Related papers: Inferring disease causing genes and their pathways…
Time plays an essential role in the diffusion of information, influence and disease over networks. In many cases we only observe when a node copies information, makes a decision or becomes infected -- but the connectivity, transmission…
Gene Regulatory Network (GRN) plays an important role in knowing insight of cellular life cycle. It gives information about at which different environmental conditions genes of particular interest get over expressed or under expressed.…
Cellular response to a perturbation is the result of a dynamic system of biological variables linked in a complex network. A major challenge in drug and disease studies is identifying the key factors of a biological network that are…
Network inference, the task of reconstructing interactions in a complex system from experimental observables, is a central yet extremely challenging problem in systems biology. While much progress has been made in the last two decades,…
Detecting the interactions of genetic compounds like genes, SNPs, proteins, metabolites, etc. can potentially unravel the mechanisms behind complex traits and common genetic disorders. Several methods have been taken into consideration for…
The recent development of single-cell transcriptomics has enabled gene expression to be measured in individual cells instead of being population-averaged. Despite this considerable precision improvement, inferring regulatory networks…
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…
Gene Regulatory Networks are networks of interactions in biological organisms responsible for determining the production levels of proteins and peptides. Proteins are workers of a cell factory, and their production defines the goal of a…
Control theory has seen recently impactful applications in network science, especially in connections with applications in network medicine. A key topic of research is that of finding minimal external interventions that offer control over…
Much of contemporary systems biology owes its success to the abstraction of a network, the idea that diverse kinds of molecular, cellular, and organismal species and interactions can be modeled as relational nodes and edges in a graph of…
New technologies have enabled the investigation of biology and human health at an unprecedented scale and in multiple dimensions. These dimensions include a myriad of properties describing genome, epigenome, transcriptome, microbiome,…
A fundamental task in developmental biology is to identify the mechanisms which drive morphogenesis. In many cases, pattern formation is driven by the positional information determined by both the gradient of maternal factors and hard-wired…
Microbiome studies increasingly indicate that disease-associated shifts cannot be understood from compositional changes alone. The functional architecture of microbial communities encoded in patterns of association among microbial gene…
Recent studies have demonstrated that network approaches are highly appropriate tools to understand the extreme complexity of the aging process. The generality of the network concept helps to define and study the aging of technological,…
Gene regulation is a series of processes that control gene expression and its extent. The connections among genes and their regulatory molecules, usually transcription factors, and a descriptive model of such connections, are known as gene…
Networks represent relationships between entities in many complex systems, spanning from online social interactions to biological cell development and brain connectivity. In many cases, relationships between entities are unambiguously…
The spread of certain diseases can be promoted, in some cases substantially, by prior infection with another disease. One example is that of HIV, whose immunosuppressant effects significantly increase the chances of infection with other…
Cancers remain the lead cause of disease-related, pediatric death in North America. The emerging field of complex systems has redefined cancer networks as a computational system with intractable algorithmic complexity. Herein, a tumor and…
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…
Antimicrobial resistance is an emerging global health crisis that is undermining advances in modern medicine and, if unmitigated, threatens to kill 10 million people per year worldwide by 2050. Research over the last decade has demonstrated…