Recent advances in constraint and machine learning-based metabolic modeling by leveraging stoichiometric balances, thermodynamic feasibility and kinetic law formalisms
Published 2020 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Recent advances in constraint and machine learning-based metabolic modeling by leveraging stoichiometric balances, thermodynamic feasibility and kinetic law formalisms
Authors
Keywords
-
Journal
METABOLIC ENGINEERING
Volume 63, Issue -, Pages 13-33
Publisher
Elsevier BV
Online
2020-12-11
DOI
10.1016/j.ymben.2020.11.013
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies
- (2020) Milenko Tokic et al. Biotechnology for Biofuels
- MEMOTE for standardized genome-scale metabolic model testing
- (2020) Christian Lieven et al. NATURE BIOTECHNOLOGY
- Flux balance analysis of metabolism during growth by osmotic cell expansion and its application to tomato fruits
- (2020) Sanu Shameer et al. PLANT JOURNAL
- Reconstruction of a regulated two-cell metabolic model to study biohydrogen production in a diazotrophic cyanobacterium Anabaena variabilis ATCC 29413
- (2020) Ali Malek Shahkouhi et al. PLoS One
- The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models
- (2020) Pierre Salvy et al. Nature Communications
- Recent Advances of CRISPR/Cas9-Based Genetic Engineering and Transcriptional Regulation in Industrial Biology
- (2020) Shangjie Zhang et al. Frontiers in Bioengineering and Biotechnology
- TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed-matter simulations
- (2020) Sree Ganesh Balasubramani et al. JOURNAL OF CHEMICAL PHYSICS
- K-FIT: An accelerated kinetic parameterization algorithm using steady-state fluxomic data
- (2020) Saratram Gopalakrishnan et al. METABOLIC ENGINEERING
- SNPeffect: identifying functional roles of SNPs using metabolic networks
- (2020) Debolina Sarkar et al. PLANT JOURNAL
- Model-based integration of genomics and metabolomics reveals SNP functionality in Mycobacterium tuberculosis
- (2020) Ove Øyås et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Integrating molecular markers into metabolic models improves genomic selection for Arabidopsis growth
- (2020) Hao Tong et al. Nature Communications
- iMM1865: A New Reconstruction of Mouse Genome-Scale Metabolic Model
- (2020) Saeideh Khodaee et al. Scientific Reports
- In Vivo Thermodynamic Analysis of Glycolysis in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum Using 13C and 2H Tracers
- (2020) Tyler B. Jacobson et al. mSystems
- In Vivo Estimates of Liver Metabolic Flux Assessed by 13C-Propionate and 13C-Lactate Are Impacted by Tracer Recycling and Equilibrium Assumptions
- (2020) Clinton M. Hasenour et al. Cell Reports
- A machine learning Automated Recommendation Tool for synthetic biology
- (2020) Tijana Radivojević et al. Nature Communications
- Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism
- (2020) Jie Zhang et al. Nature Communications
- Development of a Genome-Scale Metabolic Model of Clostridium thermocellum and Its Applications for Integration of Multi-Omics Datasets and Computational Strain Design
- (2020) Sergio Garcia et al. Frontiers in Bioengineering and Biotechnology
- Metabolic flux analysis reaching genome wide coverage: lessons learned and future perspectives
- (2020) John I Hendry et al. Current Opinion in Chemical Engineering
- DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression
- (2019) Laurence Yang et al. BMC Systems Biology
- Glycerol metabolism of Pichia pastoris (Komagataella spp.) characterised by 13C-based metabolic flux analysis
- (2019) Màrius Tomàs-Gamisans et al. New Biotechnology
- A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types
- (2019) Yara Seif et al. PLoS Computational Biology
- Tandem Mass Spectrometry for 13C Metabolic Flux Analysis: Methods and Algorithms Based on EMU Framework
