Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution (Q35024015)

5 August 2017

title

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

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David Haussler

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Laura Elnitski

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object named as

Laura Elnitski

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Francesca Chiaromonte

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object named as

Francesca Chiaromonte

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Mark Diekhans

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Webb Miller

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W James Kent

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Krishna M Roskin

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Arian Smit

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Shan Yang

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Ryan Weber

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Jia Li

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Michael O'Connor

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Diana Kolbe

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Scott Schwartz

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Simon Whelan

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publication date

1 January 2003

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5 August 2017

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volume

13

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5 August 2017

issue

1

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5 August 2017

page(s)

13-26

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Human-mouse alignments with BLASTZ

5 August 2017

cites work

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Distinguishing regulatory DNA from neutral sites

8 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Initial sequencing and comparative analysis of the mouse genome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Deterministic mutation rate variation in the human genome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Human SNP variability and mutation rate are higher in regions of high recombination

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

A high-resolution recombination map of the human genome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

The human genome browser at UCSC

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Genomewide comparison of DNA sequences between humans and chimpanzees

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Genes on human chromosome 19 show extreme divergence from the mouse orthologs and a high GC content

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

BLAT—The BLAST-Like Alignment Tool

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Mutation rates in mammalian genomes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Generation and comparative analysis of approximately 3.3 Mb of mouse genomic sequence orthologous to the region of human chromosome 7q11.23 implicated in Williams syndrome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Association between divergence and interspersed repeats in mammalian noncoding genomic DNA.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Late Cretaceous relatives of rabbits, rodents, and other extant eutherian mammals.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Misunderstandings about isochores. Part 1

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

The evolution of isochores

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Selective constraint in intergenic regions of human and mouse genomes.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Molecular phylogenetics: state-of-the-art methods for looking into the past

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Sequence conservation at human and mouse orthologous common fragile regions, FRA3B/FHIT and Fra14A2/Fhit

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Genomic strategies to identify mammalian regulatory sequences

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Comparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Initial sequencing and analysis of the human genome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Long-range comparison of human and mouse SCL loci: localized regions of sensitivity to restriction endonucleases correspond precisely with peaks of conserved noncoding sequences

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

RefSeq and LocusLink: NCBI gene-centered resources

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Conserved noncoding sequences are reliable guides to regulatory elements.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Comparative genomic sequence analysis of the human and mouse cystic fibrosis transmembrane conductance regulator genes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Isochores and the evolutionary genomics of vertebrates

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Comparative sequence analysis of the mouse and human Lgn1/SMA interval

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Chromosomal location effects on gene sequence evolution in mammals

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Models of molecular evolution and phylogeny

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Synonymous and nonsynonymous substitution distances are correlated in mouse and rat genes.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Evolutionary parameters of the transcribed mammalian genome: an analysis of 2,820 orthologous rodent and human sequences

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

PAML: a program package for phylogenetic analysis by maximum likelihood

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Large-scale comparative sequence analysis of the human and murine Bruton's tyrosine kinase loci reveals conserved regulatory domains

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Comparative analysis of 1196 orthologous mouse and human full-length mRNA and protein sequences

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Sequence analysis of the ERCC2 gene regions in human, mouse, and hamster reveals three linked genes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Human/mouse homology relationships

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Deleterious background selection with recombination

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

A molecular approach to estimating the human deleterious mutation rate.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Mammalian gene evolution: nucleotide sequence divergence between mouse and rat

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

The isochore organization of the human genome and its evolutionary history--a review

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

A codon-based model of nucleotide substitution for protein-coding DNA sequences

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Genomic sequence comparison of the human and mouse XRCC1 DNA repair gene regions

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Human and rodent DNA sequence comparisons: a mosaic model of genomic evolution

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

The hitch-hiking effect of a favourable gene

8 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

8 July 2018

https://pubmed.ncbi.nlm.nih.gov/12529302

12 December 2020

Amino acid composition and the evolutionary rates of protein-coding genes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Compositional constraints and genome evolution

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Nucleotide sequence of the BALB/c mouse beta-globin complex

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Mutation rates differ among regions of the mammalian genome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Complete nucleotide sequence of the rabbit beta-like globin gene cluster. Analysis of intergenic sequences and comparison with the human beta-like globin gene cluster

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Mammalian DNA replication: mutation biases and the mutation rate.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Sequence and comparative analysis of the rabbit alpha-like globin gene cluster reveals a rapid mode of evolution in a G + C-rich region of mammalian genomes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Significance of interspecies matches when evolutionary rate varies.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Is the synonymous substitution rate in mammals gene-specific?

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Genomic divergence between human and chimpanzee estimated from large-scale alignments of genomic sequences

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Covariation of GC content and the silent site substitution rate in rodents: implications for methodology and for the evolution of isochores.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

A test of translational selection at 'silent' sites in the human genome: base composition comparisons in alternatively spliced genes.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

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

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Comparative sequence analysis of a gene-rich cluster at human chromosome 12p13 and its syntenic region in mouse chromosome 6.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

The size differences among mammalian introns are due to the accumulation of small deletions

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

A model for the correlation of mutation rate with GC content and the origin of GC-rich isochores.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

A first-generation linkage disequilibrium map of human chromosome 22

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=430971

Local Rates of Recombination Are Positively Correlated with GC Content in the Human Genome

9 December 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/12529302

12 December 2020

Mutation pattern variation among regions of the primate genome

1 reference

https://pubmed.ncbi.nlm.nih.gov/12529302

12 December 2020

Long Human–Mouse Sequence Alignments Reveal Novel Regulatory Elements: A Reason to Sequence the Mouse Genome

1 reference

https://pubmed.ncbi.nlm.nih.gov/12529302

12 December 2020

Sensitivity of patterns of molecular evolution to alterations in methodology: a critique of Hughes and Yeager

1 reference

https://pubmed.ncbi.nlm.nih.gov/12529302

12 December 2020

Natural selection at major histocompatibility complex loci of vertebrates

1 reference

https://pubmed.ncbi.nlm.nih.gov/12529302

12 December 2020

Nucleic acid composition, codon usage, and the rate of synonymous substitution in protein-coding genes

1 reference

https://pubmed.ncbi.nlm.nih.gov/12529302

12 December 2020

Estimating the pattern of nucleotide substitution

1 reference

https://pubmed.ncbi.nlm.nih.gov/12529302

12 December 2020

Striking sequence similarity over almost 100 kilobases of human and mouse T–cell receptor DNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/12529302

12 December 2020

The effect of background selection against deleterious mutations on weakly selected, linked variants

1 reference

https://pubmed.ncbi.nlm.nih.gov/12529302

12 December 2020

Concerted evolution of mammalian cardiac myosin heavy chain genes

1 reference

https://pubmed.ncbi.nlm.nih.gov/12529302

12 December 2020

The proteins of linked genes evolve at similar rates

1 reference

https://pubmed.ncbi.nlm.nih.gov/12529302

12 December 2020

Identifiers

DOI

10.1101/GR.844103

1 reference

release_3lzkuu4rj5h33hyneyeazj7asq

5 August 2017

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/3lzkuu4rj5h33hyneyeazj7asq

24 November 2022

mapped directly with Wikidata item

PMC publication ID

430971

1 reference

5 August 2017

1 reference