Lina-Liv Willruth

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 introduces deconvMe, an R package for DNA methylation-based cell-type deconvolution, and compares its results to gene expression and experimental data.

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 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.

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.