Chen Sun

  • Publications
  • Contact Info
  • Links
  • I am a final year Computer Science Ph.D. student at Pennsylvania State University.

    My research covers

    • Algorithms for Bioinformatics
    • Data Mining(Graph/Network Data, Big Text Data)
    • Machine Learning

    I design algorithms and tools for human genetic variants analysis, genome assembly, and transcriptome data analysis.
    I am lucky to have Paul Medvedev as my advisor.

    Selected Publications( Google Scholar)

    (* co-first author)
    1. Chen Sun and Paul Medvedev.
      Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.
      Bioinformatics, 2018. [preprint]
    2. Guanjue Xiang, Belinda Giardine, Lin An, Chen Sun, Cheryl Keller, Elisabeth Heuston, David Bodine, Ross Hardison, Yu Zhang.
      Snapshot: clustering and visualizing epigenetic history during cell differentiation.
      Submitted, under review. [preprint]
    3. Chen Sun*, Robert Harris*, Rayan Chikhi, Paul Medvedev.
      AllSome Sequence Bloom Trees.
      The 21th International Conference on Research in Computational Molecular Biology
      (RECOMB, 2017)
      journal version: Journal of Computational Biology, 2018.
      the result is reported by Cell Systems, 2017.
    4. Chen Sun, David Stein, Ke Wu, Joel Young.
      Distribution-level feature monitoring and consistency reporting.
      US Patent Pend.
    5. Yongbing Zhao*, Chen Sun*, Dongyu Zhao*, et al.
      PGAP-X: Extension on pan-genome analysis pipeline.
      BMC Genomics, 2017.
    6. Chen Sun and Paul Medvedev.
      VarMatch: Robust Matching of Small Variant Datasets Using Flexible Scoring Schemes.
      Bioinformatics, 2016.
      presented at Intelligent Systems for Molecular Biology (ISMB) HitSeq 2016.
    7. Arkarachai Fungtammasan, Guruprasad Ananda, Suzanne Hile, Marcia Su, Chen Sun, Robert Harris, Paul Medvedev, Kristin Eckert and Kateryna Makova.
      Accurate typing of short tandem repeats from genome-wide sequencing data and its applications.
      Genome Research, 2015.

    I am also a reviewer of peer review journals and conferences, including ISMB, RECOMB.

    Contact Information

    Useful Links


    One thing at a time: "If you chase two rabbits, you will catch neither one."


    Long-distance running (5k, 10k, chasing rabbit...)