Global assessment of imprinted gene expression in the bovine conceptus by next generation sequencing

What’s in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual

(2015) Lynsey K. Whitacre et al.   BMC GENOMICS

The landscape of genomic imprinting across diverse adult human tissues

(2015) Yael Baran et al.   GENOME RESEARCH

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Bovine Genome Database: new tools for gleaning function from theBos taurusgenome

(2015) Christine G. Elsik et al.   NUCLEIC ACIDS RESEARCH

Morphological and Gene Expression Changes in Cattle Embryos from Hatched Blastocyst to Early Gastrulation Stages after Transfer of In Vitro Produced Embryos

(2015) Jessica van Leeuwen et al.   PLoS One

Characterization of global loss of imprinting in fetal overgrowth syndrome induced by assisted reproduction

(2015) Zhiyuan Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA editing by ADAR1 prevents MDA5 sensing of endogenous dsRNA as nonself

(2015) B. J. Liddicoat et al.   SCIENCE

One Size Doesn't Fit All - RefEditor: Building Personalized Diploid Reference Genome to Improve Read Mapping and Genotype Calling in Next Generation Sequencing Studies

(2015) Shuai Yuan et al.   PLoS Computational Biology

Sexual Dimorphism in Developmental Programming of the Bovine Preimplantation Embryo Caused by Colony-Stimulating Factor 21

(2014) Kyle B. Dobbs et al.   BIOLOGY OF REPRODUCTION

Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing

(2014) Coline Billerey et al.   BMC GENOMICS

RNA-Seq Alignment to Individualized Genomes Improves Transcript Abundance Estimates in Multiparent Populations

(2014) Steven C. Munger et al.   GENETICS

Using next-generation RNA sequencing to identify imprinted genes

(2014) X Wang et al.   HEREDITY

Epigenetics and imprinting in human disease

(2014) Jennifer M. Kalish et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

The role of genomic imprinting in biology and disease: an expanding view

(2014) Jo Peters   NATURE REVIEWS GENETICS

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

(2014) Q. Deng et al.   SCIENCE

Lineage-specific regulation of imprinted X inactivation in extraembryonic endoderm stem cells

(2014) Sarra Merzouk et al.   Epigenetics & Chromatin

Mammalian conserved ADAR targets comprise only a small fragment of the human editosome

(2014) Yishay Pinto et al.   GENOME BIOLOGY

Reliable Identification of Genomic Variants from RNA-Seq Data

(2013) Robert Piskol et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

X-Inactivation, Imprinting, and Long Noncoding RNAs in Health and Disease

(2013) Jeannie T. Lee et al.   CELL

Large offspring syndrome

(2013) Zhiyuan Chen et al.   Epigenetics

Identifying RNA editing sites using RNA sequencing data alone

(2013) Gokul Ramaswami et al.   NATURE METHODS

Deciphering the functions and regulation of brain-enriched A-to-I RNA editing

(2013) Jin Billy Li et al.   NATURE NEUROSCIENCE

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

(2013) Simon Anders et al.   Nature Protocols

RefSeq: an update on mammalian reference sequences

(2013) Kim D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

RADAR: a rigorously annotated database of A-to-I RNA editing

(2013) Gokul Ramaswami et al.   NUCLEIC ACIDS RESEARCH

Loss of DNMT1o Disrupts Imprinted X Chromosome Inactivation and Accentuates Placental Defects in Females

(2013) Serge McGraw et al.   PLoS Genetics

Genomic Imprinting in Farm Animals

(2013) Xiuchun (Cindy) Tian   Annual Review of Animal Biosciences

Random X inactivation in the mule and horse placenta

(2012) X. Wang et al.   GENOME RESEARCH

Ube3a-ATS is an atypical RNA polymerase II transcript that represses the paternal expression of Ube3a

(2012) Linyan Meng et al.   HUMAN MOLECULAR GENETICS

Accurate identification of human Alu and non-Alu RNA editing sites

(2012) Gokul Ramaswami et al.   NATURE METHODS

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Brian DeVeale et al.   PLoS Genetics

High levels of RNA-editing site conservation amongst 15 laboratory mouse strains

(2012) Petr Daneck et al.   GENOME BIOLOGY

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Mammalian Genomic Imprinting

(2011) M. S. Bartolomei et al.   Cold Spring Harbor Perspectives in Biology

Functions and Regulation of RNA Editing by ADAR Deaminases

(2010) Kazuko Nishikura   Annual Review of Biochemistry

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

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

(2010) Mark D Robinson et al.   GENOME BIOLOGY

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Characterization of Conserved and Nonconserved Imprinted Genes in Swine1

(2009) Steve R. Bischoff et al.   BIOLOGY OF REPRODUCTION

Characterization of the Bovine Pseudoautosomal Region and Comparison with Sheep, Goat, and Other Mammalian Pseudoautosomal Regions

(2009) P.J. Das et al.   CYTOGENETIC AND GENOME RESEARCH

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Global Survey of Genomic Imprinting by Transcriptome Sequencing

(2008) Tomas Babak et al.   CURRENT BIOLOGY

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

(2008) Xu Wang et al.   PLoS One

Imprinting of an evolutionarily conserved antisense transcript gene APeg3

(2007) Jung Ha Choo et al.   GENE