(Q33741021)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28402545%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

title

ORIO (Online Resource for Integrative Omics): a web-based platform for rapid integration of next generation sequencing data (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28402545%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

author

Christopher A Lavender

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28402545%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

Karen Adelman

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28402545%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

author name string

Andrew J Shapiro

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28402545%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

Adam B Burkholder

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28402545%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

Brian D Bennett

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28402545%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

David C Fargo

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28402545%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

language of work or name

English

0 references

publication date

1 June 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28402545%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

published in

Nucleic Acids Research

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28402545%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

volume

45

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28402545%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

issue

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28402545%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

page(s)

5678-5690

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28402545%20AND%20SRC:MED&resulttype=core&format=json

Downstream Antisense Transcription Predicts Genomic Features That Define the Specific Chromatin Environment at Mammalian Promoters.

17 March 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

An interactive environment for agile analysis and visualization of ChIP-sequencing data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

Chromatin and RNA Maps Reveal Regulatory Long Noncoding RNAs in Mouse.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

Pausing of RNA polymerase II regulates mammalian developmental potential through control of signaling networks.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

deepTools: a flexible platform for exploring deep-sequencing data.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

An atlas of active enhancers across human cell types and tissues

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

RefSeq: an update on mammalian reference sequences

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

Landscape of transcription in human cells

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

An integrated encyclopedia of DNA elements in the human genome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

An encyclopedia of mouse DNA elements (Mouse ENCODE).

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

ChromHMM: automating chromatin-state discovery and characterization

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

D³: Data-Driven Documents

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

An integrated ChIP-seq analysis platform with customizable workflows

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

FIMO: scanning for occurrences of a given motif

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

Histone H3K27ac separates active from poised enhancers and predicts developmental state

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

BigWig and BigBed: enabling browsing of large distributed datasets

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

c-Myc regulates transcriptional pause release

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

Widespread transcription at neuronal activity-regulated enhancers

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

Histone modification levels are predictive for gene expression

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

BEDTools: a flexible suite of utilities for comparing genomic features

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

Genome-wide analysis of histone methylation reveals chromatin state-based regulation of gene transcription and function of memory CD8+ T cells

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

MEME SUITE: tools for motif discovery and searching

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

RNA-Seq: a revolutionary tool for transcriptomics

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

Accurate whole human genome sequencing using reversible terminator chemistry

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

Model-based analysis of ChIP-Seq (MACS)

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

Genome-wide mapping of in vivo protein-DNA interactions

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

Polycomb complexes repress developmental regulators in murine embryonic stem cells

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

DAVID: Database for Annotation, Visualization, and Integrated Discovery

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

The human genome browser at UCSC

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5449597

Cutadapt removes adapter sequences from high-throughput sequencing reads

14 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKX270

Matplotlib: A 2D Graphics Environment

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKX270

The NumPy Array: A Structure for Efficient Numerical Computation

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKX270

GeneProf: analysis of high-throughput sequencing experiments

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28402545

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKX270

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28402545%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28402545%20AND%20SRC:MED&resulttype=core&format=json

17 March 2020

PubMed publication ID

28402545

1 reference