• Chang, Y., P.F Suthers and C.D. Maranas (2008), "Identification of optimal measurement sets for complete flux elucidation in MFA experiments," Biotechnology and Bioenginering, accepted.

  • Dasika, M.S. and C.D. Maranas (2008), "OptCircuit: An optimization based method for computational design of genetic circuits," BMC Systerms Biology, 2, 24.

  • Gianchandani, E.P., M.A. Oberhardt, A.P. Burgard, C.D. Maranas and J.A. Papin, (2008), "Predicting biological system objectives de novo from internal state measurements," BMC Bioinformatics, 9, 43.

  • Pantazes, R.J., M.C. Saraf and C.D. Maranas (2007), "Optimal protein library design using recombination or point mutations based on sequence-based scoring functions," Protein Engineering, Design & Selection, 20(8), 361-373.

  • Suthers, P.F, A.P. Burgard, M.S. Dasika, F. Nowroozi, S. Van Dien, J.D. Keasling and C.D. Maranas (2007), "Metabolic flux elucidation for large-scale models using 13C labeled isotopes," Metabolic Engineering, 9(5-6), 387-405.

  • Satish Kumar, V., M.S. Dasika and C.D. Maranas (2007), "Optimization based automated curation of metabolic reconstructions," BMC Bioinformatics, 8, 212.

  • Fazelinia, H., P.C. Cirino and C.D. Maranas (2007), "Extending Iterative Protein Redesign and Optimization (IPRO) in protein library design for ligand specificity," Biophysical Journal, 92(6), 2120-2130.

  • Vital-Lopez, F.G., C.D. Maranas and A. Armaou (2006), "A computational procedure for optimal engineering interventions using kinetic models of metabolism," Biotechnology Progress, 22(6), 1507-1517.

  • Christensen, C., A. Gupta, C.D. Maranas and R. Albert (2006), "Large-scale inference and graph theoretical analysis of gene-regulatory networks in B. subtilis," Physica A, 373, 796-810.

  • Dasika, M.S., A. Burgard and C.D. Maranas (2006), "A computational framework for the topological analysis and targeted disruption of signal transduction networks," Biophysical Journal, 91, 382-398.

  • Vital-Lopez, F.G., C.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, Minneapolis, MN.

  • Gupta, A., C.D. Maranas and R. Albert (2006), "Elucidation of Directionality for Co-Expressed Genes: Predicting Intra-Operon Termination Sites," Bioinformatics, 22, 209-214.

  • Saraf, M.C., G.L. Moore, N.M. Goodey, V.Y. Cao, S.J. Benkovic and Costas D. Maranas (2006), "IPRO: An Iterative Computational Protein Library Redesign and Optimization Procedure," Biophysical Journal, 90, 4167-4180.

  • Pharkya, P. and C.D. Maranas (2006), "An Optimization Framework for Identifying Reaction Activation/Inhibition or Elimination Candidates for Overproduction in Microbial Systems," Metabolic Engineering, 8, 1-13.

  • Saraf, M.C., Gupta, A., Maranas, C.D. (2005), "Design of combinatorial protein libraries of optimal size," Proteins, 60, 769-777.

  • Nikolaev, E.V., P. Pharkya, C. 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, Prague, Czech Republic, 6 pages.

  • Pharkya, P. and C.D. Maranas (2005), "A hierarchical framework for metabolic pathway discovery and strain design," FOSBE 2005 Proceedings, 141-144.

  • Fong, S.S., Burgard, A.P., Herring, C.D., Knight, E.M., Blattner, F.R., Maranas, C.D., Palsson, B.O. (2005), "In silico design and adaptive evolution of Escherichia coli for production of lactic acid," Biotechnol Bioeng., 91, 643-648.

  • Nikolaev, E.V., Burgard, A.P., Maranas, C.D. (2005), "Elucidation and Structural Analysis of Conserved Pools for Genome-Scale Metabolic Reconstructions," Biophysical Journal, 88, 37-49.

