Paola Benaglio

Functional genomics reveals mediators of beta cell survival in ER stress and type 2 diabetes risk

The paper identifies gene regulators of ER stress in beta cells and links them to type 2 diabetes risk through functional genomics and CRISPR screening.

Integrating Natural and Engineered Genetic Variation to Decode Regulatory Influence on Blood Traits

The paper combines natural and engineered genetic variation to identify 22 non-coding variants affecting haematological traits and shows how a CUX1 variant impacts megakaryopoiesis.

Multi-omic QTL mapping in early developmental tissues reveals phenotypic and temporal complexity of regulatory variants underlying GWAS loci

The paper identifies multi-omic QTLs in early developmental tissues and shows that GWAS loci often involve complex regulatory variants not captured by eQTLs alone.

Genetic discovery and risk prediction for type 1 diabetes in individuals without high-risk HLA-DR3/DR4 haplotypes

This study identifies genetic risk factors for type 1 diabetes in individuals without high-risk HLA-DR3/DR4 haplotypes and develops a new risk score for better classification.

Single cell multiome profiling of pancreatic islets reveals physiological changes in cell type-specific regulation associated with diabetes risk

The paper uses single-cell multiome profiling to identify gene regulatory changes in pancreatic islets linked to diabetes risk factors like age, sex, and genetic variants.

Analysis of regulatory network modules in hundreds of human stem cell lines reveals complex epigenetic and genetic factors contribute to pluripotency state differences between subpopulations

The paper identifies regulatory network modules in human stem cells, showing epigenetic and genetic factors influence pluripotency state differences.

eQTL mapping in fetal-like pancreatic progenitor cells reveals early developmental insights into diabetes risk

The paper maps eQTLs in fetal-like pancreatic progenitor cells, identifying regulatory variants that influence diabetes risk by affecting gene expression and splicing in early development.

An integrated map of cell type-specific gene expression in pancreatic islets

The paper creates an integrated gene expression map of pancreatic islet cell types from healthy and diabetic donors, identifying marker genes and differential expression patterns.

Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease

This study identifies causal genetic variants for cardiac traits by integrating spatiotemporal eQTL analysis with GWAS data, showing stage- and tissue-specific effects.

Type 1 diabetes risk genes mediate pancreatic beta cell survival in response to proinflammatory cytokines

The paper identifies T1D risk genes and regulatory elements that influence beta cell survival under proinflammatory cytokine exposure using functional genomics and genetics.

Large-scale genetic association and single cell accessible chromatin mapping defines cell type-specific mechanisms of type 1 diabetes risk

This study combines large-scale GWAS and single-cell epigenomics to identify cell type-specific mechanisms of type 1 diabetes risk.

Glucocorticoid signaling in pancreatic islets modulates gene regulatory programs and genetic risk of type 2 diabetes

This study identifies glucocorticoid-responsive gene regulatory programs in pancreatic islets and links them to type 2 diabetes risk through chromatin and gene expression analysis.

Mapping genetic effects on cell type-specific chromatin accessibility and annotating complex trait variants using single nucleus ATAC-seq

The paper uses snATAC-seq to map chromatin accessibility QTLs in immune cell types and fine-maps complex trait loci, identifying cell type-specific causal variants.

Allele-specific NKX2-5 binding underlies multiple genetic associations with human EKG traits

The paper identifies allele-specific NKX2-5 binding variants associated with EKG traits by integrating iPSC-CM data and GWAS, showing their role in heart rate loci and cardiac enhancer activity.

Human iPSC-derived retinal pigment epithelium: a model system for identifying and functionally characterizing causal variants at AMD risk loci

The paper uses iPSC-derived retinal pigment epithelium to identify and functionally characterize causal variants at AMD risk loci, finding rs943080 as the probable causal variant at VEGFA.

Chromatin co-accessibility is highly structured, spans entire chromosomes, and mediates long range regulatory genetic effects

The paper analyzes co-accessibility across chromosomes using ATAC-seq and identifies its regulatory effects on gene expression and disease-relevant genes.

Integration of phased Hi-C and molecular phenotype data to study genetic and epigenetic effects on chromatin looping

The paper investigates how genetic and epigenetic factors influence chromatin looping strength across cell types and haplotypes, finding that loop strength changes correlate with significant gene expression differences.

Insights into the mutational burden of human induced pluripotent stem cells using an integrative omics approach

This study analyzes the mutational burden in human iPSCs using whole genome sequencing and integrates transcriptome and epigenome data to identify mutation patterns and their impact on gene expression.