Directory

 

 
 
General InformationPublications

  • V G Poosarla, T Li, B C Goh, K Schulten, Thomas Wood and Costas D Maranas, 2017, "Computational de novo design of antibodies binding to a peptide with high affinity.", Biotechnology and bioengineering
  • A Khodayari and Costas D Maranas, 2016, "A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains.", Nature communications, 7, pp. 13806
  • Liang Zhang, C Xie, Renea Nichols, S H Chan, C Jiang, R Hao, Patricck Smith, J Cai, M N Simons, E Hatzakis, Costas D Maranas, F J Gonzalez and Andrew David Patterson, 2016, "Farnesoid X Receptor Signaling Shapes the Gut Microbiota and Controls Hepatic Lipid Metabolism.", mSystems, 1, (5)
  • C Y Ng, A Chowdhury and Costas D Maranas, 2016, "A microbial factory for diverse chemicals.", Nature biotechnology, 34, (5), pp. 513-5
  • R Saha, David X Liu, A Hoynes-O'Connor, M Liberton, Jia Yu, M Bhattacharyya-Pakrasi, A Balassy, Fan Zhang, T S Moon, Costas D Maranas and H B Pakrasi, 2016, "Diurnal Regulation of Cellular Processes in the Cyanobacterium Synechocystis sp. Strain PCC 6803: Insights from Transcriptomic, Fluxomic, and Physiological Analyses.", mBio, 7, (3)
  • T J Mueller, E A Welsh, H B Pakrasi and Costas D Maranas, 2016, "Identifying Regulatory Changes to Facilitate Nitrogen Fixation in the Nondiazotroph Synechocystis sp. PCC 6803.", ACS synthetic biology, 5, (3), pp. 250-8
  • Muyun Lihan, Boon Chong Goh, Tong Li, Costas D Maranas and Klaus Shulten, 2016, "de novo Design and in silico Optimization of Antibody-Like Binders Targeting Ebola Viral Antigen", Biophysical Journal, 110, (3), pp. 537a
  • Costas D Maranas and Ali R Zomorrodi, 2016, Optimization Methods in Metabolic Networks, John Wiley & Sons
  • Hadi Nazem-Bokaee, Saratram Gopalakrishnan, James G Ferry, Thomas Wood and Costas D Maranas, 2016, "Assessing methanotrophy and carbon fixation for biofuel production by Methanosarcina acetivorans", Microbial cell factories, 15, (1)
  • V W Soo, M J McAnulty, A Tripathi, F Zhu, Liang Zhang, E Hatzakis, Patricck Smith, S Agrawal, H Nazem-Bokaee, S Gopalakrishnan, Howard M Salis, James G Ferry, Costas D Maranas, Andrew David Patterson and Thomas Wood, 2016, "Reversing methanogenesis to capture methane for liquid biofuel precursors.", Microbial cell factories, 15, pp. 11
  • Chiam Yu Ng, Satyakam Dash and Costas D Maranas, 2016, "Metabolic modeling of clostridia: current developments and applications", FEMS microbiology letters, 363, (4)
  • Anupam Chowdhury, Ali Khodayari and Costas D Maranas, 2015, "Improving prediction fidelity of cellular metabolism with kinetic descriptions", Current opinion in biotechnology, 36, pp. 57–64
  • Thomas J Mueller, Eric A Welsh, Himadri B Pakrasi and Costas D Maranas, 2015, "Identifying regulatory changes to facilitate nitrogen fixation in the non-diazotroph Synechocystis sp. PCC 6803", ACS synthetic Biology, 5, (3), pp. 250–258
  • Saratram Gopalakrishnan and Costas D Maranas, 2015, "13C metabolic flux analysis at a genome-scale", Metabolic Engineering, 32, pp. 12-22
  • Anupam Chowdhury and Costas D Maranas, 2015, "Designing overall stoichiometric conversions and intervening metabolic reactions", Scientific reports, 5
  • Chiam Yu Ng, Ali Khodayari, Anupam Chowdhury and Costas D Maranas, 2015, "Advances in de novo strain design using integrated systems and synthetic biology tools", Current opinion in chemical biology, 28, pp. 105-114
  • Anupam Chowdhury and Costas D Maranas, 2015, "Personalized Kinetic Models for Predictive Healthcare", Cell Systems, 1, (4), pp. 250-251
  • Bertram M Berla, Rajib Saha, Costas D Maranas and Himadri B Pakrasi, 2015, "Cyanobacterial Alkanes Modulate Photosynthetic Cyclic Electron Flow to Assist Growth under Cold Stress", Scientific reports, 5
  • Ratul Chowdhury, Anupam Chowdhury and Costas D Maranas, 2015, "Using gene essentiality and synthetic lethality information to correct yeast and cho cell genome-scale models", Metabolites, 5, (4), pp. 536-570
  • Saratram Gopalakrishnan and Costas D Maranas, 2015, "Achieving Metabolic Flux Analysis for S. cerevisiae at a Genome-Scale: Challenges, Requirements, and Considerations", Metabolites, 5, (3), pp. 521-535
