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Items: 1 to 50 of 96

1.

Ion Mobility Spectrometry and the Omics: Distinguishing Isomers, Molecular Classes and Contaminant Ions in Complex Samples.

Burnum-Johnson KE, Zheng X, Dodds JN, Ash J, Fourches D, Nicora CD, Wendler JP, Metz TO, Waters KM, Jansson JK, Smith RD, Baker ES.

Trends Analyt Chem. 2019 Jul;116:292-299. doi: 10.1016/j.trac.2019.04.022. Epub 2019 Apr 29.

PMID:
31798197
2.

Broad Substrate-Specific Phosphorylation Events Are Associated With the Initial Stage of Plant Cell Wall Recognition in Neurospora crassa.

Horta MAC, Thieme N, Gao Y, Burnum-Johnson KE, Nicora CD, Gritsenko MA, Lipton MS, Mohanraj K, de Assis LJ, Lin L, Tian C, Braus GH, Borkovich KA, Schmoll M, Larrondo LF, Samal A, Goldman GH, Benz JP.

Front Microbiol. 2019 Nov 1;10:2317. doi: 10.3389/fmicb.2019.02317. eCollection 2019.

3.

Exploiting the Semidestructive Nature of Gas Cluster Ion Beam Time-of-Flight Secondary Ion Mass Spectrometry Imaging for Simultaneous Localization and Confident Lipid Annotations.

Angerer TB, Velickovic D, Nicora CD, Kyle JE, Graham DJ, Anderton C, Gamble LJ.

Anal Chem. 2019 Dec 3;91(23):15073-15080. doi: 10.1021/acs.analchem.9b03763. Epub 2019 Nov 11.

PMID:
31659904
4.

Tandem Mass Tag Labeling Facilitates Reversed-Phase Liquid Chromatography-Mass Spectrometry Analysis of Hydrophilic Phosphopeptides.

Tsai CF, Smith JS, Krajewski K, Zhao R, Moghieb AM, Nicora CD, Xiong X, Moore RJ, Liu T, Smith RD, Jacobs JM, Rajagopal S, Shi T.

Anal Chem. 2019 Sep 17;91(18):11606-11613. doi: 10.1021/acs.analchem.9b01814. Epub 2019 Aug 28.

PMID:
31418558
5.

Detection of Organohalide-Respiring Enzyme Biomarkers at a Bioaugmented TCE-Contaminated Field Site.

Heavner GLW, Mansfeldt CB, Wilkins MJ, Nicora CD, Debs GE, Edwards EA, Richardson RE.

Front Microbiol. 2019 Jun 27;10:1433. doi: 10.3389/fmicb.2019.01433. eCollection 2019.

6.

In situ transformation of ethoxylate and glycol surfactants by shale-colonizing microorganisms during hydraulic fracturing.

Evans MV, Getzinger G, Luek JL, Hanson AJ, McLaughlin MC, Blotevogel J, Welch SA, Nicora CD, Purvine SO, Xu C, Cole DR, Darrah TH, Hoyt DW, Metz TO, Lee Ferguson P, Lipton MS, Wilkins MJ, Mouser PJ.

ISME J. 2019 Nov;13(11):2690-2700. doi: 10.1038/s41396-019-0466-0. Epub 2019 Jun 26.

PMID:
31243331
7.

Deep-Subsurface Pressure Stimulates Metabolic Plasticity in Shale-Colonizing Halanaerobium spp.

Booker AE, Hoyt DW, Meulia T, Eder E, Nicora CD, Purvine SO, Daly RA, Moore JD, Wunch K, Pfiffner SM, Lipton MS, Mouser PJ, Wrighton KC, Wilkins MJ.

Appl Environ Microbiol. 2019 May 30;85(12). pii: e00018-19. doi: 10.1128/AEM.00018-19. Print 2019 Jun 15.

8.

Gut anatomical properties and microbial functional assembly promote lignocellulose deconstruction and colony subsistence of a wood-feeding beetle.

Ceja-Navarro JA, Karaoz U, Bill M, Hao Z, White RA 3rd, Arellano A, Ramanculova L, Filley TR, Berry TD, Conrad ME, Blackwell M, Nicora CD, Kim YM, Reardon PN, Lipton MS, Adkins JN, Pett-Ridge J, Brodie EL.

Nat Microbiol. 2019 May;4(5):864-875. doi: 10.1038/s41564-019-0384-y. Epub 2019 Mar 11.

9.

Insights into the histology of planarian flatworm Phagocata gracilis based on location specific, intact lipid information provided by GCIB-ToF-SIMS imaging.

Angerer TB, Chakravarty N, Taylor MJ, Nicora CD, Graham DJ, Anderton CR, Chudler EH, Gamble LJ.

Biochim Biophys Acta Mol Cell Biol Lipids. 2019 May;1864(5):733-743. doi: 10.1016/j.bbalip.2019.01.011. Epub 2019 Feb 4.

PMID:
30731132
10.

Multiomics resolution of molecular events during a day in the life of Chlamydomonas.

Strenkert D, Schmollinger S, Gallaher SD, Salomé PA, Purvine SO, Nicora CD, Mettler-Altmann T, Soubeyrand E, Weber APM, Lipton MS, Basset GJ, Merchant SS.

Proc Natl Acad Sci U S A. 2019 Feb 5;116(6):2374-2383. doi: 10.1073/pnas.1815238116. Epub 2019 Jan 18.

11.

Carrier-Assisted Single-Tube Processing Approach for Targeted Proteomics Analysis of Low Numbers of Mammalian Cells.

Zhang P, Gaffrey MJ, Zhu Y, Chrisler WB, Fillmore TL, Yi L, Nicora CD, Zhang T, Wu H, Jacobs J, Tang K, Kagan J, Srivastava S, Rodland KD, Qian WJ, Smith RD, Liu T, Wiley HS, Shi T.

Anal Chem. 2019 Jan 15;91(2):1441-1451. doi: 10.1021/acs.analchem.8b04258. Epub 2018 Dec 28.

12.

Rare Earth Elements Alter Redox Balance in Methylomicrobium alcaliphilum 20ZR.

Akberdin IR, Collins DA, Hamilton R, Oshchepkov DY, Shukla AK, Nicora CD, Nakayasu ES, Adkins JN, Kalyuzhnaya MG.

Front Microbiol. 2018 Nov 27;9:2735. doi: 10.3389/fmicb.2018.02735. eCollection 2018.

13.

Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem.

Solden LM, Naas AE, Roux S, Daly RA, Collins WB, Nicora CD, Purvine SO, Hoyt DW, Schückel J, Jørgensen B, Willats W, Spalinger DE, Firkins JL, Lipton MS, Sullivan MB, Pope PB, Wrighton KC.

Nat Microbiol. 2018 Nov;3(11):1274-1284. doi: 10.1038/s41564-018-0225-4. Epub 2018 Oct 24.

14.

Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cells.

Shi T, Gaffrey MJ, Fillmore TL, Nicora CD, Yi L, Zhang P, Shukla AK, Wiley HS, Rodland KD, Liu T, Smith RD, Qian WJ.

Commun Biol. 2018 Aug 6;1:103. doi: 10.1038/s42003-018-0107-6. eCollection 2018.

15.

Genome-centric view of carbon processing in thawing permafrost.

Woodcroft BJ, Singleton CM, Boyd JA, Evans PN, Emerson JB, Zayed AAF, Hoelzle RD, Lamberton TO, McCalley CK, Hodgkins SB, Wilson RM, Purvine SO, Nicora CD, Li C, Frolking S, Chanton JP, Crill PM, Saleska SR, Rich VI, Tyson GW.

Nature. 2018 Aug;560(7716):49-54. doi: 10.1038/s41586-018-0338-1. Epub 2018 Jul 16.

PMID:
30013118
16.

Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales.

