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A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies

Citations

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Cited by:

  1. Celine A. Manigbas & Bharati Jadhav & Paras Garg & Mariya Shadrina & William Lee & Gabrielle Altman & Alejandro Martin-Trujillo & Andrew J. Sharp, 2024. "A phenome-wide association study of tandem repeat variation in 168,554 individuals from the UK Biobank," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
  2. Thorunn A. Olafsdottir & Gudmar Thorleifsson & Aitzkoa Lopez de Lapuente Portilla & Stefan Jonsson & Lilja Stefansdottir & Abhishek Niroula & Aslaug Jonasdottir & Hannes P. Eggertsson & Gisli H. Halld, 2024. "Sequence variants influencing the regulation of serum IgG subclass levels," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  3. Zhenhua Zhang & Wenchao Li & Qiuyao Zhan & Michelle Aillaud & Javier Botey-Bataller & Martijn Zoodsma & Rob Horst & Leo A. B. Joosten & Christoph Bock & Leon N. Schulte & Cheng-Jian Xu & Mihai G. Nete, 2025. "Unveiling genetic signatures of immune response in immune-related diseases through single-cell eQTL analysis across diverse conditions," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
  4. Satria P. Sajuthi & Jamie L. Everman & Nathan D. Jackson & Benjamin Saef & Cydney L. Rios & Camille M. Moore & Angel C. Y. Mak & Celeste Eng & Ana Fairbanks-Mahnke & Sandra Salazar & Jennifer Elhawary, 2022. "Nasal airway transcriptome-wide association study of asthma reveals genetically driven mucus pathobiology," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
  5. Seong Kyu Han & Michelle T. McNulty & Christopher J. Benway & Pei Wen & Anya Greenberg & Ana C. Onuchic-Whitford & Dongkeun Jang & Jason Flannick & Noël P. Burtt & Parker C. Wilson & Benjamin D. Humph, 2023. "Mapping genomic regulation of kidney disease and traits through high-resolution and interpretable eQTLs," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  6. M. A. Zouache & B. T. Richards & C. M. Pappas & R. A. Anstadt & J. Liu & T. Corsetti & S. Matthews & N. A. Seager & S. Schmitz-Valckenberg & M. Fleckenstein & W. C. Hubbard & J. Thomas & J. L. Hageman, 2024. "Levels of complement factor H-related 4 protein do not influence susceptibility to age-related macular degeneration or its course of progression," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
  7. Ryo Yamamoto & Ryan Chung & Juan Manuel Vazquez & Huanjie Sheng & Philippa L. Steinberg & Nilah M. Ioannidis & Peter H. Sudmant, 2022. "Tissue-specific impacts of aging and genetics on gene expression patterns in humans," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
  8. Nicoló Fusi & Oliver Stegle & Neil D Lawrence, 2012. "Joint Modelling of Confounding Factors and Prominent Genetic Regulators Provides Increased Accuracy in Genetical Genomics Studies," PLOS Computational Biology, Public Library of Science, vol. 8(1), pages 1-9, January.
  9. Barbara E Stranger & Stephen B Montgomery & Antigone S Dimas & Leopold Parts & Oliver Stegle & Catherine E Ingle & Magda Sekowska & George Davey Smith & David Evans & Maria Gutierrez-Arcelus & Alkes P, 2012. "Patterns of Cis Regulatory Variation in Diverse Human Populations," PLOS Genetics, Public Library of Science, vol. 8(4), pages 1-13, April.
  10. repec:plo:pgen00:1002078 is not listed on IDEAS
  11. Chuan Gao & Ian C McDowell & Shiwen Zhao & Christopher D Brown & Barbara E Engelhardt, 2016. "Context Specific and Differential Gene Co-expression Networks via Bayesian Biclustering," PLOS Computational Biology, Public Library of Science, vol. 12(7), pages 1-39, July.
  12. repec:plo:pone00:0068141 is not listed on IDEAS
  13. Jin Hyun Ju & Sushila A Shenoy & Ronald G Crystal & Jason G Mezey, 2017. "An independent component analysis confounding factor correction framework for identifying broad impact expression quantitative trait loci," PLOS Computational Biology, Public Library of Science, vol. 13(5), pages 1-26, May.
  14. Nikolaos Ignatiadis & Wolfgang Huber, 2021. "Covariate powered cross‐weighted multiple testing," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 83(4), pages 720-751, September.
