Corresponding author: *; equal contribution: **; undergraduates: underlined.

Year 2024

63. Dooley, D., Ryu, S., Jackson, E., Giannone, R., Dien, B., Trinh, C.T.*, 2024. Expanded Genome and Proteome Reallocation in A Novel, Robust Bacillus coagulans Capable of Utilizing Pentose and Hexose Sugars, mSystems, accepted.

62. Cotter, C.J., Trinh, C.T.*, 2024. CRISPR-GRIT: Guide-RNAs with Integrated Repair Templates Enable Precise Multiplexed Genome Editing in the Diploid Fungal Pathogen Candida albicans, CRISPR Journal, in revision.

61. Klein, B.C., Scheidemantle, B., Hanes, R., Bartling, A., Grundl, N., Biddy, M., Tao, L., Trinh, C.T., Guss, A., Wyman, C.E., Ragauskas, A.J., Webb, E.G., Davison, B.H., Cai, C.M.*, 2024. Economics and global warming potential of a commercial-scale delignifying biorefinery based on Co-solvent Enhanced Lignocellulosic Fractionation, Energy Environ Sci, 17, 1202-1215.

60. Seo, H., Castro, G., Trinh, C.T.*, 2024. Engineering a Syntrophic Escherichia coli Coculture for Compartmentalized de novo Biosynthesis of Isobutyl Butyrate from Mixed Sugars, ACS Synthetic Biology,13 (1), 259-268.

Year 2023

59. Mendoza, B., Zheng, X., Clements J.§, Cotter, C., Trinh, C.T.*, 2023. Potency of CRISPR-Cas Antifungals Is Enhanced by Co-targeting DNA Repair and Growth Regulatory Machinery at the Genetic Level, ACS Infectious Diseases, 9: 2494–2503.

58. Walker, C., Mortensen, M., Poudel, B., Cotter, C., Okekeogbu, I., Ryu, S., Khomami, B., Giannone, R.J., Laursen, S., Trinh, C.T.*, 2023. Proteomes Reveal Metabolic Capabilities of Yarrowia lipolytica for Biological Upcycling of Polyethylene into High-Value Chemicals, mSystems, e00741-23.

57. Seo, H., Singh, P., Wyman, C., Cai, C., Trinh, C.T.*, 2023. Rewiring metabolism of Clostridium thermocellum for consolidated bioprocessing of lignocellulosic biomass poplar to produce short-chain esters, Bioresource Technol, 384 (2023): 129263.

Year 2022

56. Walker, C., Ryu, S., Garica, S., Dooley, D., Mendoza, B., Trinh, C.T.* 2022. Gene Co-expression Connectivity Predicts Gene Targets Underlying High Ionic Liquid Tolerance in Yarrowia lipolytica, mSystems, 7(4): e00348-22.

55. Mendoza, B.**, Fry, T.**, Dooley, D.**, Herman J., Trinh, C.T.*, 2022. CASPER: An integrated software platform for rapid development of CRISPR tools, CRISPR J, 5(4): 609-617 .

54. Seo, H., Giannone, R.J., Yang, Y.H., Trinh, C.T.* 2022. Proteome reallocation enables the selective de novo biosynthesis of non-linear, branched-chain acetate esters, Metab Eng, 73, 38-49.

53. Lynd, L.R., Beckham, G.T., Guss, A.M., Jayakody, L., Karp, E.M., Maranas, C., McCormick, R.L., Amador-Noguez, D., Bomble, Y., Davison, B.H., Foster, C., Himmel, M., Holwerda, E., Laser, M.S., Ng, C.Y., Olson, D.G., Román-Leshkov, Y., Trinh, C.T., Tuskan, G.A., Upadhayay, V., Vardon, D.R., Wang, L., Wyman, C.A., 2022. Toward low-cost biological and hybrid biological/catalytic conversion of cellulosic biomass to fuels, Energy Environ Sci, 15: 938-990.

52. Lee, J., Trinh, C.T.*, 2022.Controlling Selectivity of Modular Microbial Biosynthesis of Butyryl-CoA-Derived Designer Esters, Metab Eng, 69: 262-274.

Year 2021

51. Lee, J., Seo, H., Young, C., Trinh, C.T.*, 2021. Probing Specificities of Alcohol Acyltransferases for Designer Ester Biosynthesis with a High-Throughput Microbial Screening Platform, Biotechnol Bioeng, 1-13.

50. Walker, C., Dien, B., Giannone, R.J., Slininger, P., Thompson, S., Trinh, C.T.*, 2021. Exploring Proteomes of Robust Yarrowia lipolytica Isolates Cultivated in Biomass Hydrolysate Reveal Key Processes Impacting Mixed Sugar Utilization, Lipid Accumulation, and Degradation, mSystems, 6(4): e00443-21.

49. Garcia, S., Trinh, C.T.*, 2021. Computational Design and Analysis of Modular Cells for Large Libraries of Exchangeable Product Synthesis Modules, Metab Eng, 67: 453-463.

48. Poudel, S., Cope, A. L., O’Dell, K., Guss, A. M., Seo, H., Trinh, C. T., Hettich, R. L., 2021. An integrated guilt-by-association approach to characterize proteins of unknown function (PUFs) in Clostridium thermocellum DSM 1313 as potential genetic engineering targets, BBIO, 14 (116): 1-19.

