Maga Rowicka

The paper introduces RepliSim, a computer model of DNA replication that reveals how checkpoint mutations and dNTP levels affect origin activation and replication fork dynamics.

The paper introduces iSeq, a tool for analyzing DSB-sequencing data, enabling identification and annotation of DSB-enriched regions across various resolutions.

This paper introduces a computational model of DNA replication that incorporates stochastic fork speed, showing it better reconstructs replication dynamics than models with constant speed.

The paper modifies Direct Coupling Analysis to predict interaction domains in large protein complexes, validated on known and unknown complexes.

The paper identifies functional interactions between 5-HT2A and 5-HT2C receptors using coevolution analysis and finds significant correlations between predicted binding interfaces and SNPs in these proteins.

qDSB-Seq quantifies absolute DNA double-strand break frequencies and their genomic coordinates across samples and organisms.

The paper estimates the high-resolution timeline of ribosomal protein gene expression in yeast, showing a 25-minute sequence with genes for mature ribosome proteins expressed later than others involved in biogenesis.

The paper estimates genome-wide protein abundances and dynamics from gene expression data without assuming steady-state conditions, validated using yeast cell cycle data.