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A Genetic Toggle for Chemical Control of Individual Plk1 Substrates.

Johnson JM, Hebert AS, Drane QH, Lera RF, Wan J, Weaver BA, Coon JJ, Burkard ME.

Cell Chem Biol. 2020 Jan 27. pii: S2451-9456(20)30007-6. doi: 10.1016/j.chembiol.2020.01.007. [Epub ahead of print]


Assessing the viability of recovering hydroxycinnamic acids from lignocellulosic biorefinery alkaline pretreatment waste streams.

Karlen SD, Fasahati P, Mazaheri M, Serate J, Smith RA, Sirobhushanam S, Chen M, Tymkhin VI, Cass CL, Liu S, Padmakshan D, Xie D, Zhang Y, McGee MA, Russell JD, Coon JJ, Kaeppler HF, de Leon N, Maravelias CT, Runge TM, Kaeppler SM, Sedbrook JC, Ralph J.

ChemSusChem. 2020 Jan 26. doi: 10.1002/cssc.201903345. [Epub ahead of print]


Mass spectrometry proteomics reveals a function for mammalian CALCOCO1 in MTOR-regulated selective autophagy.

Stefely JA, Zhang Y, Freiberger EC, Kwiecien NW, Thomas HE, Davis AM, Lowry ND, Vincent CE, Shishkova E, Clark NA, Medvedovic M, Coon JJ, Pagliarini DJ, Mercer CA.

Autophagy. 2020 Feb 2:1-19. doi: 10.1080/15548627.2020.1719746. [Epub ahead of print]


Capillary Zone Electrophoresis-Tandem Mass Spectrometry with Activated Ion Electron Transfer Dissociation for Large-scale Top-down Proteomics.

McCool EN, Lodge JM, Basharat AR, Liu X, Coon JJ, Sun L.

J Am Soc Mass Spectrom. 2019 Dec 1;30(12):2470-2479.


The genetic basis of aneuploidy tolerance in wild yeast.

Hose J, Escalante LE, Clowers KJ, Dutcher HA, Robinson D, Bouriakov V, Coon JJ, Shishkova E, Gasch AP.

Elife. 2020 Jan 7;9. pii: e52063. doi: 10.7554/eLife.52063.


Multiomic Fermentation Using Chemically Defined Synthetic Hydrolyzates Revealed Multiple Effects of Lignocellulose-Derived Inhibitors on Cell Physiology and Xylose Utilization in Zymomonas mobilis.

Zhang Y, Vera JM, Xie D, Serate J, Pohlmann E, Russell JD, Hebert AS, Coon JJ, Sato TK, Landick R.

Front Microbiol. 2019 Nov 7;10:2596. doi: 10.3389/fmicb.2019.02596. eCollection 2019.


Real-time health monitoring through urine metabolomics.

Miller IJ, Peters SR, Overmyer KA, Paulson BR, Westphall MS, Coon JJ.

NPJ Digit Med. 2019 Nov 11;2:109. doi: 10.1038/s41746-019-0185-y. eCollection 2019.


Proteomic and transcriptomic analyses of early and late-chronic Toxoplasma gondii infection shows novel and stage specific transcripts.

Garfoot AL, Wilson GM, Coon JJ, Knoll LJ.

BMC Genomics. 2019 Nov 14;20(1):859. doi: 10.1186/s12864-019-6213-0.


Genome Wide Phosphoproteome Analysis of Zymomonas mobilis Under Anaerobic, Aerobic, and N2-Fixing Conditions.

Tatli M, Hebert AS, Coon JJ, Amador-Noguez D.

Front Microbiol. 2019 Sep 4;10:1986. doi: 10.3389/fmicb.2019.01986. eCollection 2019.


Learning Drug Functions from Chemical Structures with Convolutional Neural Networks and Random Forests.

Meyer JG, Liu S, Miller IJ, Coon JJ, Gitter A.

