Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data

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

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals

(2013) A. Battle et al.   GENOME RESEARCH

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

Somatic Point Mutation Calling in Low Cellularity Tumors

(2013) Karin S. Kassahn et al.   PLoS One

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

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

(2012) Cole Trapnell et al.   Nature Protocols

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

The Brisbane Systems Genetics Study: Genetical Genomics Meets Complex Trait Genetics

(2012) Joseph E. Powell et al.   PLoS One

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

(2012) Brian DeVeale et al.   PLoS 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

Chromosome-Wide Analysis of Parental Allele-Specific Chromatin and DNA Methylation

(2011) P. Singh et al.   MOLECULAR AND CELLULAR BIOLOGY

Regulation of X-chromosome inactivation by the X-inactivation centre

(2011) Sandrine Augui et al.   NATURE REVIEWS GENETICS

Genomic imprinting: the emergence of an epigenetic paradigm

(2011) Anne C. Ferguson-Smith   NATURE REVIEWS GENETICS

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

(2011) Ernest Turro et al.   GENOME BIOLOGY

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

(2010) Heng Li et al.   BIOINFORMATICS

MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes

(2010) Yun Li et al.   GENETIC EPIDEMIOLOGY

Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome

(2010) R. Shoemaker et al.   GENOME RESEARCH

RNA sequencing reveals the role of splicing polymorphisms in regulating human gene expression

(2010) E. Lalonde et al.   GENOME RESEARCH

An imbalance of human complement regulatory proteins CFHR1, CFHR3 and factor H influences risk for age-related macular degeneration (AMD)

(2010) Lars G. Fritsche et al.   HUMAN MOLECULAR GENETICS

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

Distinct Patterns of Gene-Specific Methylation in Mammalian Placentas: Implications for Placental Evolution and Function

(2010) H.K. Ng et al.   PLACENTA

Variation in Transcription Factor Binding Among Humans

(2010) M. Kasowski et al.   SCIENCE

The study of eQTL variations by RNA-seq: from SNPs to phenotypes

(2010) Jacek Majewski et al.   TRENDS IN GENETICS

Balancing Selection Maintains a Form of ERAP2 that Undergoes Nonsense-Mediated Decay and Affects Antigen Presentation

(2010) Aida M. Andrés et al.   PLoS Genetics

Mutations in the Beta Propeller WDR72 Cause Autosomal-Recessive Hypomaturation Amelogenesis Imperfecta

(2009) Walid El-Sayed et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2009) Jacob F. Degner et al.   BIOINFORMATICS

integrOmics: an R package to unravel relationships between two omics datasets

(2009) Kim-Anh Lê Cao et al.   BIOINFORMATICS

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Common polymorphic transcript variation in human disease

(2009) H. B. Fraser et al.   GENOME RESEARCH

A regulatory single nucleotide polymorphism in the ubiquitin D gene associated with celiac disease

(2009) Ainara Castellanos-Rubio et al.   HUMAN IMMUNOLOGY

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

To localize or not to localize: mRNA fate is in 3′UTR ends

(2009) Catia Andreassi et al.   TRENDS IN CELL BIOLOGY

Allele-specific gene expression patterns in primary leukemic cells reveal regulation of gene expression by CpG site methylation

(2008) L. Milani et al.   GENOME RESEARCH

Genetics of gene expression and its effect on disease

(2008) Valur Emilsson et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Allele-Specific Up-Regulation of FGFR2 Increases Susceptibility to Breast Cancer

(2008) Kerstin B Meyer et al.   PLOS BIOLOGY

Mapping the Genetic Architecture of Gene Expression in Human Liver

(2008) Eric E Schadt et al.   PLOS BIOLOGY