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C. Maranas · SciRah

Researcher profile · Semantic Scholar

C. Maranas

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C. Maranas — researcher profile on SciRah

h-index: 81
Works: 344
Citations: 22K

Most-cited papers

Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0
Laurent Heirendt, Sylvain Arreckx, T. Pfau, Sebastián N. Mendoza +51 more
2019Nature Protocols1,072 citations Open access
Semantic Scholar
Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer
S. Kuchipudi, Meera Surendran-Nair, R. Ruden, Michele Yon +14 more
2022Proceedings of the National Academy of Sciences of the United States of America195 citations Open access
Semantic Scholar
Toward low-cost biological and hybrid biological/catalytic conversion of cellulosic biomass to fuels
L. Lynd, G. Beckham, A. Guss, L. Jayakody +19 more
2022Energy & Environmental Science164 citations Open access
Semantic Scholar
Artificial Water Channels Enable Fast and Selective Water Permeation Through Water-Wire Networks
Woochul Song, Himanshu Joshi, Ratul Chowdhury, Joseph S. Najem +13 more
2019Nature Nanotechnology144 citations Open access
Semantic Scholar
Bacterial colonization reprograms the neonatal gut metabolome
K. Bittinger, Chunyu Zhao, Yun Li, Eileen Ford +25 more
2020Nature Microbiology111 citations Open access
Semantic Scholar
EcoFABs: advancing microbiome science through standardized fabricated ecosystems
K. Zengler, K. Hofmockel, N. Baliga, Scott W. Behie +15 more
2019Nature Methods111 citations Open access
Semantic Scholar
Mitochondrial ATP generation is more proteome efficient than glycolysis
Yihui Shen, Hoang V. Dinh, Edward Cruz, Zi-Hong Chen +19 more
2024Nature Chemical Biology103 citations Open access
Semantic Scholar
CatPred: a comprehensive framework for deep learning in vitro enzyme kinetic parameters
V. Boorla, C. Maranas
2025Nature Communications102 citations Open access
Semantic Scholar
Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2
Chen Chen, V. Boorla, Deepro Banerjee, Ratul Chowdhury +8 more
2021Proceedings of the National Academy of Sciences of the United States of America76 citations Open access
Semantic Scholar
Building kinetic models for metabolic engineering.
Charles J. Foster, Lin Wang, Hoang V. Dinh, P. Suthers +1 more
2020Current Opinion in Biotechnology64 citations Open access
Semantic Scholar
A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data
Hoang V. Dinh, P. Suthers, S. H. Chan, Yi-Hui Shen +7 more
2019bioRxiv60 citations Open access
Semantic Scholar
K-FIT: An accelerated kinetic parameterization algorithm using steady-state fluxomic data
Saratram Gopalakrishnan, Satyakam Dash, C. Maranas
2019bioRxiv51 citations Open access
Semantic Scholar
Developmental changes in lignin composition are driven by both monolignol supply and laccase specificity
C. Zhuo, Xin Wang, Maite L. Docampo-Palacios, Brian C. Sanders +6 more
2022Science Advances49 citations Open access
Semantic Scholar
Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2
J. Patino-Galindo, I. Filip, Ratul Chowdhury, C. Maranas +3 more
2020Genome Medicine46 citations Open access
Semantic Scholar
In Vivo Thermodynamic Analysis of Glycolysis in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum Using 13C and 2H Tracers
Tyler B. Jacobson, Travis Korosh, D. Stevenson, Charles J. Foster +4 more
2020mSystems42 citations Open access
Semantic Scholar
Computational biophysical characterization of the SARS-CoV-2 spike protein binding with the ACE2 receptor and implications for infectivity
Ratul Chowdhury, V. Boorla, C. Maranas
2020Computational and Structural Biotechnology Journal41 citations Open access
Semantic Scholar
Metabolic engineering of Rhodotorula toruloides IFO0880 improves C16 and C18 fatty alcohol production from synthetic media
