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The response to a knockout of a node is a characteristic feature of a networked dynamical system. Knockout resilience in the dynamics of the remaining nodes is a sign of robustness. Here we study the effect of knockouts for binary state sequences and their implementations in terms of Boolean threshold networks. Beside random sequences with biologically plausible constraints, we analyze the cell cycle sequence of the species Saccharomyces cerevisiae and the Boolean networks implementing it. Comparing with an appropriate null model we do not find evidence that the yeast wildtype network is optimized for high knockout resilience. Our notion of knockout resilience weakly correlates with the size of the basin of attraction, which has also been considered a measure of robustness.
Characterizing the capabilities, criticalities and response to perturbations of genome-scale metabolic networks is a basic problem with important applications. A key question concerns the identification of the potentially most harmful knockouts. The
Continuous cultures of mammalian cells are complex systems displaying hallmark phenomena of nonlinear dynamics, such as multi-stability, hysteresis, as well as sharp transitions between different metabolic states. In this context mathematical models
To estimate the time, many organisms, ranging from cyanobacteria to animals, employ a circadian clock which is based on a limit-cycle oscillator that can tick autonomously with a nearly 24h period. Yet, a limit-cycle oscillator is not essential for k
A fundamental question in biology is how cell populations evolve into different subtypes based on homogeneous processes at the single cell level. Here we show that population bimodality can emerge even when biological processes are homogenous at the
In this paper we suggest that, under suitable conditions, supervised learning can provide the basis to formulate at the microscopic level quantitative questions on the phenotype structure of multicellular organisms. The problem of explaining the robu