Sheng‐Kai Hsu

BryoCAD improves DNA foundation model performance for bryophytes by continuing pre-training on their genomes, enhancing motif recovery and gene annotation across multiple species.

This study identifies convergent genomic and gene-level constraints in grasses adapting to extreme environments using phylogenomic data and large language models.

This study identifies 9 QTLs associated with freezing tolerance in Tripsacum dactyloides using bulk segregant analysis and regression-based allele frequency imputation.

The paper constructs a transcriptomic atlas of grass senescence to identify molecular mechanisms of nitrogen recycling, finding divergent underground sink networks in annual crops.

The paper identifies a conserved cis-regulatory code across 589 grass species and finds that motif conservation declines rapidly but remains significant over evolutionary time, with adaptive changes linked to ecological transitions.

GeneCAD improves gene annotation in plant genomes using a DNA foundation model, achieving higher accuracy than existing tools across diverse species.

reelGene evaluates gene models using machine learning and evolutionary data, finding 28% of maize gene models are incorrectly annotated or nonfunctional.

The paper examines nitrogen dynamics in Andropogoneae grasses, finding annual species conserve nitrogen while perennials vary in their impact on nitrification and nitrate loss.

The paper compares cold-responsive proteomes across five PACMAD grasses to assess conservation of protein-level responses and identifies LEA3 as a key cold-tolerant protein.

The paper examines how pleiotropy influences parallel gene expression evolution in Drosophila simulans adapted to a new temperature regime, finding both direct and indirect effects of pleiotropy on parallelism.

The paper examines genome evolution in maize and related grasses, revealing variable outcomes of polyploidy across species.