Improving prediction fidelity of cellular metabolism with kinetic descriptions
- Authors:
- Publication Date:
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1250370
- Grant/Contract Number:
- SC0008091; SC0012377; EEC-0813570
- Resource Type:
- Publisher's Accepted Manuscript
- Journal Name:
- Current Opinion in Biotechnology
- Additional Journal Information:
- Journal Name: Current Opinion in Biotechnology Journal Volume: 36 Journal Issue: C; Journal ID: ISSN 0958-1669
- Publisher:
- Elsevier
- Country of Publication:
- United Kingdom
- Language:
- English
Citation Formats
Chowdhury, Anupam, Khodayari, Ali, and Maranas, Costas D. Improving prediction fidelity of cellular metabolism with kinetic descriptions. United Kingdom: N. p., 2015.
Web. doi:10.1016/j.copbio.2015.08.011.
Chowdhury, Anupam, Khodayari, Ali, & Maranas, Costas D. Improving prediction fidelity of cellular metabolism with kinetic descriptions. United Kingdom. https://doi.org/10.1016/j.copbio.2015.08.011
Chowdhury, Anupam, Khodayari, Ali, and Maranas, Costas D. Tue .
"Improving prediction fidelity of cellular metabolism with kinetic descriptions". United Kingdom. https://doi.org/10.1016/j.copbio.2015.08.011.
@article{osti_1250370,
title = {Improving prediction fidelity of cellular metabolism with kinetic descriptions},
author = {Chowdhury, Anupam and Khodayari, Ali and Maranas, Costas D.},
abstractNote = {},
doi = {10.1016/j.copbio.2015.08.011},
journal = {Current Opinion in Biotechnology},
number = C,
volume = 36,
place = {United Kingdom},
year = {Tue Dec 01 00:00:00 EST 2015},
month = {Tue Dec 01 00:00:00 EST 2015}
}
Free Publicly Available Full Text
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https://doi.org/10.1016/j.copbio.2015.08.011
https://doi.org/10.1016/j.copbio.2015.08.011
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Cited by: 24 works
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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
A kinetic model for curcumin production in Escherichia coli
journal, November 2014
- Machado, Daniel; Rodrigues, Lígia R.; Rocha, Isabel
- Biosystems, Vol. 125
Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression
journal, February 2013
- Qi, Lei S.; Larson, Matthew H.; Gilbert, Luke A.
- Cell, Vol. 152, Issue 5, p. 1173-1183
Metabolic control analysis of biochemical pathways based on a thermokinetic description of reaction rates
journal, January 1997
- Nielsen, Jens
- Biochemical Journal, Vol. 321, Issue 1
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
Towards the computational design of protein post-translational regulation
journal, June 2015
- Strumillo, Marta; Beltrao, Pedro
- Bioorganic & Medicinal Chemistry, Vol. 23, Issue 12
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 General Framework for Thermodynamically Consistent Parameterization and Efficient Sampling of Enzymatic Reactions
journal, April 2015
- Saa, Pedro; Nielsen, Lars K.
- PLOS Computational Biology, Vol. 11, Issue 4
Metabolic ensemble modeling for strain engineers
journal, October 2011
- Tan, Yikun; Liao, James C.
- Biotechnology Journal, Vol. 7, Issue 3
Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism
journal, April 2014
- Machado, Daniel; Herrgård, Markus
- PLoS Computational Biology, Vol. 10, Issue 4
Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis
journal, November 2013
- Blohm, Philipp; Frishman, Goar; Smialowski, Pawel
- Nucleic Acids Research, Vol. 42, Issue D1
How do base-pairing small RNAs evolve?
journal, April 2015
- Updegrove, Taylor B.; Shabalina, Svetlana A.; Storz, Gisela
- FEMS Microbiology Reviews, Vol. 39, Issue 3
Quantitative analysis of the fermentative metabolism of glycerol in Escherichia coli
journal, August 2011
- Cintolesi, Angela; Clomburg, James M.; Rigou, Venetia
- Biotechnology and Bioengineering, Vol. 109, Issue 1
Bilevel optimization techniques in computational strain design
journal, January 2015
- Chowdhury, Anupam; Zomorrodi, Ali R.; Maranas, Costas D.
