% csauthors.net - beta - BibTeX bibliography of Costas D. Maranas
@article{journals/anor/MaranasF93,
title = {Global optimization for molecular conformation problems.},
year = {1993},
journal = {Ann. Oper. Res.},
author = {{Costas D. Maranas} and {Christodoulos A. Floudas}}
}
@article{journals/jgo/MaranasF94,
title = {Global minimum potential energy conformations of small molecules.},
year = {1994},
journal = {J. Glob. Optim.},
author = {{Costas D. Maranas} and {Christodoulos A. Floudas}}
}
@inproceedings{conf/dimacs/MaranasAF95,
title = {A deterministic global optimization approach for the protein folding problem.},
year = {1995},
booktitle = {Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding},
author = {{Costas D. Maranas} and {Ioannis P. Androulakis} and {Christodoulos A. Floudas}},
publisher = {DIMACS/AMS},
booktitle = {Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, Proceedings of a DIMACS Workshop, USA, March 20-21, 1995}
}
@article{journals/dm/MaranasFP95,
title = {New results in the packing of equal circles in a square.},
year = {1995},
journal = {Discret. Math.},
author = {{Costas D. Maranas} and {Christodoulos A. Floudas} and {Panos M. Pardalos}}
}
@article{journals/jgo/AndroulakisMF95,
title = {αBB: A global optimization method for general constrained nonconvex problems.},
year = {1995},
journal = {J. Glob. Optim.},
author = {{Ioannis P. Androulakis} and {Costas D. Maranas} and {Christodoulos A. Floudas}}
}
@article{journals/jgo/MaranasF95,
title = {Finding all solutions of nonlinearly constrained systems of equations.},
year = {1995},
journal = {J. Glob. Optim.},
author = {{Costas D. Maranas} and {Christodoulos A. Floudas}}
}
@article{journals/jgo/AndroulakisMF97,
title = {Prediction of Oligopeptide Conformations via Deterministic Global Optimization.},
year = {1997},
journal = {J. Glob. Optim.},
author = {{Ioannis P. Androulakis} and {Costas D. Maranas} and {Christodoulos A. Floudas}}
}
@article{journals/cce/GuptaM03,
title = {Managing demand uncertainty in supply chain planning.},
year = {2003},
journal = {Comput. Chem. Eng.},
author = {{Anshuman Gupta} and {Costas D. Maranas}}
}
@inproceedings{conf/psb/DasikaGMV04,
title = {A Mixed Integer Linear Programming (MILP) Framework for Inferring Time Delay in Gene Regulatory Networks.},
year = {2004},
booktitle = {Pacific Symposium on Biocomputing},
author = {{Madhukar S. Dasika} and {Anshuman Gupta} and {Costas D. Maranas} and {Jeffrey D. Varner}},
publisher = {World Scientific},
booktitle = {Biocomputing 2004, Proceedings of the Pacific Symposium, Hawaii, USA, 6-10 January 2004}
}
@article{journals/cce/GuptaVM05,
title = {Large-scale inference of the transcriptional regulation of Bacillus subtilis.},
year = {2005},
journal = {Comput. Chem. Eng.},
author = {{Anshuman Gupta} and {Jeffrey D. Varner} and {Costas D. Maranas}}
}
@article{journals/cce/MaranasH05,
title = {Preface.},
year = {2005},
journal = {Comput. Chem. Eng.},
author = {{Costas D. Maranas} and {Vassily Hatzimanikatis}}
}
@inproceedings{conf/amcc/Vital-LopezMA06,
title = {Bifurcation analysis of the metabolism of E. coli at optimal enzyme levels.},
year = {2006},
booktitle = {ACC},
author = {{Reza G. Vital-Lopez} and {Costas D. Maranas} and {Antonios Armaou}},
publisher = {IEEE},
booktitle = {American Control Conference, ACC 2006, Minneapolis, MN, USA, 14-16 June, 2006}
}
@article{journals/bioinformatics/GuptaMA06,
title = {Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites.},
year = {2006},
journal = {Bioinform.},
author = {{Anshuman Gupta} and {Costas D. Maranas} and {Réka Albert}}
}
@article{journals/bmcbi/KumarDM07,
title = {Optimization based automated curation of metabolic reconstructions.},
year = {2007},
journal = {BMC Bioinform.},
author = {{Vinay Satish Kumar} and {Madhukar S. Dasika} and {Costas D. Maranas}}
}
@article{journals/bmcbi/GianchandaniOBMP08,
title = {Predicting biological system objectives de novo from internal state measurements.},
