Madhukar S. Dasika, Anthony Burgard, Costas D. Maranas
ABSTRACT In this article, optimization-based frameworks are introduced for elucidating the input-output structure of signaling networks and for pinpointing targeted disruptions leading to the...
Anshuman Gupta, Costas D. Maranas, Réka Albert
Figure S1 shows the co-expression network at the chosen similarity threshold value of 0.90. The network was composed of 262 nodes connected by a total of 530 edges while the remaining 484 nodes were...
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Anshuman Gupta, Costas D. Maranas, Réka Albert
Vol. 22 no. 2 2006, pages 209–214 doi:10.1093/bioinformatics/bti780 Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites
Priti Pharkya, Costas D. Maranas
In this contribution, we will discuss a hierarchical procedure termed OptStrain aimed at guiding pathway modifications, through pathway additions and deletions, of microbial networks for the...
OptCircuit: An optimization based method for computational design of genetic circuits (2008)
Dasika, Madhukar S, Maranas, Costas D
Abstract Background Recent years has witnessed an increasing number of studies on constructing simple synthetic genetic circuits that exhibit desired properties such as oscillatory behavior, inducer...
Predicting biological system objectives de novo from internal state measurements (2008)
Gianchandani, Erwin P, Oberhardt, Matthew A, Burgard, Anthony P, Maranas, Costas D, Papin, Jason A
Abstract Background Optimization theory has been applied to complex biological systems to interrogate network properties and develop and refine metabolic engineering strategies. For example, methods...
BMC Systems Biology BioMed Central Methodology article (2008)
Madhukar S Dasika, Costas D Maranas, Madhukar S Dasika, Costas D Maranas
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Background: Recent years has witnessed an increasing number of studies on...
Pantazes, Robert J., Saraf, Manish C., Maranas, Costas D.
In this paper, we introduce and test two new sequence-based protein scoring systems (i.e. S1, S2) for assessing the likelihood that a given protein hybrid will be functional. By binning together...
Optimization based automated curation of metabolic reconstructions (2007)
Satish Kumar, Vinay, Dasika, Madhukar S, Maranas, Costas D
Abstract Background Currently, there exists tens of different microbial and eukaryotic metabolic reconstructions (e.g., Escherichia coli, Saccharomyces cerevisiae , Bacillus subtilis ) with many more...
This un-edited manuscript has been accepted for publication in (2006)
Madhukar S. Dasika, Anthony Burgard, Costas D. Maranas
Biophysical Journal and is freely available on BioFast at
Gupta, Anshuman, Maranas, Costas D., Albert, Réka
Motivation: In this paper, we present a novel framework for inferring regulatory and sequence-level information from gene co-expression networks. The key idea of our methodology is the systematic...
Gupta, Anshuman, Maranas, Costas D., Albert, Reka
We present a novel framework for inferring regulatory and sequence-level information from gene co-expression networks. The key idea of our methodology is the systematic integration of network...
Evgeni V. Nikolaev, Anthony P. Burgard, Costas D. Maranas
ABSTRACT In this article, we introduce metabolite concentration coupling analysis (MCCA) to study conservation relationships for metabolite concentrations in genome-scale metabolic networks. The...
Gupta, Anshuman, Maranas, Costas D., Albert, Réka
Motivation: In this paper, we present a novel framework for inferring regulatory and sequence-level information from gene co-expression networks. The key idea of our methodology is the systematic...
Flux Coupling Analysis of Genome-Scale Metabolic Network Reconstructions (2004)
Burgard, Anthony P., Nikolaev, Evgeni V., Schilling, Christophe H., Maranas, Costas D.
In this paper, we introduce the Flux Coupling Finder (FCF) framework for elucidating the topological and flux connectivity features of genome-scale metabolic networks. The framework is demonstrated...
OptStrain: A computational framework for redesign of microbial production systems (2004)
Pharkya, Priti, Burgard, Anthony P., Maranas, Costas D.
This paper introduces the hierarchical computational framework OptStrain aimed at guiding pathway modifications, through reaction additions and deletions, of microbial networks for the overproduction...
Flux Coupling Analysis of Genome-Scale Metabolic Network Reconstructions (2004)
Burgard, Anthony P., Nikolaev, Evgeni V., Schilling, Christophe H., Maranas, Costas D.
In this paper, we introduce the Flux Coupling Finder (FCF) framework for elucidating the topological and flux connectivity features of genome-scale metabolic networks. The framework is demonstrated...