Borton MA, Hoyt DW, Roux S, Daly RA, Welch SA, Nicora CD, Purvine S, Eder EK, Hanson AJ, Sheets JM, Morgan DM, Wolfe RA, Sharma S, Carr TR, Cole DR, Mouser PJ, Lipton MS, Wilkins MJ, Wrighton KC.

Proc Natl Acad Sci U S A. 2018 Jul 10;115(28):E6585-E6594. doi: 10.1073/pnas.1800155115. Epub 2018 Jun 25.

17.

Multi 'omics comparison reveals metabolome biochemistry, not microbiome composition or gene expression, corresponds to elevated biogeochemical function in the hyporheic zone.

Graham EB, Crump AR, Kennedy DW, Arntzen E, Fansler S, Purvine SO, Nicora CD, Nelson W, Tfaily MM, Stegen JC.

Sci Total Environ. 2018 Nov 15;642:742-753. doi: 10.1016/j.scitotenv.2018.05.256. Epub 2018 Jun 17.

PMID:
29920461
18.

The MPLEx Protocol for Multi-omic Analyses of Soil Samples.

Nicora CD, Burnum-Johnson KE, Nakayasu ES, Casey CP, White RA 3rd, Roy Chowdhury T, Kyle JE, Kim YM, Smith RD, Metz TO, Jansson JK, Baker ES.

J Vis Exp. 2018 May 30;(135). doi: 10.3791/57343.

19.

Urinary Virome Perturbations in Kidney Transplantation.

Sigdel TK, Mercer N, Nandoe S, Nicora CD, Burnum-Johnson K, Qian WJ, Sarwal MM.

Front Med (Lausanne). 2018 Apr 19;5:72. doi: 10.3389/fmed.2018.00072. eCollection 2018.

20.

Optimization for Peptide Sample Preparation for Urine Peptidomics.

Sigdel TK, Nicora CD, Qian WJ, Sarwal MM.

Methods Mol Biol. 2018;1788:63-72. doi: 10.1007/7651_2017_90.

PMID:
29623538
21.

Salmonella-Mediated Inflammation Eliminates Competitors for Fructose-Asparagine in the Gut.

Wu J, Sabag-Daigle A, Borton MA, Kop LFM, Szkoda BE, Deatherage Kaiser BL, Lindemann SR, Renslow RS, Wei S, Nicora CD, Weitz KK, Kim YM, Adkins JN, Metz TO, Boyaka P, Gopalan V, Wrighton KC, Wysocki VH, Ahmer BMM.

Infect Immun. 2018 Apr 23;86(5). pii: e00945-17. doi: 10.1128/IAI.00945-17. Print 2018 May.

22.

Structure Elucidation of Unknown Metabolites in Metabolomics by Combined NMR and MS/MS Prediction.

Boiteau RM, Hoyt DW, Nicora CD, Kinmonth-Schultz HA, Ward JK, Bingol K.

Metabolites. 2018 Jan 17;8(1). pii: E8. doi: 10.3390/metabo8010008.

23.

MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape.

Menachery VD, Schäfer A, Burnum-Johnson KE, Mitchell HD, Eisfeld AJ, Walters KB, Nicora CD, Purvine SO, Casey CP, Monroe ME, Weitz KK, Stratton KG, Webb-Robertson BM, Gralinski LE, Metz TO, Smith RD, Waters KM, Sims AC, Kawaoka Y, Baric RS.

Proc Natl Acad Sci U S A. 2018 Jan 30;115(5):E1012-E1021. doi: 10.1073/pnas.1706928115. Epub 2018 Jan 16.

24.

Multiplexed targeted mass spectrometry assays for prostate cancer-associated urinary proteins.

Shi T, Quek SI, Gao Y, Nicora CD, Nie S, Fillmore TL, Liu T, Rodland KD, Smith RD, Leach RJ, Thompson IM, Vitello EA, Ellis WJ, Liu AY, Qian WJ.

Oncotarget. 2017 Oct 9;8(60):101887-101898. doi: 10.18632/oncotarget.21710. eCollection 2017 Nov 24.