  • Sarah-Maria Fendt and Costas D Maranas, 2015, "Systems biology: Advances diseases understanding and metabolic engineering", Current opinion in biotechnology, 34, pp. v-vi
  • S M Fendt and Costas D Maranas, 2015, "Editorial overview: Systems biology: Advances diseases understanding and metabolic engineering.", Current opinion in biotechnology, 34, pp. v-vi
  • Chiam Yu Ng, Iman Farasat, Costas D Maranas and Howard M Salis, 2015, "Rational design of a synthetic Entner–Doudoroff pathway for improved and controllable NADPH regeneration", Metabolic engineering, 29, pp. 86-96
  • Thomas K Mueller, Matthew J Grisewood, Hadi Nazem-Bokaee, Saratram Gopalakrishnan, James G Ferry, Thomas Wood and Costas D Maranas, 2015, "Methane oxidation by anaerobic archaea for conversion to liquid fuels", Journal of industrial microbiology & biotechnology, 42, (3), pp. 391-401
  • Robert J Pantazes, Matthew J Grisewood, Tong Li, Nathanael P Gifford and Costas D Maranas, 2015, "The Iterative Protein Redesign and Optimization (IPRO) suite of programs", Journal of computational chemistry, 36, (4), pp. 251-63
  • Anupam Chowdhury, Ali R Zomorrodi and Costas D Maranas, 2015, "Bilevel optimization techniques in computational strain design", Computers & Chemical Engineering, 72, pp. 363–372
  • Akhil Kumar and Costas D Maranas, 2014, "CLCA: maximum common molecular substructure queries within the MetRxn database.", Journal of chemical information and modeling, 54, (12), pp. 3417-38
  • M Simons, R Saha, N Amiour, Akhil Kumar, L Guillard, G Clément, M Miquel, Z Li, G Mouille, P J Lea, B Hirel and Costas D Maranas, 2014, "Assessing the metabolic impact of nitrogen availability using a compartmentalized maize leaf genome-scale model.", Plant physiology, 166, (3), pp. 1659-74
  • M Simons, R Saha, L Guillard, G Clément, P Armengaud, R Cañas, Costas D Maranas, P J Lea and B Hirel, 2014, "Nitrogen-use efficiency in maize (Zea mays L.): from 'omics' studies to metabolic modelling.", Journal of experimental botany, 65, (19), pp. 5657-71
  • R Saha, A Chowdhury and Costas D Maranas, 2014, "Recent advances in the reconstruction of metabolic models and integration of omics data.", Current opinion in biotechnology, 29, pp. 39-45
  • A Khodayari, A R Zomorrodi, Jingang Liao and Costas D Maranas, 2014, "A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data.", Metabolic engineering, 25, pp. 50-62
  • T W Tee, A Chowdhury, Costas D Maranas and J V Shanks, 2014, "Systems metabolic engineering design: fatty acid production as an emerging case study.", Biotechnology and bioengineering, 111, (5), pp. 849-57
  • A R Zomorrodi, M M Islam and Costas D Maranas, 2014, "d-OptCom: Dynamic multi-level and multi-objective metabolic modeling of microbial communities.", ACS synthetic biology, 3, (4), pp. 247-57
  • A Chowdhury, A R Zomorrodi and Costas D Maranas, 2014, "k-OptForce: integrating kinetics with flux balance analysis for strain design.", PLoS computational biology, 10, (2), pp. e1003487
  • T Li, R J Pantazes and Costas D Maranas, 2014, "OptMAVEn--a new framework for the de novo design of antibody variable region models targeting specific antigen epitopes.", PloS one, 9, (8), pp. e105954
  • A Khodayari, A Chowdhury and Costas D Maranas, 2014, "Succinate Overproduction: A Case Study of Computational Strain Design Using a Comprehensive Escherichia coli Kinetic Model.", Frontiers in bioengineering and biotechnology, 2, pp. 76
  • S Dash, T J Mueller, K P Venkataramanan, E T Papoutsakis and Costas D Maranas, 2014, "Capturing the response of Clostridium acetobutylicum to chemical stressors using a regulated genome-scale metabolic model.", Biotechnology for biofuels, 7, (1), pp. 144
  • T J Mueller, M J Grisewood, H Nazem-Bokaee, S Gopalakrishnan, James G Ferry, Thomas Wood and Costas D Maranas, 2014, "Methane oxidation by anaerobic archaea for conversion to liquid fuels.", Journal of industrial microbiology & biotechnology, 42, (3), pp. 391-401
  • W M Aumiller, B W Davis, N Hashemain, Costas D Maranas, Antonios Armaou and C D Keating, 2014, "Coupled Enzyme Reactions Performed in Heterogeneous Reaction Media: Experiments and Modeling for Glucose Oxidase and Horseradish Peroxidase in PEG/Citrate Aqueous Two-Phase System", J. Phys. Chem. B DOI: 10.1021/jp501126v.
