Costas D. Maranas

Costas D. Maranas's AcademicInfluence.com Rankings

Costas D. Maranas

Engineering

#4341

World Rank

#5532

Historical Rank

Applied Physics

#1030

World Rank

#1055

Historical Rank

engineering Degrees

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Engineering

Costas D. Maranas's Degrees

Bachelors Chemical Engineering National Technical University of Athens

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Costas D. Maranas's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization (2003) (1179)
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0 (2019) (596)
Managing demand uncertainty in supply chain planning (2003) (538)
αBB: A global optimization method for general constrained nonconvex problems (1995) (486)
OptStrain: a computational framework for redesign of microbial production systems. (2004) (470)
Flux coupling analysis of genome-scale metabolic network reconstructions. (2004) (378)
OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions (2010) (373)
In silico design and adaptive evolution of Escherichia coli for production of lactic acid. (2005) (361)
OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities (2012) (328)
Optimization based automated curation of metabolic reconstructions (2007) (328)
An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems. (2006) (310)
Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA. (2011) (308)
Synthetic biology of cyanobacteria: unique challenges and opportunities (2013) (259)
Finding all solutions of nonlinearly constrained systems of equations (1995) (225)
GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions (2009) (208)
Global Optimization in Generalized Geometric Programming (1997) (200)
Optimization-based framework for inferring and testing hypothesized metabolic objective functions. (2003) (199)
Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism (2011) (191)
Global minimum potential energy conformations of small molecules (1994) (181)
A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains (2016) (175)
Multiperiod Planning and Scheduling of Multiproduct Batch Plants under Demand Uncertainty (1997) (169)
Creating multiple-crossover DNA libraries independent of sequence identity (2001) (167)
Genome-scale gene/reaction essentiality and synthetic lethality analysis (2009) (163)
Minimal Reaction Sets for Escherichia coli Metabolism under Different Growth Requirements and Uptake Environments (2001) (159)
A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data. (2014) (156)
A Two-Stage Modeling and Solution Framework for Multisite Midterm Planning under Demand Uncertainty (2000) (151)
Mid-term supply chain planning under demand uncertainty: customer demand satisfaction and inventory management (2000) (150)
d-OptCom: Dynamic multi-level and multi-objective metabolic modeling of microbial communities. (2014) (149)
A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189 (2009) (148)
MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases (2012) (142)
A global optimization approach for Lennard‐Jones microclusters (1992) (139)
Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock (2003) (139)
Mathematical optimization applications in metabolic networks. (2012) (131)
Rational design of a synthetic Entner-Doudoroff pathway for improved and controllable NADPH regeneration. (2015) (128)
Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0. (2017) (126)
A global optimization method, αBB, for process design (1996) (126)
SteadyCom: Predicting microbial abundances while ensuring community stability (2017) (120)
k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design (2014) (120)
Recent advances in the reconstruction of metabolic models and integration of omics data. (2014) (115)
Real Options Based Analysis of Optimal Pharmaceutical Research and Development Portfolios (2002) (113)
Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions. (2001) (112)
Reversing methanogenesis to capture methane for liquid biofuel precursors (2016) (112)
Metabolic flux elucidation for large-scale models using 13C labeled isotopes. (2007) (112)
Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data (2010) (107)
An integrated computational and experimental study for overproducing fatty acids in Escherichia coli. (2012) (104)
Predicting biological system objectives de novo from internal state measurements (2008) (103)
A deterministic global optimization approach for molecular structure determination (1994) (100)
