Identifying small interfering RNA loci from high-throughput sequencing data

miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants

(2011) Xiaozeng Yang et al.   BIOINFORMATICS

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

Finding sRNA generative locales from high-throughput sequencing data with NiBLS

(2010) Daniel MacLean et al.   BMC 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

Origins and Mechanisms of miRNAs and siRNAs

(2009) Richard W. Carthew et al.   CELL

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

A toolkit for analysing large-scale plant small RNA datasets

(2008) S. Moxon et al.   BIOINFORMATICS

Discovering microRNAs from deep sequencing data using miRDeep

(2008) Marc R Friedländer et al.   NATURE BIOTECHNOLOGY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS