Yuanning Li

Hologenomics of xylotrophic bivalves reveals a minimalist, remote-acting evolutionary strategy of wood digestion

This study investigates the hologenomic strategy of wood-digesting bivalves, revealing a streamlined symbiotic system for efficient cellulose breakdown.

Augmented prediction of multi-species protein--RNA interactions using evolutionary conservation of RNA-binding proteins

MuSIC predicts cross-species RBP-RNA interactions using evolutionary conservation and label smoothing, outperforming existing methods and quantifying variant effects on binding.

Learning the native-like codons with a 5'UTR and RNA secondary structure aided species-informed transformer model

TransCodon is a Transformer-based model that predicts optimal synonymous codons by integrating species-specific information, 5'UTRs, and RNA structure, improving translational efficiency in heterologous hosts.

Deciphering the thiolactonization mechanism in thiolactomycin biosynthesis

This paper identifies the enzymatic mechanism for forming the gamma-thiolactone ring in thiolactomycin biosynthesis, revealing the roles of TlnCCy and TlnA.

Unique trajectory of gene family evolution from genomic analysis of nearly all known species in an ancient yeast lineage

The paper analyzes gene family evolution across nearly all known Saccharomycotina yeast species, finding distinct evolutionary patterns with gene loss linked to metabolic and genomic changes.

BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data

BioKIT provides a unified toolkit for processing and analyzing diverse sequence data, demonstrating its utility through quality assessments and codon usage analysis across multiple datasets.