Publications

2022

Wentao Dong, M.A. Keibler,  Sun Jin Moon, P. C., Nian Liu, C.J. Berrios, J.K. Kelleher, H.D. Sikes, O. Iliopoulos, J.L. Coloff, M.G. Vander Heiden and Gregory Stephanopoulos. “Oncogenic metabolic rewiring independent of proliferative control in human mammary epithelial cells,” bioRxiv, 2022.
10.1101/2022.04.08.486845

Yongshuo Ma, Nian Liu, Greisen, J. Li, Kangjian Qiao, S. Huang and G. Stephanoopoulos, “Removal of lycopene substrate inhibition enables high carotenoid productivity in Yarrowia lipolytica,” Nature Communications 13:572, 2022.
10.1038/s41467-022-28277-w

Xiaoqiang Ma, Hong Liang, Qiuchi Pan, Kristala Jones Prather, Anthony J. Sinskey, Gregory Stephanopoulos, Kang Zhou. “Optimization of isopentenol utilization pathway for producing isoprenoids in Escherichia coli,” Agricultural and Food Chemistry, 2022.
10.1021/acs.jafc.2c00014

Dong W, Rawat ES, Stephanopoulos G, Abu-Remaileh M. “Isotope tracing in health and disease,” Current Opinion in Biotechnology. Aug;76:102739, 2022.
10.1016/j.copbio.2022.102739

Pan Q, Ma X, Liang H, Liu Y, Zhou Y, Stephanopoulos G, Zhou K. “Biosynthesis of geranate via isopentenol utilization pathway in Escherichia coli,” Biotechnol Bioeng. 2023 Jan;120(1):230-238. Epub 2022 Nov 1.
10.1002/bit.28255

Zhang, J., Keibler, M. A., Dong, W., Ghelfi J., Cordes, T., Kanashova, T., Pailot, A., Dittmar, G., Metallo, C. M., Lautenschlaeger, T., Linster, C., Hiller, K., & Stephanopoulos, G. “Non-targeted metabolomics identifies erythronate accumulation in cancer cells,” bioRxiv 12.04.519010,2022.
10.1101/2022.12.04.519010

2021

Woolston, B. M., & Stephanopoulos, G. “Engineering E. coli to Grow on Methanol”. Joule, 4(10), 2070–2072, 2021
10.1016/j.joule.2020.09.019

Li, Jingbo, Yongshuo Ma, Nian Liu, Bekir E. Eser, Zheng Guo, Peter Ruhdal Jensen, and Gregory Stephanopoulos. “Synthesis of High-Titer Alka(e)Nes in Yarrowia Lipolytica Is Enabled by a Discovered Mechanism.” Nature Communications, 11(1): 1-13, 2021.
10.1038/s41467-020-19995-0

Katsimpouras and G. Stephanopoulos, “Enzymes in biotechnology: Critical platform technologies for bioprocess development,” Current Opinion in Biotechnology, 69: 91-102, 2021
10.1016/j.copbio.2020.12.003

M.A. Keibler, W. Dong, J.L. Coloff, K.D. Korthauer, A.M. Hosios, L.B. Sullivan, O.D. Arevalo, A.S. Rhanse, J. Lee, K. Ho, J.K. Kelleher, O. Iliopoulos, M.G. VanderHeiden and G. Stephanopoulos, “Differential substrate use in EGF- and KRAS-stimulated human mammary epithelial cells,” FEBS Journal, 288(19), 5629–5649, 2021.
10.1111/febs.15858

Suvi Santala, Ville Santala, Nian Liu, and Gregory Stephanopoulos, “Partitioning metabolism between growth and product synthesis for coordinated production of wax esters in Acinetobacter baylyi ADP1”. Biotechnology and Bioengineering, 118(6), 2283–2292, 2021.
10.1002/bit.27740

Yurou Liu, Xiaoqiang Ma, Hong Liang, Gregory Stephanopoulos and Kang Zhou, “Monoterpenoid biosynthesis by engineered microbes,” Journal of Industrial Microbiology & Biotechnology, 48(9–10), 2021.
10.1093/jimb/kuab065

Lam, F. H., Turanlı-Yıldız, B., Liu, D., Resch, M. G., Fink, G. R., & Stephanopoulos, G. “Engineered yeast tolerance enables efficient production from toxified lignocellulosic feedstocks”. Science Advances, 7(26), eabf7613, 2021.
10.1126/sciadv.abf7613

Yongshuo Ma, Sanwen Huang^, and Gregory Stephanopoulos, “Targeting pathway expression to subcellular organelles improves astaxanthin synthesis in Yarrowia lipolytica,” Metabolic Engineering, 2021.
10.1016/j.ymben.2021.10.004

Cheng Li, C.A. Swofford, C. Rückert, A.O. Chatzivasileiou, Ruiwen Ou, P. Opdensteinen, T. Luttermann, Kang Zhou, Gregory Stephanopoulos, K.L. Jones Prather, S. Liang, S. Zheng, Ying Lin, A.J. Sinskey, “Heterologous production of α-carotene in Corynebacterium glutamicum using a multicopy chromosomal integration method,” Bioresource Technology 341(3):125782, 2021.
10.1016/j.biortech.2021.125782

Nian Liu and G. Stephanopoulos, “Metabolic Engineering Perspectives,” chapter in book Metabolic Enginering, Concepts and Applications, edited by S.Y. Lee, J. Nielsen and G. Stephanopoulos, Volume 13A of Advanced Biotechnology series, S.Y. Lee, J. Nielsen and G. Stephanopoulos (editors), John Wiley, Weinheim, Germany (2021).

