Samuel J. Kaplan

FourC identifies significant and differential contacts in 4C-seq data using a Bayesian model and Gaussian processes to address duplication and model spatial patterns.

The paper identifies pre-established chromatin regions in human ESCs that enable rapid activation of lineage-specific genes during differentiation.

This paper develops a human organoid model of early PDAC that identifies genetic and epigenetic barriers to lineage plasticity, showing CDKN2A loss is essential with KRAS/TP53 mutations and TET1 suppression links ERK signaling to transcription factor silencing.

The paper uses CRISPR-Cas9 screens to identify genes affecting stem cell fitness versus pluripotency identity, finding distinct and overlapping roles for chromatin and metabolic regulators.

The paper identifies a long-range enhancer for ONECUT1 involved in pancreatic differentiation and links a diabetes risk variant to disrupted transcription factor binding.