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Untargeted Soil Metabolomics Using Liquid Chromatography-Mass Spectrometry and Gas Chromatography-Mass Spectrometry.

Swenson TL, Northen TR.

Methods Mol Biol. 2019;1859:97-109. doi: 10.1007/978-1-4939-8757-3_4.


Rapid characterization of the activities of lignin-modifying enzymes based on nanostructure-initiator mass spectrometry (NIMS).

Deng K, Zeng J, Cheng G, Gao J, Sale KL, Simmons BA, Singh AK, Adams PD, Northen TR.

Biotechnol Biofuels. 2018 Sep 27;11:266. doi: 10.1186/s13068-018-1261-2. eCollection 2018.


Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes.

Kosina SM, Greiner AM, Lau RK, Jenkins S, Baran R, Bowen BP, Northen TR.

BMC Microbiol. 2018 Sep 12;18(1):115. doi: 10.1186/s12866-018-1256-y.


Insulator Nanostructure Desorption Ionization Mass Spectrometry.

Duncombe TA, Raad M, Bowen BP, Singh AK, Northen TR.

Anal Chem. 2018 Aug 21;90(16):9657-9661. doi: 10.1021/acs.analchem.8b01989. Epub 2018 Aug 6.


Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry.

Zhalnina K, Zengler K, Newman D, Northen TR.

MBio. 2018 Jul 17;9(4). pii: e01175-18. doi: 10.1128/mBio.01175-18.


Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions.

Gao J, Sasse J, Lewald KM, Zhalnina K, Cornmesser LT, Duncombe TA, Yoshikuni Y, Vogel JP, Firestone MK, Northen TR.

J Vis Exp. 2018 Apr 10;(134). doi: 10.3791/57170.


Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly.

Zhalnina K, Louie KB, Hao Z, Mansoori N, da Rocha UN, Shi S, Cho H, Karaoz U, Loqué D, Bowen BP, Firestone MK, Northen TR, Brodie EL.

Nat Microbiol. 2018 Apr;3(4):470-480. doi: 10.1038/s41564-018-0129-3. Epub 2018 Mar 19.


An integrated workflow for phenazine-modifying enzyme characterization.

Coates RC, Bowen BP, Oberortner E, Thomashow L, Hadjithomas M, Zhao Z, Ke J, Silva L, Louie K, Wang G, Robinson D, Tarver A, Hamilton M, Lubbe A, Feltcher M, Dangl JL, Pati A, Weller D, Northen TR, Cheng JF, Mouncey NJ, Deutsch S, Yoshikuni Y.

J Ind Microbiol Biotechnol. 2018 Jul;45(7):567-577. doi: 10.1007/s10295-018-2025-5. Epub 2018 Mar 15.


Construction of Viable Soil Defined Media Using Quantitative Metabolomics Analysis of Soil Metabolites.

Jenkins S, Swenson TL, Lau R, Rocha AM, Aaring A, Hazen TC, Chakraborty R, Northen TR.

Front Microbiol. 2017 Dec 22;8:2618. doi: 10.3389/fmicb.2017.02618. eCollection 2017.


Linking soil biology and chemistry in biological soil crust using isolate exometabolomics.

Swenson TL, Karaoz U, Swenson JM, Bowen BP, Northen TR.

Nat Commun. 2018 Jan 2;9(1):19. doi: 10.1038/s41467-017-02356-9.


Key Metabolites and Mechanistic Changes for Salt Tolerance in an Experimentally Evolved Sulfate-Reducing Bacterium, Desulfovibrio vulgaris.

Zhou A, Lau R, Baran R, Ma J, von Netzer F, Shi W, Gorman-Lewis D, Kempher ML, He Z, Qin Y, Shi Z, Zane GM, Wu L, Bowen BP, Northen TR, Hillesland KL, Stahl DA, Wall JD, Arkin AP, Zhou J.

MBio. 2017 Nov 14;8(6). pii: e01780-17. doi: 10.1128/mBio.01780-17.


SbCOMT (Bmr12) is involved in the biosynthesis of tricin-lignin in sorghum.

Eudes A, Dutta T, Deng K, Jacquet N, Sinha A, Benites VT, Baidoo EEK, Richel A, Sattler SE, Northen TR, Singh S, Simmons BA, Loqué D.

PLoS One. 2017 Jun 8;12(6):e0178160. doi: 10.1371/journal.pone.0178160. eCollection 2017.


Morphology-Driven Control of Metabolite Selectivity Using Nanostructure-Initiator Mass Spectrometry.

Gao J, Louie KB, Steinke P, Bowen BP, Raad M, Zuckermann RN, Siuzdak G, Northen TR.

Anal Chem. 2017 Jun 20;89(12):6521-6526. doi: 10.1021/acs.analchem.7b00599. Epub 2017 May 26.


Widespread adenine N6-methylation of active genes in fungi.

Mondo SJ, Dannebaum RO, Kuo RC, Louie KB, Bewick AJ, LaButti K, Haridas S, Kuo A, Salamov A, Ahrendt SR, Lau R, Bowen BP, Lipzen A, Sullivan W, Andreopoulos BB, Clum A, Lindquist E, Daum C, Northen TR, Kunde-Ramamoorthy G, Schmitz RJ, Gryganskyi A, Culley D, Magnuson J, James TY, O'Malley MA, Stajich JE, Spatafora JW, Visel A, Grigoriev IV.

Nat Genet. 2017 Jun;49(6):964-968. doi: 10.1038/ng.3859. Epub 2017 May 8.


A fungal transcription factor essential for starch degradation affects integration of carbon and nitrogen metabolism.

Xiong Y, Wu VW, Lubbe A, Qin L, Deng S, Kennedy M, Bauer D, Singan VR, Barry K, Northen TR, Grigoriev IV, Glass NL.

PLoS Genet. 2017 May 3;13(5):e1006737. doi: 10.1371/journal.pgen.1006737. eCollection 2017 May.


OpenMSI Arrayed Analysis Toolkit: Analyzing Spatially Defined Samples Using Mass Spectrometry Imaging.

de Raad M, de Rond T, Rübel O, Keasling JD, Northen TR, Bowen BP.

Anal Chem. 2017 Jun 6;89(11):5818-5823. doi: 10.1021/acs.analchem.6b05004. Epub 2017 May 15.


Determination of glycoside hydrolase specificities during hydrolysis of plant cell walls using glycome profiling.

Walker JA, Pattathil S, Bergeman LF, Beebe ET, Deng K, Mirzai M, Northen TR, Hahn MG, Fox BG.

Biotechnol Biofuels. 2017 Feb 2;10:31. doi: 10.1186/s13068-017-0703-6. eCollection 2017.


Dynamic substrate preferences predict metabolic properties of a simple microbial consortium.

Erbilgin O, Bowen BP, Kosina SM, Jenkins S, Lau RK, Northen TR.

BMC Bioinformatics. 2017 Jan 23;18(1):57. doi: 10.1186/s12859-017-1478-2.


Extensive Turnover of Compatible Solutes in Cyanobacteria Revealed by Deuterium Oxide (D2O) Stable Isotope Probing.

Baran R, Lau R, Bowen BP, Diamond S, Jose N, Garcia-Pichel F, Northen TR.

ACS Chem Biol. 2017 Mar 17;12(3):674-681. doi: 10.1021/acschembio.6b00890. Epub 2017 Jan 18.


On-chip integration of droplet microfluidics and nanostructure-initiator mass spectrometry for enzyme screening.

Heinemann J, Deng K, Shih SC, Gao J, Adams PD, Singh AK, Northen TR.

Lab Chip. 2017 Jan 17;17(2):323-331. doi: 10.1039/c6lc01182a.


A robust gene-stacking method utilizing yeast assembly for plant synthetic biology.

Shih PM, Vuu K, Mansoori N, Ayad L, Louie KB, Bowen BP, Northen TR, Loqué D.

Nat Commun. 2016 Oct 26;7:13215. doi: 10.1038/ncomms13215.


Smartphone Analytics: Mobilizing the Lab into the Cloud for Omic-Scale Analyses.

Montenegro-Burke JR, Phommavongsay T, Aisporna AE, Huan T, Rinehart D, Forsberg E, Poole FL, Thorgersen MP, Adams MW, Krantz G, Fields MW, Northen TR, Robbins PD, Niedernhofer LJ, Lairson L, Benton HP, Siuzdak G.

Anal Chem. 2016 Oct 4;88(19):9753-9758. Epub 2016 Sep 15.


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.


Comprehensive in Vitro Analysis of Acyltransferase Domain Exchanges in Modular Polyketide Synthases and Its Application for Short-Chain Ketone Production.

Yuzawa S, Deng K, Wang G, Baidoo EE, Northen TR, Adams PD, Katz L, Keasling JD.

ACS Synth Biol. 2017 Jan 20;6(1):139-147. doi: 10.1021/acssynbio.6b00176. Epub 2016 Sep 6.


Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges.

Blaser MJ, Cardon ZG, Cho MK, Dangl JL, Donohue TJ, Green JL, Knight R, Maxon ME, Northen TR, Pollard KS, Brodie EL.

MBio. 2016 May 13;7(3). pii: e00714-16. doi: 10.1128/mBio.00714-16.


Belowground Response to Drought in a Tropical Forest Soil. I. Changes in Microbial Functional Potential and Metabolism.

