Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

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3. quantro: a data-driven approach to guide the choice of an appropriate normalization method
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4. The NSL complex maintains nuclear architecture stability via lamin A/C acetylation
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5. Molecular QTL discovery incorporating genomic annotations using Bayesian false discovery rate control
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6. A transcriptome-wide association study of high-grade serous epithelial ovarian cancer identifies new susceptibility genes and splice variants
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7. Dynamic Role of trans Regulation of Gene Expression in Relation to Complex Traits
   Yao, Chen, Joehanes, Roby, Johnson, Andrew D., Huan, Tianxiao, Liu, Chunyu, Freedman, Jane E., Munson, Peter J., Hill, David E., Vidal, Marc, Levy, Daniel · 2017 · The American Journal of Human Genetics
8. Accurate modeling of confounding variation in eQTL studies leads to a great increase in power to detect trans-regulatory effects
   Nicolò Fusi, Oliver Stegle, Neil David Lawrence · 2011 · Nature Precedings
9. scPower accelerates and optimizes the design of multi-sample single cell transcriptomic studies
   Schmid, Katharina T., Höllbacher, Barbara, Cruceanu, Cristiana, Böttcher, Anika, Lickert, Heiko, Binder, Elisabeth B., Theis, Fabian J., Heinig, Matthias · 2021 · Nature Communications
10. Computational approaches for interpreting sc<scp>RNA</scp>‐seq data
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11. In vivo functional analysis of non-conserved human lncRNAs associated with cardiometabolic traits
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12. Systematic integrated analysis of genetic and epigenetic variation in diabetic kidney disease
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13. Genetic control of the human brain proteome
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14. Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cells
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15. TIGER: The gene expression regulatory variation landscape of human pancreatic islets
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16. A molecular quantitative trait locus map for osteoarthritis
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17. Statistical Methods in Integrative Genomics
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18. Genetic Variation in the Social Environment Contributes to Health and Disease
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19. Pan-cancer proteogenomics characterization of tumor immunity
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20. Insight into Genotype-Phenotype Associations through eQTL Mapping in Multiple Cell Types in Health and Immune-Mediated Disease
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21. Variable number tandem repeats mediate the expression of proximal genes
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22. Genetic Regulatory Mechanisms of Smooth Muscle Cells Map to Coronary Artery Disease Risk Loci
    Liu, Boxiang, Pjanic, Milos, Wang, Ting, Nguyen, Trieu, Gloudemans, Michael, Rao, Abhiram, Castano, Victor G., Nurnberg, Sylvia, Rader, Daniel J., Elwyn, Susannah et al. · 2018 · The American Journal of Human Genetics
23. Integration of human adipocyte chromosomal interactions with adipose gene expression prioritizes obesity-related genes from GWAS
    David Z. Pan, Kristina M. Garske, Marcus Alvarez, Yash V. Bhagat, James Boocock, Elina Nikkola, Zong Miao, Chelsea K. Raulerson, Rita M. Cantor, Mete Civelek et al. · 2018 · Nature Communications
24. Genomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat
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25. Machine learning-enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions
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26. The genetic heterogeneity and drug resistance mechanisms of relapsed refractory multiple myeloma
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27. The effect of X-linked dosage compensation on complex trait variation
    Sidorenko, Julia, Kassam, Irfahan, Kemper, Kathryn E., Zeng, Jian, Lloyd-Jones, Luke R., Montgomery, Grant W., Gibson, Greg, Metspalu, Andres, Esko, Tonu, Yang, Jian et al. · 2019 · Nature Communications
28. A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit
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29. Genetic regulation of gene expression across multiple tissues in chickens
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30. Anchor Regression: Heterogeneous Data Meet Causality
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31. Gene expression in African Americans, Puerto Ricans and Mexican Americans reveals ancestry-specific patterns of genetic architecture
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32. Regulatory controls of duplicated gene expression during fiber development in allotetraploid cotton
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33. A Burden of Rare Variants Associated with Extremes of Gene Expression in Human Peripheral Blood
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34. Cross-Population Joint Analysis of eQTLs: Fine Mapping and Functional Annotation
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35. Rare and common epilepsies converge on a shared gene regulatory network providing opportunities for novel antiepileptic drug discovery
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36. CancerSplicingQTL: a database for genome-wide identification of splicing QTLs in human cancer
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37. Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans
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38. Genetic Architecture of Gene Expression in European and African Americans: An eQTL Mapping Study in GENOA
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39. Transcriptome-wide association analysis identifies DACH1 as a kidney disease risk gene that contributes to fibrosis
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40. Genetic determinants of telomere length from 109,122 ancestrally diverse whole-genome sequences in TOPMed
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41. PCA outperforms popular hidden variable inference methods for molecular QTL mapping
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42. Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks
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43. Genome-wide identification of circulating-miRNA expression quantitative trait loci reveals the role of several miRNAs in the regulation of cardiometabolic phenotypes
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44. Adipose Tissue Gene Expression Associations Reveal Hundreds of Candidate Genes for Cardiometabolic Traits
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45. Genetic regulation of gene expression and splicing during a 10-year period of human aging
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46. Evolutionary and functional impact of common polymorphic inversions in the human genome
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47. Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations
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48. A deep population reference panel of tandem repeat variation
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49. Mitochondrial DNA variants modulate N-formylmethionine, proteostasis and risk of late-onset human diseases
    Cai, Na, Gomez-Duran, Aurora, Yonova-Doing, Ekaterina, Kundu, Kousik, Burgess, Annette I., Golder, Zoe J., Calabrese, Claudia, Bonder, Marc J., Camacho, Marta, Lawson, Rachael A. et al. · 2021 · Nature Medicine
