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 Metabolic Fluxes Genome Metabolism Biomass Metabolites Genes Enzymes Kinetics Fatty Acids Metabolic Networks And Pathways Metabolite Ethanol Uncertainty Strain Pharmacological Metabolism Clostridium Thermocellum Metabolic Engineering Glucose Enzyme Kinetics Genomics Reaction Yield Application Pyrophosphatases

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

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 Robert Werner, Ernest Hovingh, Scott E. Lindner, Deepanker Tewari, Vivek Kapur, Kurt 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

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

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

Niaz Chowdhury, Wheaton Schroeder, Debolina Sarkar, Nardjis Amiour, Isabelle Quillere, Bertrand Hirel, Costas Maranas, Rajib Saha, 2022, JOURNAL OF EXPERIMENTAL BOTANY on p. 275-291

Assessing the impact of substrate-level enzyme regulations limiting ethanol titer in Clostridium thermocellum using a core kinetic model

Charles Foster, Veda Sheersh Boorla, Satyakam Dash, Saratram Gopalakrishnan, Tyler B. Jacobson, Daniel G. Olson, Daniel Amador-Noguez, Lee R. Lynd, Costas D. Maranas, 2022, Metabolic Engineering on p. 286-301

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

OptCom

Ali R. Zomorrodi, Costas D. Maranas, 2012, PLoS Computational Biology on p. e1002363

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

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

Mathematical optimization applications in metabolic networks

Ali R. Zomorrodi, Patrick F. Suthers, Sridhar Ranganathan, Costas D. Maranas, 2012, Metabolic Engineering on p. 672-686

MetRxn

Akhil Kumar, Patrick F. Suthers, Costas D. Maranas, 2012, BMC Bioinformatics

An integrated computational and experimental study for overproducing fatty acids in Escherichia coli

Sridhar Ranganathan, Ting Wei Tee, Anupam Chowdhury, Ali R. Zomorrodi, Jong Moon Yoon, Yanfen Fu, Jacqueline V. Shanks, Costas D. Maranas, 2012, Metabolic Engineering on p. 687-704

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.