- (2019) Jungik Choi et al. Frontiers in Microbiology
- Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen
- (2019) Joanne K. Liu et al. PLoS Computational Biology
- Pareto Optimality Explanation of the Glycolytic Alternatives in Nature
- (2019) Chiam Yu Ng et al. Scientific Reports
- Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0
- (2019) Laurent Heirendt et al. Nature Protocols
- Metastasis of pancreatic cancer: An uninflamed liver micromilieu controls cell growth and cancer stem cell properties by oxidative phosphorylation in pancreatic ductal epithelial cells
- (2019) Alexander Fabian et al. CANCER LETTERS
- Predicting pK a for Small Molecules on Public and In‐house Datasets Using Fast Prediction Methods Combined with Data Fusion
- (2019) Tuomo Kalliokoski et al. Molecular Informatics
- Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions
- (2019) Anne Richelle et al. PLoS Computational Biology
- Reconciling high-throughput gene essentiality data with metabolic network reconstructions
- (2019) Anna S. Blazier et al. PLoS Computational Biology
- BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data
- (2019) Jean-Christophe Lachance et al. PLoS Computational Biology
- A benchmark-driven approach to reconstruct metabolic networks for studying cancer metabolism
- (2019) Oveis Jamialahmadi et al. PLoS Computational Biology
- 13C-Metabolic Flux Analysis Reveals Effect of Phenol on Central Carbon Metabolism in Escherichia coli
- (2019) Sayaka Kitamura et al. Frontiers in Microbiology
- The Design of FluxML: A Universal Modeling Language for 13C Metabolic Flux Analysis
- (2019) Martin Beyß et al. Frontiers in Microbiology
- 2H and 13C metabolic flux analysis elucidates in vivo thermodynamics of the ED pathway in Zymomonas mobilis
- (2019) Tyler B. Jacobson et al. METABOLIC ENGINEERING
- A Mixed Quantum Chemistry/Machine Learning Approach for the Fast and Accurate Prediction of Biochemical Redox Potentials and Its Large-Scale Application to 315 000 Redox Reactions
- (2019) Adrian Jinich et al. ACS Central Science
- Predicting the Longitudinally and Radially Varying Gut Microbiota Composition Using Multi-Scale Microbial Metabolic Modeling
- (2019) Chan et al. Processes
- Kinetic ensemble model of gas fermenting Clostridium autoethanogenum for improved ethanol production
- (2019) Jennifer Greene et al. BIOCHEMICAL ENGINEERING JOURNAL
- A generalized computational framework to streamline thermodynamics and kinetics analysis of metabolic pathways
- (2019) Chao Wu et al. METABOLIC ENGINEERING
- Automated generation of bacterial resource allocation models
- (2019) Ana Bulović et al. METABOLIC ENGINEERING
- Metabolic flux responses to deletion of 20 core enzymes reveal flexibility and limits of E. coli metabolism
- (2019) Christopher P. Long et al. METABOLIC ENGINEERING
- Thermodynamic analysis of the pathway for ethanol production from cellobiose in Clostridium thermocellum
- (2019) Satyakam Dash et al. METABOLIC ENGINEERING
- High-resolution 13C metabolic flux analysis
- (2019) Christopher P. Long et al. Nature Protocols
- Flexible heuristic algorithm for automatic molecule fragmentation: application to the UNIFAC group contribution model
- (2019) Simon Müller Journal of Cheminformatics
- From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline
- (2019) Charles J. Foster et al. PLoS Computational Biology
- Molecular Transformer: A Model for Uncertainty-Calibrated Chemical Reaction Prediction
- (2019) Philippe Schwaller et al. ACS Central Science
- Multi-tissue to whole plant metabolic modelling
- (2019) Rahul Shaw et al. CELLULAR AND MOLECULAR LIFE SCIENCES
- Metabolic kinetic modeling provides insight into complex biological questions, but hurdles remain
- (2019) Jonathan Strutz et al. CURRENT OPINION IN BIOTECHNOLOGY