Kang Zhou and G, Stephanopoulos. “Harnessing Yarrowia lipolytica to make small molecule products,” chapter in book: Metabolic Enginering, Concepts and Applications, edited by S.Y. Lee, J. Nielsen and G. Stephanopoulos, Volume 13A of Advanced Biotechnology series, S.Y. Lee, J. Nielsen and G. Stephanopoulos (editors), John Wiley, Weinheim, Germany (2021).

Isidor, M. S., Dong, W., Servin-Uribe, R. I., Villarroel, J., Altıntaş, A., Ayala-Sumuano, J. T., Varela-Echavarría, A., Barrès, R., Stephanopoulos, G., Macotela, Y., & Emanuelli, B. “Insulin resistance rewires the metabolic gene program and glucose utilization in human white adipocytes”. International Journal of Obesity (2005), 2021.
10.1038/s41366-021-01021-y

Biggs, B. W., Alper, H. S., Pfleger, B. F., Tyo, K. E. J., Santos, C. N. S., Ajikumar, P. K., & Stephanopoulos, G. “Enabling commercial success of industrial biotechnology.” Science (New York, N.Y.), 374(6575), 1563–1565, 2021.
10.1126/science.abj5040

Sheneman, G. Stephasnopoulos and A.E. Vasdekis, “Deep learning classification of lipid dropletsin qualtitative phase images,” PLoS ONE 16(4): e0249196, 2021.
10.1371/journal.pone.0249196

Cheuk Him Man, Francois Mercier, Nian Liu, Wentao Dong, Gregory Stephanopoulos, Li Jiang, Yookyung Jung, Charles Lin, Anskar Leung, and David Scadden, “Proton/lactate export causes intracellular alkalinization that enforces anabolic carbon metabolism to drive mammalian cell growth,” Blood 139 (4): 502–522, 2021.
10.1182/blood.2021011563

2020

Liu, N., Santala, S., & Stephanopoulos, G. “Mixed carbon substrates: a necessary nuisance or a missed opportunity?” Current Opinion in Biotechnology 62: 5–21, 2020.
10.1016/j.copbio.2019.07.003

Mano, Junichi, Nian Liu, John H. Hammond, Devin H. Currie, and Gregory Stephanopoulos. “Engineering Yarrowia Lipolytica for the Utilization of Acid Whey.” Metabolic Engineering 57: 43–50, 2020
10.1016/j.ymben.2019.09.010

Yurou Liu, Xiaoqiang Ma, Zhen Jie Low, Hong Liang, A. Sinskey, G. Stephanopoulos, Kang Zhou. “Using biopolymer bodies for in vivo encapsulation of hydrophobic products,” Metabolic Engineering, 2020.
10.1016/j.ymben.2020.04.006

Georgios Daletos and G. Stephanopoulos. “Protein engineering strategies for microbial production of isoprenoids,” Metabolic Engineering Communications, 11, 2020.
10.1016/j.mec.2020.e00129

Daletos, Georgios, Constantinos Katsimpouras, and Gregory Stephanopoulos. “Novel Strategies and Platforms for Industrial Isoprenoid Engineering.” Trends in Biotechnology, 38(7): 811-822, 2020.
10.1016/j.tibtech.2020.03.009

Yusuf, Rushdia, Borja Saez, Azeem Sharda, Nick van Gastel, Vionnie Yu, Ninib Baryawno, Elizabeth W Scadden, et al. “Aldehyde Dehydrogenase 3a2 Protects AML Cells from Oxidative Death and the Synthetic Lethality of Ferroptosis Inducers.” Blood, 2020.
10.1182/blood.2019001808

Liu, Yurou, Zhen Jie Low, Xiaoqiang Ma, Hong Liang, Anthony J. Sinskey, Gregory Stephanopoulos, and Kang Zhou. “Using Biopolymer Bodies for Encapsulation of Hydrophobic Products in Bacterium.” Metabolic Engineering, 61: 206–14, 2020.
10.1016/j.ymben.2020.04.006

Luo, Zhengshan, Nian Liu, Zbigniew Lazar, Alkiviadis Chatzivasileiou, Valerie Ward, Jian Chen, Jingwen Zhou, and Gregory Stephanopoulos. “Enhancing Isoprenoid Synthesis in Yarrowia Lipolytica by Expressing the Isopentenol Utilization Pathway and Modulating Intracellular Hydrophobicity.” Metabolic Engineering, 61: 344–51, 2020.
10.1016/j.ymben.2020.07.010

Liang, Hong, Xiaoqiang Ma, Wenbo Ning, Yurou Liu, Anthony Sinskey, Gregory Stephanopoulos, and Kang Zhou. “Constructing an Ethanol Utilization Pathway in Escherichia Coli to Produce Acetyl-CoA Derived Compounds.” Metabolic Engineering, 2020.
10.1016/j.ymben.2020.11.010

