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Hi there, welcome to my GitHub 👋

🐵 About me

  • Ph.D. candidate in Dr. David Koslicki's lab, Penn State University
  • Domain: Bioinformatics, Metagenomics, Genomics data science
  • Email: [email protected]
  • Resume

🐝 Currently working on

  • Metagenomic analysis and method development
  • Knowledge graph and graph learning

🏆 Selected projects:

  • Knowledge graph and graph-based genomic data science:
    1. MetagenomicKG: construction of a metagenomic-specific knowledge graph and how it can be used for metagenomic data mining.
    2. ARAX: a knowledge-graph-based computational reasoning tool for translational biomedicine.
  • Metagenomic analysis and algorithm development:
    1. CMash: a modified containment MinHash algorithm for multi-resolution k-mer-based similarity estimation.
    2. FracMinHash vs Syncmer: bridging the FracMinHash algorithm with syncmers for metagenomic analysis.
    3. FracMinHash for functional profiling: utilization of the FracMinHash algorithm for metagenomic functional profiles.
  • Genomic data analysis
    1. AIAP: an integrative pipeline for comprehensive analysis of ATAC-seq dataset implemented in Docker and Singularity.

⚒️ Tech stack

python R bash
git Github
Markdown YAML neo4j
mysql jekyll HTML5

Shaopeng Liu's Projects

Shaopeng Liu doesn’t have any public repositories yet.

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