Literature DB >> 18026122

New surveyor tools for charting microbial metabolic maps.

Rainer Breitling1, Dennis Vitkup, Michael P Barrett.   

Abstract

The computational reconstruction and analysis of cellular models of microbial metabolism is one of the great success stories of systems biology. The extent and quality of metabolic network reconstructions is, however, limited by the current state of biochemical knowledge. Can experimental high-throughput data be used to improve and expand network reconstructions to include unexplored areas of metabolism? Recent advances in experimental technology and analytical methods bring this aim an important step closer to realization. Data integration will play a particularly important part in exploiting the new experimental opportunities.

Mesh：

Year:  2008        PMID： 18026122     DOI： 10.1038/nrmicro1797

Source DB:  PubMed          Journal:  Nat Rev Microbiol        ISSN： 1740-1526            Impact factor:   60.633


  33 in total

Review 1.  Carbon metabolism of intracellular bacterial pathogens and possible links to virulence.

Authors:  Wolfgang Eisenreich; Thomas Dandekar; Jürgen Heesemann; Werner Goebel
Journal:  Nat Rev Microbiol       Date:  2010-05-10       Impact factor: 60.633

Review 2.  Computational tools for the synthetic design of biochemical pathways.

Authors:  Marnix H Medema; Renske van Raaphorst; Eriko Takano; Rainer Breitling
Journal:  Nat Rev Microbiol       Date:  2012-01-23       Impact factor: 60.633

3.  Prediction of metabolic fluxes by incorporating genomic context and flux-converging pattern analyses.

Authors:  Jong Myoung Park; Tae Yong Kim; Sang Yup Lee
Journal:  Proc Natl Acad Sci U S A       Date:  2010-08-02       Impact factor: 11.205

Review 4.  Systematizing the generation of missing metabolic knowledge.

Authors:  Jeffrey D Orth; Bernhard Ø Palsson
Journal:  Biotechnol Bioeng       Date:  2010-10-15       Impact factor: 4.530

Review 5.  Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content.

Authors:  Nathan E Lewis; Byung-Kwan Cho; Eric M Knight; Bernhard O Palsson
Journal:  J Bacteriol       Date:  2009-04-10       Impact factor: 3.490

Review 6.  The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli.

Authors:  Adam M Feist; Bernhard Ø Palsson
Journal:  Nat Biotechnol       Date:  2008-06       Impact factor: 54.908

7.  A systems biology framework for modeling metabolic enzyme inhibition of Mycobacterium tuberculosis.

Authors:  Xin Fang; Anders Wallqvist; Jaques Reifman
Journal:  BMC Syst Biol       Date:  2009-09-15

8.  BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions.

Authors:  Jan Schellenberger; Junyoung O Park; Tom M Conrad; Bernhard Ø Palsson
Journal:  BMC Bioinformatics       Date:  2010-04-29       Impact factor: 3.169

9.  Reconstruction and validation of RefRec: a global model for the yeast molecular interaction network.

Authors:  Tommi Aho; Henrikki Almusa; Jukka Matilainen; Antti Larjo; Pekka Ruusuvuori; Kaisa-Leena Aho; Thomas Wilhelm; Harri Lähdesmäki; Andreas Beyer; Manu Harju; Sharif Chowdhury; Kalle Leinonen; Christophe Roos; Olli Yli-Harja
Journal:  PLoS One       Date:  2010-05-14       Impact factor: 3.240

10.  Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network.

Authors:  Germán Plata; Tzu-Lin Hsiao; Kellen L Olszewski; Manuel Llinás; Dennis Vitkup
Journal:  Mol Syst Biol       Date:  2010-09-07       Impact factor: 11.429
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