Application Note HMMoC – a compiler for hidden Markov models (2008)
Summary: Hidden Markov models are widely applied within computational biology. The large datasets and complex models involved demand optimized implementations, while efficient exploration of model...
statistical insertion–deletion (2008)
Gerton Lunter, István Miklós, Alexei Drummond, Jens Ledet Jensen, Jotun Hein
phylogenetic inference under a
Investigating selection on viruses: a statistical alignment approach (2008)
De Groot, Saskia, Mailund, Thomas, Lunter, Gerton, Hein, Jotun
Abstract Background Two problems complicate the study of selection in viral genomes: Firstly, the presence of genes in overlapping reading frames implies that selection in one reading frame can bias...
Summary: Hidden Markov models are widely applied within computational biology. The large data sets and complex models involved demand optimized implementations, while efficient exploration of model...
Uncertainty in homology inferences: Assessing and improving genomic sequence alignment (2008)
Lunter, Gerton, Rocco, Andrea, Mimouni, Naila, Heger, Andreas, Caldeira, Alexandre, Hein, Jotun
Sequence alignment underpins all of comparative genomics, yet it remains an incompletely solved problem. In particular, the statistical uncertainty within inferred alignments is often disregarded,...
HMMoC a compiler for hidden Markov models (2007)
Summary: Hidden Markov models are widely applied within computational biology. The large data sets and complex models involved demand optimized implementations, while efficient exploration of model...
Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes (2007)
Motivation: The two mutation processes that have the largest impact on genome evolution at small scales are substitutions, and sequence insertions and deletions (indels). While the former have been...
Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs (2007)
Ponjavic, Jasmina, Ponting, Chris P., Lunter, Gerton
Long transcripts that do not encode protein have only rarely been the subject of experimental scrutiny. Presumably, this is owing to the current lack of evidence of their functionality, thereby...
Genome-Wide Identification of Human Functional DNA Using a Neutral Indel Model (2006)
Gerton Lunter, Chris P. Ponting, Jotun Hein
It has become clear that a large proportion of functional DNA in the human genome does not code for protein. Identification of this non-coding functional sequence using comparative approaches is...
Signatures of adaptive evolution within human non-coding sequence (2006)
Ponting, Chris P., Lunter, Gerton
The human genome is often portrayed as consisting of three sequence types, each distinguished by their mode of evolution. Purifying selection is estimated to act on 2.5–5.0% of the genome, whereas...
Genome-wide identification of human functional DNA using a neutral indel model (2005)
Gerton Lunter, Chris P Ponting, Jotun Hein
It has recently become clear that a large proportion of functional DNA in the human genome does not code for protein. Identification of this non-coding functional sequence using comparative...
Bayesian coestimation of phylogeny and sequence alignment (2005)
Lunter, Gerton, Miklós, István, Drummond, Alexei, Jensen, Jens, Hein, Jotun
Abstract Background Two central problems in computational biology are the determination of the alignment and phylogeny of a set of biological sequences. The traditional approach to this problem is to...
Gerton Lunter, István Miklós, Alexei Drummond, Jens Ledet Jensen, Alexei Drummond, Jens Ledet Jensen, ...
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
A nucleotide substitution model with nearest-neighbour interactions (2004)
Motivation: It is well known that neighbouring nucleotides in DNA sequences do not mutate independently of each other. In this paper, we introduce a context-dependent substitution model and derive an...
Bayesian coestimation of phylogeny and sequence alignment
Lunter, Gerton, Miklós, István, Drummond, Alexei, Jensen, Jens Ledet, Hein, Jotun
Genome-Wide Identification of Human Functional DNA Using a Neutral Indel Model
Lunter, Gerton, Ponting, Chris P, Hein, Jotun
It has become clear that a large proportion of functional DNA in the human genome does not code for protein. Identification of this non-coding functional sequence using comparative approaches is...
Bayesian coestimation of phylogeny and sequence alignment
Lunter, Gerton, Miklós, István, Drummond, Alexei, Jensen, Jens Ledet, Hein, Jotun
Genome-Wide Identification of Human Functional DNA Using a Neutral Indel Model
Lunter, Gerton, Ponting, Chris P, Hein, Jotun
It has become clear that a large proportion of functional DNA in the human genome does not code for protein. Identification of this non-coding functional sequence using comparative approaches is...
Novel Type IV Secretion System Involved in Propagation of Genomic Islands▿
Juhas, Mario, Crook, Derrick W., Dimopoulou, Ioanna D., Lunter, Gerton, Harding, Rosalind M., Ferguson, David J. P., ...
Type IV secretion systems (T4SSs) mediate horizontal gene transfer, thus contributing to genome plasticity, evolution of infectious pathogens, and dissemination of antibiotic resistance and other...
Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs
Ponjavic, Jasmina, Ponting, Chris P., Lunter, Gerton
Long transcripts that do not encode protein have only rarely been the subject of experimental scrutiny. Presumably, this is owing to the current lack of evidence of their functionality, thereby...
Investigating selection on viruses: a statistical alignment approach
De Groot, Saskia, Mailund, Thomas, Lunter, Gerton, Hein, Jotun
Uncertainty in homology inferences: Assessing and improving genomic sequence alignment
Lunter, Gerton, Rocco, Andrea, Mimouni, Naila, Heger, Andreas, Caldeira, Alexandre, Hein, Jotun
Sequence alignment underpins all of comparative genomics, yet it remains an incompletely solved problem. In particular, the statistical uncertainty within inferred alignments is often disregarded,...
Ponjavic, Jasmina, Oliver, Peter L., Lunter, Gerton, Ponting, Chris P.
Besides protein-coding mRNAs, eukaryotic transcriptomes include many long non-protein-coding RNAs (ncRNAs) of unknown function that are transcribed away from protein-coding loci. Here, we have...