(Q30670345)

19 August 2017

Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data (English)

1 reference

19 August 2017

Jason Piper

1

0 references

Constanze Bonifer

object named as

Constanze Bonifer

5

0 references

Peter N Cockerill

object named as

Peter N Cockerill

4

0 references

author name string

Markus C Elze

2

1 reference

19 August 2017

Pierre Cauchy

3

1 reference

19 August 2017

Sascha Ott

6

1 reference

19 August 2017

language of work or name

English

0 references

publication date

25 September 2013

1 reference

19 August 2017

Nucleic Acids Research

1 reference

19 August 2017

41

1 reference

19 August 2017

21

1 reference

19 August 2017

e201

1 reference

Creative Commons Attribution 3.0 Unported

19 August 2017

start time

4 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Chromatin accessibility data sets show bias due to sequence specificity of the DNase I enzyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

ENCODE data in the UCSC Genome Browser: year 5 update

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

Current bioinformatic approaches to identify DNase I hypersensitive sites and genomic footprints from DNase-seq data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

An expansive human regulatory lexicon encoded in transcription factor footprints

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

An integrated encyclopedia of DNA elements in the human genome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

Transcription factors: from enhancer binding to developmental control

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

Dynamic exchange at regulatory elements during chromatin remodeling underlies assisted loading mechanism

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

Structure and function of active chromatin and DNase I hypersensitive sites.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

Runx1 binds as a dimeric complex to overlapping Runx1 sites within a palindromic element in the human GM-CSF enhancer

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

Combinatorial binding predicts spatio-temporal cis-regulatory activity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

Detection of nonneutral substitution rates on mammalian phylogenies

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

Computation for ChIP-seq and RNA-seq studies

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

A census of human transcription factors: function, expression and evolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

A conserved insulator that recruits CTCF and cohesin exists between the closely related but divergently regulated interleukin-3 and granulocyte-macrophage colony-stimulating factor genes.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

High-resolution mapping and characterization of open chromatin across the genome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

High-resolution profiling of histone methylations in the human genome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

Assessing computational tools for the discovery of transcription factor binding sites

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

The ENCODE (ENCyclopedia Of DNA Elements) Project

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

DNAase footprinting a simple method for the detection of protein-DNA binding specificity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays

20 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKT850

Structural and functional characterization of the human FMR1 promoter reveals similarities with the hnRNP-A2 promoter region.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKT850

Conserved E boxes function as part of the enhancer in hypersensitive site 2 of the beta-globin locus control region. Role of basic helix-loop-helix proteins.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKT850

In vivo genomic footprinting using LM-PCR methods.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3834841

25 November 2018

Identifiers

DOI

10.1093/NAR/GKT850

1 reference

19 August 2017

1 reference

19 August 2017

PubMed publication ID

24071585

1 reference