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Items: 1 to 50 of 87

1.

Learning representations of microbe-metabolite interactions.

Morton JT, Aksenov AA, Nothias LF, Foulds JR, Quinn RA, Badri MH, Swenson TL, Van Goethem MW, Northen TR, Vazquez-Baeza Y, Wang M, Bokulich NA, Watters A, Song SJ, Bonneau R, Dorrestein PC, Knight R.

Nat Methods. 2019 Dec;16(12):1306-1314. doi: 10.1038/s41592-019-0616-3. Epub 2019 Nov 4.

PMID:
31686038
2.

Impacts of Maize Domestication and Breeding on Rhizosphere Microbial Community Recruitment from a Nutrient Depleted Agricultural Soil.

Brisson VL, Schmidt JE, Northen TR, Vogel JP, Gaudin ACM.

Sci Rep. 2019 Oct 30;9(1):15611. doi: 10.1038/s41598-019-52148-y.

3.

Taxonomic and Metabolic Incongruence in the Ancient Genus Streptomyces.

Chevrette MG, Carlos-Shanley C, Louie KB, Bowen BP, Northen TR, Currie CR.

Front Microbiol. 2019 Sep 20;10:2170. doi: 10.3389/fmicb.2019.02170. eCollection 2019.

4.

Cooking shapes the structure and function of the gut microbiome.

Carmody RN, Bisanz JE, Bowen BP, Maurice CF, Lyalina S, Louie KB, Treen D, Chadaideh KS, Maini Rekdal V, Bess EN, Spanogiannopoulos P, Ang QY, Bauer KC, Balon TW, Pollard KS, Northen TR, Turnbaugh PJ.

Nat Microbiol. 2019 Dec;4(12):2052-2063. doi: 10.1038/s41564-019-0569-4. Epub 2019 Sep 30.

PMID:
31570867
5.

Probing the active fraction of soil microbiomes using BONCAT-FACS.

Couradeau E, Sasse J, Goudeau D, Nath N, Hazen TC, Bowen BP, Chakraborty R, Malmstrom RR, Northen TR.

Nat Commun. 2019 Jun 24;10(1):2770. doi: 10.1038/s41467-019-10542-0.

6.

EcoFABs: advancing microbiome science through standardized fabricated ecosystems.

Zengler K, Hofmockel K, Baliga NS, Behie SW, Bernstein HC, Brown JB, Dinneny JR, Floge SA, Forry SP, Hess M, Jackson SA, Jansson C, Lindemann SR, Pett-Ridge J, Maranas C, Venturelli OS, Wallenstein MD, Shank EA, Northen TR.

Nat Methods. 2019 Jul;16(7):567-571. doi: 10.1038/s41592-019-0465-0. No abstract available.

7.

A High-Throughput Mass Spectrometric Enzyme Activity Assay Enabling the Discovery of Cytochrome P450 Biocatalysts.

de Rond T, Gao J, Zargar A, de Raad M, Cunha J, Northen TR, Keasling JD.

Angew Chem Int Ed Engl. 2019 Jul 22;58(30):10114-10119. doi: 10.1002/anie.201901782. Epub 2019 Jun 13.

PMID:
31140688
8.

Optimizing de novo genome assembly from PCR-amplified metagenomes.

Roux S, Trubl G, Goudeau D, Nath N, Couradeau E, Ahlgren NA, Zhan Y, Marsan D, Chen F, Fuhrman JA, Northen TR, Sullivan MB, Rich VI, Malmstrom RR, Eloe-Fadrosh EA.

PeerJ. 2019 May 9;7:e6902. doi: 10.7717/peerj.6902. eCollection 2019.

9.

Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms.

Diamond S, Andeer PF, Li Z, Crits-Christoph A, Burstein D, Anantharaman K, Lane KR, Thomas BC, Pan C, Northen TR, Banfield JF.

Nat Microbiol. 2019 Aug;4(8):1356-1367. doi: 10.1038/s41564-019-0449-y. Epub 2019 May 20.

10.

Lessons from Two Design-Build-Test-Learn Cycles of Dodecanol Production in Escherichia coli Aided by Machine Learning.

Opgenorth P, Costello Z, Okada T, Goyal G, Chen Y, Gin J, Benites V, de Raad M, Northen TR, Deng K, Deutsch S, Baidoo EEK, Petzold CJ, Hillson NJ, Garcia Martin H, Beller HR.

ACS Synth Biol. 2019 Jun 21;8(6):1337-1351. doi: 10.1021/acssynbio.9b00020. Epub 2019 May 24.

PMID:
31072100
11.

Enzyme promiscuity shapes adaptation to novel growth substrates.

Guzmán GI, Sandberg TE, LaCroix RA, Nyerges Á, Papp H, de Raad M, King ZA, Hefner Y, Northen TR, Notebaart RA, Pál C, Palsson BO, Papp B, Feist AM.

Mol Syst Biol. 2019 Apr 8;15(4):e8462. doi: 10.15252/msb.20188462.

12.

A New Method to Correct for Habitat Filtering in Microbial Correlation Networks.

Brisson V, Schmidt J, Northen TR, Vogel JP, Gaudin A.

Front Microbiol. 2019 Mar 20;10:585. doi: 10.3389/fmicb.2019.00585. eCollection 2019.

13.

MAGI: A Method for Metabolite Annotation and Gene Integration.

Erbilgin O, Rübel O, Louie KB, Trinh M, Raad M, Wildish T, Udwary D, Hoover C, Deutsch S, Northen TR, Bowen BP.

ACS Chem Biol. 2019 Apr 19;14(4):704-714. doi: 10.1021/acschembio.8b01107. Epub 2019 Apr 4.

PMID:
30896917
14.

Regulation of Oxygenic Photosynthesis during Trophic Transitions in the Green Alga Chromochloris zofingiensis.

Roth MS, Gallaher SD, Westcott DJ, Iwai M, Louie KB, Mueller M, Walter A, Foflonker F, Bowen BP, Ataii NN, Song J, Chen JH, Blaby-Haas CE, Larabell C, Auer M, Northen TR, Merchant SS, Niyogi KK.

Plant Cell. 2019 Mar;31(3):579-601. doi: 10.1105/tpc.18.00742. Epub 2019 Feb 20.

15.

Microbial Ecology on Solar Panels in Berkeley, CA, United States.

Porcar M, Louie KB, Kosina SM, Van Goethem MW, Bowen BP, Tanner K, Northen TR.

Front Microbiol. 2018 Dec 11;9:3043. doi: 10.3389/fmicb.2018.03043. eCollection 2018.

16.

Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass.

Sasse J, Kant J, Cole BJ, Klein AP, Arsova B, Schlaepfer P, Gao J, Lewald K, Zhalnina K, Kosina S, Bowen BP, Treen D, Vogel J, Visel A, Watt M, Dangl JL, Northen TR.

New Phytol. 2019 Apr;222(2):1149-1160. doi: 10.1111/nph.15662. Epub 2019 Jan 24.

17.

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.

PMID:
30421224
18.

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.

19.

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.

20.

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.

PMID:
30063326
21.

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.

22.

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.

23.

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.

PMID:
29556109
24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

PMID:
28520405
30.

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.

31.

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.

32.

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.

PMID:
28467051
33.

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.

34.

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.

35.

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.

36.

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.

PMID:
27957569
37.

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.

38.

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.

39.

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.

40.

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.

PMID:
27548700
41.

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.

42.

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.

43.

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.

44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

PMID:
26544850
49.

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.

50.

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.

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