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

Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556 · see citing works

RNA-Seq: a revolutionary tool for transcriptomics

Wang, Z., Gerstein, M., & Snyder, M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2484 · Cited by 13,174 · see citing works

TopHat: discovering splice junctions with RNA-Seq

Trapnell, C., Pachter, L. S., & Salzberg, S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp120 · Cited by 11,477 · see citing works

Alternative isoform regulation in human tissue transcriptomes

Wang, E. T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S. F., Schroth, G. P., & Burge, C. B. (2008) · Nature · doi:10.1038/nature07509 · Cited by 5,181 · see citing works

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

Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., Aach, J., Ansorge, W., Ball, C. A., Causton, H. C., et al. (2001) · Nature Genetics · doi:10.1038/ng1201-365 · Cited by 4,109 · see citing works

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

Hindorff, L. A., Sethupathy, P., Junkins, H. A., Ramos, E. M., Mehta, J. P., Collins, F. S., & Manolio, T. A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0903103106 · Cited by 4,013 · see citing works

ChIP–seq: advantages and challenges of a maturing technology

Park, P. J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2641 · Cited by 2,217 · see citing works

Expansion of the eukaryotic proteome by alternative splicing

Nilsen, T. W., & Graveley, B. R. (2010) · Nature · doi:10.1038/nature08909 · Cited by 2,172 · see citing works

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

Yeo, G. W.-M., & Burge, C. B. (2004) · Journal of Computational Biology · doi:10.1089/1066527041410418 · Cited by 2,042 · see citing works

Genetics of gene expression surveyed in maize, mouse and man

Schadt, E., Monks, S. A., Drake, T., Lusis, A., Che, N., Colinayo, V. V., Ruff, T., Milligan, S. B., Lamb, J., Cavet, G., et al. (2003) · Nature · doi:10.1038/nature01434 · Cited by 1,594 · see citing works

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

Botstein, D., & Risch, N. (2003) · Nature Genetics · doi:10.1038/ng1090 · Cited by 1,503 · see citing works

Genetic Mapping in Human Disease

Altshuler, D., Daly, M. J., & Lander, E. S. (2008) · Science · doi:10.1126/science.1156409 · Cited by 1,452 · see citing works

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

Bosma, P. J., Chowdhury, J. R., Bakker, C., Gantla, S., Boer, A. M. T., Oostra, B. A., Lindhout, D., Tytgat, G. N. J., Jansen, P. L. M., Elferink, R. P. J. O., et al. (1995) · New England Journal of Medicine · doi:10.1056/nejm199511023331802 · Cited by 1,439 · see citing works

Genetic Dissection of Transcriptional Regulation in Budding Yeast

Brem, R. B., Yvert, G., Clinton, R., & Kruglyak, L. (2002) · Science · doi:10.1126/science.1069516 · Cited by 1,392 · see citing works

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

Sandberg, R., Neilson, J. R., Sarma, A., Sharp, P. A., & Burge, C. B. (2008) · Science · doi:10.1126/science.1155390 · Cited by 1,349 · see citing works

Genetics of gene expression and its effect on disease

Emilsson, V., Thorleifsson, G., Zhang, B., Leonardson, A. S., Zink, F., Zhu, J., Carlson, S., Helgason, A., Walters, G. B., Gunnarsdottir, S., et al. (2008) · Nature · doi:10.1038/nature06758 · Cited by 1,296 · see citing works

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

Nicolae, D. L., Gamazon, E., Zhang, W., Duan, S., Dolan, M. E., & Cox, N. J. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1000888 · Cited by 1,292 · see citing works

Understanding mechanisms underlying human gene expression variation with RNA sequencing

Pickrell, J. K., Marioni, J. C., Pai, A. A., Degner, J. F., Engelhardt, B. E., Nkadori, E., Veyrieras, J.-B., Stephens, M., Gilad, Y., & Pritchard, J. K. (2010) · Nature · doi:10.1038/nature08872 · Cited by 1,256 · see citing works

Pre-mRNA splicing and human diseasePreprint

Faustino, N. A., & Cooper, T. A. (2003) · Genes & Development · doi:10.1101/gad.1048803 · Cited by 1,248 · see citing works

Genetic analysis of genome-wide variation in human gene expression

Morley, M. P., Molony, C. M., Weber, T. M., Devlin, J. L., Ewens, K. G., Spielman, R. S., & Cheung, V. G. (2004) · Nature · doi:10.1038/nature02797 · Cited by 1,207 · see citing works

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

Musunuru, K., Strong, A., Frank-Kamenetsky, M., Lee, N. E., Ahfeldt, T., Sachs, K. V., Li, X., Li, H., Kuperwasser, N., Ruda, V. M., et al. (2010) · Nature · doi:10.1038/nature09266 · Cited by 1,140 · see citing works

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

Lu, P., Vogel, C., Wang, R., Yao, X., & Marcotte, E. M. (2007) · Nature Biotechnology · doi:10.1038/nbt1270 · Cited by 1,139 · see citing works