Genome Scale Reconstruction of a Salmonella Metabolic Model (2009) (100)
Computational tools for metabolic engineering. (2012) (99)
Solving long-term financial planning problems via global optimization (1997) (98)
Optimal Computer-Aided Molecular Design: A Polymer Design Case Study (1996) (94)
Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer (2022) (91)
Recent advances in computational protein design. (2011) (90)
Optimization in polymer design using connectivity indices (1999) (89)
Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803 (2012) (88)
Computational design of Candida boidinii xylose reductase for altered cofactor specificity (2009) (87)
Analysis of NADPH supply during xylitol production by engineered Escherichia coli (2009) (86)
OptCircuit: An optimization based method for computational design of genetic circuits (2008) (83)
A review of computational tools for design and reconstruction of metabolic pathways (2017) (83)
Optimal molecular design under property prediction uncertainty (1997) (82)
Comparative genomics reveals the molecular determinants of rapid growth of the cyanobacterium Synechococcus elongatus UTEX 2973 (2018) (82)
Diurnal Regulation of Cellular Processes in the Cyanobacterium Synechocystis sp. Strain PCC 6803: Insights from Transcriptomic, Fluxomic, and Physiological Analyses (2016) (81)
A Hierarchical Lagrangean Relaxation Procedure for Solving Midterm Planning Problems (1999) (80)
New results in the packing of equal circles in a square (1995) (79)
Deciphering cyanobacterial phenotypes for fast photoautotrophic growth via isotopically nonstationary metabolic flux analysis (2017) (78)
Assessing the Metabolic Impact of Nitrogen Availability Using a Compartmentalized Maize Leaf Genome-Scale Model1[C][W][OPEN] (2014) (78)
Farnesoid X Receptor Signaling Shapes the Gut Microbiota and Controls Hepatic Lipid Metabolism (2016) (78)
Standardizing biomass reactions and ensuring complete mass balance in genome‐scale metabolic models (2017) (76)
13C metabolic flux analysis at a genome-scale. (2015) (75)
Nitrogen-use efficiency in maize (Zea mays L.): from 'omics' studies to metabolic modelling. (2014) (75)
Artificial water channels enable fast and selective water permeation through water-wire networks (2019) (74)
Predicting crossover generation in DNA shuffling (2001) (73)
FamClash: A method for ranking the activity of engineered enzymes (2004) (71)
OptCDR: a general computational method for the design of antibody complementarity determining regions for targeted epitope binding. (2010) (70)
Systems metabolic engineering design: Fatty acid production as an emerging case study (2014) (67)
Computational Redesign of Acyl-ACP Thioesterase with Improved Selectivity toward Medium-Chain-Length Fatty Acids. (2017) (67)
Modeling DNA mutation and recombination for directed evolution experiments. (2000) (67)
Multilevel engineering of the upstream module of aromatic amino acid biosynthesis in Saccharomyces cerevisiae for high production of polymer and drug precursors. (2017) (66)
OptMAVEn – A New Framework for the de novo Design of Antibody Variable Region Models Targeting Specific Antigen Epitopes (2014) (63)
Pathway design using de novo steps through uncharted biochemical spaces (2018) (63)
Prediction of Oligopeptide Conformations via Deterministic Global Optimization (1997) (62)
IPRO: an iterative computational protein library redesign and optimization procedure. (2006) (61)
Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans (2011) (60)
Do genome-scale models need exact solvers or clearer standards? (2015) (60)
A computational framework for the topological analysis and targeted disruption of signal transduction networks. (2006) (60)
Locating all homogeneous azeotropes in multicomponent mixtures (1997) (59)
Optimization in product design with properties correlated with topological indices (1998) (56)
Optimal synthesis of refrigeration cycles and selection of refrigerants (1999) (55)
Capturing the response of Clostridium acetobutylicum to chemical stressors using a regulated genome-scale metabolic model (2014) (55)
Design of Single-Product Campaign Batch Plants under Demand Uncertainty (1998) (54)
EcoFABs: advancing microbiome science through standardized fabricated ecosystems (2019) (53)
Microbial 1-butanol production: Identification of non-native production routes and in silico engineering interventions. (2010) (52)
Bacterial colonization reprograms the neonatal gut metabolome (2020) (52)
Synthesis of Mixed Refrigerant Cascade Cycles (2002) (52)
Highly Active C8-Acyl-ACP Thioesterase Variant Isolated by a Synthetic Selection Strategy. (2018) (51)
Identifying the Metabolic Differences of a Fast-Growth Phenotype in Synechococcus UTEX 2973 (2017) (50)
Construction of an E. Coli genome‐scale atom mapping model for MFA calculations (2011) (50)
Exploiting the Genetic Diversity of Maize Using a Combined Metabolomic, Enzyme Activity Profiling, and Metabolic Modeling Approach to Link Leaf Physiology to Kernel Yield (2017) (49)
Succinate Overproduction: A Case Study of Computational Strain Design Using a Comprehensive Escherichia coli Kinetic Model (2015) (49)
Elucidation and structural analysis of conserved pools for genome-scale metabolic reconstructions. (2005) (48)
From directed evolution to computational enzyme engineering—A review (2020) (48)
A Mixed Integer Linear Programming (MILP) Framework for Inferring Time Delay in Gene Regulatory Networks (2003) (47)
Facile Affinity Maturation of Antibody Variable Domains Using Natural Diversity Mutagenesis (2017) (47)
Identifying residue–residue clashes in protein hybrids by using a second-order mean-field approach (2003) (45)
Metabolic modeling of clostridia: current developments and applications. (2016) (45)
Designing overall stoichiometric conversions and intervening metabolic reactions (2015) (43)
Using multiple sequence correlation analysis to characterize functionally important protein regions. (2003) (43)
Genome-Scale Fluxome of Synechococcus elongatus UTEX 2973 Using Transient 13C-Labeling Data1 (2018) (42)
Review of the BRENDA Database. (2003) (42)
Optimization Methods in Metabolic Networks: Maranas/Optimization Methods in Metabolic Networks (2016) (41)
Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2 (2021) (41)
Global optimization for molecular conformation problems (1993) (39)
Bilevel optimization techniques in computational strain design (2015) (39)
A Computational Procedure for Optimal Engineering Interventions Using Kinetic Models of Metabolism (2006) (39)
Elucidation of photoautotrophic carbon flux topology in Synechocystis PCC 6803 using genome-scale carbon mapping models. (2018) (39)
Identification of optimal measurement sets for complete flux elucidation in metabolic flux analysis experiments. (2008) (39)
Cyanobacterial Alkanes Modulate Photosynthetic Cyclic Electron Flow to Assist Growth under Cold Stress (2015) (39)
PoreDesigner for tuning solute selectivity in a robust and highly permeable outer membrane pore (2018) (38)
Optimal protein library design using recombination or point mutations based on sequence-based scoring functions. (2007) (38)
Improved computational performance of MFA using elementary metabolite units and flux coupling. (2010) (37)
Impact of Stoichiometry Representation on Simulation of Genotype-Phenotype Relationships in Metabolic Networks (2012) (37)
Assessing methanotrophy and carbon fixation for biofuel production by Methanosarcina acetivorans (2016) (36)
OptGraft: A computational procedure for transferring a binding site onto an existing protein scaffold (2008) (36)
OptMAVEn-2.0: De novo Design of Variable Antibody Regions against Targeted Antigen Epitopes (2018) (36)
Using Gene Essentiality and Synthetic Lethality Information to Correct Yeast and CHO Cell Genome-Scale Models (2015) (36)
Computational challenges in combinatorial library design for protein engineering (2004) (35)
A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data (2019) (34)
Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2 (2020) (34)
CLCA: Maximum Common Molecular Substructure Queries within the MetRxn Database (2014) (34)
Improving prediction fidelity of cellular metabolism with kinetic descriptions. (2015) (34)
Development of a core Clostridium thermocellum kinetic metabolic model consistent with multiple genetic perturbations (2017) (31)
Quantitative assessment of uncertainty in the optimization of metabolic pathways. (1997) (31)
MinGenome: An In Silico Top-Down Approach for the Synthesis of Minimized Genomes. (2017) (31)
Computational biophysical characterization of the SARS-CoV-2 spike protein binding with the ACE2 receptor and implications for infectivity (2020) (30)
The Iterative Protein Redesign and Optimization (IPRO) suite of programs (2015) (30)
Creation and analysis of biochemical constraint-based models : the COBRA Toolbox v 3 . 0 26 th February 2018 (2018) (30)
