Comprehensive processing of high-throughput small RNA sequencing data including quality checking, normalization, and differential expression analysis using the UEA sRNA Workbench

Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies

(2015) Lars Barquist et al.   Annual Review of Genetics

Identification of miRNAs with potential roles in regulation of anther development and male-sterility in 7B-1 male-sterile tomato mutant

(2015) Vahid Omidvar et al.   BMC GENOMICS

sRNAtoolbox: an integrated collection of small RNA research tools

(2015) Antonio Rueda et al.   NUCLEIC ACIDS RESEARCH

The genomes of two key bumblebee species with primitive eusocial organization

(2015) Ben M Sadd et al.   GENOME BIOLOGY

Integrated analysis of microRNA and mRNA expression and association with HIF binding reveals the complexity of microRNA expression regulation under hypoxia

(2014) Carme Camps et al.   Molecular Cancer

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

(2014)   NATURE BIOTECHNOLOGY

Robustly detecting differential expression in RNA sequencing data using observation weights

(2014) Xiaobei Zhou et al.   NUCLEIC ACIDS RESEARCH

Small RNA Analysis in Sindbis Virus Infected Human HEK293 Cells

(2014) Andras Donaszi-Ivanov et al.   PLoS One

Small RNA Profile in Moso Bamboo Root and Leaf Obtained by High Definition Adapters

(2014) Ping Xu et al.   PLoS One

omiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data

(2013) Sören Müller et al.   BIOINFORMATICS

TCC: an R package for comparing tag count data with robust normalization strategies

(2013) Jianqiang Sun et al.   BMC BIOINFORMATICS

A comparison of methods for differential expression analysis of RNA-seq data

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots

(2013) Elena A Vidal et al.   BMC GENOMICS

Kraken: A set of tools for quality control and analysis of high-throughput sequence data

(2013) Matthew P.A. Davis et al.   METHODS

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

(2013) Simon Anders et al.   Nature Protocols

Argonaute proteins: functional insights and emerging roles

(2013) Gunter Meister   NATURE REVIEWS GENETICS

Bidirectional processing of pri-miRNAs with branched terminal loops by Arabidopsis Dicer-like1

(2013) Hongliang Zhu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Biases in small RNA deep sequencing data

(2013) Carsten A. Raabe et al.   NUCLEIC ACIDS RESEARCH

Plant MicroRNAs Display Differential 3' Truncation and Tailing Modifications That Are ARGONAUTE1 Dependent and Conserved Across Species

(2013) J. Zhai et al.   PLANT CELL

CoLIde

(2013) Irina Mohorianu et al.   RNA Biology

ShortStack: Comprehensive annotation and quantification of small RNA genes

(2013) M. J. Axtell   RNA

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

(2013) Franck Rapaport et al.   GENOME BIOLOGY

shortran: a pipeline for small RNA-seq data analysis

(2012) Vikas Gupta et al.   BIOINFORMATICS

The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets

(2012) M. B. Stocks et al.   BIOINFORMATICS

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

Small RNAs in development – insights from plants

(2012) Xuemei Chen   CURRENT OPINION IN GENETICS & DEVELOPMENT

Cyber-T web server: differential analysis of high-throughput data

(2012) M. A. Kayala et al.   NUCLEIC ACIDS RESEARCH

RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics

(2012) M. Lohse et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Diverse correlation patterns between microRNAs and their targets during tomato fruit development indicates different modes of microRNA actions

(2012) Sara Lopez-Gomollon et al.   PLANTA

Normalization, testing, and false discovery rate estimation for RNA-sequencing data

(2011) J. Li et al.   BIOSTATISTICS

Deep sequencing of small RNAs in plants: applied bioinformatics

(2011) D. J. Studholme   Briefings in Functional Genomics

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments

(2011) Mario Fasold et al.   NUCLEIC ACIDS RESEARCH

Profiling of short RNAs during fleshy fruit development reveals stage-specific sRNAome expression patterns

(2011) Irina Mohorianu et al.   PLANT JOURNAL

RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries

(2010) Lukas Habegger et al.   BIOINFORMATICS

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

(2010) James H Bullard et al.   BMC BIOINFORMATICS

baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data

(2010) Thomas J Hardcastle et al.   BMC BIOINFORMATICS

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Structural and Functional Analysis of Viral siRNAs

(2010) Gyorgy Szittya et al.   PLoS Pathogens

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Origin, Biogenesis, and Activity of Plant MicroRNAs

(2009) Olivier Voinnet   CELL

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

Origins and Mechanisms of miRNAs and siRNAs

(2009) Richard W. Carthew et al.   CELL

A toolkit for analysing large-scale plant small RNA datasets

(2008) S. Moxon et al.   BIOINFORMATICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS