Kevin Brennan

EpiMix identifies differential DNA methylation in large cohorts with higher sensitivity than existing methods, revealing novel epigenetic mechanisms in childhood food allergy and lung cancer.

This paper benchmarks lncRNA quantification methods on cancer RNA-Seq data, finding that pseudoalignment methods with full transcriptome annotation outperform alignment-based methods.

The paper introduces ProteoMix, a method using proteomic data to identify epigenetic driver genes, finding that DNA methylation effects are often buffered at the protein level and enriched for cancer-related processes and markers.

This paper introduces AMARETTO, a multi-omics integration algorithm that identifies pancancer driver genes related to smoking and antiviral responses by analyzing eleven cancer types.