- Simultaneous repression of multiple bacterial genes using nonrepetitive extra-long sgRNA arrays
- (2019) Alexander C. Reis et al. NATURE BIOTECHNOLOGY
- Towards a fully automated algorithm driven platform for biosystems design
- (2019) Mohammad HamediRad et al. Nature Communications
- Bayesian inference of metabolic kinetics from genome-scale multiomics data
- (2019) Peter C. St. John et al. PLoS Computational Biology
- Statistical inference in ensemble modeling of cellular metabolism
- (2019) Tuure Hameri et al. PLoS Computational Biology
- Recent advances on constraint-based models by integrating machine learning
- (2019) Pratip Rana et al. CURRENT OPINION IN BIOTECHNOLOGY
- Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method
- (2018) Bin Du et al. BIOPHYSICAL JOURNAL
- Modeling the multi-scale mechanisms of macromolecular resource allocation
- (2018) Laurence Yang et al. CURRENT OPINION IN MICROBIOLOGY
- Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures
- (2018) Hiroyuki Kurata et al. JOURNAL OF BIOSCIENCE AND BIOENGINEERING
- Elucidation of photoautotrophic carbon flux topology in Synechocystis PCC 6803 using genome-scale carbon mapping models
- (2018) Saratram Gopalakrishnan et al. METABOLIC ENGINEERING
- Automated Network Generation and Analysis of Biochemical Reaction Pathways Using RING
- (2018) Udit Gupta et al. METABOLIC ENGINEERING
- Recon3D enables a three-dimensional view of gene variation in human metabolism
- (2018) Elizabeth Brunk et al. NATURE BIOTECHNOLOGY
- KBase: The United States Department of Energy Systems Biology Knowledgebase
- (2018) Adam P Arkin et al. NATURE BIOTECHNOLOGY
- Fast automated reconstruction of genome-scale metabolic models for microbial species and communities
- (2018) Daniel Machado et al. NUCLEIC ACIDS RESEARCH
- HMMER web server: 2018 update
- (2018) Simon C Potter et al. NUCLEIC ACIDS RESEARCH
- Pathway design using de novo steps through uncharted biochemical spaces
- (2018) Akhil Kumar et al. Nature Communications
- The role of dynamic enzyme assemblies and substrate channelling in metabolic regulation
- (2018) Lee J. Sweetlove et al. Nature Communications
- Traceability, reproducibility and wiki-exploration for “à-la-carte” reconstructions of genome-scale metabolic models
- (2018) Méziane Aite et al. PLoS Computational Biology
- COBRAme: A computational framework for genome-scale models of metabolism and gene expression
- (2018) Colton J. Lloyd et al. PLoS Computational Biology
- Reserve Flux Capacity in the Pentose Phosphate Pathway Enables Escherichia coli 's Rapid Response to Oxidative Stress
- (2018) Dimitris Christodoulou et al. Cell Systems
- Uniform resolution of compact identifiers for biomedical data
- (2018) Sarala M. Wimalaratne et al. Scientific Data
- Comparative Studies of Glycolytic Pathways and Channeling under In Vitro and In Vivo Modes
- (2018) Mary H. Abernathy et al. AICHE JOURNAL
- Methods for automated genome-scale metabolic model reconstruction
- (2018) José P. Faria et al. BIOCHEMICAL SOCIETY TRANSACTIONS
- Effect of macromolecular crowding on the kinetics of glycolytic enzymes and the behaviour of glycolysis in yeast
- (2018) Henrik S. Thoke et al. Integrative Biology
- OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO2 fixation potential of Escherichia coli
- (2018) Oliver Hädicke et al. PLoS Computational Biology
- Systematic selection of chemical fingerprint features improves the Gibbs energy prediction of biochemical reactions
- (2018) Meshari Alazmi et al. BIOINFORMATICS
- The poly-omics of ageing through individual-based metabolic modelling
- (2018) Elisabeth Yaneske et al. BMC BIOINFORMATICS
- Automated generation of genome-scale metabolic draft reconstructions based on KEGG
- (2018) Emil Karlsen et al. BMC BIOINFORMATICS
- Machine Learning Guided Atom Mapping of Metabolic Reactions
- (2018) Eleni E. Litsa et al. Journal of Chemical Information and Modeling
