Engineering microbial chemical factories using metabolic models
- Authors:
- Publication Date:
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1618982
- Resource Type:
- Published Article
- Journal Name:
- BMC Chemical Engineering
- Additional Journal Information:
- Journal Name: BMC Chemical Engineering Journal Volume: 1 Journal Issue: 1; Journal ID: ISSN 2524-4175
- Publisher:
- Springer Science + Business Media
- Country of Publication:
- Country unknown/Code not available
- Language:
- English
Citation Formats
Sarkar, Debolina, and Maranas, Costas D. Engineering microbial chemical factories using metabolic models. Country unknown/Code not available: N. p., 2019.
Web. doi:10.1186/s42480-019-0021-9.
Sarkar, Debolina, & Maranas, Costas D. Engineering microbial chemical factories using metabolic models. Country unknown/Code not available. https://doi.org/10.1186/s42480-019-0021-9
Sarkar, Debolina, and Maranas, Costas D. Fri .
"Engineering microbial chemical factories using metabolic models". Country unknown/Code not available. https://doi.org/10.1186/s42480-019-0021-9.
@article{osti_1618982,
title = {Engineering microbial chemical factories using metabolic models},
author = {Sarkar, Debolina and Maranas, Costas D.},
abstractNote = {},
doi = {10.1186/s42480-019-0021-9},
journal = {BMC Chemical Engineering},
number = 1,
volume = 1,
place = {Country unknown/Code not available},
year = {2019},
month = {11}
}
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1186/s42480-019-0021-9
https://doi.org/10.1186/s42480-019-0021-9
Other availability
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Systematic Construction of Kinetic Models from Genome-Scale Metabolic Networks
journal, November 2013
- Stanford, Natalie J.; Lubitz, Timo; Smallbone, Kieran
- PLoS ONE, Vol. 8, Issue 11
The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization
journal, November 2016
- Noor, Elad; Flamholz, Avi; Bar-Even, Arren
- PLOS Computational Biology, Vol. 12, Issue 11
Metabolic states with maximal specific rate carry flux through an elementary flux mode
journal, February 2014
- Wortel, Meike T.; Peters, Han; Hulshof , Josephus
- FEBS Journal, Vol. 281, Issue 6
A blueprint for human whole-cell modeling
journal, February 2018
- Szigeti, Balázs; Roth, Yosef D.; Sekar, John A. P.
- Current Opinion in Systems Biology, Vol. 7
New types of experimental data shape the use of enzyme kinetics for dynamic network modeling
journal, November 2013
- Tummler, Katja; Lubitz, Timo; Schelker, Max
- FEBS Journal, Vol. 281, Issue 2
The control of flux
journal, May 1995
- Kacser, H.; Burns, J. A.; Kacser, H.
- Biochemical Society Transactions, Vol. 23, Issue 2
Environments that Induce Synthetic Microbial Ecosystems
journal, November 2010
- Klitgord, Niels; Segrè, Daniel
- PLoS Computational Biology, Vol. 6, Issue 11
In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
journal, February 2001
- Edwards, Jeremy S.; Ibarra, Rafael U.; Palsson, Bernhard O.
- Nature Biotechnology, Vol. 19, Issue 2
Correlation between TCA cycle flux and glucose uptake rate during respiro-fermentative growth of Saccharomyces cerevisiae
journal, December 2009
- Heyland, Jan; Fu, Jianan; Blank, Lars M.
- Microbiology, Vol. 155, Issue 12
Incorporating genome-wide DNA sequence information into a dynamic whole-cell model of Escherichia coli: application to DNA replication
journal, September 2008
- Shuler, M. L.; Atlas, J. C.; Browning, S. T.
- IET Systems Biology, Vol. 2, Issue 5
Gobal optimization of hybrid kinetic/FBA models via outer-approximation
journal, January 2015
- Pozo, Carlos; Miró, Antoni; Guillén-Gosálbez, Gonzalo
- Computers & Chemical Engineering, Vol. 72
Computational evaluation of Synechococcus sp. PCC 7002 metabolism for chemical production
journal, April 2013
- Vu, Trang T.; Hill, Eric A.; Kucek, Leo A.
