PEDLA: predicting enhancers with a deep learning-based algorithmic framework. (Q37027516)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27329130%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

title

PEDLA: predicting enhancers with a deep learning-based algorithmic framework (English)

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14 March 2020

0 references

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14 March 2020

Feng Liu

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14 March 2020

Hao Li

series ordinal

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14 March 2020

Chao Ren

series ordinal

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14 March 2020

Xiaochen Bo

series ordinal

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14 March 2020

language of work or name

English

0 references

publication date

22 June 2016

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14 March 2020

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14 March 2020

volume

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14 March 2020

page(s)

28517

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Human-level concept learning through probabilistic program induction

14 March 2020

cites work

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29 September 2017

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29 September 2017

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29 September 2017

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29 September 2017

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Global view of enhancer-promoter interactome in human cells.

29 September 2017

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A high-resolution map of the three-dimensional chromatin interactome in human cells

29 September 2017

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Super-enhancers in the control of cell identity and disease

29 September 2017

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Predicting enhancer transcription and activity from chromatin modifications

29 September 2017

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Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome

29 September 2017

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Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

29 September 2017

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Selective inhibition of tumor oncogenes by disruption of super-enhancers

29 September 2017

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Master transcription factors and mediator establish super-enhancers at key cell identity genes

29 September 2017

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

29 September 2017

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Modification of enhancer chromatin: what, how, and why?

29 September 2017

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Genome organization and long-range regulation of gene expression by enhancers

29 September 2017

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29 September 2017

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Understanding transcriptional regulation by integrative analysis of transcription factor binding data.

29 September 2017

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An integrated encyclopedia of DNA elements in the human genome

29 September 2017

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Noncoding transcription at enhancers: general principles and functional models

29 September 2017

1 reference

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Unsupervised pattern discovery in human chromatin structure through genomic segmentation

29 September 2017

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ChromHMM: automating chromatin-state discovery and characterization

29 September 2017

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Genome-wide enhancer prediction from epigenetic signatures using genetic algorithm-optimized support vector machines.

29 September 2017

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Large-scale discovery of enhancers from human heart tissue

29 September 2017

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Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart.

29 September 2017

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PU.1 and C/EBPα synergistically program distinct response to NF-κB activation through establishing monocyte specific enhancers

29 September 2017

1 reference

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Enhancer function: new insights into the regulation of tissue-specific gene expression

29 September 2017

1 reference

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FIMO: scanning for occurrences of a given motif

29 September 2017

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Functional and Mechanistic Diversity of Distal Transcription Enhancers

29 September 2017

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

29 September 2017

1 reference

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Histone H3K27ac separates active from poised enhancers and predicts developmental state

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916453

Transcriptional Enhancers in Animal Development and Evolution

29 September 2017

1 reference

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ChIP-Seq identification of weakly conserved heart enhancers

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916453

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916453

Distinct epigenomic landscapes of pluripotent and lineage-committed human cells.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916453

Widespread transcription at neuronal activity-regulated enhancers

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916453

Enhancers: the abundance and function of regulatory sequences beyond promoters

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916453

Finding distal regulatory elements in the human genome

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916453

Genomic views of distant-acting enhancers

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916453

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916453

ChIP-seq accurately predicts tissue-specific activity of enhancers

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916453

Prediction of regulatory elements in mammalian genomes using chromatin signatures.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916453

Model-based analysis of ChIP-Seq (MACS)

29 September 2017

1 reference

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Integration of external signaling pathways with the core transcriptional network in embryonic stem cells

29 September 2017

1 reference

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Combinatorial patterns of histone acetylations and methylations in the human genome

29 September 2017

1 reference

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

29 September 2017

1 reference

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Ultraconservation identifies a small subset of extremely constrained developmental enhancers

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916453

High-resolution profiling of histone methylations in the human genome

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916453

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916453

In vivo enhancer analysis of human conserved non-coding sequences

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916453

Close sequence comparisons are sufficient to identify human cis-regulatory elements.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916453

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916453

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916453

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916453

Scanning Human Gene Deserts for Long-Range Enhancers

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916453

Comparing the success of different prediction software in sequence analysis: a review

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916453

Identification of a Coordinate Regulator of Interleukins 4, 13, and 5 by Cross-Species Sequence Comparisons

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916453

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916453

DEEP: a general computational framework for predicting enhancers

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916453

Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4916453

4 September 2018

Identifiers

DOI

10.1038/SREP28517

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27329130%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27329130%20AND%20SRC:MED&resulttype=core&format=json

14 March 2020

PubMed publication ID

27329130

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27329130%20AND%20SRC:MED&resulttype=core&format=json