Improving prediction fidelity of cellular metabolism with kinetic descriptions

Current Opinion in Biotechnology
Anupam ChowdhuryCostas D Maranas

Abstract

Several modeling frameworks for describing and redirecting cellular metabolism have been developed keeping pace with the rapid development in high-throughput data generation and advances in metabolic engineering techniques. The incorporation of kinetic information within stoichiometry-only modeling techniques offers potential advantages for improved phenotype prediction and consequently more precise computational strain design. In addition to substrate-level kinetic regulatory information, the integration of a number of additional layers of regulation at the transcription, translation, and post-translation levels is sought after by many research groups. However, the practical integration of these complex biological processes into a unified framework amenable to design remains an ongoing challenge.

References

Sep 2, 2003·Metabolic Engineering·Diana Visser, Joseph J Heijnen
Oct 7, 2004·Biophysical Journal·Liqing WangVassily Hatzimanikatis
Dec 31, 2005·Nucleic Acids Research·Gary D BaderChris Sander
Dec 19, 2006·Theoretical Biology & Medical Modelling·Wolfram Liebermeister, Edda Klipp
Apr 18, 2007·Proceedings of the National Academy of Sciences of the United States of America·Alexandre V Morozov, Eric D Siggia
Aug 20, 2009·Molecular Systems Biology·Desmond S LunGeorge M Church
Mar 10, 2010·Molecular Systems Biology·Oliver KotteMatthias Heinemann
Sep 2, 2010·Nature Reviews. Microbiology·Riet De Smet, Kathleen Marchal
May 24, 2011·Methods in Enzymology·Howard M Salis
Aug 23, 2011·Biotechnology and Bioengineering·Angela CintolesiRamon Gonzalez
Oct 25, 2011·Biotechnology Journal·Yikun Tan, James C Liao
Oct 29, 2011·BMC Bioinformatics·Shashank AgarwalIssac Kohane
Nov 2, 2011·Proceedings of the National Academy of Sciences of the United States of America·Xingye YuChaitan Khosla
May 10, 2012·PLoS Computational Biology·Karen van EunenBarbara M Bakker
Jul 17, 2012·Nature Methods·Daniel MarbachGustavo Stolovitzky
Jul 24, 2012·Cell·Jonathan R KarrMarkus W Covert
Aug 31, 2012·Frontiers in Physiology·Anna S Blazier, Jason A Papin
Oct 3, 2012·Metabolic Engineering·Ali R ZomorrodiCostas D Maranas
Dec 19, 2012·Molecular BioSystems·Daniel R HydukeBernhard Ø Palsson
Dec 11, 2013·PloS One·Natalie J StanfordWolfram Liebermeister
Feb 19, 2014·Current Opinion in Biotechnology·Hannes LinkUwe Sauer
Mar 4, 2014·PLoS Computational Biology·Anupam ChowdhuryCostas D Maranas
Apr 22, 2014·Metabolic Engineering·Joachim AlmquistMats Jirstrand
Apr 30, 2014·Nature Reviews. Genetics·Kevin V Morris, John S Mattick
Jun 6, 2014·PLoS Computational Biology·Steven W SowaLydia M Contreras
Jun 15, 2014·Metabolic Engineering·Ali KhodayariCostas D Maranas
Jun 24, 2014·Molecular Systems Biology·Iman FarasatHoward M Salis
Jul 2, 2014·Biotechnology and Bioengineering·Lane J WeaverJay D Keasling
Jul 6, 2014·Molecular Systems Biology·Javier CarreraIlias Tagkopoulos
Jul 17, 2014·Molecular Systems Biology·Aaron N BrooksNitin S Baliga
Sep 15, 2014·Bio Systems·Daniel MachadoIsabel Rocha
Jan 13, 2015·Current Opinion in Biotechnology·Zachary A KingBernhard O Palsson

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Citations

Jan 13, 2016·FEMS Microbiology Letters·Satyakam DashCostas D Maranas
Jul 16, 2016·Scientific Reports·Pedro A Saa, Lars K Nielsen
Dec 20, 2017·Proceedings of the National Academy of Sciences of the United States of America·Christopher P LongMaciek R Antoniewicz
Nov 5, 2019·PLoS Computational Biology·Peter C St JohnYannick J Bomble
Apr 7, 2016·NPJ Systems Biology and Applications·Victor ChubukovHéctor García Martín
Sep 7, 2017·Biophysical Journal·Jennifer L GreeneLinda J Broadbelt

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