Markus Hoffmann

SATB1 is a targetable modulator of JAK-STAT signaling and cytokines in human Treg and Tconv cells

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.

Detection of Candidate Circular RNAs to Monitor Anti-Hormonal Response in the Mammary Gland

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.

Common Pitfalls in CircRNA Detection and Quantification

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.

Comprehensive benchmark of differential transcript usage analysis for static and dynamic conditions

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

RNA sequencing depth guidelines for the study of alternative splicing

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.

Network medicine-based epistasis detection in complex diseases: ready for quantum computing

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.

Blood transcriptomics analysis offers insights into variant-specific immune response to SARS-CoV-2

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: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape

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

circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging

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: a java pipeline to prioritize condition-specific transcription factors

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