skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Improving prediction fidelity of cellular metabolism with kinetic descriptions

Journal Article · · Current Opinion in Biotechnology

Sponsoring Organization:
USDOE
Grant/Contract Number:
SC0008091; SC0012377; EEC-0813570
OSTI ID:
1250370
Journal Information:
Current Opinion in Biotechnology, Journal Name: Current Opinion in Biotechnology Vol. 36 Journal Issue: C; ISSN 0958-1669
Publisher:
ElsevierCopyright Statement
Country of Publication:
United Kingdom
Language:
English
Citation Metrics:
Cited by: 24 works
Citation information provided by
Web of Science

References (61)

Systematic Construction of Kinetic Models from Genome-Scale Metabolic Networks journal November 2013
A kinetic model for curcumin production in Escherichia coli journal November 2014
Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression journal February 2013
Metabolic control analysis of biochemical pathways based on a thermokinetic description of reaction rates journal January 1997
Gobal optimization of hybrid kinetic/FBA models via outer-approximation journal January 2015
Towards the computational design of protein post-translational regulation journal June 2015
Large‐scale 13 C‐flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli journal January 2011
A General Framework for Thermodynamically Consistent Parameterization and Efficient Sampling of Enzymatic Reactions journal April 2015
Metabolic ensemble modeling for strain engineers journal October 2011
Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism journal April 2014
Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis journal November 2013
How do base-pairing small RNAs evolve? journal April 2015
Quantitative analysis of the fermentative metabolism of glycerol in Escherichia coli journal August 2011
Bilevel optimization techniques in computational strain design journal January 2015
High-yield hydrogen production from biomass by in vitro metabolic engineering: Mixed sugars coutilization and kinetic modeling journal April 2015
Expression Atlas update—a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments journal December 2013
A Whole-Cell Computational Model Predicts Phenotype from Genotype journal July 2012
Evolution for exogenous octanoic acid tolerance improves carboxylic acid production and membrane integrity journal May 2015
Integrated 13 C-metabolic flux analysis of 14 parallel labeling experiments in Escherichia coli journal March 2015
A kinetic-based approach to understanding heterologous mevalonate pathway function in E. coli : A Kinetic-Based Approach to Understanding Heterologous journal August 2014
Dynamic strain scanning optimization: an efficient strain design strategy for balanced yield, titer, and productivity. DySScO strategy for strain design journal January 2013
Kinetic modelling of the Zymomonas mobilis Entner-Doudoroff pathway: insights into control and functionality journal October 2013
Testing Biochemistry Revisited: How In Vivo Metabolism Can Be Understood from In Vitro Enzyme Kinetics journal April 2012
Tracing the molecular basis of transcriptional dynamics in noisy data by using an experiment-based mathematical model journal December 2014
Mathematical optimization applications in metabolic networks journal November 2012
Large‐scale identification of genetic design strategies using local search journal January 2009
BioN∅T: A searchable database of biomedical negated sentences journal January 2011
A Semiquantitative Framework for Gene Regulatory Networks: Increasing the Time and Quantitative Resolution of Boolean Networks journal June 2015
A system‐level model for the microbial regulatory genome journal July 2014
Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria journal June 2014
An extended dynamic model of Lactococcus lactis metabolism for mannitol and 2,3-butanediol production journal January 2014
The rise of regulatory RNA journal April 2014
Dynamic simulation and metabolic re-design of a branched pathway using linlog kinetics journal July 2003
A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data journal September 2014
Analysis of omics data with genome-scale models of metabolism journal January 2013
Optimizing Metabolite Production Using Periodic Oscillations journal June 2014
Unraveling condition‐dependent networks of transcription factors that control metabolic pathway activity in yeast journal January 2010
k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design journal February 2014
Metabolic Control Analysis under Uncertainty: Framework Development and Case Studies journal December 2004
Integration of expression data in genome-scale metabolic network reconstructions journal January 2012
Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites journal November 2013
In vitro reconstitution and steady-state analysis of the fatty acid synthase from Escherichia coli journal October 2011
Wisdom of crowds for robust gene network inference journal July 2012
A Mass Spectrometry Platform for a Streamlined Investigation of Proteasome Integrity, Posttranslational Modifications, and Inhibitor Binding journal March 2015
Bringing metabolic networks to life: convenience rate law and thermodynamic constraints journal December 2006
Bacterial adaptation through distributed sensing of metabolic fluxes journal January 2010
Posttranslational regulation of microbial metabolism journal October 2015
Advancing metabolic models with kinetic information journal October 2014
An integrative, multi‐scale, genome‐wide model reveals the phenotypic landscape of E scherichia coli journal July 2014
Pathguide: a Pathway Resource List journal January 2006
Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments journal July 2010
Connecting protein structure with predictions of regulatory sites journal April 2007
Riboswitches: still a lot of undiscovered country journal March 2015
Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints journal August 2013
Cooperativity and saturation in biochemical networks: A saturable formalism using Taylor series approximations journal January 2007
Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models journal January 2013
Kinetic models in industrial biotechnology – Improving cell factory performance journal July 2014
Advantages and limitations of current network inference methods journal August 2010
Next-generation genome-scale models for metabolic engineering journal December 2015
Computing the functional proteome: recent progress and future prospects for genome-scale models journal August 2015
Optimization-driven identification of genetic perturbations accelerates the convergence of model parameters in ensemble modeling of metabolic networks journal June 2013

Similar Records

A review of computational tools for design and reconstruction of metabolic pathways
Journal Article · Wed Nov 15 00:00:00 EST 2017 · Synthetic and Systems Biotechnology · OSTI ID:1250370

Succinate Overproduction: A Case Study of Computational Strain Design Using a Comprehensive Escherichia coli Kinetic Model
Journal Article · Mon Jan 05 00:00:00 EST 2015 · Frontiers in Bioengineering and Biotechnology · OSTI ID:1250370

Pathway design using de novo steps through uncharted biochemical spaces
Journal Article · Fri Jan 12 00:00:00 EST 2018 · Nature Communications · OSTI ID:1250370

Related Subjects