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Träfflista för sökning "WFRF:(Heinemann Matthias) srt2:(2008-2009)"

Sökning: WFRF:(Heinemann Matthias) > (2008-2009)

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1.
  • de Graaf, Albert A, et al. (författare)
  • Nutritional systems biology modeling: from molecular mechanisms to physiology.
  • 2009
  • Ingår i: PLoS computational biology. - : Public Library of Science (PLoS). - 1553-7358 .- 1553-734X. ; 5:11
  • Forskningsöversikt (refereegranskat)abstract
    • The use of computational modeling and simulation has increased in many biological fields, but despite their potential these techniques are only marginally applied in nutritional sciences. Nevertheless, recent applications of modeling have been instrumental in answering important nutritional questions from the cellular up to the physiological levels. Capturing the complexity of today's important nutritional research questions poses a challenge for modeling to become truly integrative in the consideration and interpretation of experimental data at widely differing scales of space and time. In this review, we discuss a selection of available modeling approaches and applications relevant for nutrition. We then put these models into perspective by categorizing them according to their space and time domain. Through this categorization process, we identified a dearth of models that consider processes occurring between the microscopic and macroscopic scale. We propose a "middle-out" strategy to develop the required full-scale, multilevel computational models. Exhaustive and accurate phenotyping, the use of the virtual patient concept, and the development of biomarkers from "-omics" signatures are identified as key elements of a successful systems biology modeling approach in nutrition research--one that integrates physiological mechanisms and data at multiple space and time scales.
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2.
  • Herrgård, Markus J, et al. (författare)
  • A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
  • 2008
  • Ingår i: Nature Biotechnology. ; 26:10, s. 1155-1160
  • Tidskriftsartikel (refereegranskat)abstract
    • Genomic data allow the large-scale manual or semi-automated assembly of metabolic network reconstructions, which provide highly curated organism-specific knowledge bases. Although several genome-scale network reconstructions describe Saccharomyces cerevisiae metabolism, they differ in scope and content, and use different terminologies to describe the same chemical entities. This make comparisons between them difficult and underscores the desirability of a consolidated metabolic network that collects and formalizes the 'community knowledge' of yeast metabolism. We describe how we have produced a consensus metabolic network reconstruction for S. cerevisiae. In drafting it, we placed special emphasis on referencing molecules to persistent databases or using database-independent forms, such as SMILES or InChl strings, as this permits their chemical structure to be represented unambiguously and in a manner that permits automated reasoning. The reconstruction is readily available via a publicly accessible database and in the Systems Biology Markup Language (http://www.comp-sys-bio.org/yeastnet). It can be maintained as a resource that serves as a common denominator for studying the systems biology of yeast. Similar strategies should benefit communities studying genome-scale metabolic networks of other organisms.
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