Benedikt Obermayer

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

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.

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.

This study uses single nucleus RNA sequencing to analyze cortical and striatal development in a mouse model of Allan-Herndon-Dudley Syndrome, identifying disruptions in oligodendrocyte lineage, cell-cell communication, and cilia formation.

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

The paper develops a 3D lung organoid model to assess antiviral T cell efficacy in vitro, demonstrating T cell-mediated cytotoxicity against influenza virus.

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

The paper develops CCISM to distinguish cancer cells from normal epithelial cells in single-cell data, identifying a novel stem-like cell state in the colorectal cancer microenvironment.

The paper identifies Pri smORF peptides as pleiotropic regulators of leg development in Drosophila, functioning through Ubr3-dependent and -independent mechanisms in patterning and cell survival.

This study uses single-nuclei transcriptomics to analyze human kidney injury responses, identifying four injury-associated cell states and showing similar gene expression changes between AKI patients with and without COVID-19.

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.

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

The paper identifies and characterizes conserved small ORFs in multiple animal species, finding novel micropeptides with evidence of translation and functional potential.

RiboTaper identifies actively translated open reading frames using spectral analysis of Ribo-seq data, revealing novel ORFs and validating peptide products in HEK293 cells.