Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data

Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance

(2015) James J Crowley et al.   NATURE GENETICS

Genetic conflict reflected in tissue-specific maps of genomic imprinting in human and mouse

(2015) Tomas Babak et al.   NATURE GENETICS

Noncoding RNAs and Epigenetic Mechanisms During X-Chromosome Inactivation

(2014) Anne-Valerie Gendrel et al.   Annual Review of Cell and Developmental Biology

Regulation of Transcription by Long Noncoding RNAs

(2014) Roberto Bonasio et al.   Annual Review of Genetics

Allele-specific expression and eQTL analysis in mouse adipose tissue

(2014) Yehudit Hasin-Brumshtein et al.   BMC GENOMICS

Allelic expression analysis of the osteoarthritis susceptibility locus that maps to chromosome 3p21 reveals cis-acting eQTLs at GNL3 and SPCS1

(2014) Fiona Gee et al.   BMC Medical Genetics

What does genetics tell us about imprinting and the placenta connection?

(2014) Susannah Varmuza et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Post-natal imprinting: evidence from marsupials

(2014) J M Stringer et al.   HEREDITY

The evolution of genomic imprinting: theories, predictions and empirical tests

(2014) M M Patten et al.   HEREDITY

Using next-generation RNA sequencing to identify imprinted genes

(2014) X Wang et al.   HEREDITY

Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells

(2014) Q. Deng et al.   SCIENCE

Genomic Imprinting in Mammals

(2014) D. P. Barlow et al.   Cold Spring Harbor Perspectives in Biology

Gene regulation by the act of long non-coding RNA transcription

(2013) Aleksandra E Kornienko et al.   BMC BIOLOGY

Whole transcriptome RNA-Seq allelic expression in human brain

(2013) Ryan M Smith et al.   BMC GENOMICS

Singular Expression of Olfactory Receptor Genes

(2013) Ivan Rodriguez   CELL

Genome-wide Generation and Systematic Phenotyping of Knockout Mice Reveals New Roles for Many Genes

(2013) Jacqueline K. White et al.   CELL

Imprinted silencing is extended over broad chromosomal domains in mouse extra-embryonic lineages

(2013) Tomasz M Kulinski et al.   CURRENT OPINION IN CELL BIOLOGY

Different flavors of X-chromosome inactivation in mammals

(2013) Cathérine Dupont et al.   CURRENT OPINION IN CELL BIOLOGY

Clustered protocadherins

(2013) W. V. Chen et al.   DEVELOPMENT

Analysis of Allele-Specific Expression in Mouse Liver by RNA-Seq: A Comparison With Cis -eQTL Identified Using Genetic Linkage

(2013) Sandrine Lagarrigue et al.   GENETICS

Characterization of the imprinting signature of mouse embryo fibroblasts by RNA deep sequencing

(2013) Diana A. Tran et al.   NUCLEIC ACIDS RESEARCH

Genetic Architecture of Skewed X Inactivation in the Laboratory Mouse

(2013) John D. Calaway et al.   PLoS Genetics

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

A simple strand-specific RNA-Seq library preparation protocol combining the Illumina TruSeq RNA and the dUTP methods

(2012) Marc Sultan et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Base-Resolution Analyses of Sequence and Parent-of-Origin Dependent DNA Methylation in the Mouse Genome

(2012) Wei Xie et al.   CELL

Large-scale profiling and identification of potential regulatory mechanisms for allelic gene expression in colorectal cancer cells

(2012) Robin Dong-Woo Lee et al.   GENE

A survey of tissue-specific genomic imprinting in mammals

(2012) Adam R. Prickett et al.   MOLECULAR GENETICS AND GENOMICS

Identification of allele-specific alternative mRNA processing via transcriptome sequencing

(2012) Gang Li et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Brian DeVeale et al.   PLoS Genetics

Autosomal monoallelic expression in the mouse

(2012) Lillian M Zwemer et al.   GENOME BIOLOGY

Next-generation DNA sequencing-based assay for measuring allelic expression imbalance (AEI) of candidate neuropsychiatric disorder genes in human brain

(2011) Xiang Xu et al.   BMC GENOMICS

Identification and resolution of artifacts in the interpretation of imprinted gene expression

(2011) C. Proudhon et al.   Briefings in Functional Genomics

Extra-embryonic-specific imprinted expression is restricted to defined lineages in the post-implantation embryo

(2011) Quanah J. Hudson et al.   DEVELOPMENTAL BIOLOGY

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

(2011) Xu Wang et al.   GENETICS

Re-investigation and RNA sequencing-based identification of genes with placenta-specific imprinted expression

(2011) Hiroaki Okae et al.   HUMAN MOLECULAR GENETICS

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

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

Global survey of escape from X inactivation by RNA-sequencing in mouse

(2010) F. Yang et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

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

(2010) C. Gregg et al.   SCIENCE

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

(2010) Jacek Majewski et al.   TRENDS IN GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The function of non-coding RNAs in genomic imprinting

(2009) M. V. Koerner et al.   DEVELOPMENT

Paternal deletion of Meg1/Grb10 DMR causes maternalization of the Meg1/Grb10 cluster in mouse proximal Chromosome 11 leading to severe pre- and postnatal growth retardation

(2009) Hirosuke Shiura et al.   HUMAN MOLECULAR GENETICS

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

Global Survey of Genomic Imprinting by Transcriptome Sequencing

(2008) Tomas Babak et al.   CURRENT BIOLOGY

Transcript- and tissue-specific imprinting of a tumour suppressor gene

(2008) Reiner Schulz et al.   HUMAN MOLECULAR GENETICS

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

(2008) Xu Wang et al.   PLoS One

Revealing the architecture of gene regulation: the promise of eQTL studies

(2008) Yoav Gilad et al.   TRENDS IN GENETICS

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