Publications

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2016
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.
Gemperline D.C, Scalf M., Smith L.M, Vierstra R.D.  2016.  Morpheus Spectral Counter: A computational tool for label-free quantitative mass spectrometry using the Morpheus search engine. Proteomics. 16:920-924.
Chen X., Lu L., Mayer K.S, Scalf M., Qian S., Lomax A., Smith L.M, Zhong X..  2016.  POWERDRESS interacts with HISTONE DEACETYLASE 9 to promote aging in Arabidopsis. Elife. 5
Li Q.Y, Chang Z., Oliveira G., Xiong M., Smith L.M, Frey B.L, Welham N.V.  2016.  Protein turnover during in vitro tissue engineering. Biomaterials. 81:104-113.
Sheynkman G.M, Shortreed M.R, Cesnik A.J, Smith L.M.  2016.  Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation. 9:521-545.
Li Q.Y, Uygun B.E, Geerts S., Ozer S., Scalf M., Gilpin S.E, Ott H.C, Yarmush M.L, Smith L.M, Welham N.V et al..  2016.  Proteomic analysis of naturally-sourced biological scaffolds. Biomaterials. 75:37-46.
Keller M.P, Paul P.K, Rabaglia M.E, Stapleton D.S, Schueler K.L, Broman A.T, Ye S.I, Leng N., Brandon C.J, Neto E.C et al..  2016.  The Transcription Factor Nfatc2 Regulates β-Cell Proliferation and Genes Associated with Type 2 Diabetes in Mouse and Human Islets. PLoS Genet. 12(e1006466)
2017
Dai Y.X, Shortreed M.R, Scalf M., Frey B.L, Cesnik A.J, Solntsev S., Schaffer L.V, Smith L.M.  2017.  Elucidating Escherichia coil Proteoform Families Using Intact-Mass Proteomics and a Global PTM Discovery Database. Journal of Proteome Research. 16:4156-4165.
Buxton K.E, Kennedy-Darling J., Shortreed M.R, Zaidan N.Z, Olivier M., Scalf M., Sridharan R., Smith L.M.  2017.  Elucidating Protein-DNA Interactions in Human Alphoid Chromatin via Hybridization Capture and Mass Spectrometry. Journal of Proteome Research. 16:3433-3442.
Knoener R.A, Becker J.T, Scalf M., Sherer N.M, Smith L.M.  2017.  Elucidating the in vivo interactome of HIV-1 RNA by hybridization capture and mass spectrometry. Scientific Reports. 7
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.
Aguilar-Hernandez V., Kim D.Y, Stankey R.J, Scalf M., Smith L.M, Vierstra R.D.  2017.  Mass Spectrometric Analyses Reveal a Central Role for Ubiquitylation in Remodeling the Arabidopsis Proteome during Photomorphogenesis. Molecular Plant. 10:846-865.
Dai Y, Kennedy-Darling J, Shortreed MR, Scalf M, Gasch AP, Smith L.M.  2017.  Multiplexed Sequence-Specific Capture of Chromatin and Mass Spectrometric Discovery of Associated Proteins. Analytical Chemistry. 89:7841-7846.
Holden M.T, Carter M.CD, Ting S.K, Lynn D.M, Smith L.M.  2017.  Parallel DNA Synthesis on Poly(ethylene terephthalate). Chembiochem. 18:1914-1916.
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
2018
Chen X.S, Lu L., Qian S.M, Scalf M., Smith L.M, Zhong X.H.  2018.  Canonical and Noncanonical Actions of Arabidopsis Histone Deacetylases in Ribosomal RNA Processing. Plant Cell. 30:134-152.
Zaidan N.Z, Walker K.J, Brown J.E, Schaffer L.V, Scalf M., Shortreed M.R, Iyer G., Smith L.M, Sridharan R..  2018.  Compartmentalization of HP1 Proteins in Pluripotency Acquisition and Maintenance. Stem Cell Reports. 10:627-641.
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.
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.
Aebersold R., Agar J.N, Amster I.J, Baker M.S, Bertozzi C.R, Boja E.S, Costello C.E, Cravatt B.F, Fenselau C., Garcia B.A et al..  2018.  How many human proteoforms are there? Nature Chemical Biology. 14:206-214.
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.
Kim S.H, Stiles S.G, Feichtmeier J.M, Ramesh N., Zhan L.H, Scalf M.A, Smith L.M, Pandey U.B, Tibbetts R.S.  2018.  Mutation-dependent aggregation and toxicity in a Drosophila model for UBQLN2-associated ALS. Human Molecular Genetics. 27:322-337.
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.
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.
Smith L.M, Kelleher N.L.  2018.  Proteoforms as the next proteomics currency. Science. 359:1106-1107.

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