Abdel-Mawgoud, A.M., and G. Stephanopoulos. “Improving CRISPR/Cas9-Mediated Genome Editing Efficiency in Yarrowia Lipolytica Using Direct TRNA-SgRNA Fusions.” Metabolic Engineering, 62: 106-115, 2020.
10.1016/j.ymben.2020.07.008

Zu, Yuexuan, Kristala LJ Prather, and Gregory Stephanopoulos. “Metabolic Engineering Strategies to Overcome Precursor Limitations in Isoprenoid Biosynthesis.” Current Opinion in Biotechnology, 66:171-178, 2020.
10.1016/j.copbio.2020.07.005

Moon, Sun Jin, Wentao Dong, Gregory N. Stephanopoulos, and Hadley D. Sikes. “Oxidative Pentose Phosphate Pathway and Glucose Anaplerosis Support Maintenance of Mitochondrial NADPH Pool under Mitochondrial Oxidative Stress.” Bioengineering & Translational Medicine, 5(3): e10184, 2020.
10.1002/btm2.10184

Kang Zhou, A.J. Sinskey and G. Stephanopoulos, “Improving production of natural produsts via Metabolic Engineering,” editorial of special issue of Metabolic Engineering Communications, 2020.

Daletos, Georgios, and Gregory Stephanopoulos. “Protein Engineering Strategies for Microbial Production of Isoprenoids.” Metabolic Engineering Communications, 11: e00129, 2020.
10.1016/j.mec.2020.e00129

Woolston, B. M., & Stephanopoulos, G. “Engineering E. coli to Grow on Methanol”. Joule, 4(10), 2070–2072, 2020.
10.1016/j.joule.2020.09.019

Li, Jingbo, Yongshuo Ma, Nian Liu, Bekir E. Eser, Zheng Guo, Peter Ruhdal Jensen, and Gregory Stephanopoulos. “Synthesis of High-Titer Alka(e)Nes in Yarrowia Lipolytica Is Enabled by a Discovered Mechanism.” Nature Communications, 11(1): 1-13, 2020.
10.1038/s41467-020-19995-0

2019

W. Dong, S.J. Moon, J.K. Kelleher, G. Stephanopoulos, “Dissecting mammalian cell metabolism through 13C- and 2H-isotope tracing: Interpretations at the molecular and systems levels”, ACS Industrial & Engineering Chemistry Research, 59, 6, 2593–2610, 2019.
10.1021/acs.iecr.9b05154

N. Liu, S. Santala, G. Stephanopoulos, “Mixed carbon substrates: a necessary nuisance or a missed opportunity?”, Current Opinion in Biotechnology, 62, 15-21, 2019.
10.1016/j.copbio.2019.07.003

V. Ward, A.O. Chatzivasileiou, G. Stephanopoulos, “Cell free biosynthesis of isoprenoids from isopentenol”, Biotechnology and Bioengineering, 116, 12, 3269-3281, 2019.
10.1002/bit.27146

D.F. Emerson, G. Stephanopoulos, “Limitations in converting waste gases to fuels and chemicals”, Current Opinion in Biotechnology, 59, 39-45, 2019.
10.1016/j.copbio.2019.02.004

F. Cheng, H. Yu, G. Stephanopoulos, “Engineering Corynebacterium glutamicum for high-titer biosynthesis of hyaluronic acid”, Metabolic Engineering, 55, 276-289, 2019.
10.1016/j.ymben.2019.07.003

A.E. Vasdekis, H. Alanazi, A.M. Silverman, C.J. Williams, A.J. Canul, J.B. Cliff, A.C. Dohnalkova, G. Stephanopoulos, “Eliciting the impacts of cellular noise on metabolic trade-offs by quantitative mass imaging”, Nature Communications, 10, 2019.
10.1038/s41467-019-08717-w

J.O. Park, N. Liu, K.M. Holinski, D.F. Emerson, K. Qiao, B.M. Woolston, J. Xu, Z. Lazar, M.A. Islam, C. Vidoudez, P.R. Girguis, G. Stephanopoulos, “Synergistic substrate cofeeding stimulates reductive metabolism”, Nature Metabolism, 1, 643-651, 2019.
10.1038/s42255-019-0077-0

T.B. Roth, B.M. Woolston, G. Stephanopoulos, D.R. Liu, “Phage-assisted evolution of Bacillus methanolicus methanol dehydrogenase 2”, ACS Synthetic Biology, 8(4), 796-806, 2019.
10.1021/acssynbio.8b00481

D.F. Emerson, B.M. Woolston, N. Liu, M. Donnelly, D.H. Currie, G. Stephanopoulos, “Enhancing hydrogen‐dependent growth of and carbon dioxide fixation by Clostridium ljungdahlii through nitrate supplementation”, Biotechnology and Bioengineering, 116(2), 294-306, 2019.
10.1002/bit.26847

A.O. Chatzivasileiou, V. Ward, S.M. Edgar, G. Stephanopoulos, “Two-step pathway for isoprenoid synthesis”, PNAS, 116(2), 506-511, 2019.
10.1073/pnas.1812935116

B. Uranukul, B.M. Woolston, G.R. Fink, G. Stephanopoulos, “Biosynthesis of monoethylene glycol in Saccharomyces cerevisiae utilizing native glycolytic enzymes”, Metabolic Engineering, 51, 20-31, 2019.
10.1016/j.ymben.2018.09.012

