Yuzhen Ye

Dr. Ye is a Professor in the Computer Science Department at the Luddy School of Informatics, Computing, and Engineering at Indiana University Bloomington, where she has served as Department Chair since 2019. She earned her Ph.D. in Computational Biology from the Chinese Academy of Sciences in 2001.

Her research centers on bioinformatics and metagenomics, with a particular focus on developing algorithms and AI models to tackle complex biological problems. Recent contributions from her lab include DCTdomain, a domain-based embedding method enabled by protein language models for protein analysis; MicroKPNN, a knowledge-primed neural network for microbiome-based host phenotype prediction; and MetaProD, a tool for metaproteomics data analysis. Dr. Ye received the NSF CAREER Award in 2009, and her research has been continuously supported by grants from the NIH and NSF.

In addition to her research, Dr. Ye teaches courses such as Introduction to Computers and Programming, Data Mining, and Data Structures. She also enjoys engaging with pre-college students through a variety of outreach activities.

• Doctor of Philosophy in Computational Biology at Shanghai Institute of Biochemistry, Chinese Academy of Sciences, China, 2001
• Bachelor of Science in Molecular Biology at Nankai University, China, 1996

• Artificial Intelligence and Machine Learning
• Bioinformatics and Computational Biology
• Data Mining
• Data Science @Luddy
• Databases and Data Mining
• Health@Luddy
• Teaching and Learning @Luddy