Dieter Beule

Kiosc: an integrated platform for managing bioinformatics data analysis containers

Kiosc simplifies managing containerized web apps for bioinformatics analysis, enabling interactive result visualization and sharing across projects and institutions.

Translating multi-omics complexity into sparse prognostic biomarkers for multiple myeloma

This paper identifies prognostic biomarkers for multiple myeloma by integrating multi-omics data and shows that proteomic features outperform genomic or transcriptomic data in classification.

Gene-specific endothelial programs drive AVM pathogenesis in SMAD4 and ALK1 loss-of-function

This study identifies gene-specific mechanisms of AVM formation in endothelial cells with SMAD4 or ALK1 loss-of-function, showing distinct molecular and cellular pathways leading to different vascular malformations.

circVDJ-seq for T cell clonotype detection in single-cell and spatial multi-omics

The paper introduces circVDJ-seq for efficient T cell receptor profiling from single-cell and spatial multi-omics data, revealing distinct immune microenvironments and T cell clonality patterns in various clinical contexts.

mehari: high-performance, strict HGVS-first variant effect prediction

mehari predicts variant effects with a strict HGVS-first approach, achieving high speed and accuracy compared to existing tools.

Endothelial YAP/TAZ rewiring under cardiometabolic stress drives sex-divergent vascular remodeling in heart failure with preserved ejection fraction

This study identifies endothelial YAP/TAZ signaling as a driver of sex-divergent vascular remodeling in HFpEF, linking cardiometabolic stress to microvascular changes through YAP1 and ESM1.

StemCNV-check: a pipeline for human pluripotent stem cell (hPSC) genomic integrity control using SNP array data and copy number variant scoring

The paper introduces StemCNV-check, a pipeline for assessing genomic integrity in human pluripotent stem cells using SNP array data and CNV scoring.

In vivo sequential mutagenesis in germinal center B cells using a dual-recombinase approach: FOXO1 re-expression upon FOXO1 knockout rescues class switch recombination

The paper introduces a dual-recombinase system for sequential mutagenesis in germinal center B cells, enabling FOXO1 knockout and subsequent re-expression to study its effects on class switch recombination.

Svirlpool: structural variant detection from long read sequencing by local assembly

Svirlpool detects structural variants from ONT data using local consensus assemblies, achieving high Mendelian consistency and outperforming existing methods in certain metrics.

Lineage origin and developmental context shape tumor states in MYCN-dependent zebrafish neuroblastoma

This study shows lineage history and developmental context jointly shape tumor-state architecture in MYCN-driven zebrafish neuroblastoma.

Cryo-mtscATAC-seq for single-cell mitochondrial DNA genotyping and clonal tracing in archived human tissues

The paper introduces Cryo-mtscATAC-seq to genotype mitochondrial DNA and trace clones in frozen human tissues, revealing clonal patterns in various diseases.

Reporter-based screening identifies RAS-RAF stabilizing mutations as drivers of resistance to broad-spectrum RAS inhibition in colorectal cancer

Formation of amyloid-like HTTex1 aggregates in neurons, downregulation of synaptic proteins and early mortality of Huntington's disease flies are causally linked

This study links mHTTex1 aggregation in neurons to synaptic dysfunction and early mortality in HD flies through machine learning analysis and RNAi knockdown experiments.

Copy-number dosage regulates telomere maintenance and disease-associated pathways in neuroblastoma

The paper identifies gene dosage effects on telomere maintenance and disease pathways in neuroblastoma using genomic and transcriptomic data from 115 tumors.

Identifying cancer cells from calling single-nucleotide variants in scRNA-seq data

CCLONE identifies cancer cells in scRNA-seq data by jointly analyzing SNVs and cell populations, showing its effectiveness in leukemia and lung cancer datasets.

Ide copy number variant does not influence lesion size and mortality in two C57BL/6J mouse models of cerebrovascular ischemia nor in human cerebrovascular disease. An exploratory study

The paper investigates whether Ide copy number variants influence vascular phenotypes in mice and humans, finding no significant association.

A transgenerational mutational signature from ionizing radiation exposure.

This study finds that paternal exposure to ionizing radiation increases clustered de novo mutations in offspring, suggesting cDNMs as a transgenerational biomarker.

Microglia undergo transcriptional, translational and functional adaptations to dark and light phases in laboratory mice

The paper investigates circadian changes in microglial transcriptional, proteomic, and functional profiles in mice, finding significant differences between light and dark phases and impaired circadian regulation in a neurodevelopmental disorder model.

A proteomics analysis of 5xFAD mouse brain regions reveals the lysosome-associated protein Arl8b as a candidate biomarker for Alzheimer's disease

This study identifies Arl8b as a potential biomarker for Alzheimer's disease by analyzing proteomic changes in 5xFAD mouse brain regions and CSF from AD patients.

SODAR: managing multi-omics study data and metadata

SODAR is a software package that manages multi-omics study data and metadata using a web interface and APIs, supporting the ISA-Tab format and iRODS storage.

Analyses of circRNA expression throughout circadian rhythm reveal a strong link between Cdr1as and light-induced phase shifts in the SCN

The paper examines circRNA expression in circadian rhythms, finding that Cdr1as shows dynamic expression in the SCN and is linked to light-induced phase shifts.

Deep Learning assisted Peak Curation for large scale LC-MS Metabolomics

NeatMS uses machine learning to automate peak curation in LC-MS metabolomics, improving robustness and scalability compared to manual methods.

Spermidine reduces neuroinflammation and soluble amyloid beta in an Alzheimer's disease mouse model

This study shows that spermidine reduces neuroinflammation and soluble amyloid beta in an Alzheimer's disease mouse model by targeting microglia and reducing inflammatory pathways.

Diverse but unique astrocytic phenotypes during embryonic stem cell differentiation, culturing and aging

The paper compares ESC-derived, neonatal, and adult astrocytes to identify functional and transcriptomic differences across age and culture conditions.

The architecture of protein synthesis in the developing neocortex at near-atomic resolution reveals Ebp1-mediated neuronal proteostasis at the 60S tunnel exit

The paper reveals Ebp1's role in neuronal proteostasis by analyzing ribosomal architecture and proteomic changes in the developing mouse neocortex.

HLA-C* 04:01 is a Genetic Risk Allele for Severe Course of COVID-19

The paper identifies HLA-C* 04:01 as a genetic risk allele associated with increased intubation risk in severe COVID-19 cases, validated across multiple cohorts.

Enzymatic dissociation induces transcriptional and proteotype bias in brain cell populations

This study shows that enzymatic dissociation of brain tissue alters transcriptomic and proteotype profiles compared to mechanical dissociation.

Concepts and Software Package for Efficient Quality Control in Targeted Metabolomics Studies - MeTaQuaC

The paper introduces MeTaQuaC, an open-source R package for quality control in targeted metabolomics, improving data reliability through systematic error detection and visualization.

SCelVis: Powerful explorative single cell data analysis on the desktop and in the cloud

SCelVis provides a flexible, user-friendly tool for visualizing and analyzing single-cell data on desktop and cloud platforms.

VarFish - Collaborative and Comprehensive Variant Analysis for Diagnosis and Research

VarFish is a web application for variant analysis in rare disease genetics, offering quality control, filtering, annotation, and collaboration tools for diagnostic and research use.