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Deciphering cyanobacterial phenotypes for fast photoautotrophic growth via isotopically nonstationary metabolic flux analysis.

Abernathy MH, Yu J, Ma F, Liberton M, Ungerer J, Hollinshead WD, Gopalakrishnan S, He L, Maranas CD, Pakrasi HB, Allen DK, Tang YJ.

Biotechnol Biofuels. 2017 Nov 16;10:273. doi: 10.1186/s13068-017-0958-y. eCollection 2017.


Isotopically Nonstationary Metabolic Flux Analysis (INST-MFA) of Photosynthesis and Photorespiration in Plants.

Ma F, Jazmin LJ, Young JD, Allen DK.

Methods Mol Biol. 2017;1653:167-194. doi: 10.1007/978-1-4939-7225-8_12.


Rerouting of carbon flux in a glycogen mutant of cyanobacteria assessed via isotopically non-stationary 13 C metabolic flux analysis.

Hendry JI, Prasannan C, Ma F, Möllers KB, Jaiswal D, Digmurti M, Allen DK, Frigaard NU, Dasgupta S, Wangikar PP.

Biotechnol Bioeng. 2017 Oct;114(10):2298-2308. doi: 10.1002/bit.26350. Epub 2017 Jun 29.


Crops In Silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform.

Marshall-Colon A, Long SP, Allen DK, Allen G, Beard DA, Benes B, von Caemmerer S, Christensen AJ, Cox DJ, Hart JC, Hirst PM, Kannan K, Katz DS, Lynch JP, Millar AJ, Panneerselvam B, Price ND, Prusinkiewicz P, Raila D, Shekar RG, Shrivastava S, Shukla D, Srinivasan V, Stitt M, Turk MJ, Voit EO, Wang Y, Yin X, Zhu XG.

Front Plant Sci. 2017 May 15;8:786. doi: 10.3389/fpls.2017.00786. eCollection 2017.


Phospholipase Dζ Enhances Diacylglycerol Flux into Triacylglycerol.

Yang W, Wang G, Li J, Bates PD, Wang X, Allen DK.

Plant Physiol. 2017 May;174(1):110-123. doi: 10.1104/pp.17.00026. Epub 2017 Mar 21.


Synergism between inositol polyphosphates and TOR kinase signaling in nutrient sensing, growth control and lipid metabolism in Chlamydomonas.

Couso I, Evans B, Li J, Liu Y, Ma F, Diamond S, Allen DK, Umen JG.

Plant Cell. 2016 Sep 6. pii: tpc.00351.2016. [Epub ahead of print]


Perspectives for a better understanding of the metabolic integration of photorespiration within a complex plant primary metabolism network.

Hodges M, Dellero Y, Keech O, Betti M, Raghavendra AS, Sage R, Zhu XG, Allen DK, Weber AP.

J Exp Bot. 2016 May;67(10):3015-26. doi: 10.1093/jxb/erw145. Epub 2016 Apr 6. Review.


Assessing compartmentalized flux in lipid metabolism with isotopes.

Allen DK.

Biochim Biophys Acta. 2016 Sep;1861(9 Pt B):1226-1242. doi: 10.1016/j.bbalip.2016.03.017. Epub 2016 Mar 18. Review.


Interactions of C4 Subtype Metabolic Activities and Transport in Maize Are Revealed through the Characterization of DCT2 Mutants.

Weissmann S, Ma F, Furuyama K, Gierse J, Berg H, Shao Y, Taniguchi M, Allen DK, Brutnell TP.

Plant Cell. 2016 Feb;28(2):466-84. doi: 10.1105/tpc.15.00497. Epub 2016 Jan 26.


Quantifying plant phenotypes with isotopic labeling & metabolic flux analysis.

Allen DK.

Curr Opin Biotechnol. 2016 Feb;37:45-52. doi: 10.1016/j.copbio.2015.10.002. Epub 2015 Nov 21. Review.


Tracking the metabolic pulse of plant lipid production with isotopic labeling and flux analyses: Past, present and future.

Allen DK, Bates PD, Tjellström H.

Prog Lipid Res. 2015 Apr;58:97-120. doi: 10.1016/j.plipres.2015.02.002. Epub 2015 Mar 13. Review.


Transcriptional response to petiole heat girdling in cassava.

Zhang Y, Ding Z, Ma F, Chauhan RD, Allen DK, Brutnell TP, Wang W, Peng M, Li P.

Sci Rep. 2015 Feb 12;5:8414. doi: 10.1038/srep08414.


Isotopically nonstationary 13C flux analysis of changes in Arabidopsis thaliana leaf metabolism due to high light acclimation.

Ma F, Jazmin LJ, Young JD, Allen DK.

Proc Natl Acad Sci U S A. 2014 Nov 25;111(47):16967-72. doi: 10.1073/pnas.1319485111. Epub 2014 Nov 3.


Cytosolic phosphorylating glyceraldehyde-3-phosphate dehydrogenases affect Arabidopsis cellular metabolism and promote seed oil accumulation.

Guo L, Ma F, Wei F, Fanella B, Allen DK, Wang X.

Plant Cell. 2014 Jul;26(7):3023-35. doi: 10.1105/tpc.114.126946. Epub 2014 Jul 2.


Analysis of isotopic labeling in peptide fragments by tandem mass spectrometry.

Allen DK, Evans BS, Libourel IG.

PLoS One. 2014 Mar 13;9(3):e91537. doi: 10.1371/journal.pone.0091537. eCollection 2014.


Quantification of peptide m/z distributions from 13C-labeled cultures with high-resolution mass spectrometry.

Allen DK, Goldford J, Gierse JK, Mandy D, Diepenbrock C, Libourel IG.

Anal Chem. 2014 Feb 4;86(3):1894-901. doi: 10.1021/ac403985w. Epub 2014 Jan 21.


Metabolic flux analysis using ¹³C peptide label measurements.

Mandy DE, Goldford JE, Yang H, Allen DK, Libourel IG.

Plant J. 2014 Feb;77(3):476-86. doi: 10.1111/tpj.12390. Epub 2014 Jan 21.


Isotopically nonstationary MFA (INST-MFA) of autotrophic metabolism.

Jazmin LJ, O'Grady JP, Ma F, Allen DK, Morgan JA, Young JD.

Methods Mol Biol. 2014;1090:181-210. doi: 10.1007/978-1-62703-688-7_12.


Isotopomer measurement techniques in metabolic flux analysis II: mass spectrometry.

Young JD, Allen DK, Morgan JA.

Methods Mol Biol. 2014;1083:85-108. doi: 10.1007/978-1-62703-661-0_7.


Carbon and nitrogen provisions alter the metabolic flux in developing soybean embryos.

Allen DK, Young JD.

Plant Physiol. 2013 Mar;161(3):1458-75. doi: 10.1104/pp.112.203299. Epub 2013 Jan 11.

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