(Q35036393)

25635462

5 August 2017

title

Enhancer evolution across 20 mammalian species (English)

1 reference

5 August 2017

1

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1 June 2020

Jonathan T Erichsen

9

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1 June 2020

Mads Frost Bertelsen

12

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1 June 2020

Paul Flicek

14

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1 June 2020

Duncan Odom

15

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1 June 2020

Camille Berthelot

2

1 reference

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1 June 2020

Tim Rayner

4

1 reference

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1 June 2020

Margus Lukk

5

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1 June 2020

13

Elizabeth P Murchison

1 reference

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1 June 2020

author name string

Sarah Aldridge

3

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1 June 2020

Miguel Pignatelli

6

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1 June 2020

Thomas J Park

7

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1 June 2020

Robert Deaville

8

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1 June 2020

Anna J Jasinska

10

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1 June 2020

James M A Turner

11

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1 June 2020

language of work or name

English

0 references

publication date

1 January 2015

1 reference

5 August 2017

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25635462%20AND%20SRC:MED&resulttype=core&format=json

1 June 2020

volume

160

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1 June 2020

issue

3

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1 June 2020

page(s)

554-566

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25635462%20AND%20SRC:MED&resulttype=core&format=json

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways

1 June 2020

cites work

1 reference

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8.2% of the Human genome is constrained: variation in rates of turnover across functional element classes in the human lineage

8 July 2018

1 reference

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Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory 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=4313353

A promoter-level mammalian expression atlas

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

An atlas of active enhancers across human cell types and tissues

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Evolutionary conservation of the eumetazoan gene regulatory landscape

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Evolution of transcription factor binding in metazoans - mechanisms and functional implications

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Rapid and pervasive changes in genome-wide enhancer usage during mammalian development

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

8 July 2018

1 reference

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Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Minke whale genome and aquatic adaptation in cetaceans

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

AHT-ChIP-seq: a completely automated robotic protocol for high-throughput chromatin immunoprecipitation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Cooperativity and rapid evolution of cobound transcription factors in closely related 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=4313353

The evolution of lineage-specific regulatory activities in the human embryonic limb

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Comparative genomics as a tool to understand evolution and disease

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

The majority of primate-specific regulatory sequences are derived from transposable 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=4313353

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Genome-wide chromatin state transitions associated with developmental and environmental cues

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Evolutionary dynamics of gene and isoform regulation in Mammalian tissues.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Genome-wide scans for candidate genes involved in the aquatic adaptation of dolphins.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Comparative epigenomic annotation of regulatory 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=4313353

DNase I sensitivity QTLs are a major determinant of human expression variation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

SAGA and ATAC histone acetyl transferase complexes regulate distinct sets of genes and ATAC defines a class of p300-independent enhancers

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

The evolution of gene expression levels in mammalian organs

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Genome sequencing reveals insights into physiology and longevity of the naked mole rat

8 July 2018

1 reference

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A high-resolution map of human evolutionary constraint using 29 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=4313353

The repatterning of eukaryotic genomes by random genetic drift

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Human-specific loss of regulatory DNA and the evolution of human-specific traits

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

FIMO: scanning for occurrences of a given motif

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Gene expression differences among primates are associated with changes in a histone epigenetic modification

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Histone H3K27ac separates active from poised enhancers and predicts developmental state

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Comparative Epigenomic Analysis of Murine and Human Adipogenesis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

GREAT improves functional interpretation of cis-regulatory 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=4313353

Widespread transcription at neuronal activity-regulated enhancers

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

An atlas of combinatorial transcriptional regulation in mouse and man

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

The Sequence Alignment/Map format and SAMtools

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Fast and accurate short read alignment with Burrows-Wheeler transform

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Conservation of core gene expression in vertebrate tissues

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Histone modifications at human enhancers reflect global cell-type-specific gene expression

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

ChIP-seq accurately predicts tissue-specific activity of enhancers

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Evolution of regulatory sequences in 12 Drosophila species

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

A large genome center's improvements to the Illumina sequencing system

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Model-based analysis of ChIP-Seq (MACS)

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Evolution of the mammalian transcription factor binding repertoire via transposable 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=4313353

Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Recent and ongoing selection 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=4313353

The evolutionary significance of cis-regulatory mutations

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers 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=4313353

In vivo enhancer analysis of human conserved non-coding 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=4313353

Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

An RNA gene expressed during cortical development evolved rapidly in humans

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Close sequence comparisons are sufficient to identify human cis-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=4313353

Evolutionary turnover of mammalian transcription start sites

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Distribution and intensity of constraint in mammalian genomic sequence

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Functional evolution of a cis-regulatory module

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Bioconductor: open software development for computational biology and bioinformatics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Active genes are tri-methylated at K4 of histone H3

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

The evolutionary landscape of alternative splicing in vertebrate species

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

Transposable elements have rewired the core regulatory network of human embryonic stem cells

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4313353

10.1016/J.CELL.2015.01.006

25 October 2018

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25635462%20AND%20SRC:MED&resulttype=core&format=json

1 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25635462%20AND%20SRC:MED&resulttype=core&format=json

1 June 2020

25635462

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25635462%20AND%20SRC:MED&resulttype=core&format=json