(Q30801567)

14 September 2017

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

1 reference

14 September 2017

0 references

1 reference

4

Eric Nestler

1 reference

14 September 2017

Li Shen

1

1 reference

14 September 2017

Ningyi Shao

series ordinal

2

1 reference

14 September 2017

Xiaochuan Liu

series ordinal

3

1 reference

14 September 2017

language of work or name

English

0 references

publication date

15 April 2014

1 reference

14 September 2017

1 reference

14 September 2017

15

1 reference

14 September 2017

284

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2164-15-284

14 September 2017

0 references

cites work

HTSeq--a Python framework to work with high-throughput sequencing data

1 reference

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STAR: an integrated solution to management and visualization of sequencing data

20 June 2018

1 reference

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The next-generation sequencing revolution and its impact on genomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Human Transcriptome and Chromatin Modifications: An ENCODE Perspective

20 June 2018

1 reference

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diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

TETonic shift: biological roles of TET proteins in DNA demethylation and transcription

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

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

20 June 2018

1 reference

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20 June 2018

1 reference

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Morphine epigenomically regulates behavior through alterations in histone H3 lysine 9 dimethylation in the nucleus accumbens

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

The UCSC Genome Browser database: extensions and updates 2013.

20 June 2018

1 reference

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Spark: a navigational paradigm for genomic data exploration

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

The accessible chromatin landscape of the human genome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

An integrated encyclopedia of DNA elements in the human genome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

ggbio: an R package for extending the grammar of graphics for genomic data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

A brief introduction to web-based genome browsers

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

A map of the cis-regulatory sequences in the mouse genome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

RSeQC: quality control of RNA-seq experiments

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Systematic evaluation of factors influencing ChIP-seq fidelity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Uncovering the role of 5-hydroxymethylcytosine in the epigenome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Cistrome: an integrative platform for transcriptional regulation studies

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Integrative genomics viewer

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Tabix: fast retrieval of sequence features from generic TAB-delimited files

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

seqMINER: an integrated ChIP-seq data interpretation platform

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

The NIH Roadmap Epigenomics Mapping Consortium

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

BigWig and BigBed: enabling browsing of large distributed datasets

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Next-generation genomics: an integrative approach

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Repitools: an R package for the analysis of enrichment-based epigenomic data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Regulation of alternative splicing by histone modifications

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

BEDTools: a flexible suite of utilities for comparing genomic features

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Essential role of the histone methyltransferase G9a in cocaine-induced plasticity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Sequencing technologies - the next generation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

CEAS: cis-regulatory element annotation system

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Nucleosomes are well positioned in exons and carry characteristic histone modifications

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

The Sequence Alignment/Map format and SAMtools

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

rtracklayer: an R package for interfacing with genome browsers

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Differential chromatin marking of introns and expressed exons by H3K36me3.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

NCBI Reference Sequences: current status, policy and new initiatives

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Model-based analysis of ChIP-Seq (MACS)

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Applications of next-generation sequencing technologies in functional genomics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Human postmortem tissue: what quality markers matter?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

A bivalent chromatin structure marks key developmental genes in embryonic stem cells

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Comparison of human (and other) genome browsers

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Galaxy: a platform for interactive large-scale genome analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Role of histone H3 lysine 27 methylation in Polycomb-group silencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

The human genome browser at UCSC

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Retinoic acid induces embryonal carcinoma cells to differentiate into neurons and glial cells

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

DNase I hypersensitive sites in Drosophila chromatin occur at the 5' ends of regions of transcription.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4028082

Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells

20 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2F1471-2164-15-284

Replacement of Oct4 by Tet1 during iPSC induction reveals an important role of DNA methylation and hydroxymethylation in reprogramming.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2F1471-2164-15-284

Next-generation sequencing data interpretation: enhancing reproducibility and accessibility

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2F1471-2164-15-284

A 200 base pair region at the 5' end of the chicken adult beta-globin gene is accessible to nuclease digestion

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24735413

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2164-15-284

1 reference

Dimensions Publication ID

14 September 2017

1 reference

9 September 2019

https://scigraph.springernature.com/pub.10.1186/1471-2164-15-284

1 reference

14 September 2017

PubMed publication ID

24735413

1 reference