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ARS Home » Midwest Area » Columbia, Missouri » Plant Genetics Research » People & Locations » Douglas Allen (Doug)

Douglas K Allen (Doug) (PhD)
Plant Genetics Research
Computational Biologist

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

975 N WARSON RD
St. Louis, MO 63132
Projects
Enhancing Stable Protein Levels in Developing Soybean Seeds
Cooperative Agreement (A)
  Accession Number: 437425
Enhancing Stable Protein Levels in Developing Soybean Seeds
Cooperative Agreement (A)
  Accession Number: 437426
Enhancing Protein Quality While Maintaining Protein Amount with Insights Generated from Soybean Mutants - (Donald Danforth Plant Science Center)
Cooperative Agreement (A)
  Accession Number: 437543
Enhancing Protein Quality While Maintaining Protein Amount with Insights Generated from Soybean Mutants - (Kansas State University)
Cooperative Agreement (A)
  Accession Number: 437544
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
Discovering New Metabolic Constraints and Regulatory Nodes in Oilseeds Engineered for Enhanced Fatty Acid Synthesis and Seed Oil
Non-Funded Cooperative Agreement (N)
  Accession Number: 436421
Enhancing Protein Quality While Maintaining Protein Amount with Insights Generated from Soybean Mutants
Reimbursable Cooperative Agreement (R)
  Accession Number: 437443
Enhancing Stable Protein Levels in Developing Soybean Seeds
Reimbursable Cooperative Agreement (R)
  Accession Number: 437309
Measurement of Acyl-ACPs and Lipid Precursors in Soybeans Over Development
Non-Assistance Cooperative Agreement (S)
  Accession Number: 436431

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
A general method for quantification and discovery of acyl groups attached to acyl carrier proteins in fatty acid metabolism using LC-MS/MS Reprint Icon - (Peer Reviewed Journal)
Nam, J., Jenkins, L.M., Li, J., Evans, B.S., Jaworski, J., Allen, D.K. 2020. A general method for quantification and discovery of acyl groups attached to acyl carrier proteins in fatty acid metabolism using LC-MS/MS. The Plant Cell. 32:820–832. https://doi.org/10.1105/tpc.19.00954.
Application of stable isotope tracing to elucidate metabolic dynamics during Yarrowia lipolytica a-ionone fermentation Reprint Icon - (Peer Reviewed Journal)
Czajka, J.J., Kambhampati, S., Tang, Y.J., Wang, Y., Allen, D.K. 2020. Application of stable isotope tracing to elucidate metabolic dynamics during Yarrowia lipolytica a-ionone fermentation. iScience. 23(2):100854. https://doi.org/10.1016/j.isci.2020.100854.
On the inverse correlation of protein and oil: Examining the effects of altered central carbon metabolism on seed composition using soybean fast neutron mutants Reprint Icon - (Peer Reviewed Journal)
Kambhampati, S., Aznar-Moreno, J.A., Hostetler, C., Caso, T., Bailey, S.R., Hubbard, A.H., Durrett, T.P., Allen, D.K. 2019. On the inverse correlation of protein and oil: Examining the effects of altered central carbon metabolism on seed composition using soybean fast neutron mutants. Metabolites. 10(1):18. https://doi.org/10.3390/metabo10010018.
Reorganization of acyl flux through the lipid metabolic network in oil-accumulating tobacco leaves Reprint Icon - (Peer Reviewed Journal)
Zhou, X., Bhandari, S., Johnson, B.S., Kotapati, H., Allen, D.K., Vanhercke, T., Bates, P.D. 2020. Reorganization of acyl flux through the lipid metabolic network in oil-accumulating tobacco leaves. Plant Physiology. 182(2):739-755. https://doi.org/10.1104/pp.19.00667.
Tracing metabolic flux through time and space with isotope labeling experiments Reprint Icon - (Peer Reviewed Journal)
Allen, D.K., Young, J.D. 2020. Tracing metabolic flux through time and space with isotope labeling experiments. Current Opinion in Biotechnology. 64:92-100. https://doi.org/10.1016/j.copbio.2019.11.003.
Accurate and efficient amino acid analysis for protein quantification using hydrophilic interaction chromatography coupled tandem mass spectrometry Reprint Icon - (Peer Reviewed Journal)
Kambhampati, S., Li, J., Evans, B.S., Allen, D.K. 2019. Accurate and efficient amino acid analysis for protein quantification using hydrophilic interaction chromatography coupled tandem mass spectrometry. Plant Methods. 15:46. https://doi.org/10.1186/s13007-019-0430-z.
Cyanobacterial carboxysome mutant analysis reveals the influence of enzyme compartmentalization on cellular metabolism and metabolic network rigidity Reprint Icon - (Peer Reviewed Journal)
Abernathy, M., Czajka, J., Allen, D.K., Hill, N.C., Cameron, J.C., Tang, Y.J. 2019. Cyanobacterial carboxysome mutant analysis reveals the influence of enzyme compartmentalization on cellular metabolism and metabolic network rigidity. Metabolic Engineering. 54:222-231. https://doi.org/10.1016/j.ymben.2019.04.010.
The interaction of the soybean seed high oleic acid oil trait with other fatty acid modifications - (Peer Reviewed Journal)
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 Reprint Icon - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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 - (Abstract Only)
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2 - (Peer Reviewed Journal)
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 - (Peer Reviewed Journal)
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.