Yingchao Liu

Decoding the Transcriptome Dark Matter: Construction of Single-Cell Whole-Transcriptome Regulatory Atlas by dropTotal

The paper introduces dropTotal, a method for single-cell total RNA-seq that detects both coding and non-coding transcripts, and applies it to human glioma nuclei to uncover ncRNA-driven regulatory landscapes.

LieOTMap: A Differentiable Approach to Cryo-EM Fitting via Lie-Theoretic Optimal Transport

LieOTMap fits high-resolution atomic models into cryo-EM maps using a differentiable framework based on Lie algebra and optimal transport, achieving accurate alignment of E. coli GroEL.

LieOTDock: A Protein Docking Framework via Lie Group Optimization and Optimal Transport

LieOTDock generates high-quality protein docking poses using Lie group optimization and optimal transport, achieving 3.43 Å RMSD on a benchmark in under three minutes.

LieOTAlign: A Differentiable Protein Structure Alignment Framework Combining Optimal Transport and Lie Algebra

LieOTAlign introduces a differentiable protein structure alignment framework using Lie algebra and optimal transport, achieving higher TM-scores on benchmark datasets.