J Chem Inf Model. 2019 Oct 28;59(10):4438-4449. doi: 10.1021/acs.jcim.9b00236. Epub 2019 Oct 3.


Maximizing Tandem Mass Spectrometry Acquisition Rates for Shotgun Proteomics.

Trujillo EA, Hebert AS, Brademan DR, Coon JJ.

Anal Chem. 2019 Oct 15;91(20):12625-12629. doi: 10.1021/acs.analchem.9b02979. Epub 2019 Oct 3.


Acetyl-CoA flux regulates the proteome and acetyl-proteome to maintain intracellular metabolic crosstalk.

Dieterich IA, Lawton AJ, Peng Y, Yu Q, Rhoads TW, Overmyer KA, Cui Y, Armstrong EA, Howell PR, Burhans MS, Li L, Denu JM, Coon JJ, Anderson RM, Puglielli L.

Nat Commun. 2019 Sep 2;10(1):3929. doi: 10.1038/s41467-019-11945-9.


Genetic determinants of gut microbiota composition and bile acid profiles in mice.

Kemis JH, Linke V, Barrett KL, Boehm FJ, Traeger LL, Keller MP, Rabaglia ME, Schueler KL, Stapleton DS, Gatti DM, Churchill GA, Amador-Noguez D, Russell JD, Yandell BS, Broman KW, Coon JJ, Attie AD, Rey FE.

PLoS Genet. 2019 Aug 29;15(8):e1008073. doi: 10.1371/journal.pgen.1008073. eCollection 2019 Aug.


Pptc7 is an essential phosphatase for promoting mammalian mitochondrial metabolism and biogenesis.

Niemi NM, Wilson GM, Overmyer KA, Vögtle FN, Myketin L, Lohman DC, Schueler KL, Attie AD, Meisinger C, Coon JJ, Pagliarini DJ.

Nat Commun. 2019 Jul 19;10(1):3197. doi: 10.1038/s41467-019-11047-6.


Accelerating Lipidomic Method Development through in Silico Simulation.

Hutchins PD, Russell JD, Coon JJ.

Anal Chem. 2019 Aug 6;91(15):9698-9706. doi: 10.1021/acs.analchem.9b01234. Epub 2019 Jul 25.


Single-Shot Capillary Zone Electrophoresis-Tandem Mass Spectrometry Produces over 4400 Phosphopeptide Identifications from a 220 ng Sample.

Zhang Z, Hebert AS, Westphall MS, Coon JJ, Dovichi NJ.

J Proteome Res. 2019 Aug 2;18(8):3166-3173. doi: 10.1021/acs.jproteome.9b00244. Epub 2019 Jun 26.


Metabolic Remodeling during Biofilm Development of Bacillus subtilis.

Pisithkul T, Schroeder JW, Trujillo EA, Yeesin P, Stevenson DM, Chaiamarit T, Coon JJ, Wang JD, Amador-Noguez D.

mBio. 2019 May 21;10(3). pii: e00623-19. doi: 10.1128/mBio.00623-19.


PKA and HOG signaling contribute separable roles to anaerobic xylose fermentation in yeast engineered for biofuel production.

Wagner ER, Myers KS, Riley NM, Coon JJ, Gasch AP.

PLoS One. 2019 May 21;14(5):e0212389. doi: 10.1371/journal.pone.0212389. eCollection 2019.


Interactive Peptide Spectral Annotator: A Versatile Web-based Tool for Proteomic Applications.

Brademan DR, Riley NM, Kwiecien NW, Coon JJ.

Mol Cell Proteomics. 2019 Aug 9;18(8 suppl 1):S193-S201. doi: 10.1074/mcp.TIR118.001209. Epub 2019 May 14.


Capillary Zone Electrophoresis-Tandem Mass Spectrometry with Activated Ion Electron Transfer Dissociation for Large-scale Top-down Proteomics.

