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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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Projects
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 ⺠Article ⺠peer-review
Little Brown Bats (Myotis lucifugus) Support the Binding of SARS-CoV-2 Spike and Are Likely Susceptible to SARS-CoV-2 Infection
Chothe, S. K., Jakka, P., Boorla, V. S., Ramasamy, S., Gontu, A., Nissly, R. H., Brown, J., Turner, G., Sewall, B. J., Reeder, D. A. M., Field, K. A., Engiles, J. B., Amirthalingam, S., Ravichandran, A., LaBella, L., Nair, M. S., Maranas, C. D. & Kuchipudi, S. V., May 2023, In: Viruses. 15, 5, 1103.Research output: Contribution to journal ⺠Article ⺠peer-review
Evaluating proteome allocation of Saccharomyces cerevisiae phenotypes with resource balance analysis
Dinh, H. V. & Maranas, C. D., May 2023, In: Metabolic engineering. 77, p. 242-255 14 p.Research output: Contribution to journal ⺠Article ⺠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 ⺠Article ⺠peer-review
A detailed genome-scale metabolic model of Clostridium thermocellum investigates sources of pyrophosphate for driving glycolysis
Schroeder, W. L., Kuil, T., van Maris, A. J. A., Olson, D. G., Lynd, L. R. & Maranas, C. D., May 2023, In: Metabolic engineering. 77, p. 306-322 17 p.Research output: Contribution to journal ⺠Article ⺠peer-review
Metabolic engineering of low-pH-tolerant non-model yeast, Issatchenkia orientalis, for production of citramalate
Wu, Z. Y., Sun, W., Shen, Y., Pratas, J., Suthers, P. F., Hsieh, P. H., Dwaraknath, S., Rabinowitz, J. D., Maranas, C. D., Shao, Z. & Yoshikuni, Y., Jun 2023, In: Metabolic Engineering Communications. 16, e00220.Research output: Contribution to journal ⺠Article ⺠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 ⺠Article ⺠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 ⺠Comment/debate ⺠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 ⺠Article ⺠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 ⺠Article ⺠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 ⺠Article ⺠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 ⺠Article ⺠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 ⺠Article ⺠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 ⺠Article ⺠peer-review
Toward low-cost biological and hybrid biological/catalytic conversion of cellulosic biomass to fuelsâ
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 ⺠Review article ⺠peer-review