Uncovering the complexity of transcriptomes with RNA‐Seq

V Costa, C Angelini, I De Feis… - BioMed Research …, 2010 - Wiley Online Library
In recent years, the introduction of massively parallel sequencing platforms for Next
Generation Sequencing (NGS) protocols, able to simultaneously sequence hundred …

High‐throughput sequencing for biology and medicine

WW Soon, M Hariharan, MP Snyder - Molecular systems biology, 2013 - embopress.org
Advances in genome sequencing have progressed at a rapid pace, with increased
throughput accompanied by plunging costs. But these advances go far beyond faster and …

Removing technical variability in RNA-seq data using conditional quantile normalization

KD Hansen, RA Irizarry, Z Wu - Biostatistics, 2012 - academic.oup.com
The ability to measure gene expression on a genome-wide scale is one of the most
promising accomplishments in molecular biology. Microarrays, the technology that first …

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case …

I Nookaew, M Papini, N Pornputtapong… - Nucleic acids …, 2012 - academic.oup.com
RNA-seq, has recently become an attractive method of choice in the studies of
transcriptomes, promising several advantages compared with microarrays. In this study, we …

[HTML][HTML] Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data

Y Guo, Q Sheng, J Li, F Ye, DC Samuels, Y Shyr - PloS one, 2013 - journals.plos.org
RNAseq and microarray methods are frequently used to measure gene expression level.
While similar in purpose, there are fundamental differences between the two technologies …

[HTML][HTML] A high-throughput method for Illumina RNA-Seq library preparation

R Kumar, Y Ichihashi, S Kimura, DH Chitwood… - Frontiers in plant …, 2012 - frontiersin.org
With the introduction of cost effective, rapid, and superior quality next generation sequencing
techniques, gene expression analysis has become viable for labs conducting small projects …

Identification and Properties of 1,119 Candidate LincRNA Loci in the Drosophila melanogaster Genome

RS Young, AC Marques, C Tibbit… - Genome biology and …, 2012 - academic.oup.com
The functional repertoire of long intergenic noncoding RNA (lincRNA) molecules has begun
to be elucidated in mammals. Determining the biological relevance and potential gene …

RNA-Seq analysis and de novo transcriptome assembly of Hevea brasiliensis

Z Xia, H Xu, J Zhai, D Li, H Luo, C He, X Huang - Plant molecular biology, 2011 - Springer
Hevea brasiliensis, being the only source of commercial natural rubber, is an extremely
economically important crop. In an effort to facilitate biological, biochemical and molecular …

Simultaneous isolation of high-quality DNA, RNA, miRNA and proteins from tissues for genomic applications

S Peña-Llopis, J Brugarolas - Nature protocols, 2013 - nature.com
Genomic technologies have revolutionized our understanding of complex Mendelian
diseases and cancer. Solid tumors present several challenges for genomic analyses, such …

A strand-specific library preparation protocol for RNA sequencing

T Borodina, J Adjaye, M Sultan - Methods in enzymology, 2011 - Elsevier
The analysis of transcriptome, which was over the past decade based mostly on microarray
technologies, is now being superseded by so-called next generation sequencing (NGS) …