Francisco Berkemeier

This study uses nanopore sequencing to determine the replication timing programme of Plasmodium falciparum and links it to DNA breaking and replication fork stalling.

The paper shows that 3D epithelial cell geometry and topology influence Notch-Delta signalling range, affecting cell fate patterning in Drosophila wing margins.

The paper introduces ORILINX, a genome language model that predicts replication origins in human and other mammalian genomes using sequence context.

The paper develops a high-resolution stochastic model of DNA replication in yeast to study replication timing and firing factor dynamics.

The paper develops a high-resolution mathematical model to map replication timing profiles across cell lines, revealing correlations between replication dynamics, transcription, and chromatin structure.

The paper analyzes the dynamics of Notch-Delta signaling models to assess their ability to explain pattern formation and differentiation, finding nonlinear effects are not captured by linear or weakly nonlinear stability analyses.