Publications by authors named "Costas D Maranas"

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Rank-ordering of known enzymes as starting points for re-engineering novel substrate activity using a convolutional neural network.
Vikas Upadhyay, Veda Sheersh Boorla, Costas D Maranas

Metab Eng· July 2023

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dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design.
Lin Wang, Vikas Upadhyay, Costas D Maranas

PLoS Comput Biol· September 2021

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Reconstruction of a resource balance analysis model of Clostridium thermocellum examines the metabolic cost of glycolytic and cellulosome enzymes.
Thomas C Willis, Wheaton L Schroeder, Daven B Khana, Xuejun Qian, Sanjeev Dahal, Costas D Maranas

Metab Eng· January 2026

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Metabolic flux and resource balance in the oleaginous yeast Rhodotorula toruloides.
Eric J Mooney, Patrick F Suthers, Wheaton L Schroeder, Hoang V Dinh, Xi Li, Costas D Maranas

Metab Eng· December 2025

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Building an expanded bio-based economy through synthetic biology.
Andrea M Garza Elizondo, Ilenne Del Valle Kessra, Erica Teixeira Prates, Evan Komp, Elise K Phillips, Costas D Maranas

Biotechnol Adv· December 2025

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Parameterization of cell-free systems with time-series data using KETCHUP.
Mengqi Hu, Syed Bilal Jilani, Daniel G Olson, Costas D Maranas

PLoS Comput Biol· November 2025

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MechFind: A computational framework for de novo prediction of enzyme mechanisms.
Austin D Hartley, Vikas Upadhyay, Veda Sheersh Boorla, Costas D Maranas

bioRxiv· September 2025

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novoStoic2.0: An integrated framework for pathway synthesis, thermodynamic evaluation, and enzyme selection.
Vikas Upadhyay, Mohit Anand, Costas D Maranas

PLoS Comput Biol· August 2025

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Reframing the role of the objective function in its proper context for metabolic network modeling.
Mohammad Mazharul Islam, William Shao, Mariska Batavia, Roseanne M Ford, Bernhard O Palsson, Costas D Maranas

Cell Syst· June 2025

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Combining Chemical Catalysis with Enzymatic Steps for the Synthesis of the Artemisinin Precursor Dihydroartemisinic Acid.
Vikas Upadhyay, Hongxiang Li, Jiachen He, Blake Edward Ocampo, Silas Cook, Costas D Maranas

ACS Synth Biol· April 2025

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minChemBio: Expanding Chemical Synthesis with Chemo-Enzymatic Pathways Using Minimal Transitions.
Mohit Anand, Vikas Upadhyay, Costas D Maranas

ACS Synth Biol· March 2025

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CatPred: a comprehensive framework for deep learning in vitro enzyme kinetic parameters.
Veda Sheersh Boorla, Costas D Maranas

Nat Commun· February 2025

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Mitochondrial ATP generation is more proteome efficient than glycolysis.
Yihui Shen, Hoang V Dinh, Edward R Cruz, Zihong Chen, Caroline R Bartman, Costas D Maranas

Nat Chem Biol· September 2024

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Current State, Challenges, and Opportunities in Genome-Scale Resource Allocation Models: A Mathematical Perspective.
Wheaton L Schroeder, Patrick F Suthers, Thomas C Willis, Eric J Mooney, Costas D Maranas

Metabolites· June 2024

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KETCHUP: Parameterizing of large-scale kinetic models using multiple datasets with different reference states.
Mengqi Hu, Patrick F Suthers, Costas D Maranas

Metab Eng· March 2024

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Genome streamlining to improve performance of a fast-growing cyanobacterium UTEX 2973.
Annesha Sengupta, Anindita Bandyopadhyay, Debolina Sarkar, John I Hendry, Max G Schubert, Costas D Maranas

mBio· March 2024

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Metabolic engineering of low-pH-tolerant non-model yeast, , for production of citramalate.
Zong-Yen Wu, Wan Sun, Yihui Shen, Jimmy Pratas, Patrick F Suthers, Costas D Maranas

Metab Eng Commun· June 2023

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Evaluating proteome allocation of Saccharomyces cerevisiae phenotypes with resource balance analysis.
Hoang V Dinh, Costas D Maranas

Metab Eng· May 2023

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A detailed genome-scale metabolic model of Clostridium thermocellum investigates sources of pyrophosphate for driving glycolysis.
Wheaton L Schroeder, Teun Kuil, Antonius J A van Maris, Daniel G Olson, Lee R Lynd, Costas D Maranas

Metab Eng· May 2023

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Little Brown Bats () Support the Binding of SARS-CoV-2 Spike and Are Likely Susceptible to SARS-CoV-2 Infection.
Shubhada K Chothe, Padmaja Jakka, Veda Sheersh Boorla, Santhamani Ramasamy, Abhinay Gontu, Costas D Maranas

Viruses· April 2023

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Comparative study of two Saccharomyces cerevisiae strains with kinetic models at genome-scale.
Mengqi Hu, Hoang V Dinh, Yihui Shen, Patrick F Suthers, Charles J Foster, Costas D Maranas

Metab Eng· March 2023

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De novo design and Rosetta-based assessment of high-affinity antibody variable regions (Fv) against the SARS-CoV-2 spike receptor binding domain (RBD).
Veda Sheersh Boorla, Ratul Chowdhury, Ranjani Ramasubramanian, Brandon Ameglio, Rahel Frick, Costas D Maranas

Proteins· February 2023

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SARS-CoV-2 Omicron (B.1.1.529) Infection of Wild White-Tailed Deer in New York City.
Kurt J Vandegrift, Michele Yon, Meera Surendran Nair, Abhinay Gontu, Santhamani Ramasamy, Costas D Maranas

Viruses· December 2022

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Examining organic acid production potential and growth-coupled strategies in Issatchenkia orientalis using constraint-based modeling.
Patrick F Suthers, Costas D Maranas

Biotechnol Prog· September 2022

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Development and Validation of Indirect Enzyme-Linked Immunosorbent Assays for Detecting Antibodies to SARS-CoV-2 in Cattle, Swine, and Chicken.
Abhinay Gontu, Erika A Marlin, Santhamani Ramasamy, Sabarinath Neerukonda, Gayatri Anil, Costas D Maranas

Viruses· June 2022

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A CNN model for predicting binding affinity changes between SARS-CoV-2 spike RBD variants and ACE2 homologues.
Chen Chen, Veda Sheersh Boorla, Ratul Chowdhury, Ruth H Nissly, Abhinay Gontu, Costas D Maranas

bioRxiv· March 2022

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