Population genomics of human gene expression

Stranger, B. E., Nica, A. C., Forrest, M. S., Dimas, A. S., Bird, C., Beazley, C., Ingle, C., Dunning, M., Flicek, P., Koller, D., et al. (2007) · Nature Genetics · doi:10.1038/ng2142 · Cited by 1,132 · see citing works

Identification of a variant associated with adult-type hypolactasia

Enattah, N. S., Sahi, T., Savilahti, E., Terwilliger, J. D., Peltonen, L., & Järvelä, I. E. (2002) · Nature Genetics · doi:10.1038/ng826 · Cited by 1,029 · see citing works

A window into third-generation sequencing

Schadt, E. E., Turner, S., & Kasarskis, A. (2010) · Human Molecular Genetics · doi:10.1093/hmg/ddq416 · Cited by 960 · see citing works

A genome-wide association study of global gene expression

Dixon, A. L., Liang, L., Moffatt, M. F., Chen, W., Heath, S. C., Wong, K., Taylor, J. C., Burnett, E. C., Gut, I. G., Farrall, M., et al. (2007) · Nature Genetics · doi:10.1038/ng2109 · Cited by 946 · see citing works

Variations in DNA elucidate molecular networks that cause disease

Chen, Y., Zhu, J., Lum, P. Y., Yang, X., Pinto, S., MacNeil, D. J., Zhang, C., Lamb, J., Edwards, S., Sieberts, S. K., et al. (2008) · Nature · doi:10.1038/nature06757 · Cited by 887 · see citing works

Evolutionary changes in cis and trans gene regulation

Wittkopp, P. J., Haerum, B. K., & Clark, A. G. (2004) · Nature · doi:10.1038/nature02698 · Cited by 873 · see citing works

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

Dressman, D. C., Yan, H., Traverso, G., Kinzler, K. W., & Vogelstein, B. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1133470100 · Cited by 845 · see citing works

Transcriptome genetics using second generation sequencing in a Caucasian population

Montgomery, S. B., Sammeth, M., Gutierrez-Arcelus, M., Lach, R. P., Ingle, C., Nisbett, J., Guigo, R., & Dermitzakis, E. T. (2010) · Nature · doi:10.1038/nature08903 · Cited by 797 · see citing works

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

Tournamille, C., Colin, Y., Cartron, J. P., & Le Van Kim, C. (1995) · Nature Genetics · doi:10.1038/ng0695-224 · Cited by 741 · see citing works

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

Gieger, C., Geistlinger, L., Altmaier, E., Hrabé de Angelis, M., Kronenberg, F., Meitinger, T., Mewes, H.-W., Wichmann, H.-E., Weinberger, K. M., Adamski, J., et al. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000282 · Cited by 737 · see citing works

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

Dimas, A. S., Deutsch, S., Stranger, B. E., Montgomery, S. B., Borel, C., Attar, H., Ingle, C., Beazley, C., Arcelus, M. G., Sekowska, M., et al. (2009) · Science · doi:10.1126/science.1174148 · Cited by 729 · see citing works

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 · see citing works

Distinguishing protein-coding and noncoding genes in the human genome

Clamp, M., Fry, B., Kamal, M., Xie, X., Cuff, J., Lin, M. F., Kellis, M., Lindblad-Toh, K., & Lander, E. S. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0709013104 · Cited by 624 · see citing works

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

The Wellcome Trust Case Control Consortium, Liu, J. Z., Tozzi, F., Waterworth, D. M., Pillai, S. G., Muglia, P., Middleton, L., Berrettini, W., Knouff, C. W., Yuan, X., et al. (2010) · Nature Genetics · doi:10.1038/ng.572 · Cited by 614 · see citing works

Options and considerations when selecting a quantitative proteomics strategy

Domon, B., & Aebersold, R. H. (2010) · Nature Biotechnology · doi:10.1038/nbt.1661 · Cited by 601 · see citing works

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

Cheung, V. G., Spielman, R. S., Ewens, K. G., Weber, T. M., Morley, M. P., & Burdick, J. T. (2005) · Nature · doi:10.1038/nature04244 · Cited by 588 · see citing works

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

Zeller, T., Wild, P. S., Szymczak, S., Rotival, M., Schillert, A., Castagné, R., Maouche, S., Germain, M., Lackner, K. J., Rossmann, H., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0010693 · Cited by 584 · see citing works

Natural variation in human gene expression assessed in lymphoblastoid cells

Cheung, V. G., Conlin, L. K., Weber, T. M., Arcaro, M., Jen, K., Morley, M. P., & Spielman, R. S. (2003) · Nature Genetics · doi:10.1038/ng1094 · Cited by 550 · see citing works

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

Veyrieras, J.-B., Kudaravalli, S., Kim, S. Y., Dermitzakis, E. T., Gilad, Y., Stephens, M., & Pritchard, J. K. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000214 · Cited by 536 · see citing works

Genome-Wide Associations of Gene Expression Variation in Humans

Stranger, B. E., Forrest, M. S., Clark, A. G., Minichiello, M. J., Deutsch, S., Lyle, R., Hunt, S. E., Kahl, B. F., Antonarakis, S. E., Tavaré, S., et al. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0010078 · Cited by 519 · see citing works

