Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison (Q24548803)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16751341%20AND%20SRC:MED&resulttype=core&format=json

29 January 2020

title

Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16751341%20AND%20SRC:MED&resulttype=core&format=json

29 January 2020

0 references

1

1 reference

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29 January 2020

author name string

Peter D Keightley

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16751341%20AND%20SRC:MED&resulttype=core&format=json

29 January 2020

language of work or name

English

0 references

publication date

2 June 2006

1 reference

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29 January 2020

1 reference

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29 January 2020

volume

16

1 reference

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29 January 2020

issue

7

1 reference

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29 January 2020

page(s)

875-884

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16751341%20AND%20SRC:MED&resulttype=core&format=json

Combined evidence annotation of transposable elements in genome sequences

29 January 2020

cites work

1 reference

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Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Evidence for widespread degradation of gene control regions in hominid genomes

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

The regulatory content of intergenic DNA shapes genome architecture

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Benchmarking tools for the alignment of functional noncoding DNA

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Conservation of regulatory elements between two species of Drosophila

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Identification of pseudogenes in the Drosophila melanogaster genome

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

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

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Pseudogene evolution and natural selection for a compact genome

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

MCALIGN2: faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

The genetic organization of chromosomes

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Intron size and exon evolution in Drosophila

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Insertion/deletion and nucleotide polymorphism data reveal constraints in Drosophila melanogaster introns and intergenic regions

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

MAVID: constrained ancestral alignment of multiple sequences

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

MCALIGN: stochastic alignment of noncoding DNA sequences based on an evolutionary model of sequence evolution

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Insertion-deletion biases and the evolution of genome size

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Distribution and characterization of regulatory elements in the human genome

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

How intron splicing affects the deletion and insertion profile in Drosophila melanogaster

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Population, evolutionary and genomic consequences of interference selection

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

An expanding universe of noncoding RNAs

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Inferring parameters of mutation, selection and demography from patterns of synonymous site evolution in Drosophila

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

The correlation between intron length and recombination in drosophila. Dynamic equilibrium between mutational and selective forces.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Pyrimidine tracts between the 5' splice site and branch point facilitate splicing and recognition of a small Drosophila intron

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Molecular evolution between Drosophila melanogaster and D. simulans: reduced codon bias, faster rates of amino acid substitution, and larger proteins in D. melanogaster

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

"Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

A survey on intron and exon lengths

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Exon/intron organization of the chicken type II procollagen gene: intron size distribution suggests a minimal intron size

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Effects of intron length on differential processing of mouse mu heavy-chain mRNA

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Splicing signals in Drosophila: intron size, information content, and consensus sequences

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Selective constraints on intron evolution in Drosophila

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

High intrinsic rate of DNA loss in Drosophila.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Evolutionary dynamics of the enhancer region of even-skipped in Drosophila.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Adaptive evolution of non-coding DNA in Drosophila

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Intragenic Hill-Robertson interference influences selection intensity on synonymous mutations in Drosophila.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Comparative sequence analysis of a gene-dense region among closely related species of Drosophila melanogaster.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

A gene expression map for the euchromatic genome of Drosophila melanogaster.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Tracing the evolutionary history of Drosophila regulatory regions with models that identify transcription factor binding sites.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Patterns of insertion and deletion in contrasting chromatin domains.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Why do genes have introns? Recombination might add a new piece to the puzzle.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Intron size and natural selection

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

The evolution of codon preferences in Drosophila: a maximum-likelihood approach to parameter estimation and hypothesis testing.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Some evolutionary consequences of deleterious mutations.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484454

Patterns in spontaneous mutation revealed by human-baboon sequence comparison

28 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16751341

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Analysis of intronic conserved elements indicates that functional complexity might represent a major source of negative selection on non-coding sequences

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16751341

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1101/GR.5022906

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16751341%20AND%20SRC:MED&resulttype=core&format=json

29 January 2020

1 reference

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16751341%20AND%20SRC:MED&resulttype=core&format=json

29 January 2020

2 references