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

Mayank Gupta

Huck Affiliations

Bioinformatics and Genomics

Molecular, Cellular, and Integrative Biosciences

Center for Biorenewables

Publication Tags

Escherichia Coli Genome Biomass Metabolism Metabolic Lipid Metabolism Genes Fluxes Phenotype Metabolites Liver Growth Uncertainty Kinetics Methane Biofuels Pharmacological Metabolism Metabolomics Obesity Metabolite Genomics Enzyme Kinetics Metabolic Engineering Strain Glucose

Most Recent Publications

Metabolic engineering of Rhodotorula toruloides IFO0880 improves C16 and C18 fatty alcohol production from synthetic media

J. Carl Schultz, Shekhar Mishra, Emily Gaither, Andrea Mejia, Hoang Dinh, Costas Maranas, Huimin Zhao, 2022, Microbial Cell Factories

Examining organic acid production potential and growth-coupled strategies in Issatchenkia orientalis using constraint-based modeling

Patrick F. Suthers, Costas D. Maranas, 2022, Biotechnology Progress

ML helps predict enzyme turnover rates

Veda Sheersh Boorla, Vikas Upadhyay, Costas D. Maranas, 2022, Nature Catalysis on p. 655-657

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, Jasmine Morgan, Meysoon Quraishi, Chen Chen, Veda Sheersh Boorla, Ruth H. Nissly, Padmaja Jakka, Shubhada K. Chothe, Abirami Ravichandran, Nishitha Kodali, Saranya Amirthalingam, Lindsey Labella, Kathleen Kelly, Pazhanivel Natesan, Allen M. Minns, Randall M. Rossi, Jacob R. Werner, Ernest Hovingh, Scott E. Lindner, Deepanker Tewari, Vivek Kapur, Kurt J. Vandegrift, Costas D. Maranas, Meera Surendran Nair, Suresh V. Kuchipudi, 2022, Viruses

Developmental changes in lignin composition are driven by both monolignol supply and laccase specificity

Chunliu Zhuo, Xin Wang, Maite Docampo-Palacios, Brian C. Sanders, Nancy L. Engle, Timothy J. Tschaplinski, John I. Hendry, Costas D. Maranas, Fang Chen, Richard A. Dixon, 2022, Science advances

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

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

Suresh V. Kuchipudi, Meera Surendran-Nair, Rachel M. Ruden, Michele Yon, Ruth H. Nissly, Kurt J. Vandegrift, Rahul K. Nelli, Lingling Li, Bhushan M. Jayarao, Costas D. Maranas, Nicole Levine, Katriina Willgert, Andrew J.K. Conlan, Randall J. Olsen, James J. Davis, James M. Musser, Peter John Hudson, Vivek Kapur, 2022, Proceedings of the National Academy of Sciences of the United States of America

Functional Analysis of H<sup>+</sup>-Pumping Membrane-Bound Pyrophosphatase, ADP-Glucose Synthase, and Pyruvate Phosphate Dikinase as Pyrophosphate Sources in Clostridium thermocellum

Teun Kuil, Shuen Hon, Johannes Yayo, Charles Foster, Giulia Ravagnan, Costas D. Maranas, Lee R. Lynd, Daniel G. Olson, Antonius J.A. van Maris, 2022, Applied and Environmental Microbiology

Dissecting the metabolic reprogramming of maize root under nitrogen-deficient stress conditions

Niaz Bahar Chowdhury, Wheaton L. Schroeder, Debolina Sarkar, Nardjis Amiour, Isabelle Quilleré, Bertrand Hirel, Costas D. Maranas, Rajib Saha, 2022, Journal of Experimental Botany on p. 275-291

Quantifying the propagation of parametric uncertainty on flux balance analysis

Hoang V. Dinh, Debolina Sarkar, Costas D. Maranas, 2022, Metabolic Engineering on p. 26-39

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

Synthetic biology of cyanobacteria: Unique challenges and opportunities

Bertram M. Berla, Rajib Saha, Cheryl M. Immethun, Costas D. Maranas, Tae Seok Moon, Himadri B. Pakrasi, 2013, Frontiers in Microbiology

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

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

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

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

SteadyCom: Predicting microbial abundances while ensuring community stability

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

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

Recent advances in the reconstruction of metabolic models and integration of omics data

Rajib Saha, Anupam Chowdhury, Costas D. Maranas, 2014, Current Opinion in Biotechnology on p. 39-45

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

News Articles Featuring Costas Maranas

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.