Related papers: Reliability of regulatory networks and its evoluti…
To model biological systems using networks, it is desirable to allow more than two levels of expression for the nodes and to allow the introduction of parameters. Various modeling and simulation methods addressing these needs using Boolean…
We study the target control of asynchronous Boolean networks, to identify efficacious interventions that can drive the dynamics of a given Boolean network from any initial state to the desired target attractor. Based on the application…
Network remodeling, or adaptation, in the presence of periodically driven forcings has hereto remained largely unexplored, despite the fact that a broad class of biological transport networks, e.g. animal vasculature, depends on periodic…
We study the reliability of large networks of coupled neural oscillators in response to fluctuating stimuli. Reliability means that a stimulus elicits essentially identical responses upon repeated presentations. We view the problem on two…
Robustness to genetic or environmental disturbances is often considered as a key property of living systems. Yet, in spite of being discussed since the 1950s, how robustness emerges from the complexity of genetic architectures and how it…
The dynamics of protection processes has been a fundamental challenge in systemic risk analysis. The conceptual principle and methodological techniques behind the mechanisms involved [in such dynamics] have been harder to grasp than…
The controllability of a network is a theoretical problem of relevance in a variety of contexts ranging from financial markets to the brain. Until now, network controllability has been characterized only on isolated networks, while the vast…
A networked dynamical system is composed of subsystems interconnected through prescribed interactions. In many engineering applications, however, one subsystem can also affect others through "unintended" interactions that can significantly…
The mammalian brain could contain dense and sparse network connectivity structures, including both excitatory and inhibitory neurons, but is without any clearly defined output layer. The neurons have time constants, which mean that the…
Precise temporal coordination of gene expression is crucial for many developmental processes. One central question in developmental biology is how such coordinated expression patterns are robustly controlled. During embryonic development of…
Nonautonomous driving of an oscillator has been shown to enlarge the Arnold tongue in parameter space, but little is known about the analogous effect for a network of oscillators. To test the hypothesis that deterministic nonautonomous…
Interactions between genes and gene products give rise to complex circuits that enable cells to process information and respond to external signals. Theoretical studies often describe these interactions using continuous, stochastic, or…
Interacting biological systems at all organizational levels display emergent behavior. Modeling these systems is made challenging by the number and variety of biological components and interactions (from molecules in gene regulatory…
Estimating the influence that individual nodes have on one another in a Boolean network is essential to predict and control the system's dynamical behavior, for example, detecting key therapeutic targets to control pathways in models of…
Robust machine learning for regulatory genomics is studied under biologically and technically induced distribution shifts. Deep convolutional and attention based models achieve strong in distribution performance on DNA regulatory sequence…
The interaction of distinct units in physical, social, biological and technological systems naturally gives rise to complex network structures. Networks have constantly been in the focus of research for the last decade, with considerable…
The editing of transcribed RNA by other molecules such that the form of the final product differs from that specified in the corresponding DNA sequence is ubiquitous. This paper uses an abstract, tunable Boolean genetic regulatory network…
We consider a system of several nonlinear equations with a distributed delay and obtain absolute asymptotic stability conditions, independent of the delay. The ideas of the proofs are based on the notion of a strong attractor. The results…
Biological phenomena differ significantly from physical phenomena. At the heart of this distinction is the fact that biological entities have computational abilities and thus they are inherently difficult to predict. This is the reason why…
Topological features of gene regulatory networks can be successfully reproduced by a model population evolving under selection for short dynamical attractors. The evolved population of networks exhibit motif statistics, summarized by…