David M. MacAlpine

The paper introduces CyCLOPS, a framework to deconvolve cell cycle chromatin occupancy in yeast, revealing dynamic chromatin and transcription patterns at high resolution.

The paper uses genetic perturbations and MNase-seq to study chromatin and TF responses in yeast, revealing chromatin-mediated regulatory mechanisms and networks.

This study investigates how CAF-1-dependent chromatin maturation affects transcription fidelity during S-phase in yeast, showing that CAF-1 loss leads to heterogeneous nucleosome assembly and transient gene silencing defects.

The paper investigates chromatin dynamics at replication origins during the cell cycle in yeast, finding that nucleosome repositioning and pre-RC assembly correlate with origin efficiency.

RoboCOP computes chromatin occupancy profiles for multiple factors from epigenomic data, showing improved accuracy over existing methods for yeast nucleosomes and 150 TFs.

The paper develops predictive models linking chromatin dynamics and transcription by analyzing chromatin and RNA data in yeast under cadmium stress.

The paper investigates how nucleosome dynamics and eviction after a double-strand break are reversible via NHEJ repair in yeast, showing re-establishment of chromatin structure in G1-arrested cells.

The paper studies helicase activation in the absence of DNA replication and finds it disrupts chromatin structure and activates the intra-S-phase checkpoint.

The paper develops NCOPs to study chromatin maturation dynamics behind the DNA replication fork and identifies locus-specific differences and factor-specific transient occupancy.