Related papers: Translating and evaluating single-cell Boolean net…
Signaling networks are designed to sense an environmental stimulus and adapt to it. We propose and study a minimal model of signaling network that can sense and respond to external stimuli of varying strength in an adaptive manner. The…
Boolean networks are powerful frameworks for capturing the logic of gene-regulatory circuits, yet their combinatorial explosion hampers exhaustive analyses. Here, we present a systematic reduction of a 31-node Boolean model that describes…
Dysregulation in signal transduction pathways can lead to a variety of complex disorders, including cancer. Computational approaches such as network analysis are important tools to understand system dynamics as well as to identify critical…
The generating functional method is employed to investigate the synchronous dynamics of Boolean networks, providing an exact result for the system dynamics via a set of macroscopic order parameters. The topology of the networks studied and…
In this study, we explored the utility of a descriptive and predictive bionetwork model for phospholipase C-coupled calcium signaling pathways, built with non-kinetic experimental information. Boolean models generated from these data yield…
This paper proposes a new method to reverse engineer gene regulatory networks from experimental data. The modeling framework used is time-discrete deterministic dynamical systems, with a finite set of states for each of the variables. The…
In this paper, we analyse large random Boolean networks in terms of a constraint satisfaction problem. We first develop an algorithmic scheme which allows to prune simple logical cascades and under-determined variables, returning thereby…
Single and collective cell migration are fundamental processes critical for physiological phenomena ranging from embryonic development and immune response to wound healing and cancer metastasis. To understand cell migration from a physical…
Dynamical systems models for controlling multi-agent swarms have demonstrated advances toward resilient, decentralized navigation algorithms. We previously introduced the NeuroSwarms controller, in which agent-based interactions were…
Boolean networks are extensively applied as models of complex dynamical systems, aiming at capturing essential features related to causality and synchronicity of the state changes of components along time. Dynamics of Boolean networks…
This paper deals with the cellular biological network analysis of the tumor-growth model, consisting of multiple spaces and time scales. In this paper, we present a model in graph simulation using ABM for tumor growth. In particular, we…
Genetic interaction can be defined as a deviation of the phenotypic quantitative effect of a double gene mutation from the effect predicted from single mutations using a simple (e.g., multiplicative or linear additive) statistical model.…
Most social, technological and biological networks are embedded in a finite dimensional space, and the distance between two nodes influences the likelihood that they link to each other. Indeed, in social systems, the chance that two…
The stability of Boolean networks has attracted much attention due to its wide applications in describing the dynamics of biological systems. During the past decades, much effort has been invested in unveiling how network structure and…
Regulatory networks describe the interactions between molecular or cellular regulators, like transcription factors and genes in gene regulatory networks, kinases and their receptors in signalling networks, or neurons in neural networks. A…
With recent and rapid advancements in artificial intelligence (AI), understanding the foundation of purposeful behaviour in autonomous agents is crucial for developing safe and efficient systems. While artificial neural networks have…
Interference mitigation techniques are essential for improving the performance of interference limited wireless networks. In this paper, we introduce novel interference mitigation schemes for wireless cellular networks with space division…
The transport of particles in cells is influenced by the properties of intracellular networks they traverse while searching for localized target regions or reaction partners. Moreover, given the rapid turnover in many intracellular…
Cellular signaling is essential in information processing and decision making. Therefore, a variety of experimental approaches have been developed to study signaling on bulk and single-cell level. Single-cell measurements of signaling…
Understanding design principles of molecular interaction networks is an important goal of molecular systems biology. Some insights have been gained into features of their network topology through the discovery of graph theoretic patterns…