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

Retrotransposition and genomic imprinting

(2011) M. Cowley et al.   Briefings in Functional Genomics

Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis

(2011) R. Yamashita et al.   GENOME RESEARCH

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

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

(2011) Ernest Turro et al.   GENOME BIOLOGY

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

(2010) Tomas Babak et al.   BMC GENOMICS

WAMIDEX: A web atlas of murine genomic imprinting and differential expression

(2010) Reiner Schulz et al.   Epigenetics

Statistical inference of allelic imbalance from transcriptome data

(2010) Michael Nothnagel et al.   HUMAN MUTATION

Key considerations for measuring allelic expression on a genomic scale using high-throughput sequencing

(2010) PIERRE FONTANILLAS et al.   MOLECULAR ECOLOGY

The coiled-coil domain containing protein CCDC40 is essential for motile cilia function and left-right axis formation

(2010) Anita Becker-Heck et al.   NATURE GENETICS

FRT-seq: amplification-free, strand-specific transcriptome sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

The UCSC Genome Browser database: update 2011

(2010) P. A. Fujita et al.   NUCLEIC ACIDS RESEARCH

High-Resolution Analysis of Parent-of-Origin Allelic Expression in the Mouse Brain

(2010) C. Gregg et al.   SCIENCE

Sex-Specific Parent-of-Origin Allelic Expression in the Mouse Brain

(2010) C. Gregg et al.   SCIENCE

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Evolution of Genomic Imprinting: Insights from Marsupials and Monotremes

(2009) Marilyn B. Renfree et al.   Annual Review of Genomics and Human Genetics

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

(2009) Jacob F. Degner et al.   BIOINFORMATICS

Allele-specific expression assays using Solexa

(2009) Bradley J Main et al.   BMC GENOMICS

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

Targeted capture and massively parallel sequencing of 12 human exomes

(2009) Sarah B. Ng et al.   NATURE

Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes

(2009) Iwanka Kozarewa et al.   NATURE METHODS

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

Non-coding RNAs in imprinted gene clusters

(2008) Hélène Royo et al.   BIOLOGY OF THE CELL

Global Survey of Genomic Imprinting by Transcriptome Sequencing

(2008) Tomas Babak et al.   CURRENT BIOLOGY

Comparative analysis of human chromosome 7q21 and mouse proximal chromosome 6 reveals a placental-specific imprinted gene, TFPI2/Tfpi2, which requires EHMT2 and EED for allelic-silencing

(2008) D. Monk et al.   GENOME RESEARCH

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

(2008) Brian T. Wilhelm et al.   NATURE

The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs

(2008) T. Mituyama et al.   NUCLEIC ACIDS RESEARCH

Transcriptome-Wide Identification of Novel Imprinted Genes in Neonatal Mouse Brain

(2008) Xu Wang et al.   PLoS One