Design and validation issues in RNA-seq experiments (Q34178885)

31 July 2017

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title

Design and validation issues in RNA-seq experiments (English)

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31 July 2017

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Xiangqin Cui

2

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author name string

Zhide Fang

series ordinal

1

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31 July 2017

language of work or name

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15 April 2011

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Briefings in Bioinformatics

31 July 2017

published in

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31 July 2017

volume

12

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31 July 2017

issue

3

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31 July 2017

page(s)

280-287

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Next-generation DNA sequencing techniques

31 July 2017

cites work

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Next-generation sequencing transforms today's biology

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Sequencing technologies - the next generation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Microbial population structures in the deep marine biosphere

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

The complete genome of an individual by massively parallel DNA sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Paired-end mapping reveals extensive structural variation in the human genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Personalized copy number and segmental duplication maps using next-generation sequencing.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Genome-wide mapping of in vivo protein-DNA interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

ChIP-seq accurately predicts tissue-specific activity of enhancers

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Mapping and quantifying mammalian transcriptomes by RNA-Seq

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Epigenetics meets next-generation sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Highly integrated single-base resolution maps of the epigenome in Arabidopsis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Stem cell transcriptome profiling via massive-scale mRNA sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Understanding mechanisms underlying human gene expression variation with RNA sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Designing deep sequencing experiments: detecting structural variation and estimating transcript abundance

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Fundamentals of experimental design for cDNA microarrays

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

The transcriptional landscape of the yeast genome defined by RNA sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

RNA-Seq: a revolutionary tool for transcriptomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Small-sample estimation of negative binomial dispersion, with applications to SAGE data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Differential expression analysis for sequence count data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

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/10.1093%2FBIB%2FBBR004

Quantitative miRNA expression analysis: comparing microarrays with next-generation sequencing.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Zipf's law in gene expression.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Universality and flexibility in gene expression from bacteria to human

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

A paired-end sequencing strategy to map the complex landscape of transcription initiation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Paired-end sequence mapping detects extensive genomic rearrangement and translocation during divergence of Francisella tularensis subsp. tularensis and Francisella tularensis subsp. holarctica populations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Detection of splice junctions from paired-end RNA-seq data by SpliceMap.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Chimeric transcript discovery by paired-end transcriptome sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Transcript length bias in RNA-seq data confounds systems biology

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Biases in Illumina transcriptome sequencing caused by random hexamer priming

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Limitations and possibilities of small RNA digital gene expression profiling

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Testing the ratio of two poisson rates

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Inferences and Power Analysis Concerning Two Negative Binomial Distributions with An Application to MRI Lesion Counts Data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Power and sample size for DNA microarray studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

The PowerAtlas: a power and sample size atlas for microarray experimental design and research

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Confirming microarray data--is it really necessary?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Microarray data analysis: from disarray to consolidation and consensus

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Molecular mechanisms of ethanol-induced pathogenesis revealed by RNA-sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Power of deep sequencing and agilent microarray for gene expression profiling study

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR -- how well do they correlate?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

Extracting transcription factor targets from ChIP-Seq data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR004

21 January 2018

Identifiers

DOI

10.1093/BIB/BBR004

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31 July 2017

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DBLP Dataset 2021-01-02

28 January 2021

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