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

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

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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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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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Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels

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Natural Variations and Genome-Wide Association Studies in Crop Plants

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Comparative studies of gene expression and the evolution of gene regulation

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Heritability and genomics of gene expression in peripheral blood

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RNA sequencing reveals the complex regulatory network in the maize kernel

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Deconstructing a Syndrome: Genomic Insights Into PCOS Causal Mechanisms and Classification

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RNA-Seq and human complex diseases: recent accomplishments and future perspectives

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The RNA N6-methyladenosine modification landscape of human fetal tissues

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The genetic basis of systemic lupus erythematosus: What are the risk factors and what have we learned

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Comparative Analysis of Gene Regulatory Networks: From Network Reconstruction to Evolution

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iPSC Disease Modeling

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Extensive compensatory cis-trans regulation in the evolution of mouse gene expressionPreprint

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A genome-wide association study identifies 6p21 as novel risk locus for dilated cardiomyopathy

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The Genetic and Mechanistic Basis for Variation in Gene Regulation

Pai, A. A., Pritchard, J. K., & Gilad, Y. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1004857 · Cited by 167

Next-Generation Sequencing Accelerates Crop Gene Discovery

Nguyen, K., Grondin, A., Courtois, B., & Gantet, P. (2018) · Trends in Plant Science · doi:10.1016/j.tplants.2018.11.008 · Cited by 167

The GATK joint genotyping workflow is appropriate for calling variants in RNA-seq experiments

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Omics and Drug Response

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Allele-specific binding of ZFP57 in the epigenetic regulation of imprinted and non-imprinted monoallelic expression

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From association to prediction: statistical methods for the dissection and selection of complex traits in plants

Lipka, A. E., Kandianis, C. B., Hudson, M. E., Yu, J., Drnevich, J. M., Bradbury, P. J., & Gore, M. A. (2015) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2015.02.010 · Cited by 154

Long-range epigenetic regulation is conferred by genetic variation located at thousands of independent loci

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Modeling Alzheimer's disease with human induced pluripotent stem (iPS) cells

Mungenast, A. E., Siegert, S., & Tsai, L. (2015) · Molecular and Cellular Neuroscience · doi:10.1016/j.mcn.2015.11.010 · Cited by 136

Genome-wide association study of behavioral, physiological and gene expression traits in outbred CFW mice

Parker, C. C., Gopalakrishnan, S., Carbonetto, P. S., Gonzales, N. M., Leung, E., Park, Y. J., Aryee, E., Davis, J. R., Blizard, D. A., Ackert‐Bicknell, C. L., et al. (2016) · Nature Genetics · doi:10.1038/ng.3609 · Cited by 120

The evolution of gene expression and the transcriptome–phenotype relationship

Harrison, P. W., Wright, A. E., & Mank, J. E. (2011) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2011.12.004 · Cited by 122

Next-generation sequencing facilitates quantitative analysis of wild-type and Nrl(-/-) retinal transcriptomes.

Brooks, M. J., Rajasimha, H. K., Roger, J. E., & Swaroop, A. (2011) · Europe PMC (PubMed Central) · Cited by 107

The Contribution of RNA Decay Quantitative Trait Loci to Inter-Individual Variation in Steady-State Gene Expression Levels

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Investigating monogenic and complex diseases with pluripotent stem cells

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A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals

Chen, J., Rozowsky, J. S., Galeev, T. R., Harmanci, A. O., Kitchen, R. R., Bedford, J., Abyzov, A. S., Kong, Y., Regan, L., & Gerstein, M. (2016) · Nature Communications · doi:10.1038/ncomms11101 · Cited by 105

Genetic Variants Contribute to Gene Expression Variability in Humans

Hulse‐Kemp, A. M., & Cai, J. J. (2012) · Genetics · doi:10.1534/genetics.112.146779 · Cited by 98

Transcriptome profile analysis of adipose tissues from fat and short-tailed sheep

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Genes, behavior and next‐generation RNA sequencing

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Analysis of variation at transcription factor binding sites in Drosophila and humans

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Using next-generation RNA sequencing to identify imprinted genes

Wang, X., & Clark, A. G. (2014) · Heredity · doi:10.1038/hdy.2014.18 · Cited by 89

Gene expression in African Americans, Puerto Ricans and Mexican Americans reveals ancestry-specific patterns of genetic architecture

Kachuri, L., Mak, A. C. Y., Hu, D., Eng, C. S., Huntsman, S., Elhawary, J. R., Gupta, N., Gabriel, S., Xiao, S., Keys, K. L., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01377-z · Cited by 94

Expression Quantitative Trait Loci Analysis Identifies Associations Between Genotype and Gene Expression in Human Intestine

