Accurate Estimation of Substitution Rates with Neighbor-Dependent Models in a Phylogenetic Context

Redefining CpG islands using hidden Markov models

(2010) H. Wu et al.   BIOSTATISTICS

Modelling the ancestral sequence distribution and model frequencies in context-dependent models for primate non-coding sequences

(2010) Guy Baele et al.   BMC EVOLUTIONARY BIOLOGY

Using Non-Reversible Context-Dependent Evolutionary Models to Study Substitution Patterns in Primate Non-Coding Sequences

(2010) Guy Baele et al.   JOURNAL OF MOLECULAR EVOLUTION

Phylogenetic distances for neighbour dependent substitution processes

(2010) Mikael Falconnet   MATHEMATICAL BIOSCIENCES

Rapid Likelihood Analysis on Large Phylogenies Using Partial Sampling of Substitution Histories

(2009) A. P. J. de Koning et al.   MOLECULAR BIOLOGY AND EVOLUTION

Is there an acceleration of the CpG transition rate during the mammalian radiation?

(2008) M. Peifer et al.   BIOINFORMATICS

A Markov chain Monte Carlo Expectation Maximization Algorithm for Statistical Analysis of DNA Sequence Evolution with Neighbor-Dependent Substitution Rates

(2008) Asger Hobolth   JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS

Genome-scale DNA methylation maps of pluripotent and differentiated cells

(2008) Alexander Meissner et al.   NATURE

A Model-Based Approach to Study Nearest-Neighbor Influences Reveals Complex Substitution Patterns in Non-coding Sequences

(2008) Guy Baele et al.   SYSTEMATIC BIOLOGY

The Impact of Recombination on Nucleotide Substitutions in the Human Genome

(2008) Laurent Duret et al.   PLoS Genetics

Solvable models of neighbor-dependent substitution processes

(2007) Jean Bérard et al.   MATHEMATICAL BIOSCIENCES