Annique Claringbould

The paper maps variant, enhancer, and gene function in primary human CD4+ T cells by combining Perturb-seq of regulatory elements and genes, identifying CRE-gene pairs and linking variants to disease-related programs.

The paper maps cis- and trans-eQTLs in blood samples to infer gene regulatory networks and prioritize trait-relevant pathways.

This study identifies CDK1 as a key regulator of CD4+ T cell effector function through integrative multi-omics analysis, showing its role in linking phosphorylation to gene regulation and immune traits.

The paper identifies USP18 as a negative regulator of interferon response at a lupus risk locus through trans-eQTL analysis in lymphoblastoid cell lines.

The paper uses single-cell CRISPRi screens to functionally assess schizophrenia-associated genes, revealing disruptions in neurodevelopmental timing and identifying key regulatory factors.

This paper links common and rare disease genetics by identifying key genes affected by common variants through gene regulatory networks, finding many key genes are outside GWAS loci.

The paper links genes in cancer-susceptibility loci to known somatic driver genes through tissue-specific co-expression networks derived from non-cancer samples.

This paper introduces SUM-seq, a scalable multiomic method for single-cell chromatin and RNA sequencing, revealing gene regulatory dynamics in macrophage polarization linked to autoimmune diseases.

OTTERS is a TWAS framework that uses summary-level eQTL reference data to estimate eQTL weights and perform omnibus TWAS, showing improved power and applicability.

The paper introduces an omics-informed quality score to improve CNV detection and association analysis by reducing false positives and increasing statistical power.

The paper introduces GRaNIE and GRaNPA, tools for inferring and evaluating enhancer-mediated gene regulatory networks in macrophages, identifying PURA as a regulator of pro-inflammatory polarization.

This study uses multiomics analysis of BMSCs to show age-related changes in enhancer activity and gene regulation contribute to immune traits and tissue-specific disorders.

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 paper identifies gene regulatory network disruptions caused by LSD1 mutations in early differentiation, showing impaired transcription factor activity and potential therapeutic targets through HDAC inhibition.

The paper uses symptom-based case predictions to conduct a GWAS on COVID-19, finding new genetic susceptibility insights and suggesting different genetic architectures for severity and susceptibility.

The paper compares two models for correcting cell type composition in blood gene expression data, finding that accounting for more cell types reduces the number of age-associated genes and highlights platelet-related pathways.

The paper identifies TRAFD1 as a master regulator of IFNγ signalling in celiac disease by systematically prioritizing candidate genes in disease loci using multiple computational methods.

The paper identifies 31 host genetic loci influencing gut microbiome composition through GWAS and suggests causal effects in inflammatory diseases.

This paper introduces MR-link, a Mendelian randomization method that identifies causal relationships between gene expression and LDL-C levels, finding 19 causally linked genes including PVRL2.

The paper uses allele-specific expression analysis in a large cohort to identify high-impact, autosomal-dominant variants that are compensated by imbalanced expression.

This study identifies 242 genetic loci for glycaemic traits using trans-ancestry meta-analysis, finding 99 novel loci and improved fine-mapping resolution compared to single-ancestry analyses.

The paper introduces Decon2, a method to deconvolute bulk blood eQTL effects into immune cell subpopulations, showing high concordance with experimental and single-cell studies.

The paper investigates sex-specific cis-eQTLs in whole blood RNA-seq data and finds they do not systematically translate into detectable sex-specific trait associations due to limited power and compensatory effects.

The paper identifies pQTLs for cardiovascular proteins and uses them to evaluate drug targets and suggest new candidates for precision medicine.

This paper introduces TWMR, a Mendelian Randomization method that identifies gene-trait associations by integrating GWAS and eQTL data, revealing 3,913 novel associations across 43 human phenotypes.

The paper identifies 49 gene drivers of downstream transcriptional changes using population genomics data and RNA-sequencing from 3,072 individuals.

This study identifies 139 common and 4 rare genetic variants associated with type 2 diabetes through GWAS and integrates gene expression and epigenomic data to highlight potential functional genes and regulatory mechanisms.

The paper identifies gene targets for brain-related traits using transcriptomic and methylomic data from blood, finding strong correlations between genetic effects in brain and blood tissues.