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Dr. SUN Yanni

PhD (Washington University in Saint Louis, USA); BS and MS (Xi'an JiaoTong University, China)

Associate Professor

Contact Information

Office: G6411 YEUNG
Phone: 34427612
Email: yannisun@cityu.edu.hk
Web: Personal website
Yanni Sun is an Associate Professor in the Department of Electronic Engineering at City University of Hong Kong. Before she joined CityU, she was an Associate Professor with tenure at Michigan State University (USA). She received the B.S. and M.S. degrees from Xi'an JiaoTong University (China), both in Computer Science. She received the Ph.D. degree in Computer Science from Washington University in Saint Louis, USA.

Her research interests include: computational biology, Bioinformatics, deep learning-based sequence analysis, BIG genomic data mining, algorithm design and software development. In particular, she is interested in applying computational models, algorithms, machine learning/deep learning/data mining methods to analyze biological data. She was a recipient of NSF CAREER Award (USA) in 2010 while she was working at MSU.

Award and Achievement

  • 2010 “NSF CAREER Award (USA) ” National Science Foundation.

Previous Experience

  • Sep 2008 - Aug 2018, Assistant and Associate Professor, Michigan State University, East Lansing, USA. Dr. Sun joined the Department of Computer Science and Engineering at MSU as an Assistant Professor in 2008. She was promoted to Associate Professor with tenure in 2015.

Research Grant

  • Intersecting computational and data science to address grand challenges in plant biology, National Science Foundation (USA), Estimated Amount: USD $3,000,000, Aug 2018 - Now, Shinhan Shiu (PI).
  • Transcriptional and Translational Regulation of Gene Expression by Gene Structure, Codon Usage and tRNAs in Grasses, National Science Foundation of USA, Amount: USD $2,561,080, Apr 2018 - Mar 2022, Kevin Childs (PI), Yanni Sun (Co-PI), Ning Jiang (Co-PI), Yinong Yang (Co-PI).
  • Developing an Effective Portable Annotation Engine for Plant Genomes, National Science Foundation of USA, Amount: USD $3,626,169, Nov 2011 - Oct 2016, Mark Yandell (PI), Yanni Sun (Co-PI), Ning Jiang (Co-PI), Shinhan Shiu (Co-PI), Kevin Childs (Co-PI).
  • The Ribosomal Database Project: Sequences and Tools for Microbial Analysis, Department of Energy (DOE), USA, Estimated Amount: USD $1,725,000, Sep 2011 - Aug 2016, James Cole (PI), James Tiedje (Co-PI), Yanni Sun (Co-PI), Charles Brown (Co-PI).
  • Deep sequence profiling of gRNA transcriptomes in two stages of Trypanosoma brucei, National Institutes of Health (NIH), USA, Amount: USD $152,000, Mar 2011 - Feb 2015, Donna Koslowsky (PI), Yanni Sun (Co-PI).
  • CAREER: New Technologies for Genome-Scale Comparative NcRNA Identification, National Science Foundation (NSF) of USA, Amount: USD $512,476, Jul 2010 - Jun 2017, Yanni Sun (PI).

Publication Show All Publications Show Prominent Publications


  • Chen, Jiao. , Zhao, Yingchao. & Sun, Yanni. (2018). De novo haplotype reconstruction in viral quasispecies using paired-end read guided path finding. Bioinformatics.
  • Techa-Angkoon, Prapaporn. , Lei, Jikai. & Sun, Yanni. (2017). A sensitive short read homology search tool for paired-end read sequencing data. BMC Bioinformatics.
  • Chen, Jiao. , Zhu, Dongxiao. & Sun, Yanni. (2017). Cap-seq reveals complicated miRNA transcriptional mechanisms in C. elegans and mouse. Quantitative Biology.
  • Park, Daewood. , Du, Nan. , Sun, Yanni. & Burton, Zachary. (2017). Rooted tRNAomes and Evolution of the Genetic Code. Transcription.
  • Kirby, Laura. , Sun, Yanni. , Judah, David. , Nowak, Scooter. & Koslowsky, Donna. (2016). Analysis of the Trypanosoma brucei EATRO 164 Bloodstream Guide RNA Transcriptome. PLOS Neglected Tropical Deceases.
  • Lei, Jikai. & Sun, Yanni. (2016). Assemble CRISPRs from metagenomic sequencing data. Bioinformatics.
  • Du, Nan. & Sun, Yanni. (2016). Improve homology search sensitivity of PacBio data by correcting frameshifts. Bioinformatics.
  • Achawayantakun, Rujira. , Chen, Jiao. , Zhang, Yuan. & Sun, Yanni. (2015). LncRNA-ID: Long non-coding RNA IDentification using balanced random forests. Bioinformatics.
  • Wang, Qiong. , Fish, Jordan. , Gilman, Mariah. , Sun, Yanni. , Brown, Titus. , Tiedje, James. & Cole, James. (2015). Xander: Employing a novel method for efficient gene-targeted metagenomic assembly. Microbiome.

Last update date : 15 Apr 2019