Costas Maranas

Donald B. Broughton Professor of Chemical Engineering

Costas Maranas

Research Summary

Computational studies of metabolism and gene regulation.

Huck Graduate Students

Huck Affiliations

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Escherichia Coli Genome Metabolism Lipid Metabolism Fluxes Genes Liver Metabolic Kinetics Phenotype Biofuels Methane Biomass Metabolomics Obesity Pharmacological Metabolism Metabolites Enzyme Kinetics Strain Metabolite Glycine Nadp Gastrointestinal Microbiome Muricholic Acid Liquids

Most Recent Publications

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, 2024, Metabolites

Data-driven and physics informed modeling of Chinese Hamster Ovary cell bioreactors

Tianqi Cui, Tom Bertalan, Nelson Ndahiro, Pratik Khare, Michael Betenbaugh, Costas Maranas, Ioannis G. Kevrekidis, 2024, Computers and Chemical Engineering

KETCHUP: Parameterizing of large-scale kinetic models using multiple datasets with different reference states

Mengqi Hu, Patrick F. Suthers, Costas D. Maranas, 2024, Metabolic Engineering on p. 123-133

Genome streamlining to improve performance of a fast-growing cyanobacterium Synechococcus elongatus UTEX 2973

Annesha Sengupta, Anindita Bandyopadhyay, Debolina Sarkar, John I. Hendry, Max G. Schubert, Deng Liu, George M. Church, Costas D. Maranas, Himadri B. Pakrasi, 2024, mBio

Proteome efficiency of bioenergetic pathways

Yihui Shen, Hoang Dinh, Edward Cruz, Zihong Chen, Caroline Bartman, Yasuo Yoshikuni, Huimin Zhao, Costas Maranas, Martin Wühr, Joshua Rabinowitz, 2024, Biophysical Journal on p. 248a

Dehydrated Biomimetic Membranes with Skinlike Structure and Function

Hyeonji Oh, Yu Ming Tu, Laximicharan Samineni, Sophie De Respino, Behzad Mehrafrooz, Himanshu Joshi, Lynnicia Massenburg, Horacio Lopez-Marques, Nada Elessawy, Woochul Song, Harekrushna Behera, Raman Dhiman, Veda Sheersh Boorla, Kartik Kher, Yi Chih Lin, Costas Maranas, Aleksei Aksimentiev, Benny D. Freeman, Manish Kumar, 2024, ACS applied materials & interfaces

A multi-tissue genome-scale model of Populus trichocarpa elucidates overexpression targets for improving drought tolerance

Juliana Simas Coutinho Barbosa, Wheaton L. Schroeder, Patrick F. Suthers, Sara S. Jawdy, Jin Gui Chen, Wellington Muchero, Costas D. Maranas, 2024, In Silico Plants

Mitochondrial ATP generation is more proteome efficient than glycolysis

Yihui Shen, Hoang V. Dinh, Edward R. Cruz, Zihong Chen, Caroline R. Bartman, Tianxia Xiao, Catherine M. Call, Rolf Peter Ryseck, Jimmy Pratas, Daniel Weilandt, Heide Baron, Arjuna Subramanian, Zia Fatma, Zong Yen Wu, Sudharsan Dwaraknath, John I. Hendry, Vinh G. Tran, Lifeng Yang, Yasuo Yoshikuni, Huimin Zhao, Costas D. Maranas, Martin Wühr, Joshua D. Rabinowitz, 2024, Nature Chemical Biology

A multi-organ maize metabolic model connects temperature stress with energy production and reducing power generation

Niaz Bahar Chowdhury, Margaret Simons-Senftle, Berengere Decouard, Isabelle Quillere, Martine Rigault, Karuna Anna Sajeevan, Bibek Acharya, Ratul Chowdhury, Bertrand Hirel, Alia Dellagi, Costas Maranas, Rajib Saha, 2023, iScience

Deuterated water as a substrate-agnostic isotope tracer for investigating reversibility and thermodynamics of reactions in central carbon metabolism

Melanie M. Callaghan, Eashant Thusoo, Bishal D. Sharma, Fitsum Getahun, David M. Stevenson, Costas Maranas, Daniel G. Olson, Lee R. Lynd, Daniel Amador-Noguez, 2023, Metabolic Engineering on p. 254-266