- Genome-scale fluxome of Synechococcus elongatus UTEX 2973 using transient 13C-labeling data
- (2018) John I. Hendry et al. PLANT PHYSIOLOGY
- Estimating Metabolic Equilibrium Constants: Progress and Future Challenges
- (2018) Bin Du et al. TRENDS IN BIOCHEMICAL SCIENCES
- Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models
- (2018) David Heckmann et al. Nature Communications
- RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor
- (2018) Hao Wang et al. PLoS Computational Biology
- Quantum chemistry reveals thermodynamic principles of redox biochemistry
- (2018) Adrian Jinich et al. PLoS Computational Biology
- Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model
- (2018) Fabian Fröhlich et al. Cell Systems
- COPASI and its applications in biotechnology
- (2017) Frank T. Bergmann et al. JOURNAL OF BIOTECHNOLOGY
- Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints
- (2017) Benjamín J Sánchez et al. Molecular Systems Biology
- The MetaCyc database of metabolic pathways and enzymes
- (2017) Ron Caspi et al. NUCLEIC ACIDS RESEARCH
- Cellular trade-offs and optimal resource allocation during cyanobacterial diurnal growth
- (2017) Alexandra-M. Reimers et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation
- (2017) Ke Chen et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- SteadyCom: Predicting microbial abundances while ensuring community stability
- (2017) Siu Hung Joshua Chan et al. PLoS Computational Biology
- Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast
- (2017) Zhuo Wang et al. PLoS Computational Biology
- Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks
- (2017) Fabian Fröhlich et al. PLoS Computational Biology
- Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli
- (2017) Pierre Millard et al. PLoS Computational Biology
- BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities
- (2017) Eugen Bauer et al. PLoS Computational Biology
- Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression
- (2017) Ding Ma et al. Scientific Reports
- Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics
- (2017) Aarash Bordbar et al. Scientific Reports
- Modeling Method for Increased Precision and Scope of Directly Measurable Fluxes at a Genome-Scale
- (2016) Douglas McCloskey et al. ANALYTICAL CHEMISTRY
- iReMet-flux: constraint-based approach for integrating relative metabolite levels into a stoichiometric metabolic models
- (2016) Max Sajitz-Hermstein et al. BIOINFORMATICS
- An algorithm for designing minimal microbial communities with desired metabolic capacities
- (2016) Alexander Eng et al. BIOINFORMATICS
- Reaction Decoder Tool (RDT): extracting features from chemical reactions
- (2016) Syed Asad Rahman et al. BIOINFORMATICS
- WUFlux: an open-source platform for 13C metabolic flux analysis of bacterial metabolism
- (2016) Lian He et al. BMC BIOINFORMATICS
- solveME: fast and reliable solution of nonlinear ME models
- (2016) Laurence Yang et al. BMC BIOINFORMATICS
- Engineering Cellular Metabolism
- (2016) Jens Nielsen et al. CELL
- Computational biology in the 21st century
- (2016) Bonnie Berger et al. COMMUNICATIONS OF THE ACM
- Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction
- (2016) Christopher S. Henry et al. JOURNAL OF CELLULAR PHYSIOLOGY
- Identification of metabolic engineering targets for the enhancement of 1,4-butanediol production in recombinant E. coli using large-scale kinetic models
- (2016) Stefano Andreozzi et al. METABOLIC ENGINEERING
- iSCHRUNK – I n S ilico Approach to Ch aracterization and R eduction of Un certainty in the K inetic Models of Genome-scale Metabolic Networks
- (2016) Stefano Andreozzi et al. METABOLIC ENGINEERING
- 13 C metabolic flux analysis of microbial and mammalian systems is enhanced with GC-MS measurements of glycogen and RNA labeling