25.

LC-SRM-Based Targeted Quantification of Urinary Protein Biomarkers.

Gao Y, Wang H, Nicora CD, Shi T, Smith RD, Sigdel TK, Sarwal MM, Camp DG 2nd, Qian WJ.

Methods Mol Biol. 2018;1788:145-156. doi: 10.1007/7651_2017_93.

PMID:
29116567
26.

Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales.

Booker AE, Borton MA, Daly RA, Welch SA, Nicora CD, Hoyt DW, Wilson T, Purvine SO, Wolfe RA, Sharma S, Mouser PJ, Cole DR, Lipton MS, Wrighton KC, Wilkins MJ.

mSphere. 2017 Jul 5;2(4). pii: e00257-17. doi: 10.1128/mSphereDirect.00257-17. eCollection 2017 Jul-Aug.

27.

Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in Yarrowia lipolytica.

Kerkhoven EJ, Kim YM, Wei S, Nicora CD, Fillmore TL, Purvine SO, Webb-Robertson BJ, Smith RD, Baker SE, Metz TO, Nielsen J.

MBio. 2017 Jun 20;8(3). pii: e00857-17. doi: 10.1128/mBio.00857-17.

28.

Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes.

Li M, Gao Y, Qian WJ, Shi L, Liu Y, Nelson WC, Nicora CD, Resch CT, Thompson C, Yan S, Fredrickson JK, Zachara JM, Liu C.

Environ Microbiol Rep. 2017 Oct;9(5):512-521. doi: 10.1111/1758-2229.12558. Epub 2017 Jul 13.

PMID:
28618201
29.

Structural reorganization of the fungal endoplasmic reticulum upon induction of mycotoxin biosynthesis.

Boenisch MJ, Broz KL, Purvine SO, Chrisler WB, Nicora CD, Connolly LR, Freitag M, Baker SE, Kistler HC.

Sci Rep. 2017 Mar 13;7:44296. doi: 10.1038/srep44296.

30.

Phycobilisome truncation causes widespread proteome changes in Synechocystis sp. PCC 6803.

Liberton M, Chrisler WB, Nicora CD, Moore RJ, Smith RD, Koppenaal DW, Pakrasi HB, Jacobs JM.

PLoS One. 2017 Mar 2;12(3):e0173251. doi: 10.1371/journal.pone.0173251. eCollection 2017.

31.

Effects of delayed NSAID administration after experimental eccentric contraction injury - A cellular and proteomics study.

Bryant AE, Aldape MJ, Bayer CR, Katahira EJ, Bond L, Nicora CD, Fillmore TL, Clauss TR, Metz TO, Webb-Robertson BJ, Stevens DL.

PLoS One. 2017 Feb 28;12(2):e0172486. doi: 10.1371/journal.pone.0172486. eCollection 2017.

32.

MPLEx: a method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling.

Burnum-Johnson KE, Kyle JE, Eisfeld AJ, Casey CP, Stratton KG, Gonzalez JF, Habyarimana F, Negretti NM, Sims AC, Chauhan S, Thackray LB, Halfmann PJ, Walters KB, Kim YM, Zink EM, Nicora CD, Weitz KK, Webb-Robertson BM, Nakayasu ES, Ahmer B, Konkel ME, Motin V, Baric RS, Diamond MS, Kawaoka Y, Waters KM, Smith RD, Metz TO.

Analyst. 2017 Jan 26;142(3):442-448. doi: 10.1039/c6an02486f.

33.

An efficient method for native protein purification in the selected range from prostate cancer tissue digests.

Ahmad R, Nicora CD, Shukla AK, Smith RD, Qian WJ, Liu AY.

Chin Clin Oncol. 2016 Dec;5(6):78. doi: 10.21037/cco.2016.12.03.

34.

New roles in hemicellulosic sugar fermentation for the uncultivated Bacteroidetes family BS11.

