Costas D. Maranas

Publication Activity (10 Years)

Years Active: 1993-2021
Publications (10 Years): 10

Top Topics

Piecewise Linear

Metabolic Engineering

Community Members

Top Venues

PLoS Comput. Biol.

BMC Syst. Biol.

Publications

Debolina Sarkar, Marine Landa, Anindita Bandyopadhyay, Himadri B. Pakrasi, Jonathan P. Zehr, Costas D. Maranas
Elucidation of trophic interactions in an unusual single-cell nitrogen-fixing symbiosis using metabolic modeling. PLoS Comput. Biol. 17 (5) (2021)
Lin Wang, Vikas Upadhyay, Costas D. Maranas
dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design. PLoS Comput. Biol. 17 (9) (2021)
Debolina Sarkar, Thomas J. Mueller, Deng Liu, Himadri B. Pakrasi, Costas D. Maranas
A diurnal flux balance model of Synechocystis sp. PCC 6803 metabolism. PLoS Comput. Biol. 15 (1) (2019)
Charles J. Foster, Saratram Gopalakrishnan, Maciek R. Antoniewicz, Costas D. Maranas
From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline. PLoS Comput. Biol. 15 (9) (2019)
Siu Hung Joshua Chan, Lin Wang, Satyakam Dash, Costas D. Maranas
Accelerating flux balance calculations in genome-scale metabolic models by localizing the application of loopless constraints. Bioinform. 34 (24) (2018)
Siu Hung Joshua Chan, Margaret N. Simons, Costas D. Maranas
SteadyCom: Predicting microbial abundances while ensuring community stability. PLoS Comput. Biol. 13 (5) (2017)
Siu Hung Joshua Chan, Jingyi Cai, Lin Wang, Margaret N. Simons-Senftle, Costas D. Maranas
Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models. Bioinform. 33 (22) (2017)
Luis Miguel Serrano-Bermúdez, Andrés Fernando González Barrios, Costas D. Maranas, Dolly Montoya Castaño
Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol. BMC Syst. Biol. 11 (1) (2017)
Robert J. Pantazes, Matthew J. Grisewood, Tong Li, Nathanael P. Gifford, Costas D. Maranas
The Iterative Protein Redesign and Optimization (IPRO) suite of programs. J. Comput. Chem. 36 (4) (2015)
Anupam Chowdhury, Ali R. Zomorrodi, Costas D. Maranas
Bilevel optimization techniques in computational strain design. Comput. Chem. Eng. 72 (2015)
Akhil Kumar, Costas D. Maranas
CLCA: Maximum Common Molecular Substructure Queries within the MetRxn Database. J. Chem. Inf. Model. 54 (12) (2014)
Anupam Chowdhury, Ali R. Zomorrodi, Costas D. Maranas
k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design. PLoS Comput. Biol. 10 (2) (2014)
Ali R. Zomorrodi, Costas D. Maranas
Coarse-grained optimization-driven design and piecewise linear modeling of synthetic genetic circuits. Eur. J. Oper. Res. 237 (2) (2014)
Thomas J. Mueller, Bertram M. Berla, Himadri B. Pakrasi, Costas D. Maranas
Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow. BMC Syst. Biol. 7 (2013)
Robert J. Pantazes, Costas D. Maranas
MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured antibodies. BMC Bioinform. 14 (2013)
Ana Rita Brochado, Sergej Andrejev, Costas D. Maranas, Kiran Raosaheb Patil
Impact of Stoichiometry Representation on Simulation of Genotype-Phenotype Relationships in Metabolic Networks. PLoS Comput. Biol. 8 (11) (2012)
Ali R. Zomorrodi, Costas D. Maranas
OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities. PLoS Comput. Biol. 8 (2) (2012)
Akhil Kumar, Patrick F. Suthers, Costas D. Maranas
MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases. BMC Bioinform. 13 (2012)
Francisco G. Vital-Lopez, Costas D. Maranas, Antonios Armaou