year = {2008},
journal = {BMC Bioinform.},
author = {{Erwin P. Gianchandani} and {Matthew A. Oberhardt} and {Anthony P. Burgard} and {Costas D. Maranas} and {Jason A. Papin}}
}
@article{journals/bmcsb/DasikaM08,
title = {OptCircuit: An optimization based method for computational design of genetic circuits.},
year = {2008},
journal = {BMC Syst. Biol.},
author = {{Madhukar S. Dasika} and {Costas D. Maranas}}
}
@article{journals/cce/Vital-LopezVMA08,
title = {Implication of dynamics in signal transduction and targeted disruption analyses of signaling networks.},
year = {2008},
journal = {Comput. Chem. Eng.},
author = {{Francisco G. Vital-Lopez} and {Amit Varshney} and {Costas D. Maranas} and {Antonios Armaou}}
}
@article{journals/ploscb/KumarM09,
title = {GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions.},
year = {2009},
journal = {PLoS Comput. Biol.},
author = {{Vinay Satish Kumar} and {Costas D. Maranas}}
}
@article{journals/ploscb/SuthersDKDGM09,
title = {A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189.},
year = {2009},
journal = {PLoS Comput. Biol.},
author = {{Patrick F. Suthers} and {Madhukar S. Dasika} and {Vinay Satish Kumar} and {Gennady Denisov} and {John I. Glass} and {Costas D. Maranas}}
}
@incollection{reference/opt/Maranas09,
title = {Global Optimization in Generalized Geometric Programming.},
year = {2009},
booktitle = {Encyclopedia of Optimization},
author = {{Costas D. Maranas}},
publisher = {Springer},
booktitle = {Encyclopedia of Optimization, Second Edition}
}
@incollection{reference/opt/Maranas09a,
title = {Global Optimization in Lennard-Jones and Morse Clusters.},
year = {2009},
booktitle = {Encyclopedia of Optimization},
author = {{Costas D. Maranas}},
publisher = {Springer},
booktitle = {Encyclopedia of Optimization, Second Edition}
}
@incollection{reference/opt/Maranas09b,
title = {Global Optimization in Weber's Problem with Attraction and Repulsion.},
year = {2009},
booktitle = {Encyclopedia of Optimization},
author = {{Costas D. Maranas}},
publisher = {Springer},
booktitle = {Encyclopedia of Optimization, Second Edition}
}
@article{journals/bmcsb/ZomorrodiM10,
title = {Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data.},
year = {2010},
journal = {BMC Syst. Biol.},
author = {{Ali R. Zomorrodi} and {Costas D. Maranas}}
}
@article{journals/ploscb/RanganathanSM10,
title = {OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions.},
year = {2010},
journal = {PLoS Comput. Biol.},
author = {{Sridhar Ranganathan} and {Patrick F. Suthers} and {Costas D. Maranas}}
}
@inproceedings{conf/amcc/Vital-LopezMA11,
title = {Modeling the effect of temozolomide treatment on orthotopic models of glioma.},
year = {2011},
booktitle = {ACC},
author = {{Francisco G. Vital-Lopez} and {Costas D. Maranas} and {Antonios Armaou}},
publisher = {IEEE},
booktitle = {American Control Conference, ACC 2011, San Francisco, CA, USA, June 29 - July 1, 2011}
}
@article{journals/bmcsb/KumarFM11,
title = {Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans.},
year = {2011},
journal = {BMC Syst. Biol.},
author = {{Vinay Satish Kumar} and {James G. Ferry} and {Costas D. Maranas}}
}
@article{journals/bmcbi/KumarSM12,
title = {MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases.},
year = {2012},
journal = {BMC Bioinform.},
author = {{Akhil Kumar 003} and {Patrick F. Suthers} and {Costas D. Maranas}}
}
@article{journals/ploscb/BrochadoAMP12,
title = {Impact of Stoichiometry Representation on Simulation of Genotype-Phenotype Relationships in Metabolic Networks.},
year = {2012},
journal = {PLoS Comput. Biol.},
author = {{Ana Rita Brochado} and {Sergej Andrejev} and {Costas D. Maranas} and {Kiran Raosaheb Patil}}
}
@article{journals/ploscb/ZomorrodiM12,
title = {OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities.},
year = {2012},
journal = {PLoS Comput. Biol.},
author = {{Ali R. Zomorrodi} and {Costas D. Maranas}}
}
@article{journals/bmcbi/PantazesM13,