Abstract Managing demand uncertainty in supply chain planning (2003)
Anshuman Gupta, Costas D. Maranas
In this work, we provide an overview of our previously published works on incorporating demand uncertainty in midterm planning of multisite supply chains. A stochastic programming based approach is...
Saraf, Manish C., Moore, Gregory L., Maranas, Costas D.
Protein co‐evolution under structural and functional constraints necessitates the preservation of important interactions. Identifying functionally important regions poses many obstacles in...
Using a residue clash map to functionally characterize protein recombination hybrids (2003)
Saraf, Manish C., Maranas, Costas D.
In this article, we introduce a rapid, protein sequence database‐driven approach to characterize all contacting residue pairs present in protein hybrids for inconsistency with protein family...
Moore, Gregory L., Maranas, Costas D.
We present a systematic computational framework, eCodonOpt, for designing parental DNA sequences for directed evolution experiments through codon usage optimization. Given a set of homologous...
Anthony P. Burgard, Costas D. Maranas
optimization-based procedure for studying the response of metabolic networks after gene knockouts or additions is introduced and applied to a linear flux balance analysis (FBA) Escherichia coli...
Global Optimization in Generalized Geometric Programming (1997)
Costas D. Maranas, Christodoulos A. Floudas
A deterministic global optimization algorithm is proposed for locating the global minimum of generalized geometric (signomial) problems (GGP). By utilizing an exponential variable transformation the...
New Results In The Packing Of Equal Circles In A Square (1995)
Costas D. Maranas, Christodoulos A. Floudas, Panos M. Pardalos
The problem of finding the maximum diameter of n equal mutually disjoint circles inside a unit square is addressed in this paper. Exact solutions exist for only n = 1; : : : ; 9; 10; 16; 25; 36 while...
A Global Optimization Approach for Lennard-Jones Microclusters (1992)
Costas D. Maranas, Christodoulos A. Floudas
A global optimization approach is proposed for finding the global minimum energy configuration of Lennard--Jones microclusters. First, the original nonconvex total potential energy function, composed...
Predicting crossover generation in DNA shuffling
Moore, Gregory L., Maranas, Costas D., Lutz, Stefan, Benkovic, Stephen J.
We introduce a quantitative framework for assessing the generation of crossovers in DNA shuffling experiments. The approach uses free energy calculations and complete sequence information to model...
Creating multiple-crossover DNA libraries independent of sequence identity
Lutz, Stefan, Ostermeier, Marc, Moore, Gregory L., Maranas, Costas D., Benkovic, Stephen J.
We have developed, experimentally implemented, and modeled in silico a methodology named SCRATCHY that enables the combinatorial engineering of target proteins, independent of sequence identity. The...
Moore, Gregory L., Maranas, Costas D.
We present a systematic computational framework, eCodonOpt, for designing parental DNA sequences for directed evolution experiments through codon usage optimization. Given a set of homologous...
Identifying residue–residue clashes in protein hybrids by using a second-order mean-field approach
Moore, Gregory L., Maranas, Costas D.
In this article, a second-order mean-field-based approach is introduced for characterizing the complete set of residue–residue couplings consistent with a given protein structure. This information...
Flux Coupling Analysis of Genome-Scale Metabolic Network Reconstructions
Burgard, Anthony P., Nikolaev, Evgeni V., Schilling, Christophe H., Maranas, Costas D.
In this paper, we introduce the Flux Coupling Finder (FCF) framework for elucidating the topological and flux connectivity features of genome-scale metabolic networks. The framework is demonstrated...
FamClash: A method for ranking the activity of engineered enzymes
Saraf, Manish C., Horswill, Alexander R., Benkovic, Stephen J., Maranas, Costas D.
This article introduces the computational procedure FamClash for analyzing incompatibilities in engineered protein hybrids by using protein family sequence data. All pairs of residue positions in the...
OptStrain: A computational framework for redesign of microbial production systems
Pharkya, Priti, Burgard, Anthony P., Maranas, Costas D.
This paper introduces the hierarchical computational framework OptStrain aimed at guiding pathway modifications, through reaction additions and deletions, of microbial networks for the overproduction...
Elucidation and Structural Analysis of Conserved Pools for Genome-Scale Metabolic Reconstructions
Nikolaev, Evgeni V., Burgard, Anthony P., Maranas, Costas D.
In this article, we introduce metabolite concentration coupling analysis (MCCA) to study conservation relationships for metabolite concentrations in genome-scale metabolic networks. The analysis...
