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  1. Hedi Ben Amor, Fabien Corblin, Eric Fanchon, Adrien Elena, Laurent Trilling, Jacques Demongeot & Nicolas Glade (forthcoming). Formal Methods for Hopfield-Like Networks. Acta Biotheoretica.
    Building a meaningful model of biological regulatory network is usually done by specifying the components (e.g. the genes) and their interactions, by guessing the values of parameters, by comparing the predicted behaviors to the observed ones, and by modifying in a trial-error process both architecture and parameters in order to reach an optimal fitness. We propose here a different approach to construct and analyze biological models avoiding the trial-error part, where structure and dynamics are represented as formal constraints. We apply (...)
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  2. Jacques Demongeot, Adrien Elena & Sylvain Sené (forthcoming). Robustness in Regulatory Networks: A Multi-Disciplinary Approach. Acta Biotheoretica.
    We give in this paper indications about the dynamical impact (as phenotypic changes) coming from the main sources of perturbation in biological regulatory networks. First, we define the boundary of the interaction graph expressing the regulations between the main elements of the network (genes, proteins, metabolites, ...). Then, we search what changes in the state values on the boundary could cause some changes of states in the core of the system (robustness to boundary conditions). After, we analyse the role of (...)
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  3. Jacques Demongeot, Nicolas Glade & Andrés Moreira (forthcoming). Evolution and RNa Relics. A Systems Biology View. Acta Biotheoretica.
    The genetic code has evolved from its initial non-degenerate wobble version until reaching its present state of degeneracy. By using the stereochemical hypothesis, we revisit the problem of codon assignations to the synonymy classes of amino-acids. We obtain these classes with a simple classifier based on physico-chemical properties of nucleic bases, like hydrophobicity and molecular weight. Then we propose simple RNA (or more generally XNA, with X for D, P or R) ring structures that present, overlap included, one and only (...)
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  4. Loïc Forest & Jacques Demongeot (forthcoming). A General Formalism for Tissue Morphogenesis Based on Cellular Dynamics and Control System Interactions. Acta Biotheoretica.
    Morphogenesis is a key process in developmental biology. An important issue is the understanding of the generation of shape and cellular organisation in tissues. Despite of their great diversity, morphogenetic processes share common features. This work is an attempt to describe this diversity using the same formalism based on a cellular description. Tissue is seen as a multi-cellular system whose behaviour is the result of all constitutive cells dynamics. Morphogenesis is then considered as a spatiotemporal organization of cells activities. We (...)
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  5. Jacques Demongeot (2010). The Isochronal Fibration: Characterization and Implication in Biology. Acta Biotheoretica 58 (2):121-142.
    Limit cycles, because they are constituted of a periodic succession of states (discrete or continuous) constitute a good manner to store information. From any points of the state space reached after a perturbation or stimulation of the cognitive system storing this information, one can aim to join through a more or less long return trajectory a precise neighbourhood of the asymptotic trajectory at a specific moment (or a specific place) on the limit cycle, i.e. where the information of interest stands. (...)
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  6. Jacques Demongeot (2009). Biological Boundaries and Biological Age. Acta Biotheoretica 57 (4).
    The chronologic age classically used in demography is often unable to give useful information about which exact stage in development or aging processes has reached an organism. Hence, we propose here to explain in some applications for what reason the chronologic age fails in explaining totally the observed state of an organism, which leads to propose a new notion, the biological age. This biological age is essentially determined by the number of divisions before the Hayflick’s limit the tissue or mitochondrion (...)
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  7. Loïc Forest, Jaime San Martín, Fernando Padilla, Fabrice Chassat, Françoise Giroud & Jacques Demongeot (2004). Morphogenetic Processes: Application to Cambial Growth Dynamics. Acta Biotheoretica 52 (4).
    Both the physiological and the pathological morphogenetic processes that we can meet in embryogenesis, neogenesis and degenerative dysgenesis present common features: they are ruled by three different kinds of mechanisms, one related to cell migration, the second to cell differentiation and the third to cell proliferation. We deal here with an application to the cambial growth which essentially involves the third type of mechanism.Woody plants produce secondary tissue (secondary xylem and phloem) from a meristematic tissue called vascular cambium, responsible for (...)
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  8. Nicolas Glade, Jacques Demongeot & James Tabony (2002). Numerical Simulations of Microtubule Self-Organisation by Reaction and Diffusion. Acta Biotheoretica 50 (4).
    This article addresses the physical chemical processes underlying biological self-organisation by which a homogenous solution of reacting chemicals spontaneously self-organises. Theoreticians have predicted that self-organisation can arise from a coupling of reactive processes with molecular diffusion. In addition, the presence of an external field, such as gravity, at a critical moment early in the process may determine the morphology that subsequently develops. The formation, in-vitro, of microtubules, a constituent of the cellular skeleton, shows this type of behaviour. The preparations spontaneously (...)
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  9. Jacques Demongeot, Paul Kulesal & James Muffay (1996). Compact Set Valued Flows: Applications in Biological Modelling. Acta Biotheoretica 44 (3-4).
    Compact set valued iterations generalize classical point iterations quite naturally by replacing the function f with a tube f in the discrete iterations equation. In Section 3, some bifurcation results about logistic tube iterations are given. In Section 4, an analogous dynamical behaviour for the phase response tube involved in the entrainment of the respiratory rhythm is studied.
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  10. François Leitner, Sylvain Paillasson, Xavier Ronot & Jacques Demongeot (1995). Dynamic Functional and Structural Analysis of Living Cells: New Tools for Vital Staining of Nuclear DNA and for Characterisation of Cell Motion. Acta Biotheoretica 43 (4).
    Increasing interest has been paid to applications of fluorescence measurements to analyze physiological mechanisms in living cells. However, few studies have taken advantage of DNA quantification by fluorometry for dynamic assessment of chromatin organization as well as cell motion during the cell cycle. This approach involves both optimal conditions for DNA staining and cell tracking methods. In this context, this report describes a stoichiometric method for nuclear DNA specific staining, using the bisbenzimidazole dye Hoechst 33342 associated with verapamil, a calcium (...)
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