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Items: 19

1.

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.

2.

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.

3.

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.

4.

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.

5.

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.

6.

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.

7.

Lineage-specific chromatin signatures reveal a regulator of lipid metabolism in microalgae.

Ngan CY, Wong CH, Choi C, Yoshinaga Y, Louie K, Jia J, Chen C, Bowen B, Cheng H, Leonelli L, Kuo R, Baran R, García-Cerdán JG, Pratap A, Wang M, Lim J, Tice H, Daum C, Xu J, Northen T, Visel A, Bristow J, Niyogi KK, Wei CL.

Nat Plants. 2015 Jul 27;1:15107. doi: 10.1038/nplants.2015.107.

PMID:
27250540
8.

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.

9.

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.

PMID:
24032353
10.

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.

11.

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
12.

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
13.

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.

14.

Metabolite identification in Synechococcus sp. PCC 7002 using untargeted stable isotope assisted metabolite profiling.

Baran R, Bowen BP, Bouskill NJ, Brodie EL, Yannone SM, Northen TR.

Anal Chem. 2010 Nov 1;82(21):9034-42. doi: 10.1021/ac1020112. Epub 2010 Oct 14.

PMID:
20945921
15.

Mass spectrometry based metabolomics and enzymatic assays for functional genomics.

Baran R, Reindl W, Northen TR.

Curr Opin Microbiol. 2009 Oct;12(5):547-52. doi: 10.1016/j.mib.2009.07.004. Epub 2009 Aug 18. Review.

PMID:
19695948
16.

Visualization of three-way comparisons of omics data.

Baran R, Robert M, Suematsu M, Soga T, Tomita M.

BMC Bioinformatics. 2007 Mar 5;8:72.

17.

MathDAMP: a package for differential analysis of metabolite profiles.

Baran R, Kochi H, Saito N, Suematsu M, Soga T, Nishioka T, Robert M, Tomita M.

BMC Bioinformatics. 2006 Dec 13;7:530.

18.

Metabolomics approach for enzyme discovery.

Saito N, Robert M, Kitamura S, Baran R, Soga T, Mori H, Nishioka T, Tomita M.

J Proteome Res. 2006 Aug;5(8):1979-87.

PMID:
16889420
19.

Differential metabolomics reveals ophthalmic acid as an oxidative stress biomarker indicating hepatic glutathione consumption.

Soga T, Baran R, Suematsu M, Ueno Y, Ikeda S, Sakurakawa T, Kakazu Y, Ishikawa T, Robert M, Nishioka T, Tomita M.

J Biol Chem. 2006 Jun 16;281(24):16768-76. Epub 2006 Apr 11.

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