2018

W.S. Ahn, W. Dong, Z. Zhang, J.R. Cantor, D.M. Sabatini, O. Illiopoulos, G. Stephanopoulos, “Glyceraldehyde 3-phosphate dehydrogenase modulates nonoxidative pentose phosphate pathway to provide anabolic precursors in hypoxic tumor cells”, AICHE Journal, 64(12), 4289-4296, 2018.
10.1002/aic.16423

Z. Lazar, N. Liu, G. Stephanopoulos, “Holistic approaches in lipid production by Yarrowia lipolytica”, Trends in Biotechnology, 36(11), 1157-1170, 2018.
10.1016/j.tibtech.2018.06.007

A.M. Abdel-Mawgoud, K.A. Markham, C.M. Palmer, N. Liu, G. Stephanopoulos, “Metabolic engineering in the host Yarrowia lipolytica”, Metabolic Engineering, 50, 192-208, 2018.
10.1016/j.ymben.2018.07.016

B.M. Woolston, D.F. Emerson, D.H. Currie, G. Stephanopoulos, “Rediverting carbon flux in Clostridium ljungdahlii using CRISPR interference (CRISPRi)”, Metabolic Engineering, 48, 243-253, 2018.
10.1016/j.ymben.2018.06.006

Z. Li, P. Hong, Y. Da, L. Li, G. Stephanopoulos, “Metabolic engineering of Escherichia coli for the production of L-malate from xylose”, Metabolic Engineering, 48, 25-32, 2018.
10.1016/j.ymben.2018.05.010

B.M. Woolston, J.R. King, M. Reiter, B. Van Hove, G. Stephanopoulos, “Improving formaldehyde consumption drives methanol assimilation in engineered E. coli”, Nature Communications, 9, 2018.
10.1038/s41467-018-04795-4

J.J. Marlow, A. Kumar, B.C. Enalls, L.M. Reynard, N. Tuross, G. Stephanopoulos, P. Girguis, “Harnessing a methane-fueled, sediment-free mixed microbial community for utilization of distributed sources of natural gas”, Biotechnology and Bioengineering, 115(6), 1450-1464, 2018.
10.1002/bit.26576

V. Ward, A.O. Chatzivasileiou, G. Stephanopoulos, “Metabolic engineering of Escherichia coli for the production of isoprenoids”, FEMS Microbiology Letters, 365(10), 2018.
10.1093/femsle/fny079

A.M. Abdel-Mawgoud, G. Stephanopoulos, “Simple glycolipids of microbes: Chemistry, biological activity and metabolic engineering”, Synthetic and Systems Biotechnology, 3(1), 3-19, 2018.
10.1016/j.synbio.2017.12.001

B.M. Woolston, T. Roth, I. Kohale, D.R. Liu, G. Stephanopoulos, “Development of a formaldehyde biosensor with application to synthetic methylotrophy”, Biotechnology and Bioengineering, 115(1), 206-215, 2018.
10.1002/bit.26455

2017

X. Chen, C. Zhang, R. Zou, G. Stephanopoulos, and H. Too, “In vitro metabolic engineering of Amorpha-4,11-diene biosynthesis at enhanced rate and specific yield of production.” ACS Syn. Bio., 6 (9), 1691-1700, 2017.
10.1021/acssynbio.6b00377

W. Dong, M.A. Keibler, and G. Stephanopoulos, “Review of metabolic pathways activated in cancer cells as determined through isotopic labeling and network analysis.” Metab. Eng., 43, 113-124, 2017.
10.1016/j.ymben.2017.02.002

D.F. Emerson, A. Al Ghatta, B.M. Woolston, A. Fay, A. Kumar, and G. Stephanopoulos, “Theoretical analysis of natural gas recovery from marginal wells with a deep well reactor.” AICHE J., 63 (9), 3642-3650, 2017.
10.1002/aic.15738

J. Xu, N. Liu, K. Qiao, S. Vogg, and G. Stephanopoulos, “Application of metabolic controls for the maximization of lipid production in semicontinuous fermentation,” Proc. Natl. Acad. Sci., 114 (27), E5308-E5316, 2017.
10.1073/pnas.1703321114

J. R. King, B. M. Woolston, and G. Stephanopoulos, “Designing a new entry point into isoprenoid metabolism by exploiting fructose-6-phosphate aldolase side-reactivity in Escherichia coli.” ACS Syn. Bio., 6 (7), 1416-1426, 2017.
10.1021/acssynbio.7b00072

P. Xu, K. Qiao, and G. Stephanopoulos, “Engineering oxidative stress defense pathways to build a robust lipid production platform in Yarrowia lipolytica,” Biotechnol. Bioeng., 114 (7), 1521–1530, 2017.
10.1002/bit.26285

M. A. Islam, N. Hadadi, M. Ataman, V. Hatzimanikatis, and G. Stephanopoulos, “Exploring biochemical pathways for mono-ethylene glycol (MEG) synthesis from synthesis gas,” Metab. Eng., 41 (December 2016), 173–181, 2017.
10.1016/j.ymben.2017.04.005

Z. J. Li, K. Qiao, N. Liu, and G. Stephanopoulos, “Engineering Yarrowia lipolytica for poly-3-hydroxybutyrate production,” J. Ind. Microbiol. Biotechnol., 44 (4-5), 605–612, 2017.
10.1007/s10295-016-1864-1