  • Costas D Maranas, 2014, "Coarse-grained optimization-driven design and piecewise linear modeling of synthetic genetic circuits", European Journal of Operational Research
  • T J Mueller, B M Berla, H B Pakrasi and Costas D Maranas, 2013, "Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow.", BMC systems biology, 7, pp. 142
  • A R Zomorrodi, J G Lafontaine Rivera, Jingang Liao and Costas D Maranas, 2013, "Optimization-driven identification of genetic perturbations accelerates the convergence of model parameters in ensemble modeling of metabolic networks.", Biotechnology journal, 8, (9), pp. 1090-104
  • R J Pantazes and Costas D Maranas, 2013, "MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured antibodies.", BMC bioinformatics, 14, pp. 168
  • A R Zomorrodi, P F Suthers, S Ranganathan and Costas D Maranas, 2012, "Mathematical optimization applications in metabolic networks.", Metabolic engineering, 14, (6), pp. 672-86
  • S Ranganathan, T W Tee, A Chowdhury, A R Zomorrodi, J M Yoon, Y Fu, J V Shanks and Costas D Maranas, 2012, "An integrated computational and experimental study for overproducing fatty acids in Escherichia coli.", Metabolic engineering, 14, (6), pp. 687-704
  • P F Suthers and Costas D Maranas, 2012, "Orchestrating hi-fi annotations.", Nature chemical biology, 8, (10), pp. 810-1
  • W B Copeland, B A Bartley, D Chandran, M Galdzicki, K H Kim, S C Sleight, Costas D Maranas and H M Sauro, 2012, "Computational tools for metabolic engineering.", Metabolic engineering, 14, (3), pp. 270-80
  • A R Zomorrodi and Costas D Maranas, 2012, "OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities.", PLoS computational biology, 8, (2), pp. e1002363
  • Akhil Kumar, P F Suthers and Costas D Maranas, 2012, "MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases.", BMC bioinformatics, 13, pp. 6
  • R Saha, A T Verseput, B M Berla, T J Mueller, H B Pakrasi and Costas D Maranas, 2012, "Reconstruction and comparison of the metabolic potential of cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803.", PloS one, 7, (10), pp. e48285
  • A R Brochado, S Andrejev, Costas D Maranas and K R Patil, 2012, "Impact of stoichiometry representation on simulation of genotype-phenotype relationships in metabolic networks.", PLoS computational biology, 8, (11), pp. e1002758
  • N. Wang, K. A. Eckert, A. R. Zomorrodi, P. Xin, W. Pan, D. A. Shearer, J. Weisz, Costas D Maranas and G. A. Clawson, 2012, "Down-Regulation of HtrA1 Activates the Epithelial-Mesenchymal Transition and ATM DNA Damage Response Pathways", PLoS ONE, 7, (6), pp. e39446
  • Ping Xu, S Ranganathan, Z L Fowler, Costas D Maranas and M A Koffas, 2011, "Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA.", Metabolic engineering, 13, (5), pp. 578-87
  • R J Pantazes, M J Grisewood and Costas D Maranas, 2011, "Recent advances in computational protein design.", Current opinion in structural biology, 21, (4), pp. 467-72
  • P Ravikirthi, P F Suthers and Costas D Maranas, 2011, "Construction of an E. Coli genome-scale atom mapping model for MFA calculations.", Biotechnology and bioengineering, 108, (6), pp. 1372-82
  • V Satish Kumar, James G Ferry and Costas D Maranas, 2011, "Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans.", BMC systems biology, 5, pp. 28
  • R Saha, P F Suthers and Costas D Maranas, 2011, "Zea mays iRS1563: a comprehensive genome-scale metabolic reconstruction of maize metabolism.", PloS one, 6, (7), pp. e21784
  • F.-G. Vital-Lopez, A. Armaou, Costas D Maranas and M. Hutnik, 2011, "Modeling the Effect of Chemotaxis In Glioblastoma Tumor Progression", AIChE J., 57, pp. 778-792
  • P. Khanna, E. Weidert, F. Vital-Lopez, A. Armaou, Costas D Maranas and C. Dong, 2011, "Model Simulations Reveal VCAM-1Augment PAK Activation Rates to Amplify p38 MAPK and VE-Cadherin Phosphorylation", Celular and Molecular Bioengineering, 4, (4), pp. 656-669
