Research progress in allele-specific expression and its regulatory mechanisms

Allele-specific expression analysis methods for high-density SNP microarray data

(2012) Ruijie Liu et al.   BIOINFORMATICS

Evidence for an epigenetic role in inbreeding depression

(2012) P. Vergeer et al.   Biology Letters

Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data

(2012) Jorge Duitama et al.   BMC GENOMICS

Single-Stranded RNAs Use RNAi to Potently and Allele-Selectively Inhibit Mutant Huntingtin Expression

(2012) Dongbo Yu et al.   CELL

Epigenetic regulation of monoallelic gene expression

(2012) Hiroshi Shiba et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

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

Effects of sequence variation on differential allelic transcription factor occupancy and gene expression

(2012) T. E. Reddy et al.   GENOME RESEARCH

Trans-Species Polymorphism and Allele-Specific Expression in the CBF Gene Family of Wild Tomatoes

(2012) Mamadou Mboup et al.   MOLECULAR BIOLOGY AND EVOLUTION

Allelic Imbalance in Drosophila Hybrid Heads: Exons, Isoforms, and Evolution

(2012) R. M. Graze et al.   MOLECULAR BIOLOGY AND EVOLUTION

Allelic gene expression imbalance of bovine IGF2, LEP and CCL2 genes in liver, kidney and pituitary

(2012) R. Olbromski et al.   MOLECULAR BIOLOGY REPORTS

Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS

(2012) Zia Khan et al.   Molecular Systems Biology

A new strategy to reduce allelic bias in RNA-Seq readmapping

(2012) Ravi Vijaya Satya et al.   NUCLEIC ACIDS RESEARCH

miRNA-Mediated Relationships between Cis-SNP Genotypes and Transcript Intensities in Lymphocyte Cell Lines

(2012) Wensheng Zhang et al.   PLoS One

A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

(2012) D. G. MacArthur et al.   SCIENCE

A genome-wide screen in human embryonic stem cells reveals novel sites of allele-specific histone modification associated with known disease loci

(2012) James G D Prendergast et al.   Epigenetics & Chromatin

Cis- and trans-regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids

(2012) Xiaoli Shi et al.   Nature Communications

Chicks and single-nucleotide polymorphisms: an entrée into identifying genes conferring disease resistance in chicken

(2012) Hans H. Cheng et al.   Animal Production Science

Cis-by-Trans Regulatory Divergence Causes the Asymmetric Lethal Effects of an Ancestral Hybrid Incompatibility Gene

(2012) Shamoni Maheshwari et al.   PLoS Genetics

Estimation of alternative splicing isoform frequencies from RNA-Seq data

(2011) Marius Nicolae et al.   Algorithms for Molecular Biology

A tissue-specific landscape of sense/antisense transcription in the mouse intestine

(2011) Ulrich C Klostermeier et al.   BMC GENOMICS

Exploring the gonad transcriptome of two extreme male pigs with RNA-seq

(2011) Anna Esteve-Codina et al.   BMC GENOMICS

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

Detecting differential allelic expression using high-resolution melting curve analysis: application to the breast cancer susceptibility gene CHEK2

(2011) Tú Nguyen-Dumont et al.   BMC Medical Genomics

Identification of imprinted genes subject to parent-of-origin specific expression in Arabidopsis thaliana seeds

(2011) Peter C McKeown et al.   BMC PLANT BIOLOGY

Dominantly Inherited Constitutional Epigenetic Silencing of MLH1 in a Cancer-Affected Family Is Linked to a Single Nucleotide Variant within the 5′UTR

(2011) Megan P. Hitchins et al.   CANCER CELL

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

Allele-specific methylation in the human genome

(2011) Emma L. Meaburn et al.   Epigenetics

Allele-specific siRNA knockdown as a personalized treatment strategy for vascular Ehlers-Danlos syndrome in human fibroblasts

(2011) Gerd A. Müller et al.   FASEB JOURNAL

Differential allelic expression of c.1568C>A at UGT2B15 is due to variation in a novel cis-regulatory element in the 3′UTR

(2011) Chang Sun et al.   GENE

SNP-based large-scale identification of allele-specific gene expression in human B cells

