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List of works by Costas D. Maranas

A computational framework for the topological analysis and targeted disruption of signal transduction networks.

scientific article

A computational procedure for optimal engineering interventions using kinetic models of metabolism

scientific article published in November 2006

A diurnal flux balance model of Synechocystis sp. PCC 6803 metabolism

scientific article published on 24 January 2019

A genome-scale metabolic reconstruction of Mycoplasma genitalium, iPS189

scientific article

A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data

scientific article

An integrated computational and experimental study for overproducing fatty acids in Escherichia coli.

scientific article

An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems

scientific article

Analysis of NADPH supply during xylitol production by engineered Escherichia coli

scientific article published in January 2009

Assessing the metabolic impact of nitrogen availability using a compartmentalized maize leaf genome-scale model

scientific article published on 23 September 2014

CLCA: maximum common molecular substructure queries within the MetRxn database.

scientific article published in December 2014

Capturing the response of Clostridium acetobutylicum to chemical stressors using a regulated genome-scale metabolic model

scientific article published on 14 October 2014

Computational design of Candida boidinii xylose reductase for altered cofactor specificity

scientific article

Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2

scientific article

Computational tools for metabolic engineering.

scientific article published on May 2012

Construction of an E. Coli genome-scale atom mapping model for MFA calculations

scientific article published on 19 February 2011

Coupled enzyme reactions performed in heterogeneous reaction media: experiments and modeling for glucose oxidase and horseradish peroxidase in a PEG/citrate aqueous two-phase system.

scientific article published on 21 February 2014

DEMSIM: a discrete event based mechanistic simulation platform for gene expression and regulation dynamics

scientific article published in January 2005

Design of combinatorial protein libraries of optimal size

scientific article published in September 2005

Elucidation and structural analysis of conserved pools for genome-scale metabolic reconstructions

scientific article

Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites

scientific article published on 15 November 2005

Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock

scientific article

Extending Iterative Protein Redesign and Optimization (IPRO) in protein library design for ligand specificity

scientific article

FamClash: a method for ranking the activity of engineered enzymes.

scientific article published on 23 February 2004

Flux coupling analysis of genome-scale metabolic network reconstructions.

scientific article

From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline

scientific article published on 10 September 2019

Functional Analysis of H<sup>+</sup>-Pumping Membrane-Bound Pyrophosphatase, ADP-Glucose Synthase, and Pyruvate Phosphate Dikinase as Pyrophosphate Sources in Clostridium thermocellum

scientific article published on 22 December 2021

Genome-Scale Fluxome of Synechococcus elongatus UTEX 2973 Using Transient 13C-Labeling Data

scientific article published on 14 December 2018

Genome-scale gene/reaction essentiality and synthetic lethality analysis

scientific article published on 18 August 2009

Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA.

scientific article

GrowMatch: an automated method for reconciling in silico/in vivo growth predictions

scientific article

IPRO: an iterative computational protein library redesign and optimization procedure

scientific article

Identification of optimal measurement sets for complete flux elucidation in metabolic flux analysis experiments

scientific article published in August 2008

Identifying residue–residue clashes in protein hybrids by using a second-order mean-field approach ⬇️

scientific article published on April 16, 2003

Impact of stoichiometry representation on simulation of genotype-phenotype relationships in metabolic networks

scientific article

Improved computational performance of MFA using elementary metabolite units and flux coupling

scientific article published on 27 October 2009

Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data

scientific article

In silico design and adaptive evolution of Escherichia coli for production of lactic acid.

scientific article published in September 2005

MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured antibodies

scientific article

MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases

scientific article

Metabolic flux elucidation for large-scale models using 13C labeled isotopes

scientific article published on 29 May 2007

Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans.

scientific article

Methane oxidation by anaerobic archaea for conversion to liquid fuels.

scientific article

Microbial 1-butanol production: Identification of non-native production routes and in silico engineering interventions

scientific article published on July 2010

Minimal reaction sets for Escherichia coli metabolism under different growth requirements and uptake environments

scientific article

Modeling DNA mutation and recombination for directed evolution experiments

article

Nitrogen-use efficiency in maize (Zea mays L.): from 'omics' studies to metabolic modelling

scientific article published on 26 May 2014

OptCDR: a general computational method for the design of antibody complementarity determining regions for targeted epitope binding.

scientific article

OptCircuit: an optimization based method for computational design of genetic circuits

scientific article

OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities

scientific article

OptForce: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions

scientific article

OptGraft: A computational procedure for transferring a binding site onto an existing protein scaffold.

scientific article

OptMAVEn--a new framework for the de novo design of antibody variable region models targeting specific antigen epitopes

scientific article

OptStrain: a computational framework for redesign of microbial production systems.

scientific article published on November 2004

OptZyme: computational enzyme redesign using transition state analogues

scientific article

Optimal protein library design using recombination or point mutations based on sequence-based scoring functions

scientific article

Optimization based automated curation of metabolic reconstructions

scientific article published on 20 June 2007

Optimization-based framework for inferring and testing hypothesized metabolic objective functions

scientific article published in June 2003

Optimization-driven identification of genetic perturbations accelerates the convergence of model parameters in ensemble modeling of metabolic networks

scientific article published on 10 June 2013

Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization

scientific article (publication date: 20 December 2003)

Orchestrating hi-fi annotations.

scientific article

Pareto Optimality Explanation of the Glycolytic Alternatives in Nature

scientific article published on 22 February 2019

PoreDesigner for tuning solute selectivity in a robust and highly permeable outer membrane pore

scientific article published in Nature Communications

Predicting biological system objectives de novo from internal state measurements

scientific article

Predicting crossover generation in DNA shuffling.

scholarly article

Predicting out-of-sequence reassembly in DNA shuffling.

scientific article published in November 2002

Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions

scientific article

Quantitative assessment of uncertainty in the optimization of metabolic pathways

scientific article

Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow

scientific article

Recent advances in computational protein design.

scientific article

Recent advances in the reconstruction of metabolic models and integration of omics data

scientific article

Reconstruction and comparison of the metabolic potential of cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803

scientific article

Review of the BRENDA Database.

scientific article

Succinate Overproduction: A Case Study of Computational Strain Design Using a Comprehensive Escherichia coli Kinetic Model

scientific article published on January 2014

Synthetic biology of cyanobacteria: unique challenges and opportunities

scientific article published on 27 August 2013

Systems metabolic engineering design: fatty acid production as an emerging case study

scientific article

The Importance and Future of Biochemical Engineering

scientific article published on 28 April 2020

The Iterative Protein Redesign and Optimization (IPRO) suite of programs

scientific article published on 2 December 2014

Using a residue clash map to functionally characterize protein recombination hybrids.

scientific article published in December 2003

Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism ⬇️

scientific article published on July 6, 2011

d-OptCom: Dynamic multi-level and multi-objective metabolic modeling of microbial communities

scientific article

dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design

scientific article published on 27 September 2021

k-OptForce: integrating kinetics with flux balance analysis for strain design

scientific article (publication date: February 2014)

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