Related papers: Dynamic networks reveal key players in aging
The principled design and discovery of biologically- and physically-informed models of neuronal dynamics has been advancing since the mid-twentieth century. Recent developments in artificial intelligence (AI) have accelerated this progress.…
Genetic mutations can cause disease by disrupting normal gene function. Identifying the disease-causing mutations from millions of genetic variants within an individual patient is a challenging problem. Computational methods which can…
At the physiological level, aging is neither rigid nor unchangeable. Instead, the molecular and mechanisms driving aging are sufficiently plastic that a variety of diverse interventions--dietary, pharmaceutical, and genetic--have been…
We explore the interplay between the topological relevance of a neuron and its dynamical traces in experimental cultured neuronal networks. We monitor the growth and development of these networks to characterise the evolution of their…
Aging is thought to be a consequence of intrinsic breakdowns in how genetic information is processed. But mounting experimental evidence suggests that aging can be slowed. To help resolve this mystery, I derive a mortality equation which…
This paper proposes the importance of age and gender information in the diagnosis of diabetic retinopathy. We utilized Deep Residual Neural Networks (ResNet) and Densely Connected Convolutional Networks (DenseNet), which are proven…
Network inference approaches are now widely used in biological applications to probe regulatory relationships between molecular components such as genes or proteins. Many methods have been proposed for this setting, but the connections and…
We increasingly rely on the network approach to understand the complexity of cellular functions. Chaperones (heat shock proteins) are key "networkers", which have among their functions to sequester and repair damaged protein. In order to…
A Boolean network (BN) with $n$ components is a discrete dynamical system described by the successive iterations of a function $f:\{0,1\}^n \to \{0,1\}^n$. This model finds applications in biology, where fixed points play a central role.…
Signaling pathways are responsible for the regulation of cell processes, such as monitoring the external environment, transmitting information across membranes, and making cell fate decisions. Given the increasing amount of biological data…
System dynamics and agent based simulation models can both be used to model and understand interactions of entities within a population. Our modeling work presented here is concerned with understanding the suitability of the different types…
Active nematics is an emerging paradigm for characterising biological systems. One aspect of particularly intense focus is the role active nematic defects play in these systems, as they have been found to mediate a growing number of…
As global life expectancy increases, so does the burden of chronic diseases, yet individuals exhibit considerable variability in the rate at which they age. Identifying biomarkers that distinguish fast from slow ageing is crucial for…
Neuronal networks constitute a special class of dynamical systems, as they are formed by individual geometrical components, namely the neurons. In the existing literature, relatively little attention has been given to the influence of…
Electronic properties of DNA are believed to play a crucial role in many phenomena in living organisms, for example the location of DNA lesions by base excision repair (BER) glycosylases and the regulation of tumor-suppressor genes such as…
Gene regulation is an important fundamental biological process. The regulation of gene expression is managed through a variety of methods including epigenetic processes (e.g., DNA methylation). Understanding the role of epigenetic changes…
Convolutional Neural Networks (CNNs) are proven to be effective when data are homogeneous such as images, or when there is a relationship between consecutive data such as time series data. Although CNNs are not famous for tabular data, we…
Understanding the structures why links are formed is an important and prominent research topic. In this paper, we therefore consider the link prediction problem in face-to-face contact networks, and analyze the predictability of new and…
Complex biological functions are carried out by the interaction of genes and proteins. Uncovering the gene regulation network behind a function is one of the central themes in biology. Typically, it involves extensive experiments of…
The function of a protein is defined by its interaction partners. Thus, topology-driven network alignment of the protein-protein interaction (PPI) networks of two species should uncover similar interaction patterns and allow identification…