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A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

Thiele, I. and Hyduke, D. R. and Steeb, B. and Fankam, G. and Allen, D. K. and Bazzani, S. and Charusanti, P. and Chen, F. -C. and Fleming, R. M. T. and Hsiung, C. A. and De Keersmaecker, S. C. J. and Liao, Y. -C. and Marchal, K. and Mo, M. L. and Ozdemir, E. and Raghunathan, A. and Reed, J. L. and Shin, S. -il and Sigurbjornsdottir, S. and Steinmann, J. and Sudarsan, S. and Swainston, N. and Thijs, I. M. and Zengler, K. and Palsson, B. O. and Adkins, J. N. and Bumann, D.. (2011) A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. BMC Systems Biology, 5 (8). pp. 1-9.

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Abstract

BACKGROUND: Metabolic reconstructions (MRs) are common denominators in systems biology and represent biochemical, genetic, and genomic (BiGG) knowledge-bases for target organisms by capturing currently available information in a consistent, structured manner. Salmonella enterica subspecies I serovar Typhimurium is a human pathogen, causes various diseases and its increasing antibiotic resistance poses a public health problem. RESULTS: Here, we describe a community-driven effort, in which more than 20 experts in S. Typhimurium biology and systems biology collaborated to reconcile and expand the S. Typhimurium BiGG knowledge-base. The consensus MR was obtained starting from two independently developed MRs for S. Typhimurium. Key results of this reconstruction jamboree include i) development and implementation of a community-based workflow for MR annotation and reconciliation; ii) incorporation of thermodynamic information; and iii) use of the consensus MR to identify potential multi-target drug therapy approaches. CONCLUSION: Taken together, with the growing number of parallel MRs a structured, community-driven approach will be necessary to maximize quality while increasing adoption of MRs in experimental design and interpretation.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Infection Biology > Molecular Microbiology (Bumann)
UniBasel Contributors:Bumann, Dirk
Item Type:Article, refereed
Article Subtype:Research Article
Bibsysno:Link to catalogue
Publisher:BioMed Central
e-ISSN:1752-0509
Note:Publication type according to Uni Basel Research Database: Journal article
Language:English
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Last Modified:22 Nov 2017 08:58
Deposited On:14 Sep 2012 06:38

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