A. Okazaki, P. A. Gameiro, D. Christodoulou, L. Laviollette, M. Schneider, F. Chaves, A. Stemmer-Rachamimov, S. A. Yazinski, R. Lee, G. Stephanopoulos, L. Zou, and O. Illiopoulos, “Glutaminase and poly(ADP-ribose) polymerase inhibitors suppress pyrimidine synthesis and VHL-deficient renal cancers,” J. Clin. Invest., 127 (5), 1631–1645, 2017.
10.1172/JCI87800

J. Yang, F. Cheng, H. Yu, J. Wang, Z. Guo, and G. Stephanopoulos, “Key Role of the Carboxyl Terminus of Hyaluronan Synthase in Processive Synthesis and Size Control of Hyaluronic Acid Polymers,” Biomacromolecules, 18 (4), 1064–1073, 2017.
10.1021/acs.biomac.6b01239

S. Edgar, F. S. Li, K. Qiao, J. K. Weng, and G. Stephanopoulos, “Engineering of Taxadiene Synthase for Improved Selectivity and Yield of a Key Taxol Biosynthetic Intermediate,” ACS Synth. Biol., 6 (2), 201–205, 2017.
10.1021/acssynbio.6b00206

K. Qiao, T. M. Wasylenko, K. Zhou, P. Xu, and G. Stephanopoulos, “Lipid production in Yarrowia lipolytica is maximized by engineering cytosolic redox metabolism,” Nat. Biotechnol., 35, 173–177, 2017.
10.1038/nbt.3763

S. M. Davidson, O. Jonas, M. A. Keibler, H. W. Hou, A. Luengo, J. R. Mayers, J. Wyckoff, A. M. Del Rosario, M. Whitman, C. R. Chin, K. J. Condon, A. Lammers, K. A. Kellersberger, B. K. Stall, G. Stephanopoulos, D. Bar-Sagi, J. Han, J. D. Rabinowitz, M. J. Cima, R. Langer, and M. G. Vander Heiden, “Direct evidence for cancer-cell-autonomous extracellular protein catabolism in pancreatic tumors,” Nat. Medicine., 23, 235–241, 2017.
10.1038/nm.4256

A. E. Vasdekis, A. M. Silverman, and G. Stephanopoulos, “Exploiting bioprocessing fluctuations to elicit the mechanistics of de Novo lipogenesis in Yarrowia lipolytica,” PLoS One, 12 (1), 1–13, 2017.
10.1371/journal.pone.0168889

P. Xu, E. A. Rizzoni, S. Y. Sul, and G. Stephanopoulos, “Improving Metabolic Pathway Efficiency by Statistical Model-Based Multivariate Regulatory Metabolic Engineering,” ACS Synth. Biol., 6 (1), 148–158, 2017.
10.1021/acssynbio.6b00187

2016

C. Berrios, M. Padi, M. A. Keibler, D. E. Park, V. Molla, J. Cheng, S. M. Lee, G. Stephanopoulos, J. Quackenbush, and J. A. DeCaprio, “Merkel Cell Polyomavirus Small T Antigen Promotes Pro-Glycolytic Metabolic Perturbations Required for Transformation,” PLoS Pathog., 12 (11), 1–21, 2016.
10.1371/journal.ppat.1006020

N. Liu, K. Qiao, and G. Stephanopoulos, “13C Metabolic Flux Analysis of acetate conversion to lipids by Yarrowia lipolytica,” Metab. Eng., 38, 86–97, 2016.
10.1016/j.ymben.2016.06.006

P. Xu, K. Qiao, W. S. Ahn, and G. Stephanopoulos, “Engineering Yarrowia lipolytica as a platform for synthesis of drop-in transportation fuels and oleochemicals.,” Proc. Natl. Acad. Sci. U. S. A., 113 (39), 10848–53, 2016.
10.1073/pnas.1607295113

M. A. Keibler, T. M. Wasylenko, J. K. Kelleher, O. Iliopoulos, M. G. Vander Heiden, and G. Stephanopoulos, “Metabolic requirements for cancer cell proliferation,” Cancer Metab., 4 (1), 16, 2016.
10.1186/s40170-016-0156-6

A. J. Shaw, F. H. Lam, M. Hamilton, A. Consiglio, K. MacEwen, E. E. Brevnova, E. Greenhagen, W. G. LaTouf, C. R. South, H. van Dijken, G. Stephanopoulos, “Metabolic engineering of microbial competitive advantage for industrial fermentation processes,” Science, 353 (6299), 583-586, 2016.
10.1126/science.aaf6159

C. Zhang, X. Chen, G. Stephanopoulos, and H. P. Too, “Efflux transporter engineering markedly improves amorphadiene production in Escherichia coli,” Biotechnol. Bioeng., 113 (8), 1755–1763, 2016.
10.1002/bit.25943

H. Zhang and G. Stephanopoulos, “Co-culture engineering for microbial biosynthesis of 3-amino-benzoic acid in Escherichia coli,” Biotechnol. J., 11 (7), 981–987, 2016.
10.1002/biot.201600013

