Daria Nogina

The paper evaluates and optimizes sequence-based gene regulatory deep learning models using a DREAM Challenge dataset, showing improvements through architectural and training strategy refinements.

LegNet is a deep learning model for predicting gene expression from DNA sequences, outperforming existing models and enabling promoter sequence design.

The paper identifies three types of A-to-I editing site clusters in cephalopods and describes structural features and mechanisms underlying their formation.

The paper introduces GRaNIE and GRaNPA, tools for inferring and evaluating enhancer-mediated gene regulatory networks in macrophages, identifying PURA as a regulator of pro-inflammatory polarization.