Literature DB >> 11246024

Metabolic modeling of microbial strains in silico.

M W Covert1, C H Schilling, I Famili, J S Edwards, I I Goryanin, E Selkov, B O Palsson.   

Abstract

The large volume of genome-scale data that is being produced and made available in databases on the World Wide Web is demanding the development of integrated mathematical models of cellular processes. The analysis of reconstructed metabolic networks as systems leads to the development of an in silico or computer representation of collections of cellular metabolic constituents, their interactions and their integrated function as a whole. The use of quantitative analysis methods to generate testable hypotheses and drive experimentation at a whole-genome level signals the advent of a systemic modeling approach to cellular and molecular biology.

Mesh:

Year:  2001        PMID: 11246024     DOI: 10.1016/s0968-0004(00)01754-0

Source DB:  PubMed          Journal:  Trends Biochem Sci        ISSN: 0968-0004            Impact factor:   13.807


  72 in total

Review 1.  Thirteen years of building constraint-based in silico models of Escherichia coli.

Authors:  Jennifer L Reed; Bernhard Ø Palsson
Journal:  J Bacteriol       Date:  2003-05       Impact factor: 3.490

2.  Design then mutate.

Authors:  Jeff Hasty
Journal:  Proc Natl Acad Sci U S A       Date:  2002-12-16       Impact factor: 11.205

3.  Extreme pathway lengths and reaction participation in genome-scale metabolic networks.

Authors:  Jason A Papin; Nathan D Price; Bernhard Ø Palsson
Journal:  Genome Res       Date:  2002-12       Impact factor: 9.043

Review 4.  It is all about metabolic fluxes.

Authors:  Jens Nielsen
Journal:  J Bacteriol       Date:  2003-12       Impact factor: 3.490

5.  Flux coupling analysis of genome-scale metabolic network reconstructions.

Authors:  Anthony P Burgard; Evgeni V Nikolaev; Christophe H Schilling; Costas D Maranas
Journal:  Genome Res       Date:  2004-01-12       Impact factor: 9.043

6.  The ERGO genome analysis and discovery system.

Authors:  Ross Overbeek; Niels Larsen; Theresa Walunas; Mark D'Souza; Gordon Pusch; Eugene Selkov; Konstantinos Liolios; Viktor Joukov; Denis Kaznadzey; Iain Anderson; Anamitra Bhattacharyya; Henry Burd; Warren Gardner; Paul Hanke; Vinayak Kapatral; Natalia Mikhailova; Olga Vasieva; Andrei Osterman; Veronika Vonstein; Michael Fonstein; Natalia Ivanova; Nikos Kyrpides
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

7.  Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices.

Authors:  Nathan D Price; Jennifer L Reed; Jason A Papin; Iman Famili; Bernhard O Palsson
Journal:  Biophys J       Date:  2003-02       Impact factor: 4.033

8.  Genome-scale metabolic model of Helicobacter pylori 26695.

Authors:  Christophe H Schilling; Markus W Covert; Iman Famili; George M Church; Jeremy S Edwards; Bernhard O Palsson
Journal:  J Bacteriol       Date:  2002-08       Impact factor: 3.490

9.  Extreme pathway analysis of human red blood cell metabolism.

Authors:  Sharon J Wiback; Bernhard O Palsson
Journal:  Biophys J       Date:  2002-08       Impact factor: 4.033

10.  Regulatory network of Escherichia coli: consistency between literature knowledge and microarray profiles.

Authors:  Rosa María Gutiérrez-Ríos; David A Rosenblueth; José Antonio Loza; Araceli M Huerta; Jeremy D Glasner; Fred R Blattner; Julio Collado-Vides
Journal:  Genome Res       Date:  2003-11       Impact factor: 9.043

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