Costas D. Maranas

46 papers C 2Misc 1Journal 39Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
Parameterization of cell-free systems with time-series data using KETCHUP.
PLoS Comput. Biol.
Mengqi Hu, Syed Bilal Jilani, Daniel G. Olson, Costas D. Maranas
2025 J jnl
novoStoic2.0: An integrated framework for pathway synthesis, thermodynamic evaluation, and enzyme selection.
PLoS Comput. Biol.
Vikas Upadhyay, Mohit Anand, Costas D. Maranas
2021 J jnl
Elucidation of trophic interactions in an unusual single-cell nitrogen-fixing symbiosis using metabolic modeling.
PLoS Comput. Biol.
Debolina Sarkar, Marine Landa, Anindita Bandyopadhyay, Himadri B. Pakrasi, Jonathan P. Zehr, Costas D. Maranas
2021 J jnl
dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design.
PLoS Comput. Biol.
Lin Wang, Vikas Upadhyay, Costas D. Maranas
2019 J jnl
A diurnal flux balance model of Synechocystis sp. PCC 6803 metabolism.
PLoS Comput. Biol.
Debolina Sarkar, Thomas J. Mueller, Deng Liu, Himadri B. Pakrasi, Costas D. Maranas
2019 J jnl
From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline.
PLoS Comput. Biol.
Charles J. Foster, Saratram Gopalakrishnan, Maciek R. Antoniewicz, Costas D. Maranas
2018 J jnl
Accelerating flux balance calculations in genome-scale metabolic models by localizing the application of loopless constraints.
Bioinform.
Siu Hung Joshua Chan, Lin Wang, Satyakam Dash, Costas D. Maranas
2017 J jnl
Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol.
BMC Syst. Biol.
Luis Miguel Serrano-Bermúdez, Andrés Fernando González Barrios, Costas D. Maranas, Dolly Montoya Castaño
2017 J jnl
Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models.
Bioinform.
Siu Hung Joshua Chan, Jingyi Cai, Lin Wang, Margaret N. Simons-Senftle, Costas D. Maranas
2017 J jnl
SteadyCom: Predicting microbial abundances while ensuring community stability.
PLoS Comput. Biol.
Siu Hung Joshua Chan, Margaret N. Simons, Costas D. Maranas
2015 J jnl
Bilevel optimization techniques in computational strain design.
Comput. Chem. Eng.
Anupam Chowdhury, Ali R. Zomorrodi, Costas D. Maranas
2015 J jnl
The Iterative Protein Redesign and Optimization (IPRO) suite of programs.
J. Comput. Chem.
Robert J. Pantazes, Matthew J. Grisewood, Tong Li, Nathanael P. Gifford, Costas D. Maranas
2014 J jnl
CLCA: Maximum Common Molecular Substructure Queries within the MetRxn Database.
J. Chem. Inf. Model.
Akhil Kumar, Costas D. Maranas
2014 J jnl
Coarse-grained optimization-driven design and piecewise linear modeling of synthetic genetic circuits.
Eur. J. Oper. Res.
Ali R. Zomorrodi, Costas D. Maranas
2014 J jnl
k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design.
PLoS Comput. Biol.
Anupam Chowdhury, Ali R. Zomorrodi, Costas D. Maranas
2013 J jnl
MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured antibodies.
BMC Bioinform.
Robert J. Pantazes, Costas D. Maranas
2013 J jnl
Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow.
BMC Syst. Biol.
Thomas J. Mueller, Bertram M. Berla, Himadri B. Pakrasi, Costas D. Maranas
2012 J jnl
Impact of Stoichiometry Representation on Simulation of Genotype-Phenotype Relationships in Metabolic Networks.
PLoS Comput. Biol.
Ana Rita Brochado, Sergej Andrejev, Costas D. Maranas, Kiran Raosaheb Patil
2012 J jnl
MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases.
BMC Bioinform.
Akhil Kumar, Patrick F. Suthers, Costas D. Maranas
2012 J jnl
OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities.
PLoS Comput. Biol.
Ali R. Zomorrodi, Costas D. Maranas
2011 J jnl
Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans.
BMC Syst. Biol.
Vinay Satish Kumar, James G. Ferry, Costas D. Maranas
2011 C conf
Modeling the effect of temozolomide treatment on orthotopic models of glioma.
