Faculty Appointments
Director of Graduate Recruiting for Chemical and Biomolecular Engineering Professor of Chemical & Biomolecular Engineering
Cornelius Vanderbilt ChairCornelius Vanderbilt ChairProfessor of Molecular Physiology & BiophysicsProfessor of Molecular Physiology & Biophysics
Education
Ph.D., Chemical Engineering, Purdue University, West Lafayette, IndianaB.S., Chemical Engineering, University of Kentucky, Lexington, Kentucky
Office Address
212B Olin Hall
Vanderbilt University
Nashville, TN 37235
Vanderbilt University
Nashville, TN 37235
Research Description
The overall goal of my lab is to develop novel metabolic engineering approaches to measure, understand, and control cellular metabolism. These approaches are being applied to a variety of research questions of relevance to medicine and biomanufacturing. In particular, we use metabolomics and metabolic flux analysis (MFA) to quantify the intracellular metabolism of a variety of cell and animal models. Although diverse in their biological scope, all projects rely on our lab's core expertise to integrate numerous metabolic measurements into a quantitative map of cell metabolism using rigorous mathematical models, with the ultimate goal of deciphering how metabolic networks are natively regulated and how they can be further engineered to achieve a desired outcome. It is expected that this work will lead to (i) new discoveries that uncover fundamental disease mechanisms and can be targeted for clinical diagnosis or treatment, or (ii) innovative metabolic engineering strategies that can be implemented to enhance production of biochemicals, biofuels, recombinant proteins, or other bioproducts.
Research Keywords
Metabolic engineering and systems biology
Publications
Pannala VR, Vinnakota KC, Rawls KD, Estes SK, O'Brien TP, Printz RL, Papin JA, Reifman J, Shiota M, Young JD, Wallqvist A. Mechanistic identification of biofluid metabolite changes as markers of acetaminophen-induced liver toxicity in rats. Toxicol. Appl. Pharmacol [print-electronic]. 2019 Jun 6/1/2019; 372: 19-32. PMID: 30974156, PII: S0041-008X(19)30127-9, DOI: 10.1016/j.taap.2019.04.001, ISSN: 1096-0333.
Vinnakota KC, Pannala VR, Wall ML, Rahim M, Estes SK, Trenary I, O'Brien TP, Printz RL, Reifman J, Shiota M, Young JD, Wallqvist A. Network Modeling of Liver Metabolism to Predict Plasma Metabolite Changes During Short-Term Fasting in the Laboratory Rat. Front Physiol. 2019; 10: 161. PMID: 30881311, PMCID: PMC6405515, DOI: 10.3389/fphys.2019.00161, ISSN: 1664-042X.
Egnatchik RA, Leamy AK, Sacco SA, Cheah YE, Shiota M, Young JD. Glutamate-oxaloacetate transaminase activity promotes palmitate lipotoxicity in rat hepatocytes by enhancing anaplerosis and citric acid cycle flux. J. Biol. Chem [print-electronic]. 2018 Dec 12/18/2018; PMID: 30563841, PII: RA118.004869, DOI: 10.1074/jbc.RA118.004869, ISSN: 1083-351X.
Pannala VR, Wall ML, Estes SK, Trenary I, O'Brien TP, Printz RL, Vinnakota KC, Reifman J, Shiota M, Young JD, Wallqvist A. Metabolic network-based predictions of toxicant-induced metabolite changes in the laboratory rat. Sci Rep. 2018 Aug 8/3/2018; 8(1): 11678. PMID: 30076366, PMCID: PMC6076258, PII: 10.1038/s41598-018-30149-7, DOI: 10.1038/s41598-018-30149-7, ISSN: 2045-2322.
Pannala VR, Wall ML, Estes SK, Trenary I, O'Brien TP, Printz RL, Vinnakota KC, Reifman J, Shiota M, Young JD, Wallqvist A. Metabolic network-based predictions of toxicant-induced metabolite changes in the laboratory rat. Sci Rep. 2018 Aug 8/3/2018; 8(1): 11678. PMID: 30076366, PMCID: PMC6076258, PII: 10.1038/s41598-018-30149-7, DOI: 10.1038/s41598-018-30149-7, ISSN: 2045-2322.
Fensterheim BA, Young JD, Luan L, Kleinbard RR, Stothers CL, Patil NK, McAtee-Pereira AG, Guo Y, Trenary I, Hernandez A, Fults JB, Williams DL, Sherwood ER, Bohannon JK. The TLR4 Agonist Monophosphoryl Lipid A Drives Broad Resistance to Infection via Dynamic Reprogramming of Macrophage Metabolism. J. Immunol [print-electronic]. 2018 Jun 6/1/2018; 200(11): 3777-89. PMID: 29686054, PMCID: PMC5964009, PII: jimmunol.1800085, DOI: 10.4049/jimmunol.1800085, ISSN: 1550-6606.
Ji X, Qian J, Rahman SMJ, Siska PJ, Zou Y, Harris BK, Hoeksema MD, Trenary IA, Heidi C, Eisenberg R, Rathmell JC, Young JD, Massion PP. XCT (SLC7A11)-mediated metabolic reprogramming promotes non-small cell lung cancer progression. Oncogene [print-electronic]. 2018 May 5/23/2018; PMID: 29789716, PII: 10.1038/s41388-018-0307-z, DOI: 10.1038/s41388-018-0307-z, ISSN: 1476-5594.
Cheah YE, Young JD. Isotopically nonstationary metabolic flux analysis (INST-MFA): putting theory into practice. Curr. Opin. Biotechnol [print-electronic]. 2018 Mar 3/6/2018; 54: 80-7. PMID: 29522915, PII: S0958-1669(17)30254-9, DOI: 10.1016/j.copbio.2018.02.013, ISSN: 1879-0429.
McAtee Pereira AG, Walther JL, Hollenbach M, Young JD. 13 C Flux Analysis Reveals that Rebalancing Medium Amino Acid Composition can Reduce Ammonia Production while Preserving Central Carbon Metabolism of CHO Cell Cultures. Biotechnol J [print-electronic]. 2018 Feb 2/6/2018; PMID: 29405605, DOI: 10.1002/biot.201700518, ISSN: 1860-7314.
Williams IM, Valenzuela FA, Kahl SD, Ramkrishna D, Mezo AR, Young JD, Wells KS, Wasserman DH. Insulin exits skeletal muscle capillaries by fluid-phase transport. J. Clin. Invest [print-electronic]. 2018 Feb 2/1/2018; 128(2): 699-714. PMID: 29309051, PMCID: PMC5785264, PII: 94053, DOI: 10.1172/JCI94053, ISSN: 1558-8238.
