Publications

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Journal Article
Guillen-Ahlers H., Shortreed M.R, Smith L.M, Olivier M..  2014.  Advanced methods for the analysis of chromatin-associated proteins. Physiological Genomics. 46:441-447.
Rabaglia M.E, Gray-Keller M.P, Frey B.L, Shortreed M.R, Smith L.M, Attie A.D.  2005.  alpha-Ketoisocaproate-induced hypersecretion of insulin by islets from diabetes-susceptible mice. American Journal of Physiology - Endocrinology & Metabolism. 289:E218-E224.
Chen S.Y, Zheng T., Shortreed M.R, Alexander C., Smith L.M.  2007.  Analysis of cell surface carbohydrate expression patterns in normal and tumorigenic human breast cell lines using lectin arrays. Analytical Chemistry. 79:5698-5702.
Sheynkman G.M, Shortreed M.R, Frey B.L, Smith L.M.  2013.  Discovery and Mass Spectrometric Analysis of Novel Splice-junction Peptides Using RNA-Seq. Molecular & Cellular Proteomics. 12:2341-2353.
Kennedy-Darling J., Guillen-Ahlers H., Shortreed M.R, Scalf M., Frey B.L, Kendziorski C., Olivier M., Gasch A.P, Smith L.M.  2014.  Discovery of Chromatin-Associated Proteins via Sequence-Specific Capture and Mass Spectrometric Protein Identification in Saccharomyces cerevisiae. Journal of Proteome Research. 13:3810-3825.
Shortreed M.R, Frey B.L, Scalf M., Knoener R.A, Cesnik A.J, Smith L.M.  2016.  Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements. Journal of Proteome Research. 15:1213-1221.
Shortreed M.R, Wenger C.D, Frey B.L, Sheynkman G.M, Scalf M., Keller M.P, Attie A.D, Smith L.M.  2015.  Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search. Journal of Proteome Research. 14:4714-4720.
Li Q., Shortreed M.R, Wenger C.D, Frey B.L, Schaffer L.V, Scalf M., Smith L.M.  2017.  Global Post-Translational Modification Discovery. J Proteome Res.
Cesnik A.J, Shortreed M.R, Sheynkman G.M, Frey B.L, Smith L.M.  2016.  Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy. Journal of Proteome Research. 15:800-808.
Guillen-Ahlers H., Rao P.K, Levenstein M.E, Kennedy-Darling J., Perumalla D.S, Jadhav A.Y, Glenn J.P, Ludwig-Kubinski A., Drigalenko E., Montoya M.J et al..  2016.  HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae. Genomics. 107:267-273.
Shortreed M.R, Lamos S.M, Frey B.L, Phillips M.F, Patel M., Belshaw P.J, Smith L.M.  2006.  Ionizable isotopic labeling reagent for relative quantification of amine metabolites by mass spectrometry. Analytical Chemistry. 78:6398-6403.
Lockett M.R, Shortreed M.R, Smith L.M.  2007.  Molecular beacon-style hybridization assay for quantitative analysis of surface invasive cleavage reactions. Analytical Chemistry. 79:6031-6036.
Torde R.G, Therrien A.J, Shortreed M.R, Smith L.M, Lamos S.M.  2013.  Multiplexed Analysis of Cage and Cage Free Chicken Egg Fatty Acids Using Stable Isotope Labeling and Mass Spectrometry. Molecules. 18:14977-14988.
Kennedy-Darling J., Holden M.T, Shortreed M.R, Smith L.M.  2014.  Multiplexed Programmable Release of Captured DNA. Chembiochem. 15:2353-2356.
Chen Y., Shortreed M.R, Olivier M., Smith L.M.  2005.  Parallel single nucleotide polymorphism genotyping by surface invasive cleavage with universal detection. Analytical Chemistry. 77:2400-2405.
Nie B., Shortreed M.R, Smith L.M.  2006.  Quantitative detection of individual cleaved DNA molecules on surfaces using gold nanoparticles and scanning electron microscope imaging. Analytical Chemistry. 78:1528-1534.
Nie B., Shortreed M.R, Smith L.M.  2005.  Scoring single-nucleotide polymorphisms at the single-molecule level by counting individual DNA cleavage events on surfaces. Analytical Chemistry. 77:6594-6600.
Wu C.H, Chen S.Y, Shortreed M.R, Kreitinger G.M, Yuan Y., Frey B.L, Zhang Y., Mirza S., Cirillo L.A, Olivier M. et al..  2011.  Sequence-Specific Capture of Protein-DNA Complexes for Mass Spectrometric Protein Identification. Plos One. 6
Peelen D., Kodoyianni V., Lee J., Zheng T., Shortreed M.R, Smith L.M.  2006.  Specific capture of mammalian cells by cell surface receptor binding to ligand immobilized on gold thin films. Journal of Proteome Research. 5:1580-1585.
Lu M.C, Hall J.G, Shortreed M.R, Wang L.M, Berggren W.T, Stevens P.W, Kelso D.M, Lyamichev V., Neri B., Skinner J.L et al..  2002.  Structure-specific DNA cleavage on surfaces. Journal of the American Chemical Society. 124:7924-7931.
Chen Y., Shortreed M.R, Peelen D., Lu M.C, Smith L.M.  2004.  Surface amplification of invasive cleavage products. Journal of the American Chemical Society. 126:3016-3017.
Lu M.C, Shortreed M.R, Hall J.G, Wang L.M, Berggren T., Stevens P.W, Kelso D.M, Lyamichev V., Neri B., Smith L.M.  2002.  A surface invasive cleavage assay for highly parallel SNP analysis. Human Mutation. 19:416-422.
Shortreed M.R, Chang S.B, Hong D.G, Phillips M., Campion B., Tulpan D.C, Andronescu M., Condon A., Hoos H.H, Smith L.M.  2005.  A thermodynamic approach to designing structure-free combinatorial DNA word sets. Nucleic Acids Research. 33:4965-4977.
Tulpan D., Andronescu M., Chang S.B, Shortreed M.R, Condon A., Hoos H.H, Smith L.M.  2005.  Thermodynamically based DNA strand design. Nucleic Acids Research. 33:4951-4964.