Advances in de novo strain design using integrated systems and synthetic biology tools. (2015) (29)
Using a residue clash map to functionally characterize protein recombination hybrids. (2003) (29)
Valuation and Design of Pharmaceutical R&D Licensing Deals (2005) (29)
A Global Optimization Method For Weber’s Problem With Attraction And Repulsion (1994) (29)
Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow (2013) (28)
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 (2014) (28)
Thermodynamic analysis of the pathway for ethanol production from cellobiose in Clostridium thermocellum. (2019) (28)
Computational de novo design of antibodies binding to a peptide with high affinity (2017) (28)
Extending Iterative Protein Redesign and Optimization (IPRO) in protein library design for ligand specificity. (2007) (28)
Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites (2005) (28)
Market-based pollution abatement strategies: Risk management using emission option contracts (2003) (28)
Methane oxidation by anaerobic archaea for conversion to liquid fuels (2015) (27)
Multiple spillovers and onward transmission of SARS-CoV-2 in free-living and captive white-tailed deer (2021) (26)
From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline (2019) (26)
Design of combinatorial protein libraries of optimal size (2005) (26)
Metabolic model guided strain design of cyanobacteria. (2020) (26)
De novo design of antibody complementarity determining regions binding a FLAG tetra-peptide (2017) (26)
A diurnal flux balance model of Synechocystis sp. PCC 6803 metabolism (2019) (25)
Optimization-driven identification of genetic perturbations accelerates the convergence of model parameters in ensemble modeling of metabolic networks. (2013) (25)
Toward low-cost biological and hybrid biological/catalytic conversion of cellulosic biomass to fuels (2022) (25)
Designing the substrate specificity of d-hydantoinase using a rational approach (2009) (25)
MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured antibodies (2013) (25)
Real-Options-Based Planning Strategies under Uncertainty (2004) (23)
Large-scale inference of the transcriptional regulation of Bacillus subtilis (2005) (22)
In Vivo Thermodynamic Analysis of Glycolysis in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum Using 13C and 2H Tracers (2020) (22)
A deterministic global optimization approach for the protein folding problem (1995) (21)
OptZyme: Computational Enzyme Redesign Using Transition State Analogues (2013) (21)
Large-scale inference and graph-theoretical analysis of gene-regulatory networks in B. Subtilis (2006) (21)
Engineering of E. coli inherent fatty acid biosynthesis capacity to increase octanoic acid production (2018) (20)
K-FIT: An accelerated kinetic parameterization algorithm using steady-state fluxomic data (2019) (20)
Building kinetic models for metabolic engineering. (2020) (20)
Predicting out-of-sequence reassembly in DNA shuffling. (2002) (19)
Biophysical characterization of the SARS-CoV-2 spike protein binding with the ACE2 receptor and implications for infectivity (2020) (19)
LOCATING ALL AZEOTROPES IN HOMOGENEOUS AZEOTROPIC SYSTEMS (1996) (19)
Identifying Regulatory Changes to Facilitate Nitrogen Fixation in the Nondiazotroph Synechocystis sp. PCC 6803. (2016) (18)
K-FIT: An accelerated kinetic parameterization algorithm using steady-state fluxomic data. (2020) (17)
A Global Optimization (1992) (17)
Accelerating flux balance calculations in genome‐scale metabolic models by localizing the application of loopless constraints (2017) (17)
Recent advances in constraint and machine learning-based metabolic modeling by leveraging stoichiometric balances, thermodynamic feasibility and kinetic law formalisms. (2020) (17)
eCodonOpt: a systematic computational framework for optimizing codon usage in directed evolution experiments. (2002) (17)
Predicting the Longitudinally and Radially Varying Gut Microbiota Composition Using Multi-Scale Microbial Metabolic Modeling (2019) (16)
Molecular Design Using Quantum Chemical Calculations for Property Estimation (2004) (16)
Pareto Optimality Explanation of the Glycolytic Alternatives in Nature (2019) (16)
Modeling the Effect of Chemotaxis In Glioblastoma Tumor Progression (2011) (16)
Optimization accounting for property prediction uncertainty in polymer design (1997) (15)
Modeling and optimization of DNA recombination (2000) (14)
