Related papers: Regulatory networks and connected components of th…

Modeling gene regulatory networks (GRNs) is an important topic in systems biology. Although there has been much work focusing on various specific systems, the generic behavior of GRNs with continuous variables is still elusive. In…

Gene regulatory networks arise in all living cells, allowing the control of gene expression patterns. The study of their topology has revealed that certain subgraphs of interactions or "motifs" appear at anomalously high frequencies. We ask…

Evolving biomolecular networks have to combine the stability against perturbations with flexibility allowing their constituents to assume new roles in the cell. Gene duplication followed by functional divergence of associated proteins is a…

The well-known issue of reconstructing regulatory networks from gene expression measurements has been somewhat disrupted by the emergence and rapid development of single-cell data. Indeed, the traditional way of seeing a gene regulatory…

This paper presents the foundation for a decomposition theory for Boolean networks, a type of discrete dynamical system that has found a wide range of applications in the life sciences, engineering, and physics. Given a Boolean network…

A Boolean network model of the cell-cycle regulatory network of fission yeast (Schizosaccharomyces Pombe) is constructed solely on the basis of the known biochemical interaction topology. Simulating the model in the computer, faithfully…

Oscillations lie at the core of many biological processes, from the cell cycle, to circadian oscillations and developmental processes. Time-keeping mechanisms are essential to enable organisms to adapt to varying conditions in environmental…

Real-world growth processes and scalings have been broadly categorized into three growth regimes with distinctly different properties and driving forces. The first two are characterized by a positive and constant feedback between growth and…

In the framework of coupled cell systems, a coupled cell network describes graphically the dynamical dependencies between individual dynamical systems, the cells. The fundamental network of a network reveals the hidden symmetries of that…

The control of complex networks is of paramount importance in areas as diverse as ecosystem management, emergency response, and cell reprogramming. A fundamental property of networks is that perturbations to one node can affect other nodes,…

Identifying features of molecular regulatory networks is an important problem in systems biology. It has been shown that the combinatorial logic of such networks can be captured in many cases by special functions called nested canalyzing in…

The complexity of gene regulatory networks in multicellular organisms makes interpretable low-dimensional models highly desirable. An attractive geometric picture, attributed to Waddington, visualizes the differentiation of a cell into…

The goal of this note is to present a general approach to define the net reproduction function for a large class of nonlinear physiologically structured population models. In particular, we are going to show that this can be achieved in a…

Biological organisms are simple at heart: cells, their basic units, perform a variety of behaviors by expressing proteins from DNA-encoded genes. Gene expression though depends on sets of often-convoluted regulatory interactions known as…

The interaction between natural selection and random mutation is frequently debated in recent years. Does similar dilemma also exist in the evolution of real networks such as biological networks? In this paper, we try to discuss this issue…

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…

Discrete-time regulatory networks are dynamical systems on directed graphs, with a structure inspired on natural systems of interacting units. There is a natural notion of determination amongst vertices, which we use to classify the nodes…

A Network Control System (NCS) consists of control components that interact with the plant over a shared network. The system dynamics of a NCS could be subject to noise arising from randomness in the times at which the data is transmitted…

Plasticity is a fundamental property of complex systems, such as the brain or an organism. Yet it typically remains a descriptive concept inferred retrospectively from observed outcomes, such as modifications in activity or morphology.…

During organismal development, biochemical reaction networks sense and respond to mechanical forces to coordinate embryonic patterning with embryo morphogenesis. Factors such as cortical tension, cell density, and matrix mechanical…