(Q28603870)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26682651%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

title

Evidence for a common evolutionary rate in metazoan transcriptional networks (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26682651%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

author

Anne-Ruxandra Carvunis

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26682651%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

Dylan Skola

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26682651%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

Jason F Kreisberg

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26682651%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

7

Trey Ideker

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26682651%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

author name string

Tina Wang

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26682651%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

Alice Yu

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26682651%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

Jonathan Chen

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26682651%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

language of work or name

English

0 references

publication date

18 December 2015

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26682651%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26682651%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

volume

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26682651%20AND%20SRC:MED&resulttype=core&format=json

The goose genome sequence leads to insights into the evolution of waterfowl and susceptibility to fatty liver

3 March 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Comparative genomics reveals insights into avian genome evolution and adaptation

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Defining functional DNA elements in the human genome

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

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

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

The duck genome and transcriptome provide insight into an avian influenza virus reservoir species

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

An integrated encyclopedia of DNA elements in the human genome

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Fast gapped-read alignment with Bowtie 2

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

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

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Does positive selection drive transcription factor binding site turnover? A test with Drosophila cis-regulatory modules

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Evaluation of algorithm performance in ChIP-seq peak detection

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

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

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

The Sequence Alignment/Map format and SAMtools

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Model-based analysis of ChIP-Seq (MACS)

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Molecular clocks: four decades of evolution

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

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

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Initial sequencing and comparative analysis of the mouse genome

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

EMBOSS: the European Molecular Biology Open Software Suite

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Trimmomatic: a flexible trimmer for Illumina sequence data

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

BEDTools: a flexible suite of utilities for comparing genomic features

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

MEME SUITE: tools for motif discovery and searching

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

The evolution of gene expression levels in mammalian organs

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Genetic dissection of transcriptional regulation in budding yeast

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Transcriptomic profiling of rat liver samples in a comprehensive study design by RNA-Seq

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

RNA-seq analysis of broiler liver transcriptome reveals novel responses to high ambient temperature

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

The UCSC Genome Browser database: 2015 update

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Comparison of the transcriptional landscapes between human and mouse tissues

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

A comparative encyclopedia of DNA elements in the mouse genome

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Genome-wide mapping of DNase I hypersensitive sites and association analysis with gene expression in MSB1 cells

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Widespread contribution of transposable elements to the innovation of gene regulatory networks

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Comparative validation of the D. melanogaster modENCODE transcriptome annotation.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Response of the hepatic transcriptome to aflatoxin B1 in domestic turkey (Meleagris gallopavo).

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Tempo and mode of regulatory evolution in Drosophila

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Identification of genetic variants that affect histone modifications in human cells

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Extensive variation in chromatin states across humans

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Effect of natural genetic variation on enhancer selection and function.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Transcriptome sequencing reveals the character of incomplete dosage compensation across multiple tissues in flycatchers.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Cooperativity and rapid evolution of cobound transcription factors in closely related mammals

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Genome-wide analysis of chromatin states reveals distinct mechanisms of sex-dependent gene regulation in male and female mouse liver

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Can ENCODE tell us how much junk DNA we carry in our genome?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Adaptive evolution and the birth of CTCF binding sites in the Drosophila genome

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Transposable elements: an abundant and natural source of regulatory sequences for host genes.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

FIMO: scanning for occurrences of a given motif

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Variation in transcription factor binding among humans

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Does CTCF mediate between nuclear organization and gene expression?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Conservation of core gene expression in vertebrate tissues

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Mapping complex disease traits with global gene expression

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Design and analysis of ChIP-seq experiments for DNA-binding proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4764585

A computational pipeline for comparative ChIP-seq analyses.

3 June 2018

1 reference

https://api.crossref.org/works/10.7554%2FELIFE.11615

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

21 January 2018

1 reference

https://api.crossref.org/works/10.7554%2FELIFE.11615

The Nearly Neutral Theory of Molecular Evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.7554%2FELIFE.11615

The relationship between non-protein-coding DNA and eukaryotic complexity.

21 January 2018

1 reference

https://api.crossref.org/works/10.7554%2FELIFE.11615

21 January 2018

Identifiers

DOI

10.7554/ELIFE.11615

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26682651%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26682651%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

1 reference