Engineering biology approaches for food and nutrient production by cyanobacteria. (2020) (14)
7-log virus removal in a simple functionalized sand filter. (2019) (13)
Development of a Genome-Scale Metabolic Model of Clostridium thermocellum and Its Applications for Integration of Multi-Omics Datasets and Computational Strain Design (2020) (13)
Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol (2017) (13)
Directed Evolution Reveals the Functional Sequence Space of an Adenylation Domain Specificity Code. (2019) (12)
Developmental changes in lignin composition are driven by both monolignol supply and laccase specificity (2022) (12)
Achieving Metabolic Flux Analysis for S. cerevisiae at a Genome-Scale: Challenges, Requirements, and Considerations (2015) (12)
Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production (2020) (11)
Review of the Enzymes and Metabolic Pathways (EMP) Database (2001) (11)
Coarse-grained optimization-driven design and piecewise linear modeling of synthetic genetic circuits (2014) (11)
SNPeffect: identifying functional roles of SNPs using metabolic networks (2020) (9)
Metabolic engineering of Rhodotorula toruloides IFO0880 improves C16 and C18 fatty alcohol production from synthetic media (2022) (9)
Review of EcoCyc and MetaCyc Databases (2001) (8)
Elucidation of trophic interactions in an unusual single-cell nitrogen-fixing symbiosis using metabolic modeling (2021) (8)
Model Simulations Reveal VCAM-1 Augment PAK Activation Rates to Amplify p38 MAPK and VE-Cadherin Phosphorylation (2011) (8)
Exploring the combinatorial space of complete pathways to chemicals. (2018) (8)
Design of Multiproduct Batch Plants under Demand Uncertainty with Staged Capacity Expansions (1998) (8)
The Importance and Future of Biochemical Engineering. (2020) (7)
Design of surfactant solutions with optimal macroscopic properties (1999) (7)
IPRO+/-: Computational Protein Design Tool Allowing for Insertions and Deletions. (2020) (7)
Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike protein and the human ACE2 receptor (2021) (7)
DEMSIM: a discrete event based mechanistic simulation platform for gene expression and regulation dynamics. (2005) (7)
Metabolic flux analysis reaching genome wide coverage: lessons learned and future perspectives (2020) (6)
Computational Modeling of Microbial Communities (2017) (6)
Maranas production systems OptStrain : A computational framework for redesign of microbial Material Supplemental (2004) (6)
RISK MANAGEMENT IN REAL OPTIONS BASED PHARMACEUTICAL PORTFOLIO PLANNING (2002) (5)
OPTIMAL SELECTION OF ENZYME LEVELS USING LARGE-SCALE KINETIC MODELS (2005) (5)
Functional Analysis of H+-Pumping Membrane-Bound Pyrophosphatase, ADP-Glucose Synthase, and Pyruvate Phosphate Dikinase as Pyrophosphate Sources in Clostridium thermocellum (2021) (5)
A Prospective Study on the Fermentation Landscape of Gaseous Substrates to Biorenewables Using Methanosarcina acetivorans Metabolic Model (2018) (5)
Bifurcation analysis of the metabolism of E. coli at optimal enzyme levels (2006) (5)
Multiperiod planning of multisite supply chains under demand uncertainty (2001) (4)
Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2 (2021) (4)
Challenges of cultivated meat production and applications of genome‐scale metabolic modeling (2020) (4)
Assessing the impact of substrate-level enzyme regulations limiting ethanol titer in Clostridium thermocellum using a core kinetic model. (2022) (4)
Engineering microbial chemical factories using metabolic models (2019) (4)
EnZymClass: Substrate specificity prediction tool of plant acyl-ACP thioesterases based on Ensemble Learning (2021) (4)
Computational Strain Design (2016) (4)
A microbial factory for diverse chemicals (2016) (4)
An integrated computational and experimental study to increase the intra-cellular malonyl-CoA: Application to flavanone synthesis (2011) (4)
Modeling Growth Kinetics, Interspecies Cell Fusion, and Metabolism of a Clostridium acetobutylicum/Clostridium ljungdahlii Syntrophic Coculture (2021) (4)
Dissecting the Metabolic Reprogramming of Maize Root under Nitrogen-Deficient Stress Condition. (2021) (3)
Review of the TEIRESIAS-based tools of the IBM Bioinformatics and Pattern Discovery Group. (2001) (3)
Computationally Prospecting Potential Pathways from Lignin Monomers and Dimers toward Aromatic Compounds. (2021) (3)
Reply to Zhou and Li: Plasticity of the genomic haplotype of Synechococcus elongatus leads to rapid strain adaptation under laboratory conditions (2019) (3)
