Publications

  1. Dufault-Thompson K, Jian H, Cheng R, Li J, Wang F, and Zhang Y*. (2017) A genome-scale model of Shewanella piezotolerans simulates mechanisms of metabolic diversity and energy conservation. mSystems (ASM), 2, e00165-16.
  2. Steffensen JL, Dufault-Thompson K, and Zhang Y*. (2016). PSAMM: a portable system for the analysis of metabolic models. PLoS Computational Biology 12(2): e1004732. doi:10.1371/journal.pcbi.1004732.
  3. Zhang Y* and Sievert SM (2014) Pan-genome analyses identify lineage- and niche-specific markers of evolution and adaptation in Epsilonproteobacteria. Front. Microbiol. 5:110. doi: 10.3389/fmicb.2014.00110 (Featured in the Frontiers top viewed microbiology research articles)
  4. Zhang Y, Zagnitko O, Rodionova I, Osterman A, Godzik A. (2011) The FGGY carbohydrate kinase family: insights into the evolution of functional specificities. PLoS Computational Biology 7(12): e1002318.
  5. Kazanov MD, Igarashi Y, Eroshkin AM, Cieplak P, Ratnikov B, Zhang Y, Li Z, Godzik A, Osterman AL, Smith JW. (2011) Structural determinants of limited proteolysis. Journal of Proteome Research 10(8): 3642-51.
  6. Zhang Y, Thiele I, Weekes D, Li Z, Jaroszewski L, Ginalski K, Deacon AM, Wooley J, Lesley SA, Wilson IA, Palsson B, Osterman A, Godzik A. (2009) Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Science 325, 1544-1549. (Press releases)
  7. Burra PV, Zhang Y, Godzik A, Stec B. (2009) Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure. Proc. Natl. Acad. Sci. U. S. A. 106, 10505-10.
  8. Igarashi Y, Heureux E, Doctor KS, Talwar P, Gramatikova S, Gramatikoff K, Zhang Y, Blinov M, Ibragimova SS, Boyd S, Ratnikov B, Cieplak P, Godzik A, Smith JW, Osterman AL, Eroshkin AM. (2009). PMAP: databases for analyzing proteolytic events and pathways. Nucleic Acids Research 37, D611-8.
  9. Zhang Y, Stec B, and Godzik A. (2007). Between order and disorder in protein structures: analysis of “dual personality” fragments in proteins.Structure 15, 1141-1147. (Press releases)
  10. Igarashi Y, Eroshkin A, Gramatikova S, Gramatikoff K, Zhang Y, Smith JW, Osterman AL, and Godzik A. (2007). CutDB: a proteolytic event database. Nucleic Acids Research 35, D546-549.

*: Corresponding author