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Methods to detect selection on noncoding DNA
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stated in
PubMed
title
Methods to detect selection on noncoding DNA
(English)
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stated in
PubMed
author
Peter Andolfatto
object named as
Peter Andolfatto
series ordinal
2
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author name string
Ying Zhen
series ordinal
1
1 reference
stated in
Crossref
language of work or name
English
1 reference
stated in
PubMed
publication date
2012
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stated in
PubMed
published in
Methods in Molecular Biology
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stated in
PubMed
volume
856
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stated in
PubMed
page(s)
141-59
1 reference
stated in
PubMed
cites work
RNA-Seq: a revolutionary tool for transcriptomics
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7 April 2017
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7 April 2017
Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila
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7 April 2017
Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison
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7 April 2017
Genome-wide identification of human functional DNA using a neutral indel model
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Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content
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7 April 2017
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
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7 April 2017
Small fitness effect of mutations in highly conserved non-coding regions
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7 April 2017
Benchmarking tools for the alignment of functional noncoding DNA
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A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep
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7 April 2017
Adaptive protein evolution at the Adh locus in Drosophila
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7 April 2017
Functional noncoding sequences derived from SINEs in the mammalian genome
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7 April 2017
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7 April 2017
Understanding mechanisms underlying human gene expression variation with RNA sequencing
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7 April 2017
The Ka/Ks ratio: diagnosing the form of sequence evolution
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Detection of nonneutral substitution rates on mammalian phylogenies
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Effective population size and the efficacy of selection on the X chromosomes of two closely related Drosophila species
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28 September 2017
Changes in selective effects over time facilitate turnover of enhancer sequences
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28 September 2017
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28 September 2017
Shifts in the intensity of purifying selection: an analysis of genome-wide polymorphism data from two closely related yeast species
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28 September 2017
Natural selection on cis and trans regulation in yeasts
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A population genetic hidden Markov model for detecting genomic regions under selection
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28 September 2017
On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila
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28 September 2017
Genome-wide scans for footprints of natural selection
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28 September 2017
Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites
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28 September 2017
Genetic recombination and molecular evolution
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28 September 2017
Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence
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28 September 2017
Pervasive natural selection in the Drosophila genome?
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28 September 2017
Pervasive hitchhiking at coding and regulatory sites in humans
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28 September 2017
Gene expression levels are a target of recent natural selection in the human genome
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28 September 2017
Similar rates of protein adaptation in Drosophila miranda and D. melanogaster, two species with different current effective population sizes
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28 September 2017
Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster
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28 September 2017
Assessing the evolutionary impact of amino acid mutations in the human genome
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28 September 2017
Positive and negative selection on noncoding DNA in Drosophila simulans
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28 September 2017
Selection on amino acid substitutions in Arabidopsis
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28 September 2017
Genomewide spatial correspondence between nonsynonymous divergence and neutral polymorphism reveals extensive adaptation in Drosophila
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28 September 2017
Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome
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28 September 2017
Adaptive gene expression divergence inferred from population genomics
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28 September 2017
Adaptive evolution of conserved noncoding elements in mammals
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28 September 2017
Human genome ultraconserved elements are ultraselected
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28 September 2017
Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution.
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28 September 2017
Recombination and linkage disequilibrium in Arabidopsis thaliana.
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28 September 2017
The evolution of gene expression QTL in Saccharomyces cerevisiae
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28 September 2017
Widely distributed noncoding purifying selection in the human genome
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28 September 2017
Transcription-related mutations and GC content drive variation in nucleotide substitution rates across the genomes of Arabidopsis thaliana and Arabidopsis lyrata
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28 September 2017
A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection
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PubMed Central
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28 September 2017
Adaptive genic evolution in the Drosophila genomes
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28 September 2017
Genomic selective constraints in murid noncoding DNA
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28 September 2017
Accelerated evolution of conserved noncoding sequences in humans
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PubMed Central
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28 September 2017
Natural selection on human microRNA binding sites inferred from SNP data
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
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28 September 2017
Selection, recombination and demographic history in Drosophila miranda
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28 September 2017
Detecting natural selection on cis-regulatory DNA.
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
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28 September 2017
MCALIGN2: faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution
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28 September 2017
Detecting selection in noncoding regions of nucleotide sequences
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28 September 2017
Population genetic and phylogenetic evidence for positive selection on regulatory mutations at the factor VII locus in humans
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28 September 2017
Bayesian analysis suggests that most amino acid replacements in Drosophila are driven by positive selection
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
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28 September 2017
MCALIGN: stochastic alignment of noncoding DNA sequences based on an evolutionary model of sequence evolution
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
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28 September 2017
Effect of misoriented sites on neutrality tests with outgroup.