Flux Balance Analysis and LP Problems (2016) (3)
The Biochemistry and Physiology of Respiratory-Driven Reversed Methanogenesis (2018) (3)
Engineering sensitivity and specificity of AraC-based biosensors responsive to triacetic acid lactone and orsellinic acid. (2020) (3)
ENGINEERING CHALLENGES AND OPPORTUNITIES IN COMPUTATIONAL BIOLOGY (2002) (3)
Global Optimization in Weber's Problem with Attraction and Repulsion (2009) (2)
Computationally Exploring and Alleviating the Kinetic Bottlenecks of Anaerobic Methane Oxidation (2018) (2)
Quantifying the propagation of parametric uncertainty on flux balance analysis (2021) (2)
Implication of dynamics in signal transduction and targeted disruption analyses of signaling networks (2008) (2)
Review of the Biocatalysis/Biodegradation Database (UM-BBD) (2002) (2)
Editorial overview: Systems biology: Advances diseases understanding and metabolic engineering. (2015) (2)
Proteome capacity constraints favor respiratory ATP generation (2022) (2)
Personalized Kinetic Models for Predictive Healthcare. (2015) (2)
Development of a genome-scale metabolic model of Clostridium thermocellum and its applications for integration of multi-omics datasets and strain design (2020) (2)
De novo design of high-affinity antibody variable regions (Fv) against the SARS-CoV-2 spike protein (2020) (2)
A Genome-Scale Metabolic Model of Anabaena 33047 to Guide Genetic Modifications to Overproduce Nylon Monomers (2021) (2)
ML helps predict enzyme turnover rates (2022) (1)
Resolving Network Gaps and Growth Prediction Inconsistencies in Metabolic Networks (2016) (1)
Global optimization in computational chemistry and process systems engineering (1995) (1)
Quantifying the propagation of parametric uncertainty on flux balance analysis. (2021) (1)
Real options based approaches to decision making under uncertainty (2003) (1)
Cyanobacterial Alkanes ModulatePhotosynthetic Cyclic ElectronFlow to Assist Growth under ColdStress (2015) (1)
Comparative study of two Saccharomyces cerevisiae strains with kinetic models at genome-scale. (2023) (1)
Locating All Homogeneous AzeotropesIn Multicomponent (1997) (1)
MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases (2012) (1)
Author Correction: Artificial water channels enable fast and selective water permeation through water-wire networks (2020) (1)
MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured antibodies (2013) (1)
Pathway design using de novo steps through uncharted biochemical spaces (2018) (1)
Modeling with Binary Variables and MILP Fundamentals (2016) (1)
SARS-CoV-2 Compatible ACE2 Receptors in Little Brown Bats ( Myotis lucifugus) (2022) (1)
SARS-CoV-2 Omicron (B.1.1.529) Infection of Wild White-Tailed Deer in New York City (2022) (1)
Modeling Plant Metabolism: Advancements and Future Capabilities (2018) (1)
PLOS Computational Biology 2017 Reviewer and Editorial Board Thank You (2018) (1)
Diurnal Regulation of Cellular Processes in the Cyanobacterium <italic toggle='yes'>Synechocystis</italic> sp. Strain PCC 6803: Insights from Transcriptomic, Fluxomic, and Physiological Analyses (2016) (1)
Thermodynamic Analysis of Metabolic Networks (2016) (1)
OPTSTRAIN : A HIERARCHICAL METABOLIC PATHWAY DISCOVERY AND DESIGN FRAMEWORK FOR MICROBIAL PRODUCTION SYSTEMS (2005) (1)
EcoFABs: advancing microbiome science through standardized fabricated ecosystems (2019) (0)
Kinetic modeling of metabolism in obligatory anaerobes (2016) (0)
De novo design and Rosetta‐based assessment of high‐affinity antibody variable regions (Fv) against the SARS‐CoV‐2 spike receptor binding domain (RBD) (2022) (0)
PoreDesigner for tuning solute selectivity in a robust and highly permeable outer membrane pore (2018) (0)
SYNECHOCOCCUS ELONGATUS UTEX 2973 , A NEW CYANOBACTERIAL STRAIN THAT EXHIBITS RAPID AUTOTROPHIC GROWTH (2016) (0)
Systems analysis of a fast growing N2-fixing cyanobacterium for production of advanced biofuels and nitrogen-containing petrochemical replacement compounds (2019) (0)
Identifying functional roles of SNPs using metabolic networks for improved plant breeding (2019) (0)
Hybrid multi-scale modeling of brain tumor progression (2008) (0)
Computational Protein Engineering (2007) (0)
A detailed genome-scale metabolic model of Clostridium thermocellum investigates sources of pyrophosphate for driving glycolysis. (2023) (0)
Identification of Connected Paths to Target Metabolites (2016) (0)