- Biotechnology Journal, Vol. 8, Issue 5
Kinetic modeling can describe in vivo glycolysis in Entamoeba histolytica: Modeling Entamoeba glycolysis
journal, August 2007
- Saavedra, Emma; Marín-Hernández, Alvaro; Encalada, Rusely
- FEBS Journal, Vol. 274, Issue 18
Large‐scale 13 C‐flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli
journal, January 2011
- Haverkorn van Rijsewijk, Bart R. B.; Nanchen, Annik; Nallet, Sophie
- Molecular Systems Biology, Vol. 7, Issue 1
A diurnal flux balance model of Synechocystis sp. PCC 6803 metabolism
journal, January 2019
- Sarkar, Debolina; Mueller, Thomas J.; Liu, Deng
- PLOS Computational Biology, Vol. 15, Issue 1
Modeling of uncertainties in biochemical reactions
journal, October 2010
- Mišković, Ljubiša; Hatzimanikatis, Vassily
- Biotechnology and Bioengineering, Vol. 108, Issue 2
Rethinking Antibiotic Research and Development: World War II and the Penicillin Collaborative
journal, March 2013
- Quinn, Roswell
- American Journal of Public Health, Vol. 103, Issue 3
Metabolomics and systems biology: making sense of the soup
journal, June 2004
- Kell, D.
- Current Opinion in Microbiology, Vol. 7, Issue 3
Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism
journal, February 1992
- Savinell, Joanne M.; Palsson, Bernhard O.
- Journal of Theoretical Biology, Vol. 154, Issue 4
Approximative kinetic formats used in metabolic network modeling
journal, January 2005
- Heijnen, Joseph J.
- Biotechnology and Bioengineering, Vol. 91, Issue 5
Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110.
journal, January 1994
- Varma, A.; Palsson, B. O.
- Applied and Environmental Microbiology, Vol. 60, Issue 10
Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations
journal, March 2019
- Hameri, Tuure; Fengos, Georgios; Ataman, Meric
- Metabolic Engineering, Vol. 52
Validation and Optimization of a Yeast Dynamic Flux Balance Model using a Parallel Bioreactor System
journal, January 2013
- Hanly, Timothy J.; Tiernan, Aubrey R.; Henson, Michael A.
- IFAC Proceedings Volumes, Vol. 46, Issue 31
Systematic design and in vitro validation of novel one-carbon assimilation pathways
journal, December 2019
- Yang, Xue; Yuan, Qianqian; Luo, Hao
- Metabolic Engineering, Vol. 56
A Whole-Cell Computational Model Predicts Phenotype from Genotype
journal, July 2012
- Karr, Jonathan R.; Sanghvi, Jayodita C.; Macklin, Derek N.
- Cell, Vol. 150, Issue 2
A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains
journal, December 2016
- Khodayari, Ali; Maranas, Costas D.
- Nature Communications, Vol. 7, Issue 1
Thermodynamic constraints on the regulation of metabolic fluxes
journal, October 2018
- Dai, Ziwei; Locasale, Jason W.
- Journal of Biological Chemistry, Vol. 293, Issue 51
Exploring the gap between dynamic and constraint-based models of metabolism
journal, March 2012
- Machado, Daniel; Costa, Rafael S.; Ferreira, Eugénio C.
- Metabolic Engineering, Vol. 14, Issue 2
Ensemble Modeling of Metabolic Networks
journal, December 2008
- Tran, Linh M.; Rizk, Matthew L.; Liao, James C.
- Biophysical Journal, Vol. 95, Issue 12
Emergent Biosynthetic Capacity in Simple Microbial Communities
journal, July 2014
- Chiu, Hsuan-Chao; Levy, Roie; Borenstein, Elhanan
- PLoS Computational Biology, Vol. 10, Issue 7
Metabolic engineering of Escherichia coli for 1-butanol production
journal, November 2008
- Atsumi, Shota; Cann, Anthony F.; Connor, Michael R.
