Related papers: Cell fate reprogramming by control of intracellula…
Identifying the nodes that have the potential to influence the state of a network is a relevant question for many complex systems. In many applications it is often essential to test the ability of an individual node to control a specific…
The links between optimal control of dynamical systems and neural networks have proved beneficial both from a theoretical and from a practical point of view. Several researchers have exploited these links to investigate the stability of…
We characterize different cell states, related to cancer and ageing phenotypes, by a measure of entropy of network ensembles, integrating gene expression values and protein interaction networks. The entropy measure estimates the parameter…
Decisions in the cell that lead to its ultimate fate are important for cellular functions such as proliferation, growth, differentiation, development and death. Understanding this decision process is imperative for advancements in the…
Recent work on synthetic rescues has shown that the targeted deletion of specific metabolic genes can often be used to rescue otherwise non-viable mutants. This raises a fundamental biophysical question: to what extent can the whole-cell…
In this paper, we address the formal characterization of targets triggering cellular trans-differentiation in the scope of Boolean networks with asynchronous dynamics. Given two fixed points of a Boolean network, we are interested in all…
Modelling gene regulatory networks not only requires a thorough understanding of the biological system depicted but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to…
Graphical models have gained a lot of attention recently as a tool for learning and representing dependencies among variables in multivariate data. Often, domain scientists are looking specifically for differences among the dependency…
Traditional approaches to understanding the brain's resilience to neuropathology have identified neurophysiological variables, often described as brain or cognitive 'reserve,' associated with better outcomes. However, mechanisms of function…
Despite the significant advances in identifying the driver nodes and energy requiring in network control, a framework that incorporates more complicated dynamics remains challenging. Here, we consider the conformity behavior into network…
Stem cells can precisely and robustly undergo cellular differentiation and lineage commitment, referred to as stemness. However, how the gene network underlying stemness regulation reliably specifies cell fates is not well understood. To…
We outline a modeling and optimization strategy for investigating dynamic metabolic engineering interventions. Our framework is particularly useful at the early stages of research and development, often constrained by limited knowledge and…
We consider the problem of a dynamical network whose dynamics is subject to external perturbations (`attacks') locally applied at a subset of the network nodes. We assume that the network has an ability to defend itself against attacks with…
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…
Pluripotent embryonic stem cells are of paramount importance for biomedical research thanks to their innate ability for self-renewal and differentiation into all major cell lines. The fateful decision to exit or remain in the pluripotent…
Cell fate decisions emerge as a consequence of a complex set of gene regulatory networks. Models of these networks are known to have more parameters than data can determine. Recent work, inspired by Waddington's metaphor of a landscape, has…
Recent research shows that a faulty or sub-optimally operating metabolic network can often be rescued by the targeted removal of enzyme-coding genes--the exact opposite of what traditional gene therapy would suggest. Predictions go as far…
Network medicine is an emerging area of research dealing with molecular and genetic interactions, network biomarkers of disease, and therapeutic target discovery. Large-scale biomedical data generation offers a unique opportunity to assess…
Cancer disease occurs because of a disorder in the cellular regulatory mechanism, Which causes cellular malformation. The genes that start the malformation are called Cancer driver genes (CDGs) . Numerous computational methods have been…
Artificial neurons built on synthetic gene networks have potential applications ranging from complex cellular decision-making to bioreactor regulation. Furthermore, due to the high information throughput of natural systems, it provides an…