All Faculty and Research Staff Publications

Export 228 results:
Filters: Author is J. J. Coon  [Clear All Filters]
2014
Peterson AC, Balloon AJ, Westphall MS, Coon JJ. Development of a GC/Quadrupole-Orbitrap Mass Spectrometer, Part II: New Approaches for Discovery Metabolomics. Analytical Chemistry. 2014 ;86:10044-10051.
Parreiras LS, Breuer RJ, Narasimhan RA, Higbee AJ, La Reau A, Tremaine M, Qin L, Willis LB, Bice BD, Bonfert BL, et al. Engineering and Two-Stage Evolution of a Lignocellulosic Hydrolysate-Tolerant Saccharomyces cerevisiae Strain for Anaerobic Fermentation of Xylose from AFEX Pretreated Corn Stover. Plos One. 2014 ;9.
Honarpour N, Rose CM, Brumbaugh J, Anderson J, Graham RLJ, Sweredoski MJ, Hess S, Coon JJ, Deshaies RJ. F-box Protein FBXL16 Binds PP2A-B55 and Regulates Differentiation of Embryonic Stem Cells along the FLK1 Lineage. Molecular & Cellular Proteomics. 2014 ;13:780-791.
Rahimi A, Ulbrich A, Coon JJ, Stahl SS. Formic-acid-induced depolymerization of oxidized lignin to aromatics. Nature. 2014 ;515:249-52.
Bailey DJ, McDevitt MT, Westphall MS, Pagliarini DJ, Coon JJ. Intelligent Data Acquisition Blends Targeted and Discovery Methods. Journal of Proteome Research. 2014 ;13:2152-2161.
Lohman DC, Forouhar F, Beebe ET, Stefely MS, Minogue CE, Ulbrich A, Stefely JA, Sukumar S, Luna-Sanchez M, Jochem A, et al. Mitochondrial COQ9 is a lipid-binding protein that associates with COQ7 to enable coenzyme Q biosynthesis. Proceedings of the National Academy of Sciences of the United States of America. 2014 ;111:E4697-E4705.
Dingley SD, Polyak E, Ostrovsky J, Srinivasan S, Lee I, Rosenfeld AB, Tsukikawa M, Xiao R, Selak MA, Coon JJ, et al. Mitochondrial DNA Variant in COX1 Subunit Significantly Alters Energy Metabolism of Geographically Divergent Wild Isolates in Caenorhabditis elegans. Journal of Molecular Biology. 2014 ;426:2199-2216.
Brumbaugh J, Russell JD, Yu PZ, Westphall MS, Coon JJ, Thomson JA. NANOG Is Multiply Phosphorylated and Directly Modified by ERK2 and CDK1 In Vitro. Stem Cell Reports. 2014 ;2:18-25.
Merrill AE, Hebert AS, MacGilvray ME, Rose CM, Bailey DJ, Bradley JC, Wood WW, M. Masri E, Westphall MS, Gasch AP, et al. NeuCode Labels for Relative Protein Quantification. Molecular & Cellular Proteomics. 2014 ;13:2503-2512.
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.
Ulbrich A, Merrill AE, Hebert AS, Westphall MS, Keller MP, Attie AD, Coon JJ. Neutron-Encoded Protein Quantification by Peptide Carbamylation. Journal of the American Society for Mass Spectrometry. 2014 ;25:6-9.
Hebert AS, Richards AL, Bailey DJ, Ulbrich A, Coughlin EE, Westphall MS, Coon JJ. The One Hour Yeast Proteome. Molecular & Cellular Proteomics. 2014 ;13:339-347.
Ulbrich A, Bailey DJ, Westphall MS, Coon JJ. Organic Acid Quantitation by NeuCode Methylamidation. Analytical Chemistry. 2014 ;86:4402-4408.
