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  Peer-reviewed articles  

* corresponding author, # equal contribution

Year 2018

41. Walker, C., Ryu, S., Trinh, C.T.*, in preparation.

40. Lee, J.W., Trinh, C.T.*, in preparation.

39. Ryu, S., Walker, C., Trinh, C.T.*, in preparation.

38. Garcia, S., Trinh, C.T.*, in preparation.

37. Garcia, S., Trinh, C.T.*, in preparation.

35. Walker, C., Ryu, S., Trinh, C.T.*, 2018, Exceptional Solvent Tolerance in Yarrowia lipolytica Is Enhanced by Sterols, under review.

34. Walker. C., Ryu, S., Na, H., Zane, M., LaButti, K., Lipzen, A., Haridas, S., Barry, K., Grigoriev, I.V., Quarterman, J., Slininger, P., Dien, B., Trinh, C.T.*, 2018, Draft Genome Assemblies for Five Robust Yarrowia lipolytica Strains Exhibiting High Lipid Production and Pentose Sugar Utilization and Sugar Alcohol Secretion from Undetoxified Lignocellulosic Biomass Hydrolysates, Microb Res Ann, in press.

33. Garcia, S., Trinh, C.T.*, 2018, Multiobjective Strain Design: A Framework for Modular Cell Engineering, Metab Eng, in press.

32. Ryu, S., Trinh, C.T.*, 2018, Methods to Activate and Elucidate Complex Endogenous Sugar Metabolism in Yarrowia lipolytica, Meth Mol Biol, in press

31. Mendoza, B., Trinh, C.T.*, 2018. In Silico Processing of the Complete CRISPR-Cas Spacer Space for Identification of PAM Sequences, Biotechnol J, in press.

30. Lee, J.W., Niraula, N., Trinh, C.T.*, 2018. Harnessing a Novel P450 Fatty Acid Decarboxylase from Macrococcus caseolyticus for Microbial Biosynthesis of Odd Chain Terminal Alkenes, Metab Eng Comm, 7: e00076.

29. Ryu, S., Trinh, C.T.*, 2018, Understanding Functional Roles of Native Pentose-Specific Transporters for Activating Dormant Pentose Metabolism in Yarrowia lipolytica, Appl Environ Microbiol, 84(3): e02146-17.

28. Mendoza, B., Trinh, C.T.*, 2018. Enhanced Guide-RNA Design and Targeting Analysis for Precise CRISPR Genome Editing of Single and Consortia of Industrially Relevant and Non-Model Organisms, Bioinformatics, 34(1):16-23.

27. Wilbanks, B., Layton, D.S., Garcia, S., Trinh, C.T.*, 2018. A Prototype for Modular Cell Engineering, ACS Synthetic Biology,7(1):187-199 .

Year 2017

26. Wilbanks, B., Trinh, C.T.*, 2017. Comprehensive Characterization of Toxicity of Fermentative Metabolites on Microbial Growth, Biotechnol Biofuels, 10:262.

25. Thompson, R.A., Trinh, C.T.*, 2017. Linking Overflow Metabolism and Growth Cessation in Clostridium thermocellum DSM1313 during High Cellulose Loading Fermentations, Biotechnol Bioeng, 114(11): 2592-2604. .

Year 2016

24. Thompson, R.A., Dahal, S., Garcia, S., Nookaew, I., Trinh, C.T.*, 2016. Exploring Complex Cellular Phenotypes and Model-Guided Strain Design with A Novel Genome-scale Metabolic Model of Clostridium thermocellum DSM 1313 Implementing an Adjustable Cellulosome, Biotechnol Biofuels, 9: 194.

23. Layton, D.S., Trinh, C.T.*, 2016. Microbial Synthesis of a Branched-Chain Ester Platform from Organic Waste Carboxylates, Metab Eng Comm, 3: 245-251.


22. Trinh, C.T.*, Mendoza, B., 2016. Modular Cell Design for Rapid, Efficient Strain Engineering  towards Industrialization of Biology, Curr Opin Chem Eng, 14:18–25.  



21. Wierzbicki, M., Niraula, N., Yarrabothula, A., Layton, D.S., Trinh, C.T.*, 2016. Engineering an Escherichia coli platform to synthesize designer biodiesels, J. Biotechnol, 224: 27-34.


20. Layton, D.S., Trinh, C.T.*, 2016. Expanding the Modular Ester Fermentative Pathways for Combinatorial Biosynthesis of Esters from Volatile Organic Acids, Biotechnol Bioeng,113: 1764-1776.



19. Ryu, S., Hipp, J, Trinh, C.T.*, 2016. Erratum for Ryu et al., Activating and Elucidating Metabolism of Complex Sugars in Yarrowia lipolytica. Appl Environ Microbiol, 82(8): 2572.

