Global optimization for molecular conformation problems. - Costas D. Maranas; Christodoulos A. Floudas (Ann. Oper. Res., 1993)

Global minimum potential energy conformations of small molecules. - Costas D. Maranas; Christodoulos A. Floudas (J. Glob. Optim., 1994)

A deterministic global optimization approach for the protein folding problem. - Costas D. Maranas; Ioannis P. Androulakis; Christodoulos A. Floudas (Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, 1995)

New results in the packing of equal circles in a square. - Costas D. Maranas; Christodoulos A. Floudas; Panos M. Pardalos (Discret. Math., 1995)

αBB: A global optimization method for general constrained nonconvex problems. - Ioannis P. Androulakis; Costas D. Maranas; Christodoulos A. Floudas (J. Glob. Optim., 1995)

Finding all solutions of nonlinearly constrained systems of equations. - Costas D. Maranas; Christodoulos A. Floudas (J. Glob. Optim., 1995)

Prediction of Oligopeptide Conformations via Deterministic Global Optimization. - Ioannis P. Androulakis; Costas D. Maranas; Christodoulos A. Floudas (J. Glob. Optim., 1997)

Managing demand uncertainty in supply chain planning. - Anshuman Gupta; Costas D. Maranas (Comput. Chem. Eng., 2003)

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 (Pacific Symposium on Biocomputing, 2004)

Large-scale inference of the transcriptional regulation of Bacillus subtilis. - Anshuman Gupta; Jeffrey D. Varner; Costas D. Maranas (Comput. Chem. Eng., 2005)

Preface. - Costas D. Maranas; Vassily Hatzimanikatis (Comput. Chem. Eng., 2005)

Bifurcation analysis of the metabolism of E. coli at optimal enzyme levels. - Reza G. Vital-Lopez; Costas D. Maranas; Antonios Armaou (ACC, 2006)

Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites. - Anshuman Gupta; Costas D. Maranas; Réka Albert (Bioinform., 2006)

Optimization based automated curation of metabolic reconstructions. - Vinay Satish Kumar; Madhukar S. Dasika; Costas D. Maranas (BMC Bioinform., 2007)

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)

OptCircuit: An optimization based method for computational design of genetic circuits. - Madhukar S. Dasika; Costas D. Maranas (BMC Syst. Biol., 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)

GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions. - Vinay Satish Kumar; Costas D. Maranas (PLoS Comput. Biol., 2009)

A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189. - Patrick F. Suthers; Madhukar S. Dasika; Vinay Satish Kumar; Gennady Denisov; John I. Glass; Costas D. Maranas (PLoS Comput. Biol., 2009)

Global Optimization in Generalized Geometric Programming. - Costas D. Maranas (Encyclopedia of Optimization, 2009)

Global Optimization in Lennard-Jones and Morse Clusters. - Costas D. Maranas (Encyclopedia of Optimization, 2009)

Global Optimization in Weber's Problem with Attraction and Repulsion. - Costas D. Maranas (Encyclopedia of Optimization, 2009)

Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data. - Ali R. Zomorrodi; Costas D. Maranas (BMC Syst. Biol., 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)

Modeling the effect of temozolomide treatment on orthotopic models of glioma. - Francisco G. Vital-Lopez; Costas D. Maranas; Antonios Armaou (ACC, 2011)

Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans. - Vinay Satish Kumar; James G. Ferry; Costas D. Maranas (BMC Syst. Biol., 2011)

MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases. - Akhil Kumar 003; Patrick F. Suthers; Costas D. Maranas (BMC Bioinform., 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)

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)

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)

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)

Coarse-grained optimization-driven design and piecewise linear modeling of synthetic genetic circuits. - Ali R. Zomorrodi; Costas D. Maranas (Eur. J. Oper. Res., 2014)

CLCA: Maximum Common Molecular Substructure Queries within the MetRxn Database. - Akhil Kumar 003; Costas D. Maranas (J. Chem. Inf. Model., 2014)

k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design. - Anupam Chowdhury; Ali R. Zomorrodi; Costas D. Maranas (PLoS Comput. Biol., 2014)

Bilevel optimization techniques in computational strain design. - Anupam Chowdhury; Ali R. Zomorrodi; Costas D. Maranas (Comput. Chem. Eng., 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)

Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models. - Siu Hung Joshua Chan; Jingyi Cai; Lin Wang 031; Margaret N. Simons-Senftle; Costas D. Maranas (Bioinform., 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)

SteadyCom: Predicting microbial abundances while ensuring community stability. - Siu Hung Joshua Chan; Margaret N. Simons; Costas D. Maranas (PLoS Comput. Biol., 2017)

Accelerating flux balance calculations in genome-scale metabolic models by localizing the application of loopless constraints. - Siu Hung Joshua Chan; Lin Wang 031; Satyakam Dash; Costas D. Maranas (Bioinform., 2018)

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)

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)

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)

dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design. - Lin Wang 031; Vikas Upadhyay; Costas D. Maranas (PLoS Comput. Biol., 2021)