Optimizing a Massive Parallel Sequencing Workflow for Quantitative miRNA Expression Analysis

Bias detection and correction in RNA-Sequencing data

(2011) Wei Zheng et al.   BMC BIOINFORMATICS

Barcoding bias in high-throughput multiplex sequencing of miRNA

(2011) S. Alon et al.   GENOME RESEARCH

Accurate Estimation of Expression Levels of Homologous Genes in RNA-seq Experiments

(2011) Bogdan Paşaniuc et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

miRNAkey: a software for microRNA deep sequencing analysis

(2010) Roy Ronen et al.   BIOINFORMATICS

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

(2010) Lihua J Zhu 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

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

MicroRazerS: rapid alignment of small RNA reads

(2009) A.-K. Emde et al.   BIOINFORMATICS

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

(2009) M. Morgan et al.   BIOINFORMATICS

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

(2009) Likun Wang et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression

(2009) Wei-Chi Wang et al.   BMC BIOINFORMATICS

BioMart – biological queries made easy

(2009) Damian Smedley et al.   BMC GENOMICS

RazerS--fast read mapping with sensitivity control

(2009) D. Weese et al.   GENOME RESEARCH

miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments

(2009) Michael Hackenberg et al.   NUCLEIC ACIDS RESEARCH

Quantitative miRNA expression analysis: Comparing microarrays with next-generation sequencing

(2009) H. Willenbrock et al.   RNA

SHRiMP: Accurate Mapping of Short Color-space Reads

(2009) Stephen M. Rumble et al.   PLoS Computational Biology

A toolkit for analysing large-scale plant small RNA datasets

(2008) S. Moxon et al.   BIOINFORMATICS

PatMaN: rapid alignment of short sequences to large databases

(2008) Kay Prüfer et al.   BIOINFORMATICS

Dissecting an alternative splicing analysis workflow for GeneChip® Exon 1.0 ST Affymetrix arrays

(2008) Cristina Della Beffa et al.   BMC GENOMICS

Discovering microRNAs from deep sequencing data using miRDeep

(2008) Marc R Friedländer et al.   NATURE BIOTECHNOLOGY