  • A R Zomorrodi and Costas D Maranas, 2010, "Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data.", BMC systems biology, 4, pp. 178
  • R J Pantazes and Costas D Maranas, 2010, "OptCDR: a general computational method for the design of antibody complementarity determining regions for targeted epitope binding.", Protein engineering, design & selection : PEDS, 23, (11), pp. 849-58
  • S Ranganathan and Costas D Maranas, 2010, "Microbial 1-butanol production: Identification of non-native production routes and in silico engineering interventions.", Biotechnology journal, 5, (7), pp. 716-25
  • S Ranganathan, P F Suthers and Costas D Maranas, 2010, "OptForce: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions.", PLoS computational biology, 6, (4), pp. e1000744
  • P F Suthers, Y J Chang and Costas D Maranas, 2010, "Improved computational performance of MFA using elementary metabolite units and flux coupling.", Metabolic engineering, 12, (2), pp. 123-8
  • M AbuOun, P F Suthers, G I Jones, B R Carter, M P Saunders, Costas D Maranas, M J Woodward and M F Anjum, 2009, "Genome scale reconstruction of a Salmonella metabolic model: comparison of similarity and differences with a commensal Escherichia coli strain.", The Journal of biological chemistry, 284, (43), pp. 29480-8
  • G A Khoury, H Fazelinia, J W Chin, R J Pantazes, Patrick C Cirino and Costas D Maranas, 2009, "Computational design of Candida boidinii xylose reductase for altered cofactor specificity.", Protein science : a publication of the Protein Society, 18, (10), pp. 2125-38
  • V S Kumar and Costas D Maranas, 2009, "GrowMatch: an automated method for reconciling in silico/in vivo growth predictions.", PLoS computational biology, 5, (3), pp. e1000308
  • P F Suthers, M S Dasika, V S Kumar, G Denisov, J I Glass and Costas D Maranas, 2009, "A genome-scale metabolic reconstruction of Mycoplasma genitalium, iPS189.", PLoS computational biology, 5, (2), pp. e1000285
  • J W Chin, R Khankal, C A Monroe, Costas D Maranas and Patrick C Cirino, 2009, "Analysis of NADPH supply during xylitol production by engineered Escherichia coli.", Biotechnology and bioengineering, 102, (1), pp. 209-20
  • H Fazelinia, Patrick C Cirino and Costas D Maranas, 2009, "OptGraft: A computational procedure for transferring a binding site onto an existing protein scaffold.", Protein science : a publication of the Protein Society, 18, (1), pp. 180-95
  • P F Suthers, A Zomorrodi and Costas D Maranas, 2009, "Genome-scale gene/reaction essentiality and synthetic lethality analysis.", Molecular systems biology, 5, pp. 301
  • S.-C. Lee, Y. J. Chang, D.-M. Shin, J. Han, M.-H. Seo, H. Fazelina, Costas D Maranas and H.-S. Kim, 2009, "Designing the substrate specificity of d-hydantoinase using a rational approach", Enzyme and Microbial Technology, 44, (3), pp. 170-175
  • Y Chang, P F Suthers and Costas D Maranas, 2008, "Identification of optimal measurement sets for complete flux elucidation in metabolic flux analysis experiments.", Biotechnology and bioengineering, 100, (6), pp. 1039-49
  • M S Dasika and Costas D Maranas, 2008, "OptCircuit: an optimization based method for computational design of genetic circuits.", BMC systems biology, 2, pp. 24
  • E P Gianchandani, M A Oberhardt, A P Burgard, Costas D Maranas and J A Papin, 2008, "Predicting biological system objectives de novo from internal state measurements.", BMC bioinformatics, 9, pp. 43
  • F. G. Vital-Lopez, A. Varshney, Costas D Maranas and A. Armaou, 2008, "Implication of dynamics in signal transduction and targeted disruption analyses of signaling networks", Comp. & Chem. Eng., 32, pp. 2065-2071
  • P F Suthers, A P Burgard, M S Dasika, F Nowroozi, S Van Dien, J D Keasling and Costas D Maranas, 2007, "Metabolic flux elucidation for large-scale models using 13C labeled isotopes.", Metabolic engineering, 9, (5-6), pp. 387-405
