Anny Usheva

Scalable DNA Feature Generation and Transcription Factor Binding Prediction via Deep Surrogate Models

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

Efficient High-Throughput DNA Breathing Features Generation Using Jax-EPBD

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.

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.