Joseph L. McClay

The paper evaluates exclusion set generation strategies in short-read sequencing, finding that pre-generated Blacklists are hard to reproduce and proposes sponge sequences as an alternative to reduce artifacts.

EpiTADformer uses epigenomic signal embeddings to detect TAD boundaries with higher resolution than Hi-C-based methods.

The paper examines age-related epigenetic changes in Sult1a1 and Ugt1a6 genes in mice, finding significant loss of DNA methylation and increased H3K9ac at Sult1a1, with H3K9ac positively correlating with gene expression.

The paper identifies TCF4 binding sites and their association with schizophrenia risk genes, showing TCF4 regulates neural development genes and interacts with SZ-related loci.