  • Rogers, M.J., M. Ding and C. D. Maranas (2005), " Valuation of Pharmaceutical R&D Licensing Deals Using a Real Options Based Approach," AIChE Journal, 51, 198-209.

  • Gupta, A., J.D. Varner and C.D. Maranas (2005), "Large-Scale Inference of the Transcriptional Regulation of Bacillus subtilis," Computers & Chemical Engineering, 29, 565-576.

  • Dasika, M.S., Gupta, A., Maranas, C.D. (2005), "DEMSIM: A Discrete Event based Mechanistic Simulation Platform for Gene Expression and Regulation Dynamics," Journal of Theoretical Biology, 232, 55-69.

  • Lehmann, A., Maranas, C.D. (2004), "Molecular Design Using Quantum Chemical Calculations for Property Estimation,"Ind. Eng. Chem. Res., 43, 3419-3432

  • Pharkya, P., Burgard, A.P., Maranas, C.D. (2004), "OptStrain: A Computational Framework for Redesign of Microbial Production Systems," Genome Research, 14(11), 2367-76. (See Universal Database)
    - Database Description
    - Universal Database

  • Dasika, M.S., Gupta, A., Maranas, C.D. (2004), "A Mixed Integer Linear Programming Framework (MILP) for Inferring Time Delay in Gene Regulatory Networks," Pacific Symposium on Biocomputing. [491 kb]

  • Saraf, M.C., Horswill, A.R., Benkovic, S.J., Maranas, C.D. (2004), "FamClash: A method for ranking the activity of engineered enzymes," Proc. Natl. Acad. Sci. USA, 101, 4142-4147. [381 kb] (See Commentary )
    - Penn State press release
    - ScienceDaily Magazine story
    - Bio.com news release

  • Rogers, M.J., M. Ding and C. D. Maranas (2004), "A Case Study on the Design of Pharmaceutical R&D Licensing Deals," FOCAPD Conference Proceedings, 475-479.

  • Moore, G.L., Maranas, C.D. (2004), "Computational Challenges in Combinatorial Library Design for Protein Engineering," AIChE Journal, 50, 262-272. [233 kb]

  • Burgard, A.P.#, E.V. Nikolaev #, C.H. Schilling, Maranas, C.D. (2004), "Flux Coupling Analysis of Genome-scale Metabolic Reconstructions," Genome Research, 14, 301-312. [600 kb] # These authors contributed equally to this work.

  • Rogers, M.J., A. Gupta, Maranas, C.D. (2003), "Real Options Based Approaches to Decision Making under Uncertainty," Process Systems Engineering

  • Saraf, M.C., Maranas, C.D. (2003), "Using a Residue Clash Map to Functionally Characterize Protein Recombination Hybrids," Protein Engineering, 16(12), 1025-1034. [447 kb]

  • Pharkya, P., A.P. Burgard, Maranas, C.D. (2003), "Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock," Biotechnology and Bioengineering, 84, 887-899. [1,411 kb]

  • Moore, G.L., Maranas, C.D. (2003), "Modeling and Optimization of Directed Evolution Protocols." Enzyme Functionality: Design, Engineering, and Screening, edited by A. Svendsen (pp. 185-212). New York, NY: Marcel Dekker, Inc.

  • Gupta, A., Maranas, C.D. (2003), "Managing demand uncertainty in supply chain planning," Computers and Chemical Engineering, 27, 1219-1227. [356 kb]

  • Pharkya, P., E.V. Nikolaev, Maranas, C.D. (2003), "Review of the BRENDA Database," Metabolic Engineering, 5, 71-73. [103 kb]

  • Burgard, A.P., Pharkya, P., Maranas, C.D. (2003), "OptKnock: A Bilevel Programming Framework for Identifying Gene Knockout Strategies for Microbial Strain Optimization," Biotechnology and Bioengineering, 84, 647-657. [221 kb]

