Author

Alexey K. Shaytan

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Open access Sep 2026

DECANT: decoupling mechanism from context in single-cell drug perturbation representation

These results support DECANT as a framework for learning context-robust, mechanism-aligned perturbation representations from single-cell transcriptional responses, providing a basis for mechanism-aligned perturbation analysis and representation-based compound prioritization.

Ren Qi, Wen-Jie Teng, Xin Yang et al. · Bioinformatics · 0 citations

Open access Aug 2026

Peptide language pragmatic analysis and two-stage hierarchical learning framework for therapeutic peptide prediction

TPpred-PepPA is developed, a two-stage hierarchical deep learning framework based on the ProtT5 pre-trained large language model that achieves state-of-the-art predictive performance and provides valuable interpretability for the discovery of multi-functional therapeutic peptides.

Ke Yan, Si-Yang Lu, Shutao Chen et al. · BMC Biology · 0 citations

Open access Jun 2026

Hybrid Approach to Protein–Protein Complex Affinity Prediction Based on Language Models and Molecular Dynamics

HyBind-NN is developed, a multimodal graph neural network that integrates protein language models (PLMs) with 3D structural and dynamic datasets to predict protein–protein and protein–peptide affinity, and it is demonstrated that combining ESM-2 sequence embeddings with precise 3D Voronoi spatial geometry enables accur...

E. A. Bogdanova, A. Chernukhin, Alexey K. Shaytan · International Journal of Mol... · 0 citations