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

Göring, H. H. H., Curran, J. E., Johnson, M. P., Dyer, T. D., Charlesworth, J., Cole, S. A., Jowett, J. B. M., Abraham, L. J., Rainwater, D. L., Comuzzie, A. G., et al. (2007) · Nature Genetics · doi:10.1038/ng2119 · Cited by 503 · see citing works

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

Degner, J. F., Marioni, J. C., Pai, A. A., Pickrell, J. K., Nkadori, E., Gilad, Y., & Pritchard, J. K. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp579 · Cited by 502 · see citing works

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

Melzer, D., Perry, J. R. B., Hernandez, D., Corsi, A.-M., Stevens, K., Rafferty, I., Lauretani, F., Murray, A., Gibbs, J. R., Paolisso, G., et al. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000072 · Cited by 480 · see citing works

A survey of genetic human cortical gene expression

Myers, A. J., Gibbs, J. R., Webster, J. A., Rohrer, K., Zhao, A., Marlowe, L., Kaleem, M., Leung, D., Bryden, L., Nath, P., et al. (2007) · Nature Genetics · doi:10.1038/ng.2007.16 · Cited by 479 · see citing works

Statistical inferences for isoform expression in RNA-Seq

Jiang, H., & Wong, W. H. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp113 · Cited by 453 · see citing works

Three functional variants of IFN regulatory factor 5 ( <i>IRF5</i> ) 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 · see citing works

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

Nica, A. C., Montgomery, S. B., Dimas, A. S., Stranger, B. E., Beazley, C., Barroso, I., & Dermitzakis, E. T. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1000895 · Cited by 423 · see citing works

Genetic basis of proteome variation in yeast

Foss, E. J., Radulovic, D., Shaffer, S. A., Ruderfer, D. M., Bedalov, A., Goodlett, D. R., & Kruglyak, L. (2007) · Nature Genetics · doi:10.1038/ng.2007.22 · Cited by 358 · see citing works

Genetic Inheritance of Gene Expression in Human Cell Lines

Monks, S. A., Leonardson, A. S., Zhu, H., Cundiff, P., Pietrusiak, P., Edwards, S. W., Phillips, J. W., Sachs, A. B., & Schadt, E. E. (2004) · The American Journal of Human Genetics · doi:10.1086/426461 · Cited by 354 · see citing works

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 · see citing works

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

Castle, J. C., Zhang, C., Shah, J. K., Kulkarni, A., Kalsotra, A., Cooper, T. A., & Johnson, J. M. (2008) · Nature Genetics · doi:10.1038/ng.264 · Cited by 319 · see citing works

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

McDaniell, R., Lee, B.-K., Song, L., Liu, Z., Boyle, A. P., Erdos, M. R., Scott, L. J., Morken, M. A., Kucera, K. S., Battenhouse, A., et al. (2010) · Science · doi:10.1126/science.1184655 · Cited by 308 · see citing works

Alternative expression analysis by RNA sequencing

Griffith, M., Griffith, O. L., Mwenifumbo, J. C., Goya, R., Morrissy, A. S., Morin, R. D., Corbett, R., Tang, M., Hou, Y. C., Pugh, T. J., et al. (2010) · Nature Methods · doi:10.1038/nmeth.1503 · Cited by 306 · see citing works

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 · see citing works

Distribution and Characterization of Regulatory Elements in the Human GenomePreprint

Majewski, J., & Ott, J. (2002) · Genome Research · doi:10.1101/gr.606402 · Cited by 304 · see citing works

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

Heinzen, E. L., Ge, D., Cronin, K. D., Maia, J. M., Shianna, K. V., Gabriel, W. N., Welsh-Bohmer, K. A., Hulette, C. M., Denny, T. N., & Goldstein, D. B. (2008) · PLoS Biology · doi:10.1371/journal.pbio.1000001 · Cited by 269 · see citing works

Cis-Acting Regulatory Variation in the Human Genome

Pastinen, T., & Hudson, T. J. (2004) · Science · doi:10.1126/science.1101659 · Cited by 265 · see citing works

The Coupling of Alternative Splicing and Nonsense-Mediated mRNA Decay

Lareau, L. F., Brooks, A. N., Soergel, D. A. W., Qi, M., & Brenner, S. E. (2007) · Advances in experimental medicine and biology · doi:10.1007/978-0-387-77374-2_12 · Cited by 253 · see citing works

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

Emison, E. S., Garcia-Barceló, M., Grice, E. A., Lantieri, F., Amiel, J., Burzynski, G. M., Fernández, R. M., Li, H., Kashuk, C., West, K. M., et al. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.06.007 · Cited by 239 · see citing works

Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes

Schrimpf, S. P., Weiss, M., Reiter, L., Ahrens, C. H., Jovanovic, M., Malmström, J., Brunner, E., Mohanty, S., Lercher, M. J., Hunziker, P. E., et al. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000048 · Cited by 229 · see citing works

Functional intronic polymorphisms: Buried treasure awaiting discovery within our genes

