Lucian Ilie

Ankh-score improves sequence alignment over AlphaFold3 structural alignments and traditional BLOSUM methods on benchmark datasets.

The paper introduces an embedding-based scoring method for protein sequence alignment, showing it outperforms BLOSUM matrices and existing tools.

C3PI is a deep learning framework for predicting protein-protein interactions that outperforms existing methods, especially on leakage-free datasets.

The paper introduces a new amino acid similarity scoring method, E-score, based on contextual embeddings from deep learning, showing improved alignment quality compared to BLOSUM matrices.

Seq-InSite predicts protein interaction sites using sequence data, outperforming sequence-based models and matching structure-based predictors.

DELPHI is a deep learning model that improves the accuracy of predicting protein-protein interaction sites by using an ensemble structure and novel features.