Chen Sun

  • Publications
  • Academic Talks
  • Course Work
  • Contact Info
  • Links
  • I am a Ph.D. candidate majored in Computer Science and Engineering from Computer Science and Engineering Department at Pennsylvania State University. I am lucky to have Paul Medvedev as my advisor.

    My research interests are

    • Computational Biology and Bioinformatics
    • Information Retrieving in Big Data: Data Management, Indexing, Compression and Searching
    • Genomic Data Science

    The bioinformatics problem I am currently working on is about genomic variants(SNP, small INDEL, structure variations), and metagenomics.

    I believe, computational methods are promising tech for solving problems in biomedical sciences.

    Linkedin Profile of Chen Sun


    Publications

    (* co-first author)
    1. Chen Sun*, Robert S. Harris*, Rayan Chikhi, Paul Medvedev.
      AllSome Sequence Bloom Trees.
      The 21st Annual International Conference on Research in Computational Molecular Biology (RECOMB 2017) [Accepted Paper List] [preprint version]
    2. Chen Sun and Paul Medvedev.
      VarMatch: Robust Matching of Small Variant Datasets Using Flexible Scoring Schemes.
      Bioinformatics 2016, advance access
    3. 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.
    4. Yongbing Zhao, Jinlong Yin, Haiyan Guo, Yuyu Zhang, Wen Xiao, Chen Sun, Jiayan Wu, Xiaobo Qu, Jun Yu, Xumin Wang and Jingfa Xiao.
      The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng.
      Frontiers in plant science, 2014.
    5. 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, 2009.
    6. 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, 2009.
    7. 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.
    Citation Information on Google Scholar


    Academic Talks

  • Biological Data Analysis 2016 by Cold Spring Harbor Laboratory
  • Title: VarMatch: Robust Matching of Small Variant Datasets Using Flexible Scoring Schemes.

  • 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


    Quote

    "Tell me and I forget, teach me and I may remember, involve me and I learn."

    ― Benjamin Franklin