(Q34871025)

5 August 2017

title

Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model (English)

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5 August 2017

6

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5 August 2017

Nadav Ahituv

8

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author name string

Robin P Smith

1

1 reference

5 August 2017

Leila Taher

2

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5 August 2017

Rupali P Patwardhan

3

1 reference

5 August 2017

Mee J Kim

4

1 reference

5 August 2017

Fumitaka Inoue

5

1 reference

5 August 2017

Ivan Ovcharenko

7

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5 August 2017

language of work or name

English

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publication date

28 July 2013

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5 August 2017

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5 August 2017

volume

45

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5 August 2017

issue

9

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5 August 2017

page(s)

1021-1028

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Accurate gene synthesis with tag-directed retrieval of sequence-verified DNA molecules

5 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775494

Transcription factors: from enhancer binding to developmental control

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775494

A map of the cis-regulatory sequences in 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=3775494

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775494

Systematic dissection and optimization of inducible enhancers in human cells 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=3775494

Massively parallel functional dissection of mammalian enhancers in vivo

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775494

Opposing functions of the ETS factor family define Shh spatial expression in limb buds and underlie polydactyly

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775494

SLiCE: a novel bacterial cell extract-based DNA cloning method

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775494

Discriminative prediction of mammalian enhancers from DNA 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=3775494

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775494

Functional characterization of liver enhancers that regulate drug-associated transporters.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775494

9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775494

ChIP-Seq identification of weakly conserved heart 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=3775494

Homotypic clusters of transcription factor binding sites are a key component of human promoters and 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=3775494

Genome-wide discovery of human heart 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=3775494

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=3775494

Diversity and complexity in DNA recognition by transcription factors

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775494

Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin 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=3775494

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=3775494

Combinatorial regulation of endothelial gene expression by ets and forkhead transcription factors

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775494

Analysis of combinatorial cis-regulation in synthetic and genomic promoters

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775494

Regulation of a remote Shh forebrain enhancer by the Six3 homeoprotein

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775494

FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775494

A single SNP in an evolutionary conserved region within intron 86 of the HERC2 gene determines human blue-brown eye color

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775494

Systematic identification of cis-regulatory sequences active in mouse and human embryonic stem cells

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775494

Genome-wide mapping of in vivo 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=3775494

Development of the mammalian liver and ventral pancreas is dependent on GATA4.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775494

VISTA Enhancer Browser--a database of tissue-specific human 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=3775494

Mulan: multiple-sequence local alignment and visualization for studying function and 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=3775494

A predictive model for regulatory sequences directing liver-specific transcription.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775494

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775494

High levels of foreign gene expression in hepatocytes after tail vein injections of naked plasmid 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=3775494

Combining evidence using p-values: application to sequence homology searches

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775494

Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775494

The peroxisome proliferator-activated receptor:retinoid X receptor heterodimer is activated by fatty acids and fibrate hypolipidaemic drugs

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775494

A muscle-specific enhancer is located at the 3' end of the myosin light-chain 1/3 gene locus

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775494

Liver-enriched transcription factor HNF-4 is a novel member of the steroid hormone receptor superfamily

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775494

Characterization of a dimerization motif in AP-2 and its function in heterologous DNA-binding proteins

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775494

The words of the regulatory code are arranged in a variable manner in highly conserved 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=3775494

Position dependencies in transcription factor binding sites

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775494

Hepatic erythropoietin gene regulation by GATA-4.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775494

Ras pathway specificity is determined by the integration of multiple signal-activated and tissue-restricted transcription factors.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3775494

Functional architecture and evolution of transcriptional elements that drive gene coexpression

26 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23892608

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Information display by transcriptional enhancers

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23892608

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NG.2713

1 reference

Dimensions Publication ID

5 August 2017

0 references

1 reference

5 August 2017

1 reference