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Indiana University Bloomington

yuhze yeYuzhen Ye

Assistant Professor

Office: Informatics West,
Room 201B

Phone: 812/855-8562

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Lab Website

Education

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

Research

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

  1. Yu-Wei Wu and Yuzhen Ye. A novel abundance-based algorithm for binning metagenomic sequences using l-tuples. (Accepted in RECOMB 2010)
  2. Yuzhen Ye and Thomas G. Doak. A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes. PLoS Computational Biology, 2009, 5(8): e1000465. doi:10.1371/journal.pcbi.1000465 (Paper link)
  3. Yuzhen Ye and Haixu Tang. An ORFome assembly approach to metagenomics sequences analysis. J Bioinform Comput Biol. 2009, 7(3):455-71 (Paper link) (an older version in the Proceedings of CSB 2008)
  4. Mallika Veeramalai, Yuzhen Ye and Adam Godzik. TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model. BMC Bioinformatics 2008, 9:358 (Paper link)
  5. Linda Z. Holland, Ricard Albalat, .., Yuzhen Ye, .., Peter W.H. Holland. The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res. 18:1100-1111, 2008. (Paper link)
  6. Qing Zhang, Christian M. Zmasek, Larry J. Dishaw, M. Gail Mueller, Yuzhen Ye, Gary W. Litman and Adam Godzik. Novel genes dramatically alter regulatory network topology in amphioxus. Genome Biology 2008, 9:R123 (Paper link)
  7. Christian M. Zmasek, Qing Zhang, Yuzhen Ye and Adam Godzik. Surprising complexity of the ancestral apoptosis network, Genome Biology, 2007, 8:R226 (Paper link)
  8. Marc Awobuluyi, Jin Yang, Yuzhen Ye, Jon E Chatterton, Adam Godzik, Stuart A Lipton, and Dongxian Zhang. Subunit-specific roles of gycine-binding domains in activation of NR1/NR3 N-methyl-D-aspartate receptors. Molecular Pharmacology, 2007, 71(1):112-122 (Paper link)
  9. Yuzhen Ye, Zhanwen Li and Adam Godzik. Modeling and Analyzing three-dimensional structures of Human disease proteins. Proceedings of Pacific Symposium on Biocomputing, 2006, 11:439-450. PDF supplementary material
  10. Zhanwen Li, Yuzhen Ye and Adam Godzik. 2006. Flexible Structural Neighborhood: a database of protein structural similarities and alignments. Nucleic Acids Research, 34(Database issue):D277-80 Full paper at NAR Server
  11. Ross Overbeek, Tadhg Begley, et al. Yuzhen Ye, Olga Zagnitko, and Veronika Vonstein. 2005. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Research, 33: 5691-5702 Full paper at NAR
  12. Yuzhen Ye and Adam Godzik. 2005. Multiple flexible structure alignment using partial order graphs. Bioinformatics, 21(10):2362-2369 PubMed (color figures 4-6) (check out the server)
  13. Yuzhen Ye, Andrei Osterman, Ross Overbeek and Adam Godzik. 2005. Automatic detection of subsystem/pathway variants in genome analysis. Bioinformatics, 21 Suppl 1:i478-i486 (ISMB 2005) PubMed (check out the supplementary material at this link or this link)
  14. Yuzhen Ye and Adam Godzik. 2004. Database searching by flexible protein structure alignment. Protein Science, 13(7):1841-1850 PubMed Server
  15. Yuzhen Ye and Adam Godzik. 2004. FATCAT: a web server for flexible structure comparison and structure similarity searching. Nucleic Acid Research, 32:W582-585 PubMed Server
  16. Iddo Friedberg, Lukasz Jaroszewski, Yuzhen Ye and Adam Godzik. 2004. The interplay of fold recognition and experimental structure determination in structural genomics. Current Opinion in Structural Biology, 14(3):307-12 PubMed
  17. Yuzhen Ye and Adam Godzik. 2004. Comparative analysis of domain organization: a graph theory approach to comparison of domain distribution in genomes. Genome Research, 14:343-353 PubMed Server
  18. Dariusz Plewczynski, Leszek Rychlewski, Yuzhen Ye, Lukasz Jaroszewski and Adam Godzik. 2004. Integrated web service for improving alignment quality based on segments comparison. BMC Bioinformatics, 22;5(1):98. PubMed
  19. Yuzhen Ye and Adam Godzik. 2003. Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics, 19(suppl.2):ii246-ii255 PubMed
  20. Yuzhen Ye, Lukasz Jaroszewski, Weizhong Li, and Adam Godzik. 2003. A segment alignment approach to protein comparison. Bioinformatics, 19(6):742-749 PubMed
  21. Tong Liu, Ana Rojas, Yuzhen Ye and Adam Godzik. 2003. Homology modeling provides insights into the binding mode of the PAAD/DAPIN/pyrin domain, a fourth member of the CARD/DD/DED domain family. Protein Science, 12(9):1872-1881 PubMed
  22. Yuzhen Ye, Hao Fei and Dafu Ding. 2001. Rational redesign of inhibitors of furin/kexin processing protease. Acta Biochimica et Biophysica Sinica (Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao), 33(5):504-512 PubMed
  23. Hao Fei, Mingjuan Luo, Yuzhen Ye, Dafu Ding and Chengwu Chi 2001. The inhibitory activities of recombinant eglin C mutants on kexin and furin, using site-directed mutagenesis and molecular modeling. Acta Biochimica et Biophysica Sinica (Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao), 33(6):591-599 PubMed
  24. Qing Zhang, Yuzhen Ye and Dafu Ding. 2001. Structural basis of functional specificity of steroid receptors. Acta Biophysica sinica, 17(4): 685-694
  25. Yuzhen Ye, Tao Xie and Dafu Ding. 2000. Protein functional-group 3D motif and its applications. Chinese Science Bulletin, 45(22):2044-2051 PDF
  26. Sheng Yang, He Huang, Shiyun Li, Yuzhen Ye, Lin Wan, Fengwen Zhang and Zhongyi Yuan. 2000. Enhancing penicillin G acylase stability by site-directed mutagenesis. Acta Biochimica et Biophysica Sinica (Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao), 32(6):581-585 PubMed
  27. Yuzhen Ye, Haixu Tang and Dafu Ding. Predicting the solvated structures of protein mutants by self-consistent ensemble optimization. Acta Biophysica Sinica (1998), 14(2):311-317
  28. Haixu Tang, Yuzhen Ye and Dafu Ding. 1998. Flexible docking of proteins and "drug-like" ligands. Acta Biochimica et Biophysica Sinica (Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao), 30(6):623-630 PubMed
  29. Yuzhen Ye, Haixu Tang and Dafu Ding. 1998. Design of protein cores by screening combinatorial sequence library. Acta Biochimica et Biophysica Sinica (Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao), 30(5):525-529 PubMed
  30. Yuzhen Ye and Dafu Ding. 1999. Construction of protein scaffold database and its applications to functional protein design. Acta Biophysica Sinica, 15(4):751-757
  31. Yuzhen Ye, Haixu Tang and Dafu Ding. 1999. Engineering novel functional proteins: grafting active sites into natural scaffolds. Acta Biochimica et Biophysica Sinica, 31(3):303-308 PubMed