Sun LL, Hebert AS, Yan XJ, Zhao YM, Westphall MS, Rush MJP, Zhu GJ, Champion MM, Coon JJ, Dovichi NJ. Over 10000 Peptide Identifications from the HeLa Proteome by Using Single-Shot Capillary Zone Electrophoresis Combined with Tandem Mass Spectrometry. Angewandte Chemie-International Edition. 2014 ;53:13931-13933.
Chasman D, Ho YH, Berry DB, Nemec CM, MacGilvray ME, Hose J, Merrill AE, Lee MV, Will JL, Coon JJ, et al. Pathway connectivity and signaling coordination in the yeast stress-activated signaling network. Molecular Systems Biology. 2014 ;10.
Bhatnagar S, Soni MS, Wrighton LS, Hebert AS, Zhou AS, Paul PK, Gregg T, Rabaglia ME, Keller MP, Coon JJ, et al. Phosphorylation and Degradation of Tomosyn-2 De-represses Insulin Secretion. Journal of Biological Chemistry. 2014 ;289:25276-25286.
Lemke RAS, Peterson AC, Ziegelhoffer EC, Westphall MS, Tjellstrom H, Coon JJ, Donohue TJ. Synthesis and scavenging role of furan fatty acids. Proceedings of the National Academy of Sciences of the United States of America. 2014 ;111:E3450-E3457.
2015
Annis DS, Ma HQ, Balas DM, Kumfer KT, Sandbo N, Potts GK, Coon JJ, Mosher DF. Absence of Vitamin K-Dependent gamma-Carboxylation in Human Periostin Extracted from Fibrotic Lung or Secreted from a Cell Line Engineered to Optimize gamma-Carboxylation. Plos One. 2015 ;10.
Riley NM, Westphall MS, Coon JJ. Activated Ion Electron Transfer Dissociation for Improved Fragmentation of Intact Proteins. Analytical Chemistry. 2015 ;87:7109-7116.
Rose CM, Rush MJP, Riley NM, Merrill AE, Kwiecien NW, Holden DD, Mullen C, Westphall MS, Coon JJ. A Calibration Routine for Efficient ETD in Large-Scale Proteomics. Journal of the American Society for Mass Spectrometry. 2015 ;26:1848-1857.
Ledvinaa AR, Coon JJ, Turecek F. Competitive hydrogen atom migrations accompanying cascade dissociations of peptide cation-radicals of the z(+center dot) type. International Journal of Mass Spectrometry. 2015 ;377:44-53.
Zhao YM, Riley NM, Sun LL, Hebert AS, Yan XJ, Westphall MS, Rush MJP, Zhu GJ, Champion MM, Medie FM, et al. Coupling Capillary Zone Electrophoresis with Electron Transfer Dissociation and Activated Ion Electron Transfer Dissociation for Top-Down Proteomics. Analytical Chemistry. 2015 ;87:5422-5429.
Lippmann ES, Williams CE, Ruhl DA, Estevez-Silva MC, Chapman ER, Coon JJ, Ashton RS. Deterministic HOX Patterning in Human Pluripotent Stem Cell-Derived Neuroectoderm. Stem Cell Reports. 2015 ;4:632-644.
Kwiecien NW, Bailey DJ, Rushp MJP, Cole JS, Ulbrich A, Hebert AS, Westphall MS, Coon JJ. High-Resolution Filtering for Improved Small Molecule Identification via GC/MS. Analytical Chemistry. 2015 ;87:8328-8335.
Overmyer KA, Evans CR, Qi NR, Minogue CE, Carson JJ, Chermside-Scabbo CJ, Koch LG, Britton SL, Pagliarini DJ, Coon JJ, et al. Maximal Oxidative Capacity during Exercise Is Associated with Skeletal Muscle Fuel Selection and Dynamic Changes in Mitochondrial Protein Acetylation. Cell Metabolism. 2015 ;21:468-478.
Austin S, Kontur WS, Ulbrich A, Oshlag JZ, Zhang WP, Higbee A, Zhang YP, Coon JJ, Hodge DB, Donohue TJ, et al. Metabolism of Multiple Aromatic Compounds in Corn Stover Hydrolysate by Rhodopseudomonas palustris. Environmental Science & Technology. 2015 ;49:8914-8922.
