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John D. Bagert Curriculum vitae February 2017 Email: [email protected] Address: Frick Chemistry Laboratory, Princeton University Princeton, NJ 08544
EDUCATION 05/2015 Ph.D, Bioengineering, Engineering and Applied Science, California Institute of Technology, Pasadena, CA 2008 B.S., Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD RESEARCH EXPERIENCE 2015–present Post‐doctoral research with Prof. Tom Muir, Princeton University. 2009–2015 Doctoral research with Prof. David Tirrell, California Institute of Technology Thesis: “Quantitative, time‐resolved proteomic analysis using bio‐orthogonal non‐canonical amino acid tagging” 2009 Pre‐doctoral research rotation with Prof. Frances Arnold, California Institute of Technology Cellulase engineering by structure‐guided SCHEMA recombination 2008 Undergraduate research with Prof. Joelle Frechette, Johns Hopkins University Production and characterization of voltage‐responsive low‐density self‐assembled monolayers PUBLICATIONS Bagert, J. D., Sweredoski, M. J., Hess, S., and D. A. Tirrell. Identification of targets of the bacterial small RNA regulators using bio‐orthogonal non‐canonical amino acid tagging. In review. Dann, G. P., Liszczak, G., Bagert J. D., Bos, J., Brown, Z. Z., Müller, M. M., Nguyen, U. T. T., Panchenko, T., Pihl, R., Pollock, S. B., Wojcik, F., and T. W. Muir. Accessory Subunits of ISWI Family Chromatin Remodelers Interpret Nucleosome Modifications to Determine Substrate Preference. In review. 2016 Weller, C. E., Dhall, A., Ding, F., Linares, E., Whedon, S. D., Senger, N. A., Tyson, E. L., Bagert, J. D., Li, X., Augusto, O. and C. Chatterjee (2016). Aromatic thiol‐mediated cleavage of N‐O bonds enables chemical ubiquitylation of folded proteins. Nat. Commun. 7: 12979. 2016 Mahdavi, A., Hamblin, G.D., Jindal, G. A., Bagert, J. D., Dong, C., Sweredoski, M. J., Hess, S. Schuman, E. M., and D. A Tirrell (2016). Engineered Aminoacyl‐tRNA Synthetase for Cell‐Selective Analysis of Mammalian Protein Synthesis. J. Am. Chem. Soc. 138: 4278–81. 2016 Bagert, J. D., van Kessel, J. C., Sweredoski, M. J., Feng, L., Hess, S., Bassler, B. L., and D. A. Tirrell (2016). Time‐resolved proteomic analysis of quorum sensing in Vibrio harveyi. Chem. Sci. 7: 1797–806. 2015 Feng, L., Rutherford, S. T., Papenfort, K., Bagert, J. D., van Kessel, J. C., Tirrell, D. A., Wingreen, N. S., and B. L. Bassler (2015). A Qrr Noncoding RNA Deploys Four Different Regulatory Mechanisms to Optimize Quorum‐Sensing Dynamics. Cell 160: 228–40. 2014 Bagert, J. D., Xie, Y. J., Sweredoski, M. J., Qi, Y., Hess, S., Schuman E. M., and D. A. Tirrell (2014). Quantitative, Time‐Resolved Proteomic Analysis by Combining Bioorthogonal Noncanonical Amino Acid Tagging and Pulsed Stable Isotope Labeling by Amino Acids in Cell Culture. Mol. Cell Proteomics 13:1352–
8. 2011 Mingardon, F., Bagert, J. D., Maisonnier, C. Trudeau, D. L. and F. H. Arnold (2011). Comparison of Family 9 Cellulases from Mesophilic and Thermophilic Bacteria. Appl. Environ. Microbiol. 77: 1436–42. 2010 Szychowski, J., Mahdavi, A., Hodas, J. J., Bagert, J. D., Ngo, J. T., Landgraf, P., Dieterich, D. C., Schuman, E. M., and D. A. Tirrell (2010). Cleavable Biotin Probes for Labeling of Biomolecules via Azide‐Alkyne Cycloaddition. J. Am. Chem. Soc. 132: 18351–60. CONFERENCE PRESENTATIONS 2014 2014 2013 2012 2011 Bagert, J. D. and D. A. Tirrell. A quantitative proteomics approach to the identification of protein targets of regulatory bacterial RNAs. Cell Symposia: Regulatory RNAs, Berkeley CA, October 19–21. Bagert, J. D. and D. A. Tirrell. Noncanonical Amino Acids for Temporally‐Resolved Proteomic Profiling. AIChE Annual Meeting, Atlanta GA, November 16–21. Bagert, J. D., Xie, Y. J., Sweredoski, M. J., Qi, Y., Hess, S., Schuman E. M., and D. A. Tirrell. Quantitative, time‐resolved proteomics by combining BONCAT and pulsed SILAC. Bioorganic Chemistry Gordon Research Conference, Andover NH, June 9–14. Bagert, J. D. and D. A. Tirrell. A Quantitative Proteomics Approach to the Identification of Protein Targets of Small Bacterial RNAs. Protein Society, San Diego CA, August 5–8. Mahdavi, A., Babin, B. M., Yuet, K. P., Bagert, J. D., Szychowski, J., Ngo, J. T., and D. A. Tirrell. Noncanonical Amino Acids for Proteomic Profiling. Institute for Collaborative Biotechnologies Conference, Santa Barbara CA, February 8–9. TEACHING EXPERIENCE AND OUTREACH California Institute of Technology Instructor of Record: Biomolecular Engineering Lab, Prof. David Tirrell Mentor for graduate research students, Prof. David Tirrell Mentor for Summer Undergraduate Research Fellows, Prof. David Tirrell Caltech Classroom Connection: John Muir High School, Chemistry Teaching Assistant: Bioengineering Boot Camp, Prof. Rob Phillips Johns Hopkins University Computational and Experimental Design of Biomolecules Spring 2012, Spring 2013 Fall 2011, Winter 2012 Summer 2011, Summer 2012 Fall 2009 Summer 2009 Winter 2008 AWARDS AND HONORS 2017 2008 2008 2007 2007 2007 NIH/NIGMS Ruth L. Kirschstein National Research Service Award (NRSA) Individual Postdoctoral Fellowship (F32) Joseph L. Katz Award, Johns Hopkins University JHU Technology Fellowship, Johns Hopkins University Merck Bio‐Oriented Research Fellowship, Johns Hopkins University Provost’s Undergraduate Research Award, Johns Hopkins University Elenora Strub Muly Award, Johns Hopkins University RELATED PROFESSIONAL SKILLS Quantitative mass spectrometry‐based proteomics, bioinformatics and statistical analysis, peptide synthesis, protein semisynthesis, metabolic incorporation of non‐canonical amino acids, cloning, gene expression, protein purification, flow cytometry and fluorescence activated cell sorting (FACS), protein modification with chemical probes, quantitative PCR, western and northern blots, Python, R, MATLAB