Kim Ø. Rasmussen

Advancing Transcription Factor Binding Site Prediction Using DNA Breathing Dynamics and Sequence Transformers via Cross Attention

The paper improves TF binding site prediction by integrating DNA biophysical properties with sequence data using a multi-modal deep learning model, achieving better performance in both in vivo and in vitro datasets.

Examining DNA Breathing with pyDNA-EPBD

The paper introduces pyDNA-EPBD, a software tool for simulating DNA breathing dynamics using the EPBD model, and demonstrates its ability to calculate DNA bubble probabilities and mutation effects.