Hughey CC, James FD, Bracy DP, Donahue EP, Young JD, Viollet B, Foretz M, Wasserman DH. Loss of hepatic AMP-activated protein kinase impedes the rate of glycogenolysis but not gluconeogenic fluxes in exercising mice. J. Biol. Chem [print-electronic]. 2017 Dec 12/8/2017; 292(49): 20125-40. PMID: 29038293, PMCID: PMC5724001, PII: M117.811547, DOI: 10.1074/jbc.M117.811547, ISSN: 1083-351X.
Faubert B, Li KY, Cai L, Hensley CT, Kim J, Zacharias LG, Yang C, Do QN, Doucette S, Burguete D, Li H, Huet G, Yuan Q, Wigal T, Butt Y, Ni M, Torrealba J, Oliver D, Lenkinski RE, Malloy CR, Wachsmann JW, Young JD, Kernstine K, DeBerardinis RJ. Lactate Metabolism in Human Lung Tumors. Cell. 2017 Oct 10/5/2017; 171(2): 358-371.e9. PMID: 28985563, PMCID: PMC5684706, PII: S0092-8674(17)31068-1, DOI: 10.1016/j.cell.2017.09.019, ISSN: 1097-4172.
Templeton N, Smith KD, McAtee-Pereira AG, Dorai H, Betenbaugh MJ, Lang SE, Young JD. Application of 13C flux analysis to identify high-productivity CHO metabolic phenotypes. Metab. Eng [print-electronic]. 2017 Sep; 43(Pt B): 218-25. PMID: 28122259, PII: S1096-7176(17)30033-2, DOI: 10.1016/j.ymben.2017.01.008, ISSN: 1096-7184.
Jazmin LJ, Xu Y, Cheah YE, Adebiyi AO, Johnson CH, Young JD. Isotopically nonstationary 13C flux analysis of cyanobacterial isobutyraldehyde production. Metab. Eng [print-electronic]. 2017 Jul; 42: 9-18. PMID: 28479191, PMCID: PMC5660605, PII: S1096-7176(16)30156-2, DOI: 10.1016/j.ymben.2017.05.001, ISSN: 1096-7184.
Egnatchik RA, Brittain EL, Shah AT, Fares WH, Ford HJ, Monahan K, Kang CJ, Kocurek EG, Zhu S, Luong T, Nguyen TT, Hysinger E, Austin ED, Skala MC, Young JD, Roberts LJ, Hemnes AR, West J, Fessel JP. Dysfunctional BMPR2 signaling drives an abnormal endothelial requirement for glutamine in pulmonary arterial hypertension. Pulm Circ. 2017 Mar; 7(1): 186-99. PMID: 28680578, PMCID: PMC5448547, PII: 10.1086_690236, DOI: 10.1086/690236, ISSN: 2045-8932.
Hardeman KN, Peng C, Paudel BB, Meyer CT, Luong T, Tyson DR, Young JD, Quaranta V, Fessel JP. Dependence On Glycolysis Sensitizes BRAF-mutated Melanomas For Increased Response To Targeted BRAF Inhibition. Sci Rep. 2017 Feb 2/16/2017; 7: 42604. PMID: 28205616, PMCID: PMC5311997, PII: srep42604, DOI: 10.1038/srep42604, ISSN: 2045-2322.
Ma F, Jazmin LJ, Young JD, Allen DK. Isotopically Nonstationary Metabolic Flux Analysis (INST-MFA) of Photosynthesis and Photorespiration in Plants. Methods Mol. Biol. 2017; 1653: 167-94. PMID: 28822133, DOI: 10.1007/978-1-4939-7225-8_12, ISSN: 1940-6029.
Hasenour CM, Ridley DE, James FD, Hughey CC, Donahue EP, Viollet B, Foretz M, Young JD, Wasserman DH. Liver AMP-Activated Protein Kinase Is Unnecessary for Gluconeogenesis but Protects Energy State during Nutrient Deprivation. PLoS ONE. 2017; 12(1): e0170382. PMID: 28107516, PMCID: PMC5249187, PII: PONE-D-16-14527, DOI: 10.1371/journal.pone.0170382, ISSN: 1932-6203.
Rahman SM, Ji X, Zimmerman LJ, Li M, Harris BK, Hoeksema MD, Trenary IA, Zou Y, Qian J, Slebos RJ, Beane J, Spira A, Shyr Y, Eisenberg R, Liebler DC, Young JD, Massion PP. The airway epithelium undergoes metabolic reprogramming in individuals at high risk for lung cancer. JCI Insight. 2016 Nov 11/17/2016; 1(19): e88814. PMID: 27882349, PMCID: PMC5111517, PII: 88814, DOI: 10.1172/jci.insight.88814.
Leamy AK, Hasenour CM, Egnatchik RA, Trenary IA, Yao CH, Patti GJ, Shiota M, Young JD. Knockdown of triglyceride synthesis does not enhance palmitate lipotoxicity or prevent oleate-mediated rescue in rat hepatocytes. Biochim. Biophys. Acta [print-electronic]. 2016 Sep; 1861(9 Pt A): 1005-14. PMID: 27249207, PMCID: PMC4947436, PII: S1388-1981(16)30142-1, DOI: 10.1016/j.bbalip.2016.05.013, ISSN: 0006-3002.
Hutton JE, Wang X, Zimmerman LJ, Slebos RJ, Trenary IA, Young JD, Li M, Liebler DC. Oncogenic KRAS and BRAF drive metabolic reprogramming in colorectal cancer. Mol. Cell Proteomics [print-electronic]. 2016 Jun 6/23/2016; PMID: 27340238, PII: M116.058925, DOI: 10.1074/mcp.M116.058925, ISSN: 1535-9484.
McCloskey D, Young JD, Xu S, Palsson BO, Feist AM. Modeling Method for Increased Precision and Scope of Directly Measurable Fluxes at a Genome-Scale. Anal. Chem [print-electronic]. 2016 Apr 4/5/2016; 88(7): 3844-52. PMID: 26981784, DOI: 10.1021/acs.analchem.5b04914, ISSN: 1520-6882.
Whang YM, Park SI, Trenary IA, Egnatchik RA, Fessel JP, Kaufman JM, Carbone DP, Young JD. LKB1 deficiency enhances sensitivity to energetic stress induced by erlotinib treatment in non-small-cell lung cancer (NSCLC) cells. Oncogene [print-electronic]. 2016 Feb 2/18/2016; 35(7): 856-66. PMID: 26119936, PMCID: PMC4486321, PII: onc2015140, DOI: 10.1038/onc.2015.140, ISSN: 1476-5594.
