Costas Maranas
Donald B. Broughton Professor of Chemical Engineering
-
126 Land and Water Research
University Park, PA - cdm8@psu.edu
- 814-863-9958
Research Summary
Computational studies of metabolism and gene regulation.
Huck Graduate Students
Huck Affiliations
- Bioinformatics and Genomics
- Molecular, Cellular, and Integrative Biosciences
- Center for Biorenewables
Links
Most Recent Publications
CatPred: a comprehensive framework for deep learning in vitro enzyme kinetic parameters
Veda Sheersh Boorla, Costas D. Maranas, 2025, Nature Communications
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, Jens Nielsen, Costas D. Maranas, Sang Yup Lee, Jason A. Papin, 2025, Cell Systems
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, Huimin Zhao, Costas D. Maranas, 2025, ACS Synthetic Biology on p. 1112-1120
minChemBio: Expanding Chemical Synthesis with Chemo-Enzymatic Pathways Using Minimal Transitions
Mohit Anand, Vikas Upadhyay, Costas D. Maranas, 2025, ACS Synthetic Biology on p. 756-770
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 on p. 1123-1132
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
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
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
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
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
Comparative genomics reveals the molecular determinants of rapid growth of the cyanobacterium Synechococcus elongatus UTEX 2973
Justin Ungerer, Kristen E. Wendt, John I. Hendry, Costas D. Maranas, Himadri B. Pakrasi, 2018, Proceedings of the National Academy of Sciences of the United States of America on p. E11761-E11770
A review of computational tools for design and reconstruction of metabolic pathways
Lin Wang, Satyakam Dash, Chiam Yu Ng, Costas D. Maranas, 2017, Synthetic and Systems Biotechnology on p. 243-252
News Articles Featuring Costas Maranas
Mar 03, 2025
'Growing Impact' discusses environmental contaminants, human health
The latest episode of Growing Impact discusses how environmental contaminants affect human health, a research focus for Penn State professors Andrew Patterson and Costas Maranas.
Full Article
Nov 03, 2021
Deer may be reservoir for SARS-CoV-2, study finds
The findings of a study by Penn State and Iowa researchers suggest that white-tailed deer may be a reservoir for the SARS-CoV-2 virus to continually circulate, and raises concerns of emergence of new strains that may prove a threat to wildlife and, possibly, to humans.
Full Article
Sep 29, 2021
New tool predicts changes that may make COVID variants more infectious
The first key step in SARS-CoV-2 infection is when the virus’ spike protein binds to the ACE2 receptor on human cells. Researchers at Penn State have created a novel framework that can predict with reasonable accuracy the amino-acid changes in the virus’ spike protein that may improve its binding to human cells and confer increased infectivity to the virus.
Full Article