(Q35617343)

9 August 2017

title

Identification of cis-regulatory sequence variations in individual genome sequences (English)

1 reference

9 August 2017

Wyeth W Wasserman

3

0 references

author name string

Rebecca Worsley-Hunt

series ordinal

1

1 reference

9 August 2017

Virginie Bernard

series ordinal

2

1 reference

9 August 2017

publication date

10 October 2011

1 reference

9 August 2017

1 reference

9 August 2017

volume

3

1 reference

9 August 2017

issue

10

1 reference

9 August 2017

page(s)

65

1 reference

A functional variant in microRNA-146a promoter modulates its expression and confers disease risk for systemic lupus erythematosus.

9 August 2017

cites work

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Quantitative analysis demonstrates most transcription factors require only simple models of specificity

12 July 2018

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12 July 2018

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A founder mutation in the Ashkenazi Jewish population affecting messenger RNA splicing of the CCM2 gene causes cerebral cavernous malformations

12 July 2018

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cis-regulatory mutations are a genetic cause of human limb malformations

12 July 2018

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MEME-ChIP: motif analysis of large DNA datasets

12 July 2018

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A framework for variation discovery and genotyping using next-generation DNA sequencing data

12 July 2018

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Mapping and analysis of chromatin state dynamics in nine human cell types

12 July 2018

1 reference

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

12 July 2018

1 reference

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In the loop: long range chromatin interactions and gene regulation

12 July 2018

1 reference

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Charting histone modifications and the functional organization of mammalian genomes

12 July 2018

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12 July 2018

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UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions

12 July 2018

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A map of human genome variation from population-scale sequencing

12 July 2018

1 reference

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Massively parallel sequencing and rare disease

12 July 2018

1 reference

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is-rSNP: a novel technique for in silico regulatory SNP detection

12 July 2018

1 reference

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Integrating common and rare genetic variation in diverse human populations

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

MicroSNiPer: a web tool for prediction of SNP effects on putative microRNA targets

12 July 2018

1 reference

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Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding 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=3239227

An 8q24 gene desert variant associated with prostate cancer risk confers differential in vivo activity to a MYC enhancer

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Screening the human exome: a comparison of whole genome and whole transcriptome sequencing

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

A paired-end sequencing strategy to map the complex landscape of transcription initiation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

A survey of sequence alignment algorithms for next-generation sequencing

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

A method and server for predicting damaging missense mutations

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

A method of predicting changes in human gene splicing induced by genetic variants in context of cis-acting elements

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Exome sequencing of a multigenerational human pedigree

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Detection of nonneutral substitution rates on mammalian phylogenies

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Comprehensive mapping of long-range interactions reveals folding principles of 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=3239227

ChIP-seq: advantages and challenges of a maturing technology

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Cis-regulatory mutations in human disease

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Chromosome conformation capture (from 3C to 5C) and its ChIP-based modification

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Long-range regulation at the SOX9 locus in development and disease

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Diversity and complexity in DNA recognition by transcription factors

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

BioMart Central Portal--unified access to biological data

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Management of gene promoter mutations in molecular diagnostics

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

ChIP-seq accurately predicts tissue-specific activity of enhancers

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding 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=3239227

MetWAMer: eukaryotic translation initiation site prediction

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Human-specific gain of function in a developmental enhancer

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

First evidence for an association of a functional variant in the microRNA-510 target site of the serotonin receptor-type 3E gene with diarrhea predominant irritable bowel syndrome

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Discovery and verification of functional single nucleotide polymorphisms in regulatory genomic regions: current and developing technologies

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

RSAT: regulatory sequence analysis tools

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Mapping and sequencing of structural variation from eight human 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=3239227

The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Searching for splicing motifs.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Splicing regulation: from a parts list of regulatory elements to an integrated splicing 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=3239227

In silico detection of sequence variations modifying transcriptional regulation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

ORegAnno: an open-access community-driven resource for regulatory annotation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Splicing in disease: disruption of the splicing code and the decoding machinery

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

A survey of genomic properties for the detection of regulatory polymorphisms

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

A common polymorphism decreases low-density lipoprotein receptor exon 12 splicing efficiency and associates with increased cholesterol.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

The evolutionary significance of cis-regulatory mutations

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

A systems approach to measuring the binding energy landscapes of transcription factors

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Insulators: exploiting transcriptional and epigenetic mechanisms

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Mammalian microRNAs: a small world for fine-tuning gene expression

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Strong bias in the location of functional promoter polymorphisms

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Applied bioinformatics for the identification of regulatory elements

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

A non-parametric model for transcription factor binding 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=3239227

Identification of conserved regulatory elements by comparative genome analysis

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Abundant raw material for cis-regulatory evolution in humans

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

TFBS: Computational framework for transcription factor binding site analysis

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Listening to silence and understanding nonsense: exonic mutations that affect 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=3239227

dbSNP: the NCBI database of genetic variation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Identification of a mutation in a GATA binding site of the platelet glycoprotein Ibbeta promoter resulting in the Bernard-Soulier syndrome

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

The genetic basis of the reduced expression of bilirubin UDP-glucuronosyltransferase 1 in Gilbert's syndrome

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

Disruption of a binding site for hepatocyte nuclear factor 4 results in hemophilia B Leyden

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

A novel mutation in the nerve-specific 5'UTR of the GJB1 gene causes X-linked Charcot-Marie-Tooth disease.

12 July 2018

1 reference

Disruption of a novel regulatory element in the erythroid-specific promoter of the human PKLR gene causes severe pyruvate kinase deficiency

21 January 2018

1 reference

De novo DNA synthesis using single molecule PCR.

21 January 2018

1 reference

The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences

21 January 2018

1 reference

Systematic analysis of disease-related regulatory mutation classes reveals distinct effects on transcription factor binding.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3239227

The c.-292C>T promoter polymorphism increases reticulocyte-type 15-lipoxygenase-1 activity and could be atheroprotective

23 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21989199

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Regulatory polymorphism in transcription factor KLF5 at the MEF2 element alters the response to angiotensin II and is associated with human hypertension

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21989199

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/GM281

1 reference

Dimensions Publication ID

9 August 2017

0 references

1 reference

9 August 2017

1 reference