Sven Bergmann

Benchmarking attention-based methods for vision transformers' interpretability in retinal fundus imaging

This study benchmarks attention-based interpretability methods for Vision Transformers in retinal fundus imaging, finding gradient-weighted attention rollout provides the most faithful and biologically relevant attributions.

Sex-specific disease association and genetic architecture of retinal vascular traits

This study identifies sex-specific genetic and environmental contributions to retinal vascular traits through GWAS and interaction analyses, highlighting the need for sex-aware approaches in precision medicine.

Genetic and Etiological Insights from Automated Lumen Diameter Measurements in Carotid Ultrasounds of the UK Biobank

The paper develops a deep learning model to measure carotid lumen diameter from ultrasounds and performs GWAS, finding cLD has higher heritability and stronger associations with cardiovascular risk factors than cIMT.

Comparing tangible retinal image characteristics with deep learning features reveals their complementarity for gene association and disease prediction

Phenotypic and Genetic Characteristics of Retinal Vascular Parameters and their Association with Diseases

The paper analyzes retinal vascular phenotypes from fundus images and their genetic and disease associations using UK Biobank data, finding novel links between vascular features and health outcomes.

Cross-organ Analysis Reveals Associations between Vascular Properties of the Retina, the Carotid and Aortic Artery, and the Brain

The paper examines cross-organ vascular correlations using UK Biobank data, finding shared genetic influences and vascular morphology links between retina, carotid, aorta, and brain.

Disentangling genetic effects on transcriptional and post-transcriptional gene regulation through integrating exon and intron expression QTLs

This study integrates exon and intron expression QTLs to disentangle genetic effects on transcriptional and post-transcriptional gene regulation, revealing shared and distinct cis-QTLs and their implications for GWAS colocalization.

Associations between common genetic variants and income provide insights about the socioeconomic health gradient

This study identifies genetic variants associated with income and shows they correlate with health outcomes and educational attainment.

Genome-wide analysis identifies genetic effects on reproductive success and ongoing natural selection at the FADS locus.

This study identifies 43 genomic loci associated with reproductive success in 785,604 individuals, showing ongoing natural selection at the FADS locus.

GWAS of Retinal Vessel Tortuosity Identifies 173 Novel Loci Revealing Genes and Pathways Associated with Vascular Pathomechanics and Cardiometabolic Diseases

This study performs a GWAS on retinal vessel tortuosity, identifying 173 novel loci and linking them to vascular pathomechanics and cardiometabolic diseases.

Cross-GWAS coherence test at the gene and pathway level

This paper introduces a method to detect genes with coherent association signals across two GWAS traits, finding shared genetic links between severe COVID-19 and several medical conditions.

Estimating RNA dynamics using one time point for one sample in a single-pulse metabolic experiment

The paper introduces a method to estimate RNA synthesis, processing, and degradation rates from a single sample in a single-pulse metabolic experiment, showing good correlation with published data.

Analysis of eukaryotic lincRNA sequences reveals signatures of repressed translation in species under strong selection

The paper analyzes lincRNA sequences across six eukaryotes to identify sequence signatures of repressed translation, finding shorter ORFs and suboptimal codon usage in species under strong selection.

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.

Shear forces drive precise patterning of hair cells in the mammalian inner ear

This study shows that shear forces and local repulsion drive the formation of the checkerboard pattern of hair cells in the mammalian inner ear.

Untargeted metabolome- and transcriptome-wide association study identifies causal genes modulating metabolite concentrations in urine

This study identifies causal genes modulating urine metabolite concentrations by integrating metabolomics and transcriptomics data through mQTL analysis and Mendelian randomization.

MONET: a toolbox integrating top-performing methods for network modularisation

MONET provides a unified toolbox for disease module identification in molecular networks using top-performing methods from the DMI DREAM Challenge.

Assessment of network module identification across complex diseases

The paper evaluates module identification methods across disease-relevant networks using GWAS data to identify top-performing algorithms and disease-associated modules.

Automated analysis of large-scale NMR data generates metabolomic signatures and links them to candidate metabolites

The paper evaluates three NMR analysis tools for metabolite identification in human urine, finding ISA and ACP robustly identify metabolites while PCA fails.

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.

Interoperable and scalable data analysis with microservices: Applications in Metabolomics

The paper introduces a microservices-based framework for scalable data analysis, validated in metabolomics, enabling dynamic scaling and integration of software tools.

PROTEIN-CODING VARIANTS IMPLICATE NOVEL GENES RELATED TO LIPID HOMEOSTASIS CONTRIBUTING TO BODY FAT DISTRIBUTION

This study identifies 15 common and 9 low-frequency protein-coding variants associated with body fat distribution, implicating novel genes related to lipid homeostasis and type 2 diabetes.

PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud

PhenoMeNal provides a cloud-based platform for metabolomics data analysis, integrating tools and workflows to enable reproducible and scalable research.

Genome-wide association between transcription factor expression and chromatin accessibility reveals chromatin state regulators

The paper identifies transcription factors associated with chromatin accessibility using a linear mixed model applied to ENCODE data, confirming known and suggesting novel regulators.

Genome-wide analysis reveals novel regulators of growth in Drosophila melanogaster

The paper performs genome-wide association analysis in Drosophila to identify genetic variants associated with size traits, finding novel regulators of growth outside canonical pathways.