All Faculty and Research Staff Publications

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Lee JH, Mand MR, Kao CH, Zhou Y, Ryu SW, Richards AL, Coon JJ, Paull TT. ATM directs DNA damage responses and proteostasis via genetically separable pathways. Science Signaling. 2018 ;11.
Bottoms S, Dickinson Q, McGee M, Hinchman L, Higbee A, Hebert A, Serate J, Xie D, Zhang YP, Coon JJ, et al. Chemical genomic guided engineering of gamma-valerolactone tolerant yeast. Microbial Cell Factories. 2018 ;17.
Reidenbach AG, Kemmerer ZA, Aydin D, Jochem A, McDevitt MT, Hutchins PD, Stark JL, Stefely JA, Reddy T, Hebert AS, et al. Conserved Lipid and Small-Molecule Modulation of COQ8 Reveals Regulation of the Ancient Kinase-like UbiB Family. Cell Chemical Biology. 2018 ;25:154-+.
Hebert AS, Thoing C, Riley NM, Kwiecien NW, Shiskova E, Huguet R, Cardasis HL, Kuehn A, Eliuk S, Zabrouskov V, et al. Improved Precursor Characterization for Data-Dependent Mass Spectrometry. Analytical Chemistry. 2018 ;90:2333-2340.
Lapointe CP, Stefely JA, Jochem A, Hutchins PD, Wilson GM, Kwiecien NW, Coon JJ, Wickens M, Pagliarini DJ. Multi-omics Reveal Specific Targets of the RNA-Binding Protein Puf3p and Its Orchestration of Mitochondrial Biogenesis. Cell Systems. 2018 ;6:125-+.
Overmyer KA, Tyanova S, Hebert AS, Westphall MS, Cox J, Coon JJ. Multiplexed proteome analysis with neutron-encoded stable isotope labeling in cells and mice. Nature Protocols. 2018 ;13:293-306.
Riley NM, Coon JJ. The Role of Electron Transfer Dissociation in Modern Proteomics. Analytical Chemistry. 2018 ;90:40-64.
Riley NM, Westphall MS, Coon JJ. Sequencing Larger Intact Proteins (30-70 kDa) with Activated Ion Electron Transfer Dissociation. Journal of the American Society for Mass Spectrometry. 2018 ;29:140-149.
Riley NM, Westphall MS, Coon JJ. Activated Ion-Electron Transfer Dissociation Enables Comprehensive Top-Down Protein Fragmentation. Journal of Proteome Research. 2017 ;16:2653-2659.
Reidenbach AG, Kemmerer ZA, Aydin D, Jochem A, McDevitt MT, Hutchins PD, Stark JL, Stefely JA, Reddy T, Hebert AS, et al. Conserved Lipid and Small-Molecule Modulation of COQ8 Reveals Regulation of the Ancient Kinase-like UbiB Family. Cell Chemical Biology. 2017 .
Velsko IM, Overmyer KA, Speller C, Klaus L, Collins MJ, Loe L, Frantz LAF, Sankaranarayanan K, Lewis CM, Martinez JBR, et al. The dental calculus metabolome in modern and historic samples. Metabolomics. 2017 ;13.
Chung J, Wittig JG, Ghamari A, Maeda M, Dailey TA, Bergonia H, Kafina MD, Coughlin EE, Minogue CE, Hebert AS, et al. Erythropoietin signaling regulates heme biosynthesis. eLife. 2017 ;6.
Hewitt KJ, Katsumura KR, Matson DR, Devadas P, Tanimura N, Hebert AS, Coon JJ, Kim JS, Dewey CN, Keles S, et al. GATA Factor-Regulated Samd14 Enhancer Confers Red Blood Cell Regeneration and Survival in Severe Anemia. Developmental Cell. 2017 ;42:213-+.
Shishkova E, Kwiecien NW, Hebert AS, Westphall MS, Prenni JE, Coon JJ. Gender Diversity in a STEM Subfield - Analysis of a Large Scientific Society and Its Annual Conferences. Journal of the American Society for Mass Spectrometry. 2017 ;28:2523-2531.
Shishkova E, Zeng H, Liu FB, Kwiecien NW, Hebert AS, Coon JJ, Xu W. Global mapping of CARM1 substrates defines enzyme specificity and substrate recognition. Nature Communications. 2017 ;8.
Jayaraman D, Richards AL, Westphall MS, Coon JJ, Ane JM. Identification of the phosphorylation targets of symbiotic receptor-like kinases using a high-throughput multiplexed assay for kinase specificity. Plant Journal. 2017 ;90:1196-1207.
