Alonso, A., Dieuaide-Noubhani, M. (2014). Plant metabolic flux analysis - Methods and Protocols.. Methods in molecular biology (Clifton, N.J.). 1090, .
Dieuaide-Noubhani, M., Alonso, A., Roby, C., Raymond, P. (2003). Mesures de flux métaboliques.. Other. 265-286. Versailles: INRA Editions.
Cocuron, J., Alonso, A. (2023). 13C-labeling reveals non-conventional pathways providing carbon for hydroxy fatty acid synthesis in Physaria fendleri. Journal of Experimental Botany. erad343, .
Castro-Morreti, F. R., Cocuron, J., Castillo-Gonzalez, H., Escudero-Leyva, E., Chaverri, P., Guerreiro-Filho, O., Slot, J. C., Alonso, A. (2023). A metabolomic platform to identify and quantify polyphenols in coffee and related species using liquid chromatography mass spectrometry. Frontiers in Plant Science.
Amir, R., Martinez-Force, E., Jianxin, S., Alonso, A. (2023). Editorial: Metabolic architecture of developing seeds and grains. Frontiers in Plant Science. 14, 1258353.
Al Sulaimi, R., Maknojia, A., Eskandari, M., Shirani, A., Gautam, B., Park, W., Whitehead, P., Alonso, A., Sedbrook, J. C., Chapman, K. D., Berman, D. (2023). Evaluating the Effects of Very Long Chain and Hydroxy Fatty Acid Content on Tribological Performance and Thermal Oxidation Behavior of Plant-Based Lubricants. Tribology International. 185, 108576.
Arias, C. L., Garcia Navarrete, L. T., Mukundi, E., Swanson, T., Yang, F., Grotewold, E., Alonso, A. (2023). Metabolic and transcriptomic study of pennycress natural variation identifies targets for oil improvement. Plant Biotechnology Journal. 21, 1887-1903.
Baker, C. R., Cocuron, J., Alonso, A., Niyogi, K. K. (2023). Time-resolved systems analysis of the induction of high photosynthetic capacity in Arabidopsis during acclimation to high light.. New Phytologist. 240(6), 2335-2352.
Sagun, J. V., Yadav, U. P., Alonso, A. (2023). Progress in understanding and improving oil content and quality in seeds. Frontiers in Plant Science. 14, 1116894.
Gentzel, I., Giese, L., Ekanayake, G., Mikhail, K., Zhao, W., Cocuron, J., Alonso, A., Mackey, D. (2022). Dynamic nutrient acquisition from a hydrated apoplast supports biotrophic proliferation of a bacterial pathogen of maize. Cell Host and Microbe. 30(4), 502-517.
Johnston, C., Carcia-Navarrete, T., Ortiz, E., Romsdahl, T. B., Guzha, A., Chapman, K. D., Grotewold, E., Alonso, A. (2022). Effective mechanisms for improving seed oil production in pennycress (Thlaspi arvense L.) highlighted by integration of comparative metabolomics and transcriptomics. Frontiers in Plant Science. 13, 943585.
Arias, C. L., Quach, T., Huynh, T., Nguyen, H., Moretti, A., Shi, Y., Guo, M., Rasoul, A., Van, K., McHale, L., Clemente, T. E., Alonso, A., Zhang, C. (2022). Expression of AtWRI1 and AtDGAT1 during soybean embryo development influences oil and carbohydrate metabolism.. Plant Biotechnology Journal. 20, 1327–1345.
Garcia-Navarrete, T., Arias, C., Mukundi, E., Alonso, A., Grotewold, E. (2022). Natural variation and improved genome annotation of the emerging biofuel crop field pennycress (Thlaspi arvense). G3: Genes, Genomes, Genetics. 12(6), jkac084.
