Publications

Recent publications

2017 2016 2015 2014 2013

 

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