Publications
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Author Title [ Type
Filters: Author is Shortreed, M. R. [Clear All Filters]
Ultrafast Peptide Label-Free Quantification with FlashLFQ. Journal of Proteome Research. 17:386-391.
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2018. Thermodynamically based DNA strand design. Nucleic Acids Research. 33:4951-4964.
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2005. A thermodynamic approach to designing structure-free combinatorial DNA word sets. Nucleic Acids Research. 33:4965-4977.
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2005. A surface invasive cleavage assay for highly parallel SNP analysis. Human Mutation. 19:416-422.
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2002. Surface amplification of invasive cleavage products. Journal of the American Chemical Society. 126:3016-3017.
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2004. Structure-specific DNA cleavage on surfaces. Journal of the American Chemical Society. 124:7924-7931.
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2002. Specific capture of mammalian cells by cell surface receptor binding to ligand immobilized on gold thin films. Journal of Proteome Research. 5:1580-1585.
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2006. Sequence-Specific Capture of Protein-DNA Complexes for Mass Spectrometric Protein Identification. Plos One. 6
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2011. Scoring single-nucleotide polymorphisms at the single-molecule level by counting individual DNA cleavage events on surfaces. Analytical Chemistry. 77:6594-6600.
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2005. Quantitative detection of individual cleaved DNA molecules on surfaces using gold nanoparticles and scanning electron microscope imaging. Analytical Chemistry. 78:1528-1534.
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2006. Proteomics in non-human primates: utilizing RNA-Seq data to improve protein identification by mass spectrometry in vervet monkeys. Bmc Genomics. 18
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2017. Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families. Journal of Proteome Research. 17:568-578.
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2018. ProForma: A Standard Proteoform Notation. Journal of Proteome Research. 17:1321-1325.
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2018. Parallel single nucleotide polymorphism genotyping by surface invasive cleavage with universal detection. Analytical Chemistry. 77:2400-2405.
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2005. Multiplexed Programmable Release of Captured DNA. Chembiochem. 15:2353-2356.
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2014. Multiplexed Analysis of Cage and Cage Free Chicken Egg Fatty Acids Using Stable Isotope Labeling and Mass Spectrometry. Molecules. 18:14977-14988.
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2013. Molecular beacon-style hybridization assay for quantitative analysis of surface invasive cleavage reactions. Analytical Chemistry. 79:6031-6036.
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2007. Long Noncoding RNAs AC009014.3 and Newly Discovered XPLAID Differentiate Aggressive and Indolent Prostate Cancers. Transl Oncol. 11:808-814.
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2018. Ionizable isotopic labeling reagent for relative quantification of amine metabolites by mass spectrometry. Analytical Chemistry. 78:6398-6403.
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2006. HyCCAPP as a tool to characterize promoter DNA-protein interactions in Saccharomyces cerevisiae. Genomics. 107:267-273.
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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.
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2016. Global Post-Translational Modification Discovery. J Proteome Res.
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2017. Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search. Journal of Proteome Research. 14:4714-4720.
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2015. Expanding Proteoform Identifications in Top-Down Proteomic Analyses by Constructing Proteoform Families. Analytical Chemistry. 90:1325-1333.
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2018. Enhanced Global Post-translational Modification Discovery with MetaMorpheus. Journal of Proteome Research. 17:1844-1851.
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2018.