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  Peer-reviewed articles  

* corresponding author, # equal contribution

Year 2018

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

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

36. Ryu, S., Trinh, C.T.*, in preparation.

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

34. Garcia, S., Trinh, C.T.*, Multiobjective Strain Design: A Framework for Modular Cell Engineering, under review.

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

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

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

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, in review. See bioRxiv

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 05.17.2018