Homepage of Leo van Iersel

University of Canterbury
Department of Mathematics and Statistics
Room 620
Private Bag 4800
Christchurch
New Zealand

I'm currently working as a postdoc with Mike Steel and Charles Semple. My main research interest is the construction of phylogenetic networks from different kinds of biological data. This has led to practical, cluster-based software for constructing phylogenetic networks and triplet-based such software. There are still lots of open problems. Also see the websites of my co-authors Matthias Mnich and Steven Kelk.

Publications

Leo van Iersel, Charles Semple and Mike Steel, Quantifying the Extent of Lateral Gene Transfer Required to Avert a 'Genome of Eden', arXiv:0911.1146v1 [q-bio.PE], submitted.

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, arXiv:0910.3082v1 [q-bio.PE], submitted.

Katharina Huber, Leo van Iersel, Steven Kelk and Radoslaw Suchecki, A Practical Algorithm for Reconstructing Level-1 Phylogenetic Networks, arXiv:0910.4067v1 [q-bio.PE], submitted.

Leo van Iersel and Steven Kelk, Constructing the Simplest Possible Phylogenetic Network from Triplets, Algorithmica, DOI: 10.1007/s00453-009-9333-0. Preliminary verion in proc. of ISAAC 2008, LNCS 5369, pp. 472-483.

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, DOI: 10.1109/TCBB.2009.22. 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.

Thesis

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

Implemented Algorithms

CASS: Integrated in Dendroscope. Combines any set of input trees into a phylogenetic network representing all clusters of the input trees. CASS uses significanly fewer reticulations than other methods. See this paper. The datasets used in the paper can be found here. This guide describes precisely how to use CASS.

LEV1ATHAN: A Practical Algorithm for Reconstructing Level-1 Phylogenetic Networks. Combines any set of trees into a level-1 phylogenetic network (i.e. a galled tree) that is consistent with a large number of the triplet topologies of the input trees. Can be downloaded here. Based on this paper.

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

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. Can be downloaded here. Based on the algorithm in this paper.

LEVEL2: Constructs a level-2 phylogenetic network consistent with a dense set of triplets, if such a network exists. Can be downloaded here. Based on the algorithm in our RECOMB 2008 paper, which can be found here.

Talks

October 29th 2009, Allan Wilson Centre Meeting, Palmerston North, New Zealand, Phylogenetic Networks Do not Need to Be Complex (slides in pdf).

December 16th 2008, International Symposium on Algorithms and Computation (ISAAC 2008), Gold Coast, Australia, Constructing the Simplest Possible Phylogenetic Network from Triplets (slides in pdf).

June 11th 2008, Mathematics and Informatics in Evolution and Phylogeny, Hameau de l'Etoile, France, Level-k Phylogenetic Networks (slides in pdf).

April 29th 2008, Algorithms seminar, Eindhoven University, The Netherlands, On the Simplicity of Evolution: Algorithms for Phylogenetic Networks (slides in pdf).

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

January 16th 2008, Conference on the Mathematics of Operations Research, Lunteren, The Netherlands, Level-k Phylogenetic Networks: Uniqueness and Complexity (slides in ppt).

November 30th 2007, DIAMANT/EIDMA Symposium, Soesterberg, The Netherlands, Constructing Evolutionary Networks from Triplets (slides in ppt).

February 14th 2007, EIDMA Seminar Combinatorial Theory, Eindhoven University, The Netherlands, Combinatorial Problems in Genetics (slides in ppt).

January 17th 2007, Conference on the Mathematics of Operations Research, Lunteren, The Netherlands, Resolving Ambiguity in Genetical Data (slides in ppt).

December 7th 2006, Genome Informatics AG-seminar, Bielefeld, Germany, Sorting pancakes (slides in ppt).

October 12th 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 13th 2006, Algorithms seminar, Eindhoven University, The Netherlands, Lots of Problems about Strings and Prefix Reversals (slides in ppt).

October 4th 2005, Workshop on Algorithms in Bioinformatics 2005, Mallorca, Spain, On the Complexity of Several Haplotyping Problems (slides in ppt).

May 11th 2005, EIDMA Seminar Combinatorial Theory, Eindhoven University, The Netherlands, Two Complexity Results in Computational Biology.