Coby Viner

This study benchmarks CUT&RUN peak callers using motif enrichment, finding that MACS2 outperforms SEACR in most scenarios with optimal preprocessing.

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 develops methods to model transcription factor binding in modified DNA by expanding the DNA alphabet and adapting existing tools to handle custom alphabets, identifying modification-sensitive motifs and validating them with experimental data.

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

DNAmod is a database that catalogs DNA modifications, providing information on their chemical properties, sequencing methods, and nomenclature.

The paper describes using Segway software to annotate genomes with chromatin data from ChIP-seq experiments, providing a semi-automated workflow for interpretation.