Cooper, D. N. (2010) · Human Genomics · doi:10.1186/1479-7364-4-5-284 · Cited by 224 · see citing works

Genetic analysis of radiation-induced changes in human gene expression

Smirnov, D., Morley, M., Shin, E., Spielman, R., & Cheung, V. (2009) · Nature · doi:10.1038/nature07940 · Cited by 221 · see citing works

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

Ge, B., Pokholok, D., Kwan, T., Grundberg, E., Morcos, L., Verlaan, D. J., Le, J. M., Koka, V., Lam, K. C. L., Gagné, V., et al. (2009) · Nature Genetics · doi:10.1038/ng.473 · Cited by 215 · see citing works

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

Wang, X., Sun, Q., McGrath, S. D., Mardis, E. R., Soloway, P. D., & Clark, A. G. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003839 · Cited by 184 · see citing works

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

Lewinsky, R., Jensen, T. G. K., Møller, J., Stensballe, A., Olsen, J., & Troelsen, J. T. (2005) · Human Molecular Genetics · doi:10.1093/hmg/ddi418 · Cited by 176 · see citing works

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

Heap, G., Yang, J. H. M., Downes, K., Healy, B. C., Hunt, K. A., Bockett, N. A., Franke, L., Dubois, P. C. A., Mein, C. A., Dobson, R., et al. (2009) · Human Molecular Genetics · doi:10.1093/hmg/ddp473 · Cited by 174 · see citing works

Functional integration of transcriptional and RNA processing machineries

Pandit, S., Wang, D., & Fu, X. (2008) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2008.03.001 · Cited by 173 · see citing works

Polymorphic Cis- and Trans-Regulation of Human Gene Expression

Cheung, V. G., Nayak, R. R., Wang, I. X., Elwyn, S., Cousins, S. M., Morley, M. P., & Spielman, R. S. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000480 · Cited by 165 · see citing works

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

Zhong, H., Beaulaurier, J., Lum, P. Y., Molony, C. M., Yang, X., MacNeil, D. J., Weingarth, D. T., Zhang, B., Greenawalt, D. M., Dobrin, R., et al. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1000932 · Cited by 164 · see citing works

Global analysis of alternative splicing differences between humans and chimpanzeesPreprint

Calarco, J. A., Xing, Y., Cáceres, M., Calarco, J. P., Xiao, X. G., Pan, Q., Lee, C. J., Preuss, T. M., & Blencowe, B. J. (2007) · Genes & Development · doi:10.1101/gad.1606907 · Cited by 158 · see citing works

Identification of Common Genetic Variation That Modulates Alternative Splicing

Hull, J., Campino, S. G., Rowlands, K., Chan, M., Copley, R. R., Taylor, M. S., Rockett, K. A., Elvidge, G. P., Keating, B. J., Knight, J. C., et al. (2007) · PLoS Genetics · doi:10.1371/journal.pgen.0030099 · Cited by 157 · see citing works

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

Zhang, K., Li, J. B., Gao, Y., Egli, D. M., Xie, B., Deng, J., Li, Z., Lee, J., Aach, J., LeProust, E. M., et al. (2009) · Nature Methods · doi:10.1038/nmeth.1357 · Cited by 156 · see citing works

Heritability of alternative splicing in the human genomePreprint

Kwan, T., Benovoy, D., Dias, C., Gurd, S., Serre, D., Zuzan, H., Clark, T. A., Schweitzer, A. C., Staples, M. K., Wang, H., et al. (2007) · Genome Research · doi:10.1101/gr.6281007 · Cited by 113 · see citing works

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

Murphy, A., Chu, J., Xu, M., Carey, V. J., Lazarus, R. M., Liu, A., Szefler, S. J., Strunk, R. C., DeMuth, K. A., Castro, M., et al. (2010) · Human Molecular Genetics · doi:10.1093/hmg/ddq392 · Cited by 105 · see citing works

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

Ingram, C. J. E., Oljira, T., Tarekegn, A., Browning, S. L., Elamin, M. F., Bekele, E., Thomas, M., Weale, M. E., Bradman, N. N., & Swallow, D. M. (2009) · Journal of Molecular Evolution · doi:10.1007/s00239-009-9301-y · Cited by 100 · see citing works

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

van Nas, A., Ingram-Drake, L. A., Sinsheimer, J. S., Wang, S. S., Schadt, E. E., Drake, T. A., & Lusis, A. J. (2010) · Genetics · doi:10.1534/genetics.110.116087 · Cited by 96 · see citing works

Population genomics in a disease targeted primary cell modelPreprint

Grundberg, E., Kwan, T., Ge, B., Lam, K. C. L., Koka, V., Kindmark, A., Mallmin, H., Dias, J., Verlaan, D. J., Ouimet, M., et al. (2009) · Genome Research · doi:10.1101/gr.095224.109 · Cited by 94 · see citing works

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

Singh, G., & Cooper, T. A. (2006) · BioTechniques · doi:10.2144/000112208 · Cited by 93 · see citing works

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

Coulombe‐Huntington, J., Lam, K. C. L., Dias, C., & Majewski, J. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000766 · Cited by 89 · see citing works