47. Seo, H., Lee, J., Dunlap, N., Giannone, R., Trinh, C.T.*, 2021. Engineering Promiscuity of Chloramphenicol Acetyltransferase for Microbial Designer Ester Biosynthesis, Metab Eng, 66: 179-190.

Year 2020

46. Yang, X, Medford, J.I., Markel, K., Shih, P., De Paoli, H.C., Trinh, C.T., McCormick, A.J., Ployet, R., Hussey, S.G., Myburg, A.A., Jensen, P.E., Hassan, M.M., Zhang, J., Muchero, W., Kalluri, U.C., Yin, H., Zhuo, R., Abraham, P., Chen, J.G., Weston, D., Yang, Y.., Liu, D., Li, Y., Labbe, J., Yang, B., Lee, J., Cottingham, R.W., Martin, A., Lu, M., Tschaplinski, T.J., Y, G., Lu, H., Ranjan, P., Mitchell, J., Wullschleger, S.D., Tuskan, G.A., 2020. Plant Biosystems Design Research Roadmap 1.0, BioDesign Research, 2020, Article ID 8051764.

45. Garcia, S., Thompson, R.A., Giannone, R., Dash, S., Maranas, C., Trinh, C.T.*, 2020. Development of a genome-scale metabolic model of Clostridium thermocellum and its applications for integration of multi-omics datasets and strain design, Frontiers Bioeng Biotechnol, 8: 1-16.

44. Garcia, S., Trinh, C.T.*, 2020. Harnessing natural modularity of cellular metabolism to design a modular chassis cell for a diverse class of products by using goal attainment optimization, ACS Synthetic Biology, 9(7): 1665–1681.

43. Seo, H., Nicely, P.N., Trinh, C.T.*, 2020. Endogenous esterases of Clostridium thermocellum are identified and disrupted for enhanced isobutyl acetate production from cellulose, Biotechnol Bioeng, 117: 2223-2236.

42. Walker, C., Ryu, S., Haridas, S., Na, H., Zane, M., Labutti, K., Lipzen, A., Barry, K., Grigoriev, I., Trinh, C.T.*, 2020. Draft Genome Assemblies of Ionic Liquid Resistant Yarrowia lipolytica PO1f and its superior evolved strain YlCW001. Microbiol Resour Announce, 9(999): e01356-19.

41. Walker, C.**, Ryu, S.**, Giannone, R.S., Garcia, S., Trinh, C.T.*, 2020. Understanding and eliminating the detrimental effect of endogenous thiamine auxotrophy on metabolism of the oleaginous yeast Yarrowia lipolytica, Appl Environ Microbiol, 86(3): e02299-19.

40. Lee, J., Trinh, C.T.*, 2020. Towards renewable flavors, fragrances, and beyond, Curr Opin Biotechnol, 61: 168-180.

Year 2019

39. Seo, H.**, Lee, J.**, Garcia, S., Trinh, C.T.*, 2019. Single mutation at a highly conserved region of chloramphenicol acetyltransferase enables thermophilic isobutyl acetate production directly from cellulose by Clostridium thermocellum, Biotechnol Biofuels, 12(1): 1-13.

38. Garcia, S., Trinh, C.T.*, 2019. Comparison of Multi-objective Evolutionary Algorithms to Solve the Modular Cell Design Problem for Novel Biocatalysis, Processes, 7(6): 361.

37. Garcia, S., Trinh, C.T.*, 2019. Modular design: Implementing proven engineering principles in biotechnology, Biotechnol Advances, 37(7):107403.

36. Lee, J.W., Trinh, C.T.*, 2019.Microbial Biosynthesis of a Lactate Ester Platform, Biotechnol Biofuels, 12: 226.

35. Liu, D., Chen, M., Cheng, H., Hu, R., Li, L., Mendoza, B., Trinh, C.T., Tuskan, G. A., Yang, X.*, 2019. CRISPR/Cas9-mediated Targeted Mutagenesis for Functional Genomics Research of Crassulacean Acid Metabolism Plants, J Exp Botany, 70(22): 6621-6629.

34. Walker, C., Ryu, S., Trinh, C.T.*, 2019. Exceptional Solvent Tolerance in Yarrowia lipolytica Is Enhanced by Sterols, Metab Eng, 51: 110-120.

Research Highlights: DOE Office of Science, Department of Chemical and Biomolecular Engineering

33. Garcia, S., Trinh, C.T.*, 2019. Multiobjective Strain Design: A Framework for Modular Cell Engineering, Metab Eng, 81(5): 813.

Year 2018

32. 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, 7(12), e01040-18.

31. Mendoza, B., Trinh, C.T.*, 2018. In Silico Processing of the Complete CRISPR-Cas Spacer Space for Identification of PAM Sequences, Biotechnol J, 3(9): 1700595.

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.

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.

3. Ryu, S., Trinh, C.T.*, 2021. Methods to Activate and Elucidate Complex Endogenous Sugar Metabolism in Yarrowia lipolytica, MIMB, 2307: 175-189.

4. Carper, D.L., Trinh, C.T., Giannone, R.J., 2024. Proteomic Analysis of the Oleaginous Yeast Yarrowia lipolytica, MIMB, in review.