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Corresponding author: *; equal contribution: **; undergraduates: underlined.
Year 2024
62. Cotter, C.J., Trinh, C.T.*, 2023. CRISPR-GRIT: Guide-RNAs with Integrated Repair Templates Enable Precise Multiplexed Genome Editing in the Diploid Fungal Pathogen Candida albicans, in review. ![](acrobat image.gif)
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.*, 2023. Economics and global warming potential of a commercial-scale delignifying biorefinery based on Co-solvent Enhanced Lignocellulosic Fractionation, Energy Environ Sci, 17, 1202-1215. ![](acrobat image.gif)
60. Seo, H., Castro, G., Trinh, C.T.*, 2023. Engineering a Syntrophic Escherichia coli Coculture for Compartmentalized de novo Biosynthesis of Isobutyl Butyrate from Mixed Sugars, ACS Synthetic Biology,13 (1), 259-268. ![](acrobat image.gif)
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.![](acrobat image.gif)
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. ![](acrobat image.gif)
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.![](acrobat image.gif)
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.![](acrobat image.gif)
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. ![](acrobat image.gif)
52. Lee, J., Trinh, C.T.*, 2022.Controlling Selectivity of Modular Microbial Biosynthesis of Butyryl-CoA-Derived Designer Esters, Metab Eng, 69: 262-274. ![](acrobat image.gif)
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.![](acrobat image.gif)
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. ![](acrobat image.gif)
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. ![](acrobat image.gif)
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. ![](acrobat image.gif)
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. ![](acrobat image.gif)
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. ![](acrobat image.gif)
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. ![](acrobat image.gif)
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.![](acrobat image.gif) |
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