McCloskey D, Young JD, Xu S, Palsson BO, Feist AM. 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. Anal. Chem [print-electronic]. 2016 Jan 1/19/2016; 88(2): 1362-70. PMID: 26666286, DOI: 10.1021/acs.analchem.5b03887, ISSN: 1520-6882.
McAtee AG, Jazmin LJ, Young JD. Application of isotope labeling experiments and (13)C flux analysis to enable rational pathway engineering. Curr. Opin. Biotechnol [print-electronic]. 2015 Dec; 36: 50-6. PMID: 26319894, PII: S0958-1669(15)00103-2, DOI: 10.1016/j.copbio.2015.08.004, ISSN: 1879-0429.
Adebiyi AO, Jazmin LJ, Young JD. 13 C flux analysis of cyanobacterial metabolism. Photosyn. Res [print-electronic]. 2015 Oct; 126(1): 19-32. PMID: 25280933, PII: 10.1007/s11120-014-0045-1, DOI: 10.1007/s11120-014-0045-1, ISSN: 1573-5079.
Buescher JM, Antoniewicz MR, Boros LG, Burgess SC, Brunengraber H, Clish CB, DeBerardinis RJ, Feron O, Frezza C, Ghesquiere B, Gottlieb E, Hiller K, Jones RG, Kamphorst JJ, Kibbey RG, Kimmelman AC, Locasale JW, Lunt SY, Maddocks OD, Malloy C, Metallo CM, Meuillet EJ, Munger J, Nöh K, Rabinowitz JD, Ralser M, Sauer U, Stephanopoulos G, St-Pierre J, Tennant DA, Wittmann C, Vander Heiden MG, Vazquez A, Vousden K, Young JD, Zamboni N, Fendt SM. A roadmap for interpreting (13)C metabolite labeling patterns from cells. Curr. Opin. Biotechnol [print-electronic]. 2015 Aug; 34: 189-201. PMID: 25731751, PMCID: PMC4552607, PII: S0958-1669(15)00022-1, DOI: 10.1016/j.copbio.2015.02.003, ISSN: 1879-0429.
Hasenour CM, Wall ML, Ridley DE, Hughey CC, James FD, Wasserman DH, Young JD. Mass spectrometry-based microassay of (2)H and (13)C plasma glucose labeling to quantify liver metabolic fluxes in vivo. Am. J. Physiol. Endocrinol. Metab [print-electronic]. 2015 Jul 7/15/2015; 309(2): E191-203. PMID: 25991647, PMCID: PMC4504936, PII: ajpendo.00003.2015, DOI: 10.1152/ajpendo.00003.2015, ISSN: 1522-1555.
Wall ML, Pound LD, Trenary I, O'Brien RM, Young JD. Novel stable isotope analyses demonstrate significant rates of glucose cycling in mouse pancreatic islets. Diabetes [print-electronic]. 2015 Jun; 64(6): 2129-37. PMID: 25552595, PMCID: PMC4439557, PII: db14-0745, DOI: 10.2337/db14-0745, ISSN: 1939-327X.
Young JD. (13)C metabolic flux analysis of recombinant expression hosts. Curr. Opin. Biotechnol [print-electronic]. 2014 Dec; 30: 238-45. PMID: 25456032, PII: S0958-1669(14)00172-4, DOI: 10.1016/j.copbio.2014.10.004, ISSN: 1879-0429.
Junker BH, Young JD. Editorial overview: pharmaceutical biotechnology: engineering cells for high quality biopharmaceuticals production [editorial]. Curr. Opin. Biotechnol. 2014 Dec; 30: viii-x. PMID: 25459164, PII: S0958-1669(14)00170-0, DOI: 10.1016/j.copbio.2014.10.002, ISSN: 1879-0429.
Ma F, Jazmin LJ, Young JD, Allen DK. Isotopically nonstationary 13C flux analysis of changes in Arabidopsis thaliana leaf metabolism due to high light acclimation. Proc. Natl. Acad. Sci. U.S.A [print-electronic]. 2014 Nov 11/25/2014; 111(47): 16967-72. PMID: 25368168, PMCID: PMC4250135, PII: 1319485111, DOI: 10.1073/pnas.1319485111, ISSN: 1091-6490.
Templeton N, Lewis A, Dorai H, Qian EA, Campbell MP, Smith KD, Lang SE, Betenbaugh MJ, Young JD. The impact of anti-apoptotic gene Bcl-2¿ expression on CHO central metabolism. Metab. Eng [print-electronic]. 2014 Sep; 25: 92-102. PMID: 25014175, PII: S1096-7176(14)00091-3, DOI: 10.1016/j.ymben.2014.06.010, ISSN: 1096-7184.
Egnatchik RA, Leamy AK, Jacobson DA, Shiota M, Young JD. ER calcium release promotes mitochondrial dysfunction and hepatic cell lipotoxicity in response to palmitate overload. Mol Metab. 2014 Aug; 3(5): 544-53. PMID: 25061559, PMCID: PMC4099508, PII: S2212-8778(14)00092-1, DOI: 10.1016/j.molmet.2014.05.004, ISSN: 2212-8778.
Leamy AK, Egnatchik RA, Shiota M, Ivanova PT, Myers DS, Brown HA, Young JD. Enhanced synthesis of saturated phospholipids is associated with ER stress and lipotoxicity in palmitate treated hepatic cells. J. Lipid Res [print-electronic]. 2014 May 5/23/2014; 55(7): 1478-88. PMID: 24859739, PMCID: PMC4076085, PII: jlr.M050237, DOI: 10.1194/jlr.M050237, ISSN: 0022-2275.
Young JD. INCA: a computational platform for isotopically non-stationary metabolic flux analysis. Bioinformatics [print-electronic]. 2014 May 5/1/2014; 30(9): 1333-5. PMID: 24413674, PMCID: PMC3998137, PII: btu015, DOI: 10.1093/bioinformatics/btu015, ISSN: 1367-4811.
Egnatchik RA, Leamy AK, Noguchi Y, Shiota M, Young JD. Palmitate-induced activation of mitochondrial metabolism promotes oxidative stress and apoptosis in H4IIEC3 rat hepatocytes. Metab. Clin. Exp [print-electronic]. 2014 Feb; 63(2): 283-95. PMID: 24286856, PMCID: PMC3946971, PII: S0026-0495(13)00341-7, DOI: 10.1016/j.metabol.2013.10.009, ISSN: 1532-8600.
