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

Genome Genes Fluxes Metabolism Escherichia Coli Metabolic Cyanobacteria Biomass Nitrogen Metabolic Networks And Pathways Metabolites Carbon Enzymes Genomics Proteins Kinetics Metabolite Pharmacological Metabolism Modeling Symbiosis Microorganisms Strain Lignin Thermodynamics Metabolic Engineering

Most Recent Papers

Computationally Prospecting Potential Pathways from Lignin Monomers and Dimers toward Aromatic Compounds

Lin Wang, Costas D. Maranas, 2021, ACS Synthetic Biology on p. 1064-1076

Elucidation of trophic interactions in an unusual single-cell nitrogen-fixing symbiosis using metabolic modeling

Debolina Sarkar, Marine Landa, Anindita Bandyopadhyay, Himadri B. Pakrasi, Jonathan P. Zehr, Costas D. Maranas, 2021, PLoS Computational Biology

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

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

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

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

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

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

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

Most-Cited Papers

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

Peng Xu, Sridhar Ranganathan, Zachary L. Fowler, Costas D. Maranas, Mattheos A.G. Koffas, 2011, Metabolic Engineering on p. 578-587

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

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

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

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

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