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Staff Bio

Jie Zheng
Experience:
  • Web Application Developer / 1999 - 2001
    Loki Technologies Inc
  • Post-doctoral Researcher / 2009 - 2011
    University of Pennsylvania
  • Research Associate / 2012 - 2014
    University of Pennsylvania
  • Senior Research Investigator / 2015 - Present
    University of Pennsylvania
Education:
  • M.S. / Computer Sciences - 1999 - Towson University
  • Ph.D. / Biology - 2009 - Queen's University
Research Interests:
  • Ontology-based biomedical and clinical metadata standardization, biomedical and clinical data integration and sharing
  • New knowledge discovery based on ontology
  • Biomedical ontology development following OBO Foundry principles
Recent Publications:
  • Zheng J, Edelman SW, Tharmarajah G, Walker DW, Pletcher SD, Seroude L. (2005) Differential patterns of apoptosis in response to aging in Drosophila. PNAS 102:12083-88.
  • Poirier L, Shane A, Zheng J, and Seroude L. (2008) Characterization of the Drosophila Gene-Switch system in aging studies: a cautionary tale. Aging Cell 7: 758-770.
  • Martin I, Jones MA, Rhodenizer D, Zheng J, Warrick JM, Seroude L, Grotewiel M (2009) Sod2 knockdown in the musculature has whole-organism consequences in Drosophila. Free Radic. Biol. Med. 47, 803–813.
  • In alphabetic order: Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Soldatova LN, Stoeckert CJ Jr, Turner JA, Zheng J, OBI consortium. (2010) Modeling biomedical experimental processes with OBI. J Biomed Semantics. 1 Suppl 1:S7.
  • Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N, Zhukova A, Brazma A, Parkinson H. (2010) Modeling sample variables with an Experimental Factor Ontology. Bioinformatics. 26(8):1112-8.
  • Zheng J, Stoyanovich J, Manduchi E, Liu J, Stoeckert CJ Jr. (2011) AnnotCompute: annotation-based exploration and meta-analysis of genomics experiments. Database (Oxford). 2011:bar045.
  • Parikh PP, Zheng J, Logan-Klumper F, Stoeckert CJ Jr, Louis C, Topalis P, Protasio AV, Sheth AP, Carrington M, Berriman M, Sahoo SS. (2012) The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms. J Biomed Semantics. 2012 May 23;3(1):5.
  • Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ Jr, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, Birren B, Brinkac L, Bruno VM, Caler E, Chapman S, Collins FH, Cuomo CA, Di Francesco V, Durkin S, Eppinger M, Feldgarden M, Fraser C, Fricke WF, Giovanni M, Henn MR, Hine E, Hotopp JD, Karsch-Mizrachi I, Kissinger JC, Lee EM, Mathur P, Mongodin EF, Murphy CI, Myers G, Neafsey DE, Nelson KE, Nierman WC, Puzak J, Rasko D, Roos DS, Sadzewicz L, Silva JC, Sobral B, Squires RB, Stevens RL, Tallon L, Tettelin H, Wentworth D, White O, Will R, Wortman J, Zhang Y, Scheuermann RH. (2014) Standardized metadata for human pathogen/vector genomic sequences. PLoS One 9(6):e99979
  • Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, Schürer SC, Pang C, Malone J, Parkinson H, Liu Y, Takatsuki T, Saijo K, Masuya H, Nakamura Y, Brush MH, Haendel MA, Zheng J, Stoeckert CJ, Peters B, Mungall CJ, Carey TE, States DJ, Athey BD, He Y. (2014) CLO: The cell line ontology. J Biomed Semantics 5(37):10-1186.
  • Zheng J, Xiang Z, Stoeckert CJ, He Y. (2014) Ontodog: a web-based ontology community view generation tool. Bioinformatics, btu008.
  • Walls R L, Guralnick R, Deck J, Buntzman A, Buttigieg PL, Davies N, Denslow MW, Gallery RE, Parnell JJ, Osumi-Sutherland D, Robbins RJ, Rocca-Serra P, Wieczorek J, Zheng, J. (2014) Meeting report: advancing practical applications of biodiversity ontologies. Standards in Genomic Sciences, 9(1):17.
  • Xiang Z, Zheng J, Lin Y, He Y. (2015) Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns. J Biomed Semantics. J Biomed Semantics 6:4.
  • Rocca-Serra P, Walls R, Parnell J, Gallery R, Zheng J, Sansone SA, Gonzalez-Beltran A. (2015) Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach. Database: The Journal of Biological Databases and Curation 2015: bau132.
  • Gutierrez, J. B., Harb, O. S., Zheng, J., Tisch, D. J., Charlebois, E. D., Stoeckert, C. J., & Sullivan, S. A. (2015). A framework for global collaborative data management for malaria research. The American journal of tropical medicine and hygiene, 93(3 Suppl), 124-132.
  • Lin, Y., Zheng, J., & He, Y. (2016). VICO: Ontology-based representation and integrative analysis of Vaccination Informed Consent forms. Journal of biomedical semantics, 7(1), 1.
  • Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L. Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, Haendel MA, He Y, Heiskanen M, Hernandez-Boussard T, Jensen M, Lin Y, Lister AL, Lord P, Malone J, Manduchi E, McGee M, Morrison N, Overton JA, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Schober D, Smith B, Soldatova LN, Stoeckert CJ Jr, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, Zheng J.(2016). The Ontology for Biomedical Investigations. PloS one, 11(4), e0154556.
  • Brochhausen, M., Zheng, J., Birtwell, D., Williams, H., Masci, A. M., Ellis, H. J., & Stoeckert, C. J. (2016). OBIB-a novel ontology for biobanking. Journal of biomedical semantics, 7(1), 1.
  • Zheng, J., Harris, M. R., Masci, A. M., Lin, Y., Hero, A., Smith, B., & He, Y. (2016). The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis. Journal of Biomedical Semantics, 7(1), 53.

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