Costas D. Maranas

According to our database, Costas D. Maranas authored at least 44 papers between 1993 and 2021.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2021

dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design.

Lin Wang, Vikas Upadhyay, Costas D. Maranas

PLoS Comput. Biol., 2021

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

PLoS Comput. Biol., 2021

2019

A diurnal flux balance model of Synechocystis sp. PCC 6803 metabolism.

Debolina Sarkar, Thomas J. Mueller, Deng Liu, Himadri B. Pakrasi, Costas D. Maranas

PLoS Comput. Biol., 2019

From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline.

Charles J. Foster, Saratram Gopalakrishnan, Maciek R. Antoniewicz, Costas D. Maranas

PLoS Comput. Biol., 2019

2018

Accelerating flux balance calculations in genome-scale metabolic models by localizing the application of loopless constraints.

Siu Hung Joshua Chan, Lin Wang, Satyakam Dash, Costas D. Maranas

Bioinform., 2018

2017

SteadyCom: Predicting microbial abundances while ensuring community stability.

Siu Hung Joshua Chan, Margaret N. Simons, Costas D. Maranas

PLoS Comput. Biol., 2017

Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol.

Luis Miguel Serrano-Bermúdez, Andrés Fernando González Barrios, Costas D. Maranas, Dolly Montoya Castaño

BMC Syst. Biol., 2017

Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models.

Siu Hung Joshua Chan, Jingyi Cai, Lin Wang, Margaret N. Simons-Senftle, Costas D. Maranas

Bioinform., 2017

2015

The Iterative Protein Redesign and Optimization (IPRO) suite of programs.

Robert J. Pantazes, Matthew J. Grisewood, Tong Li, Nathanael P. Gifford, Costas D. Maranas

J. Comput. Chem., 2015

Bilevel optimization techniques in computational strain design.

Anupam Chowdhury, Ali R. Zomorrodi, Costas D. Maranas

Comput. Chem. Eng., 2015

2014

k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design.

Anupam Chowdhury, Ali R. Zomorrodi, Costas D. Maranas

PLoS Comput. Biol., 2014

CLCA: Maximum Common Molecular Substructure Queries within the MetRxn Database.

Akhil Kumar, Costas D. Maranas

J. Chem. Inf. Model., 2014

Coarse-grained optimization-driven design and piecewise linear modeling of synthetic genetic circuits.

Ali R. Zomorrodi, Costas D. Maranas

Eur. J. Oper. Res., 2014

2013

Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow.

Thomas J. Mueller, Bertram M. Berla, Himadri B. Pakrasi, Costas D. Maranas

BMC Syst. Biol., 2013

MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured antibodies.

Robert J. Pantazes, Costas D. Maranas

BMC Bioinform., 2013

2012

OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities.

Ali R. Zomorrodi, Costas D. Maranas

PLoS Comput. Biol., 2012

Impact of Stoichiometry Representation on Simulation of Genotype-Phenotype Relationships in Metabolic Networks.

Ana Rita Brochado, Sergej Andrejev, Costas D. Maranas, Kiran Raosaheb Patil

PLoS Comput. Biol., 2012

MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases.

Akhil Kumar, Patrick F. Suthers, Costas D. Maranas

BMC Bioinform., 2012

2011

Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans.

Vinay Satish Kumar, James G. Ferry, Costas D. Maranas

BMC Syst. Biol., 2011

Modeling the effect of temozolomide treatment on orthotopic models of glioma.

Francisco G. Vital-Lopez, Costas D. Maranas, Antonios Armaou

Proceedings of the American Control Conference, 2011

2010

OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions.

Sridhar Ranganathan, Patrick F. Suthers, Costas D. Maranas

PLoS Comput. Biol., 2010

Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data.

Ali R. Zomorrodi, Costas D. Maranas

BMC Syst. Biol., 2010

2009

Global Optimization in Weber's Problem with Attraction and Repulsion.

