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

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

TopHat: discovering splice junctions with RNA-Seq

Trapnell, C., Pachter, L. S., & Salzberg, S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp120 · Cited by 11,682

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

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

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

Expansion of the eukaryotic proteome by alternative splicing

Nilsen, T. W., & Graveley, B. R. (2010) · Nature · doi:10.1038/nature08909 · Cited by 2,270

ChIP–seq: advantages and challenges of a maturing technology

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

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

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

Genetic and Genomic Approaches to Acute Lung Injury

Yang, I. V. (2016) · Respiratory medicine · doi:10.1007/978-3-319-46527-2_9

Multipronged Approach to Study Glaucoma-Associated Phenotypes

Chintalapudi, S. R. (2016) · doi:10.21007/etd.cghs.2016.0410

Functional genomics of the VNN1 gene

Diepeveen, L. A. (2013) · UWA Profiles and Research Repository (UWA)

Identifying expression quantitative trait loci in genome wide association studies

Moradi, F. (2017) · ERA: Education and Research Archive (University of Alberta) · doi:10.7939/r3hd7p49q

An Introduction to Tools, Databases, and Practical Guidelines for NGS Data Analysis

Kanterakis, A., Potamias, G., & Patrinos, G. P. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-809414-3.00004-8

rs12287003 modifies the susceptibility to breast cancer by altering the interactions between KDM2A and miRNAs

Miralaei, N., Hoghoughi, N., Azadeh, M., Alborzian, K., & Ghaedi, K. (2021) · Gene Reports · doi:10.1016/j.genrep.2021.101148

Rare Coding Variants Associated with Breast Cancer

Han, M.-R. (2021) · Advances in experimental medicine and biology · doi:10.1007/978-981-32-9620-6_23

Faculty Opinions recommendation of Pleiotropy in complex traits: challenges and strategies.

Tiemeier, H. W. (2013) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.718019787.793478516

Transcriptome

Louder, M. I. M., & Balakrishnan, C. N. (2019) · Springer eBooks · doi:10.1007/978-3-319-47829-6_163-1

Transcriptome

Louder, M. I. M., & Balakrishnan, C. N. (2022) · Springer eBooks · doi:10.1007/978-3-319-55065-7_163

549. Bioinformatics workflow for the detection of eQTL in the cattle genome using Nextflow DSL2

Chitneedi, P., Hadlich, F., & Kuehn, C. (2022) · World Congress on Genetics Applied to Livestock Production (WCGALP) · doi:10.3920/978-90-8686-940-4_549

Cis-eQTL discovery of immune related molecular phenotypes in sheep

Dubarry, K., Woolley, S. A., Fairlie‐Clarke, K. J., Matthews, J., Coffey, M., & Clark, E. L. (2023) · Animal - science proceedings · doi:10.1016/j.anscip.2023.01.499

Additional file 1 of A map of cis-regulatory modules and constituent transcription factor binding sites in 80% of the mouse genome

Ni, P., Wilson, D., & Su, Z. (2022) · Figshare · doi:10.6084/m9.figshare.21365999

Additional file 1 of Genetic evidence for a causal relationship between type 2 diabetes and peripheral artery disease in both Europeans and East Asians

Xiu, X., Zhang, H., Xue, A., Cooper, D. N., Li, Y., Yang, Y., Yang, Y., & Zhao, H. (2022) · Figshare · doi:10.6084/m9.figshare.20745245

Additional file 2 of Genetic evidence for a causal relationship between type 2 diabetes and peripheral artery disease in both Europeans and East Asians

Xiu, X., Zhang, H., Xue, A., Cooper, D. N., Li, Y., Yang, Y., Yang, Y., & Zhao, H. (2022) · Figshare · doi:10.6084/m9.figshare.20745248

eQTL-Detect: nextflow-based pipeline for eQTL detection in modular format with sharable and parallelizable scripts

Chitneedi, P., Hadlich, F., Moreira, G. C. M., Espinosa‐Carrasco, J., Li, C., Plastow, G. S., Fischer, D., Charlier, C., Rocha, D., Chamberlain, A. J., et al. (2024) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqae122

Addressing Sample Mix‐Ups: Tools and Approaches for Large‐Scale Multi‐Omics Studies

Fu, Y., Yuan, Z., Wu, L., Peng, J., Wang, X., & High, A. A. (2024) · PROTEOMICS · doi:10.1002/pmic.202400271

Selection and validation of reference genes for quantitative real-time PCR during the developmental stages of seeds in Sophora davidii

Li, J., Han, S., Xu, Z., Deng, B., Zheng, N., Su, Y., Qiao, Z., Yang, Y., Zhang, H., Liang, Z., et al. (2025) · Frontiers in Plant Science · doi:10.3389/fpls.2025.1485586

Advancing RNA-Seq Methodologies: Enhancing Efficiency and Unveiling Novel Biological Insights through Extensive Sample Examination

Kashima, M. (2025) · Hikaku seiri seikagaku(Comparative Physiology and Biochemistry) · doi:10.3330/hikakuseiriseika.42.114

Languages of Hereditary Information Unfolding in Development: Linguistic Analogies and Semiotic Aspects

Spirov, A. V. (2025) · Biosystems · doi:10.1016/j.biosystems.2025.105629

Additional file 2 of Allele-specific binding variants causing ChIP-seq peak height of histone modification are not enriched in expression QTL annotations

