All Faculty and Research Staff Publications

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2020
Gamba IM, Smith LM, Tran MB. On the wave turbulence theory for stratified flows in the ocean. Mathematical Models & Methods in Applied Sciences. 2020 ;30:105-137.
2019
Wetzel AN, Smith LM, Stechmann SN, Martin JE. Balanced and Unbalanced Components of Moist Atmospheric Flows with Phase Changes. Chinese Annals of Mathematics Series B. 2019 ;40:1005-1038.
Donnelly DP, Rawlins CM, DeHart CJ, Fornelli L, Schachner LF, Lin ZQ, Lippens JL, Aluri KC, Sarin R, Chen BF, et al. Best practices and benchmarks for intact protein analysis for top-down mass spectrometry. Nature Methods. 2019 ;16:587-594.
Spiniello M, Steinbrink MI, Cesnik AJ, Miller RM, Scalf M, Shortreed MR, Smith LM. Comprehensive in vivo identification of the c-Myc mRNA protein interactome using HyPR-MS. RNA. 2019 ;25:1337-1352.
Dai YX, Buxton KE, Schaffer LV, Miller RM, Millikin RJ, Scalf M, Frey BL, Shortreed MR, Smith LM. Constructing Human Proteoform Families Using Intact-Mass and Top-Down Proteomics with a Multi-Protease Global Post-Translational Modification Discovery Database. Journal of Proteome Research. 2019 ;18:3671-3680.
Wetzel AN, Smith LM, Stechmann SN. DISCONTINUOUS FRONTS AS EXACT SOLUTIONS TO PRECIPITATING QUASI-GEOSTROPHIC EQUATIONS. Siam Journal on Applied Mathematics. 2019 ;79:1341-1366.
Holden MT, Smith LM. Encrypted Oligonucleotide Arrays for Molecular Authentication. ACS Combinatorial Science. 2019 ;21:562-567.
Marsico DH, Smith LM, Stechmann SN. Energy Decompositions for Moist Boussinesq and Anelastic Equations with Phase Changes. Journal of the Atmospheric Sciences. 2019 ;76:3569-3587.
Miller RM, Millikin RJ, Hoffmann CV, Solntsev SK, Sheynkman GM, Shortreed MR, Smith LM. Improved Protein Inference from Multiple Protease Bottom-Up Mass Spectrometry Data. Journal of Proteome Research. 2019 ;18:3429-3438.
Schaffer LV, Tucholski T, Shortreed MR, Ge Y, Smith LM. Intact-Mass Analysis Facilitating the Identification of Large Human Heart Proteoforms. Analytical Chemistry. 2019 ;91:10937-10942.
Gemperline DC, Marshall RS, Lee KH, Zhao QZ, Hu WM, McLoughlin F, Scalf M, Smith LM, Vierstra RD. Proteomic analysis of affinity-purified 26S proteasomes identifies a suite of assembly chaperones in Arabidopsis. Journal of Biological Chemistry. 2019 ;294:17570-17592.
Hernandez-Duenas G, Smith LM, Stechmann SN. Weak- and strong-friction limits of parcel models: Comparisons and stochastic convective initiation time. Quarterly Journal of the Royal Meteorological Society. 2019 ;145:2272-2291.
2017
Dai YX, Shortreed MR, Scalf M, Frey BL, Cesnik AJ, Solntsev S, Schaffer LV, Smith LM. Elucidating Escherichia coil Proteoform Families Using Intact-Mass Proteomics and a Global PTM Discovery Database. Journal of Proteome Research. 2017 ;16:4156-4165.
Buxton KE, Kennedy-Darling J, Shortreed MR, Zaidan NZ, Olivier M, Scalf M, Sridharan R, Smith LM. Elucidating Protein-DNA Interactions in Human Alphoid Chromatin via Hybridization Capture and Mass Spectrometry. Journal of Proteome Research. 2017 ;16:3433-3442.
Knoener RA, Becker JT, Scalf M, Sherer NM, Smith LM. Elucidating the in vivo interactome of HIV-1 RNA by hybridization capture and mass spectrometry. Scientific Reports. 2017 ;7.
Li QY, Shortreed MR, Wenger CD, Frey BL, Schaffer LV, Scalf M, Smith LM. Global Post-Translational Modification Discovery. Journal of Proteome Research. 2017 ;16:1383-1390.
Aguilar-Hernandez V, Kim DY, Stankey RJ, Scalf M, Smith LM, Vierstra RD. Mass Spectrometric Analyses Reveal a Central Role for Ubiquitylation in Remodeling the Arabidopsis Proteome during Photomorphogenesis. Molecular Plant. 2017 ;10:846-865.
Dai Y, Kennedy-Darling J, Shortreed MR, Scalf M, Gasch AP, Smith LM. Multiplexed Sequence-Specific Capture of Chromatin and Mass Spectrometric Discovery of Associated Proteins. Analytical Chemistry. 2017 ;89:7841-7846.
