BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC (2009)
Satija, Rahul, Novák, Ádám, Miklós, István, Lyngsø, Rune, Hein, Jotun
Abstract Background We have previously combined statistical alignment and phylogenetic footprinting to detect conserved functional elements without assuming a fixed alignment. Considering a...
Counting All Possible Ancestral Configurations of Sample Sequences in Population Genetics (2009)
Yun S. Song, Rune Lyngsø, Jotun Hein
Abstract — Given a set D of input sequences, a genealogy for D can be constructed backwards in time, using such evolutionary events as mutation, coalescent and recombination. An ancestral...
An Analysis of Structural Influences on Selection in RNA Genes (2009)
Mimouni, Naila K., Lyngsø, Rune B., Griffiths-Jones, Sam, Hein, Jotun
Noncoding RNAs (ncRNAs) are transcripts that do not code for protein but rather function as RNA in catalytic, regulatory, or structural roles in the cell. ncRNAs are involved in universally conserved...
A stochastic model for the evolution of metabolic networks with neighbor dependence (2009)
Mithani, Aziz, Preston, Gail M., Hein, Jotun
Motivation: Most current research in network evolution focuses on networks that follow a Duplication Attachment model where the network is only allowed to grow. The evolution of metabolic networks,...
Rahnuma: hypergraph-based tool for metabolic pathway prediction and network comparison (2009)
Mithani, Aziz, Preston, Gail M., Hein, Jotun
Summary:We present a tool called Rahnuma for prediction and analysis of metabolic pathways and comparison of metabolic networks. Rahnuma represents metabolic networks as hypergraphs and computes all...
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...
The TPS algorithm & the Evolutionary Path of Protein Structures 1.12.07 (2008)
Tom Darden, Jotun Hein, Mark Sansom, Lee Pedersen, Willie Taylor
Comparing homologous objects are central to biology and the last decade have been dominated by this in the field of comparative genomics. However, many other objects than sequences in biology are...
Annotation of Selection Strengths in Viral Genomes (2008)
Stephen Mccauley, Saskia De Groot, Thomas Mailund, Jotun Hein
Motivation: Viral genomes tend to code in overlapping reading frames to maximize informational content. This may result in atypical codon bias and particular evolutionary constraints. Due to the fast...
• Whole Genome Alignment: • Sequence Level Alignment • Protein Gene Finding (2008)
Jotun Hein, Vasile Palade, Rna Gene Finding, Regulatory Element Characterisation
Annotate 12 Drosophila genomes for regulatory signals.
How reliably can we predict the reliability of protein structure predictions? (2008)
Miklós, István, Novák ', Ádám, Dombai, Balázs, Hein, Jotun
Abstract Background Comparative methods have been the standard techniques for in silico protein structure prediction. The prediction is based on a multiple alignment that contains both reference...
BIOINFORMATICS APPLICATIONS NOTE (2008)
Thomas Mailund, Mikkel H. Schierup, Jesper N. Madsen, Jotun Hein, Leif Schauser
Genetics and population analysis Vol. 22 no. 18 2006, pages 2317–2318 doi:10.1093/bioinformatics/btl153 GeneRecon—a coalescent based tool for fine-scale association mapping
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,...
Novák, Ádám, Miklós, István, Lyngsø, Rune, Hein, Jotun
Motivation: Bayesian analysis is one of the most popular methods in phylogenetic inference. The most commonly used methods fix a single multiple alignment and consider only substitutions as...
Combining statistical alignment and phylogenetic footprinting to detect regulatory elements (2008)
Satija, Rahul, Pachter, Lior, Hein, Jotun
Motivation: Traditional alignment-based phylogenetic footprinting approaches make predictions on the basis of a single assumed alignment. The predictions are therefore highly sensitive to alignment...
Comparison of Coding DNA (2007)
. We discuss a model for the evolutionary distance between two coding DNA sequences which specializes to the DNA/protein model proposed in Hein [4]. We discuss the DNA/protein model in details and...
Abstract. We discuss a model for the evolutionary distance between two coding DNA sequences which specializes to the DNA/protein model proposed in Hein [4]. We discuss the DNA/protein model in...
Roald Forsberg, Martin B. Oleksiewicz, Jotun Hein, Anette Bøtner, Torben Storgaard
The disease caused by porcine reproductive and respiratory syndrome virus (PRRSV) emerged independently and almost simultaneously in Europe (1990) and North America (1987). The original reservoir of...
