Costas Maranas

Donald B. Broughton Professor of Chemical Engineering

Costas Maranas

Research Summary

Computational studies of metabolism and gene regulation.

Huck Affiliations

Links

Publication Tags

Genes Genome Metabolism Fluxes Escherichia Coli Biomass Metabolic Networks And Pathways Metabolites Kinetics Metabolic Engineering Cyanobacteria Proteins Carbon Enzymes Nutrients Thermodynamics Parameterization Machine Learning Enzyme Kinetics Microorganisms Nadp Growth Biosynthesis Biofuels Acids

Most Recent Papers

A genome-scale metabolic model of anabaena 33047 to guide genetic modifications to overproduce nylon monomers

John I. Hendry, Hoang V. Dinh, Debolina Sarkar, Lin Wang, Anindita Bandyopadhyay, Himadri B. Pakrasi, Costas D. Maranas, 2021, Metabolites

Building kinetic models for metabolic engineering

Charles J. Foster, Lin Wang, Hoang V. Dinh, Patrick F. Suthers, Costas D. Maranas, 2021, Current Opinion in Biotechnology on p. 35-41

Engineering biology approaches for food and nutrient production by cyanobacteria

Deng Liu, Michelle Liberton, John I. Hendry, Javad Aminian-Dehkordi, Costas D. Maranas, Himadri B. Pakrasi, 2021, Current Opinion in Biotechnology on p. 1-6

Recent advances in constraint and machine learning-based metabolic modeling by leveraging stoichiometric balances, thermodynamic feasibility and kinetic law formalisms

Patrick F. Suthers, Charles J. Foster, Debolina Sarkar, Lin Wang, Costas D. Maranas, 2021, Metabolic Engineering on p. 13-33

Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production

Patrick Suthers, Hoang V. Dinh, Zia Fatma, Yihui Shen, Siu Hung Joshua Chan, Joshua D. Rabinowitz, Huimin Zhao, Costas D. Maranas, 2020, Metabolic Engineering Communications

IPRO+/−: Computational Protein Design Tool Allowing for Insertions and Deletions

Ratul Chowdhury, Matthew Grisewood, Veda Boorla, Qiang Yan, Brian Pfleger, Costas Maranas, 2020, Structure with Folding & design on p. 1344-1357.e4

Metabolic flux analysis reaching genome wide coverage

John I. Hendry, Hoang V. Dinh, Charles Foster, Saratram Gopalakrishnan, Lin Wang, Costas D. Maranas, 2020, Current Opinion in Chemical Engineering on p. 17-25

Engineering sensitivity and specificity of AraC-based biosensors responsive to triacetic acid lactone and orsellinic acid

Zhiqing Wang, Aarti Doshi, Ratul Chowdhury, Yixi Wang, Costas D. Maranas, Patrick C. Cirino, 2020, Protein Engineering, Design and Selection

K-FIT: An accelerated kinetic parameterization algorithm using steady-state fluxomic data

Saratram Gopalakrishnan, Satyakam Dash, Costas Maranas, 2020, Metabolic Engineering on p. 197-205

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. Adam Thompson, Richard J. Giannone, Satyakam Dash, Costas D. Maranas, Cong T. Trinh, 2020, Frontiers in Bioengineering and Biotechnology

Most-Cited Papers

Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA.

Ping Xu, S Ranganathan, Z Fowler, Costas Maranas, M Koffas, 2011, Metabolic Engineering on p. 578-587

OptCom

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

Synthetic biology of cyanobacteria

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

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

Zea mays irs1563

Rajib Saha, Patrick F. Suthers, Costas D. Maranas, 2011, PLoS One

D-OptCom

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

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

Mathematical optimization applications in metabolic networks

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

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

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