Modeling the effect of temozolomide treatment on orthotopic models of glioma. ACC (2011)
Vinay Satish Kumar, James G. Ferry, Costas D. Maranas
Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans. BMC Syst. Biol. 5 (2011)
Ali R. Zomorrodi, Costas D. Maranas
Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data. BMC Syst. Biol. 4 (2010)
Sridhar Ranganathan, Patrick F. Suthers, Costas D. Maranas
OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions. PLoS Comput. Biol. 6 (4) (2010)
Patrick F. Suthers, Madhukar S. Dasika, Vinay Satish Kumar, Gennady Denisov, John I. Glass, Costas D. Maranas
PS189. PLoS Comput. Biol. 5 (2) (2009)
Vinay Satish Kumar, Costas D. Maranas
Growth Predictions. PLoS Comput. Biol. 5 (3) (2009)
Erwin P. Gianchandani, Matthew A. Oberhardt, Anthony P. Burgard, Costas D. Maranas, Jason A. Papin
Predicting biological system objectives de novo from internal state measurements. BMC Bioinform. 9 (2008)
Francisco G. Vital-Lopez, Amit Varshney, Costas D. Maranas, Antonios Armaou
Implication of dynamics in signal transduction and targeted disruption analyses of signaling networks. Comput. Chem. Eng. 32 (9) (2008)
Madhukar S. Dasika, Costas D. Maranas
OptCircuit: An optimization based method for computational design of genetic circuits. BMC Syst. Biol. 2 (2008)
Vinay Satish Kumar, Madhukar S. Dasika, Costas D. Maranas
Optimization based automated curation of metabolic reconstructions. BMC Bioinform. 8 (2007)
Reza G. Vital-Lopez, Costas D. Maranas, Antonios Armaou
Bifurcation analysis of the metabolism of E. coli at optimal enzyme levels. ACC (2006)
Anshuman Gupta, Costas D. Maranas, Réka Albert
Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites. Bioinform. 22 (2) (2006)
Anshuman Gupta, Jeffrey D. Varner, Costas D. Maranas
Large-scale inference of the transcriptional regulation of Bacillus subtilis. Comput. Chem. Eng. 29 (3) (2005)
Costas D. Maranas, Vassily Hatzimanikatis
Preface. Comput. Chem. Eng. 29 (3) (2005)
Madhukar S. Dasika, Anshuman Gupta, Costas D. Maranas, Jeffrey D. Varner
A Mixed Integer Linear Programming (MILP) Framework for Inferring Time Delay in Gene Regulatory Networks. Pacific Symposium on Biocomputing (2004)
Anshuman Gupta, Costas D. Maranas
Managing demand uncertainty in supply chain planning. Comput. Chem. Eng. 27 (8-9) (2003)
Ioannis P. Androulakis, Costas D. Maranas, Christodoulos A. Floudas
Prediction of Oligopeptide Conformations via Deterministic Global Optimization. J. Glob. Optim. 11 (1) (1997)
Costas D. Maranas, Christodoulos A. Floudas, Panos M. Pardalos
New results in the packing of equal circles in a square. Discret. Math. 142 (1-3) (1995)
Costas D. Maranas, Christodoulos A. Floudas
Finding all solutions of nonlinearly constrained systems of equations. J. Glob. Optim. 7 (2) (1995)
Costas D. Maranas, Ioannis P. Androulakis, Christodoulos A. Floudas
A deterministic global optimization approach for the protein folding problem. Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding (1995)
Ioannis P. Androulakis, Costas D. Maranas, Christodoulos A. Floudas
αBB: A global optimization method for general constrained nonconvex problems. J. Glob. Optim. 7 (4) (1995)
Costas D. Maranas, Christodoulos A. Floudas
Global minimum potential energy conformations of small molecules. J. Glob. Optim. 4 (2) (1994)
Costas D. Maranas, Christodoulos A. Floudas
Global optimization for molecular conformation problems. Ann. Oper. Res. 42 (1) (1993)