puma 3.0: improved uncertainty propagation methods for gene and transcript expression analysis

Identifying differentially expressed transcripts from RNA-seq data with biological variation

(2012) Peter Glaus et al.   BIOINFORMATICS

Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling

(2011) Paweł P. Łabaj et al.   BIOINFORMATICS

Comprehensive exon array data processing method for quantitative analysis of alternative spliced variants

(2011) Ping Chen et al.   NUCLEIC ACIDS RESEARCH

GATExplorer: Genomic and Transcriptomic Explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs

(2010) Alberto Risueño 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

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

puma: a Bioconductor package for propagating uncertainty in microarray analysis

(2009) Richard D Pearson et al.   BMC BIOINFORMATICS

MMBGX: a method for estimating expression at the isoform level and detecting differential splicing using whole-transcript Affymetrix arrays

(2009) Ernest Turro et al.   NUCLEIC ACIDS RESEARCH

FIRMA: a method for detection of alternative splicing from exon array data

(2008) E. Purdom et al.   BIOINFORMATICS

MADS: A new and improved method for analysis of differential alternative splicing by exon-tiling microarrays

(2008) Y. Xing et al.   RNA

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE