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Douglas K Allen (Doug)
Plant Genetics Research
Computational Biologist

Phone: (314) 587-1460
Fax: (314) 587-1560

975 N WARSON RD
St. Louis , MO 63132
Projects
Soybean Improvement through Quantitative and Computational Assessments of Phenotypic and Genotypic Diversity of Elemental, Central Carbon Metabolism, and Lipid Profiles
In-House Appropriated (D)
  Accession Number: 435034
Engineering C4 Photosynthesis in Maize to Enhance Nitrogen Utilization
Non-Funded Cooperative Agreement (N)
  Accession Number: 435190
Blocking Production of Non-metabolizable Carbohydrates by Enhancing Stable Oil Levels in Developing Soybean Seeds
Non-Funded Cooperative Agreement (N)
  Accession Number: 434071

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
The interaction of the soybean seed high oleic acid oil trait with other fatty acid modifications -
Bilyeu, K.D., Skrabisova, M., Allen, D.K., Rajcan, I., Palmquist, D.E., Gillen, A.M., Mian, R.M., Jo, H. 2018. The interaction of the soybean seed high oleic acid oil trait with other fatty acid modifications. Journal of the American Oil Chemists' Society. 95:39-49. https://doi.org/10.1002/aocs.12025.
Deciphering cyanobacterial phenotypes for fast photoautotrophic growth via isotopically nonstationary metabolic flux analysis -
Abernathy, M.H., Yu, J., Ma, F., Liberton, M., Ungerer, J., Hollinshead, W., Gopalakrishnan, S., He, L., Maranas, C.D., Pakrasi, H., Allen, D.K., Tang, Y. 2017. Deciphering cyanobacterial phenotypes for fast photoautotrophic growth via isotopically nonstationary metabolic flux analysis. Biotechnology for Biofuels. 10:273. https://doi.org/10.1186/s13068-017-0958-y.
Isotopically nonstationary metabolic flux analysis (INST-MFA) of photosynthesis and photorespiration in plants -
Rerouting of carbon flux in a glycogen mutant of cyanobacteria assessed via isotopically non-stationary 13C metabolic flux analysis Reprint Icon -
Hendry, J.I., Prasannan, C., Ma, F., Mollers, B., Jaiswal, D., Digmurti, M., Allen, D.K., Frigaard, N., Dasgupta, S., Wangikar, P.P. 2017. Rerouting of carbon flux in a glycogen mutant of cyanobacteria assessed via isotopically non-stationary 13C metabolic flux analysis. Biotechnology and Bioengineering. 114(10):2298-2308. doi: 10.1002/bit.26350.
Crops in silico: Generating virtual crops using an integrative and multi-scale modeling platform -
Marshall-Colon, A., Long, S.P., Allen, D.K., Allen, G.D., Beard, D., Benes, B., Caemmerer, S., Christensen, A., Cox, D.J., Hart, J., Hirst, P., Kannan, K., Katz, D.S., Lynch, J., Millar, A., Panneerselvan, B., Price, N., Prusinkiewicz, P., Raila, D., Shekar, R.G., Shrivastava, S., Shukla, D., Srinivasan, V., Stitt, M., Turk, M.J., Voit, E.O., Wang, Y., Yin, X., Zhu, X. 2017. Crops in silico: Generating virtual crops using an integrative and multi-scale modeling platform. Frontiers in Plant Science. 8:786. doi: 10.3389/fpls.2017.00786.
Phospholipase D¿ enhances diacylglycerol flux into triacylglycerol -
Yang, W., Wang, G., Li, J., Bates, P.D., Wang, X., Allen, D.K. 2017. Phospholipase D enhances diacylglycerol flux into triacylglycerol. Plant Physiology. 174(1):110-123. doi: 10.1104/pp.17.00026.
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, D.K., Umen, J.G. 2016. Synergism between inositol polyphosphates and TOR kinase signaling in nutrient sensing, growth control, and lipid metabolism in Chlamydomonas. The Plant Cell. 28(5):2026-2042. doi: 10.1105/tpc.16.00351.
Perspectives for a better understanding of the metabolic integration of photorespiration within a complex plant primary metabolism network Reprint Icon -
Hodges, M., Dellero, Y., Keech, O., Betti, M., Raghavendra, A.S., Sage, R., Zhu, X., Allen, D.K., Weber, A.P. 2016. Perspectives for a better understanding of the metabolic integration of photorespiration within a complex plant primary metabolism network. Journal of Experimental Botany. 67(10):3015-3026. doi:10.1093/jxb/erw145.
Assessing compartmentalized flux in lipid metabolism with isotopes Reprint Icon -
Allen, D.K. 2016. Assessing compartmentalized flux in lipid metabolism with isotopes. Biochimica et Biophysica Acta. doi:10.1016/j.bbalip.2016.03.017.
Interactions of C4 subtype metabolic activities and transport in maize are revealed through the characterization of DCT2 mutants Reprint Icon -
Weissmann, S., Ma, F., Furuyama, K., Gierse, J.K., Berg, H., Shao, Y., Taniguchi, M., Allen, D.K., Brutnell, T.P. 2016. Interactions of C4 subtype metabolic activities and transport in maize are revealed through the characterization of DCT2 mutants. The Plant Cell. 28:466-484.
Quantifying plant phenotypes with isotopic labeling and metabolic flux analysis Reprint Icon -
Allen, D.K. 2016. Quantifying plant phenotypes with isotopic labeling and metabolic flux analysis. Current Opinion in Biotechnology. 37:45-52. doi:10.1016/j.copbio.2015.10.002.
Tracking the metabolic pulse of plant lipid production with isotopic labeling and flux analyses: Past, present and future Reprint Icon -
Allen, D.K., Bates, P.D., Tjellstrom, H. 2015. Tracking the metabolic pulse of plant lipid production with isotopic labeling and flux analyses: Past, present and future. Progress in Lipid Research. 58:97-120.
Transcriptional response to petiole heat girdling in cassava Reprint Icon -
Zhang, Y., Ding, Z., Ma, F., Chauhan, R.D., Allen, D.K., Brutnell, T., Wang, W., Peng, M., Li, P. 2015. Transcriptional response to petiole heat girdling in cassava. Scientific Reports. 5:8414.
Isotopically nonstationary 13C flux analysis of changes in Arabidopsis thaliana leaf metabolism due to high light acclimation Reprint Icon -
Ma, F., Jazmin, L.J., Young, J.D., Allen, D.K. 2014. Isotopically nonstationary 13C flux analysis of changes in Arabidopsis thaliana leaf metabolism due to high light acclimation. Proceedings of the National Academy of Sciences. 111(47):16967-16972.
Analysis of isotopic labeling in peptide fragments by tandem mass spectrometry Reprint Icon -
Allen, D.K., Libourel, I.G. 2014. Analysis of isotopic labeling in peptide fragments by tandem mass spectrometry. PLoS One. 9(3):e91537. DOI:10.1371/journal.pone.0091537.
Quantification of peptide m/z distributions from 13C-labeled cultures with high resolution mass spectrometry Reprint Icon -
Allen, D.K., Goldford, J., Gierse, J.K., Mandy, D., Diepenbrock, C.H., Libourel, I. 2014. Quantification of peptide m/z distributions from 13C-labeled cultures with high resolution mass spectrometry. Analytical Chemistry. 86:1894-1901.
Metabolic flux analysis using 13C peptide label measurements Reprint Icon -
Mandy, D., Goldford, J., Yang, H., Allen, D.K., Libourel, I. 2013. Metabolic flux analysis using 13C peptide label measurements. Plant Journal. 77:476-486.
Carbon and nitrogen provisions alter the metabolic flux in developing soybean embryos Reprint Icon -
Allen, D.K., Young, J.D. 2013. Carbon and nitrogen provisions alter the metabolic flux in developing soybean embryos. Plant Physiology. 161:1458-1475.
Isotope labeling of rubisco subunits provides in vivo information on subcellular biosynthesis and exchange of amino acids between compartments. Reprint Icon -
Allen, D.K., Laclair, R.W., Ohlrogge, J.B., Shachar-Hill, Y. 2012. Isotope labeling of rubisco subunits provides in vivo information on subcellular biosynthesis and exchange of amino acids between compartments. Plant Cell and Environment. 35(7):1232-1244.
Rapid kinetic labeling of Arabidopsis cell suspension cultures: Implications for models of lipid export from plastids Reprint Icon -
Tjellstrom, H., Yang, Z., Allen, D.K., Ohlrogge, J.B. 2011. Rapid kinetic labeling of Arabidopsis cell suspension cultures: Implications for models of lipid export from plastids. Plant Physiology. 158:601-611.
Insights into primary metabolism in oilseeds from labeling and flux analysis -
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2 -
Thiele, I., Huduke, D.R., Steeb, B., Fankam, G., Allen, D.K., Bazzani, S., Charusanti, P., Chen, F., Fleming, R.M., Hsiung, C.A., Dekeersmaecker, S.C., Liao, Y., Marchal, K., Mo, M.L., Ozdemir, E., Raghunathan, A., Reed, J.L., Shin, S., Sigurbjornsdottir, S., Steinmann, J., Sudarsan, S., Swainston, N., Thijs, I.M., Zengler, K., Palsson, B.O., Adkins, J.N., Dirk, B. 2011. A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella typhimurium LT2. BMC Systems Biology. 5:8.
Synergy between 13C-metabolic flux analysis and flux balance analysis for understanding metabolic adaption to anaerobiosis in e. coli -
Chen, X., Alonso, A.P., Allen, D.K., Reed, J.L., Shachar-Hill, Y. 2010. Synergy between 13C-metabolic flux analysis and flux balance analysis for understanding metabolic adaption to anaerobiosis in E. coli. Metabolic Engineering. 13:38-48.