- Metabolic Engineering, Vol. 10, Issue 6, p. 305-311
Metabolite concentrations, fluxes and free energies imply efficient enzyme usage
journal, May 2016
- Park, Junyoung O.; Rubin, Sara A.; Xu, Yi-Fan
- Nature Chemical Biology, Vol. 12, Issue 7
Transgenic plants in the biopharmaceutical market
journal, February 2005
- Twyman, Richard M.; Schillberg, Stefan; Fischer, Rainer
- Expert Opinion on Emerging Drugs, Vol. 10, Issue 1
Design principles and operating principles: the yin and yang of optimal functioning
journal, March 2003
- Voit, Eberhard O.
- Mathematical Biosciences, Vol. 182, Issue 1
Metabolic flux distributions inCorynebacterium glutamicum during growth and lysine overproduction
journal, March 2000
- Vallino, Joseph J.; Stephanopoulos, Gregory
- Biotechnology and Bioengineering, Vol. 67, Issue 6
Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry: Do we understand yeast glycolysis?
journal, September 2000
- Teusink, Bas; Passarge, Jutta; Reijenga, Corinne A.
- European Journal of Biochemistry, Vol. 267, Issue 17
Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis–Menten and approximate kinetic equations
journal, May 2010
- Costa, Rafael S.; Machado, Daniel; Rocha, Isabel
- Biosystems, Vol. 100, Issue 2
A probabilistic approach to identify putative drug targets in biochemical networks
journal, December 2010
- Murabito, Ettore; Smallbone, Kieran; Swinton, Jonathan
- Journal of The Royal Society Interface, Vol. 8, Issue 59
Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates.
journal, January 1993
- Varma, A.; Boesch, B. W.; Palsson, B. O.
- Applied and Environmental Microbiology, Vol. 59, Issue 8
Using Gene Essentiality and Synthetic Lethality Information to Correct Yeast and CHO Cell Genome-Scale Models
journal, September 2015
- Chowdhury, Ratul; Chowdhury, Anupam; Maranas, Costas
- Metabolites, Vol. 5, Issue 4
Reducing the allowable kinetic space by constructing ensemble of dynamic models with the same steady-state flux
journal, January 2011
- Tan, Yikun; Lafontaine Rivera, Jimmy G.; Contador, Carolina A.
- Metabolic Engineering, Vol. 13, Issue 1
Kinetic modelling of plant metabolic pathways
journal, March 2012
- Rohwer, Johann M.
- Journal of Experimental Botany, Vol. 63, Issue 6
Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol
journal, May 2011
- Yim, Harry; Haselbeck, Robert; Niu, Wei
- Nature Chemical Biology, Vol. 7, Issue 7
Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation
journal, April 2010
- Liebermeister, Wolfram; Uhlendorf, Jannis; Klipp, Edda
- Bioinformatics, Vol. 26, Issue 12
Structural kinetic modeling of metabolic networks
journal, July 2006
- Steuer, R.; Gross, T.; Selbig, J.
- Proceedings of the National Academy of Sciences, Vol. 103, Issue 32
Improving prediction fidelity of cellular metabolism with kinetic descriptions
journal, December 2015
- Chowdhury, Anupam; Khodayari, Ali; Maranas, Costas D.
- Current Opinion in Biotechnology, Vol. 36
Kinetic modeling of the Calvin cycle identifies flux control and stable metabolomes in Synechocystis carbon fixation
journal, October 2018
- Janasch, Markus; Asplund-Samuelsson, Johannes; Steuer, Ralf
- Journal of Experimental Botany
Cofactor Specificity of the Bifunctional Alcohol and Aldehyde Dehydrogenase (AdhE) in Wild-Type and Mutant Clostridium thermocellum and Thermoanaerobacterium saccharolyticum
journal, May 2015
- Zheng, Tianyong; Olson, Daniel G.; Tian, Liang
- Journal of Bacteriology, Vol. 197, Issue 15
Metabolite profiling: from diagnostics to systems biology
journal, September 2004
- Fernie, Alisdair R.; Trethewey, Richard N.; Krotzky, Arno J.