Riley NM, Westphall MS, Hebert AS, Coon JJ. Implementation of Activated Ion Electron Transfer Dissociation on a Quadrupole-Orbitrap-Linear Ion Trap Hybrid Mass Spectrometer. Analytical Chemistry. 2017 ;89:6358-6366.
Mondal A, Dawson AR, Potts GK, Freiberger EC, Baker SF, Moser LA, Bernard KA, Coon JJ, Mehle A. Influenza virus recruits host protein kinase C to control assembly and activity of its replication machinery. eLife. 2017 ;6.
Guo X, Niemi NM, Coon JJ, Pagliarini DJ. Integrative proteomics and biochemical analyses define Ptc6p as the Saccharomyces cerevisiae pyruvate dehydrogenase phosphatase. Journal of Biological Chemistry. 2017 ;292:11751-11759.
Potts GK, McNally RM, Blanco R, You JS, Hebert AS, Westphall MS, Coon JJ, Hornberger TA. A map of the phosphoproteomic alterations that occur after a bout of maximal-intensity contractions. Journal of Physiology-London. 2017 ;595:5209-5226.
Veling MT, Reidenbach AG, Freiberger EC, Kwiecien NW, Hutchins PD, Drahnak MJ, Jochem A, Ulbrich A, Rush MJP, Russell JD, et al. Multi-omic Mitoprotease Profiling Defines a Role for Oct1p in Coenzyme Q Production. Molecular Cell. 2017 ;68:970-+.
Leach FE, Riley NM, Westphall MS, Coon JJ, Amster IJ. Negative Electron Transfer Dissociation Sequencing of Increasingly Sulfated Glycosaminoglycan Oligosaccharides on an Orbitrap Mass Spectrometer. Journal of the American Society for Mass Spectrometry. 2017 ;28:1844-1854.
Riley NM, Hebert AS, Durnberger G, Stanek F, Mechtler K, Westphall MS, Coon JJ. Phosphoproteomics with Activated Ion Electron Transfer Dissociation. Analytical Chemistry. 2017 ;89:6367-6376.
Peuchen EH, Cox OF, Sun LL, Hebert AS, Coon JJ, Champion MM, Dovichi NJ, Huber PW. Phosphorylation Dynamics Dominate the Regulated Proteome during Early Xenopus Development. Scientific Reports. 2017 ;7.
Guo X, Niemi NM, Hutchins PD, Condon SGF, Jochem A, Ulbrich A, Higbee AJ, Russell JD, Senes A, Coon JJ, et al. Ptc7p Dephosphorylates Select Mitochondrial Proteins to Enhance Metabolic Function. Cell Reports. 2017 ;18:307-313.
Diaz JE, Morgan CW, Minogue CE, Hebert AS, Coon JJ, Wells JA. A Split-Abl Kinase for Direct Activation in Cells. 2017 ;24:1250-+.
Rush MJP, Riley NM, Westphall MS, Syka JEP, Coon JJ. Sulfur Pentafluoride is a Preferred Reagent Cation for Negative Electron Transfer Dissociation. Journal of the American Society for Mass Spectrometry. 2017 ;28:1324-1332.
Stefely JA, Licitra F, Laredj L, Reidenbach AG, Kemmerer ZA, Grangeray A, Jaeg-Ehret T, Minogue CE, Ulbrich A, Hutchins PD, et al. Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity. Molecular Cell. 2016 ;63:608-620.
Lera RF, Potts GK, Suzuki A, Johnson JM, Salmon ED, Coon JJ, Burkard ME. Decoding Polo-like kinase 1 signaling along the kinetochore-centromere axis. Nature Chemical Biology. 2016 ;12:411-U61.
Sato TK, Tremaine M, Parreiras LS, Hebert AS, Myers KS, Higbee AJ, Sardi M, McIlwain SJ, Ong IM, Breuer RJ, et al. Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae. Plos Genetics. 2016 ;12.
Riley NM, Mullen C, Weisbrod CR, Sharma S, Senko MW, Zabrouskov V, Westphall MS, Syka JEP, Coon JJ. Enhanced Dissociation of Intact Proteins with High Capacity Electron Transfer Dissociation. Journal of the American Society for Mass Spectrometry. 2016 ;27:520-531.
Riley NM, Bern M, Westphall MS, Coon JJ. Full-Featured Search Algorithm for Negative Electron-Transfer Dissociation. Journal of Proteome Research. 2016 ;15:2768-2776.