Metabolic engineering of low-pH-tolerant non-model yeast, Issatchenkia orientalis, for production of citramalate (2023) (0)
Examining organic acid production potential and growth‐coupled strategies in Issatchenkia orientalis using constraint‐based modeling (2022) (0)
Biomimetic Membrane Design Principles for Angstrom Scale Separation (2018) (0)
Appendix A Coding Optimization Models in GAMS (2016) (0)
Little Brown Bats (Myotis lucifugus) Support the Binding of SARS-CoV-2 Spike and Are Likely Susceptible to SARS-CoV-2 Infection (2023) (0)
K-FIT: Parameterizing kinetic models of metabolism using multiple fluxomic datasets (2019) (0)
MINLP Fundamentals and Applications (2016) (0)
Dissecting the Metabolic Reprogramming of Maize Root under Nitrogen Limiting Stress Condition (2021) (0)
Multiscale Systems Engineering I - In Honor of Professor Christodoulos A. Floudas (Invited Talks) (2017) (0)
NLP Applications in Metabolic Networks (2016) (0)
Using Systems Engineering to Reconstruct, Analyze and Redesign Metabolism (2009) (0)
Mathematical Optimization Fundamentals (2016) (0)
Computational redesign of acyl-ACP thioesterase with improved selectivity towards medium chain fatty acids at high production levels (2017) (0)
MATERIALS AND INTERFACES Optimization in Polymer Design Using Connectivity Indices (2009) (0)
De novo design of antibody complementarity determining regions binding a FLAG tetra-peptide (2017) (0)
dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design (2021) (0)
Improving computational strain design strategies by incorporation of kinetic information (2015) (0)
Genome-scalegene/reaction essentialityandsynthetic lethality analysis (2009) (0)
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0 (2019) (0)
13C Metabolic flux analysis and kinetic modeling of Clostridium thermocellum grown on cellobiose (2020) (0)
Procede de determination de strategies d'inactivation genique (2003) (0)
Orchestrating hi-fi annotations. (2012) (0)
Modeling and Optimization of Directed Evolution Protocols (2003) (0)
PoreDesigner: A computational tool for the design of membrane pores for separations (2019) (0)
Evaluating proteome allocation of Saccharomyces cerevisiae phenotypes with resource balance analysis (2022) (0)
A CASE STUDY ON THE DESIGN OF PHARMACEUTICAL R & D LICENSING DEALS (2004) (0)
A CNN model for predicting binding affinity changes between SARS-CoV-2 spike RBD variants and ACE2 homologues (2022) (0)
Engineering sensitivity and specificity of AraC-based biosensors responsive to triacetic acid lactone and orsellinic acid (2020) (0)
Assessing methanotrophic capabilities of Methanosarcina acetivorans for bioproduction (2016) (0)
Inference and analysis of gene-regulatory networks in the bacterium B.subtilis (2006) (0)
Metabolic Reconstruction , Analysis and Design of Metabolic Pathways (2018) (0)
1050 Metabolic Capacity Estimation of Escherichia coli as a Platform for Redox Biocatalysis: Constraint-Based Modeling and Experimental Verifi cation (2008) (0)
Global Optimization in Lennard-Jones and Morse Clusters (2009) (0)
Ensemble cell-wide kinetic modeling of anaerobic organisms to support fuels and chemicals production (2018) (0)
Development and Validation of Indirect Enzyme-Linked Immunosorbent Assays for Detecting Antibodies to SARS-CoV-2 in Cattle, Swine, and Chicken (2022) (0)
GenomeScaleReconstructionofaSalmonellaMetabolicModel COMPARISONOFSIMILARITYANDDIFFERENCESWITHACOMMENSALESCHERICHIA COLISTRAIN (2009) (0)
Pareto Optimality Explanation of the Glycolytic Alternatives in Nature (2019) (0)
LP and Duality Theory (2016) (0)
Optimization in molecular design and bioinformatics (2001) (0)
Modeling the effect of temozolomide treatment on orthotopic models of glioma (2011) (0)
Computational analysis and design for altered cofactor specificity (2008) (0)
Bacterial colonization reprograms the neonatal gut metabolome (2020) (0)
Development of Computational Tools for Metabolic Model Curation, Flux Elucidation and Strain Design (2012) (0)
Genome-scale mapping models and algorithms for stationary and instationary MFA-based metabolic flux elucidation (2017) (0)
American Chemical Society: Biotechnology Progress Table of Contents (2007) (0)
de novo Design and in silico Optimization of Antibody-Like Binders Targeting Ebola Viral Antigen (2016) (0)
A hierarchy of modeling frameworks for cyanobacterial metabolism: From gsms to ME models (2016) (0)
Nature inspired antibody design and optimization (2017) (0)

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