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ARS Home Midwest Area Columbia, Missouri Plant Genetics Research People & Locations







Douglas K Allen

(Doug)                                                                (PhD)
                        Plant Genetics Research

                        




                        
                        Computational Biologist
                        Phone: (314) 587-1460
                        
                        
                        Fax: (314) 587-1560(Employee information on this page comes from the REE Directory. Please contact your front office staff to update the REE Directory.)
                            ProjectsImproving Soybean Seed Composition, Plant Productivity, and Resilience to Climate Change Through Biological Network Modification
                                                    In-House Appropriated
                                                                    (D)Accession Number: 444222Beyond Static Metabolic Maps - Understanding the Cellular Organization and Dynamics of Lipid Flux For Enhanced Seed Oil Production
                                                    Non-Funded Cooperative Agreement
                                                                    (N)Accession Number: 443786Measurement of Acyl-ACPs and Lipid Precursors in Soybeans Over Development
                                                    Non-Assistance Cooperative Agreement
                                                                    (S)Accession Number: 436431Characterization of Lipid Turnover in Soybeans Over Development
                                                    Non-Assistance Cooperative Agreement
                                                                    (S)Accession Number: 442792**Publications**
                                                (Clicking on the reprint icon
                                                    Reprint Icon
                                                    will take you to the publication reprint.)SIMPEL: using stable isotopes to elucidate dynamics of context specific metabolism
                                                        

- (Peer Reviewed Journal)Kambhampati, S., Hubbard, A.H., Koley, S., Gomez, J.D., Marsolais, F., Evans, B.S., Young, J.D., Allen, D.K. 2024. SIMPEL: using stable isotopes to elucidate dynamics of context specific metabolism. Communications Biology. 7. Article 172. https://doi.org/10.1038/s42003-024-05844-z.Program for integration and rapid analysis of mass isotopomer distributions (PIRAMID)
                                                        

- (Peer Reviewed Journal)Gomez Castro, J.D., Wall, M.L., Rahim, M., Kambhampati, S., Evans, B.S., Allen, D.K., Antoniewicz, M.R., Young, J. 2023. Program for integration and rapid analysis of mass isotopomer distributions (PIRAMID). Bioinformatics. 39(11). Article btad661. https://doi.org/10.1093/bioinformatics/btad661.Physcomitrium patens response to elevated CO2 is flexible and
determined by an interaction between sugar and nitrogen
availability
                                                        

- (Peer Reviewed Journal)Mohanasundaram, B., Koley, S., Allen, D.K., Pandey, S. 2024. Physcomitrium patens response to elevated CO2 is flexible and determined by an interaction between sugar and nitrogen availability. New Phytologist. 241(3):1222-1235. https://doi.org/10.1111/nph.19348.Arabidopsis acyl carrier protein 4 and rhomboid like 10 act independently in chloroplast phosphatidic acid assembly

- (Peer Reviewed Journal)GmMFT: A potential step forward in soybean breeding for high oil and yield
                                                        

- (Other)Mukherjee, T., Tully, T., Allen, D.K. 2023. GmMFT: A potential step forward in soybean breeding for high oil and yield. New Phytologist. 239(3):815-817. https://doi.org/10.1111/nph.18950.Expression of malic enzyme reveals subcellular carbon partitioning for storage reserve production in soybeans
                                                        

- (Peer Reviewed Journal)Morley, S.A., Ma, F., Alazem, M., Frankfater, C., Yi, H., Burch-Smith, T., Clemente, T.E., Veena, V., Nguyen, H., Allen, D.K. 2023. Expression of malic enzyme reveals subcellular carbon partitioning for storage reserve production in soybeans. New Phytologist. 239(5):1834-1851. https://doi.org/10.1111/nph.18835.Depleting cationic lipids involved in antimicrobial resistance drives adaptive lipid remodeling in Enterococcus faecalis
                                                        

- (Peer Reviewed Journal)Rashid, R., Nair, Z.J., Chia, D.M., Chong, K.K., Gassiot, A.C., Morley, S.A., Allen, D.K., Chen, S.L., Chng, S.S., Wenk, M.R., Kline, K.A. 2023. Depleting cationic lipids involved in antimicrobial resistance drives adaptive lipid remodeling in Enterococcus faecalis. mBio. 14(1). https://doi.org/10.1128/mbio.03073-22.Metabolic synergy in Camelina reproductive tissues for seed development
                                                        

- (Peer Reviewed Journal)Koley, S., Chu, K.L., Mukherjee, T., Morley, S.A., Klebanovych, A., Czymmek, K.J., Allen, D.K. 2022. Metabolic synergy in Camelina reproductive tissues for seed development. Science Advances. 8(43). Article eabo7683. https://doi.org/10.1126/sciadv.abo7683.Comparative metabolic analysis reveals a metabolic switch in mature, hydrated, and germinated pollen in arabidopsis thaliana
                                                        

