Emmanouil T. Dermitzakis

Integrated cell type-specific analysis of blood and gut identifies matching eQTL for 140 IBD risk loci and entrectinib as possible repurposing candidate.

The paper identifies 140 IBD risk loci with matching eQTL in blood and gut tissues and suggests entrectinib as a potential repurposing drug.

Pharmacogenomics of GLP-1 Receptor Agonists: A genome-wide analysis of observational data and large randomized controlled trials

This study identifies genetic variants associated with glycaemic response to GLP-1 receptor agonists using observational and trial data, finding variants in GLP-1R and ARRB1 linked to HbA1c reduction.

Leveraging interindividual variability of regulatory activity refines genetic regulation of gene expression in schizophrenia

The paper integrates regulatory activity variability with gene expression and genotype data to identify genetic regulation changes in schizophrenia.

Genetic variation in correlated regulatory region of Immunity

The paper identifies regulatory domains in immune cells using genomic and epigenomic data, revealing cell-type specific gene regulation and genetic control of regulatory elements.

Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR

The paper introduces MAGAR, a framework to identify methylation quantitative trait loci (methQTLs) and distinguish common from cell-type-specific effects using DNA methylation and genotyping data.

Unraveling the polygenic architecture of complex traits using blood eQTL meta-analysis

The paper uses blood eQTL meta-analysis to explore the polygenic architecture of complex traits, finding that trans-eQTLs are more informative for identifying causal genes than cis-eQTLs.

The molecular basis, genetic control and pleiotropic effects of local gene co-expression

The paper identifies local gene co-expression patterns across human tissues and links them to eQTLs associated with multiple traits.

A novel anti-influenza combined therapy assessed by single cell RNA-sequencing

This study evaluates a combined anti-influenza therapy using single cell RNA sequencing to show its effectiveness in inhibiting viral replication across different epithelial cell types.

Specific transcriptomic signatures and dual regulation of steroidogenesis between fetal and adult mouse Leydig cells

The paper compares transcriptomes of fetal and adult Leydig cells in mice to identify gene expression differences and regulatory mechanisms of steroidogenesis.

Single cell transcriptomics reveal temporal dynamics of critical regulators of germ cell fate during mouse sex determination

The paper uses single-cell RNA sequencing to study gene expression dynamics in mouse germ cells during sex determination, identifying sex-specific regulatory patterns and meiotic gene regulation.

Extensive fragmentation and re-organization of gene co-expression patterns underlie the progression of Systemic Lupus Erythematosus

This study identifies disease-associated alterations in gene co-regulation patterns in SLE, showing fragmentation and redistribution of co-expression domains correlate with disease activity and biological pathways.

Influence of genetic variants on gene expression in human pancreatic islets - implications for type 2 diabetes

The paper investigates how genetic variants affect gene expression in human pancreatic islets and identifies candidate genes linked to type 2 diabetes.

A vast resource of allelic expression data spanning human tissues

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.

Cell type specific genetic regulation of gene expression across human tissues

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.

Determinants of telomere length across human tissues

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.

Diverse transcriptomic signatures across human tissues identify functional rare genetic variation

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

A Quantitative Proteome Map of the Human Body

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

Predicting and elucidating the etiology of fatty liver disease using a machine learning-based approach: an IMI DIRECT study

This study develops machine learning models to predict liver fat content using multi-omic and clinical data from NAFLD patients, achieving higher accuracy than existing tools.

Integrative haplotype estimation with sub-linear complexity

SHAPEIT4 improves haplotype estimation with sub-linear scaling, high accuracy, and integration of external phasing information using UK Biobank and Genome In A Bottle datasets.

The GTEx Consortium atlas of genetic regulatory effects across human tissues

GTEx v8 maps expression and splicing QTLs in 49 tissues from 838 donors: cis-eQTLs cover 94.7% of protein-coding genes, and cross-tissue QTL sharing mirrors cell-type composition.

Intra- and inter-chromosomal chromatin interactions mediate genetic effects on regulatory networks

The paper combines regulatory element activity, gene expression, and genetic variation data across cell types to show how chromatin structure influences regulatory networks and genetic effects.

Expression estimation and eQTL mapping for HLA genes with a personalized pipeline

The paper develops a personalized pipeline to estimate HLA gene expression and map eQTLs, showing improved accuracy and better eQTL results compared to standard methods.

Single-cell transcriptomics of the mouse gonadal soma reveals the establishment of sexual dimorphism in distinct cell lineages

The paper uses single-cell RNA sequencing to study sex determination in mouse gonadal somatic cells, identifying early progenitors and sex-specific fate acquisition in different cell lineages.

Hundreds of putative non-coding cis-regulatory drivers in chronic lymphocytic leukaemia and skin cancer

This study identifies non-coding cis-regulatory domains in CLL and skin cancer by analyzing somatic mutations in histone modification patterns, revealing functional regulatory regions and their associated genes.

Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics

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.

Deciphering cell lineage specification during male sex determination with single-cell RNA sequencing

Time-course single-cell RNA-seq of NR5A1-GFP+ mouse XY gonad cells points to one multipotent somatic progenitor pool that yields Sertoli cells and, progressively, steroidogenic Leydig precursors.

Genomic dissection of Systemic Lupus Erythematosus: Distinct Susceptibility, Activity and Severity Signatures

This study identifies distinct susceptibility and activity/severity signatures in SLE using transcriptomics and genetics, enabling improved diagnosis and personalized therapy.

Age-dependent changes in mean and variance of gene expression across tissues in a twin cohort

The paper quantifies age-related changes in gene expression levels, splicing, and variance across tissues and identifies environmental and genetic influences on these changes in a twin cohort.

Predicting causal variants affecting expression using whole genome sequence and RNA-seq from multiple human tissues.

The paper uses whole genome sequence and RNA-seq to predict causal variants affecting gene expression and identifies high confidence causal variants enriched in GWAS associations.

Alternative splicing QTLs in European and African populations using Altrans, a novel method for splice junction quantification

This paper introduces Altrans, a method for discovering alternative splicing QTLs, and compares its performance to Cufflinks in European and African populations, finding more asQTLs with Altrans.