Jazmin LJ, O'Grady JP, Ma F, Allen DK, Morgan JA, Young JD. Isotopically nonstationary MFA (INST-MFA) of autotrophic metabolism. Methods Mol. Biol. 2014; 1090: 181-210. PMID: 24222417, DOI: 10.1007/978-1-62703-688-7_12, ISSN: 1940-6029.
Young JD, Allen DK, Morgan JA. Isotopomer measurement techniques in metabolic flux analysis II: mass spectrometry. Methods Mol. Biol. 2014; 1083: 85-108. PMID: 24218212, DOI: 10.1007/978-1-62703-661-0_7, ISSN: 1940-6029.
Young JD. Metabolic flux rewiring in mammalian cell cultures. Curr. Opin. Biotechnol [print-electronic]. 2013 Dec; 24(6): 1108-15. PMID: 23726154, PMCID: PMC3775942, PII: S0958-1669(13)00114-6, DOI: 10.1016/j.copbio.2013.04.016, ISSN: 1879-0429.
Templeton N, Dean J, Reddy P, Young JD. Peak antibody production is associated with increased oxidative metabolism in an industrially relevant fed-batch CHO cell culture. Biotechnol. Bioeng [print-electronic]. 2013 Jul; 110(7): 2013-24. PMID: 23381838, DOI: 10.1002/bit.24858, ISSN: 1097-0290.
Murphy TA, Young JD. ETA: robust software for determination of cell specific rates from extracellular time courses. Biotechnol. Bioeng [print-electronic]. 2013 Jun; 110(6): 1748-58. PMID: 23296385, PMCID: PMC3863648, DOI: 10.1002/bit.24836, ISSN: 1097-0290.
Allen DK, Young JD. Carbon and nitrogen provisions alter the metabolic flux in developing soybean embryos. Plant Physiol [print-electronic]. 2013 Mar; 161(3): 1458-75. PMID: 23314943, PMCID: PMC3585609, PII: pp.112.203299, DOI: 10.1104/pp.112.203299, ISSN: 1532-2548.
Murphy TA, Dang CV, Young JD. Isotopically nonstationary 13C flux analysis of Myc-induced metabolic reprogramming in B-cells. Metab. Eng [print-electronic]. 2013 Jan; 15: 206-17. PMID: 22898717, PMCID: PMC3535509, PII: S1096-7176(12)00078-X, DOI: 10.1016/j.ymben.2012.07.008, ISSN: 1096-7184.
Duckwall CS, Murphy TA, Young JD. Mapping cancer cell metabolism with(13)C flux analysis: Recent progress and future challenges. J Carcinog. 2013; 12: 13. PMID: 23961260, PMCID: PMC3746411, PII: JC-12-13, DOI: 10.4103/1477-3163.115422, ISSN: 1477-3163.
Jazmin LJ, Young JD. Isotopically nonstationary 13C metabolic flux analysis. Methods Mol. Biol. 2013; 985: 367-90. PMID: 23417813, DOI: 10.1007/978-1-62703-299-5_18, ISSN: 1940-6029.
Leamy AK, Egnatchik RA, Young JD. Molecular mechanisms and the role of saturated fatty acids in the progression of non-alcoholic fatty liver disease. Prog. Lipid Res [print-electronic]. 2013 Jan; 52(1): 165-74. PMID: 23178552, PMCID: PMC3868987, PII: S0163-7827(12)00058-6, DOI: 10.1016/j.plipres.2012.10.004, ISSN: 1873-2194.
Strand DW, Jiang M, Murphy TA, Yi Y, Konvinse KC, Franco OE, Wang Y, Young JD, Hayward SW. PPAR-gamma isoforms differentially regulate metabolic networks to mediate mouse prostatic epithelial differentiation. Cell Death Dis. 2012; 3: e361. PMID: 22874998, PMCID: PMC3434663, PII: cddis201299, DOI: 10.1038/cddis.2012.99, ISSN: 2041-4889.
Young JD, Shastri AA, Stephanopoulos G, Morgan JA. Mapping photoautotrophic metabolism with isotopically nonstationary (13)C flux analysis. Metab. Eng [print-electronic]. 2011 Nov; 13(6): 656-65. PMID: 21907300, PMCID: PMC3210925, PII: S1096-7176(11)00088-7, DOI: 10.1016/j.ymben.2011.08.002, ISSN: 1096-7184.
Noguchi Y, Young JD, Aleman JO, Hansen ME, Kelleher JK, Stephanopoulos G. Tracking cellular metabolomics in lipoapoptosis- and steatosis-developing liver cells. Mol Biosyst [print-electronic]. 2011 May; 7(5): 1409-19. PMID: 21327189, DOI: 10.1039/c0mb00309c, ISSN: 1742-2051.
Srour O, Young JD, Eldar YC. Fluxomers: a new approach for 13C metabolic flux analysis. BMC Syst Biol. 2011; 5: 129. PMID: 21846358, PMCID: PMC3750106, PII: 1752-0509-5-129, DOI: 10.1186/1752-0509-5-129, ISSN: 1752-0509.
Noguchi Y, Nishikata N, Shikata N, Kimura Y, Aleman JO, Young JD, Koyama N, Kelleher JK, Takahashi M, Stephanopoulos G. Ketogenic essential amino acids modulate lipid synthetic pathways and prevent hepatic steatosis in mice. PLoS ONE. 2010; 5(8): e12057. PMID: 20706589, PMCID: PMC2919399, DOI: 10.1371/journal.pone.0012057, ISSN: 1932-6203.
Reed JL, Senger RS, Antoniewicz MR, Young JD. Computational approaches in metabolic engineering [editorial]. J. Biomed. Biotechnol [print-electronic]. 2010; 2010: 207414. PMID: 21584279, PMCID: PMC3092504, DOI: 10.1155/2010/207414, ISSN: 1110-7251.
Noguchi Y, Young JD, Aleman JO, Hansen ME, Kelleher JK, Stephanopoulos G. Effect of anaplerotic fluxes and amino acid availability on hepatic lipoapoptosis. J. Biol. Chem [print-electronic]. 2009 Nov 11/27/2009; 284(48): 33425-36. PMID: 19758988, PMCID: PMC2785187, PII: M109.049478, DOI: 10.1074/jbc.M109.049478, ISSN: 1083-351X.