J. Schultz, Shekhar Mishra, E. Gaither, A. Mejía +3 more
2022Microbial Cell Factories40 citations Open access
Semantic Scholar
Metabolic model guided strain design of cyanobacteria.
John I Hendry, A. Bandyopadhyay, Shyam Srinivasan, H. Pakrasi +1 more
2020Current Opinion in Biotechnology40 citations Open access
Semantic Scholar
Multiple spillovers and onward transmission of SARS-CoV-2 in free-living and captive white-tailed deer
S. Kuchipudi, Meera Surendran-Nair, R. Ruden, Michelle Yon +14 more
2021bioRxiv34 citations Open access
Semantic Scholar
Recent advances in constraint and machine learning-based metabolic modeling by leveraging stoichiometric balances, thermodynamic feasibility and kinetic law formalisms.
P. Suthers, Charles J. Foster, Debolina Sarkar, Lin Wang +1 more
2020Metabolic Engineering33 citations Open access
Semantic Scholar
Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production
P. Suthers, Hoang V. Dinh, Z. Fatma, Yi-Hui Shen +4 more
2020Metabolic Engineering Communications33 citations Open access
Semantic Scholar
From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline
Charles J. Foster, Saratram Gopalakrishnan, M. Antoniewicz, C. Maranas
2019PLoS Comput. Biol.31 citations Open access
Semantic Scholar
SNPeffect: identifying functional roles of SNPs using metabolic networks
Debolina Sarkar, C. Maranas
2020The Plant Journal30 citations Open access
Semantic Scholar
Engineering biology approaches for food and nutrient production by cyanobacteria.
Deng Liu, M. Liberton, John I Hendry, Javad Aminian-Dehkordi +2 more
2020Current Opinion in Biotechnology29 citations Open access
Semantic Scholar
Rank-ordering of known enzymes as starting points for re-engineering novel substrate activity using a convolutional neural network.
Vikas Upadhyay, V. Boorla, C. Maranas
2023Metabolic Engineering27 citations Open access
Semantic Scholar
SARS-CoV-2 Omicron (B.1.1.529) Infection of Wild White-Tailed Deer in New York City
K. Vandegrift, Michele Yon, Meera Surendran Nair, Abhinay Gontu +30 more
2022Viruses27 citations Open access
Semantic Scholar
Dissecting the Metabolic Reprogramming of Maize Root under Nitrogen-Deficient Stress Condition.
Niaz Chowdhury, Wheaton L. Schroeder, Debolina Sarkar, N. Amiour +4 more
2021Journal of Experimental Botany24 citations Open access
Semantic Scholar
Current State, Challenges, and Opportunities in Genome-Scale Resource Allocation Models: A Mathematical Perspective
Wheaton L. Schroeder, P. Suthers, Thomas C. Willis, Eric J Mooney +1 more
2024Metabolites23 citations Open access
Semantic Scholar
Development of a Genome-Scale Metabolic Model of Clostridium thermocellum and Its Applications for Integration of Multi-Omics Datasets and Computational Strain Design
Sergio Garcia, R. A. Thompson, R. Giannone, Satyakam Dash +2 more
2020Frontiers in Bioengineering and Biotechnology23 citations Open access
Semantic Scholar
Pareto Optimality Explanation of the Glycolytic Alternatives in Nature
Chiam Yu Ng, Lin Wang, A. Chowdhury, C. Maranas
2019Scientific Reports22 citations Open access
Semantic Scholar
Comparative study of two Saccharomyces cerevisiae strains with kinetic models at genome-scale.
Mengqi Hu, Hoang V. Dinh, Yi-Hui Shen, P. Suthers +8 more
2023Metabolic Engineering21 citations Open access
Semantic Scholar
A multi-organ maize metabolic model connects temperature stress with energy production and reducing power generation
N. B. Chowdhury, Margaret Simons-Senftle, Bérengère Découard, I. Quilléré +8 more
2023iScience21 citations Open access
Semantic Scholar
Data-driven and Physics Informed Modelling of Chinese Hamster Ovary Cell Bioreactors
Tian-Qi Cui, Tom S. Bertalan, N. Ndahiro, Pratik Khare +3 more
2023Computers and Chemical Engineering21 citations Open access
Semantic Scholar