Kabakchiev, B., & Silverberg, M. S. (2013) · Gastroenterology · doi:10.1053/j.gastro.2013.03.001 · Cited by 87

Next Generation Sequencing Based Forward Genetic Approaches for Identification and Mapping of Causal Mutations in Crop Plants: A Comprehensive Review

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Epistatic Selection between Coding and Regulatory Variation in Human Evolution and Disease

Lappalainen, T., Montgomery, S. B., Nica, A. C., & Dermitzakis, E. T. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.08.004 · Cited by 74

Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research

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Molecular advances in QTL discovery and application in pig breeding

Ernst, C. W., & Steibel, J. P. (2013) · Trends in Genetics · doi:10.1016/j.tig.2013.02.002 · Cited by 83

Bayesian Detection of Expression Quantitative Trait Loci Hot Spots

Bottolo, L., Petretto, E. G., Blankenberg, S., Cambien, F., Cook, S. A., Tiret, L., & Richardson, S. T. (2011) · Genetics · doi:10.1534/genetics.111.131425 · Cited by 71

Expression quantitative trait locus analysis for translational medicine

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A meta-analysis of gene expression quantitative trait loci in brain

Kim, Y., Xia, K., Tao, R., Giusti-Rodriguez, P., Vladimirov, V, van den Oord, E., & Sullivan, P. F. (2014) · Translational Psychiatry · doi:10.1038/tp.2014.96 · Cited by 73

Allele-specific expression and eQTL analysis in mouse adipose tissue

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Age-Specific Variation in Immune Response inDrosophila melanogasterHas a Genetic Basis

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A genomic portrait of the genetic architecture and regulatory impact of microRNA expression in response to infectionPreprint

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Population-scale study of eRNA transcription reveals bipartite functional enhancer architecture

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Identification and characterization of transcript polymorphisms in soybean lines varying in oil composition and content

Goettel, W., Xia, E., Upchurch, R. G., Wang, M.-L., Chen, P., & An, Y. C. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-299 · Cited by 65

Whole transcriptome RNA-Seq allelic expression in human brain

Smith, R. M., Webb, A., Papp, A. C., Newman, L. C., Handelman, S. K., Suhy, A., Mascarenhas, R., Oberdick, J., & Sadée, W. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-571 · Cited by 67

CRISPR-Based Synthetic Transcription Factors In Vivo: The Future of Therapeutic Cellular Programming

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Elucidating the molecular responses of apple rootstock resistant to ARD pathogens: challenges and opportunities for development of genomics-assisted breeding tools

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C-reactive protein upregulates the whole blood expression of CD59 - an integrative analysis

Lepik, K., Annilo, T., Kukuškina, V., eQTLGen Consortium, Kisand, K., Kutalik, Z., Peterson, P., & Peterson, H. (2017) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1005766 · Cited by 48

Long non-coding RNA-mediated regulation of glucose homeostasis and diabetes.

Sun, X., & Wong, D. (2016) · Europe PMC (PubMed Central) · Cited by 61

Genomics and the evolution of phenotypic traits

Wray, G. A. (2013) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev-ecolsys-110512-135828 · Cited by 68

A network perspective on nitrogen metabolism from model to crop plants using integrated ‘omics’ approaches

Fukushima, A., & Kusano, M. (2014) · Journal of Experimental Botany · doi:10.1093/jxb/eru322 · Cited by 61

Genetic variation of pre‐mRNA alternative splicing in human populations

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Genomic modulators of the immune response

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Using RNA-seq data to select reference genes for normalizing gene expression in apple roots

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Global Properties and Functional Complexity of Human Gene Regulatory Variation

Gaffney, D. J. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003501 · Cited by 61

Transcriptome sequencing study implicates immune-related genes differentially expressed in schizophrenia: new data and a meta-analysis

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Embracing new-generation 'omics' tools to improve drought tolerance in cereal and food-legume crops

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The potential of the riboSNitch in personalized medicine

Solem, A., Halvorsen, M., Ramos, S. B. V., & Laederach, A. (2015) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1291 · Cited by 56

Natural genetic variation impacts expression levels of coding, non‐coding, and antisense transcripts in fission yeast

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The Impact of 3′UTR Variants on Differential Expression of Candidate Cancer Susceptibility Genes

Skeeles, L. E., Fleming, J. L., Mahler, K. L., & Toland, A. E. (2013) · PLoS ONE · doi:10.1371/journal.pone.0058609 · Cited by 54

Genes controlling vaccine responses and disease resistance to respiratory viral pathogens in cattle