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

Pinyol, M., Beà, S., Plà, L., Ribrag, V., Bosq, J., Rosenwald, A., Campo, E., & Jares, P. (2007) · Blood · doi:10.1182/blood-2006-11-057208 · Cited by 85 · see citing works

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

Hsieh, T., Shiu, T., Huang, S., Lin, H., Lee, T.-C., Chen, P., Chu, H.-C., Chang, W., Jeng, K.-S., Lai, M. M. C., et al. (2007) · Pharmacogenetics and Genomics · doi:10.1097/fpc.0b013e328012d0da · Cited by 82 · see citing works

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

FONTANILLAS, P., LANDRY, C. R., WITTKOPP, P. J., RUSS, C., GRUBER, J. D., NUSBAUM, C., & HARTL, D. L. (2010) · Molecular Ecology · doi:10.1111/j.1365-294x.2010.04472.x · Cited by 76 · see citing works

Targeted screening of cis- regulatory variation in human haplotypesPreprint

Verlaan, D. J., Ge, B., Grundberg, E., Hoberman, R., Lam, K. C. L., Koka, V., Dias, J., Gurd, S., Martín, N. W., Mallmin, H., et al. (2008) · Genome Research · doi:10.1101/gr.084798.108 · Cited by 74 · see citing works

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

Benovoy, D., Kwan, T., & Majewski, J. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn409 · Cited by 68 · see citing works

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

Lee, J., Park, I., Gao, Y., Li, J. B., Li, Z., Daley, G. Q., Zhang, K., & Church, G. M. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000718 · Cited by 66 · see citing works

Identifiability of isoform deconvolution from junction arrays and RNA-Seq

Hiller, D. J., Jiang, H., Xu, W., & Wong, W. H. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp544 · Cited by 65 · see citing works

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

Strassburg, C. P. (2009) · Drug Metabolism Reviews · doi:10.3109/03602530903209429 · Cited by 59 · see citing works

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

Babak, T., Garrett-Engele, P. W., Armour, C. D., Raymond, C. K., Keller, M. P., Chen, R., Rohl, C. A., Johnson, J. M., Attie, A., Fraser, H. B., et al. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-473 · Cited by 32 · see citing works

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

ElSharawy, A., Hundrieser, B., Brosch, M., Wittig, M., Huse, K., Platzer, M., Becker, A. J., Simon, M., Rosenstiel, P. C., Schreiber, S., et al. (2009) · Human Mutation · doi:10.1002/humu.20906 · Cited by 28 · see citing works

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

Multicenter Genetic Studies of Schizophrenia Consortium, Ripke, S., Psychosis Endophenotypes International Consortium, Wellcome Trust Case Control Consortium 2, O'Dushlaine, C., Chambert, K., Moran, J. L., Kähler, A. K., Akterin, S., Bergen, S. E., et al. (2013) · Nature Genetics · doi:10.1038/ng.2742 · Cited by 1,496 · see citing works

Rare and common variants: twenty arguments

Gibson, G. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3118 · Cited by 1,278 · see citing works

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

Rohland, N., & Reich, D. (2012) · Genome Research · doi:10.1101/gr.128124.111 · Cited by 1,159 · see citing works

Pleiotropy in complex traits: challenges and strategies

Solovieff, N., Cotsapas, C., Lee, P. H., Purcell, S. M., & Smoller, J. W. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3461 · Cited by 1,085 · see citing works

RNA Sequencing and Analysis

Kukurba, K. R., & Montgomery, S. B. (2015) · Cold Spring Harbor Protocols · doi:10.1101/pdb.top084970 · Cited by 924 · see citing works

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

Li, H., Peng, Z., Yang, X., Wang, W., Fu, J., Wang, J., Han, Y., Chai, Y., Guo, T., Yang, N., et al. (2012) · Nature Genetics · doi:10.1038/ng.2484 · Cited by 841 · see citing works

Natural Variations and Genome-Wide Association Studies in Crop Plants

Huang, X., & Han, B. (2013) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-050213-035715 · Cited by 745 · see citing works

Comparative studies of gene expression and the evolution of gene regulation

Romero, I. G., Ruvinsky, I., & Gilad, Y. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3229 · Cited by 488 · see citing works

Heritability and genomics of gene expression in peripheral blood

Wright, F. A., Sullivan, P. F., Brooks, A. I., Zou, F., Sun, W., Xia, K., Madar, V., Jansen, R., Chung, W., Zhou, Y.-H., et al. (2014) · Nature Genetics · doi:10.1038/ng.2951 · Cited by 362 · see citing works

RNA sequencing reveals the complex regulatory network in the maize kernel

Fu, J., Cheng, Y., Linghu, J., Yang, X., Kang, L., Zhang, Z., Zhang, J., He, C., Du, X., Peng, Z., et al. (2013) · Nature Communications · doi:10.1038/ncomms3832 · Cited by 298 · see citing works

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

Dapas, M., & Dunaif, A. (2022) · Endocrine Reviews · doi:10.1210/endrev/bnac001 · Cited by 300 · see citing works

