Yuzhen Ye

Prof. Yuzhen Ye is a Professor in the School of Informatics, Computing, and Engineering. Prof. Ye, obtained her B.Sc. in Molecular Biology at Nankai University in 1996 and her PhD in Computational Biology at the Shanghai Institute of Biochemistry in 2001. Before joining the School of Informatics, Computing, and Engineering in August 2007, Ye was a Research Assistant Professor in the Burnham Institute for Medical Research (2004-2007), and was a post-doc working with Prof. Adam Godzik in the same institution from 2001 to 2004. Prof. Ye is broadly interested in computational metagenomics, protein Bioinformatics (sequence, structure & function), and biological pathway reconstruction/analysis. Notably, she and her team develop new algorithms and tools using a subtractive assembly approaches for inferring disease-associated microbial genes and pathways from microbiome sequencing data.

Ye’s team has developed bioinformatics tools for functional metagenomics as well as metaproteomics, such as Fun4me and MinPath for functional metagenomic annotation and pathways reconstruction and FragGeneScan for gene prediction in short reads, contigs, or even complete genomes, as well as a  sister program TransGeneScan for finding genes in metatranscriptomic sequences. The also developed Graph2Pep and Graph2Pro, which are graph-centric tools for protein identification from MS/MS spectra data of microbial communities Gene prediction, and assembly and similarity search. Those tools are currently being heavily incorporated in metaproteomic pipelines and of great interest for the community.