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From proteomics to systems biology of bacterial pathogens: approaches, tools, and applications.

Plikat, Uwe and Voshol, Johannes and Dangendorf, Yvonne and Wiedmann, Brigitte and Devay, Piroska and Mueller, Dieter and Wirth, Urs and Szustakowski, Joseph and Chirn, Gung-Wei and Inverardi, Bruno and Puyang, Xiaoling and Brown, Karen and Kamp, Heather and Hoving, Sjouke and Ruchti, Alexandra and Brendlen, Nathalie and Peterson, Ron and Buco, Jennifer and Van Oostrum, Jan and Peitsch, Manuel (2007) From proteomics to systems biology of bacterial pathogens: approaches, tools, and applications. Proteomics, 7 (6). pp. 992-1003. ISSN 1615-9853

Abstract

The hallmark of a systems biology approach is the integration of computational tools with experimental data encompassing multiple classes of biomolecules across different functional levels. Equally important as the availability of reasonably comprehensive information at the gene, protein, and metabolite levels is the development of adequate analysis and visualization tools to reduce the inherent complexity to interpretable dimensions. In this paper, we describe the integration of a 2-D gel-based proteome map of Staphylococcus aureus Mu50 with genomic and transcriptomic information through a customized data integration and user interface built on the Ensembl genome browser. We illustrate its application and potential through the analysis of a defined system perturbation caused by a mutation in the formyltransferase gene. We envision that this software package, which we called Insieme, can support the development of novel antibiotics by allowing a systems-based view of the bacterial response pathways.

Item Type: Article
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Additional Information: archiving not allowed on institutional repository
Keywords: Population proteomics; Staphylococcus aureus; Systems biology; Transcriptomics
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Date Deposited: 14 Dec 2009 13:59
Last Modified: 14 Dec 2009 13:59
URI: https://oak.novartis.com/id/eprint/456

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