Johanna Klughammer

The paper identifies sequence variation in 5S rRNA genes across human populations and shows that variants disrupting ribosome assembly activate p53 and are selected against.

scDynOmics is a transformer model for single-cell multiomics data that outperforms existing models and provides interpretable insights into cellular dynamics.

This paper benchmarks 26 spatial domain detection methods across real and semi-synthetic spatial transcriptomics data to identify performance drivers and introduce a modular benchmarking framework.

This study identifies truncating RELA variants causing autoinflammation and autoimmunity by disrupting NF-κB feedback control and immune homeostasis.

This paper introduces a FACS-based preprocessing workflow for PBMCs that improves scRNA-seq throughput and preserves biological integrity while enabling rare cell enrichment and cross-donor multiplexing.

SlideCNA detects spatial copy number alterations from Slide-seq data to identify sub-clones in metastatic breast cancer.

SCHAF generates spatially resolved single-cell transcriptomes from H&E histology images using vision transformers and adversarial learning, showing good agreement with ground-truth data.

TACCO is a framework for annotating cell identities in single-cell and spatial omics data, excelling in speed and performance across datasets.

The paper maps DNA methylation in 580 animal species, revealing conserved and evolving patterns across vertebrates and invertebrates.

SM-Omics is a platform that combines spatial transcriptomics and proteomics to analyze tissue samples at scale.

The paper identifies genetic variants influencing DNA methylation in blood and shows their associations with complex traits and diseases, but finds limited direct causality.

ExSeq enables multiplexed RNA mapping at nanoscale resolution by expanding biological specimens for in situ sequencing.

The paper develops a toolbox for scRNA-Seq and snRNA-Seq of fresh and frozen human tumors, testing it across eight tumor types and optimizing protocols for different tissue characteristics.

This paper introduces HDST, a high-resolution spatial transcriptomics method, and demonstrates its application in mouse brain tissue to resolve spatial expression patterns and cell types.

This study maps DNA methylation changes in glioblastoma tumors over time and space, revealing heterogeneity and links to tumor microenvironment and patient survival.

This paper combines CRISPR genome editing with single-cell RNA sequencing to enable high-throughput screening with complex molecular read-outs.