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2020 – today
- 2021
[j37]Debolina Sarkar, Marine Landa
, Anindita Bandyopadhyay, Himadri B. Pakrasi, Jonathan P. Zehr, Costas D. Maranas:
Elucidation of trophic interactions in an unusual single-cell nitrogen-fixing symbiosis using metabolic modeling. PLoS Comput. Biol. 17(5) (2021)- [j36]Lin Wang, Vikas Upadhyay, Costas D. Maranas:
dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design. PLoS Comput. Biol. 17(9) (2021)
2010 – 2019
- 2019
- [j35]Debolina Sarkar, Thomas J. Mueller, Deng Liu, Himadri B. Pakrasi, Costas D. Maranas:
A diurnal flux balance model of Synechocystis sp. PCC 6803 metabolism. PLoS Comput. Biol. 15(1) (2019) - [j34]Charles J. Foster, Saratram Gopalakrishnan, Maciek R. Antoniewicz, Costas D. Maranas:
From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline. PLoS Comput. Biol. 15(9) (2019) - 2018
- [j33]Siu Hung Joshua Chan, Lin Wang, Satyakam Dash, Costas D. Maranas:
Accelerating flux balance calculations in genome-scale metabolic models by localizing the application of loopless constraints. Bioinform. 34(24): 4248-4255 (2018) - 2017
- [j32]Siu Hung Joshua Chan, Jingyi Cai, Lin Wang, Margaret N. Simons-Senftle, Costas D. Maranas:
Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models. Bioinform. 33(22): 3603-3609 (2017) - [j31]Luis Miguel Serrano-Bermúdez, Andrés Fernando González Barrios, Costas D. Maranas, Dolly Montoya Castaño:
Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol. BMC Syst. Biol. 11(1): 58:1-58:13 (2017) - [j30]Siu Hung Joshua Chan, Margaret N. Simons, Costas D. Maranas:
SteadyCom: Predicting microbial abundances while ensuring community stability. PLoS Comput. Biol. 13(5) (2017) - 2015
- [j29]Anupam Chowdhury, Ali R. Zomorrodi, Costas D. Maranas:
Bilevel optimization techniques in computational strain design. Comput. Chem. Eng. 72: 363-372 (2015) - [j28]Robert J. Pantazes, Matthew J. Grisewood, Tong Li, Nathanael P. Gifford, Costas D. Maranas:
The Iterative Protein Redesign and Optimization (IPRO) suite of programs. J. Comput. Chem. 36(4): 251-263 (2015) - 2014
- [j27]Ali R. Zomorrodi, Costas D. Maranas:
Coarse-grained optimization-driven design and piecewise linear modeling of synthetic genetic circuits. Eur. J. Oper. Res. 237(2): 665-676 (2014) - [j26]Akhil Kumar, Costas D. Maranas:
CLCA: Maximum Common Molecular Substructure Queries within the MetRxn Database. J. Chem. Inf. Model. 54(12): 3417-3438 (2014) - [j25]Anupam Chowdhury, Ali R. Zomorrodi, Costas D. Maranas:
k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design. PLoS Comput. Biol. 10(2) (2014) - 2013
- [j24]Robert J. Pantazes, Costas D. Maranas:
MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured antibodies. BMC Bioinform. 14: 168 (2013) - [j23]Thomas J. Mueller, Bertram M. Berla, Himadri B. Pakrasi, Costas D. Maranas:
Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow. BMC Syst. Biol. 7: 142 (2013) - 2012
- [j22]Akhil Kumar, Patrick F. Suthers, Costas D. Maranas:
MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases. BMC Bioinform. 13: 6 (2012) - [j21]Ali R. Zomorrodi, Costas D. Maranas:
OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities. PLoS Comput. Biol. 8(2) (2012) - [j20]Ana Rita Brochado, Sergej Andrejev, Costas D. Maranas, Kiran Raosaheb Patil:
Impact of Stoichiometry Representation on Simulation of Genotype-Phenotype Relationships in Metabolic Networks. PLoS Comput. Biol. 8(11) (2012) - 2011
- [j19]Vinay Satish Kumar, James G. Ferry, Costas D. Maranas:
Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans. BMC Syst. Biol. 5: 28 (2011) - [c4]Francisco G. Vital-Lopez, Costas D. Maranas, Antonios Armaou:
Modeling the effect of temozolomide treatment on orthotopic models of glioma. ACC 2011: 2969-2974 - 2010
- [j18]Ali R. Zomorrodi, Costas D. Maranas:
Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data. BMC Syst. Biol. 4: 178 (2010) - [j17]Sridhar Ranganathan, Patrick F. Suthers, Costas D. Maranas:
OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions. PLoS Comput. Biol. 6(4) (2010)
2000 – 2009
- 2009
- [j16]Patrick F. Suthers, Madhukar S. Dasika, Vinay Satish Kumar, Gennady Denisov, John I. Glass, Costas D. Maranas:
A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189. PLoS Comput. Biol. 5(2) (2009) - [j15]Vinay Satish Kumar, Costas D. Maranas:
GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions. PLoS Comput. Biol. 5(3) (2009) - [r3]Costas D. Maranas:
Global Optimization in Generalized Geometric Programming. Encyclopedia of Optimization 2009: 1333-1337 - [r2]Costas D. Maranas:
Global Optimization in Lennard-Jones and Morse Clusters. Encyclopedia of Optimization 2009: 1350-1354 - [r1]Costas D. Maranas:
Global Optimization in Weber's Problem with Attraction and Repulsion. Encyclopedia of Optimization 2009: 1423-1427 - 2008
- [j14]Erwin P. Gianchandani, Matthew A. Oberhardt, Anthony P. Burgard, Costas D. Maranas, Jason A. Papin:
Predicting biological system objectives de novo from internal state measurements. BMC Bioinform. 9 (2008) - [j13]Madhukar S. Dasika, Costas D. Maranas:
OptCircuit: An optimization based method for computational design of genetic circuits. BMC Syst. Biol. 2: 24 (2008) - [j12]Francisco G. Vital-Lopez, Amit Varshney, Costas D. Maranas, Antonios Armaou:
Implication of dynamics in signal transduction and targeted disruption analyses of signaling networks. Comput. Chem. Eng. 32(9): 2065-2071 (2008) - 2007
- [j11]Vinay Satish Kumar, Madhukar S. Dasika, Costas D. Maranas:
Optimization based automated curation of metabolic reconstructions. BMC Bioinform. 8 (2007) - 2006
- [j10]Anshuman Gupta, Costas D. Maranas, Réka Albert:
Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites. Bioinform. 22(2): 209-214 (2006) - [c3]Reza G. Vital-Lopez, Costas D. Maranas, Antonios Armaou:
Bifurcation analysis of the metabolism of E. coli at optimal enzyme levels. ACC 2006: 1-6 - 2005
- [j9]Costas D. Maranas, Vassily Hatzimanikatis:
Preface. Comput. Chem. Eng. 29(3): 405-406 (2005) - [j8]Anshuman Gupta, Jeffrey D. Varner, Costas D. Maranas:
Large-scale inference of the transcriptional regulation of Bacillus subtilis. Comput. Chem. Eng. 29(3): 565-576 (2005) - 2004
- [c2]Madhukar S. Dasika, Anshuman Gupta, Costas D. Maranas, Jeffrey D. Varner:
A Mixed Integer Linear Programming (MILP) Framework for Inferring Time Delay in Gene Regulatory Networks. Pacific Symposium on Biocomputing 2004: 474-485 - 2003
- [j7]Anshuman Gupta, Costas D. Maranas:
Managing demand uncertainty in supply chain planning. Comput. Chem. Eng. 27(8-9): 1219-1227 (2003)
1990 – 1999
- 1997
- [j6]Ioannis P. Androulakis, Costas D. Maranas, Christodoulos A. Floudas:
Prediction of Oligopeptide Conformations via Deterministic Global Optimization. J. Glob. Optim. 11(1): 1-34 (1997) - 1995
- [j5]Costas D. Maranas, Christodoulos A. Floudas, Panos M. Pardalos:
New results in the packing of equal circles in a square. Discret. Math. 142(1-3): 287-293 (1995) - [j4]Costas D. Maranas, Christodoulos A. Floudas:
Finding all solutions of nonlinearly constrained systems of equations. J. Glob. Optim. 7(2): 143-182 (1995) - [j3]Ioannis P. Androulakis, Costas D. Maranas, Christodoulos A. Floudas:
αBB: A global optimization method for general constrained nonconvex problems. J. Glob. Optim. 7(4): 337-363 (1995) - [c1]Costas D. Maranas, Ioannis P. Androulakis, Christodoulos A. Floudas:
A deterministic global optimization approach for the protein folding problem. Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding 1995: 133-150 - 1994
- [j2]Costas D. Maranas, Christodoulos A. Floudas:
Global minimum potential energy conformations of small molecules. J. Glob. Optim. 4(2): 135-170 (1994) - 1993
- [j1]Costas D. Maranas, Christodoulos A. Floudas:
Global optimization for molecular conformation problems. Ann. Oper. Res. 42(1): 85-117 (1993)
Coauthor Index
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