All Faculty and Research Staff Publications

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2018
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.
Rhoads TW, Burhans MS, Chen VB, Hutchins PD, Rush MJP, Clark JP, Stark JL, McIlwain SJ, Eghbalnia HR, Pavelec DM, et al. Caloric Restriction Engages Hepatic RNA Processing Mechanisms in Rhesus Monkeys. Cell Metabolism. 2018 ;27:677-+.
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.
Hebert AS, Prasad S, Belford MW, Bailey DJ, McAlister GC, Abbatiello SE, Huguet R, Wouters ER, Dunyach JJ, Brademan DR, et al. Comprehensive Single-Shot Proteomics with FAIMS on a Hybrid Orbitrap Mass Spectrometer. Analytical Chemistry. 2018 ;90:9529-9537.
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-+.
Ho YH, Shishkova E, Hose J, Coon JJ, Gasch AP. Decoupling Yeast Cell Division and Stress Defense Implicates mRNA Repression in Translational Reallocation during Stress. Current Biology. 2018 ;28:2673-+.
Zhang YP, Oates LG, Serate J, Xie D, Pohlmann E, Bukhman YV, Karlen SD, Young MK, Higbee A, Eilert D, et al. Diverse lignocellulosic feedstocks can achieve high field-scale ethanol yields while providing flexibility for the biorefinery and landscape-level environmental benefits. Global Change Biology Bioenergy. 2018 ;10:825-840.
Turton KB, Wilkerson EM, Hebert AS, Fogerty FJ, Schira HM, Botros FE, Coon JJ, Mosher DF. Expression of novel "LOCGEF" isoforms of ARHGEF18 in eosinophils. Journal of Leukocyte Biology. 2018 ;104:135-145.
Tanimura N, Liao RQ, Wilson GM, Dent MR, Cao M, Burstyn JN, Hematti P, Liu X, Zhang YY, Zheng Y, et al. GATA/Heme Multi-omics Reveals a Trace Metal-Dependent Cellular Differentiation Mechanism. Developmental Cell. 2018 ;46:581-+.
Jha P, McDevitt MT, Halilbasic E, Williams EG, Quiros PM, Gariani K, Sleiman MB, Gupta R, Ulbrich A, Jochem A, et al. Genetic Regulation of Plasma Lipid Species and Their Association with Metabolic Phenotypes. Cell Systems. 2018 ;6:709-+.
Taggart J, Wang Y, Weisenhorn E, MacDiarmid CW, Russell J, Coon JJ, Eide DJ. The GIS2 Gene Is Repressed by a Zinc-Regulated Bicistronic RNA in Saccharomyces cerevisiae
. Genes (Basel). 2018 ;9.
Wilson GM, Blanco R, Coon JJ, Hornberger TA. Identifying Novel Signaling Pathways: An Exercise Scientists Guide to Phosphoproteomics. Exercise and Sport Sciences Reviews. 2018 ;46:76-85.
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.
Mitok KA, Freiberger EC, Schueler KL, Rabaglia ME, Stapleton DS, Kwiecien NW, Malec PA, Hebert AS, Broman AT, Kennedy RT, et al. Islet proteomics reveals genetic variation in dopamine production resulting in altered insulin secretion. Journal of Biological Chemistry. 2018 ;293:5860-5877.
Das A, Rahimi A, Ulbrich A, Alherech M, Motagamwala AH, Bhalla A, Sousa LD, Balan V, Dumesic JA, Hegg EL, et al. Lignin Conversion to Low-Molecular-Weight Aromatics via an Aerobic Oxidation-Hydrolysis Sequence: Comparison of Different Lignin Sources. Acs Sustainable Chemistry & Engineering. 2018 ;6:3367-3374.
Hutchins PD, Russell JD, Coon JJ. LipiDex: An Integrated Software Package for High-Confidence Lipid Identification. Cell Systems. 2018 ;6:621-+.
Vakirlis N, Hebert AS, Opulente DA, Achaz G, Hittinger CT, Fischer G, Coon JJ, Lafontaine I. A Molecular Portrait of De Novo Genes in Yeasts. Molecular Biology and Evolution. 2018 ;35:631-645.
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.
MacGilvray ME, Shishkova E, Chasman D, Place M, Gitter A, Coon JJ, Gasch AP. Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response. Plos Computational Biology. 2018 ;14.
Kontur WS, Bingman CA, Olmsted CN, Wassarman DR, Ulbrich A, Gall DL, Smith RW, Yusko LM, Fox BG, Noguera DR, et al. Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the beta-aryl ether bond of lignin. Journal of Biological Chemistry. 2018 ;293:4955-4968.
Zhang Z, Hebert AS, Westphall MS, Qu Y, Coon JJ, Dovichi NJ. Production of Over 27 000 Peptide and Nearly 4400 Protein Identifications by Single-Shot Capillary-Zone Electrophoresis-Mass Spectrometry via Combination of a Very-Low-Electroosmosis Coated Capillary, a Third-Generation Electrokinetically-Pumped Sheath-Fl. Analytical Chemistry. 2018 ;90:12090-12093.
Esnault S, Hebert AS, Jarjour NN, Coon JJ, Mosher DF. Proteomic and Phosphoproteomic Changes Induced by Prolonged Activation of Human Eosinophils with IL-3. Journal of Proteome Research. 2018 ;17:2102-2111.
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.
Jha P, McDevitt MT, Gupta R, Quiros PM, Williams EG, Gariani K, Sleiman MB, Diserens L, Jochem A, Ulbrich A, et al. Systems Analyses Reveal Physiological Roles and Genetic Regulators of Liver Lipid Species. Cell Systems. 2018 ;6:722-+.
Rush MJP, Riley NM, Westphall MS, Coon JJ. Top-Down Characterization of Proteins with Intact Disulfide Bonds Using Activated-Ion Electron Transfer Dissociation. Analytical Chemistry. 2018 ;90:8946-8953.
Shishkova E, Hebert AS, Westphall MS, Coon JJ. Ultra-High Pressure (>30,000 psi) Packing of Capillary Columns Enhancing Depth of Shotgun Proteomic Analyses. Analytical Chemistry. 2018 ;90:11503-11508.
Riley NM, Sikora JW, Seckler HS, Greer JB, Fellers RT, Leduc RD, Westphall MS, Thomas PM, Kelleher NL, Coon JJ. The Value of Activated Ion Electron Transfer Dissociation for High-Throughput Top-Down Characterization of Intact Proteins. Analytical Chemistry. 2018 ;90:8553-8560.
2017
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.

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