Stefely JA, Reidenbach AG, Ulbrich A, Oruganty K, Floyd BJ, Jochem A, Saunders JM, Johnson IE, Minogue CE, Wrobel RL, et al. Mitochondrial ADCK3 Employs an Atypical Protein Kinase-like Fold to Enable Coenzyme Q Biosynthesis. Molecular Cell. 2015 ;57:83-94.
Minogue CE, Hebert AS, Rensvold JW, Westphall MS, Pagliarini DJ, Coon JJ. Multiplexed Quantification for Data-Independent Acquisition. Analytical Chemistry. 2015 ;87:2570-2575.
Riley NM, Rush MJP, Rose CM, Richards AL, Kwiecien NW, Bailey DJ, Hebert AS, Westphall MS, Coon JJ. The Negative Mode Proteome with Activated Ion Negative Electron Transfer Dissociation (AI-NETD). Molecular & Cellular Proteomics. 2015 ;14:2644-2660.
Rhoads TW, Prasad A, Kwiecien NW, Merrill AE, Zawack K, Westphall MS, Schroeder FC, Kimble J, Coon JJ. NeuCode Labeling in Nematodes: Proteomic and Phosphoproteomic Impact of Ascaroside Treatment in Caenorhabditis elegans. Molecular & Cellular Proteomics. 2015 ;14:2922-2935.
Richards AL, Hebert AS, Ulbrich A, Bailey DJ, Coughlin EE, Westphall MS, Coon JJ. One-hour proteome analysis in yeast. Nature Protocols. 2015 ;10:701-714.
Mondal A, Potts GK, Dawson AR, Coon JJ, Mehle A. Phosphorylation at the Homotypic Interface Regulates Nucleoprotein Oligomerization and Assembly of the Influenza Virus Replication Machinery. Plos Pathogens. 2015 ;11.
Nguyen TT, Volkening JD, Rose CM, Venkateshwaran M, Westphall MS, Coon JJ, Ane JM, Sussman MR. Potential regulatory phosphorylation sites in a Medicago truncatula plasma membrane proton pump implicated during early symbiotic signaling in roots. FEBS Letters. 2015 ;589:2186-2193.
Huang MW, Hebert AS, Coon JJ, Hull CM. Protein Composition of Infectious Spores Reveals Novel Sexual Development and Germination Factors in Cryptococcus. Plos Genetics. 2015 ;11.
Richards AL, Merrill AE, Coon JJ. Proteome sequencing goes deep. Current Opinion in Chemical Biology. 2015 ;24:11-17.
Venkateshwaran M, Jayaraman D, Chabaud M, Genre A, Balloon AJ, Maeda J, Forshey K, D. Os den, Kwiecien NW, Coon JJ, et al. A role for the mevalonate pathway in early plant symbiotic signaling. Proceedings of the National Academy of Sciences of the United States of America. 2015 ;112:9781-9786.
Nguyen HTH, Shaffer CJ, Ledvina AR, Coon JJ, Turecek F. Serine effects on collision-induced dissociation and photodissociation of peptide cation radicals of the z(+O)-type. International Journal of Mass Spectrometry. 2015 ;378:20-30.
Tagliabracci VS, Wiley SE, Guo X, Kinch LN, Durrant E, Wen JZ, Xiao JY, Cui JX, Nguyen KB, Engel JL, et al. A Single Kinase Generates the Majority of the Secreted Phosphoproteome. Cell. 2015 ;161:1619-1632.
Dittenhafer-Reed KE, Richards AL, Fan J, Smallegan MJ, Siahpirani AF, Kemmerer ZA, Prolla TA, Roy S, Coon JJ, Denu JM. SIRT3 Mediates Multi-Tissue Coupling for Metabolic Fuel Switching. Cell Metabolism. 2015 ;21:637-646.
2016
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.

Pages