- Nature Reviews Molecular Cell Biology, Vol. 5, Issue 9
Toward Scalable Whole-Cell Modeling of Human Cells
conference, January 2016
- Goldberg, Arthur P.; Chew, Yin Hoon; Karr, Jonathan R.
- Proceedings of the 2016 annual ACM Conference on SIGSIM Principles of Advanced Discrete Simulation - SIGSIM-PADS '16
Expanding a dynamic flux balance model of yeast fermentation to genome-scale
journal, January 2011
- Vargas, Felipe A.; Pizarro, Francisco; Pérez-Correa, J. Ricardo
- BMC Systems Biology, Vol. 5, Issue 1
Models describing the kinetics of ribulose biphosphate carboxylase-oxygenase
journal, April 1979
- Farquhar, Graham D.
- Archives of Biochemistry and Biophysics, Vol. 193, Issue 2
The challenges of in silico biology
journal, November 2000
- Palsson, Bernhard
- Nature Biotechnology, Vol. 18, Issue 11
Metabolic Control Analysis under Uncertainty: Framework Development and Case Studies
journal, December 2004
- Wang, Liqing; Birol, Inanç; Hatzimanikatis, Vassily
- Biophysical Journal, Vol. 87, Issue 6
Multilevel engineering of the upstream module of aromatic amino acid biosynthesis in Saccharomyces cerevisiae for high production of polymer and drug precursors
journal, July 2017
- Suástegui, Miguel; Yu Ng, Chiam; Chowdhury, Anupam
- Metabolic Engineering, Vol. 42
Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism
journal, February 2014
- Noor, Elad; Bar-Even, Arren; Flamholz, Avi
- PLoS Computational Biology, Vol. 10, Issue 2
Thermodynamic analysis of the pathway for ethanol production from cellobiose in Clostridium thermocellum
journal, September 2019
- Dash, Satyakam; Olson, Daniel G.; Joshua Chan, Siu Hung
- Metabolic Engineering, Vol. 55
Metabolic gene–deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes
journal, September 2004
- Fong, Stephen S.; Palsson, Bernhard Ø
- Nature Genetics, Vol. 36, Issue 10
Something from nothing − bridging the gap between constraint-based and kinetic modelling: Constraint-based meets kinetic modelling
journal, October 2007
- Smallbone, Kieran; Simeonidis, Evangelos; Broomhead, David S.
- FEBS Journal, Vol. 274, Issue 21
Bringing metabolic networks to life: convenience rate law and thermodynamic constraints
journal, December 2006
- Liebermeister, Wolfram; Klipp, Edda
- Theoretical Biology and Medical Modelling, Vol. 3, Issue 1
Diurnal Regulation of Cellular Processes in the Cyanobacterium Synechocystis sp. Strain PCC 6803: Insights from Transcriptomic, Fluxomic, and Physiological Analyses
journal, May 2016
- Saha, Rajib; Liu, Deng; Hoynes-O’Connor, Allison
- mBio, Vol. 7, Issue 3
Simulation of cellular biochemical system kinetics: Simulation of cellular biochemical system kinetics
journal, December 2010
- Beard, Daniel A.
- Wiley Interdisciplinary Reviews: Systems Biology and Medicine, Vol. 3, Issue 2
Fat synthesis in adipose tissue. An examination of stoichiometric constraints
journal, September 1986
- Fell, D. A.; Small, J. R.
- Biochemical Journal, Vol. 238, Issue 3
Assessing the Metabolic Impact of Nitrogen Availability Using a Compartmentalized Maize Leaf Genome-Scale Model
journal, September 2014
- Simons, M.; Saha, R.; Amiour, N.
- PLANT PHYSIOLOGY, Vol. 166, Issue 3
Simple constrained-optimization view of acetate overflow inE. coli
journal, March 1990
- Majewski, R. A.; Domach, M. M.
