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Computational Systems Biology 2010

  1. Research

    Phase computations and phase models for discrete molecular oscillators

    Biochemical oscillators perform crucial functions in cells, e.g., they set up circadian clocks. The dynamical behavior of oscillators is best described and analyzed in terms of the scalar quantity, phase. A rigor...

    Onder Suvak and Alper Demir

    EURASIP Journal on Bioinformatics and Systems Biology 2012 2012:6

    Published on: 11 June 2012

  2. Research

    A visual analytics approach for models of heterogeneous cell populations

    In recent years, cell population models have become increasingly common. In contrast to classic single cell models, population models allow for the study of cell-to-cell variability, a crucial phenomenon in mo...

    Jan Hasenauer, Julian Heinrich, Malgorzata Doszczak, Peter Scheurich, Daniel Weiskopf and Frank Allgöwer

    EURASIP Journal on Bioinformatics and Systems Biology 2012 2012:4

    Published on: 31 May 2012

  3. Research

    Determination of minimal transcriptional signatures of compounds for target prediction

    The identification of molecular target and mechanism of action of compounds is a key hurdle in drug discovery. Multiplexed techniques for bead-based expression profiling allow the measurement of transcriptiona...

    Florian Nigsch, Janna Hutz, Ben Cornett, Douglas W Selinger, Gregory McAllister, Somnath Bandyopadhyay, Joseph Loureiro and Jeremy L Jenkins

    EURASIP Journal on Bioinformatics and Systems Biology 2012 2012:2

    Published on: 10 May 2012

  4. Research

    Unscented Kalman filter with parameter identifiability analysis for the estimation of multiple parameters in kinetic models

    In systems biology, experimentally measured parameters are not always available, necessitating the use of computationally based parameter estimation. In order to rely on estimated parameters, it is critical to...

    Syed Murtuza Baker, C Hart Poskar and Björn H Junker

    EURASIP Journal on Bioinformatics and Systems Biology 2011 2011:7

    Published on: 11 October 2011

  5. Research

    Detecting controlling nodes of boolean regulatory networks

    Boolean models of regulatory networks are assumed to be tolerant to perturbations. That qualitatively implies that each function can only depend on a few nodes. Biologically motivated constraints further show ...

    Steffen Schober, David Kracht, Reinhard Heckel and Martin Bossert

    EURASIP Journal on Bioinformatics and Systems Biology 2011 2011:6

    Published on: 11 October 2011

  6. Research

    Measuring and analyzing tissue specificity of human genes and protein complexes

    Proteins and their interactions are essential for the survival of each human cell. Knowledge of their tissue occurrence is important for understanding biological processes. Therefore, we analyzed microarray an...

    Dorothea Emig, Tim Kacprowski and Mario Albrecht

    EURASIP Journal on Bioinformatics and Systems Biology 2011 2011:5

    Published on: 4 August 2011

  7. Research

    Modeling time delay in the NFκB signaling pathway following low dose IL-1 stimulation

    Stimulation of human epithelial cells with IL-1 (10 ng/ml) + UVB radiation results in sustained NFκB activation caused by continuous IKKβ phosphorylation. We have recently published a strictly reduced ordinary...

    Johannes Witt, Sandra Barisic, Oliver Sawodny, Michael Ederer, Dagmar Kulms and Thomas Sauter

    EURASIP Journal on Bioinformatics and Systems Biology 2011 2011:3

    Published on: 17 June 2011

  8. Research

    A systems biology approach to analyse leaf carbohydrate metabolism in Arabidopsis thaliana

    Plant carbohydrate metabolism comprises numerous metabolite interconversions, some of which form cycles of metabolite degradation and re-synthesis and are thus referred to as futile cycles. In this study, we p...

    Sebastian Henkel, Thomas Nägele, Imke Hörmiller, Thomas Sauter, Oliver Sawodny, Michael Ederer and Arnd G Heyer

    EURASIP Journal on Bioinformatics and Systems Biology 2011 2011:2

    Published on: 17 June 2011