Costas D. Maranas

Proceedings of the Encyclopedia of Optimization, Second Edition, 2009

Global Optimization in Lennard-Jones and Morse Clusters.

Costas D. Maranas

Proceedings of the Encyclopedia of Optimization, Second Edition, 2009

Global Optimization in Generalized Geometric Programming.

Costas D. Maranas

Proceedings of the Encyclopedia of Optimization, Second Edition, 2009

A Genome-Scale Metabolic Reconstruction of <i>Mycoplasma genitalium</i>, <i>i</i>PS189.

Patrick F. Suthers, Madhukar S. Dasika, Vinay Satish Kumar, Gennady Denisov, John I. Glass, Costas D. Maranas

PLoS Comput. Biol., 2009

GrowMatch: An Automated Method for Reconciling <i>In Silico</i>/<i>In Vivo</i> Growth Predictions.

Vinay Satish Kumar, Costas D. Maranas

PLoS Comput. Biol., 2009

2008

Implication of dynamics in signal transduction and targeted disruption analyses of signaling networks.

Francisco G. Vital-Lopez, Amit Varshney, Costas D. Maranas, Antonios Armaou

Comput. Chem. Eng., 2008

OptCircuit: An optimization based method for computational design of genetic circuits.

Madhukar S. Dasika, Costas D. Maranas

BMC Syst. Biol., 2008

Predicting biological system objectives de novo from internal state measurements.

Erwin P. Gianchandani, Matthew A. Oberhardt, Anthony P. Burgard, Costas D. Maranas, Jason A. Papin

BMC Bioinform., 2008

2007

Optimization based automated curation of metabolic reconstructions.

Vinay Satish Kumar, Madhukar S. Dasika, Costas D. Maranas

BMC Bioinform., 2007

2006

Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites.

Anshuman Gupta, Costas D. Maranas, Réka Albert

Bioinform., 2006

Bifurcation analysis of the metabolism of E. coli at optimal enzyme levels.

Reza G. Vital-Lopez, Costas D. Maranas, Antonios Armaou

Proceedings of the American Control Conference, 2006

2005

Preface.

Costas D. Maranas, Vassily Hatzimanikatis

Comput. Chem. Eng., 2005

Large-scale inference of the transcriptional regulation of Bacillus subtilis.

Anshuman Gupta, Jeffrey D. Varner, Costas D. Maranas

Comput. Chem. Eng., 2005

2004

A Mixed Integer Linear Programming (MILP) Framework for Inferring Time Delay in Gene Regulatory Networks.

Madhukar S. Dasika, Anshuman Gupta, Costas D. Maranas, Jeffrey D. Varner

Proceedings of the Biocomputing 2004, 2004

2003

Managing demand uncertainty in supply chain planning.

Anshuman Gupta, Costas D. Maranas

Comput. Chem. Eng., 2003

1997

Prediction of Oligopeptide Conformations via Deterministic Global Optimization.

Ioannis P. Androulakis, Costas D. Maranas, Christodoulos A. Floudas

J. Glob. Optim., 1997

1995

Finding all solutions of nonlinearly constrained systems of equations.

Costas D. Maranas, Christodoulos A. Floudas

J. Glob. Optim., 1995

αBB: A global optimization method for general constrained nonconvex problems.

Ioannis P. Androulakis, Costas D. Maranas, Christodoulos A. Floudas

J. Glob. Optim., 1995

New results in the packing of equal circles in a square.

Costas D. Maranas, Christodoulos A. Floudas, Panos M. Pardalos

Discret. Math., 1995

A deterministic global optimization approach for the protein folding problem.

Costas D. Maranas, Ioannis P. Androulakis, Christodoulos A. Floudas

Proceedings of the Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, 1995

1994

Global minimum potential energy conformations of small molecules.

Costas D. Maranas, Christodoulos A. Floudas

J. Glob. Optim., 1994

1993

Global optimization for molecular conformation problems.

Costas D. Maranas, Christodoulos A. Floudas

Ann. Oper. Res., 1993