Jotun Hein, Tao Jiang, Lusheng Wang, Kaizhong Zhang
x We study the computational complexity and approximation of several problems arising in the comparison of evolutionary trees. It is shown that the maximum agreement subtree (MAST) problem for three...
Comparative annotation of viral genomes with non-conserved gene structure (2007)
De Groot, Saskia, Mailund, Thomas, Hein, Jotun
Motivation: Detecting genes in viral genomes is a complex task. Due to the biological necessity of them being constrained in length, RNA viruses in particular tend to code in overlapping reading...
Stephen Mccauley, Saskia De Groot, Thomas Mailund, Jotun Hein
Motivation: Viral genomes tend to code in overlapping reading frames to maximize informational content. This may result in atypical codon bias and particular evolutionary constraints. Due to the fast...
Comparative Annotation of Viral Genomes with Non-Conserved Gene Structure (2007)
De Groot, Saskia, Mailund, Thomas, Hein, Jotun
Motivation: Detecting genes in viral genomes is a complex task. Due to the biological necessity of them being constrained in length, RNA viruses in particular tend to code in overlapping reading...
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...
BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm078 Sequence analysis (2006)
Saskia De Groot, Thomas Mailund, Jotun Hein
Comparative annotation of viral genomes with non-conserved gene structure
Using hidden Markov models and observed evolution to annotate viral genomes (2006)
McCauley, Stephen, Hein, Jotun
Motivation: ssRNA (single stranded) viral genomes are generally constrained in length and utilize overlapping reading frames to maximally exploit the coding potential within the genome length...
GeneRecon--a coalescent based tool for fine-scale association mapping (2006)
Mailund, Thomas, Schierup, Mikkel H., Pedersen, Christian N. S., Madsen, Jesper N., Hein, Jotun, Schauser, Leif
Summary: GeneRecon is a tool for fine-scale association mapping using a coalescence model. GeneRecon takes as input case–control data from phased or unphased SNP and microsatellite genotypes. The...
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...
Tree measures and the number of segregating sites in time-structured population samples (2005)
Forsberg, Roald, Drummond, Alexei J, Hein, Jotun
Abstract Background Time-structured genetic samples are a valuable source of information in population genetics because they provide several correlated observations of the underlying evolutionary...
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...
Schizophrenia Mendelian & Complex diseases (2005)
Leif Schauser, Thomas Mailund, Jesper N. Madsen, Jotun Hein, Mikkel H. Schierup, Cystic Fibrosis
The concept of mapping in case-control studies Pr (Disease gene location | data)
Constructing minimal ancestral recombination graphs (2005)
By viewing the ancestral recombination graph as defining a sequence of trees, we show how possible evolutionary histories consistent with given data can be constructed using the minimum number of...
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
Constructing minimal ancestral recombination graphs (2005)
By viewing the ancestral recombination graph as defining a sequence of trees, we show how possible evolutionary histories consistent with given data can be constructed using the minimum number of...
An Evolutionary Model for Protein-Coding Regions with Conserved RNA Structure (2004)
Pedersen, Jakob Skou, Forsberg, Roald, Meyer, Irmtraud Margret, Hein, Jotun
Here we present a model of nucleotide substitution in protein-coding regions that also encode the formation of conserved RNA structures. In such regions, apparent evolutionary context dependencies...
Pedersen, Jakob Skou, Meyer, Irmtraud Margret, Forsberg, Roald, Simmonds, Peter, Hein, Jotun
Existing computational methods for RNA secondary-structure prediction tacitly assume RNA to only encode functional RNA structures. However, experimental studies have revealed that some RNA sequences,...
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...
An Evolutionary Model for Protein-Coding Regions with Conserved RNA Structure (2004)
Pedersen, Jakob Skou, Forsberg, Roald, Meyer, Irmtraud Margret, Hein, Jotun
Here we present a model of nucleotide substitution in protein-coding regions that also encode the formation of conserved RNA structures. In such regions, apparent evolutionary context dependencies...
An Evolutionary Model for Protein-Coding Regions with Conserved RNA Structure (2004)
Pedersen, Jakob Skou, Forsberg, Roald, Meyer, Irmtraud Margret, Hein, Jotun
Here we present a model of nucleotide substitution in protein-coding regions that also encode the formation of conserved RNA structures. In such regions, apparent evolutionary context dependencies...
Gene finding with a hidden Markov model of genome structure and evolution (2003)
Pedersen, Jakob Skou, Hein, Jotun
Motivation: A growing number of genomes are sequenced. The differences in evolutionary pattern between functional regions can thus be observed genome-wide in a whole set of organisms. The diverse...