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

Costa, V., Aprile, M., Esposito, R., & Ciccodicola, A. (2012) · European Journal of Human Genetics · doi:10.1038/ejhg.2012.129 · Cited by 266 · see citing works

The RNA N6-methyladenosine modification landscape of human fetal tissues

Xiao, S., Cao, S., Huang, Q., Xia, L., Deng, M., Yang, M., Jia, G., Liu, X., Shi, J., Wang, W., et al. (2019) · Nature Cell Biology · doi:10.1038/s41556-019-0315-4 · Cited by 177 · see citing works

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

Teruel, M., & Alarcón-Riquelme, M. E. (2016) · Journal of Autoimmunity · doi:10.1016/j.jaut.2016.08.001 · Cited by 177 · see citing works

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

Thompson, D. A., Regev, A., & Roy, S. (2015) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-100913-012908 · Cited by 170 · see citing works

iPSC Disease Modeling

Soldner, F., & Jaenisch, R. (2012) · Science · doi:10.1126/science.1227682 · Cited by 176 · see citing works

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

Gonçalves, Â., Leigh-Brown, S., Thybert, D., Stefflova, K., Turro, E., Flicek, P., Brāzma, A., Odom, D. T., & Marioni, J. C. (2012) · Genome Research · doi:10.1101/gr.142281.112 · Cited by 173 · see citing works

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

Meder, B., Rühle, F., Weis, T., Homuth, G., Keller, A., Franke, J., Peil, B., Bermejo, J. L., Frese, K., Huge, A., et al. (2013) · European Heart Journal · doi:10.1093/eurheartj/eht251 · Cited by 172 · see citing works

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 158 · see citing works

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 164 · see citing works

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

Brouard, J., Schenkel, F. S., Marete, A., & Bissonnette, N. (2019) · Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology · doi:10.1186/s40104-019-0359-0 · Cited by 158 · see citing works

Omics and Drug Response

Meyer, U. A., Zanger, U. M., & Schwab, M. (2013) · Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev-pharmtox-010510-100502 · Cited by 157 · see citing works

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

Strogantsev, R., Krueger, F., Yamazawa, K., Shi, H., Gould, P., Goldman-Roberts, M., McEwen, K., Sun, B., Pedersen, R., & Ferguson-Smith, A. C. (2015) · Genome Biology · doi:10.1186/s13059-015-0672-7 · Cited by 152 · see citing works

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 149 · see citing works

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

Lemire, M., Zaidi, S. H. E., Ban, M., Ge, B., Aïssi, D., Germain, M., Kassam, I., Wang, M., Zanke, B. W., Gagnon, F., et al. (2015) · Nature Communications · doi:10.1038/ncomms7326 · Cited by 133 · see citing works

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 127 · see citing works

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 119 · see citing works

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 121 · see citing works

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 108 · see citing works

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

Pai, A. A., Cain, C. E., Mizrahi-Man, O., Leon, S. D., Lewellen, N., Veyrieras, J., Degner, J. F., Gaffney, D. J., Pickrell, J. K., Stephens, M., et al. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1003000 · Cited by 108 · see citing works

Investigating monogenic and complex diseases with pluripotent stem cells

Zhu, H., Lensch, M. W., Cahan, P., & Daley, G. (2011) · Nature reviews genetics · doi:10.1038/nrg2951 · Cited by 112 · see citing works

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 100 · see citing works

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 · see citing works

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

Wang, X., Zhou, G., Xu, X., Geng, R., Zhou, J., Yang, Y., Yang, Z., & Chen, Y. (2014) · Gene · doi:10.1016/j.gene.2014.07.072 · Cited by 90 · see citing works

Genes, behavior and next‐generation <scp>RNA</scp> sequencing

Hitzemann, R., Bottomly, D., Darakjian, P., Walter, N., Iancu, O., Searles, R., Wilmot, B., & McWeeney, S. (2013) · Genes, Brain and Behavior · doi:10.1111/gbb.12007 · Cited by 88 · see citing works

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

Spivakov, M., Akhtar, J., Kheradpour, P., Beal, K., Girardot, C., Koscielny, G., Herrero, J., Kellis, M., Furlong, E. E., & Birney, E. (2012) · Genome Biology · doi:10.1186/gb-2012-13-9-r49 · Cited by 94 · see citing works

Using next-generation RNA sequencing to identify imprinted genes

Wang, X., & Clark, A. G. (2014) · Heredity · doi:10.1038/hdy.2014.18 · Cited by 88 · see citing works

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 87 · see citing works

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 84 · see citing works

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

Sahu, P. K., Sao, R., Mondal, S., Vishwakarma, G., Gupta, S. K., Kumar, V., Singh, S. K., Sharma, D., & Das, B. K. (2020) · Plants · doi:10.3390/plants9101355 · Cited by 80 · see citing works

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 79 · see citing works

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

Chaitankar, V., Karakülah, G., Ratnapriya, R., Giuste, F., Brooks, M. J., & Swaroop, A. (2016) · Progress in Retinal and Eye Research · doi:10.1016/j.preteyeres.2016.06.001 · Cited by 79 · see citing works

