Girke Lab Research and Teaching Site

Eddie Cao



Graduate Student in Genetics, Computer Science (UCR) ChemGen IGERT Fellow



  • University of California, Riverside, CA - PhD in Computer Science, 2010 (expected)
  • National University of Singapore - Master of Engineering in Electrical and Computer Engineering, 2005
    • Thesis title: Distributed and Parallel Computing Techniques in Biomedical Engineering
  • Tsinghua University, Beijing, P.R.China - B.S in Electrical Engineering, 2003
    • Thesis title: Net-based Self-organized Anti-virus System Research

Research Interests

Algorithm, cheminformatics and bioinformatics. My research interests include graph matching, machine learning, information retrieval, similarity measure of chemical compound, and ligand- and receptor-based virtual screening of chemical compound libraries.


  • Cao Y, Jiang T, Girke T (2010) Accelerated Similarity Searching and Clustering of Large Compound Sets by Geometric Embedding and Locality Sensitive. Bioinformatics: epub.

  • Cao Y, Charisi A, Cheng LC, Jiang T, Girke T (2008) ChemmineR: A Compound Mining Framework for R. Bioinformatics: 24, 1733-1734.

  • Cao Y, Jiang T, Girke T (2008) A maximum common substructure-based algorithm for searching and predicting drug-like compounds. Bioinformatics: 24, i366-374.

  • John J. Irwin, Brian K. Shoichet, Michael M. Mysinger, Niu Huang, Francesco Colizzi, Pascal Wassam, Yiqun Cao (2009) Automated Docking Screens: A Feasibility Study. J Med Chem 52(18).


  • Cheminformatics algorithms: MCS, EI
  • Web services for cheminformatics: ChemMine Web Tools, EI
  • Databases: ChemMine, BAP DB
  • Environments: ChemmineR