Diabetes and Obesity

  1. Egnatchik, R. A., Brittain, E. L., Shah, A. T., Fares, W. H., Ford, H. J., Monahan, K., ... & J. D. Young. Dysfunctional BMPR2 signaling drives an abnormal endothelial requirement for glutamine in pulmonary arterial hypertension. Pulmonary Circulation, 7(1), 186-199, 2017. [Link to article]
  2. C. M. Hasenour, D. E. Ridley, F. D. James, E. P. Donahue, B. Viollet, M. Foretz, J. D. Young, D. H. Wasserman. Liver AMP-activated protein kinase is unnecessary for gluconeogenesis but protects energy state during nutrient deprivation. PLoS ONE 12:e0170382, 2017. [Link to article]
  3. A. K. Leamy, C. M. Hasenour, R. A. Egnatchik, I. A. Trenary, C. Yao, G. J. Patti, M. Shiota, J. D. Young. Knockdown of triglyceride synthesis does not enhance palmitate lipotoxicity or prevent oleate-mediated rescue in rat hepatocytes. BBA-Molecular and Cell Biology of Lipids 1861:1005-1014, 2016. [Link to article]
  4. C.M. Hasenour, M.L. Wall, D.E. Ridley, C.C. Hughey, F.D. James, D.H. Wasserman J.D. Young. Mass Spectrometry-Based Microassay of 2H and 13C Plasma Glucose Labeling to Quantify Liver Metabolic Fluxes In vivo. American Journal of Physiology 309:E191-E203, 2015.  [Link to article]
  5. M.L. Wall, L.D. Pound, I. Trenary, R.M. O'Brien, J.D. Young. Novel stable isotope analyses demonstrate significant rates of glucose cycling in mouse pancreatic islets. Diabetes 64:2129-2137, 2015.  [Link to article]
  6. A.K. Leamy, R.A. Egnatchik, M. Shiota, P.T. Ivanova, D.S. Myers, H.A. Brown, J.D. Young. Enhanced synthesis of saturated phospholipids is associated with ER stress and lipotoxicity in palmitate treated hepatic cells. Journal of Lipid Research 55:1478-88, 2014.  [Link to article]
  7. R.A. Egnatchik, A.K. Leamy, D.A. Jacobson, M. Shiota, J.D. Young. ER calcium release promotes mitochondrial dysfunction and hepatic cell lipotoxicity in response to palmitate overload. Molecular Metabolism 3:544-553, 2014.  [Link to article]
  8. R. A. Egnatchik, A. K. Leamy, Y. Noguchi, M. Shiota, J. D. Young. Palmitate-induced activation of mitochondrial metabolism promotes oxidative stress and apoptosis in H4IIEC3 rat hepatocytes. Metabolism 63:283-295, 2014.  [Link to article]
  9. A. K. Leamy1, R. A. Egnatchik1, J. D. Young. Molecular mechanisms and the role of saturated fatty acids in the progression of non-alcoholic fatty liver disease. Progress in Lipid Research 52:165–174, 2013.  [Link to article]
  10. Y. Noguchi, J. D. Young, J. O. Aleman, M. E. Hansen, J. K. Kelleher, G. Stephanopoulos. Tracking cellular metabolomics in lipoapoptosis- and steatosis-developing liver cells. Molecular BioSystems 7:1409–19, 2011.  [Link to article]
  11. Y. Noguchi1, N. Shikata1, N. Nishikata1, Y. Hara1, J. O. Aleman, J. D. Young, S. Kurihara, N. Koyama, J. K. Kelleher, T. Michio, G. Stephanopoulos. Ketogenic essential amino acids modulate lipid synthetic pathways and prevent hepatic steatosis in mice. PLoS ONE 5:e12057, 2010.  [Link to article]
  12. Y. Noguchi1, J. D. Young1, J. O. Aleman, M. E. Hansen, J. K. Kelleher, G. Stephanopoulos. Effect of anaplerotic fluxes and amino acid availability on hepatic lipoapoptosis. Journal of Biological Chemistry 284: 33425–36, 2009.  [Link to article]

1Equal contributions.