McCool EN, Lodge JM, Basharat AR, Liu X, Coon JJ, Sun L.

J Am Soc Mass Spectrom. 2019 Dec;30(12):2470-2479. doi: 10.1007/s13361-019-02206-6. Epub 2019 May 9.


Capturing site-specific heterogeneity with large-scale N-glycoproteome analysis.

Riley NM, Hebert AS, Westphall MS, Coon JJ.

Nat Commun. 2019 Mar 21;10(1):1311. doi: 10.1038/s41467-019-09222-w.


Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast.

Myers KS, Riley NM, MacGilvray ME, Sato TK, McGee M, Heilberger J, Coon JJ, Gasch AP.

PLoS Genet. 2019 Mar 11;15(3):e1008037. doi: 10.1371/journal.pgen.1008037. eCollection 2019 Mar.


Polo-like kinase 4 maintains centriolar satellite integrity by phosphorylation of centrosomal protein 131 (CEP131).

Denu RA, Sass MM, Johnson JM, Potts GK, Choudhary A, Coon JJ, Burkard ME.

J Biol Chem. 2019 Apr 19;294(16):6531-6549. doi: 10.1074/jbc.RA118.004867. Epub 2019 Feb 25.


Systems-Level Analysis of Oxygen Exposure in Zymomonas mobilis: Implications for Isoprenoid Production.

Martien JI, Hebert AS, Stevenson DM, Regner MR, Khana DB, Coon JJ, Amador-Noguez D.

mSystems. 2019 Feb 12;4(1). pii: e00284-18. doi: 10.1128/mSystems.00284-18. eCollection 2019 Jan-Feb.


Mapping Lipid Fragmentation for Tailored Mass Spectral Libraries.

Hutchins PD, Russell JD, Coon JJ.

J Am Soc Mass Spectrom. 2019 Apr;30(4):659-668. doi: 10.1007/s13361-018-02125-y. Epub 2019 Feb 12.


Proteomic Atlas of the Human Brain in Alzheimer's Disease.

McKetney J, Runde RM, Hebert AS, Salamat S, Roy S, Coon JJ.

J Proteome Res. 2019 Mar 1;18(3):1380-1391. doi: 10.1021/acs.jproteome.9b00004. Epub 2019 Feb 20.


S-adenosylmethionine biosynthesis is a targetable metabolic vulnerability of cancer stem cells.

Strekalova E, Malin D, Weisenhorn EMM, Russell JD, Hoelper D, Jain A, Coon JJ, Lewis PW, Cryns VL.

Breast Cancer Res Treat. 2019 May;175(1):39-50. doi: 10.1007/s10549-019-05146-7. Epub 2019 Feb 2.


Coenzyme Q biosynthetic proteins assemble in a substrate-dependent manner into domains at ER-mitochondria contacts.

Subramanian K, Jochem A, Le Vasseur M, Lewis S, Paulson BR, Reddy TR, Russell JD, Coon JJ, Pagliarini DJ, Nunnari J.

J Cell Biol. 2019 Apr 1;218(4):1353-1369. doi: 10.1083/jcb.201808044. Epub 2019 Jan 23.


An Isoprene Lipid-Binding Protein Promotes Eukaryotic Coenzyme Q Biosynthesis.

Lohman DC, Aydin D, Von Bank HC, Smith RW, Linke V, Weisenhorn E, McDevitt MT, Hutchins P, Wilkerson EM, Wancewicz B, Russell J, Stefely MS, Beebe ET, Jochem A, Coon JJ, Bingman CA, Dal Peraro M, Pagliarini DJ.

Mol Cell. 2019 Feb 21;73(4):763-774.e10. doi: 10.1016/j.molcel.2018.11.033. Epub 2019 Jan 17.


MS-Helios: a Circos wrapper to visualize multi-omic datasets.

Marx H, Coon JJ.

BMC Bioinformatics. 2019 Jan 11;20(1):21. doi: 10.1186/s12859-018-2564-9.