Solden LM, Hoyt DW, Collins WB, Plank JE, Daly RA, Hildebrand E, Beavers TJ, Wolfe R, Nicora CD, Purvine SO, Carstensen M, Lipton MS, Spalinger DE, Firkins JL, Wolfe BA, Wrighton KC.

ISME J. 2017 Mar;11(3):691-703. doi: 10.1038/ismej.2016.150. Epub 2016 Dec 13.

35.

Proteome Remodeling in Response to Sulfur Limitation in "Candidatus Pelagibacter ubique".

Smith DP, Nicora CD, Carini P, Lipton MS, Norbeck AD, Smith RD, Giovannoni SJ.

mSystems. 2016 Jul 12;1(4). pii: e00068-16. eCollection 2016 Jul-Aug.

36.

Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes.

White RA 3rd, Bottos EM, Roy Chowdhury T, Zucker JD, Brislawn CJ, Nicora CD, Fansler SJ, Glaesemann KR, Glass K, Jansson JK.

mSystems. 2016 Jun 28;1(3). pii: e00045-16. eCollection 2016 May-Jun.

37.

MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses.

Nakayasu ES, Nicora CD, Sims AC, Burnum-Johnson KE, Kim YM, Kyle JE, Matzke MM, Shukla AK, Chu RK, Schepmoes AA, Jacobs JM, Baric RS, Webb-Robertson BJ, Smith RD, Metz TO.

mSystems. 2016 May 10;1(3). pii: e00043-16. eCollection 2016 May-Jun.

38.

The fungal cultivar of leaf-cutter ants produces specific enzymes in response to different plant substrates.

Khadempour L, Burnum-Johnson KE, Baker ES, Nicora CD, Webb-Robertson BM, White RA 3rd, Monroe ME, Huang EL, Smith RD, Currie CR.

Mol Ecol. 2016 Nov;25(22):5795-5805. doi: 10.1111/mec.13872. Epub 2016 Oct 26.

39.

Corrigendum: The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol.

Sun J, Todd JD, Thrash JC, Qian Y, Qian MC, Temperton B, Guo J, Fowler EK, Aldrich JT, Nicora CD, Lipton MS, Smith RD, De Leenheer P, Payne SH, Johnston AW, Davie-Martin CL, Halsey KH, Giovannoni SJ.

Nat Microbiol. 2016 Oct 3;1(11):16210. doi: 10.1038/nmicrobiol.2016.210. No abstract available.

PMID:
27694837
40.

The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol.

Sun J, Todd JD, Thrash JC, Qian Y, Qian MC, Temperton B, Guo J, Fowler EK, Aldrich JT, Nicora CD, Lipton MS, Smith RD, De Leenheer P, Payne SH, Johnston AW, Davie-Martin CL, Halsey KH, Giovannoni SJ.

Nat Microbiol. 2016 May 16;1(8):16065. doi: 10.1038/nmicrobiol.2016.65. Erratum in: Nat Microbiol. 2016 Oct 03;1(11):16210.

PMID:
27573103
41.

Comparative Community Proteomics Demonstrates the Unexpected Importance of Actinobacterial Glycoside Hydrolase Family 12 Protein for Crystalline Cellulose Hydrolysis.

Hiras J, Wu YW, Deng K, Nicora CD, Aldrich JT, Frey D, Kolinko S, Robinson EW, Jacobs JM, Adams PD, Northen TR, Simmons BA, Singer SW.

MBio. 2016 Aug 23;7(4). pii: e01106-16. doi: 10.1128/mBio.01106-16.

42.

Unambiguous metabolite identification in high-throughput metabolomics by hybrid 1D 1 H NMR/ESI MS1 approach.

Walker LR, Hoyt DW, Walker SM 2nd, Ward JK, Nicora CD, Bingol K.

Magn Reson Chem. 2016 Dec;54(12):998-1003. doi: 10.1002/mrc.4503. Epub 2016 Sep 16. No abstract available.

PMID:
27539910
43.

Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway.