  • R J Pantazes, M C Saraf and Costas D Maranas, 2007, "Optimal protein library design using recombination or point mutations based on sequence-based scoring functions.", Protein engineering, design & selection : PEDS, 20, (8), pp. 361-73
  • V Satish Kumar, M S Dasika and Costas D Maranas, 2007, "Optimization based automated curation of metabolic reconstructions.", BMC bioinformatics, 8, pp. 212
  • H Fazelinia, Patrick C Cirino and Costas D Maranas, 2007, "Extending Iterative Protein Redesign and Optimization (IPRO) in protein library design for ligand specificity.", Biophysical journal, 92, (6), pp. 2120-30
  • C. Christensen, A. Gupta, Costas D Maranas and R. Albert, 2007, "Large-scale inference and Graph Theoretical Analysis of Gene-Regulatory Networks", B. Subtilis. Physica A, 373, pp. 796-810
  • F G Vital-Lopez, Antonios Armaou, E V Nikolaev and Costas D Maranas, 2006, "A computational procedure for optimal engineering interventions using kinetic models of metabolism.", Biotechnology progress, 22, (6), pp. 1507-17
  • M S Dasika, A Burgard and Costas D Maranas, 2006, "A computational framework for the topological analysis and targeted disruption of signal transduction networks.", Biophysical journal, 91, (1), pp. 382-98
  • M C Saraf, Gregory Moore, N M Goodey, V Y Cao, Stephen J Benkovic and Costas D Maranas, 2006, "IPRO: an iterative computational protein library redesign and optimization procedure.", Biophysical journal, 90, (11), pp. 4167-80
  • A Gupta, Costas D Maranas and Reka Albert, 2006, "Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites.", Bioinformatics (Oxford, England), 22, (2), pp. 209-14
  • P Pharkya and Costas D Maranas, 2006, "An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems.", Metabolic engineering, 8, (1), pp. 1-13
  • F. Vital-Lopez, Costas D Maranas and A. Armaou, 2006, "Bifurcation analysis of the metabolism of E. coli at optimal enzyme levels", Proceedings of the 2006 American Control Conference
  • S S Fong, A P Burgard, C D Herring, E M Knight, F R Blattner, Costas D Maranas and B O Palsson, 2005, "In silico design and adaptive evolution of Escherichia coli for production of lactic acid.", Biotechnology and bioengineering, 91, (5), pp. 643-8
  • M C Saraf, A Gupta and Costas D Maranas, 2005, "Design of combinatorial protein libraries of optimal size.", Proteins, 60, (4), pp. 769-77
  • M S Dasika, A Gupta and Costas D Maranas, 2005, "DEMSIM: a discrete event based mechanistic simulation platform for gene expression and regulation dynamics.", Journal of theoretical biology, 232, (1), pp. 55-69
  • E V Nikolaev, A P Burgard and Costas D Maranas, 2005, "Elucidation and structural analysis of conserved pools for genome-scale metabolic reconstructions.", Biophysical journal, 88, (1), pp. 37-49
  • Costas D Maranas and Min Ding, 2005, "Valuation and Design of Pharmaceutical R&D,", 51, (1), pp. 198-209
  • E. V. Nikolaev, P. Pharkya, Costas D Maranas and A. Armaou, 2005, "Optimal selection of enzyme levels using large-scale kinetic models", Proceedings of 16th International Federation of Automatic Control World Congress, pp. 6
  • P. Pharkya and Costas D Maranas, 2005, "A hierarchical framework for metabolic pathway discovery and strain design", FOSBE 2005 Proceedings, pp. 141-144
  • M. Rogers, M. Ding and Costas D Maranas, 2005, "Valuation of Pharmaceutical R&D Licensing Deals Using a Real Options Based Approach", AIChE Journal, 51, (1), pp. 198-209
  • A. Gupta, J. Varner and Costas D Maranas, 2005, "Large-Scale Inference of the Transcriptional Regulation of Bacillus Subtilis", Computers & Chemical Engineering, 29, pp. 565-576
  • P Pharkya, A P Burgard and Costas D Maranas, 2004, "OptStrain: a computational framework for redesign of microbial production systems.", Genome research, 14, (11), pp. 2367-76
