Alexander J. Hartemink

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.

SCARlink predicts gene expression from chromatin accessibility in single-cell multiome data, identifies enhancers, and enables chromatin potential analysis for developmental trajectories.

The paper introduces TOP, a Bayesian framework that quantifies TF occupancy across many conditions using a single DNase-seq experiment, showing changes in 1500 TF motifs across cell types, hormone exposure, and genetic backgrounds.

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 introduces MATCHER, a method that aligns single cell transcriptomic and epigenomic data to infer shared trajectories, revealing correlations between gene expression and epigenetic changes in mouse embryonic stem cells.

The paper analyzes growth and division dependencies in budding yeast, finding new inter-cycle correlations and developing a hierarchical model to capture these dependencies.

The paper examines chromatin interactions in yeast and finds that transcriptional activity correlates with chromosomal interactions.