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Items: 1 to 50 of 234

1.

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

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

J Proteome Res. 2019 Jun 10. doi: 10.1021/acs.jproteome.9b00244. [Epub ahead of print]

PMID:
31180221
2.

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.

3.

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.

4.

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

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

Mol Cell Proteomics. 2019 May 14. pii: mcp.TIR118.001209. doi: 10.1074/mcp.TIR118.001209. [Epub ahead of print]

5.

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 May 9. doi: 10.1007/s13361-019-02206-6. [Epub ahead of print]

PMID:
31073891
6.

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.

7.

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.

8.

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.

PMID:
30804208
9.

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.

10.

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.

PMID:
30756325
11.

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.

PMID:
30735395
12.

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.

PMID:
30712196
13.

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.

PMID:
30674579
14.

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.

PMID:
30661980
15.

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.

16.

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.

17.

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.

18.

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.

PMID:
30358795
19.

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.

21.

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.

PMID:
30179449
22.

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.

PMID:
30122630
23.

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.

PMID:
30078561
24.

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.

25.

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.

PMID:
29949341
26.

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.

PMID:
29924586
27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

PMID:
29601110
34.

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.

35.

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.

36.

Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin.

Kontur WS, Bingman CA, Olmsted CN, Wassarman DR, Ulbrich A, Gall DL, Smith RW, Yusko LM, Fox BG, Noguera DR, Coon JJ, Donohue TJ.

J Biol Chem. 2018 Apr 6;293(14):4955-4968. doi: 10.1074/jbc.RA117.001268. Epub 2018 Feb 15.

37.

Identifying Novel Signaling Pathways: An Exercise Scientists Guide to Phosphoproteomics.

Wilson GM, Blanco R, Coon JJ, Hornberger TA.

Exerc Sport Sci Rev. 2018 Apr;46(2):76-85. doi: 10.1249/JES.0000000000000146. Review.

38.

Chemical genomic guided engineering of gamma-valerolactone tolerant yeast.

Bottoms S, Dickinson Q, McGee M, Hinchman L, Higbee A, Hebert A, Serate J, Xie D, Zhang Y, Coon JJ, Myers CL, Landick R, Piotrowski JS.

Microb Cell Fact. 2018 Jan 12;17(1):5. doi: 10.1186/s12934-017-0848-9.

39.

Multiplexed proteome analysis with neutron-encoded stable isotope labeling in cells and mice.

Overmyer KA, Tyanova S, Hebert AS, Westphall MS, Cox J, Coon JJ.

Nat Protoc. 2018 Jan;13(1):293-306. doi: 10.1038/nprot.2017.121. Epub 2018 Jan 11.

40.

ATM directs DNA damage responses and proteostasis via genetically separable pathways.

Lee JH, Mand MR, Kao CH, Zhou Y, Ryu SW, Richards AL, Coon JJ, Paull TT.

Sci Signal. 2018 Jan 9;11(512). pii: eaan5598. doi: 10.1126/scisignal.aan5598.

41.

Improved Precursor Characterization for Data-Dependent Mass Spectrometry.

Hebert AS, Thöing C, Riley NM, Kwiecien NW, Shiskova E, Huguet R, Cardasis HL, Kuehn A, Eliuk S, Zabrouskov V, Westphall MS, McAlister GC, Coon JJ.

Anal Chem. 2018 Feb 6;90(3):2333-2340. doi: 10.1021/acs.analchem.7b04808. Epub 2018 Jan 11.

42.

Multi-omics Reveal Specific Targets of the RNA-Binding Protein Puf3p and Its Orchestration of Mitochondrial Biogenesis.

Lapointe CP, Stefely JA, Jochem A, Hutchins PD, Wilson GM, Kwiecien NW, Coon JJ, Wickens M, Pagliarini DJ.

Cell Syst. 2018 Jan 24;6(1):125-135.e6. doi: 10.1016/j.cels.2017.11.012. Epub 2017 Dec 13.

43.

Multi-omic Mitoprotease Profiling Defines a Role for Oct1p in Coenzyme Q Production.

Veling MT, Reidenbach AG, Freiberger EC, Kwiecien NW, Hutchins PD, Drahnak MJ, Jochem A, Ulbrich A, Rush MJP, Russell JD, Coon JJ, Pagliarini DJ.

Mol Cell. 2017 Dec 7;68(5):970-977.e11. doi: 10.1016/j.molcel.2017.11.023.

44.

A Molecular Portrait of De Novo Genes in Yeasts.

Vakirlis N, Hebert AS, Opulente DA, Achaz G, Hittinger CT, Fischer G, Coon JJ, Lafontaine I.

Mol Biol Evol. 2018 Mar 1;35(3):631-645. doi: 10.1093/molbev/msx315.

45.

Conserved Lipid and Small-Molecule Modulation of COQ8 Reveals Regulation of the Ancient Kinase-like UbiB Family.

Reidenbach AG, Kemmerer ZA, Aydin D, Jochem A, McDevitt MT, Hutchins PD, Stark JL, Stefely JA, Reddy T, Hebert AS, Wilkerson EM, Johnson IE, Bingman CA, Markley JL, Coon JJ, Dal Peraro M, Pagliarini DJ.

Cell Chem Biol. 2018 Feb 15;25(2):154-165.e11. doi: 10.1016/j.chembiol.2017.11.001. Epub 2017 Nov 30.

46.

The Role of Electron Transfer Dissociation in Modern Proteomics.

Riley NM, Coon JJ.

Anal Chem. 2018 Jan 2;90(1):40-64. doi: 10.1021/acs.analchem.7b04810. Epub 2017 Dec 12. Review. No abstract available.

47.

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. 2017 Nov 15;7(1):15647. doi: 10.1038/s41598-017-15936-y. Erratum in: Sci Rep. 2018 Nov 21;8(1):17393.

48.

The dental calculus metabolome in modern and historic samples.

Velsko IM, Overmyer KA, Speller C, Klaus L, Collins MJ, Loe L, Frantz LAF, Sankaranarayanan K, Lewis CM Jr, Martinez JBR, Chaves E, Coon JJ, Larson G, Warinner C.

Metabolomics. 2017;13(11):134. doi: 10.1007/s11306-017-1270-3. Epub 2017 Oct 3.

49.

Proteomics of Eosinophil Activation.

Mosher DF, Wilkerson EM, Turton KB, Hebert AS, Coon JJ.

Front Med (Lausanne). 2017 Sep 29;4:159. doi: 10.3389/fmed.2017.00159. eCollection 2017. Review.

50.

Sequencing Larger Intact Proteins (30-70 kDa) with Activated Ion Electron Transfer Dissociation.

Riley NM, Westphall MS, Coon JJ.

J Am Soc Mass Spectrom. 2018 Jan;29(1):140-149. doi: 10.1007/s13361-017-1808-7. Epub 2017 Oct 12.

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