Stephan Ossowski

Unsupervised prioritization of gene-regulatory variants with isolation forests

The paper introduces eQIF, an unsupervised machine-learning method that integrates Enformer predictions to prioritize gene-regulatory variants, showing strong performance in predicting eQTLs and GWAS variants.

Long-read genome sequencing resolves complex structural variants in exome-negative developmental and epileptic encephalopathy

This study evaluates the diagnostic value of long-read genome sequencing in DEE patients, finding it particularly effective for resolving complex structural variants not detected by short-read sequencing.

Genomic correlates of metastatic competence and progression in human melanoma

This study identifies genomic features, particularly copy-number alterations, that predict metastatic progression in melanoma and defines a six-gene signature associated with relapse.

aiDIVA - Diagnostics of Rare Genetic Diseases Using Large Language Models

aiDIVA uses AI and LLMs to prioritize causal genetic variants in rare diseases, achieving high accuracy in identifying top candidates.

MethylBench: A comprehensive benchmark of DNA methylation profiling methods across diverse sequencing platforms

MethylBench benchmarks DNA methylation profiling methods across sequencing platforms, finding consistent DMC hotspots and highlighting platform-specific strengths and limitations.

Single-Platform Nanopore Sequencing Enables Diploid Telomere-to-Telomere Genome Assembly and Haplotype-Resolved 3D Chromatin Maps

This paper presents a Nanopore-only workflow for diploid T2T genome assembly and haplotype-resolved 3D chromatin maps, achieving high accuracy without hybrid polishing.

Long-Read RNA-sequencing reveals transcript-specific regulation in human-derived cortical neurons

This study uses long-read RNA sequencing to analyze transcript diversity and regulation in human fibroblasts, induced pluripotent stem cells, and cortical neurons, revealing transcript-specific changes in disease-related genes.

Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes

This study uses ultra-deep metagenomic sequencing to analyze soil microbes, revealing extensive microbial diversity and biosynthetic potential previously unexplored.

Comprehensive reanalysis for CNVs in exome sequencing data from unsolved rare disease cases results in new diagnoses

The paper reanalyzes exome sequencing data from rare disease cases to identify previously undetected copy number variants, resulting in diagnoses for 51 families and partial explanations for 34 individuals.

Structural variant calling and clinical interpretation in 6224 unsolved rare disease exomes

This study identifies structural variants in 6224 rare disease exomes, finding 0.4% diagnostic yield with 8 previously undetected pathogenic SVs.

Unravelling undiagnosed rare disease cases by HiFi long-read genome sequencing

The paper uses HiFi long-read sequencing to identify genetic variants in undiagnosed rare disease families, finding novel diagnoses in 13% of cases and candidate variants in 4.3%.

A unified data infrastructure to support large-scale rare disease research

The paper describes a unified data infrastructure for rare disease research, enabling collaborative analysis of multi-omics data across institutions.

ClinCNV: multi-sample germline CNV detection in NGS data

ClinCNV detects germline CNVs in NGS data using multi-sample normalization and an algorithm combining circular binary segmentation and Hidden Markov models.

Exome-wide analysis of copy number variation shows association of the human leukocyte antigen region with asthma in UK Biobank

The paper identifies two independent asthma-associated loci in the HLA region using exome-wide CNV analysis in UK Biobank, highlighting challenges with CNV detection in complex genomic regions.

Swarm Learning as a privacy-preserving machine learning approach for disease classification

This paper introduces Swarm Learning, a decentralized machine learning approach for disease classification using transcriptomic data, demonstrating its effectiveness in developing classifiers for COVID-19, tuberculosis, and leukemias while preserving privacy.

Environmental enrichment induces epigenomic and genome organization changes relevant for cognitive function

This study shows environmental enrichment alters chromatin structure, transcription factor binding, and 3D genome organization in mice, affecting cognitive function and gene regulation.

Efficient and Flexible Integration of Variant Characteristics in Rare Variant Association Studies Using Integrated Nested Laplace Approximation

The paper introduces BATI, a Bayesian rare variant association test that outperforms existing methods in detecting rare variants associated with complex diseases, especially when genetic variation explains little phenotypic variance.

Nuclear gene proximity and protein interactions shape transcript covariances in mammalian single cells

The paper identifies >80,000 gene pairs with intrinsic covariance in mouse embryonic stem cells, showing nuclear organization and protein interactions drive transcript covariances.

Tracking of antibiotic resistance transfer and rapid plasmid evolution in a hospital setting by Nanopore sequencing

The paper uses Nanopore sequencing to track antibiotic resistance plasmid evolution and transfer between bacterial species in a hospital setting, identifying plasmid fusion and gene rearrangements.

The rate and spectrum of mosaic mutations during embryogenesis revealed by RNA sequencing of 49 tissues

The paper uses RNA sequencing from 49 tissues to estimate the rate and spectrum of mosaic mutations during embryogenesis, finding a similar frequency to germline de novo mutations and identifying a new mutational signature in the gastrointestinal tract.

Genomic footprints of activated telomere maintenance mechanisms in cancer

The paper analyzes whole-genome sequencing data from cancer samples to identify genomic footprints of telomere maintenance mechanisms, finding specific telomere variant repeat patterns associated with ATRX/DAXX mutations.

Spatial Genome Organization as a Framework for Somatic Alterations in Human Cancer

The paper examines how somatic structural variations affect TAD boundaries and gene regulation in human cancers using whole genome sequencing data.

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

This study analyzes chromothripsis in 2,658 cancers using whole-genome sequencing, finding it prevalent across multiple cancer types with complex structural alterations.

Wengan: Efficient and high quality hybrid de novo assembly of human genomes

The paper introduces WO_SCPCAPENGANC_SCPCAP, a hybrid de novo assembler for human genomes that improves contiguity and quality using long and short reads, achieving results better than the current reference genome.

ClinCNV: novel method for allele-specific somatic copy-number alterations detection

ClinCNV detects allele-specific somatic copy-number alterations in NGS data using a statistical approach, showing performance on WES and TPS cohorts.

Genome-wide active enhancer identification using cell type-specific signatures of epigenomic activity

The paper introduces a machine learning method to identify active enhancers using cell type-specific epigenomic signatures, showing improved performance and generalizability across human and mouse tissues.

Multi-omics approach identifies novel pathogen-derived prognostic biomarkers in patients with Pseudomonas aeruginosa bloodstream infection

The paper identifies novel pathogen-derived biomarkers associated with mortality in Pseudomonas aeruginosa bloodstream infections using a multi-omics approach.

Bayesian Inference Of Cancer Driver Genes Using Signatures Of Positive Selection

This study introduces a Bayesian model to identify cancer driver genes by integrating evolutionary signatures, revealing novel gene-tumor type associations and highlighting chromatin modifiers as key targets.