Glass, E. J., Baxter, R., Leach, R. J., & Jann, O. (2011) · Veterinary Immunology and Immunopathology · doi:10.1016/j.vetimm.2011.05.009 · Cited by 53

miRNA regulatory variation in human evolution

Li, J., & Zhang, Z. (2012) · Trends in Genetics · doi:10.1016/j.tig.2012.10.008 · Cited by 52

Mapping eQTLs with RNA-seq reveals novel susceptibility genes, non-coding RNAs and alternative-splicing events in systemic lupus erythematosus

Odhams, C. A., Cortini, A., Chen, L., Roberts, A. L., Viñuela, A., Buil, A., Small, K. S., Dermitzakis, E. T., Morris, D. L., Vyse, T. J., et al. (2016) · Human Molecular Genetics · doi:10.1093/hmg/ddw417 · Cited by 47

Transcriptomic basis of genome by genome variation in a legume‐rhizobia mutualism

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Natural variation in non-coding regions underlying phenotypic diversity in budding yeast

Salinas, F., de Boer, C. G., Abarca, V., García, V., Cuevas, M., Araos, S., Larrondo, L. F., Martı́nez, C., & Cubillos, F. A. (2016) · Scientific Reports · doi:10.1038/srep21849 · Cited by 48

Reduced representation approaches to interrogate genome diversity in large repetitive plant genomes

Hirsch, C. D., Evans, J., Buell, C. R., & Hirsch, C. N. (2014) · Briefings in Functional Genomics · doi:10.1093/bfgp/elt051 · Cited by 44

Contribution of unfixed transposable element insertions to human regulatory variation

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Genomic reaction norms inform predictions of plastic and adaptive responses to climate change

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Structural effects of linkage disequilibrium on the transcriptome

Martin, J. S., Halvorsen, M., Davis-Neulander, L., Ritz, J., Gopinath, C., Beauregard, A., & Laederach, A. (2011) · RNA · doi:10.1261/rna.029900.111 · Cited by 43

Impact of common regulatory single-nucleotide variants on gene expression profiles in whole blood

Mehta, D., Heim, K., Herder, C., Carstensen, M., Eckstein, G., Schurmann, C., Homuth, G., Nauck, M. A., Völker, U., Roden, M., et al. (2012) · European Journal of Human Genetics · doi:10.1038/ejhg.2012.106 · Cited by 42

Allelic variation in transcription factor PtoWRKY68 contributes to drought tolerance in Populus

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Genetic dissection of the gene coexpression network underlying photosynthesis in Populus

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

Andergassen, D., Dotter, C. P., Kuliński, T. M., Guenzl, P. M., Bammer, P. C., Barlow, D. P., Pauler, F. M., & Hudson, Q. J. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv727 · Cited by 37

Genetic architecture of retinal and macular degenerative diseases: the promise and challenges of next-generation sequencing

Ratnapriya, R., & Swaroop, A. (2013) · Genome Medicine · doi:10.1186/gm488 · Cited by 38

Expression level polymorphisms: heritable traits shaping natural variation

Delker, C., & Quint, M. (2011) · Trends in Plant Science · doi:10.1016/j.tplants.2011.05.009 · Cited by 38

Differential Gene Expression in Age-Related Macular DegenerationPreprint

Morgan, D. J., & DeAngelis, M. M. (2014) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a017210 · Cited by 36

The consequences of genomic architecture on ecological speciation in postglacial fishes

Rogers, S. M., Mee, J. A., & Bowles, E. (2013) · Current Zoology · doi:10.1093/czoolo/59.1.53 · Cited by 37

Comparative analysis of pathology and behavioural phenotypes in mouse models of Huntington's disease

Brooks, S. P., Jones, L., & Dunnett, S. B. (2011) · Brain Research Bulletin · doi:10.1016/j.brainresbull.2011.10.002 · Cited by 40

An integrative functional genomics framework for effective identification of novel regulatory variants in genome–phenome studies

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Translating Lung Function Genome-Wide Association Study (GWAS) Findings

Kheirallah, A. K., Miller, S., Hall, I. P., & Sayers, I. (2016) · Advances in genetics · doi:10.1016/bs.adgen.2015.12.002 · Cited by 36

Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes

Hasin-Brumshtein, Y., Khan, A. H., Hormozdiari, F., Pan, C., Parks, B. W., Petyuk, V., Piehowski, P., Brümmer, A., Pellegrini, M. A., Xiao, X. G., et al. (2016) · eLife · doi:10.7554/elife.15614 · Cited by 34

Predominant contribution of cis‐regulatory divergence in the evolution of mouse alternative splicing

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Drosophila melanogaster as a model for lead neurotoxicology and toxicogenomics research

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