Stephanopoulos has authored more than 400 journal articles on the topics of biotechnology, bioinformatics, and metabolic engineering.  These include:
* Gregory Stephanopoulos, R. Aris, A. G. Fredrickson. "A stochastic analysis of the growth of competing microbial populations in a continuous biochemical reactor", Mathematical Biosciences 45, 99-135, (1979).
* Gregory Stephanopoulos, R. Aris, A. G. Fredrickson. "The growth of competing microbial populations in a CSTR with periodically varying inputs", AIChE Journal 25, 863-872, (1979).
* G. Stephanopoulos, A. G. Fredrickson. ""Coexistence of Photosynthetic Microorganisms with Growth Rates Depending on the Spectral Quality of Light", Bulletin of Mathematical Biology 41, 525-542, (1979).
* G. Stephanopoulos, A. G. Fredrickson. "The Effect of Spatial Inhomogeneities on the Coexistence of Competing Microbial Populations", Biotechnology and Bioengineering 21, 1491-1498, (1979).
* Rahul Singhvi, Amit Kumar, Gabriel P. Lopez, Gregory N. Stephanopoulos, D. I. Wang, George M. Whitesides, Donald E. Ingber "Engineering cell shape and function", Science, 264(5159), 696-698, (1994).
* Hal Alper, Curt Fischer, Elke Nevoigt, Gregory Stephanopoulos. "Tuning genetic control through promoter engineering", Proceedings of the National Academy of Sciences, 102(36), 12678, (2005).
* Parayil Kumaran Ajikumar, Wen-Hai Xiao, Keith E. J. Tyo, Yong Wang, Fritz Simeon, Effendi Leonard, Oliver Mucha, Too Heng Phon, Blaine Pfeifer, Gregory Stephanopoulos. "Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli", Science, 330(6000), 70-74, (2010).
* Christian M Metallo, Paulo A. Gameiro, Eric L. Bell, Katherine R. Mattaini, Juanjuan Yang, Karsten Hiller, Christopher M Jewell, Zachary R Johnson, Darrell J. Irvine, Leonard Guarente, Joanne K. Kelleher, Matthew G. Vander Heiden, Othon Iliopoulos, Gregory Stephanopoulos. "Reductive glutamine metabolism by IDH1 mediates lipogenesis under hypoxia", Nature, 481(7381), 380, (2012).