Holden MT, Carter MCD, Ting SK, Lynn DM, Smith LM. Parallel DNA Synthesis on Poly(ethylene terephthalate). Chembiochem. 2017 ;18:1914-1916.
Proffitt JM, Glenn J, Cesnik AJ, Jadhav A, Shortreed MR, Smith LM, Kavanagh K, Cox LA, Olivier M. Proteomics in non-human primates: utilizing RNA-Seq data to improve protein identification by mass spectrometry in vervet monkeys. Bmc Genomics. 2017 ;18.
2016
Shortreed MR, Frey BL, Scalf M, Knoener RA, Cesnik AJ, Smith LM. Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements. Journal of Proteome Research. 2016 ;15:1213-1221.
Cesnik AJ, Shortreed MR, Sheynkman GM, Frey BL, Smith LM. Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy. Journal of Proteome Research. 2016 ;15:800-808.
Chen XS, Lu L, Mayer KS, Scalf M, Qian SM, Lomax A, Smith LM, Zhong XH. POWERDRESS interacts with HISTONE DEACETYLASE 9 to promote aging in Arabidopsis. eLife. 2016 ;5.
Li QY, Chang Z, Oliveira G, Xiong M, Smith LM, Frey BL, Welham NV. Protein turnover during in vitro tissue engineering. Biomaterials. 2016 ;81:104-113.
Sheynkman GM, Shortreed MR, Cesnik AJ, Smith LM. Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation. In: Bohn PW, Pemberton JE Vol. 9. Palo Alto: Annual Reviews; 2016. pp. 521-545.
Li QY, Uygun BE, Geerts S, Ozer S, Scalf M, Gilpin SE, Ott HC, Yarmush ML, Smith LM, Welham NV, et al. Proteomic analysis of naturally-sourced biological scaffolds. Biomaterials. 2016 ;75:37-46.
Keller MP, Paul PK, Rabaglia ME, Stapleton DS, Schueler KL, Broman AT, Ye SI, Leng N, Brandon CJ, Neto EC, et al. The Transcription Factor Nfatc2 Regulates beta-Cell Proliferation and Genes Associated with Type 2 Diabetes in Mouse and Human Islets. Plos Genetics. 2016 ;12.
2014
Guillen-Ahlers H, Shortreed MR, Smith LM, Olivier M. Advanced methods for the analysis of chromatin-associated proteins. Physiological Genomics. 2014 ;46:441-447.
Liu RR, Li QY, Smith LM. Detection of Large Ions in Time-of-Flight Mass Spectrometry: Effects of Ion Mass and Acceleration Voltage on Microchannel Plate Detector Response. Journal of the American Society for Mass Spectrometry. 2014 ;25:1374-1383.
Kennedy-Darling J, Guillen-Ahlers H, Shortreed MR, Scalf M, Frey BL, Kendziorski C, Olivier M, Gasch AP, Smith LM. Discovery of Chromatin-Associated Proteins via Sequence-Specific Capture and Mass Spectrometric Protein Identification in Saccharomyces cerevisiae. Journal of Proteome Research. 2014 ;13:3810-3825.
Wu CH, Holden MT, Smith LM. Enzymatic Fabrication of High-Density RNA Arrays. Angewandte Chemie-International Edition. 2014 ;53:13514-13517.
Jagtap PD, Johnson JE, Onsongo G, Sadler FW, Murray K, Wang YB, Shenykrnan GM, Bandhakavi S, Smith LM, Griffin TJ. Flexible and Accessible Workflows for Improved Proteogenomic Analysis Using the Galaxy Framework. Journal of Proteome Research. 2014 ;13:5898-5908.
Cesnik AJ, Shortreed MR, Sheynkman GM, Frey BL, Smith LM. In-Depth Identification of Protein Sequence Variants and Posttranslational Modifications in 10 Human Cell Lines. Molecular & Cellular Proteomics. 2014 ;13:S49-S49.
Sheynkman GM, Shortreed MR, Frey BL, Scalf M, Smith LM. Large-Scale Mass Spectrometric Detection of Variant Peptides Resulting from Nonsynonymous Nucleotide Differences. Journal of Proteome Research. 2014 ;13:228-240.
Kennedy-Darling J, Smith LM. Measuring the Formaldehyde Protein-DNA Cross-Link Reversal Rate. Analytical Chemistry. 2014 ;86:5678-5681.
Ladror DT, Frey BL, Scalf M, Levenstein ME, Artymiuk JM, Smith LM. Methylation of yeast ribosomal protein S2 is elevated during stationary phase growth conditions. Biochemical and Biophysical Research Communications. 2014 ;445:535-541.
Kennedy-Darling J, Holden MT, Shortreed MR, Smith LM. Multiplexed Programmable Release of Captured DNA. Chembiochem. 2014 ;15:2353-2356.
Rhoads TW, Rose CM, Bailey DJ, Riley NM, Molden RC, Nestler AJ, Merrill AE, Smith LM, Hebert AS, Westphall MS, et al. Neutron-Encoded Mass Signatures for Quantitative Top-Down Proteomics. Analytical Chemistry. 2014 ;86:2314-2319.

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