Cancer Metabolism

  1. K. Hardeman, C. Peng, B. Paudel, C. Meyer, T. Luong, D. Tyson, J. D. Young, V. Quaranta, and J. Fessel. Dependence on glycolysis sensitizes BRAF-mutated melanomas for increased response to targeted BRAF inhibition. Scientific Reports 7:42604, 2017. [Link to article]
  2. S. M. J. Rahman, X. Ji, L. J. Zimmerman, M. Li, B. K. Harris, M. D. Hoeksema, I. A Trenary, Y. Zou, J. Qian, R. J. C. Slebos, J. Beane, A. Spira, Y. Shyr, R. Eisenberg, D. C. Liebler, J. D. Young, P. P. Massion. The airway epithelium undergoes metabolic reprogramming in individuals at high risk for lung cancer. JCI Insight 1:e88814, 2016. [Link to article]
  3. J. E. Hutton, X. Wang, L. J. Zimmerman, R. J. C. Slebos, I. A. Trenary, J. D. Young, M. Li, D. C. Liebler. Oncogenic KRAS and BRAF drive metabolic reprogramming in colorectal cancer. Molecular and Cellular Proteomics 15:2924-2938, 2016.  [Link to article]
  4. Y.M. Whang, S.I. Park, I.A. Trenary, R.A. Egnatchik, J.P. Fessel, J.M. Kaufman, D.P. Carbone, J.D. Young. LKB1 deficiency enhances sensitivity to energetic stress induced by erlotinib treatment in non-small-cell lung cancer (NSCLC) cells. Oncogene 35:856-866, 2016.  [Link to article]
  5. C. S. Duckwall, T. A. Murphy, J. D. Young. Mapping cancer cell metabolism with 13C flux analysis: Recent progress and future challenges. Journal of Carcinogenesis 12:13, 2013.  [Link to article]
  6. T. A. Murphy, C. V. Dang, J. D. Young. Isotopically nonstationary 13C flux analysis of Myc-induced metabolic reprogramming in B-cells. Metabolic Engineering 15:206–217, 2013.   [Link to article]
  7. D. W. Strand, M. Jiang, T. A. Murphy, Y. Yi, K. C. Konvinse, O. E. Franco, Y. Wang, J. D. Young, S. W. Hayward. PPAR-gamma isoforms differentially regulate metabolic networks to mediate mouse prostatic epithelial differentiation. Cell Death and Disease 3:e361, 2012.  [Link to article]

Cell Culture Engineering

  1. N. Templeton, K. D. Smith, A. G. McAtee-Pereira, H. Dorai, M. J. Betenbaugh, S. E. Lang, J. D. Young. Application of 13C flux analysis to identify high-productivity CHO metabolic phenotypes. Metabolic Engineering, accepted. [Link to article]
  2. Junker, Beth H., and Jamey D. Young. Editorial overview: pharmaceutical biotechnology: engineering cells for high quality biopharmaceuticals production. Current opinion in biotechnology 30: viii. 2014. [Link to article]
  3. J.D. Young. 13C metabolic flux analysis of recombinant expression hosts. Current Opinion in Biotechnology 30:238-245, 2014.  [Link to article]
  4. N. Templeton, A. Lewis, H. Dorai, E.A. Qian, M.P. Campbell, K.D. Smith, S.E. Lang, M.J. Betenbaugh, J.D. Young. The impact of anti-apoptotic gene Bcl-2? expression on CHO central metabolism. Metabolic Engineering 25:92-102, 2014.  [Link to article]
  5. A.G. McAtee, N. Templeton, J.D. Young. Role of Chinese hamster ovary central carbon metabolism in controlling the quality of secreted biotherapeutic proteins. Pharmaceutical Bioprocessing 2:63-74, 2014.  [Link to article]
  6. J. D. Young. Metabolic flux rewiring in mammalian cell cultures. Current Opinion in Biotechnology 24:1108–1115, 2013. [Link to article]
  7. N. Templeton, J. Dean, P. Reddy, J. D. Young. Peak antibody production is associated with increased oxidative metabolism in an industrially relevant fed-batch CHO cell culture. Biotechnology and Bioengineering 110:2013–2024, 2013.  [Link to article]

Photosynthesis Research

  1. Jazmin, L. J., Xu, Y., Cheah, Y. E., Adebiyi, A. O., Johnson, C. H., & Young, J. D. Isotopically nonstationary 13C flux analysis of cyanobacterial isobutyraldehyde production. Metabolic Engineering. 2017 [Link to article]
  2. A.O. Adebiyi, L.J. Jazmin, J.D. Young. 13C flux analysis of cyanobacterial metabolism. Photosynthesis Research, 126:19-32, 2014.  [Link to article]
  3. F. Ma, L.J. Jazmin, J.D. Young, D.K. Allen. Isotopically nonstationary 13C flux analysis of changes in Arabidopsis thaliana leaf metabolism due to high light acclimation. PNAS 111:16967-16972, 2014.  [Link to article]
  4. L.J. Jazmin, J.P. O'Grady, F. Ma, D.K. Allen, J.A. Morgan, J.D. Young. Isotopically nonstationary MFA (INST-MFA) of autotrophic metabolism. Methods in Molecular Biology 1090:181-210, 2014.  [Link to article]
  5. D. K. Allen, J. D. Young. Carbon and nitrogen provisions alter the metabolic flux in developing soybean embryos. Plant Physiology 161:1458–1475, 2013.  [Link to article]
  6. J. D. Young1, A. A. Shastri1, G. Stephanopoulos, J. A. Morgan. Mapping photoautotrophic metabolism with isotopically nonstationary 13C flux analysis. Metabolic Engineering 13:656–65, 2011.  [Link to article]

1Equal contributions.