(2011) Min-Young Song et al.   GENE

Quantitative Epigenetics Through Epigenomic Perturbation of Isogenic Lines

(2011) Frank Johannes et al.   GENETICS

Analysis of allelic differential expression in the human genome using allele-specific serial analysis of gene expression tags

(2011) Daniel Onofre Vidal et al.   GENOME

Genetic architecture of regulatory variation in Arabidopsis thaliana

(2011) X. Zhang et al.   GENOME RESEARCH

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

Development of an Allele-Specific Real-Time PCR Assay for Discrimination and Quantification of p63 R279H Mutation in EEC Syndrome

(2011) Vanessa Barbaro et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Application of allele-specific RNAi in hepatitis B virus lamivudine resistance

(2011) X. Teng et al.   JOURNAL OF VIRAL HEPATITIS

Allele-specific gene expression in a wild nonhuman primate population

(2011) J. TUNG et al.   MOLECULAR ECOLOGY

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Epigenome-wide association studies for common human diseases

(2011) Vardhman K. Rakyan et al.   NATURE REVIEWS GENETICS

Deep sequencing of virus-infected cells reveals HIV-encoded small RNAs

(2011) N. C. T. Schopman et al.   NUCLEIC ACIDS RESEARCH

The Effect of ACACB cis-Variants on Gene Expression and Metabolic Traits

(2011) Lijun Ma et al.   PLoS One

A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq

(2011) Lin Wang et al.   PLoS One

Comparing Methods for Mapping cis Acting Polymorphisms Using Allelic Expression Ratios

(2011) Marion Dawn Teare et al.   PLoS One

Allele-specific expression analysis reveals CD79B has a cis-acting regulatory element that responds to Marek's disease virus infection in chickens

(2011) H. Meydan et al.   POULTRY SCIENCE

The evolution of gene expression and the transcriptome–phenotype relationship

(2011) Peter W. Harrison et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Partitioning Transcript Variation in Drosophila : Abundance, Isoforms, and Alleles

(2011) Yajie Yang et al.   G3-Genes Genomes Genetics

Analysis of DNA Methylation in a Three-Generation Family Reveals Widespread Genetic Influence on Epigenetic Regulation

(2011) Jason Gertz et al.   PLoS Genetics

Allelic Skewing of DNA Methylation Is Widespread across the Genome

(2010) Leonard C. Schalkwyk et al.   AMERICAN JOURNAL OF HUMAN GENETICS

MLH1 Differential Allelic Expression in Mutation Carriers and Controls

(2010) Mauro Santibanez Koref et al.   ANNALS OF HUMAN GENETICS

Analysis of DNA strand-specific differential expression with high density tiling microarrays

(2010) Luis Quintales et al.   BMC BIOINFORMATICS

Cis -acting genetic variation at an E2F1/YY1 response site and putative p53 site is associated with altered allele-specific expression of ERCC5 (XPG) transcript in normal human bronchial epithelium

(2010) Thomas M. Blomquist et al.   CARCINOGENESIS

The hunt for the epiallele

(2010) Sarah Finer et al.   ENVIRONMENTAL AND MOLECULAR MUTAGENESIS

Regulatory divergence in Drosophila revealed by mRNA-seq

(2010) C. J. McManus et al.   GENOME RESEARCH

Strand-specific deep sequencing of the transcriptome

(2010) A. P. Vivancos et al.   GENOME RESEARCH

Coevolution within a transcriptional network by compensatory trans and cis mutations

(2010) D. Kuo et al.   GENOME RESEARCH

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

(2010) R. Shoemaker et al.   GENOME RESEARCH

Natural selection on cis and trans regulation in yeasts

(2010) J. J. Emerson et al.   GENOME RESEARCH

Development of a versatile, target-oriented tiling microarray assay for measuring allele-specific gene expression

(2010) Hang He et al.   GENOMICS

Allele-specific and heritable chromatin signatures in humans

(2010) E. Birney et al.   HUMAN MOLECULAR GENETICS

Allelic expression imbalance at high-density lipoprotein cholesterol locus MMAB-MVK

