(Q36085119)

12 August 2017

A synergistic DNA logic predicts genome-wide chromatin accessibility (English)

1 reference

12 August 2017

9

Tommi Jaakkola

1 reference

12 August 2017

Tatsunori Hashimoto

1

1 reference

12 August 2017

Richard I Sherwood

2

1 reference

12 August 2017

Daniel D Kang

3

1 reference

12 August 2017

Nisha Rajagopal

4

1 reference

12 August 2017

Amira A Barkal

5

1 reference

12 August 2017

Haoyang Zeng

6

1 reference

12 August 2017

Bart J M Emons

7

1 reference

12 August 2017

Sharanya Srinivasan

8

1 reference

12 August 2017

David K Gifford

10

1 reference

12 August 2017

25 July 2016

1 reference

12 August 2017

1 reference

12 August 2017

26

1 reference

12 August 2017

10

1 reference

12 August 2017

1430-1440

1 reference

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

12 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

Predicting effects of noncoding variants with deep learning-based sequence model

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

Regulation of RNA polymerase II activation by histone acetylation in single living cells.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

Saturation editing of genomic regions by multiplex homology-directed repair

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

Enhanced regulatory sequence prediction using gapped k-mer features

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

An atlas of active enhancers across human cell types and tissues

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

Identification of genetic variants that affect histone modifications in human cells

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

Developmental fate and cellular maturity encoded in human regulatory DNA landscapes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

RNA-guided human genome engineering via Cas9

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

Multiplex genome engineering using CRISPR/Cas systems

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

Facilitators and impediments of the pluripotency reprogramming factors' initial engagement with the genome

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

The accessible chromatin landscape of the human genome

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

An integrated encyclopedia of DNA elements in the human genome

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

Metazoan promoters: emerging characteristics and insights into transcriptional regulation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

ChromHMM: automating chromatin-state discovery and characterization

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

Pioneer transcription factors: establishing competence for gene expression

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

Discriminative prediction of mammalian enhancers from DNA sequence.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

DECOD: fast and accurate discriminative DNA motif finding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

DREME: motif discovery in transcription factor ChIP-seq data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

A map of open chromatin in human pancreatic islets

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

A sigmoidal transcriptional response: cooperativity, synergy and dosage effects

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

Chromosomal subunits in active genes have an altered conformation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

Hepatic specification of the gut endoderm in vitro: cell signaling and transcriptional control.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

The 5' ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5052050

Universality of core promoter elements?

23 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27456004

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1101/GR.199778.115

1 reference

12 August 2017

1 reference

12 August 2017

PubMed publication ID

27456004

1 reference