- (Peer Reviewed Journal)Wang, J., Kambhampati, S., Allen, D.K., Chen, L. 2022. Comparative metabolic analysis reveals a metabolic switch in mature, hydrated, and germinated pollen in arabidopsis thaliana. Frontiers in Plant Science. 13. Article 836665. https://doi.org/10.3389/fpls.2022.836665.Suppression of SDP1 improves soybean seed composition by increasing oil and reducing undigestible oligosaccharides
                                                        

- (Peer Reviewed Journal)Aznar-Moreno, J.A., Mukherjee, T., Morley, S.A., Duressa, D., Kambhampati, S., Chu, K.L., Koley, S., Allen, D.K., Durrett, T.P. 2022. Suppression of SDP1 improves soybean seed composition by increasing oil and reducing undigestible oligosaccharides. Plant Biotechnology Journal. 13. Article 863254. https://doi.org/10.3389/fpls.2022.863254.An efficient LC-MS method for isomer separation and detection of sugars, phosphorylated sugars, and organic acids
                                                        

- (Peer Reviewed Journal)Koley, S., Chu, K.L., Gill, S.S., Allen, D.K. 2022. An efficient LC-MS method for isomer separation and detection of sugars, phosphorylated sugars, and organic acids. Journal of Experimental Botany. 73(9):2938–2952. https://doi.org/10.1093/jxb/erac062.Metabolic flux analysis of the non-transitory starch tradeoff for lipid production in mature tobacco leaves
                                                        

- (Peer Reviewed Journal)Chu, K.L., Koley, S., Jenkins, L.M., Bailey, S.R., Kambhampati, S., Foley, K., Arp, J.J., Morley, S.A., Czymmek, K., Bates, P.D., Allen, D.K. 2022. Metabolic flux analysis of the non-transitory starch tradeoff for lipid production in mature tobacco leaves. Metabolic Engineering. 69:231-248. https://doi.org/10.1016/j.ymben.2021.12.003.Metabolic flux analysis of the non-transitory starch tradeoff for lipid production in mature tobacco leaves
                                                        

- (Peer Reviewed Journal)Chu, K.L., Koley, S., Jenkins, L.M., Bailey, S.R., Kambhampati, S., Foley, K., Arp, J.J., Morley, S.A., Czymmek, K.J., Bates, P.D., Allen, D.K. 2021. Metabolic flux analysis of the non-transitory starch tradeoff for lipid production in mature tobacco leaves. Plant Physiology. 69:231-248. https://doi.org/10.1016/j.ymben.2021.12.003.Sterile spikelets contribute to yield in sorghum and related grasses
                                                        

- (Peer Reviewed Journal)Aubuchon-Elder, T., Coneva, V., Goad, D.M., Jenkins, L.M., Yu, Y., Allen, D.K., Kellogg, E.A. 2020. Sterile spikelets contribute to yield in sorghum and related grasses. The Plant Cell. 32(11):3500-3518. https://doi.org/10.1105/tpc.20.00424.Analyzing mass spectrometry imaging data of 13C-labeled phospholipids in camelina sativa and thlaspi arvense (pennycress) embryos
                                                        

- (Peer Reviewed Journal)Romsdahl, T.B., Kambhampati, S., Koley, S., Yadav, U.P., Alonso, A.P., Allen, D.K., Chapman, K.D. 2021. Analyzing mass spectrometry imaging data of 13C-labeled phospholipids in camelina sativa and thlaspi arvense (pennycress) embryos. Metabolites. 11(3). Article e148. https://doi.org/10.3390/metabo11030148.Temporal changes in metabolism late in seed development affect biomass composition
                                                        

- (Peer Reviewed Journal)Kambhampati, S., Aznar-Moreno, J.A., Bailey, S.R., Arp, J.J., Chu, K., Bilyeu, K.D., Durrett, T.P., Allen, D.K. 2021. Temporal changes in metabolism late in seed development affect biomass composition. Plant Physiology. 186(2):874-890. https://doi.org/10.1093/plphys/kiab116.Quantification of acyl-acyl carrier proteins for fatty acid synthesis using LC-MS/MS
                                                        

- (Book / Chapter)Jenkins, L.M., Nam, J., Evans, B.S., Allen, D.K. 2021. Quantification of acyl-acyl carrier proteins for fatty acid synthesis using LC-MS/MS. Methods in Molecular Biology. 2295:219-247. https://doi.org/10.1007/978-1-0716-1362-7_13.A general method for quantification and discovery of acyl
groups attached to acyl carrier proteins in fatty acid
metabolism using LC-MS/MS
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (Book / Chapter)Fangfang, M., Jazmin, L.J., Young, J.D., Allen, D.K. 2017. Isotopically nonstationary metabolic flux analysis (INST-MFA) of photosynthesis and photorespiration in plants. Methods in Molecular Biology. 1653: 167-194. https://doi.org/10.1007/978-1-4939-7225-8_12.Rerouting of carbon flux in a glycogen mutant of cyanobacteria assessed via isotopically non-stationary 13C metabolic flux analysis
                                                        

- (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

- (Review Article)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
                                                        

- (Review Article)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
                                                        

- (Review Article)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
                                                        

- (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
                                                        

- (Review Article)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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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

- (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.

- (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

- (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.


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