Costas D. Maranas
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Engineering
Costas D. Maranas's Degrees
- Bachelors Chemical Engineering National Technical University of Athens
Why Is Costas D. Maranas Influential?
(Suggest an Edit or Addition)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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