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



Associate Professor


Contact Information Office: G6411YEUNG
Phone: 34427612
Email: yannisun@cityu.edu.hk
Web: Personal website

Research Interests Bioinformatics, deep learning for genomic data



Yanni Sun is an Associate Professor in the Department of Electrical 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., M.S. degrees from Xi'an JiaoTong University (China), and the Ph.D. degree from Washington University in Saint Louis, USA, all in Computer Science.
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.


Awards and Achievements 2010 “NSF CAREER Award (USA) ” National Science Foundation.
2019 “Outstanding Teacher Award” Electrical Engineering Department, City University of Hong Kong. Department teaching award.
2021 “Outstanding Teacher Award” Electrical Engineering Department, City University of Hong Kong. Department teaching award.



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 Grants Viral metagenomic sequencing as a broad-spectrum pathogen detection technology for viral diseases, ITF-MRP, Apr 2021 - Dec 2024, Yanni Sun (PI), Mang Shi (Co-I), Sibo Wang (Co-I).
Strain-level composition analysis for RNA viral sequencing data, Hong Kong RGC RGF, Amount: HKD $838,393, Jan 2021 - Dec 2024, Yanni Sun (PI).
Characterizing quasispecies of known and novel viruses from metagenomic data, Hong Kong RGC RGF, Amount: HKD $731,089, 1 Jan 2020 - 31 Dec 2022, Yanni Sun (PI).
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).



Publications Show All Publications Show Prominent Publications
Journal Li, Yang. , Jiang, Ning. & Sun, Yanni. (Oct 2021). AnnoSINE: a new SINE annotation tool for plant genomes.
Shang, Jiayu. , Jiang, Jingzhe. & Sun, Yanni. (Jul 2021). Bacteriophage classification for assembled contigs using Graph Convolutional Network. Bioinformatics (also appeared in ISMB/ECCB 2021).
Shang, Jiayu. & Sun, Yanni. (May 2021). CHEER: HierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning. Methods.
Guo, Jiarong. , Quensen, John. F. , Sun, Yanni. , Wang, Qiong. , Brown, Titus. C. , Cole, James. R. & Tiedje, James. M. (Oct 2019). Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes. Frontiers in Genetics.
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.


Conference Paper Shang, Jiayu. , Jiang, Jinzhe. & Sun, Yanni. (summer Jul 2021). Bacteriophage classification for assembled contigs using Graph Convolutional Network. ISMB/ECCB 2021 (acceptance rate 18%).
Lei, Jikai. & Sun, Yanni. (Sep 2016). Assemble CRISPRs from metagenomic sequencing data. The 15th European Conference on Computational Biology (ECCB 2016).
Du, Nan. & Sun, Yanni. (Sep 2016). Improve homology search sensitivity of PacBio data by correcting frameshifts. The 15th European Conference on Computational Biology (ECCB 2016).
Yuan, Cheng. , Lei, Jikai. , Cole, James. R. & Sun, Yanni. (Jul 2015). Reconstructing 16S rRNA genes in metagenomic data. The 23rd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2015).
Sun, Yanni. & Buhler, Jeremy. (Jan 2006). Designing patterns for profile HMM search. The 5th European Conference on Computational Biology (ECCB06).
Sun, Yanni. & Buhler, Jeremy. (Mar 2004). Designing multiple simultaneous seeds for DNA similarity search. The Eighth Annual International Conference on Computational Molecular Biology (RECOMB04).
(Apr 2003). Designing seeds for similarity search in genomic DNA. The Seventh Annual International Conference on Computational Molecular Biology (RECOMB03).




Last update date : 23 Jan 2022