- Computers & Chemical Engineering, Vol. 72
High-yield hydrogen production from biomass by in vitro metabolic engineering: Mixed sugars coutilization and kinetic modeling
journal, April 2015
- Rollin, Joseph A.; Martin del Campo, Julia; Myung, Suwan
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 16
Expression Atlas update—a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments
journal, December 2013
- Petryszak, Robert; Burdett, Tony; Fiorelli, Benedetto
- Nucleic Acids Research, Vol. 42, Issue D1
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
Evolution for exogenous octanoic acid tolerance improves carboxylic acid production and membrane integrity
journal, May 2015
- Royce, Liam A.; Yoon, Jong Moon; Chen, Yingxi
- Metabolic Engineering, Vol. 29
Integrated 13 C-metabolic flux analysis of 14 parallel labeling experiments in Escherichia coli
journal, March 2015
- Crown, Scott B.; Long, Christopher P.; Antoniewicz, Maciek R.
- Metabolic Engineering, Vol. 28
A kinetic-based approach to understanding heterologous mevalonate pathway function in E. coli : A Kinetic-Based Approach to Understanding Heterologous
journal, August 2014
- Weaver, Lane J.; Sousa, Mirta M. L.; Wang, George
- Biotechnology and Bioengineering, Vol. 112, Issue 1
Dynamic strain scanning optimization: an efficient strain design strategy for balanced yield, titer, and productivity. DySScO strategy for strain design
journal, January 2013
- Zhuang, Kai; Yang, Laurence; Cluett, William R.
- BMC Biotechnology, Vol. 13, Issue 1
Kinetic modelling of the Zymomonas mobilis Entner-Doudoroff pathway: insights into control and functionality
journal, October 2013
- Rutkis, R.; Kalnenieks, U.; Stalidzans, E.
- Microbiology, Vol. 159, Issue Pt_12
Testing Biochemistry Revisited: How In Vivo Metabolism Can Be Understood from In Vitro Enzyme Kinetics
journal, April 2012
- van Eunen, Karen; Kiewiet, José A. L.; Westerhoff, Hans V.
- PLoS Computational Biology, Vol. 8, Issue 4
Tracing the molecular basis of transcriptional dynamics in noisy data by using an experiment-based mathematical model
journal, December 2014
- Rybakova, Katja N.; Tomaszewska, Aleksandra; van Mourik, Simon
- Nucleic Acids Research, Vol. 43, Issue 1
Mathematical optimization applications in metabolic networks
journal, November 2012
- Zomorrodi, Ali R.; Suthers, Patrick F.; Ranganathan, Sridhar
- Metabolic Engineering, Vol. 14, Issue 6
Large‐scale identification of genetic design strategies using local search
journal, January 2009
- Lun, Desmond S.; Rockwell, Graham; Guido, Nicholas J.
- Molecular Systems Biology, Vol. 5, Issue 1
BioN∅T: A searchable database of biomedical negated sentences
journal, January 2011
- Agarwal, Shashank; Yu, Hong; Kohane, Issac
- BMC Bioinformatics, Vol. 12, Issue 1
A Semiquantitative Framework for Gene Regulatory Networks: Increasing the Time and Quantitative Resolution of Boolean Networks
journal, June 2015
- Kerkhofs, Johan; Geris, Liesbet
- PLOS ONE, Vol. 10, Issue 6
A system‐level model for the microbial regulatory genome
journal, July 2014
- Brooks, Aaron N.; Reiss, David J.; Allard, Antoine
- Molecular Systems Biology, Vol. 10, Issue 7
Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria
journal, June 2014
- Farasat, I.; Kushwaha, M.; Collens, J.
- Molecular Systems Biology, Vol. 10, Issue 6, p. 731-731
An extended dynamic model of Lactococcus lactis metabolism for mannitol and 2,3-butanediol production
journal, January 2014
- Costa, Rafael S.; Hartmann, Andras; Gaspar, Paula
- Molecular BioSystems, Vol. 10, Issue 3
The rise of regulatory RNA
journal, April 2014
- Morris, Kevin V.; Mattick, John S.
- Nature Reviews Genetics, Vol. 15, Issue 6
Dynamic simulation and metabolic re-design of a branched pathway using linlog kinetics
journal, July 2003
- Visser, Diana; Heijnen, Joseph J.
- Metabolic Engineering, Vol. 5, Issue 3
A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data
journal, September 2014
- Khodayari, Ali; Zomorrodi, Ali R.; Liao, James C.
- Metabolic Engineering, Vol. 25
Analysis of omics data with genome-scale models of metabolism
journal, January 2013
- Hyduke, Daniel R.; Lewis, Nathan E.; Palsson, Bernhard Ø.
