The next generation: using new sequencing technologies to analyse gene regulation (Q37809563)

23 August 2017

The next generation: using new sequencing technologies to analyse gene regulation (English)

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23 August 2017

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Pamela A. Hoodless

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author name string

Rebecca Cullum

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23 August 2017

1 February 2011

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23 August 2017

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16

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23 August 2017

210-222

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Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays

23 August 2017

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https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

21 January 2018

The year of sequencing.

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https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

The impact of next-generation sequencing technology on genetics

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Sequencing technologies - the next generation

21 January 2018

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3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

RNA-Seq: a revolutionary tool for transcriptomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

RNA-Seq analysis to capture the transcriptome landscape of a single cell

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Construction of small RNA cDNA libraries for deep sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Serial analysis of gene expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Using the transcriptome to annotate the genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Next-generation tag sequencing for cancer gene expression profiling

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Deep SAGE analysis of the Caenorhabditis elegans transcriptome

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

A combination of LongSAGE with Solexa sequencing is well suited to explore the depth and the complexity of transcriptome

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Mapping and quantifying mammalian transcriptomes by RNA-Seq

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

CAGE: cap analysis of gene expression

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Massive transcriptional start site analysis of human genes in hypoxia cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Deep sequencing of the zebrafish transcriptome response to mycobacterium infection.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Both noncoding and protein-coding RNAs contribute to gene expression evolution in the primate brain

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Understanding PRRSV infection in porcine lung based on genome-wide transcriptome response identified by deep sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Use of serial analysis of gene expression to reveal the specific regulation of gene expression profile in asthmatic rats treated by acupuncture

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Identification of novel lung genes in bronchial epithelium by serial analysis of gene expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Serial analysis of gene expression profiles of developmental stages in non-small cell lung carcinoma

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

The transcriptional landscape of the yeast genome defined by RNA sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

De novo transcriptome assembly with ABySS.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Defining transcribed regions using RNA-seq

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

The antisense transcriptomes of human cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

FRT-seq: amplification-free, strand-specific transcriptome sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

3'-end sequencing for expression quantification (3SEQ) from archival tumor samples

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Digital transcriptome profiling from attomole-level RNA samples

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Transcription regulation through promoter-proximal pausing of RNA polymerase II.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Screening the human exome: a comparison of whole genome and whole transcriptome sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Transcriptome and targetome analysis in MIR155 expressing cells using RNA-seq

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

ISOLATE: a computational strategy for identifying the primary origin of cancers using high-throughput sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Deep sequencing of human nuclear and cytoplasmic small RNAs reveals an unexpectedly complex subcellular distribution of miRNAs and tRNA 3' trailers

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Ultra-high throughput sequencing-based small RNA discovery and discrete statistical biomarker analysis in a collection of cervical tumours and matched controls

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

A myriad of miRNA variants in control and Huntington's disease brain regions detected by massively parallel sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Serum microRNA signatures identified in a genome-wide serum microRNA expression profiling predict survival of non-small-cell lung cancer.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Identification of differentially expressed miRNAs in chicken lung and trachea with avian influenza virus infection by a deep sequencing approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

High-resolution genome-wide mapping of histone modifications

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Defining the CREB regulon: a genome-wide analysis of transcription factor regulatory regions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Identification of the mismatch repair genes PMS2 and MLH1 as p53 target genes by using serial analysis of binding elements

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

A global map of p53 transcription-factor binding sites in the human genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Global mapping of c-Myc binding sites and target gene networks in human B cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

ChIP-seq: advantages and challenges of a maturing technology

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Genome-wide histone methylation profile for heart failure

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Fast and accurate short read alignment with Burrows-Wheeler transform

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Fast and accurate long-read alignment with Burrows-Wheeler transform

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Computation for ChIP-seq and RNA-seq studies

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Evaluation of algorithm performance in ChIP-seq peak detection

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Genome-wide mapping of in vivo protein-DNA interactions

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

GREAT improves functional interpretation of cis-regulatory regions

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

GADEM: a genetic algorithm guided formation of spaced dyads coupled with an EM algorithm for motif discovery

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis.

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Nucleosome dynamics define transcriptional enhancers

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Translating the Histone Code

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Determination of enriched histone modifications in non-genic portions of the human genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

HHMD: the human histone modification database

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Hyperphosphorylation of the C-terminal repeat domain of RNA polymerase II facilitates dissociation of its complex with mediator

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

RNA polymerase is poised for activation across the genome

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

NA-Seq: a discovery tool for the analysis of chromatin structure and dynamics during differentiation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Mapping networks of physical interactions between genomic elements using 5C technology

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

An evaluation of 3C-based methods to capture DNA interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

An oestrogen-receptor-α-bound human chromatin interactome

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Whole genome DNA methylation analysis based on high throughput sequencing technology

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Dynamic changes in the human methylome during differentiation

21 January 2018

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https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

Human general transcription factor IIH phosphorylates the C-terminal domain of RNA polymerase II

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1440-1843.2010.01899.X

10.1111/J.1440-1843.2010.01899.X

21 January 2018

Identifiers

DOI

1 reference

23 August 2017

1 reference

PubMed ID

21077988