- Biotechnology and Bioengineering, Vol. 35, Issue 7
2H and 13C metabolic flux analysis elucidates in vivo thermodynamics of the ED pathway in Zymomonas mobilis
journal, July 2019
- Jacobson, Tyler B.; Adamczyk, Paul A.; Stevenson, David M.
- Metabolic Engineering, Vol. 54
Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli
journal, May 2005
- Alper, Hal; Jin, Yong-Su; Moxley, J. F.
- Metabolic Engineering, Vol. 7, Issue 3
Control of Bacterial Fermentations
journal, November 1987
- Bajpai, Rakesh
- Annals of the New York Academy of Sciences, Vol. 506, Issue 1 Biochemical E
Metabolic Control Analysis: A Tool for Designing Strategies to Manipulate Metabolic Pathways
journal, January 2008
- Moreno-Sánchez, Rafael; Saavedra, Emma; Rodríguez-Enríquez, Sara
- Journal of Biomedicine and Biotechnology, Vol. 2008
Fed-batch cultivation of animal cells using different medium design concepts and feeding strategies
journal, January 2006
- Xie, Liangzhi; Wang, Daniel I. C.
- Biotechnology and Bioengineering, Vol. 95, Issue 2
Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli
journal, September 2002
- Mahadevan, Radhakrishnan; Edwards, Jeremy S.; Doyle, Francis J.
- Biophysical Journal, Vol. 83, Issue 3
Dynamic flux balance modeling to increase the production of high-value compounds in green microalgae
journal, August 2016
- Flassig, Robert J.; Fachet, Melanie; Höffner, Kai
- Biotechnology for Biofuels, Vol. 9, Issue 1
Clostridium butyricum population balance model: Predicting dynamic metabolic flux distributions using an objective function related to extracellular glycerol content
journal, December 2018
- Serrano-Bermúdez, Luis Miguel; González Barrios, Andrés Fernando; Montoya, Dolly
- PLOS ONE, Vol. 13, Issue 12
Predictions for oxygen supply control to enhance population stability of engineered production strains
journal, February 1994
- Varma, Amit; Palsson, Bernhard O.
- Biotechnology and Bioengineering, Vol. 43, Issue 4
Multidimensional Optimality of Microbial Metabolism
journal, May 2012
- Schuetz, R.; Zamboni, N.; Zampieri, M.
- Science, Vol. 336, Issue 6081
Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints
journal, August 2013
- Chakrabarti, Anirikh; Miskovic, Ljubisa; Soh, Keng Cher
- Biotechnology Journal, Vol. 8, Issue 9
The stability and robustness of metabolic states: identifying stabilizing sites in metabolic networks
journal, January 2007
- Grimbs, Sergio; Selbig, Joachim; Bulik, Sascha
- Molecular Systems Biology, Vol. 3, Issue 1
Estimating optimal profiles of genetic alterations using constraint-based models
journal, January 2004
- Gadkar, Kapil G.; Doyle III, Francis J.; Edwards, Jeremy S.
- Biotechnology and Bioengineering, Vol. 89, Issue 2
What is flux balance analysis?
journal, March 2010
- Orth, Jeffrey D.; Thiele, Ines; Palsson, Bernhard Ø
- Nature Biotechnology, Vol. 28, Issue 3
iML1515, a knowledgebase that computes Escherichia coli traits
journal, October 2017
- Monk, Jonathan M.; Lloyd, Colton J.; Brunk, Elizabeth
- Nature Biotechnology, Vol. 35, Issue 10
Glycolysis in Entamoeba histolytica: Biochemical characterization of recombinant glycolytic enzymes and flux control analysis
journal, March 2005
- Saavedra, Emma; Encalada, Rusely; Pineda, Erika
- FEBS Journal, Vol. 272, Issue 7
Optimization-driven identification of genetic perturbations accelerates the convergence of model parameters in ensemble modeling of metabolic networks
journal, June 2013
- Zomorrodi, Ali R.; Lafontaine Rivera, Jimmy G.; Liao, James C.
- Biotechnology Journal, Vol. 8, Issue 9