Citations
| 132 |
Systems Biology : Properties of Reconstructed Networks
- Palsson
- 2006
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Citation Context ...2, 3]sto the analysis of complex biological systems have proven to be very useful.sThis difference between the physicochemical sciencessand the physical sciences or engineering is illustrated insRef. =-=[14]-=-. All theory-based considerations (i.e., engineering and physics) lead one to attempt to seek an “exact” solution, and typically computed based on the lawssof physics and chemistry. However, constrain... |
| 130 |
Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network
- Förster, Famili, et al.
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Citation Context ...truction consisting of the chemicalsreactions that transport and interconvert metabolitesswithin yeast. This network reconstruction was based on asprevious reconstruction, termed S. cerevisiae_iFF708s=-=[15]-=-. The general features of S. cerevisiae_iND750 aresshown in the Table 1 of Ref. [9].sA SBML format file to the model S. cerevisiae_iND750 can be downloaded from the supplementary information of Ref. [... |
| 113 |
A genomescale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Molecular systems biology
- Feist, Henry, et al.
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Citation Context ...nerated. Gene-protein-reactions(GPR) associated models can keep track of associationssbetween genes, proteins, and reactions [4], and thereshave been several genome-scale GPR models, such as E.scol i =-=[4,5]-=- , S. aureus [6], H. pylori [7], M. barkeri[8], S.scerevisiae [9] and B. subtilis [10]. A reconstruction issherein defined as the list of biochemical reactions occurring in a particular cellular syste... |
| 78 |
Reconstruction and validation of saccharomyces cerevisiae ind750, a fully compartmentalized genome-scale metabolic model
- Duarte, Herrgard, et al.
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Citation Context ...ck of associationssbetween genes, proteins, and reactions [4], and thereshave been several genome-scale GPR models, such as E.scol i [4,5] , S. aureus [6], H. pylori [7], M. barkeri[8], S.scerevisiae =-=[9]-=- and B. subtilis [10]. A reconstruction issherein defined as the list of biochemical reactions occurring in a particular cellular system and the associationssbetween these reactions and relevant prote... |
| 75 | Global organization of metabolic fluxes in the bacterium Escherichia coli. - Almaas, Kovacs, et al. - 2004 |
| 75 | Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast - Papp, Pal, et al. |
| 61 | Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network.” - Famili, Forster, et al. - 2003 |
| 53 |
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA
- Becker, Feist, et al.
- 2007
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Citation Context ...red research, we here calculated the flux distribution of S. cerevisiae_iND750 [9].sWhat we use is Sc_iND750_GlcMM.xml, the SBML filesthat is presented with the reconstruction of S. cerevisiae_iND750 =-=[11]-=-. The computational method we usedsis flux balance analysis (FBA) [11], one of the most fundamental genome-scale phenotypic calculations, whichscan simulate cellular growth. FBA is based on linearsopt... |
| 51 |
Genome-scale reconstruction of the metabolic network in staphylococcus aureus n315: an initial draft to the two-dimensional annotation
- Becker, Palsson
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Citation Context ...ein-reactions(GPR) associated models can keep track of associationssbetween genes, proteins, and reactions [4], and thereshave been several genome-scale GPR models, such as E.scol i [4,5] , S. aureus =-=[6]-=-, H. pylori [7], M. barkeri[8], S.scerevisiae [9] and B. subtilis [10]. A reconstruction issherein defined as the list of biochemical reactions occurring in a particular cellular system and the associ... |
| 33 |
Expanded metabolic reconstruction of helicobacter pylori (iit341 gsm/gpr): an in silico genome-scale characterization of single- and double-deletion mutants
- Thiele, Vo, et al.
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Citation Context ...PR) associated models can keep track of associationssbetween genes, proteins, and reactions [4], and thereshave been several genome-scale GPR models, such as E.scol i [4,5] , S. aureus [6], H. pylori =-=[7]-=-, M. barkeri[8], S.scerevisiae [9] and B. subtilis [10]. A reconstruction issherein defined as the list of biochemical reactions occurring in a particular cellular system and the associationssbetween ... |
| 23 | Modeling methanogenesis with a genome-scale metabolic reconstruction ofMethanosarcina barkeri,”Molecular Systems Biology,
- Feist, Scholten, et al.
- 2006
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Citation Context ...models can keep track of associationssbetween genes, proteins, and reactions [4], and thereshave been several genome-scale GPR models, such as E.scol i [4,5] , S. aureus [6], H. pylori [7], M. barkeri=-=[8]-=-, S.scerevisiae [9] and B. subtilis [10]. A reconstruction issherein defined as the list of biochemical reactions occurring in a particular cellular system and the associationssbetween these reactions... |
| 22 | Large-scale evaluation of in silico gene deletions in saccharomyces cerevisiae - Forster, Famili, et al. - 2003 |
| 14 | Schilling CH & Mahadevan R (2007) Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data - YK, BO, et al. |
| 14 | Properties of metabolic networks: structure versus function’, - Mahadevan, Palsson - 2005 |
| 4 |
Is there biological research beyond Systems Biology? A comparative analysis of terms. Molecular Systems Biology.1: Art
- Bork
- 2005
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Citation Context ...ilable,sbiology has transited from a data-poor to a data-rich environment. This has underscored the need for systemssanalysis in biology and systems biology has become asrapidly growing field as well =-=[1]-=-.sA change in mathematical modeling philosophy, i.e.,sbuilding and validating in silico models is also necessitated. Modern biological models need to meet new setssof criteria: organism-specific, data... |
| 4 |
2004 Genomescale models of microbial cells: evaluating the consequences of constraints
- Price, Reed, et al.
- 2005
(Show Context)
Citation Context ...needed, it is currently difficult to use these methods tosmodel genome-scale networks. To date, genome-scalesmodels of metabolism have only been analyzed with thesconstraint-based modeling philosophy =-=[2, 3]-=-. Genome-scale network models of diverse cellular processesssuch as signal transduction, transcriptional regulation andsmetabolism have been generated. Gene-protein-reactions(GPR) associated models ca... |
| 3 |
Genomescale microbial in silico models: the constraints-based approach. Trends in Biotechnology 21
- ND, JA, et al.
- 2003
(Show Context)
Citation Context ...needed, it is currently difficult to use these methods tosmodel genome-scale networks. To date, genome-scalesmodels of metabolism have only been analyzed with thesconstraint-based modeling philosophy =-=[2, 3]-=-. Genome-scale network models of diverse cellular processesssuch as signal transduction, transcriptional regulation andsmetabolism have been generated. Gene-protein-reactions(GPR) associated models ca... |
| 2 |
An expanded genome scale model of Escherichia coli K-12, Genome Biol
- Reed, Vo, et al.
- 2003
(Show Context)
Citation Context ...signal transduction, transcriptional regulation andsmetabolism have been generated. Gene-protein-reactions(GPR) associated models can keep track of associationssbetween genes, proteins, and reactions =-=[4]-=-, and thereshave been several genome-scale GPR models, such as E.scol i [4,5] , S. aureus [6], H. pylori [7], M. barkeri[8], S.scerevisiae [9] and B. subtilis [10]. A reconstruction issherein defined ... |
| 1 | amage, Nada Amin, Benno Schwikowski and Trey Ideker. (2003) Cytoscape: a software environment for integrated models of biomo- lecular interaction networks - Shannon, Markiel, et al. |
