Markus Hoffmann

This study identifies SATB1 as a regulator of JAK-STAT signaling and cytokines in human Treg and Tconv cells, showing its potential as a target for CAR T cell therapy.

The paper identifies circular RNAs that change in response to anti-hormonal treatments in mouse models, suggesting potential as non-invasive biomarkers for therapeutic response.

This study highlights issues with circRNA detection in poly(A)-enriched RNA-seq data, showing it leads to false positives and recommends total RNA-seq with rRNA depletion for accurate profiling.

The paper benchmarks differential transcript usage analysis tools across static and dynamic conditions, finding optimal tools for different data types and experimental settings.

The paper provides sequencing depth guidelines for comprehensive alternative splicing analysis across tissues, showing that current depths are insufficient and recommending deeper sequencing or long-read technologies.

The paper introduces NeEDL, a network medicine-based method for detecting higher-order epistatic interactions in complex diseases, showing improved statistical significance and applicability across eight diseases.

The paper uses bulk RNA-seq to analyze immune responses to SARS-CoV-2 variants, showing that 10 million reads per sample can estimate immune cell composition and BCR/TCR sequences.

spongEffects identifies patient-specific ceRNA modules to provide insights into miRNA regulatory activity using gene expression data alone.

The paper introduces circRNA-sponging, a pipeline to analyze circRNA expression and miRNA sponging, identifying two types of circRNAs based on binding site ratios.

TF-Prioritizer identifies condition-specific transcription factors using multi-modal genomic data and generates an interactive web report.