Predicting crossover generation in DNA shuffling
Moore, Gregory L., Maranas, Costas D., Lutz, Stefan, Benkovic, Stephen J.
We introduce a quantitative framework for assessing the generation of crossovers in DNA shuffling experiments. The approach uses free energy calculations and complete sequence information to model...
Creating multiple-crossover DNA libraries independent of sequence identity
Lutz, Stefan, Ostermeier, Marc, Moore, Gregory L., Maranas, Costas D., Benkovic, Stephen J.
We have developed, experimentally implemented, and modeled in silico a methodology named SCRATCHY that enables the combinatorial engineering of target proteins, independent of sequence identity. The...
Moore, Gregory L., Maranas, Costas D.
We present a systematic computational framework, eCodonOpt, for designing parental DNA sequences for directed evolution experiments through codon usage optimization. Given a set of homologous...
Identifying residue–residue clashes in protein hybrids by using a second-order mean-field approach
Moore, Gregory L., Maranas, Costas D.
In this article, a second-order mean-field-based approach is introduced for characterizing the complete set of residue–residue couplings consistent with a given protein structure. This information...
Flux Coupling Analysis of Genome-Scale Metabolic Network Reconstructions
Burgard, Anthony P., Nikolaev, Evgeni V., Schilling, Christophe H., Maranas, Costas D.
In this paper, we introduce the Flux Coupling Finder (FCF) framework for elucidating the topological and flux connectivity features of genome-scale metabolic networks. The framework is demonstrated...
FamClash: A method for ranking the activity of engineered enzymes
Saraf, Manish C., Horswill, Alexander R., Benkovic, Stephen J., Maranas, Costas D.
This article introduces the computational procedure FamClash for analyzing incompatibilities in engineered protein hybrids by using protein family sequence data. All pairs of residue positions in the...
OptStrain: A computational framework for redesign of microbial production systems
Pharkya, Priti, Burgard, Anthony P., Maranas, Costas D.
This paper introduces the hierarchical computational framework OptStrain aimed at guiding pathway modifications, through reaction additions and deletions, of microbial networks for the overproduction...
Elucidation and Structural Analysis of Conserved Pools for Genome-Scale Metabolic Reconstructions
Nikolaev, Evgeni V., Burgard, Anthony P., Maranas, Costas D.
In this article, we introduce metabolite concentration coupling analysis (MCCA) to study conservation relationships for metabolite concentrations in genome-scale metabolic networks. The analysis...
IPRO: An Iterative Computational Protein Library Redesign and Optimization Procedure
Saraf, Manish C., Moore, Gregory L., Goodey, Nina M., Cao, Vania Y., Benkovic, Stephen J., Maranas, Costas D.
A number of computational approaches have been developed to reengineer promising chimeric proteins one at a time through targeted point mutations. In this article, we introduce the computational...
Dasika, Madhukar S., Burgard, Anthony, Maranas, Costas D.
In this article, optimization-based frameworks are introduced for elucidating the input-output structure of signaling networks and for pinpointing targeted disruptions leading to the silencing of...
Predicting biological system objectives de novo from internal state measurements
Gianchandani, Erwin P, Oberhardt, Matthew A, Burgard, Anthony P, Maranas, Costas D, Papin, Jason A
Fazelinia, Hossein, Cirino, Patrick C., Maranas, Costas D.
In this article we extend the Iterative Protein Redesign and Optimization (IPRO) framework for the design of protein libraries with targeted ligand specificity. Mutations that minimize the binding...
A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189
Suthers, Patrick F., Dasika, Madhukar S., Kumar, Vinay Satish, Denisov, Gennady, Glass, John I., Maranas, Costas D.
With a genome size of ∼580 kb and approximately 480 protein coding regions, Mycoplasma genitalium is one of the smallest known self-replicating organisms and, additionally, has extremely fastidious...
GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions
Kumar, Vinay Satish, Maranas, Costas D.
Genome-scale metabolic reconstructions are typically validated by comparing in silico growth predictions across different mutants utilizing different carbon sources with in vivo growth data. This...
Genome-scale gene/reaction essentiality and synthetic lethality analysis
Suthers, Patrick F, Zomorrodi, Alireza, Maranas, Costas D
Synthetic lethals are to pairs of non-essential genes whose simultaneous deletion prohibits growth. One can extend the concept of synthetic lethality by considering gene groups of increasing size...