Dokwal, D., Alonso, A., Cocuron, J., Dickstein, R. (2022). Metabolite shift in Medicago truncatula occurs in phosphorus deprivation. Journal of Experimental Botany. https://academic.oup.com/jxb/advance-article/doi/10.1093/jxb/erab559/6491222
Romsdahl, T. B., Cocuron, J. C., Pearson, M. J., Alonso, A., Chapman, K. D. (2022). A lipidomics platform to analyze the fatty acid compositions of non-polar and polar lipid molecular species from plant tissues: Examples from developing seeds and seedlings of pennycress (Thlaspi arvense).. Frontiers in Plant Science. 13, 1038161.
Destailleur, A., Poucet, T., Cabasson, C., Alonso, A., Cocuron, J., Larbat, R., Vercambe, G., Colombie, S., Petriaq, P., Andrieu, M., Beauvoit, B., Gibon, Y., Dieuaide-Noubhani, M. (2021). The evolution of leaf function during development is reflected in profound changes in the metabolic composition of the vacuole.. Metabolites. 11(12), 848.
Dokwal, D., Romsdahl, T. B., Kunz, D. A., Alonso, A., Dickstein, R. (2021). Phosphorus deprivation affects composition and spatial distribution of membrane lipids in legume nodules. Plant Physiology. https://watermark.silverchair.com/kiaa115.pdf
Castro-Moretti, F. R., Cocuron, J., Cia, M. C., Catacldi, T. R., Labate, C. A., Alonso, A., Camargo, L. E. (2021). Targeted metabolic profiles of leaves and xylem sap of two sugarcane genotypes infected with the vascular bacterial pathogen Leifsonia xyli subsp. xyli.. Metabolites. 11, 234.
Romsdahl, T. B., Kambhampati, S., Koley, S., Yadav, U. P., Alonso, A., Allen, D. K., Chapman, K. D. (2021). Analyzing Mass Spectrometry Imaging Data of <sup>13</sup>C-Labeled Phospholipids in <i>Camelina sativa</i> and <i>Thlaspi arvense</i> (Pennycress) Embryos.. Metabolites. 11(3), .
Moretti, A. R., Arias, C. L., Mozzoni, L. A., Chen, P., McNeece, B. T., Mian, M. R., McHale, L. K., Alonso, A. (2020). Workflow for the quantification of soluble and insoluble carbohydrates in soybean seed.. Molecules. 25(17), 3806.
Tsogtbaatar, E., Cocuron, J. C., Alonso, A. (2020). Non-conventional pathways enable pennycress (Thlaspi arvense L.) embryos to achieve high biosynthetic efficiency. Journal of Experimental Botany. 71(10), 3037-3051.
Castro-Moretti, F. R., Gentzel, I., Mackey, D., Alonso, A. (2020). Metabolomics as an emerging tool for the study of plant-pathogen interactions. Metabolites. 10(2), 52.
Castro-Moretti, F. R., Cocuron, J., Vega, F., Alonso, A. (2020). Differential Metabolic Responses Caused by the Most Important Insect Pest of Coffee Worldwide, the Coffee Berry Borer (Hypothenemus hampei). Journal of Agricultural and Food Chemistry. 68(8), 2597-2605.
Cocuron, J., Ross, Z., Alonso, A. (2020). Liquid Chromatography tandem Mass Spectrometry (LC-MS/MS) Quantification of 13C-Labeling in Sugars. Metabolites. 10(1), 30.
Cocuron, J., Koubaa, M., Kimmelfield, R., Ross, Z., Alonso, A. (2019). A Combined Metabolomics and Fluxomics Analysis Identifies Steps Limiting Oil Synthesis in Maize Embryos. Plant Physiology. 181, 961-975.
Huseby, C. J., Hoffman, C. N., Cooper, G. L., Cocuron, J. C., Alonso, A., Thomas, S. N., Yang, A. J., Kuret, J. (2019). Quantification of Tau Protein Lysine Methylation in Aging and Alzheimer's Disease. Journal of Alzheimer's Disease. 71(3), 979-991.
Gentzel, I., Giese, L., Zhao, W., Alonso, A., Mackey, D. (2019). A simple method for measuring apoplast hydration and collecting apoplast contents in maize. Plant Physiology. 179, 1265-1272.
