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Affiliate Researcher
Titles and Affiliations
Donald B. Broughton Professor, Chemical Engineering
Research Summary
Research interests include modeling/optimization of directed evolution protocols for protein engineering, optimization in metabolic engineering and bioinformatics, molecular and product design, and supply chain planning and scheduling.In the News
Research Keywords
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Recent Publications
De novo design and Rosetta-based assessment of high-affinity antibody variable regions (Fv) against the SARS-CoV-2 spike receptor binding domain (RBD)
Boorla, V. S., Chowdhury, R., Ramasubramanian, R., Ameglio, B., Frick, R., Gray, J. J. & Maranas, C. D., Feb 2023, In: Proteins: Structure, Function and Bioinformatics. 91, 2, p. 196-208 13 p.Research output: Contribution to journal › Article › peer-review
Comparative study of two Saccharomyces cerevisiae strains with kinetic models at genome-scale
Hu, M., Dinh, H. V., Shen, Y., Suthers, P. F., Foster, C. J., Call, C. M., Ye, X., Pratas, J., Fatma, Z., Zhao, H., Rabinowitz, J. D. & Maranas, C. D., Mar 2023, In: Metabolic engineering. 76, p. 1-17 17 p.Research output: Contribution to journal › Article › peer-review
EnZymClass: Substrate specificity prediction tool of plant acyl-ACP thioesterases based on ensemble learning
Banerjee, D., Jindra, M. A., Linot, A. J., Pfleger, B. F. & Maranas, C. D., Jan 2022, In: Current Research in Biotechnology. 4, p. 1-9 9 p.Research output: Contribution to journal › Article › peer-review
ML helps predict enzyme turnover rates
Boorla, V. S., Upadhyay, V. & Maranas, C. D., Aug 2022, In: Nature Catalysis. 5, 8, p. 655-657 3 p.Research output: Contribution to journal › Comment/debate › peer-review
Dissecting the metabolic reprogramming of maize root under nitrogen-deficient stress conditions
Chowdhury, N. B., Schroeder, W. L., Sarkar, D., Amiour, N., Quilleré, I., Hirel, B., Maranas, C. D. & Saha, R., Jan 5 2022, In: Journal of experimental botany. 73, 1, p. 275-291 17 p.Research output: Contribution to journal › Article › peer-review
Quantifying the propagation of parametric uncertainty on flux balance analysis
Dinh, H. V., Sarkar, D. & Maranas, C. D., Jan 2022, In: Metabolic engineering. 69, p. 26-39 14 p.Research output: Contribution to journal › Article › peer-review
Assessing the impact of substrate-level enzyme regulations limiting ethanol titer in Clostridium thermocellum using a core kinetic model
Foster, C., Boorla, V. S., Dash, S., Gopalakrishnan, S., Jacobson, T. B., Olson, D. G., Amador-Noguez, D., Lynd, L. R. & Maranas, C. D., Jan 2022, In: Metabolic engineering. 69, p. 286-301 16 p.Research output: Contribution to journal › Article › peer-review
Development and Validation of Indirect Enzyme-Linked Immunosorbent Assays for Detecting Antibodies to SARS-CoV-2 in Cattle, Swine, and Chicken
Gontu, A., Marlin, E. A., Ramasamy, S., Neerukonda, S., Anil, G., Morgan, J., Quraishi, M., Chen, C., Boorla, V. S., Nissly, R. H., Jakka, P., Chothe, S. K., Ravichandran, A., Kodali, N., Amirthalingam, S., Labella, L., Kelly, K., Natesan, P., Minns, A. M., Rossi, R. M., & 9 others, Jul 2022, In: Viruses. 14, 7, 1358.Research output: Contribution to journal › Article › peer-review
Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer
Kuchipudi, S. V., Surendran-Nair, M., Ruden, R. M., Yon, M., Nissly, R. H., Vandegrift, K. J., Nelli, R. K., Li, L., Jayarao, B. M., Maranas, C. D., Levine, N., Willgert, K., Conlan, A. J. K., Olsen, R. J., Davis, J. J., Musser, J. M., Hudson, P. J. & Kapur, V., Feb 8 2022, In: Proceedings of the National Academy of Sciences of the United States of America. 119, 6, e2121644119.Research output: Contribution to journal › Article › peer-review
Functional Analysis of H+-Pumping Membrane-Bound Pyrophosphatase, ADP-Glucose Synthase, and Pyruvate Phosphate Dikinase as Pyrophosphate Sources in Clostridium thermocellum
Kuil, T., Hon, S., Yayo, J., Foster, C., Ravagnan, G., Maranas, C. D., Lynd, L. R., Olson, D. G. & van Maris, A. J. A., Feb 2022, In: Applied and environmental microbiology. 88, 4, e01857.Research output: Contribution to journal › Article › peer-review
Toward low-cost biological and hybrid biological/catalytic conversion of cellulosic biomass to fuels†
Lynd, L. R., Beckham, G. T., Guss, A. M., Jayakody, L. N., Karp, E. M., Maranas, C., McCormick, R. L., Amador-Noguez, D., Bomble, Y. J., Davison, B. H., Foster, C., Himmel, M. E., Holwerda, E. K., Laser, M. S., Ng, C. Y., Olson, D. G., Román-Leshkov, Y., Trinh, C. T., Tuskan, G. A., Upadhayay, V., & 3 others, Feb 9 2022, In: Energy and Environmental Science. 15, 3, p. 938-990 53 p.Research output: Contribution to journal › Review article › peer-review
Metabolic engineering of Rhodotorula toruloides IFO0880 improves C16 and C18 fatty alcohol production from synthetic media
Schultz, J. C., Mishra, S., Gaither, E., Mejia, A., Dinh, H., Maranas, C. & Zhao, H., Dec 2022, In: Microbial Cell Factories. 21, 1, 26.Research output: Contribution to journal › Article › peer-review
Examining organic acid production potential and growth-coupled strategies in Issatchenkia orientalis using constraint-based modeling
Suthers, P. F. & Maranas, C. D., Sep 1 2022, In: Biotechnology progress. 38, 5, e3276.Research output: Contribution to journal › Article › peer-review
SARS-CoV-2 Omicron (B.1.1.529) Infection of Wild White-Tailed Deer in New York City
Vandegrift, K. J., Yon, M., Surendran Nair, M., Gontu, A., Ramasamy, S., Amirthalingam, S., Neerukonda, S., Nissly, R. H., Chothe, S. K., Jakka, P., LaBella, L., Levine, N., Rodriguez, S., Chen, C., Sheersh Boorla, V., Stuber, T., Boulanger, J. R., Kotschwar, N., Aucoin, S. G., Simon, R., & 14 others, Dec 2022, In: Viruses. 14, 12, 2770.Research output: Contribution to journal › Article › peer-review
Developmental changes in lignin composition are driven by both monolignol supply and laccase specificity
Zhuo, C., Wang, X., Docampo-Palacios, M., Sanders, B. C., Engle, N. L., Tschaplinski, T. J., Hendry, J. I., Maranas, C. D., Chen, F. & Dixon, R. A., Mar 2022, In: Science Advances. 8, 10, eabm8145.Research output: Contribution to journal › Article › peer-review