  • Saraf, M.C., Moore, G.L., Maranas, C.D. (2003), "Using multiple sequence correlation analysis to characterize functionally important protein regions," Protein Engineering, 16, 397-406. [352 kb]

  • Moore, G.L., Maranas, C.D. (2003), "Identifying Residue-Residue Clashes in Protein Hybrids by Using a Second-order Mean-field Approach," Proc. Natl. Acad. Sci. USA, 100, 5091-5096. [256 kb] (download archived supplemental information [1751 kb])
    - Chemical & Engineering News

  • Burgard, A.P., Maranas, C.D. (2003), "Optimization-Based Framework for Inferring and Testing Hypothesized Metabolic Objective Functions," Biotechnology and Bioengineering, 82, 670-677. [221 kb]

  • Gupta, A., Maranas, C.D. (2003), "Market-Based Pollution Abatement Strategies: Risk Management Using Emission Option Contracts," Industrial & Engineering Chemistry Research, 42 802-810. [103 kb]

  • Maranas, C.D., G.L. Moore, A.P. Burgard, and A. Gupta (2003), "Systems Engineering Challenges And Opportunities In Computational Biology," FOCAPO 2003, 13-26. [418 kb]

  • Rogers, M.J., Gupta, A., Maranas, C.D. (2003), "Risk Management in Real Options Based Pharmaceutical Portfolio Planning," FOCAPO 2003, 241-244. [195 kb]

  • Rogers, M.J., Gupta, A., Maranas, C.D. (2002), "Real Options Based Analysis of Optimal Pharmaceutical R&D Portfolios," Industrial & Engineering Chemistry Research, 41, 6607-6620. [210 kb]

  • Moore, G.L., Maranas, C.D. (2002), "Predicting Out-of-Sequence Reassembly in DNA Shuffling," Journal of Theoretical Biology, 219, 9-17. [502 kb]

  • Vaidyaraman, S., Maranas, C.D. (2002), "Synthesis of Mixed Refrigerant Cascade Cycles," Chemical Engineering Communications, 189, 1057-1078.

  • Moore, G.L., Maranas, C.D. (2002), "eCodonOpt: A Systematic Computational Framework for Optimizing Codon Usage in Directed Evolution Experiments," Nucleic Acids Research, 30, 2407-2416. [1113 kb] (download Supplementary material)

  • Burgard, A.P., Maranas, C.D. (2002), "Review of the Biocatalysis/Biodegradation Database (UM-BBD)," Metabolic Engineering, 4, 111-113. [60 kb]

  • Burgard, A.P., S. Vaidyaraman, Maranas, C.D. (2001), "Minimal Reaction Sets for Escherichia Coli Metabolism under Different Growth Requirements and Uptake Environments," Biotechnology Progress, 17, 791-797. [75 kb]

  • Burgard, A.P., G.L. Moore, and C. D. Maranas (2001), "Review of the TEIRESIAS-based Tools of the IBM Bioinformatics and Pattern Discovery Group," Metabolic Engineering, 3, 285-288. [133 kb]

  • Lutz, S., M. Ostermeier, G.L. Moore, C.D. Maranas, and S.J. Benkovic (2001), "Creating multiple-crossover DNA libraries independent of sequence identity," Proc. Natl. Acad. Sci. USA, 98, 11248-11253. [385 kb] (download supplemental Table 1, Figure 9, Figure 10)

  • Burgard, A.P., Maranas, C.D. (2001), "Review of Enzymes and Metabolic Pathways (EMP) database," Metabolic Engineering, 3, 193-194. [105 kb]

  • Burgard, A.P., Maranas, C.D. (2001), "Probing the Performance Limits of the Escherichia coli Metabolic Network Subject to Gene Additions or Deletions," Biotechnology and Bioengineering, 74, 364-375. [238 kb]

  • Gupta, A., Maranas, C.D. (2001), "Multiperiod Planning of Multisite Supply Chains Under Demand Uncertainty," European Symposium on Computer Aided Process Engineering, 11, 871-882. [935 kb]