(2010) Marie P. Fogarty et al.   HUMAN MOLECULAR GENETICS

Allele-specific DNA methylation: beyond imprinting

(2010) B. Tycko   HUMAN MOLECULAR GENETICS

Single Nucleotide Polymorphisms in the Chicken Mx gene at Position 2032 by Real-time Allele-specific PCR Melting-curve Analysis

(2010) Xiangqun Ye et al.   JOURNAL OF POULTRY SCIENCE

Trans-acting small RNA determines dominance relationships in Brassica self-incompatibility

(2010) Yoshiaki Tarutani et al.   NATURE

Transcriptome genetics using second generation sequencing in a Caucasian population

(2010) Stephen B. Montgomery et al.   NATURE

A map of open chromatin in human pancreatic islets

(2010) Kyle J Gaulton et al.   NATURE GENETICS

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

(2010) Lira Mamanova et al.   NATURE METHODS

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

Genome-wide allele-specific analysis: insights into regulatory variation

(2010) Tomi Pastinen   NATURE REVIEWS GENETICS

Highly parallel SNP genotyping reveals high-resolution landscape of mono-allelic Ube3a expression associated with locus-wide antisense transcription

(2010) Koji Numata et al.   NUCLEIC ACIDS RESEARCH

Allele-specific differences in ryanodine receptor 1 mRNA expression levels may contribute to phenotypic variability in malignant hyperthermia

(2010) Hilbert Grievink et al.   Orphanet Journal of Rare Diseases

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

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

Integrated Genetic and Epigenetic Analysis Identifies Haplotype-Specific Methylation in the FTO Type 2 Diabetes and Obesity Susceptibility Locus

(2010) Christopher G. Bell et al.   PLoS One

Tailor-made RNAi knockdown against triplet repeat disease-causing alleles

(2010) M. Takahashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small RNA profiling reveals antisense transcription throughout the KSHV genome and novel small RNAs

(2010) Y.-T. Lin et al.   RNA

Variation in Transcription Factor Binding Among Humans

(2010) M. Kasowski et al.   SCIENCE

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

Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans

(2010) R. McDaniell et al.   SCIENCE

Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same

(2010) Matthew T. Weirauch et al.   TRENDS IN GENETICS

Extensive sequence-influenced DNA methylation polymorphism in the human genome

(2010) Asaf Hellman et al.   Epigenetics & Chromatin

Polymorphic Cis- and Trans-Regulation of Human Gene Expression

(2010) Vivian G. Cheung et al.   PLOS BIOLOGY

Allele-Specific Down-Regulation of RPTOR Expression Induced by Retinoids Contributes to Climate Adaptations

(2010) Chang Sun et al.   PLoS Genetics

Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species

(2010) Moran Yassour et al.   GENOME BIOLOGY

Allele-Specific Chromatin Remodeling in the ZPBP2/GSDMB/ORMDL3 Locus Associated with the Risk of Asthma and Autoimmune Disease

(2009) Dominique J. Verlaan et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Allele-specific expression assays using Solexa

(2009) Bradley J Main et al.   BMC GENOMICS

Dual effect of a single nucleotide polymorphism in the first intron of the porcine Secreted phosphoprotein 1 gene: allele-specific binding of C/EBP beta and activation of aberrant splicing

(2009) Eduard Muráni et al.   BMC MOLECULAR BIOLOGY

Genome-Wide Identification of Allelic Expression in Hypertensive Rats

(2009) Renata I. Dmitrieva et al.   Circulation-Cardiovascular Genetics

A Genomewide Assessment of Inbreeding Depression: Gene Number, Function, and Mode of Action

(2009) JULIEN F. AYROLES et al.   CONSERVATION BIOLOGY

Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes

(2009) J. Reinders et al.   GENES & DEVELOPMENT

A single-base resolution map of an archaeal transcriptome

(2009) O. Wurtzel et al.   GENOME RESEARCH

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

Allelic imbalance (AI) identifies novel tissue-specificcis-regulatory variation for humanUGT2B15

(2009) Chang Sun et al.   HUMAN MUTATION

Allele-specific regulation ofMTTPexpression influences the risk of ischemic heart disease

