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

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RNA-Seq: a revolutionary tool for transcriptomics

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TopHat: discovering splice junctions with RNA-Seq

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Alternative isoform regulation in human tissue transcriptomes

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Minimum information about a microarray experiment (MIAME)-toward standards for microarray data

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Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

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Expansion of the eukaryotic proteome by alternative splicing

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ChIP–seq: advantages and challenges of a maturing technology

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Maximum Entropy Modeling of Short Sequence Motifs with Applications to RNA Splicing Signals

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Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease

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Genetics of gene expression surveyed in maize, mouse and man

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Genetic Mapping in Human Disease

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The Genetic Basis of the Reduced Expression of Bilirubin UDP-Glucuronosyltransferase 1 in Gilbert's Syndrome

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Genetic Dissection of Transcriptional Regulation in Budding Yeast

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Proliferating Cells Express mRNAs with Shortened 3' Untranslated Regions and Fewer MicroRNA Target Sites

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Genetics of gene expression and its effect on disease

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Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS

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Understanding mechanisms underlying human gene expression variation with RNA sequencing

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Pre-mRNA splicing and human diseasePreprint

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Genetic analysis of genome-wide variation in human gene expression

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Population genomics of human gene expression

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From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus

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Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation

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Identification of a variant associated with adult-type hypolactasia

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A window into third-generation sequencing

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A genome-wide association study of global gene expression

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Variations in DNA elucidate molecular networks that cause disease

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Evolutionary changes in cis and trans gene regulation

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Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations

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Transcriptome genetics using second generation sequencing in a Caucasian population

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Disruption of a GATA motif in the Duffy gene promoter abolishes erythroid gene expression in Duffy-negative individuals

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

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Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum

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Allelic Variation in Human Gene Expression

Yan, H., Yuan, W., Velculescu, V. E., Vogelstein, B., & Kinzler, K. W. (2002) · Science · doi:10.1126/science.1072545 · Cited by 625

Distinguishing protein-coding and noncoding genes in the human genome

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Options and considerations when selecting a quantitative proteomics strategy

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Meta-analysis and imputation refines the association of 15q25 with smoking quantity

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Genetics and Beyond – The Transcriptome of Human Monocytes and Disease Susceptibility

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Mapping determinants of human gene expression by regional and genome-wide association

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Natural variation in human gene expression assessed in lymphoblastoid cells

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High-Resolution Mapping of Expression-QTLs Yields Insight into Human Gene Regulation

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Genome-Wide Associations of Gene Expression Variation in Humans

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Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes

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

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A genome-wide association study identifies protein quantitative trait loci (pQTLs)

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A survey of genetic human cortical gene expression

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Statistical inferences for isoform expression in RNA-Seq

Jiang, H., & Wong, W. H. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp113 · Cited by 468

Three functional variants of IFN regulatory factor 5 ( IRF5 ) define risk and protective haplotypes for human lupus

Graham, R. R., Kyogoku, C., Sigurdsson, S., Vlasova, I. A., Davies, L. R. L., Baechler, E. C., Plenge, R. M., Koeuth, T., Ortmann, W. A., Hom, G., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0701266104 · Cited by 450

Candidate Causal Regulatory Effects by Integration of Expression QTLs with Complex Trait Genetic Associations

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Genetic basis of proteome variation in yeast

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Genetic Inheritance of Gene Expression in Human Cell Lines

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

Gregg, C. J., Zhang, J., Butler, J. E., Haig, D., & Dulac, C. G. (2010) · Science · doi:10.1126/science.1190831 · Cited by 347

Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines

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Alternative expression analysis by RNA sequencing

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

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Genome-wide analysis of transcript isoform variation in humans

Kwan, T., Benovoy, D., Dias, C., Gurd, S., Provencher, C., Beaulieu, P., Hudson, T. J., SLADEK, R. M., & Majewski, J. (2008) · Nature Genetics · doi:10.1038/ng.2007.57 · Cited by 305

Distribution and Characterization of Regulatory Elements in the Human GenomePreprint

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Tissue-Specific Genetic Control of Splicing: Implications for the Study of Complex Traits

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Cis-Acting Regulatory Variation in the Human Genome

Pastinen, T., & Hudson, T. J. (2004) · Science · doi:10.1126/science.1101659 · Cited by 266

The Coupling of Alternative Splicing and Nonsense-Mediated mRNA Decay

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Differential Contributions of Rare and Common, Coding and Noncoding Ret Mutations to Multifactorial Hirschsprung Disease Liability

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Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes

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Functional intronic polymorphisms: Buried treasure awaiting discovery within our genes

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Genetic analysis of radiation-induced changes in human gene expression

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

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

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T −13910 DNA variant associated with lactase persistence interacts with Oct-1 and stimulates lactase promoter activity in vitro

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Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing

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Functional integration of transcriptional and RNA processing machineries

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Polymorphic Cis- and Trans-Regulation of Human Gene Expression

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Global analysis of alternative splicing differences between humans and chimpanzeesPreprint

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Liver and Adipose Expression Associated SNPs Are Enriched for Association to Type 2 Diabetes

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Identification of Common Genetic Variation That Modulates Alternative Splicing

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Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human

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Heritability of alternative splicing in the human genomePreprint

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Mapping of numerous disease-associated expression polymorphisms in primary peripheral blood CD4+ lymphocytes

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Multiple Rare Variants as a Cause of a Common Phenotype: Several Different Lactase Persistence Associated Alleles in a Single Ethnic Group

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Expression Quantitative Trait Loci: Replication, Tissue- and Sex-Specificity in Mice

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Population genomics in a disease targeted primary cell modelPreprint

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Minigene reporter for identification and analysis of cis elements and trans factors affecting pre-mRNA splicing

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Fine-Scale Variation and Genetic Determinants of Alternative Splicing across Individuals

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Inactivation of RB1 in mantle-cell lymphoma detected by nonsense-mediated mRNA decay pathway inhibition and microarray analysis

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Molecular pathogenesis of Gilbert's syndrome: decreased TATA-binding protein binding affinity of UGT1A1 gene promoter

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

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Targeted screening of cis- regulatory variation in human haplotypesPreprint

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A Robust Approach to Identifying Tissue-Specific Gene Expression Regulatory Variants Using Personalized Human Induced Pluripotent Stem Cells

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Effect of polymorphisms within probe–target sequences on olignonucleotide microarray experiments

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Identifiability of isoform deconvolution from junction arrays and RNA-Seq

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Gilbert-Meulengracht’s syndrome and pharmacogenetics: is jaundice just the tip of the iceberg?

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

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Systematic evaluation of the effect of common SNPs on pre-mRNA splicing

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Genome-wide association analysis identifies 13 new risk loci for schizophrenia

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Rare and common variants: twenty arguments

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Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capturePreprint

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Pleiotropy in complex traits: challenges and strategies

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RNA Sequencing and Analysis

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ReQTL – an allele-level measure of variation-expression genomic relationshipsPreprint

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Dissecting the regulation of expression quantitative trait loci using RNA sequencing technology

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eQTL Mapping Using RNA-seq Data

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From expression QTLs to personalized transcriptomics

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RNA sequencing reveals the role of splicing polymorphisms in regulating human gene expression

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