Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes (Q35493886)

8 August 2017

title

Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes (English)

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8 August 2017

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8 August 2017

Manolis Kellis

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8 August 2017

Pouya Kheradpour

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8 August 2017

Michael F Lin

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8 August 2017

Stefan Washietl

series ordinal

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8 August 2017

Brian J Parker

series ordinal

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8 August 2017

publication date

12 October 2011

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8 August 2017

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8 August 2017

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8 August 2017

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8 August 2017

page(s)

1916-1928

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New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes

8 August 2017

cites work

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Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content

12 July 2018

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Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons

12 July 2018

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COMIT: identification of noncoding motifs under selection in coding sequences

12 July 2018

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12 July 2018

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Detection of nonneutral substitution rates on mammalian phylogenies

12 July 2018

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Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches

12 July 2018

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The coexistence of the nucleosome positioning code with the genetic code on eukaryotic genomes

12 July 2018

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12 July 2018

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Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing

12 July 2018

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Identifying novel constrained elements by exploiting biased substitution patterns

12 July 2018

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VARNA: Interactive drawing and editing of the RNA secondary structure

12 July 2018

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Reliabilities of identifying positive selection by the branch-site and the site-prediction methods

12 July 2018

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Conserved elements within open reading frames of mammalian Hox genes

12 July 2018

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Poly(dA:dT) tracts: major determinants of nucleosome organization

12 July 2018

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Posttranscriptional crossregulation between Drosha and DGCR8.

12 July 2018

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A regulatory module embedded in the coding region of Hoxa2 controls expression in rhombomere 2

12 July 2018

1 reference

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Evidence for common short natural trans sense-antisense pairing between transcripts from protein coding genes

12 July 2018

1 reference

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The trouble with sliding windows and the selective pressure in BRCA1.

12 July 2018

1 reference

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The impact of the nucleosome code on protein-coding sequence evolution in yeast

12 July 2018

1 reference

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Models of coding sequence evolution

12 July 2018

1 reference

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Mutations of LRTOMT, a fusion gene with alternative reading frames, cause nonsyndromic deafness in humans

12 July 2018

1 reference

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Investigating protein-coding sequence evolution with probabilistic codon substitution models

12 July 2018

1 reference

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Ultraconserved coding regions outside the homeobox of mammalian Hox genes

12 July 2018

1 reference

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Bayesian comparisons of codon substitution models

12 July 2018

1 reference

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Measuring the prevalence of regional mutation rates: an analysis of silent substitutions in mammals, fungi, and insects

12 July 2018

1 reference

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An ultraconserved Hox-Pbx responsive element resides in the coding sequence of Hoxa2 and is active in rhombomere 4.

12 July 2018

1 reference

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The computational detection of functional nucleotide sequence motifs in the coding regions of organisms

12 July 2018

1 reference

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Dynamic regulation of nucleosome positioning in the human genome

12 July 2018

1 reference

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Bioinformatics prediction of overlapping frameshifted translation products in mammalian transcripts

12 July 2018

1 reference

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Prominent roles for odorant receptor coding sequences in allelic exclusion

12 July 2018

1 reference

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MicroRNA targeting specificity in mammals: determinants beyond seed pairing

12 July 2018

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Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

12 July 2018

1 reference

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Widespread positive selection in synonymous sites of mammalian genes

12 July 2018

1 reference

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A first look at ARFome: dual-coding genes in mammalian genomes

12 July 2018

1 reference

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An empirical codon model for protein sequence evolution

12 July 2018

1 reference

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Splicing and the evolution of proteins in mammals

12 July 2018

1 reference

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The genetic code is nearly optimal for allowing additional information within protein-coding sequences

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Detecting non-coding selective pressure in coding regions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

A machine learning strategy to identify candidate binding sites in human protein-coding sequence

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Comparative analysis identifies exonic splicing regulatory sequences--The complex definition of enhancers and silencers

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

A periodic pattern of mRNA secondary structure created by the genetic code

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Identification and classification of conserved RNA secondary structures in the human genome

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Regions of extreme synonymous codon selection in mammalian genes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

GONOME: measuring correlations between GO terms and genomic positions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Can RNA selection pressure distort the measurement of Ka/Ks?

