COBRApy: COnstraints-Based Reconstruction and Analysis for Python.
作者： Ali Ebrahim , Joshua A Lerman , Bernhard O Palsson , Daniel R Hyduke
关键词:
摘要: … We have previously published the COBRA Toolbox [19] for MATLAB to … Flux variability analyses can be used to identify problems in model structure [40] or ‘pinch-points’ in a metabolic …
biomedcentral.com
springer.com
core.ac.uk
paperity.org参考文章(42)
Marnix H. Medema, Renske van Raaphorst, Eriko Takano, Rainer Breitling, Computational tools for the synthetic design of biochemical pathways Nature Reviews Microbiology. ,vol. 10, pp. 191- 202 ,(2012) , 10.1038/NRMICRO2717
Il-Kwon Kim, António Roldão, Verena Siewers, Jens Nielsen, A systems-level approach for metabolic engineering of yeast cell factories Fems Yeast Research. ,vol. 12, pp. 228- 248 ,(2012) , 10.1111/J.1567-1364.2011.00779.X
K. R. Patil, J. Nielsen, Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 102, pp. 2685- 2689 ,(2005) , 10.1073/PNAS.0406811102
Christian Frezza, Liang Zheng, Ori Folger, Kartik N. Rajagopalan, Elaine D. MacKenzie, Livnat Jerby, Massimo Micaroni, Barbara Chaneton, Julie Adam, Ann Hedley, Gabriela Kalna, Ian P. M. Tomlinson, Patrick J. Pollard, Dave G. Watson, Ralph J. Deberardinis, Tomer Shlomi, Eytan Ruppin, Eyal Gottlieb, Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase Nature. ,vol. 477, pp. 225- 228 ,(2011) , 10.1038/NATURE10363
Daniel R. Hyduke, Bernhard Ø. Palsson, Towards genome-scale signalling-network reconstructions Nature Reviews Genetics. ,vol. 11, pp. 297- 307 ,(2010) , 10.1038/NRG2750
Markus W. Covert, Bernhard Ø. Palsson, Transcriptional regulation in constraints-based metabolic models of Escherichia coli Journal of Biological Chemistry. ,vol. 277, pp. 28058- 28064 ,(2002) , 10.1074/JBC.M201691200
Alexei Vazquez, Qasim K Beg, Marcio A deMenezes, Jason Ernst, Ziv Bar-Joseph, Albert-László Barabási, László G Boros, Zoltán N Oltvai, Impact of the solvent capacity constraint on E. coli metabolism. BMC Systems Biology. ,vol. 2, pp. 7- 7 ,(2008) , 10.1186/1752-0509-2-7
Erwin P. Gianchandani, Andrew R. Joyce, Bernhard Ø. Palsson, Jason A. Papin, Functional States of the Genome-Scale Escherichia Coli Transcriptional Regulatory System PLoS Computational Biology. ,vol. 5, pp. e1000403- ,(2009) , 10.1371/JOURNAL.PCBI.1000403
J. C. Liao, R. Boscolo, Y.-L. Yang, L. M. Tran, C. Sabatti, V. P. Roychowdhury, Network component analysis: Reconstruction of regulatory signals in biological systems Proceedings of the National Academy of Sciences of the United States of America. ,vol. 100, pp. 15522- 15527 ,(2003) , 10.1073/PNAS.2136632100
Steffen Klamt, Axel von Kamp, An application programming interface for CellNetAnalyzer BioSystems. ,vol. 105, pp. 162- 168 ,(2011) , 10.1016/J.BIOSYSTEMS.2011.02.002