- (2016) Christopher P. Long et al. METABOLIC ENGINEERING
- A method for analysis and design of metabolism using metabolomics data and kinetic models: Application on lipidomics using a novel kinetic model of sphingolipid metabolism
- (2016) Georgios Savoglidis et al. METABOLIC ENGINEERING
- Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli
- (2016) Nusrat Jahan et al. Microbial Cell Factories
- Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering
- (2016) Andrew D Garst et al. NATURE BIOTECHNOLOGY
- Metabolite concentrations, fluxes and free energies imply efficient enzyme usage
- (2016) Junyoung O Park et al. Nature Chemical Biology
- BRENDA in 2017: new perspectives and new tools in BRENDA
- (2016) Sandra Placzek et al. NUCLEIC ACIDS RESEARCH
- KEGG: new perspectives on genomes, pathways, diseases and drugs
- (2016) Minoru Kanehisa et al. NUCLEIC ACIDS RESEARCH
- Molecular thermodynamics of metabolism: hydration quantities and the equation-of-state approach
- (2016) C. Panayiotou et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Systems-level analysis of mechanisms regulating yeast metabolic flux
- (2016) S. R. Hackett et al. SCIENCE
- A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains
- (2016) Ali Khodayari et al. Nature Communications
- Multi-omic data integration enables discovery of hidden biological regularities
- (2016) Ali Ebrahim et al. Nature Communications
- Construction of feasible and accurate kinetic models of metabolism: A Bayesian approach
- (2016) Pedro A. Saa et al. Scientific Reports
- Reconstruction of Tissue-Specific Metabolic Networks Using CORDA
- (2016) André Schultz et al. PLoS Computational Biology
- Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets
- (2016) Daniel Hartleb et al. PLoS Computational Biology
- SUMOFLUX: A Generalized Method for Targeted 13C Metabolic Flux Ratio Analysis
- (2016) Maria Kogadeeva et al. PLoS Computational Biology
- Constrained Allocation Flux Balance Analysis
- (2016) Matteo Mori et al. PLoS Computational Biology
- Metabolic Network Prediction of Drug Side Effects
- (2016) Itay Shaked et al. Cell Systems
- Kinetic study of butanol production from various sugars by Clostridium acetobutylicum using a dynamic model
- (2015) Francesca Raganati et al. BIOCHEMICAL ENGINEERING JOURNAL
- Context-specific metabolic network reconstruction of a naphthalene-degrading bacterial community guided by metaproteomic data
- (2015) Luis Tobalina et al. BIOINFORMATICS
- Integrated metabolic modelling reveals cell-type specific epigenetic control points of the macrophage metabolic network
- (2015) Maria Pires Pacheco et al. BMC GENOMICS
- Robust and efficient parameter estimation in dynamic models of biological systems
- (2015) Attila Gábor et al. BMC Systems Biology
- Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology
- (2015) Peter D. Karp et al. BRIEFINGS IN BIOINFORMATICS
- Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome
- (2015) Saeed Shoaie et al. Cell Metabolism
- Improving prediction fidelity of cellular metabolism with kinetic descriptions
- (2015) Anupam Chowdhury et al. CURRENT OPINION IN BIOTECHNOLOGY
- Heading in the right direction: thermodynamics-based network analysis and pathway engineering
- (2015) Meric Ataman et al. CURRENT OPINION IN BIOTECHNOLOGY
- Benefit of Retraining pKa Models Studied Using Internally Measured Data
- (2015) Peter Gedeck et al. Journal of Chemical Information and Modeling
- Quantitative prediction of genome-wide resource allocation in bacteria
- (2015) Anne Goelzer et al. METABOLIC ENGINEERING
- 13 C-metabolic flux analysis of co-cultures: A novel approach
- (2015) Nikodimos A. Gebreselassie et al. METABOLIC ENGINEERING
- Integrated 13 C-metabolic flux analysis of 14 parallel labeling experiments in Escherichia coli
- (2015) Scott B. Crown et al. METABOLIC ENGINEERING
