Gerton Lunter

Contact details:	MRC Functional Genetics Unit
	Department of Physiology Anatomy & Genetics
	University of Oxford
	1 South Parks Road,
	Oxford OX1 3QX, UK
	Telephone: 01865 285854
	Fax: 01865 285862
	E-mail: gerton.lunter @ dpag.ox.ac.uk

Research

I am based in the Comparative Genomics Group headed by Chris Ponting, in the MRC Functional Genetics Unit at Oxford university.

My research focuses on the development of methods to study evolution, in particular the evolution of non-coding DNA. I'm especially interested in studying and exploiting the evolutionary imprint of indels.

Other interests include probabilistic sequence alignment, phylogenetic inference, the structured coalescent model, and the evolution of gene expression levels.

Software

HMMoC - generates efficient C++ code from a high-level description of a hidden Markov model (see the paper)
GRAPe - (Beta version) Probabilistic whole-genome re-alignment tool; annotates alignments with reliability scores
Gapscan - Python script to identify indel-purified segments from genome alignments (see the paper)

Data

Human indel-purified sequence, with links to the UCSC en Ensembl browsers. Bulk download (hg17) here.
Human-mouse posterior decoding alignments computed by GRAPe, and annotated with local reliabilities.

Short CV

1989-1994	Mathematics and Physics (Groningen, The Netherlands)
1994-1999	PhD in mathematics, dynamical systems (Groningen, The Netherlands)
2000-2002	Senior Scientist, Philips NatLab (Eindhoven, The Netherlands).
2002-2005	Postdoctoral researcher with Jotun Hein (Oxford)
2005-now	MRC Bioinformatics Fellow, with Chris Ponting (Oxford)

Recent publications

S. de Groot, T. Mailund, G.A. Lunter and Jotun Hein (2008). Investigating selection on viruses: a statistical alignment approach BMC Bioinformatics 9:304. Journal link
G.A. Lunter, A. Rocco, N. Mimouni, A. Heger, A. Caldeira and J. Hein (2007). Uncertainty in homology inferences: Assessing and improving genomic sequence alignment Genome Res. (Epub before print). Journal link. Simulated data used for the paper is here.
G.A. Lunter (2007) Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes Bioinformatics 2007; doi:10.1093/bioinformatics/btm185 Journal link
G.A. Lunter (2007) HMMoC - a compiler for hidden Markov models Bioinformatics 2007; doi:10.1093/bioinformatics/btm350 Journal link

J. Ponjavic, C.P. Ponting, G.A. Lunter (2007) Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs Genome Res. 17:556-565, 2007 Journal link

G.A. Lunter (2007) Dog as an outgroup to human and mouse. PLoS Comput Biol 3(4):e74 Journal link PubMed archive

M. Jugas, D.W. Crook, I.D. Dimopoulou, G.A. Lunter, R.M. Harding, D.J.P. Ferguson, D.W. Hood (2007) Novel type IV secretion systems involved in propagation of genomic islands J. Bacteriol 189(3):761-71 Journal link

C.P. Ponting, G. Lunter (2006) Signatures of adaptive evolution within human non-coding sequence. Hum Mol Genet. 15 Spec No 2:R170-5. Review. Journal link

C.P. Ponting, G. Lunter (2006) Human brain gene wins genome race. Nature. 443(7108):149-50. Journal link

G Lunter, CP Ponting, J Hein (2006) Genome-wide identification of human functional DNA using a neutral indel model PLoS Comput Biol. 2006 Jan;2(1):e5 Journal link

G.A. Lunter, I. Miklós, A.J. Drummond, J.L. Jensen and J. Hein (2005) Bayesian Coestimation of Phylogeny and Sequence Alignment BMC Bioinformatics 2005, 6:83. journal link

G.A. Lunter and J. Hein (2004) A nucleotide substitution model with nearest-neighbour interactions Bioinformatics 20(supp. 1):i216-i223 pdf Journal link

G.A. Lunter, A.J. Drummond, I. Miklós and J. Hein (2004), Statistical Alignment: Recent Progress, New Applications, and Challenges, in: Rasmus Nielsen (ed.), "Statistical methods in Molecular Evolution", Springer Verlag's Series in Statistics in Health and Medicine. Publisher link pdf

I. Miklós, G.A. Lunter and I. Holmes (2004) A "long indel" model for evolutionary sequence alignment. Mol. Biol. Evol. 21(3):529-540. Journal link pdf

G.A. Lunter, I. Miklós, Y.S. Song and J. Hein (2003) An efficient algorithm for statistical multiple alignment on arbitrary phylogenetic trees. J. Comp. Biol., 10(6):869-889. pdf Journal link

G.A. Lunter, I. Miklós, A.J. Drummond, J.L. Jensen and J. Hein (2003) Bayesian phylogenetic inference under a statistical indel model. Lecture Notes in Bioinformatics, Proceedings of WABI'03, 2812:228-244. pdf Link to publisher

Selected older publications:

G.A. Lunter, Bifurcations in Hamiltonian systems, Computing singularities by Gröbner bases, published as Lecture Notes in Mathematics 1806 (2003), ISBN 3-540-00403-3. Link to publisher.

H.W. Broer, I. Hoveijn, G.A. Lunter, G. Vegter, Resonances in a spring-pendulum: algorithms for equivariant singularity theory, Nonlinearity 11 (1998), 1569-1605. pdf

G.A. Lunter, New proofs and a generalisation of inequalities of Fan, Taussky and Todd, J. of Math. Anal. and Appl. 185 no. 2 (1994), 464-476. pdf

G.A. Lunter, B.S.J.M. van Wayenburg, Het idee van Fourier (Dutch), in: "Speeltuin van de wiskunde", B. de Smit and J. Top (eds.), ISBN: 907698820X (2003). link to publisher pdf

Other things

My Sinclair ZX Spectrum emulator WinZ80 (click here to download) is still good for playing games - some of which can be found here.