đź—¨ About Me
I am a full-time Lab Specialist at the Center for Public Health Genomics in University of Virginia School of Medicine advised by Prof. Chongzhi Zang.
Previously, I received my Master’s degree in Computer Science from Johns Hopkins University and Bachelor’s degree in Computer Science from Wenzhou-Kean University. I did my master thesis advised by Prof. Kimia Ghobadi at Johns Hopkins on multi-agent simulation. I was fortunate to work with Prof. Aloysius Wong’s group where I first stepped into the field of bioinformatics. In addition, I developed a deep learning model for RNA-ligand affinity prediction with Prof. Yanjun Li at UFL and later participated in developing a single-cell foundation model in Prof. Xiaojie Qiu’s Lab at Stanford.
I mainly work on the intersection of machine learning and biology in a broad scope. I am interested in foundation models and LLMs for science including single-cell, RNA, and protein, and how to use them to discover and interpret the biological mechanism.
Research Interests:
- Single-cell Multi-omics
- Deep learning for Cancer Biology and Chemical Biology
- AI for Drug Discovery
đź“– Educations
- 2022.08 - 2023.12, Master of Science in Engineering, Computer Science. Johns Hopkins University. Baltimore, MD
- 2018.08 - 2022.05, Bachelor of Science, Computer Science. Wenzhou-Kean University. Wenzhou, China
đź“° News
đź“ť Publications
Simulating Disease Spread During Disaster Scenarios
Shiyu Jiang, Heejoong Kim, Fabio Henrique Tanaka, Claus Aranha, Anna Bogdanova, Kimia Ghobadi, Anton Dahbura. The International Conference on Artificial Life, 2023.
HNOXPred: a web tool for the prediction of gas-sensing H-NOX proteins from amino acid sequence
Shiyu Jiang, Hemn Barzan Abdalla, Chuyun Bi, Yi Zhu, Xuechen Tian, Yixin Yang, Aloysius Wong. Bioinformatics, 2022
Deblur-yolo: Real-time object detection with efficient blind motion deblurring
Shen Zheng, Yuxiong Wu, Shiyu Jiang, Changjie Lu, Gaurav Gupta. International Joint Conference on Neural Networks, 2021
🧑‍💻 Research Experience
- 2023.06 - Present, Lab Specialist, Chongzhi Zang Lab, Center for Public Health Genomics, University of Virginia, Charlottesville, VA.
- 2023.08 - Present, Remote Research Assistant, Xiaojie Qiu Lab, Stanford School of Medicine, Remote.
- 2023.06 - 2024.03, Remote Research Assistant, Yanjun Li Lab, University of Florida College of Pharmacy, Remote.
- 2022.09 - 2023.12, Postgraduate Research Assistant, Kimia Ghobadi Lab, Johns Hopkins Withing School of Engineering, Baltimore, MD.
- 2021.08 - 2022.06, Undergraduate Research Assistant, Aloysius Wong Lab, Wenzhou-Kean University Department of Biology, Wenzhou, China.
🧑‍💻 Professional Experience
- 2022.06 - 2022.08, Software Engineer Intern, Alibaba Cloud - PolarDB, Hangzhou, China.
- 2021.09 - 2022.03, Applied Research Intern, Institute of Automation, Chinese Academy of Sciences, Beijing, China.
🔨 Tools
Model
- Koudou: an agent-based model that simulates the infectious diseases.
Web server
- HNOXPred (Prediction of Heme-Nitric oxide/OXygen domains): a web server that predicts gas-sensing H-NOX proteins from amino acid sequences.
Python Package
- SICER 2.0 (Spatial-clustering Identification of ChIP-Enriched Regions): a ChIP-Seq broad peak calling data analysis method.
🌎 Miscellaneous
Soccer (Visca Barça), Gym, Table tennis, Piano, Travel, etc.
