Related papers: Cell biology: Networks, regulation, pathways
Metabolism is a fascinating cell machinery underlying life and disease and genome-scale reconstructions provide us with a captivating view of its complexity. However, deciphering the relationship between metabolic structure and function…
Mathematical and computational models can assist in gaining an understanding of cell behavior at many levels of organization. Here, we review models in the literature that focus on eukaryotic cell motility at 3 size scales: intracellular…
In this article, we propose a general framework to study the dynamics and topology of cellular networks that capture the geometry of cell packings in two-dimensional tissues. Such epithelia undergo large-scale deformation during…
Graph Theoretic Process Network Synthesis is described as an introduction to biological networks. Genetic, protein and metabolic systems are considered. The theoretical work of Kauffman is discussed and amplified by critical property…
The world of network science is fascinating and filled with complex phenomena that we aspire to understand. One of them is the dynamics of spreading processes over complex networked structures. Building the knowledge-base in the field where…
Networks effectively capture interactions among components of complex systems, and have thus become a mainstay in many scientific disciplines. Growing evidence, especially from biology, suggest that networks undergo changes over time, and…
Understanding large molecular networks consisting of entities such as genes, proteins or RNAs that interact in complex ways to drive the cellular machinery has been an active focus of systems biology. Computational approaches have played a…
With the increasing availability and size of multi-omics datasets, investigating the casual relationships between molecular phenotypes has become an important aspect of exploring underlying biology and genetics. This paper aims to introduce…
Droplet formation has emerged as an essential concept for the spatiotemporal organisation of biomolecules in cells. However, classical descriptions of droplet dynamics based on passive liquid-liquid phase separation cannot capture the…
This chapter reviews the purpose and use of models from the field of complex systems and, in particular, the implications of trying to use models to understand or make decisions within complex situations, such as policy makers usually face.…
This thesis is a compendium of research which brings together ideas from the fields of Complex Networks and Computational Neuroscience to address two questions regarding neural systems: 1) How the activity of neurons, via synaptic changes,…
An outline of recent work on complex networks is given from the point of view of a physicist. Motivation, achievements and goals are discussed with some of the typical applications from a wide range of academic fields. An introduction to…
We analyze a science collaboration network, i.e. a network whose nodes are scientists with edges connecting them for each paper published together. Furthermore we develop a model for the simulation of discontiguous small-world networks that…
Discrete and Continuous Dynamics is the first in a series of articles on Network Models for Epidemiology. This project began in the Fall quarter of 2014 in my continuous modeling course. Since then, it has taken off and turned into a series…
Characterization of the differences between biological and random networks can reveal the design principles that enable the robust realization of crucial biological functions including the establishment of different cell types. Previous…
Networks have in recent years emerged as an invaluable tool for describing and quantifying complex systems in many branches of science. Recent studies suggest that networks often exhibit hierarchical organization, where vertices divide into…
A modeling formalism is proposed for the description and study of living and life-like systems. It provides an abstract conceptual model framework for real life and evolution of biological organisms. It is proposed, that this model…
Computational modeling is crucial for understanding and analyzing complex systems. In biology, model creation is a human dependent task that requires reading hundreds of papers and conducting wet lab experiments, which would take days or…
Breast cancer cell lines are indispensable tools for unraveling disease mechanisms, enabling drug discovery, and developing personalized treatments, yet their heterogeneity and inconsistent classification pose significant challenges in…
Link prediction in complex networks has attracted considerable attention from interdisciplinary research communities, due to its ubiquitous applications in biological networks, social networks, transportation networks, telecommunication…