Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery.
暂无分享,去创建一个
Aarash Bordbar | Ines Thiele | Jan Schellenberger | Ronan M T Fleming | Bernhard Ø Palsson | B. Palsson | R. Fleming | A. Bordbar | Jan Schellenberger | I. Thiele
[1] R. Mahadevan,et al. The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. , 2003, Metabolic engineering.
[2] Bernhard O. Palsson,et al. Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation , 2009, BMC Systems Biology.
[3] Bernhard O. Palsson,et al. Functional States of the Genome-Scale Escherichia Coli Transcriptional Regulatory System , 2009, PLoS Comput. Biol..
[4] Vassily Hatzimanikatis,et al. An algorithmic framework for genome-wide modeling and analysis of translation networks. , 2006, Biophysical journal.
[5] I. Jolliffe. Principal Component Analysis , 2002 .
[6] Tsutomu Suzuki,et al. molecular mechanism of lysidine synthesis that determines tRNA identity and codon recognition. , 2005, Molecular cell.
[7] B. Palsson,et al. Biochemical production capabilities of escherichia coli , 1993, Biotechnology and bioengineering.
[8] H. Mori,et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection , 2006, Molecular systems biology.
[9] V. Schachter,et al. Genome-scale models of bacterial metabolism: reconstruction and applications , 2008, FEMS microbiology reviews.
[10] Jason A. Papin,et al. Genome-scale microbial in silico models: the constraints-based approach. , 2003, Trends in biotechnology.
[11] Bernhard O. Palsson,et al. Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling , 2009, PLoS Comput. Biol..
[12] B. Palsson,et al. Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[13] M L Shuler,et al. Ribosomal protein limitations in Escherichia coli under conditions of high translational activity , 1994, Biotechnology and bioengineering.
[14] Peter D. Karp,et al. EcoCyc: a comprehensive database resource for Escherichia coli , 2004, Nucleic Acids Res..
[15] Bernhard O. Palsson,et al. Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition , 2006, BMC Bioinformatics.
[16] B. Palsson,et al. Candidate Metabolic Network States in Human Mitochondria , 2005, Journal of Biological Chemistry.
[17] Bernhard O. Palsson,et al. Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes , 2009, BMC Systems Biology.
[18] Daniel A Beard,et al. Extreme pathways and Kirchhoff's second law. , 2002, Biophysical journal.
[19] Ronan M. T. Fleming,et al. Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization , 2009, PLoS Comput. Biol..
[20] B. Palsson,et al. Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states. , 2004, Genome research.
[21] J. Keasling,et al. Mathematical Model of the lac Operon: Inducer Exclusion, Catabolite Repression, and Diauxic Growth on Glucose and Lactose , 1997, Biotechnology progress.
[22] Neal S. Holter,et al. Dynamic modeling of gene expression data. , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[23] G. Stephanopoulos,et al. Metabolic flux analysis of postburn hepatic hypermetabolism. , 2000, Metabolic engineering.
[24] Bernhard Ø Palsson,et al. In silico biotechnology. Era of reconstruction and interrogation. , 2004, Current opinion in biotechnology.
[25] T. Moon,et al. Mathematical Methods and Algorithms for Signal Processing , 1999 .
[26] D. J. Naylor,et al. Proteome-wide Analysis of Chaperonin-Dependent Protein Folding in Escherichia coli , 2005, Cell.
[27] Jason A. Papin,et al. Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk. , 2004, Journal of theoretical biology.
[28] Neal S. Holter,et al. Fundamental patterns underlying gene expression profiles: simplicity from complexity. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[29] F. Hartl,et al. Molecular Chaperones in the Cytosol: from Nascent Chain to Folded Protein , 2002, Science.
[30] S. Ueda,et al. Regulation of RNA polymerase sigma subunit synthesis in Escherichia coli: intracellular levels of four species of sigma subunit under various growth conditions , 1996, Journal of bacteriology.
[31] M C Mackey,et al. Dynamic regulation of the tryptophan operon: a modeling study and comparison with experimental data. , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[32] M. Nomura,et al. Regulation of Ribosome Biosynthesis in Escherichia coli and Saccharomyces cerevisiae: Diversity and Common Principles , 1999, Journal of bacteriology.
[33] B. Palsson,et al. Flux-concentration duality in dynamic nonequilibrium biological networks. , 2009, Biophysical journal.
[34] D. Botstein,et al. Singular value decomposition for genome-wide expression data processing and modeling. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[35] Holger Patzelt,et al. Trigger Factor and DnaK possess overlapping substrate pools and binding specificities , 2003, Molecular microbiology.
[36] B. Palsson,et al. Genome-scale models of microbial cells: evaluating the consequences of constraints , 2004, Nature Reviews Microbiology.
[37] M. Ehrenberg,et al. Free RNA polymerase and modeling global transcription in Escherichia coli. , 2003, Biochimie.
[38] Adam M. Feist,et al. Reconstruction of biochemical networks in microorganisms , 2009, Nature Reviews Microbiology.
[39] Markus J. Herrgård,et al. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. , 2004, Genome research.
[40] L Alberghina,et al. Analysis of a cell cycle model for Escherichia coli , 1980, Journal of mathematical biology.
[41] B. Palsson,et al. A protocol for generating a high-quality genome-scale metabolic reconstruction , 2010 .
[42] B. Palsson,et al. Towards multidimensional genome annotation , 2006, Nature Reviews Genetics.