Holger Prokisch

This study uses RNA sequencing to identify pathogenic variants in mitochondrial disease patients who were undiagnosed by DNA sequencing, revealing cryptic splicing and regulatory events.

The paper identifies contmeQTLs linking childhood adversity to epigenetic changes in immune cells, which are associated with disease risk and inflammatory profiles.

The paper uses fibroblast RNA-seq to improve molecular diagnosis in dystonia patients by identifying RNA expression and splicing defects missed by genomic sequencing.

This study integrates single-cell spatial transcriptomics with bulk and single-cell RNA sequencing to reveal the molecular heterogeneity and mechanisms of atherosclerotic carotid artery plaques.

PROTRIDER detects protein expression outliers in proteomics data using conditional autoencoders, outperforming existing methods and revealing enrichments of pathogenic variants in outliers.

This study identifies the MCUR1-CCDC90B complex as a mitochondrial scaffold regulating metabolic homeostasis, showing its role in amino acid metabolism and linking its deficiency to neurometabolic disease.

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

This study identifies novel and known genetic contributors to hypertension using RNA-seq and eQTL analyses, highlighting potential drug targets and pathways.

The paper develops an interpretable multimodal machine learning framework to predict distal sensorimotor polyneuropathy using clinical and molecular data, identifying key biomarkers and improving prediction accuracy with additional molecular modalities.

The paper maps tissue-specific mtDNA heteroplasmy and its associations with age and mtDNA gene expression using bulk RNAseq data from GTEx.

This study identifies biallelic DAP3 variants causing mitoribosomal dysfunction, leading to combined oxidative phosphorylation deficiency and Perrault syndrome-like features.

The paper reports a cohort of 35 individuals with CUL3 variants causing a syndromic neurodevelopmental disorder, showing loss-of-function variants disrupt protein homeostasis by impairing proteasomal degradation of CUL3 substrates.

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.

This paper identifies nuclear genetic factors modifying the clinical phenotype of m.3243A>G mitochondrial disease using genetic linkage analysis across 76 pedigrees.

The paper reconstructs regulatory networks underlying trans-QTL hotspots using human multi-omics data and biological priors, identifying novel networks related to schizophrenia and lean body mass.

The paper predicts tissue-specific aberrant splicing by improving DNA-based models with RNA-seq data and benchmarking over 8.8 million variants across 49 human tissues.

The paper implements RNA-seq in diagnostics for Mendelian diseases, achieving a 16% diagnosis rate in WES-inconclusive cases by detecting aberrant expression, splicing, and mono-allelic expression.

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.

This study analyzes 2,023 pediatric exomes to diagnose mitochondrial disease, identifying 1,109 molecular diagnoses and 62 novel disease genes through exome sequencing and functional studies.

Adding tandem mass tag proteomics to genome and transcriptome data resolved 22% of 121 unsolved suspected mitochondrial disease cases and surfaced two new disease genes.

FRASER detects aberrant splicing events in RNA-seq data, identifying pathogenic intron retention and improving sensitivity over z-score methods.

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.

This study identifies novel ELAC2 variants linked to hypertrophic cardiomyopathy and mitochondrial dysfunction, confirms their pathogenicity through in vitro analysis, and links one variant to prostate cancer.

The paper quantifies protein-to-mRNA (PTR) ratios across 29 human tissues and identifies sequence determinants influencing these ratios, finding many new post-transcriptional regulatory elements.

OUTRIDER detects aberrantly expressed genes in RNA-seq data by modeling co-variation and using significance-based thresholds to identify outliers.

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.

This study develops OCR-Stats, a statistical method to improve the accuracy of mitochondrial respiration measurements from Seahorse XF Analyzer data by addressing noise and variation across plates and wells.

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.

This study identifies genetic loci associated with early childhood growth phenotypes and links them to later adiposity traits, suggesting potential targets for obesity prevention.

This study uses RNA sequencing to identify genetic diagnoses in mitochondrial disease patients by detecting aberrant gene expression and splicing events.