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Biochemistry and Biophysics

John Wrobel, PhD

Research Interests:

  • Breast Cancer Proteogenomics and Biomarker Assay Development for CPTAC (Clinical Proteomics Tumor Analysis Consortium)
  • Proteogenomics for the ENCODE (ENCyclopedia Of DNA Elements) project

Education:

  • Ph.D. Microbiology and Immunology (1996) University of North Carolina, Chapel Hill, NC
  • B.A. Biology (1987) College of the Holy Cross, Worcester, MA
  • A.A.S. Computer Programming (2008) Wake Technical Community College, Raleigh, NC
  • A.A.S. Database Management (2007) Wake Technical Community College, Raleigh, NC
  • Certification: Oracle PL/SQL Developer Certified Associate (OCA)

Professional Experience:

  • Research Associate (2013 – present), Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, Advisor: Dr. Xian Chen
  • Research Associate (2012 – 2013), Postdoctoral Research Associate (2011 – 2012), College of Arts and Sciences, Boise State University, Boise, ID, Advisor: Dr. Morgan Giddings,
  • Database Developer (2009 – 2010), Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC Advisor: Dr. Morgan Giddings
  • Database Developer (2006 – 2009) North Carolina Institute for Public Health University of North Carolina, Chapel Hill, NC
  • Research Associate (2003 – 2006) Postdoctoral Research Associate (1996 – 2003) Department of Microbiology and Immunology University of North Carolina, Chapel Hill, NC Advisor: Dr. Clyde A. Hutchison III

Publications:

  • Gunawardena, H.P., Feltcher, M.E., Wrobel, J.A., Gu, S., Braunstein, M., and Chen, X. (2013). Comparison of the Membrane Proteome of Virulent Mycobacterium tuberculosis and the Attenuated Mycobacterium bovis BCG Vaccine Strain by Label-Free Quantitative Proteomics. Journal of Proteome Research 12, 5463-5474.
  • Khatun, J., Yu, Y, Wrobel, J.A., Risk, B.A., Gunawardena, H.P., Secrest, A., Spitzer, W.J., Ling, X., Wang, L., Chen, X., and Giddings, M.C. (2013). Whole human genome proteogenomic mapping for ENCODE cell line data: identifying protein-coding regions. BMC Genomics 14, 141.
  • The ENCODE Project Consortium. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74.
  • Djebali, S. et al. (2012). Landscape of transcription in human cells. Nature 489, 101-108.
  • Wrobel, J.A., Conrad, M.J., Bloedon, E., Swanstrom, R., and Hutchison, C.A., III. (2000). Analysis of HIV type 1 Reverse Transcriptase: Comparing Sequences of Viral Isolates with Mutational Data. AIDS Research and Human Retroviruses 16, 2049-2054.
  • Wrobel, J.A., Chao, S.-F., Conrad, M.J., Merker, J.D., Swanstrom, R., Pielak, G.J., and Hutchison, C.A., III. (1998). A Genetic Approach for Identifying Critical Residues in the Fingers and Palm Subdomains of HIV-1 Reverse Transcriptase. Proc. Natl. Acad. Sci. USA 95, 638-645.
  • Hoffmann, G.R., Sprague, K.M., Wrobel, J.A., and Wroblewski, D.H. (1987). A Recombinagenic Effect of Strychnine in Salmonella typhimurium. Environmental and Molecular Mutagenesis 10, 27-33.

Invited Talks:

  • Proteogenomics for the ENCODE project: Investigating genome-wide translation. Midwest Mass Spectrometry Discussion Group, Washington University School of Medicine, St. Louis, Missouri (December 4, 2012).

Conference Abstracts:

  • Wrobel, J., Risk, B., Gunawardena, H., Fenyö, D., Ruggles, K., Davies, S., Ding, L., Townsend, R., Ellis, M., Giddings, M., and Chen, X. Proteogenomic analysis of patient derived xenograft mouse models of luminal and basal breast cancer subtyptes. (Abstract for Poster Session at The Clinical Proteomic Tumor Analysis Consortium First Annual Scientific Symposium: Connecting Genome Alterations to Cancer Biology with Proteomics, National Institutes of Health, Bethesda, Maryland, November 2013).
  • Meyer, M.R., Erdmann-Gilmore, P., Wrobel, J., Ruggles, K., Hoog, J., Li, S., Kitchens, R.T., Snider, J., Davies, S.R., Fenyö, D., Ellis, M.J., and Townsend, R.R. Development of Multiplex Parallel Reaction Monitoring Assays for the AKT Kinases and Activating Phosphorylation Sites in Patient-Derived Breast Cancer Xenografts. (Abstract for Poster Session at The Clinical Proteomic Tumor Analysis Consortium First Annual Scientific Symposium: Connecting Genome Alterations to Cancer Biology with Proteomics, National Institutes of Health, Bethesda, Maryland, November 2013).
  • Gunawardena, H., O’Brien, J., Wrobel, J., Xie, L., Wang, L., Davies, S., Li, S., Kitchens, R., Snider, J., Erdmann-Gilmore, P., Ruggles, K., Teubl, J., Fenyö, D., Townsend, R., Ellis, M., and Chen, X. A hybrid label-free quantitation (LFQ) and spike-in metabolic labeling for comprehensive quantitative coverage of both global and phosphoproteomic changes between breast cancer subtypes. (Abstract for Poster Session at The Clinical Proteomic Tumor Analysis Consortium First Annual Scientific Symposium: Connecting Genome Alterations to Cancer Biology with Proteomics, National Institutes of Health, Bethesda, Maryland, November 2013).
  • Wrobel, J., Gunawardena, H.P., Khatun, J., Risk, B., Yu, Y., Giddings, M.C., and Chen, X. Proteogenomics for the ENCODE project: Investigating genome-wide translation. (Abstract for Poster Session at 61st ASMS Conference on Mass Spectrometry and Allied Topics, Minneapolis, Minnesota, June 2013).
  • Wrobel, J., Khatun, J., Risk, B., Ellis, M., Giddings, M., and Townsend, R. (2011). Proteogenomic mapping of breast cancer amplicons reveals unannotated homologs of gene families. (Abstract for Poster Session at The Cancer Genome Atlas’ 1st Annual Scientific Symposium: Enabling Cancer Research Through TCGA, National Harbor, Maryland, November 2011).