(Q37682396)

22 August 2017

Improved regulatory element prediction based on tissue-specific local epigenomic signatures (English)

1 reference

22 August 2017

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28193886%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

Diane E. Dickel

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28193886%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

Axel Visel

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28193886%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

Joseph R. Ecker

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28193886%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

9

Len A Pennacchio

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28193886%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

author name string

Yupeng He

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28193886%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

Joseph R Nery

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28193886%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

Rosa G Castanon

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28193886%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

Ah Young Lee

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28193886%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

Yin Shen

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28193886%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

Bing Ren

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28193886%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

language of work or name

English

0 references

publication date

13 February 2017

1 reference

Proceedings of the National Academy of Sciences of the United States of America

22 August 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28193886%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

volume

114

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28193886%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

issue

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28193886%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

page(s)

E1633-E1640

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28193886%20AND%20SRC:MED&resulttype=core&format=json

PEDLA: predicting enhancers with a deep learning-based algorithmic framework.

11 June 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Differential sensitivity to methylated DNA by ETS-family transcription factors is intrinsically encoded in their DNA-binding domains

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Prediction of promoters and enhancers using multiple DNA methylation-associated features

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

DELTA: A Distal Enhancer Locating Tool Based on AdaBoost Algorithm and Shape Features of Chromatin Modifications

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Non-CG Methylation in the Human Genome.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Human body epigenome maps reveal noncanonical DNA methylation variation

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Inferring regulatory element landscapes and transcription factor networks from cancer methylomes

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Base-resolution methylation patterns accurately predict transcription factor bindings in vivo

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Integrative analysis of haplotype-resolved epigenomes across human tissues.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Integrative analysis of 111 reference human epigenomes

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

A comparative encyclopedia of DNA elements in the mouse genome

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Abnormalities in human pluripotent cells due to reprogramming mechanisms

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Integrating diverse datasets improves developmental enhancer prediction

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

CTCF: an architectural protein bridging genome topology and function

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Charting a dynamic DNA methylation landscape of the human genome

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Epigenomic analysis of multilineage differentiation of human embryonic stem cells

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

RFECS: a random-forest based algorithm for enhancer identification from chromatin state

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

DNA methylation: roles in mammalian development

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Dynamic DNA methylation across diverse human cell lines and tissues

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

'Leveling' the playing field for analyses of single-base resolution DNA methylomes.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

GENCODE: the reference human genome annotation for The ENCODE Project

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Systematic localization of common disease-associated variation in regulatory DNA

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

An integrated encyclopedia of DNA elements in the human genome

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Functions of DNA methylation: islands, start sites, gene bodies and beyond

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

BEDOPS: high-performance genomic feature operations

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

ChromHMM: automating chromatin-state discovery and characterization

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Histone H3K27ac separates active from poised enhancers and predicts developmental state

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Discover regulatory DNA elements using chromatin signatures and artificial neural network.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

BEDTools: a flexible suite of utilities for comparing genomic features

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Genome-wide discovery of human heart enhancers

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Human DNA methylomes at base resolution show widespread epigenomic differences

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

ChIP-seq: advantages and challenges of a maturing technology

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Fast and accurate short read alignment with Burrows-Wheeler transform

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Histone modifications at human enhancers reflect global cell-type-specific gene expression

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Prediction of regulatory elements in mammalian genomes using chromatin signatures.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Model-based analysis of ChIP-Seq (MACS)

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

VISTA Enhancer Browser--a database of tissue-specific human enhancers

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

In vivo enhancer analysis of human conserved non-coding sequences

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Long-range control of gene expression: emerging mechanisms and disruption in disease

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

The human genome browser at UCSC

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

DNA methylation patterns and epigenetic memory

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Progress and challenges in bioinformatics approaches for enhancer identification

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Statistical methods for detecting differentially methylated loci and regions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

High-throughput mapping of regulatory DNA.

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Transcriptional enhancers in development and disease

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Recruitment of CBP/p300 by the IFN beta enhanceosome is required for synergistic activation of transcription

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Inducible expression of an hsp68-lacZ hybrid gene in transgenic mice

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Estimation of false discovery rate using sequential permutation p-values.

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

DNA-binding factors shape the mouse methylome at distal regulatory regions

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Elimination of a long-range cis-regulatory module causes complete loss of limb-specific Shh expression and truncation of the mouse limb.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5338528

Corrigendum: DNA-binding factors shape the mouse methylome at distal regulatory regions

1 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.1618353114

Connecting rules from paired miRNA and mRNA expression data sets of HCV patients to detect both inverse and positive regulatory relationships

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.1618353114

Identifying Important Risk Factors for Survival in Kidney Graft Failure Patients Using Random Survival Forests

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.1618353114

C/EBPβ (CEBPB) protein binding to the C/EBP|CRE DNA 8-mer TTGC|GTCA is inhibited by 5hmC and enhanced by 5mC, 5fC, and 5caC in the CG dinucleotide

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28193886

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.1618353114

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28193886%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28193886%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

PubMed publication ID

28193886

1 reference