Novel Method for Analysis of Allele Specific Expression in Triploid Oryzias latipes Reveals Consistent Pattern of Allele Exclusion

Sources of bias in measures of allele-specific expression derived from RNA-seq data aligned to a single reference genome

(2013) Kraig R Stevenson et al.   BMC GENOMICS

Identification of Transcriptome SNPs for Assessing Allele-Specific Gene Expression in a Super-Hybrid Rice Xieyou9308

(2013) Rongrong Zhai et al.   PLoS One

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Genomic expression dominance in allopolyploids

(2012) Ryan A Rapp et al.   BMC BIOLOGY

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Ploidy mosaicism and allele-specific gene expression differences in the allopolyploid Squalius alburnoides

(2011) Isa Matos et al.   BMC GENETICS

A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data

(2011) D. A. Skelly et al.   GENOME RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes

(2009) Francesco Santini et al.   BMC EVOLUTIONARY BIOLOGY

Evolutionary Genetics of Genome Merger and Doubling in Plants

(2008) Jeff J. Doyle et al.   Annual Review of Genetics