All Faculty and Research Staff Publications

Export 226 results:
Filters: Author is J. J. Coon  [Clear All Filters]
Hutchins PD, Russell JD, Coon JJ. Accelerating Lipidomic Method Development through in Silico Simulation. Analytical Chemistry. 2019 ;91:9698-9706.
Dieterich IA, Lawton AJ, Peng YJ, Yu Q, Rhoads TW, Overmyer KA, Cui YS, Armstrong EA, Howell PR, Burhans MS, et al. Acetyl-CoA flux regulates the proteome and acetyl-proteome to maintain intracellular metabolic crosstalk. Nature Communications. 2019 ;10.
Riley NM, Hebert AS, Westphall MS, Coon JJ. Capturing site-specific heterogeneity with large-scale N-glycoproteome analysis. Nature Communications. 2019 ;10.
Subramanian K, Jochem A, Le Vasseur M, Lewis S, Paulson BR, Reddy TR, Russell JD, Coon JJ, Pagliarini DJ, Nunnari J. Coenzyme Q biosynthetic proteins assemble in a substrate-dependent manner into domains at ER-mitochondria contacts. Journal of Cell Biology. 2019 ;218:1352-1368.
Brademan DR, Riley NM, Kwiecien NW, Coon JJ. Interactive Peptide Spectral Annotator: A Versatile Web-based Tool for Proteomic Applications. Molecular & Cellular Proteomics. 2019 ;18:S193-S201.
Lohman DC, Aydin D, Von Bank HC, Smith RW, Linke V, Weisenhorn E, McDevitt MT, Hutchins P, Wilkerson EM, Wancewicz B, et al. An Isoprene Lipid-Binding Protein Promotes Eukaryotic Coenzyme Q Biosynthesis. Molecular Cell. 2019 ;73:763-+.
Hutchins PD, Russell JD, Coon JJ. Mapping Lipid Fragmentation for Tailored Mass Spectral Libraries. Journal of the American Society for Mass Spectrometry. 2019 ;30:659-668.
Marx H, Coon JJ. MS-Helios: a Circos wrapper to visualize multi-omic datasets. Bmc Bioinformatics. 2019 ;20:21.
Ghosh IN, Martien J, Hebert AS, Zhang YP, Coon JJ, Amador-Noguez D, Landick R. OptSSeq explores enzyme expression and function landscapes to maximize isobutanol production rate. Metabolic Engineering. 2019 ;52:324-340.
Wagner ER, Myers KS, Riley NM, Coon JJ, Gasch AP. PKA and HOG signaling contribute separable roles to anaerobic xylose fermentation in yeast engineered for biofuel production. Plos One. 2019 ;14.
Denu RA, Sass MM, Johnson JM, Potts GK, Choudhary A, Coon JJ, Burkard ME. Polo-like kinase 4 maintains centriolar satellite integrity by phosphorylation of centrosomal protein 131 (CEP131). Journal of Biological Chemistry. 2019 ;294:6531-6549.
Niemi NM, Wilson GM, Overmyer KA, Vogtle FN, Myketin L, Lohman DC, Schueler KL, Attie AD, Meisinger C, Coon JJ, et al. Pptc7 is an essential phosphatase for promoting mammalian mitochondrial metabolism and biogenesis. Nature Communications. 2019 ;10.
McKetney J, Runde RM, Hebert AS, Salamat S, Roy S, Coon JJ. Proteomic Atlas of the Human Brain in Alzheimer's Disease. Journal of Proteome Research. 2019 ;18:1380-1391.
Myers KS, Riley NM, MacGilvray ME, Sato TK, McGee M, Heilberger J, Coon JJ, Gasch AP. Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast. Plos Genetics. 2019 ;15.
Strekalova E, Malin D, Weisenhorn EMM, Russell JD, Hoelper D, Jain A, Coon JJ, Lewis PW, Cryns VL. S-adenosylmethionine biosynthesis is a targetable metabolic vulnerability of cancer stem cells. Breast Cancer Research and Treatment. 2019 ;175:39-50.
Zhang ZB, Hebert AS, Westphall MS, Coon JJ, Dovichi NJ. Single-Shot Capillary Zone Electrophoresis-Tandem Mass Spectrometry Produces over 4400 Phosphopeptide Identifications from a 220 ng Sample. Journal of Proteome Research. 2019 ;18:3166-3173.
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-+.
Wang YR, Weisenhorn E, MacDiarmid CW, Andreini C, Bucci M, Taggart J, Banci L, Russell J, Coon JJ, Eide DJ. The cellular economy of the Saccharomyces cerevisiae zinc proteome. Metallomics. 2018 ;10.
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-+.
Tanimura N, Liao RQ, Wilson GM, Dent MR, Cao M, Burstyn JN, Hematti P, Liu X, Zhang YN, Zheng Y, et al. GATA/Heme Multi-Omics Reveals a Trace Metal-Dependent Erythrocyte Developmental Mechanism. Blood. 2018 ;132.
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.