18. Ryu, S., Hipp, J, Trinh, C.T.*, 2016. Activating and Elucidating Complex Sugar Metabolism in Yarrowia lipolytica, Appl Environ Microbiol, 82: 1334-1345.


Year 2015

17. Thompson, R.A., Layton, D.S., Guss, A.M., Olson, D.G., Lynd, L.R., Trinh, C.T.*, 2015. Elucidating Central Metabolic Redox Obstacles Hindering Ethanol Production in Clostridium thermocellum, Metab Eng, 32: 207-219.


16. Trinh, C.T.*, Liu, Y., Conner, D.J., 2015. Rational Design of Efficient Modular Cells, Metab Eng, 32:220–231.


15. Ryu, S., Labbe, N., Trinh, C.T.*, 2015. Simultaneous saccharification and fermentation of cellulose in ionic liquid for efficient production of alpha-ketoglutaric acid in Yarrowia lipolytica, Appl Microbiol Biotechnol, 99(10): 4237-4244.


Year 2014

14. Layton, D.S., Trinh, C.T.*, 2014. Engineering Modular Ester Fermentative Pathways in Escherichia coli, Metab Eng, 26:77–88.


13. Thompson, R.A., Trinh, C.T.*, 2014. Enhancing Fatty Acid Ethyl Ester Production in Saccharomyces cerevisiae through Metabolic Engineering and Medium Optimization, Biotechnol Bioeng 111(11): 2200-2208.


Year 2013

12. Flowers, D., Thompson, R. A., Birdwell, D., Wang, T.*, Trinh, C.T.*, 2013. SMET: Systematic Multiple Enzyme Targeting - A Novel Method To Rationally Design Optimal Strains For Target Chemical Overproduction, Biotechnol J 8(5): 605-618. DOI: 10.1002/biot.201200233.



Year 2012

11. Trinh, C.T.*, 2012. Elucidating and reprogramming Escherichia coli metabolism for obligate anaerobic butanol and isobutanol production. Appl Microbiol Biotechnol 95(4): 1083-1094.

Year 2011

10. Trinh, C.T., Li, J., Blanch, H.W., Clark, D.S., 2011. Redesigning Escherichia coli metabolism for anaerobic production of isobutanol. Appl Environ Microbiol 77(14): 4894-4904.

9. Jevremovic, D., Trinh, C.T., Srienc, F., Sosa, C.P., Boley, D., 2011.  Parallelization of null space algorithm for the computation of metabolic pathways. Parallel Computing 37: 261-278.

Year 2010

8. Trinh, C.T., Huffer, S., Clark, M.E., Blanch, H.W., Clark, D.S., 2010. Elucidating Mechanisms of Solvent Toxicity in ethanologenic Escherichia coli. Biotechnol Bioeng 106(5):721-730. 

7.  Unrean, P., Trinh, C.T., Srienc, F., 2010.  Rational design and construction of an efficient E. coli for production of diapolycopendioic acid.  Metab Eng 12(2):112-122.

6. Jevremovic, D., Trinh, C.T., Srienc, F., Boley, D., 2010. On Algebraic Properties of Extreme Pathways in Metabolic Networks. J Comp Biol 17(2):107-19.

Year 2009

5.  Trinh, C.T., Srienc, F., 2009. Metabolic Engineering of Escherichia coli for Efficient Conversion of Glycerol into Ethanol.  Appl Environ Microbiol 75(21): 6696-6705.

4. Trinh, C.T., Wlaschin, A.P., Srienc, F., 2009. Elementary Mode Analysis: A Useful Metabolic Pathway Analysis Tool for Characterizing Cellular Metabolism.  Appl Microbiol Biotechnol 81(5): 813-826.

Year 2008

3. Trinh, C.T., Unrean, P., Srienc, F., 2008. A minimal Escherichia coli cell for most efficient ethanol production from hexoses and pentoses. Appl Environ Microbiol 7: 3634-3643.

Year 2006

2. Trinh, C.T., Carlson, R., Wlaschin, A.P., Srienc, F., 2006. Design, construction and performance of the most efficient biomass producing E. coli bacterium. Metab Eng 8: 628-638.

1. Wlaschin, A.P., Trinh, C.T., Carlson, R., Srienc, F., 2006. The fractional contributions of elementary modes to the metabolism of E. coli and their estimation from reaction entropies.  Metab Eng 8: 338-352.

  Book chapters and editors  

1. Trinh, C.T., Thompson, R.A., 2012. Elementary Mode Analysis: A Useful Metabolic Pathway Analysis Tool for Reprogramming Microbial Metabolic Pathways. Reprogramming Microbial Metabolic Pathways, p. 21-42. In X. Wang, J. Chen, and P. Quinn (ed.), vol. 64. Springer Netherlands.

2. Eckert, C., Trinh, C.T., 2016.  “Biotechnology for Biofuel Production and Optimization”. Elsevier.





  Updated on 09.19.2018