Shaopeng Liu

The paper investigates sex-specific molecular responses to early-life toxicant exposures in mice across multiple life stages using transcriptomic and epigenomic data.

The paper introduces MetagenomicKG, a knowledge graph integrating metagenomic data with biomedical knowledge to enable hypothesis generation and pathogen prediction.

The paper characterizes persistent epigenomic and transcriptomic changes in mice exposed to environmental toxicants across life stages, revealing widespread gene expression and chromatin alterations.

The paper shows that open syncmer sketches are equivalent to FracMinHash sketches for k-mer similarities but offer better distance distribution and conservation, and extends them for metagenomic and sequence comparison applications.

This paper introduces fmh-funprofiler, a fast and lightweight metagenomic functional profiler using FracMinHash sketches, showing improved purity and speed compared to alignment-based methods.

CMash provides a fast, multi-resolution method to estimate k-mer-based Jaccard and containment indices without reconstructing k-mer sets for different k values.

The paper introduces AIAP, an ATAC-seq analysis package that improves quality control and analysis, showing increased sensitivity in peak calling and differential analysis.