Chen Sun

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

    My Ph.D. research covers Algorithms for Bioinformatics, Information Retrieving of Big-Data, and Machine Learning.

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

    Biomedical science is the cornerstone of human health and happiness. I believe computational methods are promising tech for solving biomedical problems.

    I also have a M.S. degree in Bioinformatics from University of Chinese Academy of Sciences.


    (* co-first author)
    1. Chen Sun and Paul Medvedev.
      Accelerating SNP genotyping from whole genome sequencing data for bedside diagnostics.
      Submitted. [preprint]
    2. 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 to appear in Journal of Comp. Bio.)
      the result is reported by Cell Systems.
    3. Chen Sun, David Stein, Ke Wu, Joel Young.
      Distribution-level feature monitoring and consistency reporting.
      Patent, all rights reserved by Microsoft, filed in 2017.
    4. Yongbing Zhao*, Chen Sun*, Dongyu Zhao*, et al.
      PGAP-X: Extension on pan-genome analysis pipeline.
      BMC Genomics, 2017.
    5. Chen Sun and Paul Medvedev.
      VarMatch: Robust Matching of Small Variant Datasets Using Flexible Scoring Schemes.
      Bioinformatics, 2016.
    6. 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.
    7. Yongbing Zhao, ..., Chen Sun(6 of 11 authors), ..., Jingfa Xiao.
      The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng.
      Frontiers in plant science, 2014 .
    8. Chen Sun, Jinglei Ren, Xiaojuan Zheng, Yonglong Wei and Xudong Zheng.
      JVMTI-based Model Enforcement on Java Platform for Model-Carrying Code.
      The 4th International Conference on Ubiquitous Information Technologies and Applications (CUTE 2009).
    9. Xudong Zheng, Jinglei Ren, Xiaojuan Zheng, Yonglong Wei and Chen Sun.
      Static Analysis of Java Source Code to Generate Security-Relevant Behavior Model Based on Extended Pushdown Automaton.
      The 2nd International Conference on Computer Science and its Applications ( CSA 2009 ).
    10. Yonglong Wei, Xiaojuan Zheng, Jinglei Ren, Xudong Zheng, Chen Sun and Zhenghao Li.
      Verification of Security-Relevant Behavior Model and Security Policy for Model-Carry Code.
      Security Technology, 2009.
    Chen Sun @ Google Scholar

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

    Academic Talks

  • Biological Data Analysis 2016 by Cold Spring Harbor Laboratory
  • Title: A fast, parallel, and memory-efficient method for the variant matching problem.

  • Genome in A Bottle Consortium Workshop 2016 by National Institute of Standards and Technology, U.S. Department of Commerce
  • Title: VarMatch: Robust Matching of Small Variant Datasets Using Flexible Scoring Schemes.

  • Intelligent Systems for Molecular Biology (ISMB 2016) High Throughput Sequencing Algorithms and Applications SIG by International Society for Computational Biology
  • Title: VarMatch: Robust Matching of Small Variant Datasets Using Flexible Scoring Schemes.

    Course Work

    I took the following graduate level courses as a matter of interest during my graduate study: I was also TA and Recitation Instructor for undergraduate level Algorithms and Data Structures course.

    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)