Young JD, Henne KL, Morgan JA, Konopka AE, Ramkrishna D. Integrating cybernetic modeling with pathway analysis provides a dynamic, systems-level description of metabolic control. Biotechnol. Bioeng. 2008 Jun 6/15/2008; 100(3): 542-59. PMID: 18438875, DOI: 10.1002/bit.21780, ISSN: 1097-0290.
Young JD, Walther JL, Antoniewicz MR, Yoo H, Stephanopoulos G. An elementary metabolite unit (EMU) based method of isotopically nonstationary flux analysis. Biotechnol. Bioeng. 2008 Feb 2/15/2008; 99(3): 686-99. PMID: 17787013, DOI: 10.1002/bit.21632, ISSN: 1097-0290.
Young JD, Ramkrishna D. On the matching and proportional laws of cybernetic models. Biotechnol. Prog. 2007 Jan; 23(1): 83-99. PMID: 17269675, DOI: 10.1021/bp060176q, ISSN: 1520-6033.
J. D. Young, K. L. Henne, J. A. Morgan, A. E. Konopka and D. Ramkrishna.. Cybernetic modeling of metabolism: towards a framework for rational design of recombinant organisms. Chemical Engineering Science. 2004; 59: 5041-9.
Vinnakota KC, Pannala VR, Wall ML, Rahim M, Estes SK, Trenary I, O'Brien TP, Printz RL, Reifman J, Shiota M, Young JD, Wallqvist A. Network Modeling of Liver Metabolism to Predict Plasma Metabolite Changes During Short-Term Fasting in the Laboratory Rat. Front Physiol. 2019; 10: 161. PMID: 30881311, PMCID: PMC6405515, DOI: 10.3389/fphys.2019.00161, ISSN: 1664-042X.
Egnatchik RA, Leamy AK, Sacco SA, Cheah YE, Shiota M, Young JD. Glutamate-oxaloacetate transaminase activity promotes palmitate lipotoxicity in rat hepatocytes by enhancing anaplerosis and citric acid cycle flux. J. Biol. Chem [print-electronic]. 2018 Dec 12/18/2018; PMID: 30563841, PII: RA118.004869, DOI: 10.1074/jbc.RA118.004869, ISSN: 1083-351X.
Pannala VR, Wall ML, Estes SK, Trenary I, O'Brien TP, Printz RL, Vinnakota KC, Reifman J, Shiota M, Young JD, Wallqvist A. Metabolic network-based predictions of toxicant-induced metabolite changes in the laboratory rat. Sci Rep. 2018 Aug 8/3/2018; 8(1): 11678. PMID: 30076366, PMCID: PMC6076258, PII: 10.1038/s41598-018-30149-7, DOI: 10.1038/s41598-018-30149-7, ISSN: 2045-2322.
Pannala VR, Wall ML, Estes SK, Trenary I, O'Brien TP, Printz RL, Vinnakota KC, Reifman J, Shiota M, Young JD, Wallqvist A. Metabolic network-based predictions of toxicant-induced metabolite changes in the laboratory rat. Sci Rep. 2018 Aug 8/3/2018; 8(1): 11678. PMID: 30076366, PMCID: PMC6076258, PII: 10.1038/s41598-018-30149-7, DOI: 10.1038/s41598-018-30149-7, ISSN: 2045-2322.
Fensterheim BA, Young JD, Luan L, Kleinbard RR, Stothers CL, Patil NK, McAtee-Pereira AG, Guo Y, Trenary I, Hernandez A, Fults JB, Williams DL, Sherwood ER, Bohannon JK. The TLR4 Agonist Monophosphoryl Lipid A Drives Broad Resistance to Infection via Dynamic Reprogramming of Macrophage Metabolism. J. Immunol [print-electronic]. 2018 Jun 6/1/2018; 200(11): 3777-89. PMID: 29686054, PMCID: PMC5964009, PII: jimmunol.1800085, DOI: 10.4049/jimmunol.1800085, ISSN: 1550-6606.
Ji X, Qian J, Rahman SMJ, Siska PJ, Zou Y, Harris BK, Hoeksema MD, Trenary IA, Heidi C, Eisenberg R, Rathmell JC, Young JD, Massion PP. XCT (SLC7A11)-mediated metabolic reprogramming promotes non-small cell lung cancer progression. Oncogene [print-electronic]. 2018 May 5/23/2018; PMID: 29789716, PII: 10.1038/s41388-018-0307-z, DOI: 10.1038/s41388-018-0307-z, ISSN: 1476-5594.
Cheah YE, Young JD. Isotopically nonstationary metabolic flux analysis (INST-MFA): putting theory into practice. Curr. Opin. Biotechnol [print-electronic]. 2018 Mar 3/6/2018; 54: 80-7. PMID: 29522915, PII: S0958-1669(17)30254-9, DOI: 10.1016/j.copbio.2018.02.013, ISSN: 1879-0429.
McAtee Pereira AG, Walther JL, Hollenbach M, Young JD. 13 C Flux Analysis Reveals that Rebalancing Medium Amino Acid Composition can Reduce Ammonia Production while Preserving Central Carbon Metabolism of CHO Cell Cultures. Biotechnol J [print-electronic]. 2018 Feb 2/6/2018; PMID: 29405605, DOI: 10.1002/biot.201700518, ISSN: 1860-7314.
Williams IM, Valenzuela FA, Kahl SD, Ramkrishna D, Mezo AR, Young JD, Wells KS, Wasserman DH. Insulin exits skeletal muscle capillaries by fluid-phase transport. J. Clin. Invest [print-electronic]. 2018 Feb 2/1/2018; 128(2): 699-714. PMID: 29309051, PMCID: PMC5785264, PII: 94053, DOI: 10.1172/JCI94053, ISSN: 1558-8238.
Hughey CC, James FD, Bracy DP, Donahue EP, Young JD, Viollet B, Foretz M, Wasserman DH. Loss of hepatic AMP-activated protein kinase impedes the rate of glycogenolysis but not gluconeogenic fluxes in exercising mice. J. Biol. Chem [print-electronic]. 2017 Dec 12/8/2017; 292(49): 20125-40. PMID: 29038293, PMCID: PMC5724001, PII: M117.811547, DOI: 10.1074/jbc.M117.811547, ISSN: 1083-351X.
Faubert B, Li KY, Cai L, Hensley CT, Kim J, Zacharias LG, Yang C, Do QN, Doucette S, Burguete D, Li H, Huet G, Yuan Q, Wigal T, Butt Y, Ni M, Torrealba J, Oliver D, Lenkinski RE, Malloy CR, Wachsmann JW, Young JD, Kernstine K, DeBerardinis RJ. Lactate Metabolism in Human Lung Tumors. Cell. 2017 Oct 10/5/2017; 171(2): 358-371.e9. PMID: 28985563, PMCID: PMC5684706, PII: S0092-8674(17)31068-1, DOI: 10.1016/j.cell.2017.09.019, ISSN: 1097-4172.