Metabolic Flux Analysis

  1. Cheah, Yi Ern, Clinton M. Hasenour, and Jamey D. Young. "13C Flux Analysis in Biotechnology and Medicine." Systems Biology 6:25, 2017. [Link to article]
  2. D. McCloskey, J. D. Young, S. Xu, B. O. Palsson, A. M. Feist. Modeling method for increased precision and scope of directly measurable fluxes at a genome-scale. Analytical Chemistry 88:3844-52, 2016. [Link to article]
  3. D. McCloskey, J. D. Young, S. Xu, B. O. Palsson, A. M. Feist. MID Max: LC-MS/MS method for measuring the precursor and product mass isotopomer distributions of metabolic intermediates and cofactors for metabolic flux analysis applications. Analytical Chemistry 88:1362-1370, 2016. [Link to article]
  4. A.G. McAtee, L.J. Jazmin, J.D. Young. Application of isotope labeling experiments and 13C flux analysis to enable rational pathway engineering. Current Opinion in Biotechnology, 36:50-56, 2015.  [Link to article]
  5. J.M. Buescher, M.R. Antoniewicz, LG. Boros, S.C. Burgess, H. Brunengraber, C.B. Clish, R.J. DeBerardinis, O. Feron, C. Frezza, B. Ghesquiere, E. Gottlieb, K. Hiller, R.G. Jones, J.J. Kamphorst, R.G. Kibbey, A.C. Kimmelman, J.W. Locasale, S.Y. Lunt, O.D.K. Maddocks, C. Malloy, C.M. Metallo, E.J. Meuillet, J. Munger, K. Noh, J.D. Rabinowitz, M. Ralser, U. Sauer, G. Stephanopoulos, J. St-Pierre, D.A. Tennant, C. Wittmann, M.G. Vander Heiden, A. Vazquez, K. Vousden, J.D. Young, N. Zamboni, S. Fendt. A roadmap for interpreting 13C metabolite labeling patterns from cells. 34:189-201, 2015. [Link to article]
  6. J.D. Young. INCA: A computational platform for isotopically nonstationary metabolic flux anlaysis. Bioinformatics 30:1333-1335, 2014.  [Link to article]
  7. J.D. Young, D.K. Allen, J.A. Morgan. Isotopmer measurement techniques in metabolic flux analysis II: Mass spectrometry. Methods in Molecular Biology 1083:85-108, 2014.  [Link to article]
  8. T. A. Murphy, J. D. Young. ETA: Robust software for determination of cell specific rates from extracellular time courses. Biotechnology and Bioengineering 110:1748–1758, 2013.  [Link to article]
  9. L. J. Jazmin, J. D. Young. Isotopically nonstationary 13C metabolic flux analysis. Methods in Molecular Biology 985:367–390, 2013. [Link to article]
  10. O. Srour, J. D. Young, Y. C. Eldar. Fluxomers – A new approach for 13C metabolic flux analysis. BMC Systems Biology 5:129, 2011.  [Link to article]
  11. J. L. Reed, R. S. Senger, M. R. Antoniewicz, J. D. Young. Computational approaches in metabolic engineering. Journal of Biomedicine and Biotechnology 2010:207414, 2010.  [Link to article]
  12. J. D. Young1, J. L. Walther1, M. R. Antoniewicz, H. Yoo, G. Stephanopoulos. An elementary metabolite unit (EMU) based method of isotopically nonstationary flux analysis. Biotechnology and Bioengineering 99: 686–99, 2008.  [Link to article]

1Equal contributions.

Cybernetic Modeling

  1. J.D. Young. Learning from the steersman: A natural history of cybernetic models. Industrial & Enginering Chemistry Research 54:10162-10169, 2015.  [Link to article]
  2. J. D. Young, K. L. Henne, J. A. Morgan, A. E. Konopka, D. Ramkrishna. Integrating cybernetic modeling with pathway analysis provides a dynamic, systems-level description of metabolic control. Biotechnology and Bioengineering 100: 542–59, 2008.  [Link to article]
  3. J. D. Young, D. Ramkrishna. On the matching and proportional laws of cybernetic models. Biotechnology Progress 23: 83–99, 2007.  [Link to article]
  4. J. D. Young, K. L. Henne, J. A. Morgan, A. E. Konopka, D. Ramkrishna. Cybernetic modeling of metabolism: towards a framework for rational design of recombinant organisms. Chemical Engineering Science 59: 5041–9, 2004.  [Link to article]