  • M C Saraf, A R Horswill, Stephen J Benkovic and Costas D Maranas, 2004, "FamClash: a method for ranking the activity of engineered enzymes.", Proceedings of the National Academy of Sciences of the United States of America, 101, (12), pp. 4142-7
  • A P Burgard, E V Nikolaev, C H Schilling and Costas D Maranas, 2004, "Flux coupling analysis of genome-scale metabolic network reconstructions.", Genome research, 14, (2), pp. 301-12
  • M S Dasika, A Gupta and Costas D Maranas, 2004, "A mixed integer linear programming (MILP) framework for inferring time delay in gene regulatory networks.", Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, pp. 474-85
  • A. Burgard, P. Pharkya and Costas D Maranas, 2004, "A Computational Procedure for Suggesting Gene Knock-out Strategies for Microbial Strain Optimization", Bioengineering & Biotechnology, 84, pp. 887-899
  • G. L. Moore and Costas D Maranas, 2004, "Perspectives: Computational Challenges in Combinatorial Library Design for Protein Engineering", AIChE Journal, 50, pp. 262-272
  • M. Rogers, A. Gupta and Costas D Maranas, 2004, "Real Options Based Approaches to Decision Making Under Uncertainty", Process Systems Engineering Conference Proceedings
  • A. Lehmann and Costas D Maranas, 2004, "Molecular Design using Quantum Chemical Calculations for Property Estimation", Industrial & Engineering Chemistry Research, 43, pp. 3419-3432
  • M. J. Rogers, M. Ding and Costas D Maranas, 2004, "A Case Study on the Design of Pharmaceutical R&D Licensing Deals", FOCAPD Conference Proceedings, pp. 475-479
  • P Pharkya, A P Burgard and Costas D Maranas, 2003, "Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock.", Biotechnology and bioengineering, 84, (7), pp. 887-99
  • A P Burgard, P Pharkya and Costas D Maranas, 2003, "Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization.", Biotechnology and bioengineering, 84, (6), pp. 647-57
  • M C Saraf and Costas D Maranas, 2003, "Using a residue clash map to functionally characterize protein recombination hybrids.", Protein engineering, 16, (12), pp. 1025-34
  • A P Burgard and Costas D Maranas, 2003, "Optimization-based framework for inferring and testing hypothesized metabolic objective functions.", Biotechnology and bioengineering, 82, (6), pp. 670-7
  • M C Saraf, Gregory Moore and Costas D Maranas, 2003, "Using multiple sequence correlation analysis to characterize functionally important protein regions.", Protein engineering, 16, (6), pp. 397-406
  • Gregory Moore and Costas D Maranas, 2003, "Identifying residue-residue clashes in protein hybrids by using a second-order mean-field approach.", Proceedings of the National Academy of Sciences of the United States of America, 100, (9), pp. 5091-6
  • P Pharkya, E V Nikolaev and Costas D Maranas, 2003, "Review of the BRENDA Database.", Metabolic engineering, 5, (2), pp. 71-3
  • A. Gupta and Costas D Maranas, 2003, "Market -Based Pollution Abatement Strategies: Risk Management Using Emission Option Contracts", Industrial & Engineering Chemistry Research, 42, pp. 802-810
  • A. P. Burgard and Costas D Maranas, 2003, "An Optimization Based Framework for Inferring and Testing Hypothesized Metabolic Objective Functions", Biotechnology & Bioengineering, 82, pp. 670-670
  • A. Gupta and Costas D Maranas, 2003, "Managing Uncertainties in Chemical Process Industry (CIP) Supply Chain Planning", Computers & Chemical Engineering, 27, pp. 1219-1227
  • M. J. Rogers, A. Gupta and Costas D Maranas, 2003, "Risk Management in Options Based Pharmaceutical Portfolio Planning", Proceedings of Foundations of Computer-Aided Process Operations IV, pp. 241-244
  • Costas D Maranas, G. L. Moore, A. P. Burgard and A. Gupta, 2003, "Systems Engineering Challenges and Opportunities in Computational Biology", Proceedings of Foundations of Computer-Aided Process Operations IV, pp. 13-26
  • G. L. Moore and Costas D Maranas, 2003, Modeling and Optimization of Directed Evolution Protocols, Marcel Dekker, Inc.
