Improving prediction fidelity of cellular metabolism with kinetic descriptions

作者: Anupam Chowdhury , Ali Khodayari , Costas D Maranas

DOI: 10.1016/J.COPBIO.2015.08.011

关键词: Metabolic engineeringFidelityBioinformaticsKinetic informationResearch groupsCellular metabolismBiologyTest data generationBiochemical engineering

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

参考文章(65)
Howard M. Salis, The ribosome binding site calculator. Methods in Enzymology. ,vol. 498, pp. 19- 42 ,(2011) , 10.1016/B978-0-12-385120-8.00002-4
Karl Kochanowski, Uwe Sauer, Elad Noor, Posttranslational regulation of microbial metabolism. Current Opinion in Microbiology. ,vol. 27, pp. 10- 17 ,(2015) , 10.1016/J.MIB.2015.05.007
Wolfram Liebermeister, Edda Klipp, Bringing metabolic networks to life: convenience rate law and thermodynamic constraints. Theoretical Biology and Medical Modelling. ,vol. 3, pp. 41- 41 ,(2006) , 10.1186/1742-4682-3-41
Kai Zhuang, Mounir Izallalen, Paula Mouser, Hanno Richter, Carla Risso, Radhakrishnan Mahadevan, Derek R Lovley, Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments. The ISME Journal. ,vol. 5, pp. 305- 316 ,(2011) , 10.1038/ISMEJ.2010.117
Ida Schomburg, Antje Chang, Sandra Placzek, Carola Söhngen, Michael Rother, Maren Lang, Cornelia Munaretto, Susanne Ulas, Michael Stelzer, Andreas Grote, Maurice Scheer, Dietmar Schomburg, BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA Nucleic Acids Research. ,vol. 41, pp. 764- 772 ,(2012) , 10.1093/NAR/GKS1049
Shashank Agarwal, Hong Yu, Issac Kohane, BioN∅T: A searchable database of biomedical negated sentences BMC Bioinformatics. ,vol. 12, pp. 420- 420 ,(2011) , 10.1186/1471-2105-12-420
Anupam Chowdhury, Ali R. Zomorrodi, Costas D. Maranas, Bilevel optimization techniques in computational strain design Computers & Chemical Engineering. ,vol. 72, pp. 363- 372 ,(2015) , 10.1016/J.COMPCHEMENG.2014.06.007
Scott B. Crown, Christopher P. Long, Maciek R. Antoniewicz, Integrated 13C-metabolic flux analysis of 14 parallel labeling experiments in Escherichia coli. Metabolic Engineering. ,vol. 28, pp. 151- 158 ,(2015) , 10.1016/J.YMBEN.2015.01.001