Ghoreishifar, M., Chamberlain, A. J., Xiang, R., Prowse-Wilkins, C., Lopdell, T., Littlejohn, M. D., Pryce, J. E., & Goddard, M. E. (2024) · Figshare · doi:10.6084/m9.figshare.26122862

Additional file 2 of A map of cis-regulatory modules and constituent transcription factor binding sites in 80% of the mouse genome

Ni, P., Wilson, D. C., & Su, Z. (2022) · Figshare · doi:10.6084/m9.figshare.21366002

Additional file 3 of Allele-specific binding variants causing ChIP-seq peak height of histone modification are not enriched in expression QTL annotations

Ghoreishifar, M., Chamberlain, A. J., Xiang, R., Prowse-Wilkins, C., Lopdell, T., Littlejohn, M. D., Pryce, J. E., & Goddard, M. E. (2024) · Figshare · doi:10.6084/m9.figshare.26740181

Additional file 2 of Genetic variation in histone modifications and gene expression identifies regulatory variants in the mammary gland of cattle

Prowse-Wilkins, C., Lopdell, T., Xiang, R., Vander-Jagt, C. J., Littlejohn, M. D., Chamberlain, A. J., & Goddard, M. E. (2023) · Figshare · doi:10.6084/m9.figshare.22616741

Additional file 1 of Allele-specific binding variants causing ChIP-seq peak height of histone modification are not enriched in expression QTL annotations

Ghoreishifar, M., Chamberlain, A. J., Xiang, R., Prowse-Wilkins, C., Lopdell, T., Littlejohn, M. D., Pryce, J. E., & Goddard, M. E. (2024) · Figshare · doi:10.6084/m9.figshare.26122591

Additional file 4 of Genetic variation in histone modifications and gene expression identifies regulatory variants in the mammary gland of cattle

Prowse-Wilkins, C., Lopdell, T., Xiang, R., Vander-Jagt, C. J., Littlejohn, M. D., Chamberlain, A. J., & Goddard, M. E. (2023) · Figshare · doi:10.6084/m9.figshare.22616747

Additional file 3 of Genetic variation in histone modifications and gene expression identifies regulatory variants in the mammary gland of cattle

Prowse-Wilkins, C., Lopdell, T., Xiang, R., Vander-Jagt, C. J., Littlejohn, M. D., Chamberlain, A. J., & Goddard, M. E. (2023) · Figshare · doi:10.6084/m9.figshare.22616744

Molecular and physiological characterization of grapevine rootstock adaptation to drought

Peccoux, A. (2011) · theses.fr (ABES) · doi:10.70675/ab4b4e5dzb19ez45d7z9b84zb37423122088

Épidémiologie épi-génétique de biomarqueurs du risque cardiovasculaire : intérêt de l’étude de la méthylation de l’ADN à partir d’échantillons sanguins

Aïssi, D. (2015) · theses.fr (ABES) · doi:10.70675/e53592fazd426z4cd5z841ez8c011a78dc45

Rôle des effets épistatiques dans l’évolution d’une population à régime de reproduction mixte, et dans la régulation de l’expression des gènes homéologues chez une espèce autogame allotétraploïde, le blé dur (Triticum turgidum).

Vagne, C. (2014) · theses.fr (ABES) · doi:10.70675/4b74cdafz5fa2z4ca1zbda0z1f3dcab738a6

Etude des facteurs génétiques de variabilité phénotypique dans les formes syndromiques d'anévrismes de l'aorte thoracique

Benarroch, L. (2018) · theses.fr (ABES) · doi:10.70675/f868034fzea81z4a04z92fbz24b35d3a07c7

Effet de la sélection fluctuante sur le pathogène du blé Zymoseptoria tritici par une approche d'évolution expérimentale

Jallet, A. (2019) · doi:10.70675/fa3366b4z3dd8z4e94za9f9za68c43575692

Caractérisation fonctionnelle d'un QTL de développement racinaire détecté par GWAS dans une collection de variétés vietnamiennes de riz

Nguyen, L. K. (2018) · theses.fr (ABES) · doi:10.70675/18f92a4ez86faz4ed9zb72bz13f6536db63f

Intégration de multiples approches omiques pour améliorer la prise en charge des patients atteints de cancer pédiatrique

Savary, C. (2020) · theses.fr (ABES) · doi:10.70675/c9668778z4218z4692z908fz449455de3a1e

Stabilizing and directional selection shape the genetic variation of gene expression in the transcriptome of Chlamydomonas

Balogun, E. J., Sztepanacz, J. L., & Ness, R. W. (2026) · Molecular Biology and Evolution · doi:10.1093/molbev/msag142

Genome-Wide association study of genetic variants influencing creatine kinase levels in Chinese winter sports athletes

Mei, T., Li, Y., Bao, D., Yang, X., & He, Z. (2026) · Gene · doi:10.1016/j.gene.2026.150275

Characterization of SIK family and GDH genes reveals ammonia-responsive expression patterns and candidate SNP markers for ammonia tolerance in yellowfin seabream (Acanthopagrus latus)Preprint

Zhou, J., Zhi-ya, Y., Chen, C.-H., Yu, F.-Z., Luo, M., Liu, B.-S., Guo, H., Zhang, N., Xian, L., Zhu, K., et al. (2026) · SSRN Electronic Journal · doi:10.2139/ssrn.7387969

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

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 82

From expression QTLs to personalized transcriptomics

Montgomery, S. B., & Dermitzakis, E. T. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2969 · Cited by 194

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