50. Genetic association and transcriptome integration identify contributing genes and tissues at cystic fibrosis modifier loci
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51. Genome-wide association and multi-omic analyses reveal ACTN2 as a gene linked to heart failure
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52. Consistent RNA sequencing contamination in GTEx and other data sets
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53. Optimizing expression quantitative trait locus mapping workflows for single-cell studies
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54. Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics
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55. Proteogenomic analysis of lung adenocarcinoma reveals tumor heterogeneity, survival determinants, and therapeutically relevant pathways
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56. Comprehensive map of age-associated splicing changes across human tissues and their contributions to age-associated diseases
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57. A reference haplotype panel for genome-wide imputation of short tandem repeats
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58. Analysis of the caudate nucleus transcriptome in individuals with schizophrenia highlights effects of antipsychotics and new risk genes
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59. Analysis and Visualization of Spatial Transcriptomic Data
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60. Blood transcriptomic comparison of individuals with and without autism spectrum disorder: A combined‐samples mega‐analysis
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62. Identifying cis -mediators for trans -eQTLs across many human tissues using genomic mediation analysis
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63. lncRNAKB, a knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA
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64. Molecular insights into genome-wide association studies of chronic kidney disease-defining traits
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65. Promoter shape varies across populations and affects promoter evolution and expression noise
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66. Uncovering genetic mechanisms of hypertension through multi-omic analysis of the kidney
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67. Sex- and age-dependent genetics of longevity in a heterogeneous mouse population
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68. Differential expression analysis for RNAseq using Poisson mixed models
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69. Chromatin domain alterations linked to 3D genome organization in a large cohort of schizophrenia and bipolar disorder brains
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70. Tissue-specific sex differences in human gene expression
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71. Using Large Datasets to Understand Nanotechnology
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72. Pancan-meQTL: a database to systematically evaluate the effects of genetic variants on methylation in human cancer
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73. A Transcriptome-Wide Association Study Among 97,898 Women to Identify Candidate Susceptibility Genes for Epithelial Ovarian Cancer Risk
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74. The non-coding variant rs1800734 enhances DCLK3 expression through long-range interaction and promotes colorectal cancer progression
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75. IL1RL1 asthma risk variants regulate airway type 2 inflammation
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76. Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate
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77. A 12 kb multi-allelic copy number variation encompassing a GC gene enhancer is associated with mastitis resistance in dairy cattle
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78. Transcriptome-wide association analyses reveal the impact of regulatory variants on rice panicle architecture and causal gene regulatory networks
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79. Learning Causal Biological Networks With the Principle of Mendelian Randomization
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80. The Farm Animal Genotype–Tissue Expression (FarmGTEx) Project
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81. Genome-wide analysis of expression quantitative trait loci (eQTLs) reveals the regulatory architecture of gene expression variation in the storage roots of sweet potato
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82. Enhancing Discovery of Genetic Variants for Posttraumatic Stress Disorder Through Integration of Quantitative Phenotypes and Trauma Exposure Information
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83. Genetic associations at regulatory phenotypes improve fine-mapping of causal variants for 12 immune-mediated diseases
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84. False positives in trans-eQTL and co-expression analyses arising from RNA-sequencing alignment errors
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85. Distinct molecular etiologies of male and female hepatocellular carcinoma
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86. Gene regulation underlies environmental adaptation in house mice
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87. Rare variants with large effects provide functional insights into the pathology of migraine subtypes, with and without aura
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88. Genome-wide association analyses of breast cancer in women of African ancestry identify new susceptibility loci and improve risk prediction
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89. An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures
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90. Aberrant Gene Expression in Humans
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91. Diagnosing rare diseases after the exome
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92. Identifying gene function and module connections by the integration of multispecies expression compendia
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93. Genetic and Epigenetic Fine Mapping of Complex Trait Associated Loci in the Human Liver
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94. Transcriptomic Insight Into the Polygenic Mechanisms Underlying Psychiatric Disorders
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95. A comprehensive analysis of SNCA ‐related genetic risk in sporadic parkinson disease
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96. ncRNA-eQTL: a database to systematically evaluate the effects of SNPs on non-coding RNA expression across cancer types
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97. Identification of trans-eQTLs using mediation analysis with multiple mediators
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98. Identification of Novel Susceptibility Loci and Genes for Prostate Cancer Risk: A Transcriptome-Wide Association Study in Over 140,000 European Descendants
    Lang Wu, Jifeng Wang, Qiuyin Cai, Taylor B. Cavazos, Nima C. Emami, Jirong Long, Xiao‐Ou Shu, Yingchang Lu, Xingyi Guo, Joshua A. Bauer et al. · 2019 · Cancer Research
99. Population-scale proteome variation in human induced pluripotent stem cells
    2020
100. Identifying Novel Susceptibility Genes for Colorectal Cancer Risk From a Transcriptome-Wide Association Study of 125,478 Subjects
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