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28 September 2017
Phylogenetic shadowing of primate sequences to find functional regions of the human genome
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28 September 2017
Adaptive protein evolution in Drosophila
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
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28 September 2017
Directional selection and the site-frequency spectrum.
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28 September 2017
The neutral theory in the genomic era.
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28 September 2017
Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences.
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
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28 September 2017
Positive and negative selection on the human genome
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
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28 September 2017
Selective constraint in intergenic regions of human and mouse genomes.
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
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28 September 2017
Endless Forms
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PubMed Central
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28 September 2017
Terumi Mukai and the riddle of deleterious mutation rates
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28 September 2017
Natural selection and the frequency distributions of "silent" DNA polymorphism in Drosophila.
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28 September 2017
Contingency tests of neutrality using intra/interspecific gene trees: the rejection of neutrality for the evolution of the mitochondrial cytochrome oxidase II gene in the hominoid primates.
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28 September 2017
Cases of ancient mobile element DNA insertions that now affect gene regulation
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28 September 2017
Amino acid substitution at the Adh locus of Drosophila is facilitated by small population size
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
28 September 2017
Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
28 September 2017
Confidence interval for the number of selectively neutral amino acid polymorphisms
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
28 September 2017
Deleterious mutations and the evolution of sexual reproduction
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
28 September 2017
Population genetics of polymorphism and divergence
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
28 September 2017
Studying patterns of recent evolution at synonymous sites and intronic sites in Drosophila melanogaster
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
31 May 2018
Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
31 May 2018
Estimating the genomewide rate of adaptive protein evolution in Drosophila
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
31 May 2018
Changing effective population size and the McDonald-Kreitman test
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
31 May 2018
Searching for regulatory elements in human noncoding sequences.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
31 May 2018
Evolutionary dynamics of the enhancer region of even-skipped in Drosophila
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
31 May 2018
A molecular approach to estimating the human deleterious mutation rate.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
31 May 2018
Positive and negative selection on noncoding DNA close to protein-coding genes in wild house mice.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
28 November 2018
Genome-wide functional element detection using pairwise statistical alignment outperforms multiple genome footprinting techniques
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
28 November 2018
Natural selection on synonymous and nonsynonymous mutations shapes patterns of polymorphism in Populus tremula.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
28 November 2018
Distributions of selectively constrained sites and deleterious mutation rates in the hominid and murid genomes.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
28 November 2018
Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
28 November 2018
Mapping regulatory elements by DNaseI hypersensitivity chip (DNase-Chip).
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
28 November 2018
Controlling type-I error of the McDonald-Kreitman test in genomewide scans for selection on noncoding DNA.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
28 November 2018
Combining statistical alignment and phylogenetic footprinting to detect regulatory elements.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
28 November 2018
Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
28 November 2018
Uncertainty in homology inferences: assessing and improving genomic sequence alignment
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
28 November 2018
Purifying selection maintains highly conserved noncoding sequences in Drosophila.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
28 November 2018
Context dependence, ancestral misidentification, and spurious signatures of natural selection.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
28 November 2018
Intron length evolution in Drosophila.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
28 November 2018
The rate of adaptive evolution in enteric bacteria.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
28 November 2018
Conserved noncoding sequences are selectively constrained and not mutation cold spots
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
28 November 2018
Adaptive evolution of non-coding DNA in Drosophila
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
28 November 2018
The genomic rate of adaptive amino acid substitution in Drosophila.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
28 November 2018
Inference of positive and negative selection on the 5' regulatory regions of Drosophila genes
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
28 November 2018
The effects of selection against spurious transcription factor binding sites.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
28 November 2018
Quantifying the Slightly Deleterious Mutation Model of Molecular Evolution
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
28 November 2018
A test for adaptive change in DNA sequences controlling transcription.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725466
retrieved
28 November 2018
Pattern of selective constraint in C. elegans and C. briggsae genomes
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/22399458
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Heads or tails: a simple reliability check for multiple sequence alignments
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/22399458
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
The Impact of Natural Selection on the Genome: Emerging Patterns in Drosophila and Arabidopsis
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1007%2F978-1-61779-585-5_6
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Identifiers
DOI
10.1007/978-1-61779-585-5_6
1 reference
stated in
PubMed
PMC publication ID
3725466
1 reference
stated in
PubMed
PubMed publication ID
22399458
1 reference
stated in
PubMed
ResearchGate publication ID
221686018
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