- 13C metabolic flux analysis at a genome-scale
- (2015) Saratram Gopalakrishnan et al. METABOLIC ENGINEERING
- Biomass composition: the “elephant in the room” of metabolic modelling
- (2015) Duygu Dikicioglu et al. Metabolomics
- MetDFBA: incorporating time-resolved metabolomics measurements into dynamic flux balance analysis
- (2015) A. Marcel Willemsen et al. Molecular BioSystems
- Extended Functional Groups (EFG): An Efficient Set for Chemical Characterization and Structure-Activity Relationship Studies of Chemical Compounds
- (2015) Elena Salmina et al. MOLECULES
- The MG-RAST metagenomics database and portal in 2015
- (2015) Andreas Wilke et al. NUCLEIC ACIDS RESEARCH
- Molecular thermodynamics of metabolism: quantum thermochemical calculations for key metabolites
- (2015) N. Hadadi et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Integration of transcriptomics and metabolomics data specifies the metabolic response of Chlamydomonas to rapamycin treatment
- (2015) Sabrina Kleessen et al. PLANT JOURNAL
- Context-Specific Metabolic Model Extraction Based on Regularized Least Squares Optimization
- (2015) Semidán Robaina Estévez et al. PLoS One
- Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli
- (2015) Sang Woo Seo et al. Nature Communications
- 150 Years of the Mass Action Law
- (2015) Eberhard O. Voit et al. PLoS Computational Biology
- Pantograph: A template-based method for genome-scale metabolic model reconstruction
- (2015) Nicolas Loira et al. Journal of Bioinformatics and Computational Biology
- Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics
- (2015) Aarash Bordbar et al. Cell Systems
- INCA: a computational platform for isotopically non-stationary metabolic flux analysis
- (2014) J. D. Young BIOINFORMATICS
- Ki MoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems
- (2014) Rafael S Costa et al. BMC Systems Biology
- CLCA: Maximum Common Molecular Substructure Queries within the MetRxn Database
- (2014) Akhil Kumar et al. Journal of Chemical Information and Modeling
- A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data
- (2014) Ali Khodayari et al. METABOLIC ENGINEERING
- Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling
- (2014) R. Agren et al. Molecular Systems Biology
- Predicting Growth Conditions from Internal Metabolic Fluxes in an In-Silico Model of E. coli
- (2014) Viswanadham Sridhara et al. PLoS One
- Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli
- (2014) Sang Woo Seo et al. Nature Communications
- Quantum Chemical Approach to Estimating the Thermodynamics of Metabolic Reactions
- (2014) Adrian Jinich et al. Scientific Reports
- d-OptCom: Dynamic Multi-level and Multi-objective Metabolic Modeling of Microbial Communities
- (2014) Ali R. Zomorrodi et al. ACS Synthetic Biology
- Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics
- (2014) William R. Harcombe et al. Cell Reports
- Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism
- (2014) Daniel Machado et al. PLoS Computational Biology
- Fast Reconstruction of Compact Context-Specific Metabolic Network Models
- (2014) Nikos Vlassis et al. PLoS Computational Biology
- A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks
- (2014) Hojung Nam et al. PLoS Computational Biology
- Contribution of Network Connectivity in Determining the Relationship between Gene Expression and Metabolite Concentration Changes
- (2014) Aleksej Zelezniak et al. PLoS Computational Biology
- OpenMebius: An Open Source Software for Isotopically Nonstationary13C-Based Metabolic Flux Analysis
- (2014) Shuichi Kajihata et al. Biomed Research International
- GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data
- (2013) Brian J. Schmidt et al. BIOINFORMATICS
- Path2Models: large-scale generation of computational models from biochemical pathway maps
- (2013) Finja Büchel et al. BMC Systems Biology
