Lude Franke

Human genetics implicates a BACH2-NRF2 axis in fetal hemoglobin activation

This study identifies a BACH2-NRF2 axis regulating fetal hemoglobin activation through genetic and functional analyses in a large multi-ancestry cohort.

Epigenome-wide association study meta-analysis of wellbeing

This study conducts an epigenome-wide association study (EWAS) meta-analysis of wellbeing using DNA methylation data, finding no significant methylation sites but suggesting the need for larger studies.

Cell-specific regulatory circuits connect genetic variation to disease susceptibility

The paper identifies dual-acting regulatory QTLs and gene regulatory networks in immune cells to better understand how genetic variation influences disease susceptibility.

Federated single-cell QTL meta-analysis reveals novel disease mechanisms

The paper performs a federated cis-eQTL meta-analysis across single-cell datasets to identify cell-type-specific genetic effects and link them to disease mechanisms.

High cell-type specificity of eQTLs revealed by single-nucleus analyses of brain and blood

The paper identifies highly cell-type-specific eQTLs using snRNA-seq data from brain and blood, showing that bulk analyses overestimate eQTL agreement.

Disease-associated variants are enriched for altering cell-type-specific gene co-expression relationships

The paper identifies co-eQTLs that alter gene co-expression relationships in specific cell types, linking these variants to immune disease associations.

Identification of (ultra-)rare functional promoter mutations in cancer using sequence-based deep learning models

This study uses sequence-based deep learning models to identify functional promoter mutations in cancer, finding enrichment in known and novel cancer genes.

Linking common and rare disease genetics through gene regulatory networks

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.

Single-cell atlas of the human immune system reveals sex-specific dynamics of immunosenescence

This study uses single-cell RNA sequencing to analyze immune aging in 982 donors, revealing sex-specific changes in immune cell composition and function during aging.

Phenotype prediction using biologically interpretable neural networks on multi-cohort multi-omics data

The paper develops interpretable neural networks for multi-omics data to predict smoking status, age, and LDL levels, showing improved performance and generalizability across cohorts.

Co-expression in tissue-specific gene networks links genes in cancer-susceptibility loci to known somatic driver genes

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

The regulatory grammar of human promoters uncovered by MPRA-trained deep learning

This paper introduces PARM, a deep learning model trained on MPRA data to predict human promoter activity and identify TF binding preferences, revealing positional and functional differences in regulatory grammar.

Distinct genetic liability profiles define clinically relevant patient strata across common diseases

The paper identifies genetically distinct patient subgroups across diseases by analyzing polygenic risk and pathway convergence.

Understanding the genetic complexity of puberty timing across the allele frequency spectrum

This study identifies genetic signals associated with age at menarche, highlights genes involved in pubertal development, and links reproductive timing to later life disease risk.

Multi-ancestry polygenic risk scores for venous thromboembolism

This study develops multi-ancestry polygenic risk scores for venous thromboembolism using diverse GWAS data and shows improved predictive performance across European- and African-ancestry populations.

Leveraging functional genomic annotations and genome coverage to improve polygenic prediction of complex traits within and between ancestries

This paper introduces SBayesRC, a method that improves polygenic prediction of complex traits by integrating GWAS summary statistics with functional genomic annotations, showing significant accuracy gains across ancestries.

Demuxafy: Improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods

Demuxafy improves droplet assignment and doublet removal in scRNA-seq by combining multiple demultiplexing and doublet detection methods.

Linking the gut microbiome to host DNA methylation by a discovery and replication epigenome-wide association study

This study identifies two CpGs associated with the gut microbiome genus Eggerthella and shows microbiome mediates environmental effects on DNA methylation.

Using brain cell-type-specific protein interactomes to interpret genetic data in schizophrenia

The paper uses brain cell-type-specific protein interactomes to interpret genetic data in schizophrenia and identifies enriched networks and genes associated with the disease.

OTTERS: A powerful TWAS framework leveraging summary-level reference data

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.

Brain expression quantitative trait locus and network analysis reveals downstream effects and putative drivers for brain-related diseases

The paper integrates brain RNA-seq and genotype data to identify eQTLs and their downstream effects on brain-related diseases.

KidneyNetwork: Using kidney-derived gene expression data to predict and prioritize novel genes involved in kidney disease

KidneyNetwork predicts kidney-specific gene functions and disease phenotypes using co-expression networks, identifying ALG6 as a candidate gene for kidney and liver cysts in undiagnosed patients.

Phenotypic and genetic factors are associated with absence of cardiomyopathy symptoms in PLN c.40_42delAGA carriers

The paper identifies shorter QRS duration in asymptomatic PLN c.40_42delAGA carriers and links it to genetic sensitivity in symptomatic carriers.

Global biobank analyses provide lessons for developing polygenic risk scores across diverse cohorts

This study evaluates polygenic risk score methods across diverse biobanks and ancestries, finding that European reference panels often yield better performance, while PRS-CS outperforms P+T for high-heritability traits.

Meta-analysis fine-mapping is often miscalibrated at single-variant resolution

This paper shows that meta-analysis fine-mapping is often miscalibrated due to cohort heterogeneity and introduces a QC method to identify suspicious loci.

Genome-wide characterization of circulating metabolic biomarkers reveals substantial pleiotropy and novel disease pathways

This study identifies 400+ genetic loci associated with circulating metabolic traits and highlights pleiotropy and novel disease pathways.

Global Biobank Meta-analysis Initiative: powering genetic discovery across human diseases

Meta-analysis of harmonized GWAS from up to 18 biobanks (six ancestry groups) across 14 endpoints replicated 320 known loci and identified 188 apparently novel loci.

Omics-informed CNV calls reduce false positive rate and improve power for CNV-trait associations

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

Unbiased identification of unknown cellular and environmental factors that mediate eQTLs using principal interaction component analysis

This paper introduces PICALO, a method to identify unknown contexts influencing eQTLs, finding 31 and 21 PICs in blood and brain datasets, respectively, associated with cell type, RNA quality, and environmental factors.

Integration of Candida albicans-induced single-cell gene expression data and circulatory protein concentrations reveal genetic regulators of inflammation

The paper integrates single-cell gene expression and circulatory protein data to identify genetic regulators of inflammation in response to Candida albicans.