Daniel Baumhoer

Persistent Staphylococcus aureus in human musculoskeletal tissues despite targeted antibiotic therapy

This study shows S. aureus persists in musculoskeletal tissues despite antibiotic therapy, with residual bacteria capable of causing relapse.

Genetic profiling of soft tissue and bone tumors using SarcDBase

SarcDBase is a tool that extracts and interprets genetic alterations from tumor sequencing data, showing high agreement with curated diagnoses in most cases.

Microgeography of staphyloccoci in human tissue explains antibiotic failure

The paper maps Staphylococcus aureus microgeography in human tissue using AI-guided imaging and finds antibiotic failure is linked to intracellular bacterial persistence and metabolic constraints.

Super-enhancer-driven CACNA2D2 is an EWSR1::WT1 signature gene encoding a diagnostic marker for desmoplastic small round cell tumor (DSRCT)

The paper identifies CACNA2D2 as a super-enhancer-driven target of EWSR1::WT1 and demonstrates its utility as a diagnostic biomarker for DSRCT.

CDK4 is co-amplified with either TP53 promoter gene fusions or MDM2 through distinct mechanisms in osteosarcoma

This study identifies four subgroups of osteosarcomas based on genomic and transcriptomic analysis, revealing distinct mechanisms of CDK4 amplification in relation to MDM2 or TP53 alterations.

scROSHI - robust supervised hierarchical identification of single cells

scROSHI identifies cell types without training data by using pre-existing gene sets and hierarchical relationships, outperforming methods in low-data and high-diversity scenarios.

SCIM: Universal Single-Cell Matching with Unpaired Feature Sets

SCIM matches single-cell measurements across technologies by learning a technology-invariant latent space and applying bipartite matching, achieving high accuracy in real-world datasets.

Germline determinants of the somatic mutation landscape in 2,642 cancer genomes

This study identifies germline genetic variants influencing somatic mutation patterns in 2,642 cancer genomes across 39 cancer types.

Comprehensive Molecular Characterization of Mitochondrial Genomes in Human Cancers

This study characterizes mitochondrial genomes in 2,700 cancer patients across 37 types using whole-genome sequencing and RNA-seq, revealing mutational patterns, truncating mutations, and nuclear transfer of mitochondrial DNA.