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Indiana University Bloomington

yuhze yeYuzhen Ye

Associate Professor, Informatics and Computing

Office: Informatics West,
Room 201B

Phone: 812/855-8562

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Lab Website


Ph.D Computational Biology, Shanghai Institute of Biochemistry, Chinese Academy of Sciences, China, 1996-2001
B.S in Molecular Biology, Nankai University, China, 1992-1996


Computational metagenomics, developing computational tools for the studies of the structure and function of microbial communities; protein structure comparison and prediction, function prediction using structure information; biological pathway reconstruction and pathway variant detection.

Peer Reviewed Publications

Quan Zhang, Mina Rho, Haixu Tang, Thomas G. Doak and Yuzhen Ye. CRISPR–Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes. Genome Biology, 14:R40 (2013)

Yu-Wei Wu, Thomas G. Doak and Yuzhen Ye. The gain and loss of chromosomal integron systems in the Treponema species. BMC Evolutionary Biology, 13:16 DOI: 10.1186/1471-2148-13-16 (2013)

Dazhi Jiao, Yuzhen Ye and Haixu Tang. Probabilistic inference of biochemical reactions in microbial communities from metagenomic sequences. PLoS Comput Biol 9(3): e1002981. doi:10.1371/journal.pcbi.1002981 (2013) 

Yu-Wei Wu, Mina Rho, Thomas G. Doak and Yuzhen Ye. Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics. Selected paper in the 12th European Conferences on Computational Biology (ECCB 2012); Bioinformatics, 28 (18): i363-i369 DOI: 10.1021/bi300140 (2012)

Yu-Wei Wu, Mina Rho, Thomas G. Doak, and Yuzhen Ye. Oral spirochetes implicated in dental diseases are widespread in normal human subjects and carry extremely diverse integron gene cassettes. Applied and Environmental Microbiology 78:5288-5296 (2012)

The Human Microbiome Project Consortium. Structure, function and diversity of the health human microbiome. Nature, 486, 207–214 (2012)

The Human Microbiome Project Consortium. A framework for human microbiome research. Nature, 486, 215–221 (2012)

Susan M. Huse, Yuzhen Ye, Yanjiao Zhou, and Anthony A. Fodor. A Core Human Microbiome as Viewed Through 16S rRNA Sequence Clusters. PLoS ONE 7(6): e34242. doi:10.1371/journal.pone.0034242 (2012)

Mina Rho, Yu-Wei Wu, Haixu Tang, Thomas G. Doak, and Yuzhen Ye. Diverse CRISPRs evolving in human microbiomes. PLoS Genetics, 8(6): e1002441. doi:10.1371/journal.pgen.1002441 (2012)

Mingjie Wang, Yuzhen Ye and Haixu Tang. A graph approach to the quantification of closely-related genomes in a microbial community. Journal of Computational Biology 19(6): 814–825. doi:10.1089/cmb.2012.0058 (2012)

Yongan Zhao, Haixu Tang and Yuzhen Ye. RAPSearch2: a fast and memory efficient protein similarity search tool for next generation sequencing data. Bioinformatics 28(1):125–126 (2012)

Quan Zhang, Thomas G. Doak and Yuzhen Ye. Artificial functional difference between microbial communities caused by length difference of sequencing reads. Proceedings of Pacific Symposium on Biocomputing (PSB) 2012, 259–70 (2012)

Yuzhen Ye, Jeong-Hyeon Choi, and Haixu Tang. RAPSearch: a fast protein similarity search tool for short reads. BMC Bioinformatics, 12:159 (2011)

Neethu Shah, Haixu Tang, Thomas G. Doak and Yuzhen Ye. Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics. Pac Symp Biocomput. 165–76 (2011)John K. Colbourne1, Michael E. Pfrender, ...,

Yuzhen Ye, ..., Jeffrey L. Boore. The Ecoresponsive Genome of Daphnia pulex. Science, 331(6017)555-561 (2011)