Miller, S., Rizzo A.D. and Waldbauer, J.R. (in revision) Postnovo: Post-Processing Enables Accurate and FDR- Controlled De Novo Peptide Sequencing. Journal of Proteome Research.

Ma, X., Coleman, M.L. and Waldbauer, J.R. Distinct molecular signatures in dissolved organic matter produced by viral lysis of marine cyanobacteria. In press, Environ Microbiol doi: 10.1111/1462‐2920.14338.

Waldbauer, J.R., Zhang, L., Rizzo, A. and Muratore, D. (2017) diDO-IPTL: A Peptide-Labeling Strategy for Precision Quantitative Proteomics. Analytical Chemistry 89: 11498-11504.

Schwartz, M., Waldbauer, J.R., Zhang, L. and Pan, T. (2016) Global tRNA misacylation induced by anaerobiosis and antibiotic exposure broadly increases stress resistance in Escherichia coli. Nucleic Acids Research 44: 10292-10303.

Moran, M.A., Kujawinski, E.B., Stubbins, A., Fatland, R., Aluwihare, L.I., Buchan, A., Crump, B.C., Dorrestein, P.C., Dyhrman, S.T., Hess, N.J., Howe, B., Longnecker, K., Medeiros, P.M., Niggemann, J., Obernosterer, I., Repeta, D.J., Waldbauer, J.R. (2016) Deciphering ocean carbon in a changing world. PNAS doi:10.1073/pnas.1514645113.

Waldbauer, J.R.*, Rodrigue, S.*, Coleman, M.L. and Chisholm, S.W. (2012) Transcriptome and proteome dynamics of a light-dark synchronized bacterial cell cycle. PLoS ONE 7: e43432. (*co-first authors)

Waldbauer, J.R., Newman, D.K. and Summons, R.E. (2011) Microaerobic steroid biosynthesis and the molecular fossil record of Archean life. Proceedings of the National Academy of Sciences 108: 13409-13414.
    Awarded the Cozzarelli Prize for Physical and Mathematical Sciences

Waldbauer, J.R., Sherman, L.S., Sumner, D.Y. and Summons, R.E. (2009) Late Archean molecular fossils from the Transvaal Supergroup record the antiquity of microbial diversity and aerobiosis. Precambrian Research 169: 28-47.

Frias-Lopez, J., Thompson, A.W., Waldbauer, J.R. and Chisholm, S.W. (2009) Use of stable isotope labeled cells to identify active grazers of picocyanobacteria in ocean surface waters. Environmental Microbiology 11: 512-525.

Martínez, A., Bradley, A.S., Waldbauer, J.R., Summons, R.E. and DeLong, E.F. (2007) Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host. Proceedings of the National Academy of Sciences 104: 5590-5595.

Knoll, A.H., Summons, R.E., Waldbauer, J.R. and Zumberge, J.E. (2007) The Geological Succession of Primary Producers in the Oceans. In The Evolution of Primary Producers in the Sea, P.G. Falkowski and A.H. Knoll, eds. Academic Press, p. 133-163.

Sherman, L.S., Waldbauer, J.R. and Summons, R.E. (2007) Improved methods for isolating and validating indigenous biomarkers in Precambrian rocks. Organic Geochemistry 38: 1987-2000.

Hayes, J.M. and Waldbauer, J.R. (2006) The carbon cycle and associated redox processes through time. Philosophical Transactions of the Royal Society B 361: 931-950.

Summons, R.E., Bradley, A.S., Jahnke, L.L. and Waldbauer, J.R. (2006) Steroids, triterpenoids and molecular oxygen. Philosophical Transactions of the Royal Society B 361: 951-968.

Chamberlain, C.P., Waldbauer, J.R., Fox-Dobbs, K., Newsome, S.D., Koch, P.L., Smith, D.R., Church, M.E., Chamberlain, S.D., Sorenson, K.J. and Risebrough, R. (2005) Pleistocene to recent dietary shifts in California condors. Proceedings of the National Academy of Sciences 102: 16707-16711.