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Computational Systems Biology 2011

  1. Research

    Properties of Boolean networks and methods for their tests

    Transcriptional regulation networks are often modeled as Boolean networks. We discuss certain properties of Boolean functions (BFs), which are considered as important in such networks, namely, membership to th...

    Johannes Georg Klotz, Ronny Feuer, Oliver Sawodny, Martin Bossert, Michael Ederer and Steffen Schober

    EURASIP Journal on Bioinformatics and Systems Biology 2013 2013:1

    Published on: 11 January 2013

  2. Research

    In vitro detection of adrenocorticotropic hormone levels by fluorescence correlation spectroscopy immunoassay for mathematical modeling of glucocorticoid-mediated feedback mechanisms

    Performing quantitative, highly sensitive measurements at a single molecule level is often necessary to address specific issues related to complex molecular and biochemical systems. For that purpose, we presen...

    Martin Gerald Puchinger, Clemens Alexander Zarzer, Philipp Kügler, Erwin Gaubitzer and Gottfried Köhler

    EURASIP Journal on Bioinformatics and Systems Biology 2012 2012:17

    Published on: 26 October 2012

  3. Research

    Model-based analysis of an adaptive evolution experiment with Escherichia coli in a pyruvate limited continuous culture with glycerol

    Bacterial strains that were genetically blocked in important metabolic pathways and grown under selective conditions underwent a process of adaptive evolution: certain pathways may have been deregulated and th...

    Ronny Feuer, Katrin Gottlieb, Gero Viertel, Johannes Klotz, Steffen Schober, Martin Bossert, Oliver Sawodny, Georg Sprenger and Michael Ederer

    EURASIP Journal on Bioinformatics and Systems Biology 2012 2012:14

    Published on: 3 October 2012

  4. Research

    The role of feedback control mechanisms on the establishment of oscillatory regimes in the Ras/cAMP/PKA pathway in S. cerevisiae

    In the yeast Saccharomyces cerevisiae, the Ras/cAMP/PKA pathway is involved in the regulation of cell growth and proliferation in response to nutritional sensing and stress conditions. The pathway is tightly regu...

    Daniela Besozzi, Paolo Cazzaniga, Dario Pescini, Giancarlo Mauri, Sonia Colombo and Enzo Martegani

    EURASIP Journal on Bioinformatics and Systems Biology 2012 2012:10

    Published on: 20 July 2012

  5. Research

    Approximate maximum likelihood estimation for stochastic chemical kinetics

    Recent experimental imaging techniques are able to tag and count molecular populations in a living cell. From these data mathematical models are inferred and calibrated. If small populations are present, discr...

    Aleksandr Andreychenko, Linar Mikeev, David Spieler and Verena Wolf

    EURASIP Journal on Bioinformatics and Systems Biology 2012 2012:9

    Published on: 18 July 2012

  6. Research

    From microscopy data to in silico environments for in vivo-oriented simulations

    In our previous study, we introduced a combination methodology of Fluorescence Correlation Spectroscopy (FCS) and Transmission Electron Microscopy (TEM), which is powerful to investigate the effect of intracel...

    Noriko Hiroi, Michael Klann, Keisuke Iba, Pablo de Heras Ciechomski, Shuji Yamashita, Akito Tabira, Takahiro Okuhara, Takeshi Kubojima, Yasunori Okada, Kotaro Oka, Robin Mange, Michael Unger, Akira Funahashi and Heinz Koeppl

    EURASIP Journal on Bioinformatics and Systems Biology 2012 2012:7

    Published on: 26 June 2012

  7. 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

  8. 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

  9. 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