Development of Strategies for SNP Detection in RNA-Seq Data: Application to Lymphoblastoid Cell Lines and Evaluation Using 1000 Genomes Data

Identification of SNPs in RNA-seq data of two cultivars of Glycine max (soybean) differing in drought resistance

(2012) Ramon Oliveira Vidal et al.   GENETICS AND MOLECULAR BIOLOGY

Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome

(2012) Zhiyu Peng et al.   NATURE BIOTECHNOLOGY

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

RNA-Seq Identifies SNP Markers for Growth Traits in Rainbow Trout

(2012) Mohamed Salem et al.   PLoS One

Screening the human exome: a comparison of whole genome and whole transcriptome sequencing

(2012) Elizabeth T Cirulli et al.   GENOME BIOLOGY

Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

(2011) S Samuel Yang et al.   BMC GENOMICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

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

(2011) Ernest Turro et al.   GENOME BIOLOGY

Gene Expression in Skin and Lymphoblastoid Cells: Refined Statistical Method Reveals Extensive Overlap in cis-eQTL Signals

(2010) Jun Ding et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The uniqueome: a mappability resource for short-tag sequencing

(2010) Ryan Koehler et al.   BIOINFORMATICS

DARNED: a DAtabase of RNa EDiting in humans

(2010) A. Kiran et al.   BIOINFORMATICS

Calling SNPs without a reference sequence

(2010) Aakrosh Ratan et al.   BMC BIOINFORMATICS

The discovery of human genetic variations and their use as disease markers: past, present and future

(2010) Chee Seng Ku et al.   JOURNAL OF HUMAN GENETICS

SNP discovery in the bovine milk transcriptome using RNA-Seq technology

(2010) Angela Cánovas et al.   MAMMALIAN GENOME

Transcriptome genetics using second generation sequencing in a Caucasian population

(2010) Stephen B. Montgomery et al.   NATURE

Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls

(2010)   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Elucidating the inosinome: global approaches to adenosine-to-inosine RNA editing

(2010) Bjorn-Erik Wulff et al.   NATURE REVIEWS GENETICS

Tumor Transcriptome Sequencing Reveals Allelic Expression Imbalances Associated with Copy Number Alterations

(2010) Brian B. Tuch et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Expression quantitative trait loci detected in cell lines are often present in primary tissues

(2009) Kevin Bullaughey et al.   HUMAN MOLECULAR GENETICS

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

Utility of lymphoblastoid cell lines

(2009) L. Sie et al.   JOURNAL OF NEUROSCIENCE RESEARCH

Targeted capture and massively parallel sequencing of 12 human exomes

(2009) Sarah B. Ng et al.   NATURE

An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells

(2009) Gene W Yeo et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq

(2009) Iouri Chepelev et al.   NUCLEIC ACIDS RESEARCH

Fidelity of SNP Array Genotyping Using Epstein Barr Virus-Transformed B-Lymphocyte Cell Lines: Implications for Genome-Wide Association Studies

(2009) Joshua T. Herbeck et al.   PLoS One

Common Regulatory Variation Impacts Gene Expression in a Cell Type-Dependent Manner

(2009) A. S. Dimas et al.   SCIENCE

Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing

(2008) Ryan D. Morin et al.   BIOTECHNIQUES

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

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

Cross-species replication of a resistin mRNA QTL, but not QTLs for circulating levels of resistin, in human and baboon

(2008) M E Tejero et al.   HEREDITY

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

Comparing whole genomes using DNA microarrays

(2008) David Gresham et al.   NATURE REVIEWS GENETICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Genomic Convergence Analysis of Schizophrenia: mRNA Sequencing Reveals Altered Synaptic Vesicular Transport in Post-Mortem Cerebellum

(2008) Joann Mudge et al.   PLoS One

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

(2008) M. Sultan et al.   SCIENCE