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

Alternative strategies for development of a reference transcriptome for quantification of allele specific expression in organisms having sparse genomic resources

(2012) Yingjia Shen et al.   Comparative Biochemistry and Physiology D-Genomics & Proteomics

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

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

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

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

Genomic Imprinting Absent in Drosophila melanogaster Adult Females

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

Critical Evaluation of Imprinted Gene Expression by RNA–Seq: A New Perspective

(2012) Brian DeVeale et al.   PLoS Genetics

Mapping personal functional data to personal genomes

(2011) M. Rivas-Astroza et al.   BIOINFORMATICS

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

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Regulatory divergence in Drosophila revealed by mRNA-seq

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

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

(2009) Jacob F. Degner et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Regulatory Divergence in Drosophila melanogaster and D. simulans, a Genomewide Analysis of Allele-Specific Expression

(2009) R. M. Graze et al.   GENETICS

Systems genetics of complex traits in Drosophila melanogaster

(2009) Julien F Ayroles et al.   NATURE GENETICS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Fast Statistical Alignment

(2009) Robert K. Bradley et al.   PLoS Computational Biology

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

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