Ong RG, Higbee A, Bottoms S, Dickinson Q, Xie D, Smith SA, Serate J, Pohlmann E, Jones AD, Coon JJ, et al. Inhibition of microbial biofuel production in drought-stressed switchgrass hydrolysate. Biotechnology for Biofuels. 2016 ;9.
Dickinson Q, Bottoms S, Hinchman L, McIlwain S, Li S, Myers CL, Boone C, Coon JJ, Hebert A, Sato TK, et al. Mechanism of imidazolium ionic liquids toxicity in Saccharomyces cerevisiae and rational engineering of a tolerant, xylose-fermenting strain. Microbial Cell Factories. 2016 ;15.
Stefely JA, Kwiecien NW, Freiberger EC, Richards AL, Jochem A, Rush MJP, Ulbrich A, Robinson KP, Hutchins PD, Veling MT, et al. Mitochondrial protein functions elucidated by multi-omic mass spectrometry profiling. Nature Biotechnology. 2016 ;34:1191-+.
Horton JL, Martin OJ, Lai L, Riley NM, Richards AL, Vega RB, Leone TC, Pagliarini DJ, Muoio DM, Bedi KC, et al. Mitochondrial protein hyperacetylation in the failing heart. Jci Insight. 2016 ;1.
Floyd BJ, Wilkerson EM, Veling MT, Minogue CE, Xia CW, Beebe ET, Wrobel RL, Cho H, Kremer LS, Alston CL, et al. Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function. Molecular Cell. 2016 ;63:621-632.
Weisenhorn EMM, Erve TJ van 't, Riley NM, Hess JR, Raife TJ, Coon JJ. Multi-omics Evidence for Inheritance of Energy Pathways in Red Blood Cells. Molecular & Cellular Proteomics. 2016 ;15:3614-3623.
Potts GK, Voigt EA, Bailey DJ, Rose CM, Westphall MS, Hebert AS, Yin J, Coon JJ. Neucode Labels for Multiplexed, Absolute Protein Quantification. Analytical Chemistry. 2016 ;88:3295-3303.
Baughman JM, Rose CM, Kolumam G, Webster JD, Wilkerson EM, Merrill AE, Rhoads TW, Noubade R, Katavolos P, Lesch J, et al. NeuCode Proteomics Reveals Bap1 Regulation of Metabolism. Cell Reports. 2016 ;16:583-595.
Shishkova E, Hebert AS, Coon JJ. Now, More Than Ever, Proteomics Needs Better Chromatography. Cell Systems. 2016 ;3:321-324.
Kuang MC, Hutchins PD, Russell JD, Coon JJ, Hittinger CT. Ongoing resolution of duplicate gene functions shapes the diversification of a metabolic network. eLife. 2016 ;5.
Wilkerson EM, Johansson MW, Hebert AS, Westphall MS, Mathur SK, Jarjour NN, Schwantes EA, Mosher DF, Coon JJ. The Peripheral Blood Eosinophil Proteome. Journal of Proteome Research. 2016 ;15:1524-1533.
Riley NM, Coon JJ. Phosphoproteomics in the Age of Rapid and Deep Proteome Profiling. Analytical Chemistry. 2016 ;88:74-94.
Marx H, Minogue CE, Jayaraman D, Richards AL, Kwiecien NW, Siahpirani AF, Rajasekar S, Maeda J, Garcia K, Del Valle-Echevarria AR, et al. A proteomic atlas of the legume Medicago truncatula and its nitrogen-fixing endosymbiont Sinorhizobium meliloti. Nature Biotechnology. 2016 ;34:1198-+.
Riley NM, Hebert AS, Coon JJ. Proteomics Moves into the Fast Lane. Cell Systems. 2016 ;2:142-143.
Sarks C, Higbee A, Piotrowski J, Xue SS, Coon JJ, Sato TK, Jin MJ, Balan V, Dale BE. Quantifying pretreatment degradation compounds in solution and accumulated by cells during solids and yeast recycling in the Rapid Bioconversion with Integrated recycling Technology process using AFEX (TM) corn stover. Bioresource Technology. 2016 ;205:24-33.
Xue L, Blythe EE, Freiberger EC, Mamrosh JL, Hebert AS, Reitsma JM, Hess S, Coon JJ, Deshaies RJ. Valosin-containing protein (VCP)-Adaptor Interactions are Exceptionally Dynamic and Subject to Differential Modulation by a VCP Inhibitor. Molecular & Cellular Proteomics. 2016 ;15:2970-2986.