Z. J. Li, K. Qiao, W. Shi, B. Pereira, H. Zhang, B. D. Olsen, and G. Stephanopoulos, “Biosynthesis of poly(glycolate-co-lactate-co-3-hydroxybutyrate) from glucose by metabolically engineered Escherichia coli,” Metab. Eng., 35, 1–8, 2016.
10.1016/j.ymben.2016.01.004

A. M. Silverman, K. Qiao, P. Xu, and G. Stephanopoulos, “Functional overexpression and characterization of lipogenesis-related genes in the oleaginous yeast Yarrowia lipolytica,” Appl. Microbiol. Biotechnol., 100 (8), 3781–3798, 2016.
10.1007/s00253-016-7376-0

W. Biggs, C. Giaw, K. Sagliani, S. Shankar, and G. Stephanopoulos, “Overcoming heterologous protein interdependency to optimize P450-mediated Taxol precursor synthesis in Escherichia coli,” Proc. Natl. Acad. Sci., 113 (12), 3209–3214, 2016.
10.1073/pnas.1515826113

F. Cheng, Q. Gong, H. Yu, and G. Stephanopoulos, “High-titer biosynthesis of hyaluronic acid by recombinant Corynebacterium glutamicum,” Biotechnol. J., 11, 574-584, 2016.
10.1002/biot.201500404

B. Pereira, Z. J. Li, M. De Mey, C. G. Lim, H. Zhang, C. Hoeltgen, and G. Stephanopoulos, “Efficient utilization of pentoses for bioproduction of the renewable two-carbon compounds ethylene glycol and glycolate,” Metab. Eng., 34, 80–87, 2016.
10.1016/j.ymben.2015.12.004

J. R. King, S. Edgar, K. Qiao, and G. Stephanopoulos,”Accessing nature’s diversity through metabolic engineering and synthetic biology,” F1000Research, 5, 397-407, 2016.
10.12688/f1000research.7311.1

S. Edgar, K. Zhou, K. Qiao, J. R. King, J. H. Simpson, and G. Stephanopoulos, “Mechanistic Insights into Taxadiene Epoxidation by Taxadiene-5α-Hydroxylase,” ACS Chem. Biol., 11, 460-469, 2016.
10.1021/acschembio.5b00767

B. Pereira, H. Zhang, M. De Mey, C. G. Lim, Z. J. Li, and G. Stephanopoulos, “Engineering a novel biosynthetic pathway in Escherichia coli for production of renewable ethylene glycol,” Biotechnol. Bioeng., 113 (2), 376–383, 2016.
10.1002/bit.25717

J. Friedlander, V. Tsakraklides, A. Kamineni, E. H. Greenhagen, A. L. Consiglio, K. MacEwen, D. V. Crabtree, J. Afshar, R. L. Nugent, M. A. Hamilton, A. Joe Shaw, C. R. South, G. Stephanopoulos, and E. E. Brevnova, “Engineering of a high lipid producing Yarrowia lipolytica strain,” Biotechnol. Biofuels, 9 (1), 77-88, 2016.
10.1186/s13068-016-0492-3

2015

A. E. Vasdekis and G. Stephanopoulos, “Review of methods to probe single cell metabolism and bioenergetics”, Metab. Eng,. 27, 115–135, 2015.
10.1016/j.ymben.2014.09.007

A. E. Vasdekis, A. M. Silverman and G. Stephanopoulos, “Origins of Cell-to-Cell Bioprocessing Diversity and Implications of the Extracellular Environment Revealed at the Single-Cell Level”, Sci. Rep., 5, 17689, 2015.
10.1038/srep17689

H. Zhang, Z. Li, B. Pereira and G. Stephanopoulos, “Engineering E. coli–E. coli cocultures for production of muconic acid from glycerol”, Microb. Cell Fact., 14, 134, 2015.
10.1186/s12934-015-0319-0

A. Okazaki, P. Gameiro, G. Stephanopoulo and O. Iliopoulos, “Glutaminase inhibitors suppress pyrimidine synthesis and promote DNA replication stress in VHL-deficient human renal cancer cells”, Cancer Research, 75(15), 1123, 2015;
10.1158/1538-7445.AM2015-1123

J. M. Buescher and G. Stephanopoulos et al, “A roadmap for interpreting 13C metabolite labeling patterns from cells”, Curr. Opin. Biotechnol. 34, 189–201, 2015.
10.1016/j.copbio.2015.02.003

V. Tsakraklides, E. Brevnova, G. Stephanopoulos and A. J. Shaw, “Improved gene targeting through cell cycle synchronization”, PLoS One, 10, 2015.
10.1371/journal.pone.0133434

H. Zhang, B. Pereira, Z Li and G. Stephanopoulos, “Engineering Escherichia coli coculture systems for the production of biochemical products”, Proc. Natl. Acad. Sci., 112, 8266–71, 2015.
10.1073/pnas.1506781112

T. M. Wasylenko, W. S. Ahn and G. Stephanopoulos, “The oxidative pentose phosphate pathway is the primary source of NADPH for lipid overproduction from glucose in Yarrowia lipolytica”, Metab. Eng., 30, 27–39, 2015.
10.1016/j.ymben.2015.02.007

K. Qiao and G. Stephanopoulos et al, “Engineering lipid overproduction in the oleaginous yeast Yarrowia lipolytica”, Metab. Eng,. 29, 56–65, 2015.
10.1016/j.ymben.2015.02.005