Metabolic engineering of low-pH-tolerant non-model yeast, Issatchenkia orientalis, for production of citramalate
Zong-Yen Wu, Wan Sun, Yi-Hui Shen, Jimmy Pratas +7 more
2023Metabolic Engineering Communications20 citations Open access
Semantic Scholar
Evaluating proteome allocation of Saccharomyces cerevisiae phenotypes with resource balance analysis
Hoang V. Dinh, C. Maranas
2022bioRxiv20 citations Open access
Semantic Scholar
Predicting the Longitudinally and Radially Varying Gut Microbiota Composition Using Multi-Scale Microbial Metabolic Modeling
S. H. Chan, E. Friedman, Gary D. Wu, C. Maranas
2019Processes20 citations Open access
Semantic Scholar
dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design
Lin Wang, Vikas Upadhyay, C. Maranas
2021bioRxiv18 citations Open access
Semantic Scholar
EnZymClass: Substrate specificity prediction tool of plant acyl-ACP thioesterases based on Ensemble Learning
Deepro Banerjee, M. Jindra, Alec J. Linot, B. Pfleger +1 more
2021bioRxiv18 citations Open access
Semantic Scholar
Biophysical characterization of the SARS-CoV-2 spike protein binding with the ACE2 receptor and implications for infectivity
Ratul Chowdhury, C. Maranas
2020bioRxiv18 citations Open access
Semantic Scholar
High yield production of 3-hydroxypropionic acid using Issatchenkia orientalis
Shih-I Tan, S. Bhagwat, T. A. Martin, P. Suthers +6 more
2026Nature Communications16 citations Open access
Semantic Scholar
Biophysical characterization of the SARS-CoV2 spike protein binding with the ACE2 receptor explains increased COVID-19 pathogenesis
Ratul Chowdhury, C. Maranas
202016 citations
Semantic Scholar
Assessing the impact of substrate-level enzyme regulations limiting ethanol titer in Clostridium thermocellum using a core kinetic model.
Charles J. Foster, V. Boorla, S. Dash, Saratram Gopalakrishnan +5 more
2022Metabolic Engineering15 citations Open access
Semantic Scholar
Elucidation of trophic interactions in an unusual single-cell nitrogen-fixing symbiosis using metabolic modeling
Debolina Sarkar, M. Landa, A. Bandyopadhyay, H. Pakrasi +2 more
2021PLoS Comput. Biol.15 citations Open access
Semantic Scholar
The Importance and Future of Biochemical Engineering
T. Whitehead, S. Banta, W. Bentley, M. Betenbaugh +15 more
2020Biotechnology and Bioengineering15 citations Open access
Semantic Scholar
Genome streamlining to improve performance of a fast-growing cyanobacterium Synechococcus elongatus UTEX 2973
Annesha Sengupta, A. Bandyopadhyay, Debolina Sarkar, John I Hendry +5 more
2024bioRxiv14 citations Open access
Semantic Scholar
A detailed genome-scale metabolic model of Clostridium thermocellum investigates sources of pyrophosphate for driving glycolysis.
Wheaton L. Schroeder, T. Kuil, A. V. van Maris, D. Olson +2 more
2023Metabolic Engineering14 citations Open access
Semantic Scholar
Functional Analysis of H+-Pumping Membrane-Bound Pyrophosphatase, ADP-Glucose Synthase, and Pyruvate Phosphate Dikinase as Pyrophosphate Sources in Clostridium thermocellum
T. Kuil, Shuen Hon, J. Yayo, Charles J. Foster +5 more
2021Applied and Environmental Microbiology14 citations Open access
Semantic Scholar
Modeling Growth Kinetics, Interspecies Cell Fusion, and Metabolism of a Clostridium acetobutylicum/Clostridium ljungdahlii Syntrophic Coculture
Charles J. Foster, Kamil Charubin, E. Papoutsakis, C. Maranas
2021mSystems14 citations Open access
Semantic Scholar
Quantifying the propagation of parametric uncertainty on flux balance analysis
Hoang V. Dinh, Debolina Sarkar, C. Maranas
2021bioRxiv14 citations Open access
Semantic Scholar
Metabolic flux analysis reaching genome wide coverage: lessons learned and future perspectives
John I Hendry, Hoang V. Dinh, Charles J. Foster, Saratram Gopalakrishnan +2 more
202014 citations Open access
Semantic Scholar

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