I am a Ph.D. candidate[CV] at WashU, advised by Dr. Jeremy Buhler. My current research interest include but not limited to
  • Sequence Comparison
  • Phylogenetics
  • Computational Complexity
Other areas/topics that I want to know more about, and very likely to work on in the future:
  • Natural Language Processing
  • Machine Learning
  • Information Retrieval




Projects


PhyMAIT(ongoing): A Software for Improving the Quality of Existing Multiple Sequence Alignments
Responsibilities: Algorithm design & implementation.
Results: higher alignment quality than most popular ab initio alignment programs.
Publication: H.Sun and J. Buhler, PhyMAIT - a Phylogenetic Multiple Alignment Improvement Tool (in preparation)

PhyMap(ongoing): Next-Generation Sequencing Read Mapping using Phylogenetic Footprint
Responsibilities: Algorithm design & implementation.
Results: more accurate than the most popular short read mapping tools.
Publication: H. Sun and J. Buhler, Next-Generation Sequencing Read Mapping using Phylogenetic Footprint. (in preparation)

PhyGRIT(ongoing): A Software for Genomic Rearrangement Inference
Responsibilities: Algorithm design & implementation.

PhyLAT(NSF Project): Next-generation Sequence Similarity Search Tool
Responsibilities: Algorithm design & implementation (LOC: 16K), and large-scale data processing.
Results: significantly more accurate than the world's most popular alignment program.
Publication: H.Sun and J.Buhler, PhyLAT - A Phylogenetic Local Alignment Tool, Oxford Bioinformatics, 2012 (IF: 4.926)

PhyloNet: A Software for Motif Discovery
Responsibilities: use of machine learning techniques to reduce program running time.
Results: reduced running time by 99%
Publication: Identifying the conserved network of cis-regulatory sites of a eukaryotic genome, PNAS, 2005






Publications


Journal Papers

H.Sun and J. Buhler, PhyMAIT - a Phylogenetic Multiple Alignment Improvement Tool (in preparation)

H. Sun and J. Buhler, Next-Generation Sequencing Read Mapping using Phylogenetic Footprint. (in preparation)

H. Sun and J. Buhler, PhyLAT - A Phylogenetic Local Alignment Tool (Oxford Bioinformatics, 2012, IF: 4.926).


Conference Papers

H. Sun, T. Liu, et. al., "Improved Exponential Time Lower Bound of Knapsack Problem Under BT Model". TAMC, 2007

H. Sun, H. Peng, et. al., "On Lower Bound of Worst Case Error Probability for Quantum Fingerprinting with Shared Entanglement" . arXiv:quant-ph/0606116v1, 2006

H. Sun and L. Zhang, "Research on Optimization Method for Extracting Parameters in BSIM3v3" . Annual Academic Conference of EECS, Peking Univ., 2003

H. Sun, "Problems in Mathematics and Their Relations to Computer Science" . Mathematics in Practice and Theory, Vol. 33, No. 1, 2003






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