(2009) Anna Aminoff et al.   JOURNAL OF LIPID RESEARCH

Differential ACE expression among tissues in allele-specific Wistar rat lines

(2009) Jelena Kamilic et al.   MAMMALIAN GENOME

Roles of Trans and Cis Variation in Yeast Intraspecies Evolution of Gene Expression

(2009) Huang-Mo Sung et al.   MOLECULAR BIOLOGY AND EVOLUTION

Direct RNA sequencing

(2009) Fatih Ozsolak et al.   NATURE

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Allelic imbalance sequencing reveals that single-nucleotide polymorphisms frequently alter microRNA-directed repression

(2009) Jinkuk Kim et al.   NATURE BIOTECHNOLOGY

Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming

(2009) Jie Deng et al.   NATURE BIOTECHNOLOGY

Global patterns of cis variation in human cells revealed by high-density allelic expression analysis

(2009) Bing Ge et al.   NATURE GENETICS

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

(2009) Jay R Hesselberth et al.   NATURE METHODS

Digital transcriptome profiling using selective hexamer priming for cDNA synthesis

(2009) Christopher D Armour et al.   NATURE METHODS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

The genetics of inbreeding depression

(2009) Deborah Charlesworth et al.   NATURE REVIEWS GENETICS

Mapping genes for complex traits in domestic animals and their use in breeding programmes

(2009) Michael E. Goddard et al.   NATURE REVIEWS GENETICS

Profiling of mismatch discrimination in RNAi enabled rational design of allele-specific siRNAs

(2009) Huang Huang et al.   NUCLEIC ACIDS RESEARCH

A simple method for directional transcriptome sequencing using Illumina technology

(2009) N. J. Croucher et al.   NUCLEIC ACIDS RESEARCH

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

Asymmetric allele-specific expression in relation to developmental variation and drought stress in barley hybrids

(2009) Maria von Korff et al.   PLANT JOURNAL

A Yeast Hybrid Provides Insight into the Evolution of Gene Expression Regulation

(2009) I. Tirosh et al.   SCIENCE

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

(2009) A. S. Dimas et al.   SCIENCE

DNA Methylation Analysis of Chromosome 21 Gene Promoters at Single Base Pair and Single Allele Resolution

(2009) Yingying Zhang et al.   PLoS Genetics

A Strand-Specific RNA–Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi

(2009) Timothy T. Perkins et al.   PLoS Genetics

Assessing the Impact of Transgenerational Epigenetic Variation on Complex Traits

(2009) Frank Johannes et al.   PLoS Genetics

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

Allele-specific silencing of the dominant disease allele in sialuria by RNA interference

(2008) Riko D. Klootwijk et al.   FASEB JOURNAL

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

Regulatory changes underlying expression differences within and between Drosophila species

(2008) Patricia J Wittkopp et al.   NATURE GENETICS

Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation

(2008) Kristi Kerkel et al.   NATURE GENETICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Detecting shared pathogenesis from the shared genetics of immune-related diseases

(2008) Alexandra Zhernakova et al.   NATURE REVIEWS GENETICS

Shared and Distinct Genetic Variants in Type 1 Diabetes and Celiac Disease

(2008) Deborah J. Smyth et al.   NEW ENGLAND JOURNAL OF MEDICINE

Allele-Specific RNA Silencing of Mutant Ataxin-3 Mediates Neuroprotection in a Rat Model of Machado-Joseph Disease

(2008) Sandro Alves et al.   PLoS One

Dominance and the evolutionary accumulation of cis- and trans-effects on gene expression

(2008) B. Lemos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Persistent epigenetic differences associated with prenatal exposure to famine in humans

(2008) B. T. Heijmans et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Species-Specific Transcription in Mice Carrying Human Chromosome 21

(2008) M. D. Wilson et al.   SCIENCE

The Antisense Transcriptomes of Human Cells

(2008) Yiping He et al.   SCIENCE

Mapping the Genetic Architecture of Gene Expression in Human Liver

(2008) Eric E Schadt et al.   PLOS BIOLOGY

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

Transcriptome content and dynamics at single-nucleotide resolution

(2008) Nicole Cloonan et al.   GENOME BIOLOGY