Comparing Computational Methods for Identification of Allele-Specific Expression based on Next Generation Sequencing Data

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

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

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

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A Survey for Novel Imprinted Genes in the Mouse Placenta by mRNA-seq

(2011) Xu Wang et al.   GENETICS

Analysis of allelic differential expression in the human genome using allele-specific serial analysis of gene expression tags

(2011) Daniel Onofre Vidal et al.   GENOME

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

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

AlleleSeq: analysis of allele-specific expression and binding in a network framework

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High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta

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Regulatory divergence in Drosophila revealed by mRNA-seq

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Transcriptome genetics using second generation sequencing in a Caucasian population

(2010) Stephen B. Montgomery et al.   NATURE

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

Genome-wide allele-specific analysis: insights into regulatory variation

(2010) Tomi Pastinen   NATURE REVIEWS GENETICS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

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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

Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing

(2009) Graham A. Heap et al.   HUMAN MOLECULAR GENETICS

Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human

(2009) Kun Zhang et al.   NATURE METHODS

Mapping complex disease traits with global gene expression

(2009) William Cookson et al.   NATURE REVIEWS GENETICS

Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer

(2009) Y. F. Chan et al.   SCIENCE

Advances in the identification and analysis of allele-specific expression

(2009) Christopher G Bell et al.   Genome Medicine

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Independent Effects of cis- and trans-regulatory Variation on Gene Expression in Drosophila melanogaster

(2008) P. J. Wittkopp et al.   GENETICS

SNP-specific array-based allele-specific expression analysis

(2008) H. T. Bjornsson et al.   GENOME RESEARCH

Differential Allelic Expression in the Human Genome: A Robust Approach To Identify Genetic and Epigenetic Cis-Acting Mechanisms Regulating Gene Expression

(2008) David Serre et al.   PLoS Genetics