title = {MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured antibodies.},
year = {2013},
journal = {BMC Bioinform.},
author = {{Robert J. Pantazes} and {Costas D. Maranas}}
}
@article{journals/bmcsb/MuellerBPM13,
title = {Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow.},
year = {2013},
journal = {BMC Syst. Biol.},
author = {{Thomas J. Mueller} and {Bertram M. Berla} and {Himadri B. Pakrasi} and {Costas D. Maranas}}
}
@article{journals/eor/ZomorrodiM14,
title = {Coarse-grained optimization-driven design and piecewise linear modeling of synthetic genetic circuits.},
year = {2014},
journal = {Eur. J. Oper. Res.},
author = {{Ali R. Zomorrodi} and {Costas D. Maranas}}
}
@article{journals/jcisd/0003M14,
title = {CLCA: Maximum Common Molecular Substructure Queries within the MetRxn Database.},
year = {2014},
journal = {J. Chem. Inf. Model.},
author = {{Akhil Kumar 003} and {Costas D. Maranas}}
}
@article{journals/ploscb/ChowdhuryZM14,
title = {k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design.},
year = {2014},
journal = {PLoS Comput. Biol.},
author = {{Anupam Chowdhury} and {Ali R. Zomorrodi} and {Costas D. Maranas}}
}
@article{journals/cce/ChowdhuryZM15,
title = {Bilevel optimization techniques in computational strain design.},
year = {2015},
journal = {Comput. Chem. Eng.},
author = {{Anupam Chowdhury} and {Ali R. Zomorrodi} and {Costas D. Maranas}}
}
@article{journals/jcc/PantazesGLGM15,
title = {The Iterative Protein Redesign and Optimization (IPRO) suite of programs.},
year = {2015},
journal = {J. Comput. Chem.},
author = {{Robert J. Pantazes} and {Matthew J. Grisewood} and {Tong Li} and {Nathanael P. Gifford} and {Costas D. Maranas}}
}
@article{journals/bioinformatics/ChanCWSM17,
title = {Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models.},
year = {2017},
journal = {Bioinform.},
author = {{Siu Hung Joshua Chan} and {Jingyi Cai} and {Lin Wang 031} and {Margaret N. Simons-Senftle} and {Costas D. Maranas}}
}
@article{journals/bmcsb/Serrano-Bermudez17,
title = {Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol.},
year = {2017},
journal = {BMC Syst. Biol.},
author = {{Luis Miguel Serrano-Bermúdez} and {Andrés Fernando González Barrios} and {Costas D. Maranas} and {Dolly Montoya Castaño}}
}
@article{journals/ploscb/ChanSM17,
title = {SteadyCom: Predicting microbial abundances while ensuring community stability.},
year = {2017},
journal = {PLoS Comput. Biol.},
author = {{Siu Hung Joshua Chan} and {Margaret N. Simons} and {Costas D. Maranas}}
}
@article{journals/bioinformatics/ChanWDM18,
title = {Accelerating flux balance calculations in genome-scale metabolic models by localizing the application of loopless constraints.},
year = {2018},
journal = {Bioinform.},
author = {{Siu Hung Joshua Chan} and {Lin Wang 031} and {Satyakam Dash} and {Costas D. Maranas}}
}
@article{journals/ploscb/FosterGAM19,
title = {From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline.},
year = {2019},
journal = {PLoS Comput. Biol.},
author = {{Charles J. Foster} and {Saratram Gopalakrishnan} and {Maciek R. Antoniewicz} and {Costas D. Maranas}}
}
@article{journals/ploscb/SarkarMLPM19,
title = {A diurnal flux balance model of Synechocystis sp. PCC 6803 metabolism.},
year = {2019},
journal = {PLoS Comput. Biol.},
author = {{Debolina Sarkar} and {Thomas J. Mueller} and {Deng Liu} and {Himadri B. Pakrasi} and {Costas D. Maranas}}
}
@article{journals/ploscb/SarkarLBPZM21,
title = {Elucidation of trophic interactions in an unusual single-cell nitrogen-fixing symbiosis using metabolic modeling.},
year = {2021},
journal = {PLoS Comput. Biol.},
author = {{Debolina Sarkar} and {Marine Landa} and {Anindita Bandyopadhyay} and {Himadri B. Pakrasi} and {Jonathan P. Zehr} and {Costas D. Maranas}}
}
@article{journals/ploscb/WangUM21,
title = {dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design.},
year = {2021},
journal = {PLoS Comput. Biol.},
author = {{Lin Wang 031} and {Vikas Upadhyay} and {Costas D. Maranas}}
}