- Algorithm for Reaction Classification
- (2013) Hans Kraut et al. Journal of Chemical Information and Modeling
- COMPLETE-MFA: Complementary parallel labeling experiments technique for metabolic flux analysis
- (2013) Robert W. Leighty et al. METABOLIC ENGINEERING
- Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction
- (2013) E. J. O{middle dot}Brien et al. Molecular Systems Biology
- Community Flux Balance Analysis for Microbial Consortia at Balanced Growth
- (2013) Ruchir A. Khandelwal et al. PLoS One
- BioMog: A Computational Framework for the De Novo Generation or Modification of Essential Biomass Components
- (2013) Christopher J. Tervo et al. PLoS One
- Glycolytic strategy as a tradeoff between energy yield and protein cost
- (2013) A. Flamholz et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Retropath: Automated Pipeline for Embedded Metabolic Circuits
- (2013) Pablo Carbonell et al. ACS Synthetic Biology
- Consistent Estimation of Gibbs Energy Using Component Contributions
- (2013) Elad Noor et al. PLoS Computational Biology
- 13CFLUX2—high-performance software suite for 13C-metabolic flux analysis
- (2012) Michael Weitzel et al. BIOINFORMATICS
- An integrated open framework for thermodynamics of reactions that combines accuracy and coverage
- (2012) Elad Noor et al. BIOINFORMATICS
- Modelling biological systems from molecules to dynamical networks
- (2012) Yong Wang et al. BMC Systems Biology
- A Whole-Cell Computational Model Predicts Phenotype from Genotype
- (2012) Jonathan R. Karr et al. CELL
- Kinetic modelling of central carbon metabolism inEscherichia coli
- (2012) Kirill Peskov et al. FEBS Journal
- Accurate Atom-Mapping Computation for Biochemical Reactions
- (2012) Mario Latendresse et al. Journal of Chemical Information and Modeling
- Wisdom of crowds for robust gene network inference
- (2012) Daniel Marbach et al. NATURE METHODS
- Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage
- (2012) Ines Thiele et al. PLoS One
- The Pathway Tools Pathway Prediction Algorithm
- (2012) Peter D. Karp et al. Standards in Genomic Sciences
- Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT
- (2012) Rasmus Agren et al. PLoS Computational Biology
- OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities
- (2012) Ali R. Zomorrodi et al. PLoS Computational Biology
- Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters
- (2012) Roi Adadi et al. PLoS Computational Biology
- The Moderately Efficient Enzyme: Evolutionary and Physicochemical Trends Shaping Enzyme Parameters
- (2011) Arren Bar-Even et al. BIOCHEMISTRY
- Bacterial growth rate reflects a bottleneck in resource allocation
- (2011) A. Goelzer et al. BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
- Recommendations for terminology and databases for biochemical thermodynamics
- (2011) Robert A. Alberty et al. BIOPHYSICAL CHEMISTRY
- A retrosynthetic biology approach to metabolic pathway design for therapeutic production
- (2011) Pablo Carbonell et al. BMC Systems Biology
- Stereochemically Consistent Reaction Mapping and Identification of Multiple Reaction Mechanisms through Integer Linear Optimization
- (2011) Eric L. First et al. Journal of Chemical Information and Modeling
- Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol
- (2011) Harry Yim et al. Nature Chemical Biology
- Comparative Analysis of Proteome and Transcriptome Variation in Mouse
- (2011) Anatole Ghazalpour et al. PLoS Genetics
- Functional integration of a metabolic network model and expression data without arbitrary thresholding
- (2010) Paul A. Jensen et al. BIOINFORMATICS
- Pathway Activity Profiling (PAPi): from the metabolite profile to the metabolic pathway activity
- (2010) Raphael B. M. Aggio et al. BIOINFORMATICS
- iMAT: an integrative metabolic analysis tool
- (2010) Hadas Zur et al. BIOINFORMATICS
