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Items: 1 to 50 of 64

1.

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.

2.

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
3.

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.

4.

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
5.

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.

6.

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.

7.

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.

8.

Towards measuring growth rates of pathogens during infections by D2 O-labeling lipidomics.

Neubauer C, Sessions AL, Booth IR, Bowen BP, Kopf SH, Newman DK, Dalleska NF.

Rapid Commun Mass Spectrom. 2018 Dec 30;32(24):2129-2140. doi: 10.1002/rcm.8288.

PMID:
30252972
9.

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.

10.

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
11.

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.

12.

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
13.

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.

14.

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.

15.

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.

16.

Role of adipocyte mitochondria in inflammation, lipemia and insulin sensitivity in humans: effects of pioglitazone treatment.

Xie X, Sinha S, Yi Z, Langlais PR, Madan M, Bowen BP, Willis W, Meyer C.

Int J Obes (Lond). 2017 Aug 14. doi: 10.1038/ijo.2017.192. [Epub ahead of print]

17.

Exometabolomic Analysis of Cross-Feeding Metabolites.

Lubbe A, Bowen BP, Northen T.

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

18.

BASTet: Shareable and Reproducible Analysis and Visualization of Mass Spectrometry Imaging Data via OpenMSI.

Rubel O, Bowen BP.

IEEE Trans Vis Comput Graph. 2018 Jan;24(1):1025-1035. doi: 10.1109/TVCG.2017.2744479. Epub 2017 Aug 29.

19.

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
20.

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.

21.

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
22.

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.

23.

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.

24.

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.

25.

Proteomics analyses of subcutaneous adipocytes reveal novel abnormalities in human insulin resistance.

Xie X, Yi Z, Sinha S, Madan M, Bowen BP, Langlais P, Ma D, Mandarino L, Meyer C.

Obesity (Silver Spring). 2016 Jul;24(7):1506-14. doi: 10.1002/oby.21528.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

An accessible, scalable ecosystem for enabling and sharing diverse mass spectrometry imaging analyses.

Fischer CR, Ruebel O, Bowen BP.

Arch Biochem Biophys. 2016 Jan 1;589:18-26. doi: 10.1016/j.abb.2015.08.021. Epub 2015 Sep 11. Review.

32.

Analysis of Metabolomics Datasets with High-Performance Computing and Metabolite Atlases.

Yao Y, Sun T, Wang T, Ruebel O, Northen T, Bowen BP.

Metabolites. 2015 Jul 20;5(3):431-42. doi: 10.3390/metabo5030431.

33.

Dirigent Protein-Mediated Lignan and Cyanogenic Glucoside Formation in Flax Seed: Integrated Omics and MALDI Mass Spectrometry Imaging.

Dalisay DS, Kim KW, Lee C, Yang H, Rübel O, Bowen BP, Davin LB, Lewis NG.

J Nat Prod. 2015 Jun 26;78(6):1231-42. doi: 10.1021/acs.jnatprod.5b00023. Epub 2015 May 17.

34.

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.

35.

Identifying important ions and positions in mass spectrometry imaging data using CUR matrix decompositions.

Yang J, Rübel O, Prabhat, Mahoney MW, Bowen BP.

Anal Chem. 2015;87(9):4658-66. doi: 10.1021/ac5040264. Epub 2015 Apr 13.

PMID:
25825055
36.

MIDAS: a database-searching algorithm for metabolite identification in metabolomics.

Wang Y, Kora G, Bowen BP, Pan C.

Anal Chem. 2014 Oct 7;86(19):9496-503. doi: 10.1021/ac5014783. Epub 2014 Sep 11.

PMID:
25157598
37.

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.

38.

"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.

PMID:
24111681
39.

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.

PMID:
24087878
40.

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.

41.

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.

PMID:
23713674
42.

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.

43.

Metabolites associated with adaptation of microorganisms to an acidophilic, metal-rich environment identified by stable-isotope-enabled metabolomics.

Mosier AC, Justice NB, Bowen BP, Baran R, Thomas BC, Northen TR, Banfield JF.

MBio. 2013 Mar 12;4(2):e00484-12. doi: 10.1128/mBio.00484-12.

44.

Differential intrahepatic phospholipid zonation in simple steatosis and nonalcoholic steatohepatitis.

Wattacheril J, Seeley EH, Angel P, Chen H, Bowen BP, Lanciault C, Caprioli RM, Abumrad N, Flynn CR.

PLoS One. 2013;8(2):e57165. doi: 10.1371/journal.pone.0057165. Epub 2013 Feb 25.

45.

Effect of exercise on the skeletal muscle proteome in patients with type 2 diabetes.

Hussey SE, Sharoff CG, Garnham A, Yi Z, Bowen BP, Mandarino LJ, Hargreaves M.

Med Sci Sports Exerc. 2013 Jun;45(6):1069-76. doi: 10.1249/MSS.0b013e3182814917.

46.

Metabolic footprinting of mutant libraries to map metabolite utilization to genotype.

Baran R, Bowen BP, Price MN, Arkin AP, Deutschbauer AM, Northen TR.

ACS Chem Biol. 2013 Jan 18;8(1):189-99. doi: 10.1021/cb300477w. Epub 2012 Oct 31.

PMID:
23082955
47.

Low-dose ionizing radiation-induced blood plasma metabolic response in a diverse genetic mouse population.

Lee DY, Bowen BP, Nguyen DH, Parsa S, Huang Y, Mao JH, Northen TR.

Radiat Res. 2012 Dec;178(6):551-5. doi: 10.1667/RR2990.1. Epub 2012 Oct 10.

PMID:
23051006
48.

Reduction in inflammatory gene expression in skeletal muscle from Roux-en-Y gastric bypass patients randomized to omentectomy.

Tamboli RA, Hajri T, Jiang A, Marks-Shulman PA, Williams DB, Clements RH, Melvin W, Bowen BP, Shyr Y, Abumrad NN, Flynn CR.

PLoS One. 2011;6(12):e28577. doi: 10.1371/journal.pone.0028577. Epub 2011 Dec 16.

49.

Untargeted metabolic footprinting reveals a surprising breadth of metabolite uptake and release by Synechococcus sp. PCC 7002.

Baran R, Bowen BP, Northen TR.

Mol Biosyst. 2011 Dec;7(12):3200-6. doi: 10.1039/c1mb05196b. Epub 2011 Sep 21.

PMID:
21935552
50.

Improved genome annotation through untargeted detection of pathway-specific metabolites.

Bowen BP, Fischer CR, Baran R, Banfield JF, Northen T.

BMC Genomics. 2011 Jun 15;12 Suppl 1:S6. doi: 10.1186/1471-2164-12-S1-S6.

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