  • C.D. Maranas (2001), "Optimization in Molecular Design and Bioinformatics," European Symposium on Computer Aided Process Engineering, 11, 1157-1164. [129 kb]

  • Maranas, C.D. and A.P. Burgard (2001), "Review of EcoCyc and MetaCyc databases," Metabolic Engineering, 3, 98-99. [70 kb]

  • Moore, G.L., C.D. Maranas, S. Lutz, and S.J. Benkovic (2001), "Predicting Crossover Generation in DNA Shuffling," Proc. Natl. Acad. Sci. USA 98, 3226-3231. [196 kb] (download Supplementary material)
    - Penn State press release
    - Collegian newspaper story
    - ScienceDaily Magazine story
    - Bioresearch Online

  • Gupta, A., C.D. Maranas, and C.M. McDonald (2000), "Midterm Supply Chain Planning Under Demand Uncertainty: Customer Demand Satisfaction and Inventory Management," Computers and Chemical Engineering, 24, 2613-2621. [156 kb]

  • Gupta, A., Maranas, C.D. (2000), "A Two-Stage Modeling and Solution Framework for Multisite Midterm Planning under Demand Uncertainty," Industrial & Engineering Chemistry Research 39, 3799-3813. [169 kb]

  • Moore, G.L., Maranas, C.D. (2000), "Modeling DNA Mutation and Recombination for Directed Evolution Experiments," Journal of Theoretical Biology 205, 483-503. [425 kb]

  • Moore, G.L., C.D. Maranas, K.R. Gutshall, and J.E. Brenchley (2000), "Modeling and Optimization of DNA Recombination," Computers and Chemical Engineering 24, 693-699. [251 kb]

  • Vaidyaraman, S., Maranas, C.D. (1999), "Simultaneous Refrigeration Cycle Synthesis and Refrigerant Selection," In proceedings of PRES'99, 2nd Conference on Process Integration, Modeling and Optimisation for Energy Saving and Pollution Reduction, May 31-June 2, Budapest, Hungary. [164 kb]

  • Camarda, K.V., B.W. Bonnell, C.D. Maranas, and R. Nagarajan (1999), "Design of Surfactant Solutions with Optimal Macroscopic Properties," Computers and Chemical Engineering 23, Suppl., 467-470. [45 kb]

  • Gupta, A., Maranas, C.D. (1999), "A Hierarchical Lagrangean Relaxation Procedure for Solving Midterm Planning Problems," Industrial & Engineering Chemistry Research 38, 1937-1947. [332 kb]

  • Camarda, K.V., Maranas, C.D. (1999), "Optimization in Polymer Design using Connectivity Indices," Industrial & Engineering Chemistry Research 38, 1884-1892. [193 kb]

  • Vaidyaraman, S., Maranas, C.D. (1999), "Optimal Refrigeration Cycle Synthesis and Refrigerant Selection," AIChE Journal 45(5), 997-1017. [657 kb]

  • Raman, V.S., Maranas, C.D. (1998), "Optimization in product design with properties correlated with topological indices," Computers and Chemical Engineering 22(6), 747-763. [312 kb]

  • Petkov, S.B., Maranas, C.D. (1998), "Design of Multiproduct Batch Plants Under Demand Uncertainty with Staged Capacity Expansions," Computers and Chemical Engineering 22, Suppl., 789-792. [102 kb]

  • Petkov, S.B., Maranas, C.D. (1998), "Design of Single-Product Campaign Batch Plants under Demand Uncertainty," AIChE Journal 44(4), 896-911. [416 kb]

  • Petkov, S.B., Maranas, C.D. (1997), "Multiperiod Planning and Scheduling of Multipurpose Batch Plants Under Demand Uncertainty," Industrial & Engineering Chemistry Research 36(11), 4864-4881. [454 kb]