- Mass Action Stoichiometric Simulation Models: Incorporating Kinetics and Regulation into Stoichiometric Models
- (2010) Neema Jamshidi et al. BIOPHYSICAL JOURNAL
- BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
- (2010) Jan Schellenberger et al. BMC BIOINFORMATICS
- DBSolve Optimum: a software package for kinetic modeling which allows dynamic visualization of simulation results
- (2010) Nail M Gizzatkulov et al. BMC Systems Biology
- Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments
- (2010) Kai Zhuang et al. ISME Journal
- Evaluation of pKaEstimation Methods on 211 Druglike Compounds
- (2010) John Manchester et al. Journal of Chemical Information and Modeling
- Extended-Connectivity Fingerprints
- (2010) David Rogers et al. Journal of Chemical Information and Modeling
- Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism
- (2010) R.M.T. Fleming et al. JOURNAL OF THEORETICAL BIOLOGY
- ISIDA Property-Labelled Fragment Descriptors
- (2010) Fiorella Ruggiu et al. Molecular Informatics
- Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models
- (2010) Nathan E Lewis et al. Molecular Systems Biology
- Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism
- (2010) Livnat Jerby et al. Molecular Systems Biology
- The BioPAX community standard for pathway data sharing
- (2010) Emek Demir et al. NATURE BIOTECHNOLOGY
- A protocol for generating a high-quality genome-scale metabolic reconstruction
- (2010) Ines Thiele et al. Nature Protocols
- Probabilistic integrative modeling of genome-scale metabolic and regulatory networks inEscherichia coliandMycobacterium tuberculosis
- (2010) Sriram Chandrasekaran et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Production of biofuels and biochemicals: in need of an ORACLE
- (2010) Ljubisa Miskovic et al. TRENDS IN BIOTECHNOLOGY
- PACKMOL: A package for building initial configurations for molecular dynamics simulations
- (2009) L. Martínez et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- OpenFLUX: efficient modelling software for 13C-based metabolic flux analysis
- (2009) Lake-Ee Quek et al. Microbial Cell Factories
- Applications of genome-scale metabolic reconstructions
- (2009) Matthew A Oberhardt et al. Molecular Systems Biology
- System-wide molecular evidence for phenotypic buffering in Arabidopsis
- (2009) Jingyuan Fu et al. NATURE GENETICS
- The PubChem chemical structure sketcher
- (2009) Wolf D Ihlenfeldt et al. Journal of Cheminformatics
- GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions
- (2009) Vinay Satish Kumar et al. PLoS Computational Biology
- Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production
- (2009) Caroline Colijn et al. PLoS Computational Biology
- Ensemble Modeling of Metabolic Networks
- (2008) Linh M. Tran et al. BIOPHYSICAL JOURNAL
- Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks
- (2008) Matthew D. Jankowski et al. BIOPHYSICAL JOURNAL
- Impact of the solvent capacity constraint on E. coli metabolism
- (2008) Alexei Vazquez et al. BMC Systems Biology
- Quantifying Reductive Carboxylation Flux of Glutamine to Lipid in a Brown Adipocyte Cell Line
- (2008) Hyuntae Yoo et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- Formulating genome-scale kinetic models in the post-genome era
- (2008) Neema Jamshidi et al. Molecular Systems Biology
- NCBI BLAST: a better web interface
- (2008) M. Johnson et al. NUCLEIC ACIDS RESEARCH
- Context-Specific Metabolic Networks Are Consistent with Experiments
- (2008) Scott A. Becker et al. PLoS Computational Biology
- An elementary metabolite unit (EMU) based method of isotopically nonstationary flux analysis
- (2007) Jamey D. Young et al. BIOTECHNOLOGY AND BIOENGINEERING
Discover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversationAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started