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 77 · see citing works

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 · see citing works

Expression quantitative trait locus analysis for translational medicine

Gibson, G. C., Powell, J. E., & Marigorta, U. M. (2015) · Genome Medicine · doi:10.1186/s13073-015-0186-7 · Cited by 74 · see citing works

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 · see citing works

Allele-specific expression and eQTL analysis in mouse adipose tissue

Hasin-Brumshtein, Y., Hormozdiari, F., Martin, L. J., van Nas, A., Eskin, E., Lusis, A., & Drake, T. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-471 · Cited by 63 · see citing works

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

Felix, T. M., Hughes, K. A., Stone, E. A., Drnevich, J. M., & Leips, J. (2012) · Genetics · doi:10.1534/genetics.112.140640 · Cited by 69 · see citing works

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

Siddle, K. J., Deschamps, M., Tailleux, L., Nédélec, Y., Pothlichet, J., Lugo‐Villarino, G., Libri, V., Gicquel, B., Neyrolles, O., Laval, G., et al. (2014) · Genome Research · doi:10.1101/gr.161471.113 · Cited by 67 · see citing works

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

Kristjánsdóttir, K., Kwak, Y., Tippens, N. D., Lis, J. T., Kang, H. M., & Kwak, H. (2020) · Nature Communications · doi:10.1038/s41467-020-19829-z · Cited by 64 · see citing works

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 · see citing works

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 65 · see citing works

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

Pandelakis, M., Delgado, E., & Ebrahimkhani, M. R. (2020) · Cell Systems · doi:10.1016/j.cels.2019.10.003 · Cited by 64 · see citing works

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

Zhu, Y., Fazio, G., & Mazzola, M. (2014) · Horticulture Research · doi:10.1038/hortres.2014.43 · Cited by 63 · see citing works

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 · see citing works

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

Sun, X., & Wong, D. (2016) · Europe PMC (PubMed Central) · Cited by 62 · see citing works

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 · see citing works

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 · see citing works

Genetic variation of pre‐mRNA alternative splicing in human populations

Lu, Z., Jiang, P., & Xing, Y. (2011) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.120 · Cited by 60 · see citing works

Genomic modulators of the immune response

Knight, J. C. (2012) · Trends in Genetics · doi:10.1016/j.tig.2012.10.006 · Cited by 57 · see citing works

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

Zhou, Z., Cong, P., Tian, Y., & Zhu, Y. (2017) · PLoS ONE · doi:10.1371/journal.pone.0185288 · Cited by 59 · see citing works

Global Properties and Functional Complexity of Human Gene Regulatory Variation

Gaffney, D. J. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003501 · Cited by 57 · see citing works

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

Sanders, A. R., Drigalenko, E. I., Duan, J., Moy, W., Freda, J., Göring, H. H. H., Gejman, P. V., & on behalf of, M. G. S. (2017) · Translational Psychiatry · doi:10.1038/tp.2017.47 · Cited by 57 · see citing works

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

Singh, B., Bohra, A., Mishra, S., Joshi, R., & Pandey, S. (2015) · Biologia Plantarum · doi:10.1007/s10535-015-0515-0 · Cited by 58 · see citing works

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 55 · see citing works

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

Clément‐Ziza, M., Marsellach, X., Codlin, S., Papadakis, M. A., Reinhardt, S., Rodríguez‐López, M., Martin, S., Marguerat, S., Schmidt, A., Lee, E., et al. (2014) · Molecular Systems Biology · doi:10.15252/msb.20145123 · Cited by 51 · see citing works

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 53 · see citing works

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 · see citing works

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 · see citing works

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 46 · see citing works

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

Burghardt, L. T., Guhlin, J. G., Chun, C. L., Liu, J., Sadowsky, M. J., Stupar, R. M., Young, N. D., & Tiffin, P. (2017) · Molecular Ecology · doi:10.1111/mec.14285 · Cited by 49 · see citing works

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 47 · see citing works

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 46 · see citing works

Contribution of unfixed transposable element insertions to human regulatory variation

Goubert, C., Zevallos, N. A., & Feschotte, C. (2020) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2019.0331 · Cited by 41 · see citing works

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

Oomen, R. A., & Hutchings, J. A. (2022) · Journal of Animal Ecology · doi:10.1111/1365-2656.13707 · Cited by 43 · see citing works

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 · see citing works

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 41 · see citing works

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

Fang, Y., Wang, D., Xiao, L., Quan, M., Qi, W., Song, F., Zhou, J., Liu, X., Qin, S., Du, Q., et al. (2023) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiad315 · Cited by 40 · see citing works

Genetic dissection of the gene coexpression network underlying photosynthesis in Populus

Xiao, L., Liu, X., Lu, W., Chen, P., Quan, M., Si, J., Du, Q., & Zhang, D. (2019) · Plant Biotechnology Journal · doi:10.1111/pbi.13270 · Cited by 40 · see citing works

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 · see citing works

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 · see citing works

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 37 · see citing works

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 · see citing works

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 36 · see citing works

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 36 · see citing works

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

Zhao, J., Cheng, F., Jia, P., Cox, N. J., Denny, J. C., & Zhao, Z. (2018) · Genome Medicine · doi:10.1186/s13073-018-0513-x · Cited by 35 · see citing works

