Martin Depken

The paper provides tools and methods for analyzing high-throughput single-molecule biophysics data using first-passage time and maximum likelihood estimation to model kinetic behavior.

This study shows that the coronavirus helicase enhances RNA synthesis through duplex RNA by tenfold by forming a directional complex with the polymerase, revealing an active coupling mechanism that modulates replication dynamics.

This study investigates how DNA supercoiling affects Cas9 off-target cleavage by mapping cleavage rates and sites across different topologies using NucleaSeq and a biophysical model.

The paper introduces CRISPRzip, a mechanistic model that predicts CRISPR-Cas9 activity based on sequence and context, validated by experimental data.

The paper shows that the SARS-CoV-2 polymerase core RTC undergoes a conformational change after RNA binding to become elongation-competent, which is essential for viral RNA synthesis.

This study systematically identifies sequence determinants of CRISPR/Cas9 specificity by analyzing off-target effects of 1,902 gRNAs on 13,314 targets, revealing three key factors and developing a predictive tool.

The paper constructs a kinetic model to predict CRISPR-Cas off-targeting based on mismatch positions and distances, explaining efficiency and specificity decoupling.