M. A. Islam, K. Zengler, E. A. Edwards, R. Mahadevan and G. Stephanopoulos, “Investigating Moorella thermoacetica metabolism with a genome-scale constraint-based metabolic model”, Integr. Biol., 7, 869–82, 2015.
10.1039/c5ib00095e

S. Y. Lunt and G. Stephanopoulos et al., “Pyruvate kinase isoform expression alters nucleotide synthesis to impact cell proliferation”, Mol. Cell, 57, 95–107, 2015.
10.1016/j.molcel.2014.10.027

T. M. Wasylenko and G. Stephanopoulos, “Metabolomic and 13C-metabolic flux analysis of a xylose-consuming Saccharomyces cerevisiae strain expressing xylose isomerase”, Biotechnol. Bioeng., 112, 470–483, 2015.
10.1002/bit.25447

K. Zhou, K. Qiao, S. Edgar and G. Stephanopoulos, “Distributing a metabolic pathway among a microbial consortium enhances production of natural products”, Nat. Biotechnol., 33, 377–383, 2015.
10.1038/nbt.3095

C. Zhang, R. Zou, X. Chen, G. Stephanopoulos and H. P. Too, “Experimental design-aided systematic pathway optimization of glucose uptake and deoxyxylulose phosphate pathway for improved amorphadiene production”, Appl. Microbiol. Biotechnol., 99, 3825–3837, 2015.
10.1007/s00253-015-6463-y

2014

J. Zhang, W. S. Ahn, P. A. Gameiro, M. A. Keibler, Z. Zhang and G. Stephanopoulos, “13C isotope-assisted methods for quantifying glutamine metabolism in cancer cells”, Methods Enzymol, 542, 369–389, 2014.
10.1016/B978-0-12-416618-9.00019-4

A. E. Vasdekis and G. Stephanopoulos, “Single Microbe Trap and Release using Sub-Microfluidics: Methods and Applications in Biopolymer Trafficking”, Biophysical Journal, 106(2), 2014.
10.1021/ac403879d

A. Wegner, D. Weindl, C. Jager, S. C. Sapcariu, X. Y. Dong, G. Stephanopoulos and K. Hiller, “Fragment formula calculator (FFC): Determination of chemical formulas for fragment ions in mass spectrometric data”, Anal. Chem., 86, 2221–2228, 2014.
10.1021/ac403879d

V. G. Yadav and G. Stephanopoulos, “Metabolic engineering: The ultimate paradigm for continuous pharmaceutical manufacturing”, ChemSusChem, 7, 1847–1853, 2014.
10.1002/cssc.201301219

P. Xu, L. Li, F. Zhang, G. Stephanopoulos and M. Koffas, “Improving fatty acids production by engineering dynamic pathway regulation and metabolic control”, Proc. Natl. Acad. Sci., 111, 11299–11304, 2014.
10.1073/pnas.1406401111

F. H. Lam, A. Ghaderi, G. R. Fink and G. Stephanopoulos, “Engineering alcohol tolerance in yeast”, Science, 346, 71–75, 2014.
10.1126/science.1257859

2013

M. Tai, G. Stephanopoulos, “Engineering the push and pull of lipid biosynthesis in oleaginous yeast Yarrowia lipolytica for biofuel production”, Metabolic Engineering, 15, 1-9, 2013.
10.1016/j.ymben.2012.08.007

B. M. Woolston, S. Edgar and G. Stephanopoulos, “Metabolic Engineering: Past and Future”, Annu. Rev. Chem. Biomol. Eng., 4, 259–288, 2013.
10.1146/annurev-chembioeng-061312-103312

B. N. Nicolay, P. A. Gameiro, K. Tschop, M. Korenjak, A. M. Heilmann, J. M. Asara, G. Stephanopoulos, O. Iliopoulos and N. J. Dyson, “Loss of RBF1 changes glutamine catabolism”, Genes and Development, 27(2), 182-196, 2013.
10.1101/gad.206227.112

P. A. Gameiro, A. Metelo, R. Pérez-Carro, A. Alexandra, Z. Wang, K. W. Rathmell, A. Olumi, P. López-Larrubia, G. Stephanopoulos and O. Iliopoulos, “Hypoxia inducible factor (HIF) promotes reductive carboxylation by regulating citrate levels and renders VHL-deficient and hypoxic cells sensitive to glutamine deprivation”, Cancer Research, 73(3), 2013.
10.1158/1538-7445

P. A. Gameiro, J. Yang, A. M. Metelo, R. Pérez-Carro, R. Baker, Z. Wang, A. Arreola, W. K. Rathmell, A. Olumi, P. López-Larrubia and G. Stephanopoulos, O. Iliopoulos, “In vivo HIF-mediated reductive carboxylation Is regulated by citrate levels and sensitizes VHL-deficient cells to glutamine deprivation”, Cell Metabolism, 17(3), 372-385, 2013.
10.1016/j.cmet.2013.02.002

H. Zhang and G. Stephanopoulos, “Engineering E. coli for caffeic acid biosynthesis from renewable sugars”, Applied Microbiology and Biotechnology, 97(8), 3333-3341
2013.10.1007/s00253-012-4544-8

