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
Data-driven and physics informed modeling of Chinese Hamster Ovary cell bioreactors
Cui, T., Bertalan, T., Ndahiro, N., Khare, P., Betenbaugh, M., Maranas, C. & Kevrekidis, I. G., Apr 2024, In: Computers and Chemical Engineering. 183, 108594.Research output: Contribution to journal › Article › peer-review
KETCHUP: Parameterizing of large-scale kinetic models using multiple datasets with different reference states
Hu, M., Suthers, P. F. & Maranas, C. D., Mar 2024, In: Metabolic engineering. 82, p. 123-133 11 p.Research output: Contribution to journal › Article › peer-review
Genome streamlining to improve performance of a fast-growing cyanobacterium Synechococcus elongatus UTEX 2973
Sengupta, A., Bandyopadhyay, A., Sarkar, D., Hendry, J. I., Schubert, M. G., Liu, D., Church, G. M., Maranas, C. D. & Pakrasi, H. B., Mar 2024, In: mBio. 15, 3Research output: Contribution to journal › Article › peer-review
Mitochondrial ATP generation is more proteome efficient than glycolysis
Shen, Y., Dinh, H. V., Cruz, E. R., Chen, Z., Bartman, C. R., Xiao, T., Call, C. M., Ryseck, R. P., Pratas, J., Weilandt, D., Baron, H., Subramanian, A., Fatma, Z., Wu, Z. Y., Dwaraknath, S., Hendry, J. I., Tran, V. G., Yang, L., Yoshikuni, Y., Zhao, H., & 3 others , 2024, (Accepted/In press) In: Nature Chemical Biology.Research output: Contribution to journal › Article › peer-review
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
Deuterated water as a substrate-agnostic isotope tracer for investigating reversibility and thermodynamics of reactions in central carbon metabolism
Callaghan, M. M., Thusoo, E., Sharma, B. D., Getahun, F., Stevenson, D. M., Maranas, C., Olson, D. G., Lynd, L. R. & Amador-Noguez, D., Nov 2023, In: Metabolic engineering. 80, p. 254-266 13 p.Research output: Contribution to journal › Article › peer-review
A single amino acid change led to structural and functional differentiation of PvHd1 to control flowering in switchgrass
Choi, S., Prabhakar, P. K., Chowdhury, R., Pendergast, T. H., Urbanowicz, B. R., Maranas, C. & Devos, K. M., Sep 29 2023, In: Journal of experimental botany. 74, 18, p. 5532-5546 15 p.Research output: Contribution to journal › Article › 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 › Article › peer-review
A multi-organ maize metabolic model connects temperature stress with energy production and reducing power generation
Chowdhury, N. B., Simons-Senftle, M., Decouard, B., Quillere, I., Rigault, M., Sajeevan, K. A., Acharya, B., Chowdhury, R., Hirel, B., Dellagi, A., Maranas, C. & Saha, R., Dec 15 2023, In: iScience. 26, 12, 108400.Research output: Contribution to journal › Article › 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 › 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
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 › Article › peer-review
Rank-ordering of known enzymes as starting points for re-engineering novel substrate activity using a convolutional neural network
Upadhyay, V., Boorla, V. S. & Maranas, C. D., Jul 2023, In: Metabolic engineering. 78, p. 171-182 12 p.Research output: Contribution to journal › Article › 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 › 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