Cocuron, J., Casas, M. I., Yang, F., Grotewold, E., Alonso, A. (2019). Beyond the wall: High-throughput quantification of plant soluble and cell-wall bound phenolics by liquid chromatography tandem mass spectrometry. Journal of Chromatography A. 1589, 93-104.
Cooper, G. L., Huseby, C. J., Chandler, C. N., Cocuron, J. C., Alonso, A., Kuret, J. (2018). A liquid chromatography tandem mass spectroscopy approach for quantification of protein methylation stoichiometry.. Analytical Biochemistry. 545, 72-77.
Dhakal, S., Balasubramaniam, V., Cocuron, J., Alonso, A., Agcam, E., Kamat, S. (2017). Pressure-thermal kinetics of furan formation in selected fruit and vegetable juices. Food and Bioprocess Technology. 10(11), 1959-1969.
Corkins, M. E., Wilson, S., Cocuron, J. C., Alonso, A., Bird, A. J. (2017). The gluconate shunt is an alternative route for directing glucose into the pentose phosphate pathway in fission yeast.. Journal of Biological Chemistry. 292(33), 13823-13832.
McClure, T., Cocuron, J. C., Osmark, V., McHale, L. K., Alonso, A. (2017). Impact of Environment on the Biomass Composition of Soybean (Glycine max) seeds.. Journal of Agricultural and Food Chemistry. 65(32), 6753-6761.
Casas, M. I., Vaughan, M. J., Bonello, P., McSpadden Gardener, B., Grotewold, E., Alonso, A. (2017). Identification of biochemical features of defective Coffea arabica L. beans.. Other. 95, 59-67.
Cocuron, J. C., Tsogtbaatar, E., Alonso, A. (2017). High-throughput quantification of the levels and labeling abundance of free amino acids by liquid chromatography tandem mass spectrometry.. Journal of Chromatography A. 1490, 148-155.
Horn, P. J., Liu, J., Cocuron, J. C., McGlew, K., Thrower, N. A., Larson, M., Lu, C., Alonso, A., Ohlrogge, J. (2016). Identification of multiple lipid genes with modifications in expression and sequence associated with the evolution of hydroxy fatty acid accumulation in Physaria fendleri.. The Plant journal : for cell and molecular biology. 86(4), 322-48.
De Souza, A. P., Cocuron, J. C., Garcia, A. C., Alonso, A., Buckeridge, M. S. (2015). Changes in Whole-Plant Metabolism during the Grain-Filling Stage in Sorghum Grown under Elevated CO2 and Drought.. Plant Physiology. 169(3), 1755-65.
Tsogtbaatar, E., Cocuron, J. C., Sonera, M. C., Alonso, A. (2015). Metabolite fingerprinting of pennycress (Thlaspi arvense L.) embryos to assess active pathways during oil synthesis.. Journal of Experimental Botany. 66(14), 4267-77.
Cocuron, J. C., Anderson, B., Boyd, A., Alonso, A. (2014). Targeted metabolomics of Physaria fendleri, an industrial crop producing hydroxy fatty acids.. Plant and Cell Physiology. 55(3), 620-33.
Dieuaide-Noubhani, M., Alonso, A. (2014). Application of metabolic flux analysis to plants.. Methods in molecular biology (Clifton, N.J.). 1090, 1-17.
Cocuron, J. C., Alonso, A. (2014). Liquid chromatography tandem mass spectrometry for measuring ¹³C-labeling in intermediates of the glycolysis and pentose phosphate pathway.. Methods in molecular biology (Clifton, N.J.). 1090, 131-42.
Chen, X., Alonso, A., Shachar-Hill, Y. (2013). Dynamic metabolic flux analysis of plant cell wall synthesis.. Other. 18, 78-85.
Koubaa, M., Cocuron, J. C., Thomasset, B., Alonso, A. (2013). Highlighting the tricarboxylic acid cycle: liquid and gas chromatography-mass spectrometry analyses of (13)C-labeled organic acids.. Analytical Biochemistry. 436(2), 151-9.