OptSSeq explores enzyme expression and function landscapes to maximize isobutanol production rate.

Ghosh IN, Martien J, Hebert AS, Zhang Y, Coon JJ, Amador-Noguez D, Landick R.

Metab Eng. 2019 Mar;52:324-340. doi: 10.1016/j.ymben.2018.12.008. Epub 2018 Dec 27.


Author Correction: Phosphorylation Dynamics Dominate the Regulated Proteome during Early Xenopus Development.

Peuchen EH, Cox OF, Sun L, Hebert AS, Coon JJ, Champion MM, Dovichi NJ, Huber PW.

Sci Rep. 2018 Nov 21;8(1):17393. doi: 10.1038/s41598-018-35442-z.


The cellular economy of the Saccharomyces cerevisiae zinc proteome.

Wang Y, Weisenhorn E, MacDiarmid CW, Andreini C, Bucci M, Taggart J, Banci L, Russell J, Coon JJ, Eide DJ.

Metallomics. 2018 Dec 12;10(12):1755-1776. doi: 10.1039/c8mt00269j.


The GIS2 Gene Is Repressed by a Zinc-Regulated Bicistronic RNA in Saccharomyces cerevisiae.

Taggart J, Wang Y, Weisenhorn E, MacDiarmid CW, Russell J, Coon JJ, Eide DJ.

Genes (Basel). 2018 Sep 19;9(9). pii: E462. doi: 10.3390/genes9090462.


Ultra-High Pressure (>30,000 psi) Packing of Capillary Columns Enhancing Depth of Shotgun Proteomic Analyses.

Shishkova E, Hebert AS, Westphall MS, Coon JJ.

Anal Chem. 2018 Oct 2;90(19):11503-11508. doi: 10.1021/acs.analchem.8b02766. Epub 2018 Sep 14.


GATA/Heme Multi-omics Reveals a Trace Metal-Dependent Cellular Differentiation Mechanism.

Tanimura N, Liao R, Wilson GM, Dent MR, Cao M, Burstyn JN, Hematti P, Liu X, Zhang Y, Zheng Y, Keles S, Xu J, Coon JJ, Bresnick EH.

Dev Cell. 2018 Sep 10;46(5):581-594.e4. doi: 10.1016/j.devcel.2018.07.022. Epub 2018 Aug 16.


Decoupling Yeast Cell Division and Stress Defense Implicates mRNA Repression in Translational Reallocation during Stress.

Ho YH, Shishkova E, Hose J, Coon JJ, Gasch AP.

Curr Biol. 2018 Aug 20;28(16):2673-2680.e4. doi: 10.1016/j.cub.2018.06.044. Epub 2018 Aug 2.


Comprehensive Single-Shot Proteomics with FAIMS on a Hybrid Orbitrap Mass Spectrometer.

Hebert AS, Prasad S, Belford MW, Bailey DJ, McAlister GC, Abbatiello SE, Huguet R, Wouters ER, Dunyach JJ, Brademan DR, Westphall MS, Coon JJ.

Anal Chem. 2018 Aug 7;90(15):9529-9537. doi: 10.1021/acs.analchem.8b02233. Epub 2018 Jul 18.


Top-Down Characterization of Proteins with Intact Disulfide Bonds Using Activated-Ion Electron Transfer Dissociation.

Rush MJP, Riley NM, Westphall MS, Coon JJ.

Anal Chem. 2018 Aug 7;90(15):8946-8953. doi: 10.1021/acs.analchem.8b01113. Epub 2018 Jul 10.


The Value of Activated Ion Electron Transfer Dissociation for High-Throughput Top-Down Characterization of Intact Proteins.

Riley NM, Sikora JW, Seckler HS, Greer JB, Fellers RT, LeDuc RD, Westphall MS, Thomas PM, Kelleher NL, Coon JJ.

