Dimitra Sarantopoulou

BEERS2: RNA-Seq simulation through high fidelity in silico modeling

BEERS2 simulates RNA-seq reads with high fidelity, incorporating detailed library preparation and sequencing steps, and evaluates its impact on the Salmon pseudoalignment algorithm.

Epigenetic signature of human immune aging: the GESTALT study.

The paper identifies age-associated DNA methylation sites in immune cells and links them to transcription factor motifs and histone modifications, suggesting adaptive responses to oxygen fluctuations in aging.

Comparative evaluation of full-length isoform quantification from RNA-Seq

This study evaluates isoform quantification methods using simulated data, finding that no method significantly outperforms a simple approach on realistic data.

Distinct vascular genomic response of proton and gamma radiation.

This study compares the genomic response of mouse aorta to proton and gamma radiation, finding differences in gene responsiveness and pathway activation.

Iso-relevance Functions - A Systematic Approach to Ranking Genomic Features by Differential Effect Size

The paper introduces a framework to rank genomic features by differential effect size, showing that pseudocounts optimize the balance between fold-change and difference sorting.