Zhiwei Qin

The evolutionary processes of bacterial aromatic polyketide ketosynthases

The paper uses a protein language model to analyze the evolutionary history of bacterial aromatic polyketide ketosynthases and chain length factors, identifying a shared ancestral cluster and distinct evolutionary paths.

DeepAden: an explainable machine learning for substrate specificity prediction in nonribosomal peptide synthetases

DeepAden predicts A-domain substrate specificities in NRPSs using a two-stage deep learning framework, achieving competitive performance and enabling the identification of novel NRP gene clusters.

Holomycin from Yersinia ruckeri mediates fish infection at low temperature

This study identifies holomycin as a key factor in Yersinia ruckeri infection of rainbow trout at low temperatures, showing it remodels host microbiota and enhances biofilm formation.

MAAPE: A Modular Approach to Evolutionary Analysis of Protein Embeddings

MAAPE integrates KNN and co-occurrence matrix analysis to extract evolutionary insights from protein embeddings, successfully reconstructing phylogenetic relationships in benchmark datasets.

DNA-SaM, a robust system for large-scale data storage

DNA-SaM improves DNA data storage by achieving high efficiency, scalability, and safety through advanced encoding and architecture.

Machine learning-guided directed evolution for the development of small-molecule antibiotics originating from antimicrobial peptides

This study uses machine learning-guided directed evolution to develop a peptide antibiotic from antimicrobial peptides, showing improved antimicrobial activity and therapeutic potential.