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Items: 1 to 50 of 111

1.

Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere.

Doud DFR, Bowers RM, Schulz F, De Raad M, Deng K, Tarver A, Glasgow E, Vander Meulen K, Fox B, Deutsch S, Yoshikuni Y, Northen T, Hedlund BP, Singer SW, Ivanova N, Woyke T.

ISME J. 2019 Nov 21. doi: 10.1038/s41396-019-0557-y. [Epub ahead of print]

PMID:
31754206
2.

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
3.

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.

4.

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.

5.

CRAGE enables rapid activation of biosynthetic gene clusters in undomesticated bacteria.

Wang G, Zhao Z, Ke J, Engel Y, Shi YM, Robinson D, Bingol K, Zhang Z, Bowen B, Louie K, Wang B, Evans R, Miyamoto Y, Cheng K, Kosina S, De Raad M, Silva L, Luhrs A, Lubbe A, Hoyt DW, Francavilla C, Otani H, Deutsch S, Washton NM, Rubin EM, Mouncey NJ, Visel A, Northen T, Cheng JF, Bode HB, Yoshikuni Y.

Nat Microbiol. 2019 Dec;4(12):2498-2510. doi: 10.1038/s41564-019-0573-8. Epub 2019 Oct 14.

PMID:
31611640
6.

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
7.

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.

8.

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.

9.

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
10.

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.

11.

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.

12.

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
13.

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.

14.

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.

15.

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
16.

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.

17.

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.

18.

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.

19.

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
20.

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.

21.

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.

22.

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
23.

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.

24.

Deciphering microbial interactions in synthetic human gut microbiome communities.

Venturelli OS, Carr AC, Fisher G, Hsu RH, Lau R, Bowen BP, Hromada S, Northen T, Arkin AP.

Mol Syst Biol. 2018 Jun 21;14(6):e8157. doi: 10.15252/msb.20178157.

25.

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.

26.

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
27.

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.

28.

Large Blooms of Bacillales (Firmicutes) Underlie the Response to Wetting of Cyanobacterial Biocrusts at Various Stages of Maturity.

Karaoz U, Couradeau E, da Rocha UN, Lim HC, Northen T, Garcia-Pichel F, Brodie EL.

MBio. 2018 Mar 6;9(2). pii: e01366-16. doi: 10.1128/mBio.01366-16.

29.

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.

30.

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.

31.

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.

32.

Feed Your Friends: Do Plant Exudates Shape the Root Microbiome?

Sasse J, Martinoia E, Northen T.

Trends Plant Sci. 2018 Jan;23(1):25-41. doi: 10.1016/j.tplants.2017.09.003. Epub 2017 Oct 17. Review.

33.

Exometabolomic Analysis of Cross-Feeding Metabolites.

Lubbe A, Bowen BP, Northen T.

Metabolites. 2017 Oct 4;7(4). pii: E50. doi: 10.3390/metabo7040050.

34.

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.

35.

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
36.

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.

37.

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.

38.

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
39.

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.

40.

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.

41.

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.

42.

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
43.

Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone.

Butterfield CN, Li Z, Andeer PF, Spaulding S, Thomas BC, Singh A, Hettich RL, Suttle KB, Probst AJ, Tringe SG, Northen T, Pan C, Banfield JF.

PeerJ. 2016 Nov 8;4:e2687. eCollection 2016.

44.

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.

45.

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.

46.

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.

47.

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
48.

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.

Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, P CAB, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N.

Nat Biotechnol. 2016 Aug 9;34(8):828-837. doi: 10.1038/nbt.3597.

49.

New insight into the role of MMP14 in metabolic balance.

Mori H, Bhat R, Bruni-Cardoso A, Chen EI, Jorgens DM, Coutinho K, Louie K, Bowen BB, Inman JL, Tecca V, Lee SJ, Becker-Weimann S, Northen T, Seiki M, Borowsky AD, Auer M, Bissell MJ.

PeerJ. 2016 Jul 13;4:e2142. doi: 10.7717/peerj.2142. eCollection 2016.

50.

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.

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