groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data (Q30980309)

5 October 2017

groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data (English)

1 reference

5 October 2017

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26173492%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

author name string

Minho Chae

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26173492%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

W Lee Kraus

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26173492%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

language of work or name

1 reference

16 July 2015

1 reference

5 October 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26173492%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

volume

16

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26173492%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

page(s)

222

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26173492%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

14 June 2020

copyright license

start time

16 July 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

edgeR

object named as

edgeR package

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

edgeR

0 references

cites work

Noncoding RNA transcription targets AID to divergently transcribed loci in B cells.

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Enhancer RNAs and regulated transcriptional programs

21 June 2018

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An atlas of active enhancers across human cell types and tissues

21 June 2018

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FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells

21 June 2018

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Function-based identification of mammalian enhancers using site-specific integration

21 June 2018

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Enhancer biology and enhanceropathies

21 June 2018

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Dynamic reorganization of the AC16 cardiomyocyte transcriptome in response to TNFα signaling revealed by integrated genomic analyses

21 June 2018

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Enhancer RNAs: the new molecules of transcription

21 June 2018

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Vespucci: a system for building annotated databases of nascent transcripts

21 June 2018

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Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs

21 June 2018

1 reference

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Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation.

21 June 2018

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Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

21 June 2018

1 reference

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Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

Enhancer transcripts mark active estrogen receptor binding sites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

Genome-wide quantitative enhancer activity maps identified by STARR-seq

21 June 2018

1 reference

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Defining the status of RNA polymerase at promoters

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

Landscape of transcription in human cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

An integrated encyclopedia of DNA elements in the human genome

21 June 2018

1 reference

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Genomic approaches towards finding cis-regulatory modules in animals

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

ChromHMM: automating chromatin-state discovery and characterization

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA.

21 June 2018

1 reference

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Discovery of active enhancers through bidirectional expression of short transcripts

21 June 2018

1 reference

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REVIGO summarizes and visualizes long lists of gene ontology terms

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

Full-length transcriptome assembly from RNA-Seq data without a reference genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

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

21 June 2018

1 reference

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Identifying dispersed epigenomic domains from ChIP-Seq data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

A signal-noise model for significance analysis of ChIP-seq with negative control

21 June 2018

1 reference

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edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

21 June 2018

1 reference

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Combinatorial binding predicts spatio-temporal cis-regulatory activity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

ChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

RNA exosome depletion reveals transcription upstream of active human promoters

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

RNA-Seq: a revolutionary tool for transcriptomics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

Model-based analysis of ChIP-Seq (MACS)

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

RNA polymerase is poised for activation across the genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

A chromatin landmark and transcription initiation at most promoters in human cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

Genome-wide analysis of estrogen receptor binding sites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

Java Treeview--extensible visualization of microarray data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502638

Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription.

21 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2FS12859-015-0656-3

BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2FS12859-015-0656-3

10.1186/S12859-015-0656-3

21 January 2018

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26173492%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

DBLP publication ID

journals/bmcbi/ChaeDK15

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26173492%20AND%20SRC:MED&resulttype=core&format=json

14 June 2020

PubMed publication ID

26173492

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26173492%20AND%20SRC:MED&resulttype=core&format=json