Costas D. Maranas

According to our database1, Costas D. Maranas authored at least 42 papers between 1993 and 2021.

Collaborative distances:



In proceedings 
PhD thesis 




dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design.
PLoS Comput. Biol., 2021

Elucidation of trophic interactions in an unusual single-cell nitrogen-fixing symbiosis using metabolic modeling.
PLoS Comput. Biol., 2021

A diurnal flux balance model of Synechocystis sp. PCC 6803 metabolism.
PLoS Comput. Biol., 2019

From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline.
PLoS Comput. Biol., 2019

Accelerating flux balance calculations in genome-scale metabolic models by localizing the application of loopless constraints.
Bioinform., 2018

SteadyCom: Predicting microbial abundances while ensuring community stability.
PLoS Comput. Biol., 2017

Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol.
BMC Syst. Biol., 2017

Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models.
Bioinform., 2017

The Iterative Protein Redesign and Optimization (IPRO) suite of programs.
J. Comput. Chem., 2015

Bilevel optimization techniques in computational strain design.
Comput. Chem. Eng., 2015

k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design.
PLoS Comput. Biol., 2014

CLCA: Maximum Common Molecular Substructure Queries within the MetRxn Database.
J. Chem. Inf. Model., 2014

Coarse-grained optimization-driven design and piecewise linear modeling of synthetic genetic circuits.
Eur. J. Oper. Res., 2014

Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow.
BMC Syst. Biol., 2013

MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured antibodies.
BMC Bioinform., 2013

OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities.
PLoS Comput. Biol., 2012

Impact of Stoichiometry Representation on Simulation of Genotype-Phenotype Relationships in Metabolic Networks.
PLoS Comput. Biol., 2012

MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases.
BMC Bioinform., 2012

Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans.
BMC Syst. Biol., 2011

OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions.
PLoS Comput. Biol., 2010

Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data.
BMC Syst. Biol., 2010

Global Optimization in Weber's Problem with Attraction and Repulsion.
Proceedings of the Encyclopedia of Optimization, Second Edition, 2009

Global Optimization in Lennard-Jones and Morse Clusters.
Proceedings of the Encyclopedia of Optimization, Second Edition, 2009

Global Optimization in Generalized Geometric Programming.
Proceedings of the Encyclopedia of Optimization, Second Edition, 2009

A Genome-Scale Metabolic Reconstruction of <i>Mycoplasma genitalium</i>, <i>i</i>PS189.
PLoS Comput. Biol., 2009

GrowMatch: An Automated Method for Reconciling <i>In Silico</i>/<i>In Vivo</i> Growth Predictions.
PLoS Comput. Biol., 2009

Implication of dynamics in signal transduction and targeted disruption analyses of signaling networks.
Comput. Chem. Eng., 2008

OptCircuit: An optimization based method for computational design of genetic circuits.
BMC Syst. Biol., 2008

Predicting biological system objectives de novo from internal state measurements.
BMC Bioinform., 2008

Optimization based automated curation of metabolic reconstructions.
BMC Bioinform., 2007

Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites.
Bioinform., 2006

Comput. Chem. Eng., 2005

Large-scale inference of the transcriptional regulation of Bacillus subtilis.
Comput. Chem. Eng., 2005

A Mixed Integer Linear Programming (MILP) Framework for Inferring Time Delay in Gene Regulatory Networks.
Proceedings of the Biocomputing 2004, 2004

Managing demand uncertainty in supply chain planning.
Comput. Chem. Eng., 2003

Prediction of Oligopeptide Conformations via Deterministic Global Optimization.
J. Glob. Optim., 1997

Finding all solutions of nonlinearly constrained systems of equations.
J. Glob. Optim., 1995

αBB: A global optimization method for general constrained nonconvex problems.
J. Glob. Optim., 1995

New results in the packing of equal circles in a square.
Discret. Math., 1995

A deterministic global optimization approach for the protein folding problem.
Proceedings of the Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, 1995

Global minimum potential energy conformations of small molecules.
J. Glob. Optim., 1994

Global optimization for molecular conformation problems.
Ann. Oper. Res., 1993