Brunilda Balliu

This study examines epigenomic and spatial changes during human reprogramming, finding distinct molecular and spatial patterns in productive versus unsuccessful trajectories.

FastGxC efficiently maps context-specific eQTLs in bulk and single-cell RNA-seq data, improving power and speed while enhancing biological relevance and trait association precision.

This study uses longitudinal single-cell adipose transcriptomics to identify genes and variants associated with weight loss after bariatric surgery and shows that BMI polygenic risk scores predict weight loss outcomes.

The paper evaluates demultiplexing methods for joint snRNA/snATAC experiments under ambient contamination and introduces a new metric to assess their performance.

The paper identifies novel transcripts, eQTLs, and caQTLs in African populations and fine-maps GWAS signals for complex diseases.

The paper identifies causal SNPs near ERAP2 that regulate its expression through long-range chromatin interactions, linking autoimmune disease risk variants to enhancer activity.

The paper introduces CONTENT, a method for multi-context genetic modeling of transcriptional regulation, which improves power and discovers more gene-phenotype associations in TWAS.

The paper explores the relationship between genomic ancestry and health outcomes using a biobank linked to electronic health records, finding disease stratification across ancestry clusters.

The paper integrates genetic colocalizations with physiological and pharmacological perturbations to identify causal genes for cardiometabolic diseases.

The paper identifies environmental modulators of genetic risk factors for complex traits by integrating perturbation data with GWAS.

This study shows that correcting background noise in microbiome data improves phenotype prediction by using unsupervised methods with appropriate transformations.

The paper presents a large ASE resource from GTEx v8 with 431 million SNP-level and 153 million haplotype-level measurements, and extends phASER to estimate cis regulatory variant effect sizes.

The paper uses bulk RNA-seq data to estimate cell type abundances and identifies cell type interaction QTLs that provide finer resolution of tissue specificity than bulk cis-eQTLs.

The paper assesses the impact of admixture and ancestry on eQTL analysis and GWAS colocalization in GTEx, finding that local ancestry adjustment improves power but has limited effect on colocalization probabilities.

The paper examines telomere length variation across 6,391 tissue samples from 952 individuals, showing tissue-specific differences, positive correlations between tissues, and associations with age and ancestry.

Integrating expression, allelic expression and splicing across tissues identifies rare variants with relevance to traits.

The paper quantifies protein levels across 32 human tissues and compares them to transcriptome data, revealing insights into post-transcriptional regulation and disease mechanisms.

The paper characterizes the dynamic multi-omic molecular response to acute exercise and identifies biomarkers of fitness.

This study identifies fRPE-specific genes and variants associated with AMD and myopia, revealing novel e/sQTL and mechanisms linking a common variant to both diseases.

The paper analyzes gene expression and splicing changes in human aging using longitudinal RNA sequencing data from the PIVUS study, finding stability in most genetic regulation but dynamic changes in a subset of genes.

This study evaluates the use of whole blood transcriptome sequencing for diagnosing rare diseases, finding an 8.5% diagnostic rate across 56 undiagnosed cases.

The paper develops S-PrediXcan to compute gene expression associations from GWAS summary data and applies it to 44 GTEx tissues and 100+ phenotypes, finding tissue-specific effects and colocalized associations.

This paper introduces a new gene-gene interaction test for trio studies called the trio correlation (TC) test, which outperforms existing methods in power and identifies a bias in previous tests.