Templeton N, Smith KD, McAtee-Pereira AG, Dorai H, Betenbaugh MJ, Lang SE, Young JD. Application of 13C flux analysis to identify high-productivity CHO metabolic phenotypes. Metab. Eng [print-electronic]. 2017 Sep; 43(Pt B): 218-25. PMID: 28122259, PII: S1096-7176(17)30033-2, DOI: 10.1016/j.ymben.2017.01.008, ISSN: 1096-7184.
Jazmin LJ, Xu Y, Cheah YE, Adebiyi AO, Johnson CH, Young JD. Isotopically nonstationary 13C flux analysis of cyanobacterial isobutyraldehyde production. Metab. Eng [print-electronic]. 2017 Jul; 42: 9-18. PMID: 28479191, PMCID: PMC5660605, PII: S1096-7176(16)30156-2, DOI: 10.1016/j.ymben.2017.05.001, ISSN: 1096-7184.
Egnatchik RA, Brittain EL, Shah AT, Fares WH, Ford HJ, Monahan K, Kang CJ, Kocurek EG, Zhu S, Luong T, Nguyen TT, Hysinger E, Austin ED, Skala MC, Young JD, Roberts LJ, Hemnes AR, West J, Fessel JP. Dysfunctional BMPR2 signaling drives an abnormal endothelial requirement for glutamine in pulmonary arterial hypertension. Pulm Circ. 2017 Mar; 7(1): 186-99. PMID: 28680578, PMCID: PMC5448547, PII: 10.1086_690236, DOI: 10.1086/690236, ISSN: 2045-8932.
Hardeman KN, Peng C, Paudel BB, Meyer CT, Luong T, Tyson DR, Young JD, Quaranta V, Fessel JP. Dependence On Glycolysis Sensitizes BRAF-mutated Melanomas For Increased Response To Targeted BRAF Inhibition. Sci Rep. 2017 Feb 2/16/2017; 7: 42604. PMID: 28205616, PMCID: PMC5311997, PII: srep42604, DOI: 10.1038/srep42604, ISSN: 2045-2322.
Ma F, Jazmin LJ, Young JD, Allen DK. Isotopically Nonstationary Metabolic Flux Analysis (INST-MFA) of Photosynthesis and Photorespiration in Plants. Methods Mol. Biol. 2017; 1653: 167-94. PMID: 28822133, DOI: 10.1007/978-1-4939-7225-8_12, ISSN: 1940-6029.
Hasenour CM, Ridley DE, James FD, Hughey CC, Donahue EP, Viollet B, Foretz M, Young JD, Wasserman DH. Liver AMP-Activated Protein Kinase Is Unnecessary for Gluconeogenesis but Protects Energy State during Nutrient Deprivation. PLoS ONE. 2017; 12(1): e0170382. PMID: 28107516, PMCID: PMC5249187, PII: PONE-D-16-14527, DOI: 10.1371/journal.pone.0170382, ISSN: 1932-6203.
Rahman SM, Ji X, Zimmerman LJ, Li M, Harris BK, Hoeksema MD, Trenary IA, Zou Y, Qian J, Slebos RJ, Beane J, Spira A, Shyr Y, Eisenberg R, Liebler DC, Young JD, Massion PP. The airway epithelium undergoes metabolic reprogramming in individuals at high risk for lung cancer. JCI Insight. 2016 Nov 11/17/2016; 1(19): e88814. PMID: 27882349, PMCID: PMC5111517, PII: 88814, DOI: 10.1172/jci.insight.88814.
Leamy AK, Hasenour CM, Egnatchik RA, Trenary IA, Yao CH, Patti GJ, Shiota M, Young JD. Knockdown of triglyceride synthesis does not enhance palmitate lipotoxicity or prevent oleate-mediated rescue in rat hepatocytes. Biochim. Biophys. Acta [print-electronic]. 2016 Sep; 1861(9 Pt A): 1005-14. PMID: 27249207, PMCID: PMC4947436, PII: S1388-1981(16)30142-1, DOI: 10.1016/j.bbalip.2016.05.013, ISSN: 0006-3002.
Hutton JE, Wang X, Zimmerman LJ, Slebos RJ, Trenary IA, Young JD, Li M, Liebler DC. Oncogenic KRAS and BRAF drive metabolic reprogramming in colorectal cancer. Mol. Cell Proteomics [print-electronic]. 2016 Jun 6/23/2016; PMID: 27340238, PII: M116.058925, DOI: 10.1074/mcp.M116.058925, ISSN: 1535-9484.
McCloskey D, Young JD, Xu S, Palsson BO, Feist AM. Modeling Method for Increased Precision and Scope of Directly Measurable Fluxes at a Genome-Scale. Anal. Chem [print-electronic]. 2016 Apr 4/5/2016; 88(7): 3844-52. PMID: 26981784, DOI: 10.1021/acs.analchem.5b04914, ISSN: 1520-6882.
Whang YM, Park SI, Trenary IA, Egnatchik RA, Fessel JP, Kaufman JM, Carbone DP, Young JD. LKB1 deficiency enhances sensitivity to energetic stress induced by erlotinib treatment in non-small-cell lung cancer (NSCLC) cells. Oncogene [print-electronic]. 2016 Feb 2/18/2016; 35(7): 856-66. PMID: 26119936, PMCID: PMC4486321, PII: onc2015140, DOI: 10.1038/onc.2015.140, ISSN: 1476-5594.
McCloskey D, Young JD, Xu S, Palsson BO, Feist AM. 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. Anal. Chem [print-electronic]. 2016 Jan 1/19/2016; 88(2): 1362-70. PMID: 26666286, DOI: 10.1021/acs.analchem.5b03887, ISSN: 1520-6882.
McAtee AG, Jazmin LJ, Young JD. Application of isotope labeling experiments and (13)C flux analysis to enable rational pathway engineering. Curr. Opin. Biotechnol [print-electronic]. 2015 Dec; 36: 50-6. PMID: 26319894, PII: S0958-1669(15)00103-2, DOI: 10.1016/j.copbio.2015.08.004, ISSN: 1879-0429.
Adebiyi AO, Jazmin LJ, Young JD. 13 C flux analysis of cyanobacterial metabolism. Photosyn. Res [print-electronic]. 2015 Oct; 126(1): 19-32. PMID: 25280933, PII: 10.1007/s11120-014-0045-1, DOI: 10.1007/s11120-014-0045-1, ISSN: 1573-5079.