Pfold: RNA secondary structure prediction using stochastic context-free grammars (2003)
RNA secondary structures are important in many biological processes and efficient structure prediction can give vital directions for experimental investigations. Many available programs for RNA...
Pfold: RNA secondary structure prediction using stochastic context-free grammars (2003)
RNA secondary structures are important in many biological processes and efficient structure prediction can give vital directions for experimental investigations. Many available programs for RNA...
Gene finding with a hidden Markov model of genome structure and evolution (2003)
Pedersen, Jakob Skou, Hein, Jotun
Motivation: A growing number of genomes are sequenced. The differences in evolutionary pattern between functional regions can thus be observed genome-wide in a whole set of organisms. The diverse...
A Simulation Study of the Reliability of Recombination Detection Methods (2001)
Wiuf, Carsten, Christensen, Thomas, Hein, Jotun
There exist many methods to detect recombination or mosaic structure in a sample of DNA sequences. But how reliable are they? Four methods were investigated with respect to their power to detect...
Discussion: recent common ancestors of all present-day individuals (1999)
Donnelly, Peter, Wiuf, Carsten, Hein, Jotun, Slatkin, Montgomery, Ewens, W. J., Kingman, J. F. C.
Recombination as a point process along sequences (1999)
Histories of sequences in the coalescent model with recombination can be simulated using an algorithm that takes as input a sample of extant sequences. The algorithm traces the history of the...
Pfold: RNA secondary structure prediction using stochastic context-free grammars
RNA secondary structures are important in many biological processes and efficient structure prediction can give vital directions for experimental investigations. Many available programs for RNA...
Recursions for statistical multiple alignment
Hein, Jotun, Jensen, Jens Ledet, Pedersen, Christian N. S.
Algorithms are presented that allow the calculation of the probability of a set of sequences related by a binary tree that have evolved according to the Thorne–Kishino–Felsenstein model for a...
A comparative method for finding and folding RNA secondary structures within protein-coding regions
Pedersen, Jakob Skou, Meyer, Irmtraud Margret, Forsberg, Roald, Simmonds, Peter, Hein, Jotun
Existing computational methods for RNA secondary-structure prediction tacitly assume RNA to only encode functional RNA structures. However, experimental studies have revealed that some RNA sequences,...
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...
Pfold: RNA secondary structure prediction using stochastic context-free grammars
RNA secondary structures are important in many biological processes and efficient structure prediction can give vital directions for experimental investigations. Many available programs for RNA...
Recursions for statistical multiple alignment
Hein, Jotun, Jensen, Jens Ledet, Pedersen, Christian N. S.
Algorithms are presented that allow the calculation of the probability of a set of sequences related by a binary tree that have evolved according to the Thorne–Kishino–Felsenstein model for a...
A comparative method for finding and folding RNA secondary structures within protein-coding regions
Pedersen, Jakob Skou, Meyer, Irmtraud Margret, Forsberg, Roald, Simmonds, Peter, Hein, Jotun
Existing computational methods for RNA secondary-structure prediction tacitly assume RNA to only encode functional RNA structures. However, experimental studies have revealed that some RNA sequences,...
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...
On Recombination-Induced Multiple and Simultaneous Coalescent Events
Davies, Joanna L., Simančík, František, Lyngsø, Rune, Mailund, Thomas, Hein, Jotun
Coalescent theory deals with the dynamics of how sampled genetic material has spread through a population from a single ancestor over many generations and is ubiquitous in contemporary molecular...
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,...
David Sankoff, Yvon Abel, Jotun Hein
Local optimization, Heuristics, Molecular evolution,
This document in subdirectoryRS/98/3/ Comparison of coding DNA
Rune B. Lyngsø, Jotun Hein, Lyngsø Jotun Hein
Reproduction of all or part of this work is permitted for educational or research use on condition that this copyright notice is included in any copy. See back inner page for a list of recent BRICS...
BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC
Satija, Rahul, Novák, Ádám, Miklós, István, Lyngsø, Rune, Hein, Jotun
Taylor, Jennifer M., Street, Teresa L., Hao, Lizhong, Copley, Richard, Taylor, Martin S., Hayden, Patrick J., ...
The mammalian epidermis is a continually renewing structure that provides the interface between the organism and an innately hostile environment. The keratinocyte is its principal cell. Keratinocyte...