIMPLISTIC: Constructs level-k phylogenetic networks from triplets. This program always returns a phylogenetic network consistent with all input triplets. Partly based on the SL-k and MINPITS algorithms in this paper. Download.

MARLON: Constructs a level-1 phylogenetic network with a minimum number of reticulations consistent with a dense set of triplets, if such a network exists. Paper. Download.

LEVEL2: Constructs a level-2 phylogenetic network consistent with a dense set of triplets, if such a network exists. Paper. Download.

Thesis

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

Talks and Posters

July 2014, Greifswald Phylogenetics Meeting, Greifswald, Hybridization Number on Three Trees.

June 2014, EUSACOU Workshop, Tinbergen Institute, Amsterdam. Parameterized algorithms for reconstructing phylogenetic networks.

November 2013, Alfréd Rényi Institute of Mathematics, Budapest, Hungary. Reconstructing Phylogenetic Networks.

July 2013, Midsummer Combinatorial Workshop (MCW), Prague, Czech Republic. Reconstructing Phylogenetic Networks (slides, abstract).

May 2013, Mathematical and Computational Evolutionary Biology (MCEB), Montpellier, France. Approximation Algorithms for Nonbinary Agreement Forests (poster).

October 2012, The Future of Phylogenetic Networks, Leiden, The Netherlands. A summary of the week (slides).

June 2012, Mathematical and Computational Evolutionary Biology (MCEB), Montpellier, France. Hybridization Networks for Multiple Trees (poster).

April 2012, University of East Anglia, United Kingdom, Minimizing Hybridizations.

January 2012, SOUTH, The 16th Annual New Zealand Phylogenetics Meeting, Kaikoura, New Zealand, Approximating the minimum number of reticulations needed to explain two conflicting gene trees (slides).

January 2012, Gijs de Leve Prijs Reward Lecture, LNMB Conference, Lunteren, Netherlands.

April 2010, Adelaide Phylogenetics Conference, Australia, Phylogenetic networks do not need to be complex.

February 2010, DOOM, The 14th Annual New Zealand Phylogenetics Meeting, Mount Ruapehu, New Zealand, Avoiding a Genome of Eden.

December 2009, TACO workshop on Treewidth and Combinatorial Optimization, Eindhoven University, The Netherlands, Treewidth and the Genome of Eden.

November 2009, Physoc Seminar, University of Canterbury, Christchurch, New Zealand, Using Mathematics to Reconstruct the Evolution of Species.

October 2009, Allan Wilson Centre Meeting, Palmerston North, New Zealand, Phylogenetic Networks Do not Need to Be Complex.

December 2008, International Symposium on Algorithms and Computation (ISAAC 2008), Gold Coast, Australia, Constructing the Simplest Possible Phylogenetic Network from Triplets.

June 2008, Mathematics and Informatics in Evolution and Phylogeny, Montpellier, France, Level-k Phylogenetic Networks.

April 2008, Algorithms seminar, Eindhoven University, The Netherlands, On the Simplicity of Evolution: Algorithms for Phylogenetic Networks.

April 2008, Conference on Research in Computational Molecular Biology (RECOMB 2008), Singapore, Constructing Level-2 Phylogenetic Networks from Triplets.

January 2008, Conference on the Mathematics of Operations Research, Lunteren, The Netherlands, Level-k Phylogenetic Networks: Uniqueness and Complexity.

November 2007, DIAMANT/EIDMA Symposium, Soesterberg, The Netherlands, Constructing Evolutionary Networks from Triplets.

February 2007, EIDMA Seminar Combinatorial Theory, Eindhoven University, The Netherlands, Combinatorial Problems in Genetics.

January 2007, Conference on the Mathematics of Operations Research, Lunteren, The Netherlands, Resolving Ambiguity in Genetical Data.

December 2006, Genome Informatics AG-seminar, Bielefeld, Germany, Sorting pancakes.

October 2006, SIREN 2006 poster presentation, Utrecht, The Netherlands, Computing evolutionary distance by genome rearrangements: a combinatorial approach, Phylogenetic trees for yeasts and Combinatorial approaches in phylogenetics: two examples.

April 2006, Algorithms seminar, Eindhoven University, The Netherlands, Lots of Problems about Strings and Prefix Reversals.

October 2005, Workshop on Algorithms in Bioinformatics 2005, Mallorca, Spain, On the Complexity of Several Haplotyping Problems.

May 2005, EIDMA Seminar Combinatorial Theory, Eindhoven University, The Netherlands, Two Complexity Results in Computational Biology.



CWI DISCLAIMER
 

 

 

 

 

 

 

 




eXTReMe Tracker