Estimates of allele-specific expression in Drosophila with a single genome sequence and RNA-seq data

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

Allelic imbalance metre (Allim), a new tool for measuring allele-specific gene expression with RNA-seq data

(2013) Ram Vinay Pandey et al.   Molecular Ecology Resources

Allelic Imbalance in Drosophila Hybrid Heads: Exons, Isoforms, and Evolution

(2012) R. M. Graze et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Drosophila melanogaster Genetic Reference Panel

(2012) Trudy F. C. Mackay et al.   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

A new strategy to reduce allelic bias in RNA-Seq readmapping

(2012) Ravi Vijaya Satya et al.   NUCLEIC ACIDS RESEARCH

Genomic Imprinting Absent in Drosophila melanogaster Adult Females

(2012) Joseph D. Coolon et al.   Cell Reports

Genomic Variation and Its Impact on Gene Expression in Drosophila melanogaster

(2012) Andreas Massouras et al.   PLoS Genetics

Accurate identification of A-to-I RNA editing in human by transcriptome sequencing

(2011) J. H. Bahn et al.   GENOME RESEARCH

Systematic Detection of Polygenic cis-Regulatory Evolution

(2011) Hunter B. Fraser et al.   PLoS Genetics

Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads

(2011) Ernest Turro et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation

(2010) Tomas Babak et al.   BMC GENOMICS

Regulatory divergence in Drosophila revealed by mRNA-seq

(2010) C. J. McManus et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Polygenic and directional regulatory evolution across pathways in Saccharomyces

(2010) J. H. Bullard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

(2009) Jacob F. Degner et al.   BIOINFORMATICS

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

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

HapCUT: an efficient and accurate algorithm for the haplotype assembly problem

(2008) V. Bansal et al.   BIOINFORMATICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS