Improving small RNA-seq by using a synthetic spike-in set for size-range quality control together with a set for data normalization

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones

(2014) Thomas R. Cech et al.   CELL

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells

(2014) Shanrong Zhao et al.   PLoS One

The Long and Short of MicroRNA

(2013) Luke A. Yates et al.   CELL

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

(2013) Peter A C 't Hoen et al.   NATURE BIOTECHNOLOGY

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs

(2013) Noah Fahlgren et al.   PLoS One

Comprehensive profiling of circulating microRNA via small RNA sequencing of cDNA libraries reveals biomarker potential and limitations

(2013) Zev Williams et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

miRNA-Seq normalization comparisons need improvement

(2013) X. Zhou et al.   RNA

Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing

(2013) Shivendra Kishore et al.   GENOME BIOLOGY

Revisiting Global Gene Expression Analysis

(2012) Jakob Lovén et al.   CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Synthetic Spike-in Standards Improve Run-Specific Systematic Error Analysis for DNA and RNA Sequencing

(2012) Justin M. Zook et al.   PLoS One

Evaluation of normalization methods in mammalian microRNA-Seq data

(2012) L. X. Garmire et al.   RNA

RNA-seq: technical variability and sampling

(2011) Lauren M McIntyre et al.   BMC GENOMICS

RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries

(2011) M. Hafner et al.   RNA

Normalization strategies for microRNA profiling experiments: a ‘normal’ way to a hidden layer of complexity?

(2010) Swanhild U. Meyer et al.   BIOTECHNOLOGY LETTERS

The widespread regulation of microRNA biogenesis, function and decay

(2010) Jacek Krol et al.   NATURE REVIEWS GENETICS

miRBase: integrating microRNA annotation and deep-sequencing data

(2010) A. Kozomara et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Small silencing RNAs: an expanding universe

(2009) Megha Ghildiyal et al.   NATURE REVIEWS GENETICS

Loqs and R2D2 act sequentially in the siRNA pathway in Drosophila

(2009) João Trindade Marques et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Computational and analytical framework for small RNA profiling by high-throughput sequencing

(2009) N. Fahlgren et al.   RNA

A Genome-Wide Characterization of MicroRNA Genes in Maize

(2009) Lifang Zhang et al.   PLoS Genetics