(Q46027168)

18 December 2017

title

A model-based approach to study nearest-neighbor influences reveals complex substitution patterns in non-coding sequences. (English)

1 reference

18 December 2017

nearest neighbour algorithm

main subject

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1

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18 December 2017

Yves Van de Peer

series ordinal

2

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18 December 2017

Stijn Vansteelandt

series ordinal

3

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18 December 2017

publication date

1 October 2008

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18 December 2017

published in

Systematic Biology

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18 December 2017

volume

57

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18 December 2017

issue

5

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18 December 2017

page(s)

675-692

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18 December 2017

DNA sequence evolution with neighbor-dependent mutation.

cites work

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Identification and measurement of neighbor-dependent nucleotide substitution processes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Frequency and spectrum of mutations produced by a single cis-syn thymine-thymine cyclobutane dimer in a single-stranded vector

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Solvable models of neighbor-dependent substitution processes

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Markov chain analysis finds a significant influence of neighboring bases on the occurrence of a base in eucaryotic nuclear DNA sequences both protein-coding and noncoding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Aligning multiple genomic sequences with the threaded blockset aligner

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Pseudo-likelihood analysis of codon substitution models with neighbor-dependent rates.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

The covariation between TpA deficiency, CpG deficiency, and G+C content of human isochores is due to a mathematical artifact.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Maximum Likelihood and Minimum-Steps Methods for Estimating Evolutionary Trees from Data on Discrete Characters

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Evolutionary trees from DNA sequences: A maximum likelihood approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

A Hidden Markov Model approach to variation among sites in rate of evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Cytosine deamination plays a primary role in the evolution of mammalian isochores

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Inference from Iterative Simulation Using Multiple Sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Reversible jump Markov chain Monte Carlo computation and Bayesian model determination

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Monte Carlo sampling methods using Markov chains and their applications

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Wide variations in neighbor-dependent substitution rates.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Inferring the root of a phylogenetic tree

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Bayesian inference of phylogeny and its impact on evolutionary biology

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Repbase update: a database and an electronic journal of repetitive elements

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

A large family of ancient repeat elements in the human genome is under strong selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

The closest living relatives of land plants

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

The UCSC Genome Browser Database

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

The human genome browser at UCSC

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

A new method for calculating evolutionary substitution rates

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Computing Bayes factors using thermodynamic integration.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Phylogenetic Tree Construction Using Markov Chain Monte Carlo

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

A nucleotide substitution model with nearest-neighbour interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Identification and characterization of multi-species conserved sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Differences between pair-wise and multi-sequence alignment methods affect vertebrate genome comparisons

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Bayesian phylogenetic inference via Markov chain Monte Carlo methods.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Equation of State Calculations by Fast Computing Machines

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Neighboring base composition and transversion/transition bias in a comparison of rice and maize chloroplast noncoding regions

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Neighboring base composition is strongly correlated with base substitution bias in a region of the chloroplast genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Protein evolution with dependence among codons due to tertiary structure.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Assessing site-interdependent phylogenetic models of sequence evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

MrBayes 3: Bayesian phylogenetic inference under mixed models

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Mechanisms underlying the evolution and maintenance of functionally heterogeneous 18S rRNA genes in Apicomplexans.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

A Stochastic Model for the Evolution of Autocorrelated DNA Sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Phylogenetic estimation of context-dependent substitution rates by maximum likelihood

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Should phylogenetic models be trying to "fit an elephant"?

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Bayesian selection of continuous-time Markov chain evolutionary models

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Comparative analyses of multi-species sequences from targeted genomic regions

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Among-site rate variation and its impact on phylogenetic analyses

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Phylogenetic analysis using parsimony and likelihood methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Branch-length prior influences Bayesian posterior probability of phylogeny.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Dependence among sites in RNA evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Model parameterization, prior distributions, and the general time-reversible model in Bayesian phylogenetics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

Markov Chasin Monte Carlo Algorithms for the Bayesian Analysis of Phylogenetic Trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F10635150802422324

10.1080/10635150802422324

21 January 2018

Identifiers

DOI

1 reference

18 December 2017

1 reference

18 December 2017