- Mol. BioSyst., Vol. 9, Issue 2
Optimizing Metabolite Production Using Periodic Oscillations
journal, June 2014
- Sowa, Steven W.; Baldea, Michael; Contreras, Lydia M.
- PLoS Computational Biology, Vol. 10, Issue 6
Unraveling condition‐dependent networks of transcription factors that control metabolic pathway activity in yeast
journal, January 2010
- Fendt, Sarah‐Maria; Oliveira, Ana Paula; Christen, Stefan
- Molecular Systems Biology, Vol. 6, Issue 1
k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design
journal, February 2014
- Chowdhury, Anupam; Zomorrodi, Ali R.; Maranas, Costas D.
- PLoS Computational Biology, Vol. 10, Issue 2
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
Integration of expression data in genome-scale metabolic network reconstructions
journal, January 2012
- Blazier, Anna S.; Papin, Jason A.
- Frontiers in Physiology, Vol. 3
Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites
journal, November 2013
- Espah Borujeni, Amin; Channarasappa, Anirudh S.; Salis, Howard M.
- Nucleic Acids Research, Vol. 42, Issue 4
In vitro reconstitution and steady-state analysis of the fatty acid synthase from Escherichia coli
journal, October 2011
- Yu, X.; Liu, T.; Zhu, F.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 46
Wisdom of crowds for robust gene network inference
journal, July 2012
- Marbach, Daniel; Costello, James C.; Küffner, Robert
- Nature Methods, Vol. 9, Issue 8
A Mass Spectrometry Platform for a Streamlined Investigation of Proteasome Integrity, Posttranslational Modifications, and Inhibitor Binding
journal, March 2015
- Gersch, Malte; Hackl, Mathias W.; Dubiella, Christian
- Chemistry & Biology, Vol. 22, Issue 3
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
Bacterial adaptation through distributed sensing of metabolic fluxes
journal, January 2010
- Kotte, Oliver; Zaugg, Judith B.; Heinemann, Matthias
- Molecular Systems Biology, Vol. 6, Issue 1
Posttranslational regulation of microbial metabolism
journal, October 2015
- Kochanowski, Karl; Sauer, Uwe; Noor, Elad
- Current Opinion in Microbiology, Vol. 27
Advancing metabolic models with kinetic information
journal, October 2014
- Link, Hannes; Christodoulou, Dimitris; Sauer, Uwe
- Current Opinion in Biotechnology, Vol. 29
An integrative, multi‐scale, genome‐wide model reveals the phenotypic landscape of E scherichia coli
journal, July 2014
- Carrera, Javier; Estrela, Raissa; Luo, Jing
- Molecular Systems Biology, Vol. 10, Issue 7
Pathguide: a Pathway Resource List
journal, January 2006
- Bader, G. D.
- Nucleic Acids Research, Vol. 34, Issue 90001
Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments
journal, July 2010
- Zhuang, Kai; Izallalen, Mounir; Mouser, Paula
- The ISME Journal, Vol. 5, Issue 2
Connecting protein structure with predictions of regulatory sites
journal, April 2007
- Morozov, A. V.; Siggia, E. D.
- Proceedings of the National Academy of Sciences, Vol. 104, Issue 17, p. 7068-7073
Riboswitches: still a lot of undiscovered country
journal, March 2015
- Batey, Robert T.
- RNA, Vol. 21, Issue 4
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
Cooperativity and saturation in biochemical networks: A saturable formalism using Taylor series approximations
journal, January 2007
- Sorribas, Albert; Hernández-Bermejo, Benito; Vilaprinyo, Ester
- Biotechnology and Bioengineering, Vol. 97, Issue 5
Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models
journal, January 2013
- Cotten, Cameron; Reed, Jennifer L.
- BMC Bioinformatics, Vol. 14, Issue 1
Kinetic models in industrial biotechnology – Improving cell factory performance
journal, July 2014
- Almquist, Joachim; Cvijovic, Marija; Hatzimanikatis, Vassily
- Metabolic Engineering, Vol. 24
Advantages and limitations of current network inference methods
journal, August 2010
- De Smet, Riet; Marchal, Kathleen
- Nature Reviews Microbiology, Vol. 8, Issue 10
Next-generation genome-scale models for metabolic engineering
journal, December 2015
- King, Zachary A.; Lloyd, Colton J.; Feist, Adam M.
- Current Opinion in Biotechnology, Vol. 35
Computing the functional proteome: recent progress and future prospects for genome-scale models
journal, August 2015
- O’Brien, Edward J.; Palsson, Bernhard O.
- Current Opinion in Biotechnology, Vol. 34
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