Buescher JM, Antoniewicz MR, Boros LG, Burgess SC, Brunengraber H, Clish CB, DeBerardinis RJ, Feron O, Frezza C, Ghesquiere B, Gottlieb E, Hiller K, Jones RG, Kamphorst JJ, Kibbey RG, Kimmelman AC, Locasale JW, Lunt SY, Maddocks OD, Malloy C, Metallo CM, Meuillet EJ, Munger J, Nöh K, Rabinowitz JD, Ralser M, Sauer U, Stephanopoulos G, St-Pierre J, Tennant DA, Wittmann C, Vander Heiden MG, Vazquez A, Vousden K, Young JD, Zamboni N, Fendt SM. A roadmap for interpreting (13)C metabolite labeling patterns from cells. Curr. Opin. Biotechnol [print-electronic]. 2015 Aug; 34: 189-201. PMID: 25731751, PMCID: PMC4552607, PII: S0958-1669(15)00022-1, DOI: 10.1016/j.copbio.2015.02.003, ISSN: 1879-0429.
Hasenour CM, Wall ML, Ridley DE, Hughey CC, James FD, Wasserman DH, Young JD. Mass spectrometry-based microassay of (2)H and (13)C plasma glucose labeling to quantify liver metabolic fluxes in vivo. Am. J. Physiol. Endocrinol. Metab [print-electronic]. 2015 Jul 7/15/2015; 309(2): E191-203. PMID: 25991647, PMCID: PMC4504936, PII: ajpendo.00003.2015, DOI: 10.1152/ajpendo.00003.2015, ISSN: 1522-1555.
Wall ML, Pound LD, Trenary I, O'Brien RM, Young JD. Novel stable isotope analyses demonstrate significant rates of glucose cycling in mouse pancreatic islets. Diabetes [print-electronic]. 2015 Jun; 64(6): 2129-37. PMID: 25552595, PMCID: PMC4439557, PII: db14-0745, DOI: 10.2337/db14-0745, ISSN: 1939-327X.
Young JD. (13)C metabolic flux analysis of recombinant expression hosts. Curr. Opin. Biotechnol [print-electronic]. 2014 Dec; 30: 238-45. PMID: 25456032, PII: S0958-1669(14)00172-4, DOI: 10.1016/j.copbio.2014.10.004, ISSN: 1879-0429.
Junker BH, Young JD. Editorial overview: pharmaceutical biotechnology: engineering cells for high quality biopharmaceuticals production [editorial]. Curr. Opin. Biotechnol. 2014 Dec; 30: viii-x. PMID: 25459164, PII: S0958-1669(14)00170-0, DOI: 10.1016/j.copbio.2014.10.002, ISSN: 1879-0429.
Ma F, Jazmin LJ, Young JD, Allen DK. Isotopically nonstationary 13C flux analysis of changes in Arabidopsis thaliana leaf metabolism due to high light acclimation. Proc. Natl. Acad. Sci. U.S.A [print-electronic]. 2014 Nov 11/25/2014; 111(47): 16967-72. PMID: 25368168, PMCID: PMC4250135, PII: 1319485111, DOI: 10.1073/pnas.1319485111, ISSN: 1091-6490.
Templeton N, Lewis A, Dorai H, Qian EA, Campbell MP, Smith KD, Lang SE, Betenbaugh MJ, Young JD. The impact of anti-apoptotic gene Bcl-2¿ expression on CHO central metabolism. Metab. Eng [print-electronic]. 2014 Sep; 25: 92-102. PMID: 25014175, PII: S1096-7176(14)00091-3, DOI: 10.1016/j.ymben.2014.06.010, ISSN: 1096-7184.
Egnatchik RA, Leamy AK, Jacobson DA, Shiota M, Young JD. ER calcium release promotes mitochondrial dysfunction and hepatic cell lipotoxicity in response to palmitate overload. Mol Metab. 2014 Aug; 3(5): 544-53. PMID: 25061559, PMCID: PMC4099508, PII: S2212-8778(14)00092-1, DOI: 10.1016/j.molmet.2014.05.004, ISSN: 2212-8778.
Leamy AK, Egnatchik RA, Shiota M, Ivanova PT, Myers DS, Brown HA, Young JD. Enhanced synthesis of saturated phospholipids is associated with ER stress and lipotoxicity in palmitate treated hepatic cells. J. Lipid Res [print-electronic]. 2014 May 5/23/2014; 55(7): 1478-88. PMID: 24859739, PMCID: PMC4076085, PII: jlr.M050237, DOI: 10.1194/jlr.M050237, ISSN: 0022-2275.
Young JD. INCA: a computational platform for isotopically non-stationary metabolic flux analysis. Bioinformatics [print-electronic]. 2014 May 5/1/2014; 30(9): 1333-5. PMID: 24413674, PMCID: PMC3998137, PII: btu015, DOI: 10.1093/bioinformatics/btu015, ISSN: 1367-4811.
Egnatchik RA, Leamy AK, Noguchi Y, Shiota M, Young JD. Palmitate-induced activation of mitochondrial metabolism promotes oxidative stress and apoptosis in H4IIEC3 rat hepatocytes. Metab. Clin. Exp [print-electronic]. 2014 Feb; 63(2): 283-95. PMID: 24286856, PMCID: PMC3946971, PII: S0026-0495(13)00341-7, DOI: 10.1016/j.metabol.2013.10.009, ISSN: 1532-8600.
Jazmin LJ, O'Grady JP, Ma F, Allen DK, Morgan JA, Young JD. Isotopically nonstationary MFA (INST-MFA) of autotrophic metabolism. Methods Mol. Biol. 2014; 1090: 181-210. PMID: 24222417, DOI: 10.1007/978-1-62703-688-7_12, ISSN: 1940-6029.
Young JD, Allen DK, Morgan JA. Isotopomer measurement techniques in metabolic flux analysis II: mass spectrometry. Methods Mol. Biol. 2014; 1083: 85-108. PMID: 24218212, DOI: 10.1007/978-1-62703-661-0_7, ISSN: 1940-6029.
Young JD. Metabolic flux rewiring in mammalian cell cultures. Curr. Opin. Biotechnol [print-electronic]. 2013 Dec; 24(6): 1108-15. PMID: 23726154, PMCID: PMC3775942, PII: S0958-1669(13)00114-6, DOI: 10.1016/j.copbio.2013.04.016, ISSN: 1879-0429.