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Hearing silence: non-neutral evolution at synonymous sites in mammals

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Comparative analysis of chimpanzee and human Y chromosomes unveils complex evolutionary pathway.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Estimating the "effective number of codons": the Wright way of determining codon homozygosity leads to superior estimates

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Sequence conservation, relative isoform frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Site-to-site variation of synonymous substitution rates

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Distribution and intensity of constraint in mammalian genomic sequence

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Recoding elements located adjacent to a subset of eukaryal selenocysteine-specifying UGA codons.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

A transcriptional regulatory element in the coding sequence of the human Bcl-2 gene.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

A comparative method for finding and folding RNA secondary structures within protein-coding regions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

An evolutionary model for protein-coding regions with conserved RNA structure

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

WebLogo: A Sequence Logo Generator

12 July 2018

1 reference

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Ultraconserved Elements in the Human Genome

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

The DNA sequence and biology of human chromosome 19

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Gene fusion and overlapping reading frames in the mammalian genes for 4E-BP3 and MASK

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

The signature of selection mediated by expression on human genes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Nervous system targets of RNA editing identified by comparative genomics

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Statistical significance for genomewide studies

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Selection for short introns in highly expressed genes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Predictive identification of exonic splicing enhancers in human genes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

The human genome browser at UCSC

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

RNA editing by adenosine deaminases that act on RNA

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

XBP1 mRNA is induced by ATF6 and spliced by IRE1 in response to ER stress to produce a highly active transcription factor

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Two overlapping reading frames in a single exon encode interacting proteins--a novel way of gene usage

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Statistical methods for detecting molecular adaptation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Codon-substitution models for heterogeneous selection pressure at amino acid sites

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

A phylogenetic analysis reveals an unusual sequence conservation within introns involved in RNA editing

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

The effect of tandem substitutions on the correlation between synonymous and nonsynonymous rates in rodents

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Regulation of alternative splicing by RNA editing

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

The INK4A/ARF locus and its two gene products

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

The 'effective number of codons' used in a gene

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Nucleosome positioning as a determinant of exon recognition

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Intron size in mammals: complexity comes to terms with economy

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Alternatively and constitutively spliced exons are subject to different evolutionary forces

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Detecting amino acid sites under positive selection and purifying selection

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Expression of IGF-I splice variants in young and old human skeletal muscle after high resistance exercise.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Is the synonymous substitution rate in mammals gene-specific?

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Appropriate likelihood ratio tests and marginal distributions for evolutionary tree models with constraints on parameters.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Evolutionary footprints of nucleosome positions in yeast

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Chromatin organization marks exon-intron structure

15 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3205576

Simulation study of the reliability and robustness of the statistical methods for detecting positive selection at single amino acid sites

15 November 2018

1 reference

12 December 2020

How Common Are Intragene Windows with K A > K S Owing to Purifying Selection on Synonymous Mutations?

1 reference

12 December 2020

Preliminary Assessment of the Impact of MicroRNA-Mediated Regulation on Coding Sequence Evolution in Mammals

1 reference

12 December 2020

Post-transcriptional regulation of thyroid hormone receptor expression by cis-acting sequences and a naturally occurring antisense RNA

1 reference

12 December 2020

Exonic Splicing Regulatory Elements Skew Synonymous Codon Usage near Intron-exon Boundaries in Mammals

1 reference

12 December 2020

Evidence for purifying selection acting on silent sites in BRCA1

1 reference

12 December 2020

Evidence for Purifying Selection Against Synonymous Mutations in Mammalian Exonic Splicing Enhancers

1 reference

12 December 2020

Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution

1 reference

12 December 2020

A high-resolution map of human evolutionary constraint using 29 mammals

1 reference

COCI

https://opencitations.net/index/coci/api/v1/citations/10.1038/NATURE10530

15 July 2023

Identifiers

DOI

10.1101/GR.108753.110

1 reference

8 August 2017

1 reference

8 August 2017

1 reference