  • Gregory Moore and Costas D Maranas, 2002, "Predicting out-of-sequence reassembly in DNA shuffling.", Journal of theoretical biology, 219, (1), pp. 9-17
  • Gregory Moore and Costas D Maranas, 2002, "eCodonOpt: a systematic computational framework for optimizing codon usage in directed evolution experiments.", Nucleic acids research, 30, (11), pp. 2407-16
  • M. J. Rogers, A. Gupta and Costas D Maranas, 2002, "Real Options Based Analysis of Optimal Pharmaceutical R&D Portfolios", Industrial & Engineering Chemistry Research, 41, pp. 6607-6620
  • S. Vaidyaraman and Costas D Maranas, 2002, "Synthesis of Mixed Refrigerant Cascade Cycles", Chemical Engineering Communications, 189, (8), pp. 1057-1078
  • A. P. Burgard and Costas D Maranas, 2002, "Review of the Biocatalysis/Biodegradation Database (UM-BBD)", Metabolic Engineering, 4, pp. 111-113
  • A P Burgard, Gregory Moore and Costas D Maranas, 2001, "Review of the TEIRESIAS-based tools of the IBM Bioinformatics and Pattern Discovery Group.", Metabolic engineering, 3, (4), pp. 285-8
  • S Lutz, M Ostermeier, Gregory Moore, Costas D Maranas and Stephen J Benkovic, 2001, "Creating multiple-crossover DNA libraries independent of sequence identity.", Proceedings of the National Academy of Sciences of the United States of America, 98, (20), pp. 11248-53
  • A P Burgard and Costas D Maranas, 2001, "Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions.", Biotechnology and bioengineering, 74, (5), pp. 364-75
  • A P Burgard, S Vaidyaraman and Costas D Maranas, 2001, "Minimal reaction sets for Escherichia coli metabolism under different growth requirements and uptake environments.", Biotechnology progress, 17, (5), pp. 791-7
  • Gregory Moore, Costas D Maranas, S Lutz and Stephen J Benkovic, 2001, "Predicting crossover generation in DNA shuffling.", Proceedings of the National Academy of Sciences of the United States of America, 98, (6), pp. 3226-31
  • A. P. Burgard and Costas D Maranas, 2001, "Review of Enzymes and Metabolic Pathways (EMP) database", Metabolic Engineering, 3, pp. 193-194
  • Costas D Maranas and A. P. Burgard, 2001, "Review of EcoCyc and MetaCyc web databases", Metabolic Engineering, 3, pp. 98-99
  • A. Gupta and Costas D Maranas, 2001, "Multiperiod Planning of Multisite Supply Chains Under Demand Uncertainty", European Symposium on Computer-Aided Process Engineering, 11, pp. 871-882
  • Costas D Maranas, 2001, "Optimization in Molecular Design and Bioinformatics", European Symposium on Computer-Aided Process Engineering, 11, pp. 1157-1164
  • Gregory Moore and Costas D Maranas, 2000, "Modeling DNA mutation and recombination for directed evolution experiments.", Journal of theoretical biology, 205, (3), pp. 483-503
  • A. Gupta, Costas D Maranas and C. M. McDonald, 2000, "Midterm Supply Chain Planning Under Uncertainty: Customer Demand Satisfaction and Inventory Management", Computers & Chemical Engineering, 24, pp. 2613-2621
  • A. Gupta and Costas D Maranas, 2000, "A Two-Stage Modeling and Solution Framework for Multisite Midterm Planning under Demand Uncertainty", Industrial & Engineering Chemistry Research, 39, pp. 3799-3813
  • G. L. Moore, Costas D Maranas, K. R. Gutshall and J. E. Brenshley, 2000, "Modeling and Optimization of DNA Recombination", Computers & Chemical Engineering, 24, pp. 693-699
  • S. Vaidyaraman and Costas D Maranas, 1999, "Simultaneous Refrigeration Cycle Synthesis and Refrigerant Selection", PRES'99, 2nd Conference on Process Integration, Modeling and Optimisation for Energy Saving and Pollution Reduction
  • K. V. Camarda, B. W. Bonnell, Costas D Maranas and R. Nagarajan, 1999, "Design of Surfactant Solutions with Optimal Macroscopic Properties", Computers & Chemical Engineering, 23, pp. 467-470
  • A. Gupta and Costas D Maranas, 1999, "A Hierarchical Lagrangean Relaxation Procedure for Solving Midterm Planning Problems", Industrial & Engineering Chemistry Research, 38, pp. 1937-1947
