Affiliation: University of Potsdam
- The mutual information: detecting and evaluating dependencies between variablesR Steuer
University Potsdam, Nonlinear Dynamics Group, Germany
Bioinformatics 18:S231-40. 2002..In particular when dealing with small datasets, finite sample effects and other sources of potentially misleading results have to be taken into account...
- A gentle guide to the analysis of metabolomic dataRalf Steuer
Institute of Biochemistry and Biology, University of Potsdam, Germany
Methods Mol Biol 358:105-26. 2007..The chapter is accompanied by a webpage, describing the application of all algorithms in a ready-to-use format...
- Estimating mutual information using B-spline functions--an improved similarity measure for analysing gene expression dataCarsten O Daub
Max Planck Institute of Molecular Plant Physiology, Potsdam, 14424, Germany
BMC Bioinformatics 5:118. 2004..Since mutual information is defined in terms of discrete variables, its application to continuous data requires the use of binning procedures, which can lead to significant numerical errors for datasets of small or moderate size...
- From structure to dynamics of metabolic pathways: application to the plant mitochondrial TCA cycleRalf Steuer
University Potsdam, Institute for Biochemistry and Biology, Haus 20, Germany
Bioinformatics 23:1378-85. 2007..Our analysis also serves as a general example how to elucidate the transition from the structure to the dynamics of metabolic pathways...
- Validation and functional annotation of expression-based clusters based on gene ontologyRalf Steuer
University Potsdam, Institute for Biochemistry and Biology, Karl Liebknecht Strasse 24 25, Haus 20, 14476 Potsdam, Germany
BMC Bioinformatics 7:380. 2006..One common approach is to look for functional annotations that are significantly enriched within a group or cluster of genes, as compared to a reference group...
- Structural kinetic modeling of metabolic networksRalf Steuer
Institute for Physics, Nonlinear Dynamics Group, University Potsdam, 14469 Potsdam, Germany
Proc Natl Acad Sci U S A 103:11868-73. 2006..The method is exemplified on two paradigmatic metabolic systems: the glycolytic pathway of yeast and a realistic-scale representation of the photosynthetic Calvin cycle...
- Review: on the analysis and interpretation of correlations in metabolomic dataRalf Steuer
University Potsdam, Insitute of Physics, Am Neuen Palais 10, Haus 19, 14469 Potsdam, Germany
Brief Bioinform 7:151-8. 2006..It is demonstrated that the comparative correlations analysis offers a way to exploit the observed correlations to obtain additional information about the physiological state of the system...
- Effects of stochasticity in models of the cell cycle: from quantized cycle times to noise-induced oscillationsRalf Steuer
Nonlinear Dynamics Group, Potsdam University, Institute of Physics, Am Neuen Palais 10, Haus 19, Potsdam 14469, Germany
J Theor Biol 228:293-301. 2004..These findings will be discussed in the light of an ongoing debate on models of cell division as limit-cycle oscillators versus checkpoint mechanisms...
- Constructive effects of fluctuations in genetic and biochemical regulatory systemsRalf Steuer
Institut für Physik der Universität Potsdam, Arbeitsgruppe Nichtlineare Dynamik, Am Neuen Palais 10, Haus 19, 14469 Potsdam, Germany
Biosystems 72:241-51. 2003..It will be demonstrated that in many typical situations biochemical and genetic regulatory systems may utilize intrinsic noise to their advantage...
- Interpreting correlations in metabolomic networksR Steuer
Arbeitsgruppe Nichtlineare Dynamik, Institut für Physik der Universität Potsdam, Am Neuen Palais 10, Haus 19, 14469 Potsdam, Germany
Biochem Soc Trans 31:1476-8. 2003..In this mini-review, we discuss the integration of these observed correlations into metabolomic networks and their relationships with the underlying biochemical pathways...
- Observing and interpreting correlations in metabolomic networksR Steuer
University Potsdam, Nonlinear Dynamics Group, Am Neuen Palais 10, 14469 Potsdam, Germany
Bioinformatics 19:1019-26. 2003..e. to recover the underlying enzymatic reaction network from data. The implications of our findings for other bioinformatics approaches are discussed...
- Computational approaches to the topology, stability and dynamics of metabolic networksRalf Steuer
Humboldt Universitat zu Berlin, Institut fur Biologie, Invalidenstr 43, 10115 Berlin, Germany
Phytochemistry 68:2139-51. 2007..Utilizing this approach, the role of feedback mechanisms in the maintenance of stability is discussed using minimal models of cellular pathways...