Wang, Y., Alonso, A., Wilkerson, C. G., Keegstra, K. (2012). Deep EST profiling of developing fenugreek endosperm to investigate galactomannan biosynthesis and its regulation.. Plant Molecular Biology. 79(3), 243-58.
Alonso, A., Val, D. L., Shachar-Hill, Y. (2011). Central metabolic fluxes in the endosperm of developing maize seeds and their implications for metabolic engineering.. Other. 13(1), 96-107.
Chen, X., Alonso, A., Allen, D. K., Reed, J. L., Shachar-Hill, Y. (2011). Synergy between (13)C-metabolic flux analysis and flux balance analysis for understanding metabolic adaptation to anaerobiosis in E. coli.. Other. 13(1), 38-48.
Alonso, A., Dale, V. L., Shachar-Hill, Y. (2010). Understanding fatty acid synthesis in developing maize embryos using metabolic flux analysis.. Other. 12(5), 488-97.
Alonso, A., Piasecki, R. J., Wang, Y., LaClair, R. W., Shachar-Hill, Y. (2010). Quantifying the labeling and the levels of plant cell wall precursors using ion chromatography tandem mass spectrometry.. Plant Physiology. 153(3), 915-24.
Dieuaide-Noubhani, M., Alonso, A., Roby, C., Raymond, P. (2007). Methods for the qualitative and quantitative analysis of metabolic fluxes. Other.
Alonso, A., Goffman, F. D., Ohlrogge, J. B., Shachar-Hill, Y. (2007). Carbon conversion efficiency and central metabolic fluxes in developing sunflower (Helianthus annuus L.) embryos.. The Plant journal : for cell and molecular biology. 52(2), 296-308.
Alonso, A., Raymond, P., Hernould, M., Rondeau-Mouro, C., de Graaf, A., Chourey, P., Lahaye, M., Shachar-Hill, Y., Rolin, D., Dieuaide-Noubhani, M. (2007). A metabolic flux analysis to study the role of sucrose synthase in the regulation of the carbon partitioning in central metabolism in maize root tips.. Other. 9(5-6), 419-32.
Alonso, A., Raymond, P., Rolin, D., Dieuaide-Noubhani, M. (2007). Substrate cycles in the central metabolism of maize root tips under hypoxia.. Phytochemistry. 68(16-18), 2222-31.
Cocuron, J. C., Lerouxel, O., Drakakaki, G., Alonso, A., Liepman, A. H., Keegstra, K., Raikhel, N., Wilkerson, C. G. (2007). A gene from the cellulose synthase-like C family encodes a beta-1,4 glucan synthase.. Proceedings of the National Academy of Sciences of the United States of America. 104(20), 8550-5.
Dieuaide-Noubhani, M., Alonso, A., Rolin, D., Eisenreich, W., Raymond, P. (2007). Metabolic flux analysis: recent advances in carbon metabolism in plants.. Other. 97, 213-43.
Alonso, A., Vigeolas, H., Raymond, P., Rolin, D., Dieuaide-Noubhani, M. (2005). A new substrate cycle in plants. Evidence for a high glucose-phosphate-to-glucose turnover from in vivo steady-state and pulse-labeling experiments with [13C]glucose and [14C]glucose.. Plant Physiology. 138(4), 2220-32.
Goffman, F. D., Alonso, A., Schwender, J., Shachar-Hill, Y., Ohlrogge, J. B. (2005). Light enables a very high efficiency of carbon storage in developing embryos of rapeseed.. Plant Physiology. 138(4), 2269-79.
Dejean, L., Beauvoit, B., Alonso, A., Bunoust, O., Guérin, B., Rigoulet, M. (2002). cAMP-induced modulation of the growth yield of Saccharomyces cerevisiae during respiratory and respiro-fermentative metabolism.. Biochimica et Biophysica Acta. 1554(3), 159-69.
