Ruishan Liu

A Taxonomy-Informed Sparse DNA Foundation Model for Microbial Genomics

A sparse mixture-of-experts DNA model conditioned on hyperbolic taxonomy embeddings learns better microbial representations than its taxonomy-free twin and comes close to Evo2-7B in probing and fine-tuning at lower compute.

Benchmarking computational methods for multi-omics biomarker discovery in cancer

This paper benchmarks 20 computational methods for multi-omics biomarker discovery in cancer using real and simulated datasets, finding that DeePathNet and Deep-KEGG perform best.

METAHICT enables comprehensive genome-resolved microbiome analysis with metagenomic Hi-C

METAHICT improves metagenomic Hi-C analysis by integrating binning, reassembly, and downstream tools to recover high-quality MAGs and reduce contamination.

Modeling Spatial Correlation of Transcripts With Application to Developing Pancreas

The paper develops a tool to analyze spatial gene expression correlations in tissue sections, applied to human fetal pancreas development.