Templeton N, Dean J, Reddy P, Young JD. Peak antibody production is associated with increased oxidative metabolism in an industrially relevant fed-batch CHO cell culture. Biotechnol. Bioeng [print-electronic]. 2013 Jul; 110(7): 2013-24. PMID: 23381838, DOI: 10.1002/bit.24858, ISSN: 1097-0290.
Murphy TA, Young JD. ETA: robust software for determination of cell specific rates from extracellular time courses. Biotechnol. Bioeng [print-electronic]. 2013 Jun; 110(6): 1748-58. PMID: 23296385, PMCID: PMC3863648, DOI: 10.1002/bit.24836, ISSN: 1097-0290.
Allen DK, Young JD. Carbon and nitrogen provisions alter the metabolic flux in developing soybean embryos. Plant Physiol [print-electronic]. 2013 Mar; 161(3): 1458-75. PMID: 23314943, PMCID: PMC3585609, PII: pp.112.203299, DOI: 10.1104/pp.112.203299, ISSN: 1532-2548.
Murphy TA, Dang CV, Young JD. Isotopically nonstationary 13C flux analysis of Myc-induced metabolic reprogramming in B-cells. Metab. Eng [print-electronic]. 2013 Jan; 15: 206-17. PMID: 22898717, PMCID: PMC3535509, PII: S1096-7176(12)00078-X, DOI: 10.1016/j.ymben.2012.07.008, ISSN: 1096-7184.
Duckwall CS, Murphy TA, Young JD. Mapping cancer cell metabolism with(13)C flux analysis: Recent progress and future challenges. J Carcinog. 2013; 12: 13. PMID: 23961260, PMCID: PMC3746411, PII: JC-12-13, DOI: 10.4103/1477-3163.115422, ISSN: 1477-3163.
Jazmin LJ, Young JD. Isotopically nonstationary 13C metabolic flux analysis. Methods Mol. Biol. 2013; 985: 367-90. PMID: 23417813, DOI: 10.1007/978-1-62703-299-5_18, ISSN: 1940-6029.
Leamy AK, Egnatchik RA, Young JD. Molecular mechanisms and the role of saturated fatty acids in the progression of non-alcoholic fatty liver disease. Prog. Lipid Res [print-electronic]. 2013 Jan; 52(1): 165-74. PMID: 23178552, PMCID: PMC3868987, PII: S0163-7827(12)00058-6, DOI: 10.1016/j.plipres.2012.10.004, ISSN: 1873-2194.
Strand DW, Jiang M, Murphy TA, Yi Y, Konvinse KC, Franco OE, Wang Y, Young JD, Hayward SW. PPAR-gamma isoforms differentially regulate metabolic networks to mediate mouse prostatic epithelial differentiation. Cell Death Dis. 2012; 3: e361. PMID: 22874998, PMCID: PMC3434663, PII: cddis201299, DOI: 10.1038/cddis.2012.99, ISSN: 2041-4889.
Young JD, Shastri AA, Stephanopoulos G, Morgan JA. Mapping photoautotrophic metabolism with isotopically nonstationary (13)C flux analysis. Metab. Eng [print-electronic]. 2011 Nov; 13(6): 656-65. PMID: 21907300, PMCID: PMC3210925, PII: S1096-7176(11)00088-7, DOI: 10.1016/j.ymben.2011.08.002, ISSN: 1096-7184.
Noguchi Y, Young JD, Aleman JO, Hansen ME, Kelleher JK, Stephanopoulos G. Tracking cellular metabolomics in lipoapoptosis- and steatosis-developing liver cells. Mol Biosyst [print-electronic]. 2011 May; 7(5): 1409-19. PMID: 21327189, DOI: 10.1039/c0mb00309c, ISSN: 1742-2051.
Srour O, Young JD, Eldar YC. Fluxomers: a new approach for 13C metabolic flux analysis. BMC Syst Biol. 2011; 5: 129. PMID: 21846358, PMCID: PMC3750106, PII: 1752-0509-5-129, DOI: 10.1186/1752-0509-5-129, ISSN: 1752-0509.
Noguchi Y, Nishikata N, Shikata N, Kimura Y, Aleman JO, Young JD, Koyama N, Kelleher JK, Takahashi M, Stephanopoulos G. Ketogenic essential amino acids modulate lipid synthetic pathways and prevent hepatic steatosis in mice. PLoS ONE. 2010; 5(8): e12057. PMID: 20706589, PMCID: PMC2919399, DOI: 10.1371/journal.pone.0012057, ISSN: 1932-6203.
Reed JL, Senger RS, Antoniewicz MR, Young JD. Computational approaches in metabolic engineering [editorial]. J. Biomed. Biotechnol [print-electronic]. 2010; 2010: 207414. PMID: 21584279, PMCID: PMC3092504, DOI: 10.1155/2010/207414, ISSN: 1110-7251.
Noguchi Y, Young JD, Aleman JO, Hansen ME, Kelleher JK, Stephanopoulos G. Effect of anaplerotic fluxes and amino acid availability on hepatic lipoapoptosis. J. Biol. Chem [print-electronic]. 2009 Nov 11/27/2009; 284(48): 33425-36. PMID: 19758988, PMCID: PMC2785187, PII: M109.049478, DOI: 10.1074/jbc.M109.049478, ISSN: 1083-351X.
Young JD, Henne KL, Morgan JA, Konopka AE, Ramkrishna D. Integrating cybernetic modeling with pathway analysis provides a dynamic, systems-level description of metabolic control. Biotechnol. Bioeng. 2008 Jun 6/15/2008; 100(3): 542-59. PMID: 18438875, DOI: 10.1002/bit.21780, ISSN: 1097-0290.
Young JD, Walther JL, Antoniewicz MR, Yoo H, Stephanopoulos G. An elementary metabolite unit (EMU) based method of isotopically nonstationary flux analysis. Biotechnol. Bioeng. 2008 Feb 2/15/2008; 99(3): 686-99. PMID: 17787013, DOI: 10.1002/bit.21632, ISSN: 1097-0290.
Young JD, Ramkrishna D. On the matching and proportional laws of cybernetic models. Biotechnol. Prog. 2007 Jan; 23(1): 83-99. PMID: 17269675, DOI: 10.1021/bp060176q, ISSN: 1520-6033.
J. D. Young, K. L. Henne, J. A. Morgan, A. E. Konopka and D. Ramkrishna.. Cybernetic modeling of metabolism: towards a framework for rational design of recombinant organisms. Chemical Engineering Science. 2004; 59: 5041-9.