Most-Cited Papers

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

Laurent Heirendt, Sylvain Arreckx, Thomas Pfau, Sebastián N. Mendoza, Anne Richelle, Almut Heinken, Hulda S. Haraldsdóttir, Jacek Wachowiak, Sarah M. Keating, Vanja Vlasov, Stefania Magnusdóttir, Chiam Yu Ng, German Preciat, Alise Žagare, Siu H.J. Chan, Maike K. Aurich, Catherine M. Clancy, Jennifer Modamio, John T. Sauls, Alberto Noronha, Aarash Bordbar, Benjamin Cousins, Diana C. El Assal, Luis V. Valcarcel, Iñigo Apaolaza, Susan Ghaderi, Masoud Ahookhosh, Marouen Ben Guebila, Andrejs Kostromins, Nicolas Sompairac, Hoai M. Le, Ding Ma, Yuekai Sun, Lin Wang, James T. Yurkovich, Miguel A.P. Oliveira, Phan T. Vuong, Lemmer P. El Assal, Inna Kuperstein, Andrei Zinovyev, H. Scott Hinton, William A. Bryant, Francisco J. Aragón Artacho, Francisco J. Planes, Egils Stalidzans, Alejandro Maass, Santosh Vempala, Michael Hucka, Michael A. Saunders, Costas D. Maranas, Nathan E. Lewis, Thomas Sauter, Bernhard Palsson, Ines Thiele, Ronan M.T. Fleming, 2019, Nature Protocols on p. 639-702

A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains

Ali Khodayari, Costas D. Maranas, 2016, Nature Communications

D-OptCom: Dynamic Multi-level and Multi-objective Metabolic Modeling of Microbial Communities

Ali R. Zomorrodi, Mohammad Mazharul Islam, Costas D. Maranas, 2014, ACS Synthetic Biology on p. 247-257

SteadyCom: Predicting microbial abundances while ensuring community stability

Siu Hung Joshua Chan, Margaret N. Simons, Costas D. Maranas, 2017, PLoS Computational Biology

Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer

Suresh V. Kuchipudi, Meera Surendran-Nair, R Ruden, M Yon, R Nissly, Kurt J. Vandegrift, R Nelli, Lingling Li, Bhushan Jayarao, Costas D. Maranas, N Levine, K Willgert, Andrew J.K. Conlan, Conlan AJK, R Olsen, J Davis, J Musser, Peter John Hudson, Vivek Kapur, 2022, Proceedings of the National Academy of Sciences of the United States of America

Rational design of a synthetic Entner-Doudoroff pathway for improved and controllable NADPH regeneration

Chiam Yu Ng, Iman Farasat, Costas D. Maranas, Howard M. Salis, 2015, Metabolic Engineering on p. 86-96

A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data

Ali Khodayari, Ali R. Zomorrodi, James C. Liao, Costas D. Maranas, 2014, Metabolic Engineering on p. 50-62

Reversing methanogenesis to capture methane for liquid biofuel precursors

Valerie W.C. Soo, Michael J. McAnulty, Arti Tripathi, Fayin Zhu, Limin Zhang, Emmanuel Hatzakis, Philip B. Smith, Saumya Agrawal, Hadi Nazem-Bokaee, Saratram Gopalakrishnan, Howard M. Salis, James G. Ferry, Costas D. Maranas, Andrew D. Patterson, Thomas K. Wood, 2016, Microbial Cell Factories on p. 11

Farnesoid X receptor signaling shapes the gut microbiota and controls hepatic lipid metabolism

Limin Zhang, Cen Xie, Robert G. Nichols, Siu H.J. Chan, Changtao Jiang, Ruixin Hao, Philip B. Smith, Jingwei Cai, Margaret N. Simons, Emmanuel Hatzakis, Costas D. Maranas, Frank J. Gonzalez, Andrew D. Patterson, 2016, mSystems on p. e00070-16

Toward low-cost biological and hybrid biological/catalytic conversion of cellulosic biomass to fuels†

Lee R. Lynd, Gregg T. Beckham, Adam M. Guss, Lahiru N. Jayakody, Eric M. Karp, Costas Maranas, Robert L. McCormick, Daniel Amador-Noguez, Yannick J. Bomble, Brian H. Davison, Charles Foster, Michael E. Himmel, Evert K. Holwerda, Mark S. Laser, Chiam Yu Ng, Daniel G. Olson, Yuriy Román-Leshkov, Cong T. Trinh, Gerald A. Tuskan, Vikas Upadhayay, Derek R. Vardon, Lin Wang, Charles E. Wyman, 2022, Energy and Environmental Science on p. 938-990