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

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Items 601–700 of 998

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6. Genotyping sequence-resolved copy number variation using pangenomes reveals paralog-specific global diversity and expression divergence of duplicated genes
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7. Multi-region m6A epitranscriptome profiling of the human brain reveals spatial and temporal variation and enrichment of disease-associated loci
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8. A computational approach to generate highly conserved gene co-expression networks with RNA-seq data
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9. Genetic regulation of lncRNA expression in whole human brain and their contribution to CNS disorders
   Yijie He, Yaqin Tang, Pengcheng Tan, Dongyu Huang, Yongheng Wang, Tong Wen, Lin Huang, Jia Wang, Lizhen Shao, Qinyu Cai et al. · 2025 · Briefings in Bioinformatics
10. A genome-wide association study integrated with single-cell and bulk profiles uncovers susceptibility genes for nasopharyngeal carcinoma involved in tumorigenesis via regulation of T cells
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11. Genetic variants associated mRNA stability in lung
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12. Sequencing-based fine-mapping and in silico functional characterization of the 10q24.32 arsenic metabolism efficiency locus across multiple arsenic-exposed populations
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13. Rare genetic variants underlie outlying levels of DNA methylation and gene-expression
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14. Shifts in isoform usage underlie transcriptional differences in regulatory T cells in type 1 diabetes
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15. Omics-based construction of regulatory variants can be applied to help decipher pig liver-related traits
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16. Genome-wide study of gene-by-sex interactions identifies risks for cleft palate
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17. Mapping dynamic regulation of gene expression using single-cell transcriptomics and application to complex disease genetics
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18. Proteogenomic and observational evidence implicate ANGPTL4 as a potential therapeutic target for colorectal cancer prevention
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19. Integrating germline and somatic genetics to identify genes associated with lung cancer
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20. Network regression analysis for binary and ordinal categorical phenotypes in transcriptome-wide association studies
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21. Mapping microRNA expression quantitative trait loci in the prenatal human brain implicates miR-1908-5p expression in bipolar disorder and other brain-related traits
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22. OCMA: Fast, Memory-Efficient Factorization of Prohibitively Large Relationship Matrices
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23. Characterization of Expression Quantitative Trait Loci in Pedigrees from Colombia and Costa Rica Ascertained for Bipolar Disorder
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24. Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis
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25. SOMSC: Self-Organization-Map for High-Dimensional Single-Cell Data of Cellular States and Their Transitions
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26. Modeling memory T cell states at single-cell resolution identifies in vivo state-dependence of eQTLs influencing disease
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27. Phenotype integration improves power and preserves specificity in biobank-based genetic studies of MDD
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28. Immune Isoform Atlas: Landscape of alternative splicing in human immune cells
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29. Long-read RNA-seq atlas of novel microglia isoforms elucidates disease-associated genetic regulation of splicing
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30. Astrocytic-supplied cholesterol drives synaptic gene expression programs in developing neurons and downstream astrocytic transcriptional programs
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31. Genetically regulated eRNA expression predicts chromatin contact frequency and reveals genetic mechanisms at GWAS loci
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32. The epigenomic landscape of primary tissues in osteoarthritis
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33. Epigenome-wide association study for dilated cardiomyopathy in left ventricular heart tissue identifies putative gene sets associated with cardiac pathology and early indicators of cardiac risk
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34. Transcriptome-wide association study of alternative polyadenylation identifies susceptibility genes in non-small cell lung cancer
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35. Long-range chromosomal interactions increase and mark repressed gene expression during adipogenesis
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36. Identification and Validation of Candidate Genes from Genome-Wide Association Studies
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37. Patterns of Unwanted Biological and Technical Expression Variation Among 49 Human Tissues
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38. Melanoma-specific mutation hotspots in distal, non-coding, promoter-interacting regions implicate novel candidate driver genes
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39. FABIO: TWAS fine-mapping to prioritize causal genes for binary traits
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40. Integrating genetic and transcriptomic data to identify genes underlying obesity risk loci
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42. Constraint and divergence of global gene expression in the mammalian embryo
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43. Detection of Regulator Genes and eQTLs in Gene Networks
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45. Using population-scale transcriptomic and genomic data to map 3′ UTR alternative polyadenylation quantitative trait loci
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48. Uncovering the role of admixture in disease and drug response: Association of hepatocyte gene expression and DNA methylation with African Ancestry in African Americans
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49. Multi-tissue analysis reveals short tandem repeats as ubiquitous regulators of gene expression and complex traits
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50. Chromatin co-accessibility is highly structured, spans entire chromosomes, and mediates long range regulatory genetic effects
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51. Impact of the X chromosome and sex on regulatory variation
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52. Genetic regulation of human aortic smooth muscle cell gene expression and splicing predict causal coronary artery disease genes
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53. PCA outperforms popular hidden variable inference methods for molecular QTL mapping
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54. SOMSC: Self-Organization-Map for High-Dimensional Single-Cell Data of Cellular States and Their Transitions
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55. Genetic Basis of Alternative Polyadenylation is an Emerging Molecular Phenotype for Human Traits and Diseases
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56. CiDRE + M2c macrophages hijacked by SARS-CoV-2 cause COVID-19 severity
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57. Multi-ancestry genetic analysis of gene regulation in coronary artery prioritizes disease risk loci
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58. Trans-ancestral Genome Wide Association Study of Sporadic and Recurrent Miscarriage
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59. Mapping multitissue regulatory variants reveals a liver-centric coexpression network associated with duck egg-laying performance
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60. Gut heavy metal and antibiotic resistome of humans living in the high Arctic
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61. Causal network inference of cis- and trans-gene regulation of expression quantitative trait loci across human tissues
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65. Circular RNA Vv‐circCOR27 modulates thermotolerance through attenuating VvHSP90 .2b‐ VvHsfA7a interaction in grapevine
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66. Expanded chromatin accessibility mapping explains genetic variation associated with complex traits in liver
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67. Tissue-resolved molecular landscape reveals hepatic regulatory networks and metabolic mediators underlying feed efficiency in chickens
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68. Cell-type-aware transcriptome-wide association studies identify 91 independent risk genes for Alzheimer’s disease dementia
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69. Integration of estimated regional gene expression with neuroimaging and clinical phenotypes at biobank scale
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70. Genetic Control of tRNA-Derived Fragments Contributes to Cancer Risk
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71. A Transcriptome‐Wide Association Study Identifies Candidate Susceptibility Loci and Genes for Lung Cancer Risk
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86. RSVP-graphs: Fast High-dimensional Covariance Matrix Estimation under Latent Confounding
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97. Impact of polymorphisms on gene expression and splicing in response to exercise and diet-induced weight loss in human skeletal muscle tissues
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