Publications

Export 35 results:
Author Title [ Type(Asc)] Year
Filters: Author is Shortreed, M. R.  [Clear All Filters]
Journal Article
Millikin R.J, Solntsev S.K, Shortreed M.R, Smith L.M.  2018.  Ultrafast Peptide Label-Free Quantification with FlashLFQ. Journal of Proteome Research. 17:386-391.
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.
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.
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.
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, 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.
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.
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
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.
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.
Proffitt J.M, Glenn J., Cesnik A.J, Jadhav A., Shortreed M.R, Smith L.M, Kavanagh K., Cox L.A, Olivier M..  2017.  Proteomics in non-human primates: utilizing RNA-Seq data to improve protein identification by mass spectrometry in vervet monkeys. Bmc Genomics. 18
Cesnik A.J, Shortreed M.R, Schaffer L.V, Knoener R.A, Frey B.L, Scalf M., Solntsev S.K, Dai Y.X, Gasch A.P, Smith L.M.  2018.  Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families. Journal of Proteome Research. 17:568-578.
Leduc R.D, Schwammle V., Shortreed M.R, Cesnik A.J, Solntsev S.K, Shaw J.B, Martin M.J, Vizcaino J.A, Alpi E., Danis P. et al..  2018.  ProForma: A Standard Proteoform Notation. Journal of Proteome Research. 17:1321-1325.
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.
Kennedy-Darling J., Holden M.T, Shortreed M.R, Smith L.M.  2014.  Multiplexed Programmable Release of Captured DNA. Chembiochem. 15:2353-2356.
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.
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.
Cesnik A.J, Yang B., Truong A., Etheridge T., Spiniello M., Steinbrink M.I, Shortreed M.R, Frey B.L, Jarrard D.F, Smith L.M.  2018.  Long Noncoding RNAs AC009014.3 and Newly Discovered XPLAID Differentiate Aggressive and Indolent Prostate Cancers. Transl Oncol. 11:808-814.
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.
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.
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.
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.
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.
Schaffer L.V, Shortreed M.R, Cesnik A.J, Frey B.L, Solntsev S.K, Scalf M., Smith L.M.  2018.  Expanding Proteoform Identifications in Top-Down Proteomic Analyses by Constructing Proteoform Families. Analytical Chemistry. 90:1325-1333.
Solntsev S.K, Shortreed M.R, Frey B.L, Smith L.M.  2018.  Enhanced Global Post-translational Modification Discovery with MetaMorpheus. Journal of Proteome Research. 17:1844-1851.

Pages