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Individual cancer cells carry a bewildering number of distinct genomic alterations i.e., copy number variations and mutations, making it a challenge to uncover genomic-driven mechanisms governing tumorigenesis. Here we performed…
A great part of the effort in the study of coarse grained models of transcription networks is directed to the analysis of their dynamical features. In this letter, we consider the \emph{equilibrium} properties of such systems, showing that…
Genes communicate with each other through different regulatory effects, which lead to the emergence of complex structures in cells, and such structures are expected to be different for normal and cancerous cells. To study breast cancer…
A biologically motivated individual-based framework for evolution in network-structured populations is developed that can accommodate eco-evolutionary dynamics. This framework is used to construct a network birth and death model. The…
Controlling a complex network is of great importance in many applications. The network can be controlled by inputting external control signals through some selected nodes, which are called input nodes. Previous works found that the majority…
Spatio-temporal network dynamics is an emergent property of many complex systems which remains poorly understood. We suggest a new approach to its study based on the analysis of dynamical motifs -- small subnetworks with periodic and…
Complexity in the temporal organization of neural systems may be a reflection of the diversity of its neural constituents. These constituents, excitatory and inhibitory neurons, comprise an invariant ratio in vivo and form the substrate for…
Living systems rely on coordinated molecular interactions, especially those related to gene expression and protein activity. The Unfolded Protein Response is a crucial mechanism in eukaryotic cells, activated when unfolded proteins exceed a…
This paper (parts I and II) provides an expository introduction to monotone and near-monotone dynamical systems associated to biochemical networks, those whose graphs are consistent or near-consistent. Many conclusions can be drawn from…
Network science provides an indispensable theoretical framework for studying the structure and function of real complex systems. Different network models are often used for finding the rules that govern their evolution, whereby the correct…
Under suitable assumptions, the dynamic behaviour of a chemical reaction network is governed by an autonomous set of polynomial ordinary differential equations over continuous variables representing the concentrations of the reactant…
Flow networks are essential for both living organisms and enginneered systems. These networks often present complex dynamics controlled, at least in part, by their topology. Previous works have shown that topologically complex networks…
The biological processes of cellular decision making and differentiation involve a plethora of signalling pathways and gene regulatory circuits. These networks, in their turn, exhibit a multitude of motifs playing crucial parts in…
Elucidating the architecture and dynamics of large scale genetic regulatory networks of cells is an important goal in systems biology. We study the system level dynamical properties of the genetic network of Escherichia coli that regulates…
In many real-world networks, nodes have class labels, attributes, or variables that affect the network's topology. If the topology of the network is known but the labels of the nodes are hidden, we would like to select a small subset of…
Tumor metastasis is one of the main factors responsible for the high fatality rate of cancer. Metastasis can occur after malignant cells transition from the epithelial phenotype to the mesenchymal phenotype. This transformation allows cells…
Reconstruction of gene regulatory networks is the process of identifying gene dependency from gene expression profile through some computation techniques. In our human body, though all cells pose similar genetic material but the activation…
The characterisation of quantum networks is fundamental to understanding how energy and information propagates through complex systems, with applications in control, communication, error mitigation and energy transfer. In this work, we…
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…
Nonlinear networked systems are of interest in several areas of research, such as multi-agent systems and social networks. In this paper, we examine the controllability of several classes of nonlinear networked dynamics on which the…