Shi T, Niepel M, McDermott JE, Gao Y, Nicora CD, Chrisler WB, Markillie LM, Petyuk VA, Smith RD, Rodland KD, Sorger PK, Qian WJ, Wiley HS.

Sci Signal. 2016 Jul 12;9(436):rs6. doi: 10.1126/scisignal.aaf0891.

44.

Mining the human urine proteome for monitoring renal transplant injury.

Sigdel TK, Gao Y, He J, Wang A, Nicora CD, Fillmore TL, Shi T, Webb-Robertson BJ, Smith RD, Qian WJ, Salvatierra O, Camp DG 2nd, Sarwal MM.

Kidney Int. 2016 Jun;89(6):1244-52. doi: 10.1016/j.kint.2015.12.049. Epub 2016 Mar 4.

45.

Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica.

Pomraning KR, Kim YM, Nicora CD, Chu RK, Bredeweg EL, Purvine SO, Hu D, Metz TO, Baker SE.

BMC Genomics. 2016 Feb 25;17:138. doi: 10.1186/s12864-016-2471-2.

46.

Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism.

Tisoncik-Go J, Gasper DJ, Kyle JE, Eisfeld AJ, Selinger C, Hatta M, Morrison J, Korth MJ, Zink EM, Kim YM, Schepmoes AA, Nicora CD, Purvine SO, Weitz KK, Peng X, Green RR, Tilton SC, Webb-Robertson BJ, Waters KM, Metz TO, Smith RD, Kawaoka Y, Suresh M, Josset L, Katze MG.

Cell Host Microbe. 2016 Feb 10;19(2):254-66. doi: 10.1016/j.chom.2016.01.002.

47.

Multi-Omic Dynamics Associate Oxygenic Photosynthesis with Nitrogenase-Mediated H2 Production in Cyanothece sp. ATCC 51142.

Bernstein HC, Charania MA, McClure RS, Sadler NC, Melnicki MR, Hill EA, Markillie LM, Nicora CD, Wright AT, Romine MF, Beliaev AS.

Sci Rep. 2015 Nov 3;5:16004. doi: 10.1038/srep16004.

48.

Correction: Enrichment and Broad Representation of Plant Biomass-Degrading Enzymes in the Specialized Hyphal Swellings of Leucoagaricus gongylophorus, the Fungal Symbiont of Leaf-Cutter Ants.

Aylward FO, Khadempour L, Tremmel DM, McDonald BR, Nicora CD, Wu S, Moore RJ, Orton DJ, Monroe ME, Piehowski PD, Purvine SO, Smith RD, Lipton MS, Burnum-Johnson KE, Currie CR.

PLoS One. 2015 Sep 23;10(9):e0139151. doi: 10.1371/journal.pone.0139151. eCollection 2015. No abstract available.

49.

Enrichment and Broad Representation of Plant Biomass-Degrading Enzymes in the Specialized Hyphal Swellings of Leucoagaricus gongylophorus, the Fungal Symbiont of Leaf-Cutter Ants.

Aylward FO, Khadempour L, Tremmel DM, McDonald BR, Nicora CD, Wu S, Moore RJ, Orton DJ, Monroe ME, Piehowski PD, Purvine SO, Smith RD, Lipton MS, Burnum-Johnson KE, Currie CR.

PLoS One. 2015 Aug 28;10(8):e0134752. doi: 10.1371/journal.pone.0134752. eCollection 2015. Erratum in: PLoS One. 2015;10(9):e0139151.

50.

Diacyltransferase Activity and Chain Length Specificity of Mycobacterium tuberculosis PapA5 in the Synthesis of Alkyl β-Diol Lipids.

Touchette MH, Bommineni GR, Delle Bovi RJ, Gadbery JE, Nicora CD, Shukla AK, Kyle JE, Metz TO, Martin DW, Sampson NS, Miller WT, Tonge PJ, Seeliger JC.

Biochemistry. 2015 Sep 8;54(35):5457-68. doi: 10.1021/acs.biochem.5b00455. Epub 2015 Aug 24.

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