  15. Jie Ping & Guochong Jia & Qiuyin Cai & Xingyi Guo & Jifeng Wang & Ran Tao & Bingshan Li & Joshua A. Bauer & Yuhan Xie & Stefan Ambs & Mollie E. Barnard & Yu Chen & Ji-Yeob Choi & Yu-Tang Gao & Montser, 2026. "Multi-ancestry transcriptome-wide association studies uncover insights into breast cancer genetics and biology," Nature Communications, Nature, vol. 17(1), pages 1-13, December.
  16. Saedis Saevarsdottir & Kristbjörg Bjarnadottir & Thorsteinn Markusson & Jonas Berglund & Thorunn A. Olafsdottir & Gisli H. Halldorsson & Gudrun Rutsdottir & Kristbjorg Gunnarsdottir & Asgeir Orn Arnth, 2024. "Start codon variant in LAG3 is associated with decreased LAG-3 expression and increased risk of autoimmune thyroid disease," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
  17. Yu Yan & Hongbo Liu & Amin Abedini & Xin Sheng & Matthew Palmer & Hongzhe Li & Katalin Susztak, 2024. "Unraveling the epigenetic code: human kidney DNA methylation and chromatin dynamics in renal disease development," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
  18. Peyton McClelland & Georgette Femerling & Rose Laflamme & Alejandro Mejia-Garcia & Mohadese Sayahian Dehkordi & Hongyu Xiao & Alex Diaz-Papkovich & Justin Pelletier & Jean-Christophe Grenier & Ken Sin, 2026. "A multi-ancestry genetic reference for the Quebec population," Nature Communications, Nature, vol. 17(1), pages 1-17, December.
  19. Brooke Szczesny & Meher Preethi Boorgula & Sameer Chavan & Monica Campbell & Randi K. Johnson & Kai Kammers & Emma E. Thompson & Madison S. Cox & Gautam Shankar & Corey Cox & Andréanne Morin & Wendy L, 2024. "Multi-omics in nasal epithelium reveals three axes of dysregulation for asthma risk in the African Diaspora populations," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
  20. repec:plo:pgen00:1008007 is not listed on IDEAS
  21. Sébastien Thériault & Zhonglin Li & Erik Abner & Jian’an Luan & Hasanga D. Manikpurage & Ursula Houessou & Pardis Zamani & Mewen Briend & Dominique K. Boudreau & Nathalie Gaudreault & Lily Frenette & , 2024. "Integrative genomic analyses identify candidate causal genes for calcific aortic valve stenosis involving tissue-specific regulation," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  22. Jacob Sampson & Ayellet V. Segrè & Kinga M. Bujakowska & Simon J. Clark & Paul N. Bishop & Steve Haynes & Diana Baralle & Jospin Al-Deek & Stacey Holden & Beverley Anderson & Andrew Hayes & Rahmat A. , 2026. "Paired DNA and RNA sequencing uncovers common and rare variation regulating human retinal gene expression," Nature Communications, Nature, vol. 17(1), pages 1-16, December.
  23. Jie Ping & Guochong Jia & Qiuyin Cai & Xingyi Guo & Ran Tao & Christine Ambrosone & Dezheng Huo & Stefan Ambs & Mollie E. Barnard & Yu Chen & Montserrat Garcia-Closas & Jian Gu & Jennifer J. Hu & Esth, 2024. "Using genome and transcriptome data from African-ancestry female participants to identify putative breast cancer susceptibility genes," Nature Communications, Nature, vol. 15(1), pages 1-8, December.
  24. Georgia Katsoula & Ana Luiza Arruda & Mauro Tutino & Ene Reimann & Norbert Bittner & Peter Kreitmaier & Karan M. Shah & Diane Swift & Lorraine Southam & Siim Suutre & Galadriel Lucía Velázquez Silva &, 2026. "Transcriptome analysis in osteoarthritis primary tissues identifies high-confidence effector genes," Nature Communications, Nature, vol. 17(1), pages 1-19, December.
  25. Xiao, Jian & Li, Shaoting & Chen, Jun & Zhu, Wensheng, 2025. "Model-free latent confounder-adjusted feature selection with FDR control," Computational Statistics & Data Analysis, Elsevier, vol. 205(C).
  26. Kaido Lepik & Tarmo Annilo & Viktorija Kukuškina & eQTLGen Consortium & Kai Kisand & Zoltán Kutalik & Pärt Peterson & Hedi Peterson, 2017. "C-reactive protein upregulates the whole blood expression of CD59 - an integrative analysis," PLOS Computational Biology, Public Library of Science, vol. 13(9), pages 1-20, September.
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