Anal Chem. 2018 Jul 17;90(14):8553-8560. doi: 10.1021/acs.analchem.8b01638. Epub 2018 Jul 5.


Systems Analyses Reveal Physiological Roles and Genetic Regulators of Liver Lipid Species.

Jha P, McDevitt MT, Gupta R, Quiros PM, Williams EG, Gariani K, Sleiman MB, Diserens L, Jochem A, Ulbrich A, Coon JJ, Auwerx J, Pagliarini DJ.

Cell Syst. 2018 Jun 27;6(6):722-733.e6. doi: 10.1016/j.cels.2018.05.016. Epub 2018 Jun 13.


Genetic Regulation of Plasma Lipid Species and Their Association with Metabolic Phenotypes.

Jha P, McDevitt MT, Halilbasic E, Williams EG, Quiros PM, Gariani K, Sleiman MB, Gupta R, Ulbrich A, Jochem A, Coon JJ, Trauner M, Pagliarini DJ, Auwerx J.

Cell Syst. 2018 Jun 27;6(6):709-721.e6. doi: 10.1016/j.cels.2018.05.009. Epub 2018 Jun 13.


Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032.

Yang S, Vera JM, Grass J, Savvakis G, Moskvin OV, Yang Y, McIlwain SJ, Lyu Y, Zinonos I, Hebert AS, Coon JJ, Bates DM, Sato TK, Brown SD, Himmel ME, Zhang M, Landick R, Pappas KM, Zhang Y.

Biotechnol Biofuels. 2018 May 2;11:125. doi: 10.1186/s13068-018-1116-x. eCollection 2018.


Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response.

MacGilvray ME, Shishkova E, Chasman D, Place M, Gitter A, Coon JJ, Gasch AP.

PLoS Comput Biol. 2018 May 8;13(5):e1006088. doi: 10.1371/journal.pcbi.1006088. eCollection 2018 May.


Proteomic and Phosphoproteomic Changes Induced by Prolonged Activation of Human Eosinophils with IL-3.

Esnault S, Hebert AS, Jarjour NN, Coon JJ, Mosher DF.

J Proteome Res. 2018 Jun 1;17(6):2102-2111. doi: 10.1021/acs.jproteome.8b00057. Epub 2018 May 4.


LipiDex: An Integrated Software Package for High-Confidence Lipid Identification.

Hutchins PD, Russell JD, Coon JJ.

Cell Syst. 2018 May 23;6(5):621-625.e5. doi: 10.1016/j.cels.2018.03.011. Epub 2018 Apr 25.


Expression of novel "LOCGEF" isoforms of ARHGEF18 in eosinophils.

Turton KB, Wilkerson EM, Hebert AS, Fogerty FJ, Schira HM, Botros FE, Coon JJ, Mosher DF.

J Leukoc Biol. 2018 Jul;104(1):135-145. doi: 10.1002/JLB.2MA1017-418RR. Epub 2018 Mar 30.


Caloric Restriction Engages Hepatic RNA Processing Mechanisms in Rhesus Monkeys.

Rhoads TW, Burhans MS, Chen VB, Hutchins PD, Rush MJP, Clark JP, Stark JL, McIlwain SJ, Eghbalnia HR, Pavelec DM, Ong IM, Denu JM, Markley JL, Coon JJ, Colman RJ, Anderson RM.

Cell Metab. 2018 Mar 6;27(3):677-688.e5. doi: 10.1016/j.cmet.2018.01.014.


Islet proteomics reveals genetic variation in dopamine production resulting in altered insulin secretion.

Mitok KA, Freiberger EC, Schueler KL, Rabaglia ME, Stapleton DS, Kwiecien NW, Malec PA, Hebert AS, Broman AT, Kennedy RT, Keller MP, Coon JJ, Attie AD.

J Biol Chem. 2018 Apr 20;293(16):5860-5877. doi: 10.1074/jbc.RA117.001102. Epub 2018 Mar 1.

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