Bouskill NJ, Wood TE, Baran R, Ye Z, Bowen BP, Lim H, Zhou J, Nostrand JD, Nico P, Northen TR, Silver WL, Brodie EL.

Front Microbiol. 2016 Apr 20;7:525. doi: 10.3389/fmicb.2016.00525. eCollection 2016.


Belowground Response to Drought in a Tropical Forest Soil. II. Change in Microbial Function Impacts Carbon Composition.

Bouskill NJ, Wood TE, Baran R, Hao Z, Ye Z, Bowen BP, Lim HC, Nico PS, Holman HY, Gilbert B, Silver WL, Northen TR, Brodie EL.

Front Microbiol. 2016 Mar 15;7:323. doi: 10.3389/fmicb.2016.00323. eCollection 2016.


Exometabolomics Assisted Design and Validation of Synthetic Obligate Mutualism.

Kosina SM, Danielewicz MA, Mohammed M, Ray J, Suh Y, Yilmaz S, Singh AK, Arkin AP, Deutschbauer AM, Northen TR.

ACS Synth Biol. 2016 Jul 15;5(7):569-76. doi: 10.1021/acssynbio.5b00236. Epub 2016 Feb 17.


Application of Black Silicon for Nanostructure-Initiator Mass Spectrometry.

Gao J, de Raad M, Bowen BP, Zuckermann RN, Northen TR.

Anal Chem. 2016 Feb 2;88(3):1625-30. doi: 10.1021/acs.analchem.5b03452. Epub 2016 Jan 21.


Multifunctional cellulase catalysis targeted by fusion to different carbohydrate-binding modules.

Walker JA, Takasuka TE, Deng K, Bianchetti CM, Udell HS, Prom BM, Kim H, Adams PD, Northen TR, Fox BG.

Biotechnol Biofuels. 2015 Dec 21;8:220. doi: 10.1186/s13068-015-0402-0. eCollection 2015.


Use of Nanostructure-Initiator Mass Spectrometry to Deduce Selectivity of Reaction in Glycoside Hydrolases.

Deng K, Takasuka TE, Bianchetti CM, Bergeman LF, Adams PD, Northen TR, Fox BG.

Front Bioeng Biotechnol. 2015 Oct 27;3:165. doi: 10.3389/fbioe.2015.00165. eCollection 2015.


High-throughput platforms for metabolomics.

de Raad M, Fischer CR, Northen TR.

Curr Opin Chem Biol. 2016 Feb;30:7-13. doi: 10.1016/j.cbpa.2015.10.012. Epub 2015 Nov 4. Review.


Development of a High Throughput Platform for Screening Glycoside Hydrolases Based on Oxime-NIMS.

Deng K, Guenther JM, Gao J, Bowen BP, Tran H, Reyes-Ortiz V, Cheng X, Sathitsuksanoh N, Heins R, Takasuka TE, Bergeman LF, Geertz-Hansen H, Deutsch S, Loqué D, Sale KL, Simmons BA, Adams PD, Singh AK, Fox BG, Northen TR.

Front Bioeng Biotechnol. 2015 Oct 13;3:153. doi: 10.3389/fbioe.2015.00153. eCollection 2015.


Exometabolite niche partitioning among sympatric soil bacteria.

Baran R, Brodie EL, Mayberry-Lewis J, Hummel E, Da Rocha UN, Chakraborty R, Bowen BP, Karaoz U, Cadillo-Quiroz H, Garcia-Pichel F, Northen TR.

Nat Commun. 2015 Sep 22;6:8289. doi: 10.1038/ncomms9289.


Gut microbiota mediate caffeine detoxification in the primary insect pest of coffee.

Ceja-Navarro JA, Vega FE, Karaoz U, Hao Z, Jenkins S, Lim HC, Kosina P, Infante F, Northen TR, Brodie EL.

Nat Commun. 2015 Jul 14;6:7618. doi: 10.1038/ncomms8618.


Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust.

Nunes da Rocha U, Cadillo-Quiroz H, Karaoz U, Rajeev L, Klitgord N, Dunn S, Truong V, Buenrostro M, Bowen BP, Garcia-Pichel F, Mukhopadhyay A, Northen TR, Brodie EL.

Front Microbiol. 2015 Apr 14;6:277. doi: 10.3389/fmicb.2015.00277. eCollection 2015.


Exometabolomics and MSI: deconstructing how cells interact to transform their small molecule environment.

Silva LP, Northen TR.

Curr Opin Biotechnol. 2015 Aug;34:209-16. doi: 10.1016/j.copbio.2015.03.015. Epub 2015 Apr 5. Review.


Nanostructure imaging mass spectrometry: the role of fluorocarbons in metabolite analysis and yoctomole level sensitivity.

