Michael A. Boemo

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

This paper introduces CAD-C, a chromatin-conformation capture method that enables high-resolution detection of sister-chromatid interactions and centromere pairing.

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

The paper identifies a third mechanism for resolving stalled RNA polymerase II by showing that transcription stalling triggers GSK3-mediated phosphorylation of Ser7 on Pol II, which primes incoming Pol II for efficient elongation.

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.

This study shows ecDNA replicates asynchronously and is vulnerable to replication stress, leading to its depletion in cancer cells.

This study identifies that high levels of DNA replication initiation factors correlate with ATR inhibitor sensitivity due to excessive origin firing in cancer cells.

This study compares DNA replication dynamics in two Plasmodium species with different A/T-content genomes, finding that P. falciparum has slower and more consistent replication fork speeds despite high A/T bias.

DNAscent v2 detects replication forks in nanopore sequencing data using a deep learning model, outperforming previous methods and tools.

The paper identifies DNA copy number alterations and chromosome-scale losses caused by replication stress in non-transformed cells, revealing their role in chromosomal instability and cancer evolution.

The paper introduces the Beacon Calculus, a process algebra for modelling biological systems, and demonstrates its application to DNA replication, DNA damage repair, and multisite phosphorylation.

This paper introduces a method to measure DNA replication dynamics on single molecules using nanopore sequencing and applies it to yeast to discover new replication origins.