  • Petkov, S.B., Maranas, C.D. (1997), "Quantitative Assessment of Uncertainty in the Optimization of Metabolic Pathways," Biotechnology and Bioengineering 56(2), 145-161. [426 kb]

  • Maranas, C.D. (1997), "Optimization Accounting for Property Prediction Uncertainty in Polymer Design," Computers and Chemical Engineering 21, Suppl., 1019-1024. [94 kb]

  • Maranas, C.D. (1997), "Optimal Molecular Design Under Property Prediction Uncertainty," AIChE Journal 43(5), 1250-1264. [454 kb]

  • Androulakis, I.P., C.D. Maranas ,and C.A. Floudas (1997), "Prediction of Oligopeptide Conformations via Deterministic Global Optimization," Journal of Global Optimization 11, 1-34.

  • Maranas, C.D. and C.A. Floudas (1997), "Global Optimization in Generalized Geometric Programming," Computers and Chemical Engineering 21(4), 351-369.

  • Harding, S.T., C.D. Maranas, C.M. McDonald, and C.A. Floudas (1997), "Locating All Homogeneous Azeotropes in Multicomponent Mixtures," Industrial & Engineering Chemistry Research 36(1), 160-178.

  • Maranas, C.D., 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), 1405-1425.

  • Maranas, C.D. (1996), "Optimal Computer-Aided Molecular Design: Application to Polymer Design," Industrial & Engineering Chemistry Research 35(10), 3403-3414. [317 kb]

  • Adjiman, C.S., I.P. Androulakis, C.D. Maranas, and C.A. Floudas (1996), "A Global Optimization Method, alphaBB, for Process Design," Computers and Chemical Engineering 20, Suppl. A, S419-S424.

  • Maranas, C.D, C.M. McDonald, S.T. Harding, and C.A. Floudas (1996), "Locating All Azeotropes in Homogeneous Azeotropic Systems," Computers and Chemical Engineering, 20, Suppl. A, S413-S418.

  • Maranas, C.D., 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, 133-150.

  • Androulakis, I.P., C.D. Maranas, and C.A. Floudas (1995), "alphaBB: A Global Optimization Method for General Constrained Nonconvex Problems," Journal of Global Optimization 7(4), 337-363.

  • Maranas, C.D. and C.A. Floudas (1995), "Finding All Solutions of Nonlinearly Constrained Systems of Equations," Journal of Global Optimization 7(2), 143-182.

  • Maranas, C.D., C.A. Floudas, and P.N. Pardalos (1995), "New Results in the Packing of Equal Circles in a Square," Discrete Mathematics 142, 287-293.

  • Maranas, C.D. and C.A. Floudas (1994), "A Deterministic Global Optimization Approach for Molecular Structure Determination," Journal of Chemical Physics 100(2), 1247-1261.

  • Maranas, C.D. and C.A. Floudas (1994), "Global Minimum Potential Energy Conformations of Small Molecules," Journal of Global Optimization 4, 135-170.

  • Maranas, C.D. and C.A. Floudas, (1993), "A Global Optimization Method For Weber's Problem With Attraction And Repulsion," Proc. of Large Scale Optimization: State of the Art Conference, (February 15-17, 1993, Florida University), Kluwer Academic Publishers B.V., 259-293.

  • Maranas, C.D. and C.A. Floudas (1993), "Global Optimization for Molecular Conformation Problems," Annals of Operations Research 42, 85-117.

  • Maranas, C.D. and C.A. Floudas (1992), "A Global Optimization Approach for Lennard-Jones Microclusters," Journal of Chemical Physics 97(10), 7667-7678.

  • Pistikopoulos, E.N., T.A. Mazzuchi, C.D. Maranas, and T.V Thomaidis (1991), "Simultaneous Assessment of Flexibility, Reliability and Availability for In-Line Blending Systems: A Unified Framework for Analysis and Retrofit Design," Proc. of Fourth International Symposium on Process Systems Engineering (PSE 91), 1.4.1-1.4.16.