Publications

Fernández Robledo JA, Yadavalli R, Allam B, Pales Espinosa E, Gerdol M, Greco S, Gomez-Chiarri M, Stevick RJ, Zhang Y, Heil C, Bishop-Bailey D, Metzger MJ. (2019) From the raw bar to the bench: Bivalves as models for human health. Developmental and Comparative Immunology 92, 260–282. doi:10.1016/j.dci.2018.11.020.

Pimentel ZT§ and Zhang Y*. (2018) Evolution of the natural transformation protein, ComEC, in Bacteria. Frontiers in Microbiology 9:2980. doi:10.3389/fmicb.2018.02980.

Mokszycki ME, Leatham-Jensen M, Steffensen JL, Zhang Y, Krogfelt KA, Caldwell ME, Conway T, and Cohen PS. (2018) A Simple In Vitro Gut Model for Studying the Interaction between Escherichia coli and the Intestinal Commensal Microbiota in Cecal Mucus. Applied and Environmental Microbiology. doi:10.1128/AEM.02166-18.

Steffensen JL§, Dufault-Thompson K§, Zhang Y*. (2018) FindPrimaryPairs: An efficient algorithm for predicting element-transferring reactant/product pairs in metabolic networks. PLoS ONE 13(2): e0192891.

Dufault-Thompson K§, Steffensen JL§, Zhang Y* (2018) Using PSAMM for the curation and analysis of genome-scale metabolic models. In: Fondi M, editor. Metabolic Network Reconstruction and Modeling: Methods and Protocols. New York, NY: Springer New York. pp. 131–150. doi:10.1007/978-1-4939-7528-0_6. (Invited book chapter)

Waite DW, Vanwonterghem I, Rinke C, Parks DH, Zhang Y, Takai K, Sievert SM, Simon J, Campbell BJ, Hanson TE, Woyke T, Klotz MG and Hugenholtz P. (2018) Addendum: Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.). Frontiers in Microbiology 9:772. doi: 10.3389/fmicb.2018.00772

Waite DW, Vanwonterghem I, Rinke C, Parks DH, Zhang Y, Takai K, Sievert SM, Simon J, Campbell BJ, Hanson TE, Woyke T, Klotz MG, Hugenholtz P. (2017) Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.). Frontiers in Microbiology. 8:682.

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. (Press release)

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.

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)

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.

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.

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)

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.

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.

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)

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 
§: Zhang lab trainees