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 35 · see citing works

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 32 · see citing works

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

Gao, Q., Sun, W., Ballegeer, M., Libert, C., & Chen, W. (2015) · Molecular Systems Biology · doi:10.15252/msb.20145970 · Cited by 34 · see citing works

Drosophila melanogaster as a model for lead neurotoxicology and toxicogenomics research

Hirsch, H. V. B., Lnenicka, G. A., Possidente, D. R., Possidente, B. P., Garfinkel, M. D., Wang, L., Lu, X., & Ruden, D. M. (2012) · Frontiers in Genetics · doi:10.3389/fgene.2012.00068 · Cited by 34 · see citing works

Extensive allele‐specific translational regulation in hybrid mice

Hou, J., Wang, X., McShane, E., Zauber, H., Sun, W., Selbach, M., & Chen, W. (2015) · Molecular Systems Biology · doi:10.15252/msb.156240 · Cited by 32 · see citing works

Genetic variation in histone modifications and gene expression identifies regulatory variants in the mammary gland of cattle

Prowse-Wilkins, C., Lopdell, T., Xiang, R., Jagt, C. J. V., Littlejohn, M. D., Chamberlain, A. J., & Goddard, M. E. (2022) · BMC Genomics · doi:10.1186/s12864-022-09002-9 · Cited by 33 · see citing works

Functional effects of variation in transcription factor binding highlight long-range gene regulation by epromoters

Mitchelmore, J., Grinberg, N. F., Wallace, C., & Spivakov, M. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa123 · Cited by 25 · see citing works

Integrative Multi-omic Analysis of Human Platelet eQTLs Reveals Alternative Start Site in Mitofusin 2.

Simon, L., Chen, E., Edelstein, L., Kong, X.-G., Bhatlekar, S., Rigoutsos, I., Bray, P., & Shaw, C. (2016) · American Journal of Human Genetics · doi:10.1016/j.ajhg.2016.03.007 · Cited by 32 · see citing works

Prospects and challenges of cancer systems medicine: from genes to disease networks

Karimi, M. R., Karimi, A. H., Abolmaali, S., Sadeghi, M., & Schmitz, U. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab343 · Cited by 33 · see citing works

Combining GWAS and TWAS to identify candidate causal genes for tocochromanol levels in maize grain

Wu, D., Li, X., Tanaka, R., Wood, J. C., Tibbs‐Cortes, L. E., Magallanes‐Lundback, M., Bornowski, N., Hamilton, J. P., Vaillancourt, B., Diepenbrock, C., et al. (2022) · Genetics · doi:10.1093/genetics/iyac091 · Cited by 30 · see citing works

Extraordinary Cancer Epigenomics: Thinking Outside the Classical Coding and Promoter Box

Murtha, M. J., & Esteller, M. (2016) · Trends in cancer · doi:10.1016/j.trecan.2016.08.004 · Cited by 30 · see citing works

Bayesian Inference of Allele-Specific Gene Expression Indicates Abundant Cis-Regulatory Variation in Natural Flycatcher Populations

Mi, W., Uebbing, S., & Ellegren, H. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx080 · Cited by 26 · see citing works

Integrated analysis of Mendelian Randomization and Bayesian colocalization reveals bidirectional causal association between inflammatory bowel disease and psoriasis

Cai, Y., Xie, S., Jia, X., Chen, D., Wu, D., Bao, W., Cai, J., Mao, J., & Ye, J. (2023) · Annals of Medicine · doi:10.1080/07853890.2023.2281658 · Cited by 27 · see citing works

Cd14 SNPs regulate the innate immune response

Liu, H.-H., Hu, Y., Zheng, M., Suhoski, M. M., Engleman, E. G., Dill, D. L., Hudnall, M. T., Wang, J., Spolski, R. J., Leonard, W. J., et al. (2012) · Molecular Immunology · doi:10.1016/j.molimm.2012.02.112 · Cited by 25 · see citing works

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

Spurr, L., Alomran, N., Słowiński, P., Li, M.-Z., Bousounis, P., Zhang, Q.-Q., Sein, J., Crandall, K., Tsaneva-Atanasova, K., & Horvath, A. (2018) · bioRxiv · doi:10.1101/464206 · Cited by 1 · see citing works

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

Wang, Z. (2016) · eScholarship@McGill (McGill) · doi:10.82308/24388

eQTL Mapping Using RNA-seq Data

Sun, W., & Hu, Y. (2012) · Statistics in Biosciences · doi:10.1007/s12561-012-9068-3 · Cited by 77 · see citing works

From expression QTLs to personalized transcriptomics

Montgomery, S. B., & Dermitzakis, E. T. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2969 · Cited by 189 · see citing works

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

Lalonde, E., Ha, K. C. H., Wang, Z., Bemmo, A., Kleinman, C. L., Kwan, T., Pastinen, T., & Majewski, J. (2011) · Genome Research · doi:10.1101/gr.111211.110 · Cited by 111 · see citing works