Zakaria Louadi

DysRegNet infers patient-specific gene-regulatory networks from bulk RNA-seq data, accounting for confounders and scaling to large sample sizes, showing age-specific bias in breast cancer.

The paper investigates how alternative splicing affects miRNA regulation by analyzing six TCGA cancer datasets, finding that transcripts with miRNA target sites in coding regions better predict miRNA expression.

Spycone analyzes alternative splicing in time course data to detect isoform switches and provides downstream analysis tools.

DICAST benchmarks alternative splicing analysis tools, showing STAR and HISAT2 perform best, and proposes a reporting standard for event detection.

The paper introduces NEASE, a tool for functional analysis of alternative splicing events, showing its ability to identify pathways related to tissue identity and cell type development, and highlight splicing-related biomarkers.