Steven Kelk's homepage @ CWI

I am currently a postdoc in the Life Sciences cluster of the Centrum voor Wiskunde en Informatica (CWI) in Amsterdam, in the subgroup Combinatorial Problems in Biology, more details about CWI are available on the CWI home page.

My staff page at CWI (complete with contact details etc.) is available here. My PGP public key is available here.

I am currently working on the combinatorial aspects of computational biology. I obtained my PhD in late 2003 from the Algorithms and Computational Complexity Research Group at the University of Warwick. My supervisor was Leslie Goldberg. My main research interests are approximation algorithms and phylogenetic networks.

Publications/Papers

(See also the website of my co-author Leo van Iersel.)

• A short note on the tractability of constructing phylogenetic networks from clusters, Leo van Iersel and Steven Kelk, arXiv pre-print 22 december 2009.
• A Practical Algorithm for Reconstructing Level-1 Phylogenetic Networks, Katharina T. Huber, Leo van Iersel, Steven Kelk, Radoslaw Suchecki, arXiv pre-print 21 october 2009. To appear in IEEE/ACM Transactions on Computational Biology and Bioinformatics.
  • LEV1ATHAN, the algorithm from the above paper, is available for download from this website.
• Phylogenetic Networks Do not Need to Be Complex: Using Fewer Reticulations to Represent Conflicting Clusters, Leo van Iersel, Steven Kelk, Regula Rupp, Daniel Huson, arXiv pre-print 16 october 2009.
  • CASS, the algorithm from the above paper, has now been incorporated into Dendroscope. CASS also has its own website, see here.
• Some mathematical refinements concerning error minimization in the genetic code, Harry Buhrman, Peter T. S. van der Gulik, Steven M. Kelk, Wouter M. Koolen, Leen Stougie, arXiv pre-print 8 september 2009. Submitted.
• An early release of SIMPLISTIC (SIMPLe network heurISTIC) is now available! SIMPLISTIC is a program, written in Java, which always returns some network consistent with 100% of the dense input triplets. See this page for code and documentation (28 july 2008). There is a poster here about SIMPLISTIC (and MARLON.)
• Constructing the Simplest Possible Phylogenetic Network from Triplets, Leo van Iersel and Steven Kelk, june 2009: to appear in Algorithmica (available on-line)
  • MARLON (Minimum Amount of Reticulation Level One Network) can be downloaded here.
  • A version of the paper has been accepted to appear in ISAAC2008.
• Uniqueness, intractability and exact algorithms: reflections on level-k phylogenetic networks, Leo van Iersel, Steven Kelk, Matthias Mnich, Journal of Bioinformatics and Computational Biology (JBCB) 7(4):597-623 (2009)
• Worst-case optimal approximation algorithms for maximizing triplet consistency within phylogenetic networks, Jaroslaw Byrka, Pawel Gawrychowski, Katharina T. Huber, Journal of Discrete Algorithms 8(1):65-75 (2010)
• In February 2008 we produced a new version of the paper, with a heavily optimized running time for the derandomization, and a very fast triplet consistency checking algorithm as subroutine.
• Slides from a presentation about this article, given at both Technische Universiteit Eindhoven and the Isaac Newton Institute (Cambridge, England).
• Constructing level-2 phylogenetic networks from triplets, Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie, Ferry Hagen, Teun Boekhout, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6(4):667-681 (2009).
  • Powerpoint slides used in presentations at University of East Anglia and University of Liverpool, summer 2007.
  • September 2007: Here is a practical implementation of the algorithm in Java: LEVEL2
  • December 2007: The article has been accepted to appear in RECOMB2008.
• Shorelines of islands of tractability: Algorithms for parsimony and perfect phylogeny haplotyping problems, Leo van Iersel, Judith Keijsper, Steven Kelk and Leen Stougie, IEEE/ACM Transactions on Computational Biology and Bioinformatics April-June 2008 (Vol. 5, No. 2) pp. 301-312. This is the journal version of the WABI paper Beaches... and contains new approximation results for PH and MPPH not found in the WABI version. The essence of the approximation results is explained in this presentation given at Bielefeld University (Germany) in November 2006.
• Beaches of islands of tractability: Algorithms for parsimony and minimum perfect phylogeny haplotyping problems, Leo van Iersel, Judith Keijsper, Steven Kelk and Leen Stougie. A conference version was presented at WABI2006. (WABI slides are available here.)
• Prefix reversals on binary and ternary strings, Cor Hurkens, Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie, John Tromp, SIAM Journal on Discrete Mathematics, 21(3), pp. 592--611 (2007).
  • There is a poster here about this paper.
  • Conference version appears in Algebraic Biology 2007, LNCS4545 pp. 292--307, DOI 10.1007/978-3-540-73433-8_21
• On the complexity of the Single Individual SNP Haplotyping Problem, Rudi Cilibrasi, Leo van Iersel, Steven Kelk and John Tromp, Algorithmica 49(1), pp. 13-36 (2007), DOI 10.1007/s00453-007-0029-z
• On the complexity of several haplotyping problems, Rudi Cilibrasi, Leo van Iersel, Steven Kelk and John Tromp, Algorithms in Bioinformatics: 5th International Workshop, WABI 2005, Mallorca, Spain, October 3-6, 2005, LNCS 3692 / 2005, pp. 128-139.
• On the relative complexity of approximately counting H-colourings, Steven Kelk, PhD Thesis, University of Warwick, 2004. (3.5mb, PDF)
• The complexity of choosing an H-colouring (nearly) uniformly at random, L.A. Goldberg, S. Kelk and M. Paterson, SICOMP, 33(2) 416-432 (2004) copyright SIAM (preliminary version STOC 2002)

Software for phylogenetic networks

• CASS
• LEV1ATHAN
• SIMPLISTIC
• MARLON
• LEVEL2

Last updated: February 28th, 2010. The solar image at the top of this page was obtained from here.