ACC
Francisco G. Vital-Lopez, Costas D. Maranas, Antonios Armaou
2010 J jnl
Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data.
BMC Syst. Biol.
Ali R. Zomorrodi, Costas D. Maranas
2010 J jnl
OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions.
PLoS Comput. Biol.
Sridhar Ranganathan, Patrick F. Suthers, Costas D. Maranas
2009 J jnl
A Genome-Scale Metabolic Reconstruction of
PLoS Comput. Biol.
Patrick F. Suthers, Madhukar S. Dasika, Vinay Satish Kumar, Gennady Denisov, John I. Glass, Costas D. Maranas
2009 — ch.
Global Optimization in Generalized Geometric Programming.
Encyclopedia of Optimization
Costas D. Maranas
2009 — ch.
Global Optimization in Lennard-Jones and Morse Clusters.
Encyclopedia of Optimization
Costas D. Maranas
2009 — ch.
Global Optimization in Weber's Problem with Attraction and Repulsion.
Encyclopedia of Optimization
Costas D. Maranas
2009 J jnl
GrowMatch: An Automated Method for Reconciling
PLoS Comput. Biol.
Vinay Satish Kumar, Costas D. Maranas
2008 J jnl
Implication of dynamics in signal transduction and targeted disruption analyses of signaling networks.
Comput. Chem. Eng.
Francisco G. Vital-Lopez, Amit Varshney, Costas D. Maranas, Antonios Armaou
2008 J jnl
OptCircuit: An optimization based method for computational design of genetic circuits.
BMC Syst. Biol.
Madhukar S. Dasika, Costas D. Maranas
2008 J jnl
Predicting biological system objectives de novo from internal state measurements.
BMC Bioinform.
Erwin P. Gianchandani, Matthew A. Oberhardt, Anthony P. Burgard, Costas D. Maranas, Jason A. Papin
2007 J jnl
Optimization based automated curation of metabolic reconstructions.
BMC Bioinform.
Vinay Satish Kumar, Madhukar S. Dasika, Costas D. Maranas
2006 C conf
Bifurcation analysis of the metabolism of E. coli at optimal enzyme levels.
ACC
Reza G. Vital-Lopez, Costas D. Maranas, Antonios Armaou
2006 J jnl
Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites.
Bioinform.
Anshuman Gupta, Costas D. Maranas, Réka Albert
2005 J jnl
Large-scale inference of the transcriptional regulation of Bacillus subtilis.
Comput. Chem. Eng.
Anshuman Gupta, Jeffrey D. Varner, Costas D. Maranas
2005 J jnl
Preface.
Comput. Chem. Eng.
Costas D. Maranas, Vassily Hatzimanikatis
2004 Misc conf
A Mixed Integer Linear Programming (MILP) Framework for Inferring Time Delay in Gene Regulatory Networks.
Pacific Symposium on Biocomputing
Madhukar S. Dasika, Anshuman Gupta, Costas D. Maranas, Jeffrey D. Varner
2003 J jnl
Managing demand uncertainty in supply chain planning.
Comput. Chem. Eng.
Anshuman Gupta, Costas D. Maranas
1997 J jnl
Prediction of Oligopeptide Conformations via Deterministic Global Optimization.
J. Glob. Optim.
Ioannis P. Androulakis, Costas D. Maranas, Christodoulos A. Floudas
1995 — conf
A deterministic global optimization approach for the protein folding problem.
Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding
Costas D. Maranas, Ioannis P. Androulakis, Christodoulos A. Floudas
1995 J jnl
Finding all solutions of nonlinearly constrained systems of equations.
J. Glob. Optim.
Costas D. Maranas, Christodoulos A. Floudas
1995 J jnl
New results in the packing of equal circles in a square.
Discret. Math.
Costas D. Maranas, Christodoulos A. Floudas, Panos M. Pardalos
1995 J jnl
αBB: A global optimization method for general constrained nonconvex problems.
J. Glob. Optim.
Ioannis P. Androulakis, Costas D. Maranas, Christodoulos A. Floudas
1994 J jnl
Global minimum potential energy conformations of small molecules.
J. Glob. Optim.
Costas D. Maranas, Christodoulos A. Floudas
1993 J jnl
Global optimization for molecular conformation problems.
Ann. Oper. Res.
Costas D. Maranas, Christodoulos A. Floudas