(Q34510016)

2 August 2017

title

Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection (English)

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2 August 2017

1 reference

3

Gregory E Crawford

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2 August 2017

4

Uwe Ohler

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2 August 2017

author name string

Galip Gürkan Yardımcı

series ordinal

1

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2 August 2017

Christopher L Frank

series ordinal

2

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2 August 2017

language of work or name

English

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publication date

7 October 2014

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2 August 2017

published in

Nucleic Acids Research

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2 August 2017

volume

42

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2 August 2017

issue

19

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2 August 2017

page(s)

11865-11878

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Creative Commons Attribution-NonCommercial 4.0 International

2 August 2017

copyright license

start time

3 May 2017

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

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7 July 2018

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Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification

7 July 2018

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Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins

7 July 2018

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7 July 2018

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

7 July 2018

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Transcriptome and genome sequencing uncovers functional variation in humans

7 July 2018

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

7 July 2018

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DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements

7 July 2018

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Probing DNA shape and methylation state on a genomic scale with DNase I.

7 July 2018

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Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions

7 July 2018

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B-lineage transcription factors and cooperating gene lesions required for leukemia development

7 July 2018

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Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity

7 July 2018

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7 July 2018

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Predicting cell-type-specific gene expression from regions of open chromatin

7 July 2018

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Systematic localization of common disease-associated variation in regulatory DNA

7 July 2018

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An expansive human regulatory lexicon encoded in transcription factor footprints

7 July 2018

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The accessible chromatin landscape of the human genome

7 July 2018

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An integrated encyclopedia of DNA elements in the human genome

7 July 2018

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Modeling gene expression using chromatin features in various cellular contexts

7 July 2018

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Unsupervised pattern discovery in human chromatin structure through genomic segmentation

7 July 2018

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

7 July 2018

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Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights

7 July 2018

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

7 July 2018

1 reference

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Epigenetic priors for identifying active transcription factor binding sites

7 July 2018

1 reference

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Cooperative transcription factor associations discovered using regulatory variation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4231734

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4231734

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4231734

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4231734

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4231734

DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4231734

Distinguishing direct versus indirect transcription factor-DNA interactions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4231734

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4231734

Diversity and complexity in DNA recognition by transcription factors

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4231734

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4231734

A transcription factor affinity-based code for mammalian transcription initiation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4231734

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4231734

F-Seq: a feature density estimator for high-throughput sequence tags

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4231734

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4231734

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4231734

Genome-wide mapping of in vivo protein-DNA interactions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4231734

The role of chromatin during transcription

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4231734

Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4231734

Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4231734

Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4231734

DNA binding sites: representation and discovery

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4231734

CoREST: a functional corepressor required for regulation of neural-specific gene expression

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4231734

NRSF/REST is required in vivo for repression of multiple neuronal target genes during embryogenesis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4231734

The transcriptional coactivators p300 and CBP are histone acetyltransferases

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4231734

High sequence specificity of micrococcal nuclease

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4231734

Nuclease hypersensitive sites in chromatin

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4231734

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4231734

7 July 2018

Identifiers

DOI

10.1093/NAR/GKU810

1 reference

2 August 2017

1 reference

2 August 2017

1 reference