Danielle Denisko

The paper introduces effect size-based methods to rank transcription factor binding motifs, showing they outperform p-value rankings under heterogeneous sample sizes.

The paper identifies inverted Alu pairs that promote exon skipping through RNA stem-loop structures and shows their evolutionary significance in hominoid genomes.

The paper introduces peaKO, a method to optimize ChIP-seq motif analysis using knockout controls, showing improved results compared to existing methods.

The paper assesses BED format interoperability using Acidbio, finding most software packages perform poorly and introduces a badge system to improve reliability.