Costas Maranas All publications ( 31 ) Chin JW. Khankal R. Monroe CA. Maranas CD. Cirino PC. Analysis of NADPH supply during xylitol production by engineered Escherichia coli. 2008 Jul 22. Biotechnol Bioeng. . Chang Y. Suthers PF. Maranas CD. Identification of optimal measurement sets for complete flux elucidation in metabolic flux analysis experiments. 2008 Aug 15. Biotechnol Bioeng. 100(6):1039-49. Suthers PF. Burgard AP. Dasika MS. Nowroozi F. Van Dien S. Keasling JD. Maranas CD. Metabolic flux elucidation for large-scale models using (13)C labeled isotopes. 2007 May 29. Metab Eng. . Fazelinia H. Cirino PC. Maranas CD. Extending Iterative Protein Redesign and Optimization (IPRO) in protein library design for ligand specificity. 2007 Mar 15. Biophys J. 92(6):2120-30. Satish Kumar V. Dasika MS. Maranas CD. Optimization based automated curation of metabolic reconstructions. 2007. BMC Bioinformatics. 8:212. Vital-Lopez FG. Armaou A. Nikolaev EV. Maranas CD. A computational procedure for optimal engineering interventions using kinetic models of metabolism. 2006 Nov-Dec. Biotechnol Prog. 22(6):1507-17. Saraf MC. Moore GL. Goodey NM. Cao VY. Benkovic SJ. Maranas CD. IPRO: an iterative computational protein library redesign and optimization procedure. 2006 Jun 1. Biophys J. 90(11):4167-80. National Institute of General Medical Sciences Dasika MS. Burgard A. Maranas CD. A computational framework for the topological analysis and targeted disruption of signal transduction networks. 2006 Jul 1. Biophys J. 91(1):382-98. Gupta A. Maranas CD. Albert R. Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites. 2006 Jan 15. Bioinformatics. 22(2):209-14. Pharkya P. Maranas CD. An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems. 2006 Jan. Metab Eng. 8(1):1-13. Saraf MC. Gupta A. Maranas CD. Design of combinatorial protein libraries of optimal size. 2005 Sep 1. Proteins. 60(4):769-77. Dasika MS. Gupta A. Maranas CD. DEMSIM: a discrete event based mechanistic simulation platform for gene expression and regulation dynamics. 2005 Jan 7. J Theor Biol. 232(1):55-69. Nikolaev EV. Burgard AP. Maranas CD. Elucidation and structural analysis of conserved pools for genome-scale metabolic reconstructions. 2005 Jan. Biophys J. 88(1):37-49. Pharkya P. Burgard AP. Maranas CD. OptStrain: a computational framework for redesign of microbial production systems. 2004 Nov. Genome Res. 14(11):2367-76. Saraf MC. Horswill AR. Benkovic SJ. Maranas CD. FamClash: a method for ranking the activity of engineered enzymes. 2004 Mar 23. Proc Natl Acad Sci U S A. 101(12):4142-7. National Institute of General Medical Sciences Burgard AP. Nikolaev EV. Schilling CH. Maranas CD. Flux coupling analysis of genome-scale metabolic network reconstructions. 2004 Feb. Genome Res. 14(2):301-12. Dasika MS. Gupta A. Maranas CD. A mixed integer linear programming (MILP) framework for inferring time delay in gene regulatory networks. 2004. Pac Symp Biocomput. 474-85. Burgard AP. Maranas CD. Optimization-based framework for inferring and testing hypothesized metabolic objective functions. 2003 Jun 20. Biotechnol Bioeng. 82(6):670-7. Saraf MC. Moore GL. Maranas CD. Using multiple sequence correlation analysis to characterize functionally important protein regions. 2003 Jun. Protein Eng. 16(6):397-406. Pharkya P. Burgard AP. Maranas CD. Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock. 2003 Dec 30. Biotechnol Bioeng. 84(7):887-99. Burgard AP. Pharkya P. Maranas CD. Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. 2003 Dec 20. Biotechnol Bioeng. 84(6):647-57. Saraf MC. Maranas CD. Using a residue clash map to functionally characterize protein recombination hybrids. 2003 Dec. Protein Eng. 16(12):1025-34. Moore GL. Maranas CD. Identifying residue-residue clashes in protein hybrids by using a second-order mean-field approach. 2003 Apr 29. Proc Natl Acad Sci U S A. 100(9):5091-6. Pharkya P. Nikolaev EV. Maranas CD. Review of the BRENDA Database. 2003 Apr. Metab Eng. 5(2):71-3. Moore GL. Maranas CD. Predicting out-of-sequence reassembly in DNA shuffling. 2002 Nov 7. J Theor Biol. 219(1):9-17. Moore GL. Maranas CD. eCodonOpt: a systematic computational framework for optimizing codon usage in directed evolution experiments. 2002 Jun 1. Nucleic Acids Res. 30(11):2407-16. Burgard AP. Vaidyaraman S. Maranas CD. Minimal reaction sets for Escherichia coli metabolism under different growth requirements and uptake environments. 2001 Sep-Oct. Biotechnol Prog. 17(5):791-7. Burgard AP. Maranas CD. Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions. 2001 Sep 5. Biotechnol Bioeng. 74(5):364-75. Burgard AP. Moore GL. Maranas CD. Review of the TEIRESIAS-based tools of the IBM Bioinformatics and Pattern Discovery Group. 2001 Oct. Metab Eng. 3(4):285-8. Moore GL. Maranas CD. Lutz S. Benkovic SJ. Predicting crossover generation in DNA shuffling. 2001 Mar 13. Proc Natl Acad Sci U S A. 98(6):3226-31. Moore GL. Maranas CD. Modeling DNA mutation and recombination for directed evolution experiments. 2000 Aug 7. J Theor Biol. 205(3):483-503.