  • K. V. Camarda and Costas D Maranas, 1999, "Optimization in Polymer Design using Connectivity Indices", Industrial & Engineering Chemistry Research, 38, pp. 1884-1892
  • S. Vaidyaraman and Costas D Maranas, 1999, "Optimal Refrigeration Cycle Synthesis and Refrigerant Selection", AIChE Journal, 45, (5), pp. 997-1017
  • V. S. Raman and Costas D Maranas, 1998, "Optimization in product design with properties correlated with topological indices", Computers & Chemical Engineering, 22, (6), pp. 747-763
  • S. B. Petkov and Costas D Maranas, 1998, "Design of Multiproduct Batch Plants Under Demand Uncertainty with Staged Capacity Expansions", Computers & Chemical Engineering, 22, pp. 789-792
  • S. B. Petkov and Costas D Maranas, 1998, "Design of Single-Product Campaign Batch Plants under Demand Uncertainty", AlChE Journal, 44, (4), pp. 896-911
  • S B Petkov and Costas D Maranas, 1997, "Quantitative assessment of uncertainty in the optimization of metabolic pathways.", Biotechnology and bioengineering, 56, (2), pp. 145-61
  • S. B. Petkov and Costas D Maranas, 1997, "Multiperiod Planning and Scheduling of Multipurpose Batch Plants Under Demand Uncertainty", Industrial & Engineering Chemistry Research, 36, (11), pp. 4864-4881
  • I. P. Androulakis, Costas D Maranas and C. A. Floudas, 1997, "Prediction of Oligopeptide Conformations via Deterministic Global Optimization", Journal of Global Optimization, 11, pp. 1-34
  • Costas D Maranas, 1997, "Optimization Accounting for Property Prediction Uncertainty in Polymer Design", Computers & Chemical Engineering, 21, pp. 1019-1024
  • Costas D Maranas, 1997, "Optimal Molecular Design Under Property Prediction Uncertainty", AIChE Journal, 43, (5), pp. 1250-1264
  • Costas D Maranas and C. A. Floudas, 1997, "Global Optimization in Generalized Geometric Programming", Computers & Chemical Engineering, 21, (4), pp. 351-369
  • S. T. Harding, Costas D Maranas, C. M. McDonald and C. A. Floudas, 1997, "Locating All Homogeneous Azeotropes in Multicomponent Mixtures", Industrial & Engineering Chemistry Research, 36, (1), pp. 160-178
  • Costas D Maranas, I. P. Androulakis, C. A. Floudas, J. M. Mulvey and A. J. Berger, 1997, "Solving Long-Term Financial Planning Problems via Global Optimization", Journal of Economics Dynamics and Control, 21, (8/9), pp. 1405-1425
  • Costas D Maranas, 1996, "Optimal Computer-Aided Molecular Design: Application to Polymer Design", Industrial & Engineering Chemistry Research, 35, (10), pp. 3403-3414
  • C. S. Adjiman, I. P. Androulakis, Costas D Maranas and C. A. Floudas, 1996, "A Global Optimization Method, BB, for Process Design", Computers & Chemical Engineering, 20, pp. S419-S424
  • Costas D Maranas, C. M. McDonald, S. T. Harding and C. A. Floudas, 1996, "Locating All Azeotropes in Homogeneous Azeotropic Systems", Computers & Chemical Engineering, 20, pp. 413-418
  • Costas D Maranas, I. P. Androulakis and C. A. Floudas, 1995, "A Deterministic Global Optimization Approach for the Protein Folding Problem", Proc. of DIMACS Series in Discrete Mathematics and Theoretical Computer Science, 23, pp. 133-150
  • I. P. Androulakis, Costas D Maranas and C. A. Floudas, 1995, "A Global Optimization Method for General Constrained Nonconvex Problems", Journal of Global Optimization, 7, (4), pp. 337-363
  • Costas D Maranas and C. A. Floudas, 1995, "Finding All Solutions of Nonlinearly Constrained Systems of Equations", Journal of Global Optimization, 7, (2), pp. 143-182
  • Costas D Maranas, C. A. Floudas and P. N. Pardalos, 1995, "New Results in the Packing of Equal Circles in a Square", Discrete Mathematics, 142, pp. 287-293
 

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The Penn State Department of Chemical Engineering, established in 1948, is recognized as one of the largest and most influential chemical engineering departments in the nation.

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Department of Chemical Engineering

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