J. L. Avalos, G. R. Fink and G. Stephanopoulos, “Compartmentalization of metabolic pathways in yeast mitochondria improves the production of branched-chain alcohols”, Nat. Biotechnol., 31, 335–341, 2013.
10.1038/nbt.2509

K. Hiller, A. Wegner, D. Weindl, T. Cordes, C. M. Metallo, J. K. Kelleher and G. Stephanopoulos, “NTFD–a stand-alone application for the non-targeted detection of stable isotope-labeled compounds in GC/MS data”, Bioinformatics, 29, 1226–1228, 2013.
10.1093/bioinformatics/btt119

P. A. Gameiro, L. A. Laviolette, J. K. Kelleher, O. Iliopoulos and G. Stephanopoulos, “Cofactor balance by nicotinamide nucleotide transhydrogenase (NNT) coordinates reductive carboxylation and glucose catabolism in the tricarboxylic acid (TCA) cycle”, J. Biol. Chem, 288, 12967–12977, 2013.
10.1074/jbc.M112.396796

A. Csibi, S. Fendt, C. Li, G. Poulogiannis, A. Y. Choo, D. J. Chapski, S. M. Jeong, J. M. Dempsey, A. Parkhitko, T. Morrison, E. P. Henske, M. C. Haigis, L. C. Cantley, G. Stephanopoulos, J. Yu and J. Blenis, “The mTORC1 Pathway Stimulates Glutamine Metabolism and Cell Proliferation by Repressing SIRT4”, Cell, 153(4), 840-854, 2013.
10.1016/j.cell.2013.04.023

S. Carlsen, P. K. Ajikumar, L. R. Formenti, K. Zhou, T. H. Phon, M. L. Nielsen, A. E. Lantz, M. C. Kielland-Brandt and G. Stephanopoulos, “Heterologous expression and characterization of bacterial 2-C-methyl-d-erythritol-4-phosphate pathway in Saccharomyces cerevisiae”, Appl. Microbiol. Biotechnol, 97, 5753–5769, 2013.
10.1007/s00253-013-4877-y

S. M. Fendt, E. L. Bell, M. A. Keibler, B. A. Olenchock, J. R. Mayers, T. M. Wasylenko, N. I. Vokes, L. Guarente, M. G. Vander Heiden and G. Stephanopoulos, “Reductive glutamine metabolism is a function of the ketoglutarate to citrate ratio in cells”, Nature Communications, 4, 1-11, 2013.
10.1038/ncomms3236

S. M. Fendt, E. L. Bell, M. A. Keibler, S. M. Davidson, G. J. Wirth, B. Fiske, J. R. Mayers, M. Schwab, G. Bellinger, A. Csibi, A. Patnaik, M. J. Blouin, L. C. Cantley, L. Guarante, J., Belnis, M. N. Pollak, A. F. Olumi, M. G. Vander Heiden and G. Stephanopoulos, “Metformin decreases glucose oxidation and increases the dependency of prostate cancer cells on reductive glutamine metabolism”, Cancer Res., 73, 4429–4438, 2013.
10.1158/0008-5472

P. Hu, H. Rismani-Yazdi and G. Stephanopoulos, “Anaerobic CO2 fixation by the acetogenic bacterium Moorella thermoacetica”, AIChE J., 59, 3176–3183, 2013.
10.1002/aic.14127

F. Ahmad, M. N. Atiyeh, B. Pereira and G. Stephanopoulos, “A review of cellulosic microbial fuel cells: Performance and challenges”, Biomass and Bioenergy, 56, 177–188, 2013.
10.1016/j.biombioe.2013.04.006

T. M. Wasylenko and G. Stephanopoulos, “Kinetic isotope effects significantly influence intracellular metabolite 13C labeling patterns and flux determination”, Biotechnol. J., 8, 1080–1089, 2013.
10.1002/biot.201200276

K. Zhou, R. Zou, C. Zhang, G. Stephanopoulos and H. P. Too, “Optimization of amorphadiene synthesis in bacillus subtilis via transcriptional, translational, and media modulation”, Biotechnol. Bioeng., 110, 2556–2561, 2013.
10.1002/bit.24900

C. Zhang, X. X. Chen, R. Y. Zou, K. Zhou and G. Stephanopoulos, “Combining Genotype Improvement and Statistical Media Optimization for Isoprenoid Production in E. coli.”, PLoS One, 8, 2013.
10.1371/journal.pone.0075164

R. Zou, K. Zhou, G. Stephanopoulos and H. P. Too, “Combinatorial Engineering of 1-Deoxy-D-Xylulose 5-Phosphate Pathway Using Cross-Lapping In Vitro Assembly (CLIVA) Method”, PLoS One, 8(11), 2013.
10.1371/journal.pone.0079557

X. Chen, C. Q. Zhang, R. Y. Zou, K. Zhou, G. Stephanopoulos and H. P. Too, “Statistical experimental design guided optimization of a one-pot biphasic multienzyme total synthesis of amorpha-4,11-diene”, PLoS One, 8, 2013.
10.1371/journal.pone.0079650

K. H. Seow, L. H. Zhou, G. Stephanopoulos and H. P. Too, “c-Jun N-terminal kinase in synergistic neurite outgrowth in PC12 cells mediated through P90RSK”, BMC NEUROSCIENCE, 14, 2013.
10.1186/1471-2202-14-153