A. R. Bishop

The paper investigates DNA breathing's role in TF-DNA interactions using in vitro and in vivo data, finding correlations between breathing features near motifs and binding affinity across multiple TFs.

The paper develops a deep surrogate model to generate DNA breathing features efficiently, improving transcription factor binding predictions.

The paper introduces JAX-EPBD, a high-throughput framework for simulating DNA breathing dynamics, showing 30x speedup and improved predictions of transcription factor binding using SELEX datasets.

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.

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.