Kurczy ME, Northen TR, Trauger SA, Siuzdak G.

Methods Mol Biol. 2015;1203:141-9. doi: 10.1007/978-1-4939-1357-2_14. Review.


Metabolic imaging using nanostructure-initiator mass spectrometry (NIMS).

Louie KB, Northen TR.

Methods Mol Biol. 2014;1198:313-29. doi: 10.1007/978-1-4939-1258-2_21.


The lethal cargo of Myxococcus xanthus outer membrane vesicles.

Berleman JE, Allen S, Danielewicz MA, Remis JP, Gorur A, Cunha J, Hadi MZ, Zusman DR, Northen TR, Witkowska HE, Auer M.

Front Microbiol. 2014 Sep 9;5:474. doi: 10.3389/fmicb.2014.00474. eCollection 2014.


Phylogenomically guided identification of industrially relevant GH1 β-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry.

Heins RA, Cheng X, Nath S, Deng K, Bowen BP, Chivian DC, Datta S, Friedland GD, D'Haeseleer P, Wu D, Tran-Gyamfi M, Scullin CS, Singh S, Shi W, Hamilton MG, Bendall ML, Sczyrba A, Thompson J, Feldman T, Guenther JM, Gladden JM, Cheng JF, Adams PD, Rubin EM, Simmons BA, Sale KL, Northen TR, Deutsch S.

ACS Chem Biol. 2014 Sep 19;9(9):2082-91. doi: 10.1021/cb500244v. Epub 2014 Jul 17.


Rapid kinetic characterization of glycosyl hydrolases based on oxime derivatization and nanostructure-initiator mass spectrometry (NIMS).

Deng K, Takasuka TE, Heins R, Cheng X, Bergeman LF, Shi J, Aschenbrener R, Deutsch S, Singh S, Sale KL, Simmons BA, Adams PD, Singh AK, Fox BG, Northen TR.

ACS Chem Biol. 2014 Jul 18;9(7):1470-9. doi: 10.1021/cb5000289. Epub 2014 May 12.


High throughput nanostructure-initiator mass spectrometry screening of microbial growth conditions for maximal β-glucosidase production.

Cheng X, Hiras J, Deng K, Bowen B, Simmons BA, Adams PD, Singer SW, Northen TR.

Front Microbiol. 2013 Dec 6;4:365. doi: 10.3389/fmicb.2013.00365. eCollection 2013.


"Replica-extraction-transfer" nanostructure-initiator mass spectrometry imaging of acoustically printed bacteria.

Louie KB, Bowen BP, Cheng X, Berleman JE, Chakraborty R, Deutschbauer A, Arkin A, Northen TR.

Anal Chem. 2013 Nov 19;85(22):10856-62. doi: 10.1021/ac402240q. Epub 2013 Oct 29.


OpenMSI: a high-performance web-based platform for mass spectrometry imaging.

Rübel O, Greiner A, Cholia S, Louie K, Bethel EW, Northen TR, Bowen BP.

Anal Chem. 2013 Nov 5;85(21):10354-61. doi: 10.1021/ac402540a. Epub 2013 Oct 25.


Functional genomics of novel secondary metabolites from diverse cyanobacteria using untargeted metabolomics.

Baran R, Ivanova NN, Jose N, Garcia-Pichel F, Kyrpides NC, Gugger M, Northen TR.

Mar Drugs. 2013 Sep 30;11(10):3617-31. doi: 10.3390/md11103617.


Robust automated mass spectra interpretation and chemical formula calculation using mixed integer linear programming.

Baran R, Northen TR.

Anal Chem. 2013 Oct 15;85(20):9777-84. doi: 10.1021/ac402180c. Epub 2013 Sep 27.


Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust.

Rajeev L, da Rocha UN, Klitgord N, Luning EG, Fortney J, Axen SD, Shih PM, Bouskill NJ, Bowen BP, Kerfeld CA, Garcia-Pichel F, Brodie EL, Northen TR, Mukhopadhyay A.

ISME J. 2013 Nov;7(11):2178-91. doi: 10.1038/ismej.2013.83. Epub 2013 Jun 6.


Stable-isotope probing reveals that hydrogen isotope fractionation in proteins and lipids in a microbial community are different and species-specific.

Fischer CR, Bowen BP, Pan C, Northen TR, Banfield JF.

ACS Chem Biol. 2013 Aug 16;8(8):1755-63. doi: 10.1021/cb400210q. Epub 2013 Jun 5.


Mass spectrometry imaging for in situ kinetic histochemistry.

Louie KB, Bowen BP, McAlhany S, Huang Y, Price JC, Mao JH, Hellerstein M, Northen TR.

Sci Rep. 2013;3:1656. doi: 10.1038/srep01656.

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