Related papers: Cell cycle and protein complex dynamics in discove…
Biological systems and processes are networks of complex nonlinear regulatory interactions between nucleic acids, proteins, and metabolites. A natural way in which to represent these interaction networks is through the use of a graph. In…
Cell signaling networks are complex and often incompletely characterized, making it difficult to obtain a comprehensive picture of the mechanisms they encode. Mathematical modeling of these networks provides important clues, but the models…
Diseases involve complex processes and modifications to the cellular machinery. The gene expression profile of the affected cells contains characteristic patterns linked to a disease. Hence, biological knowledge pertaining to a disease can…
Genomic alterations lead to cancer complexity and form a major hurdle for a comprehensive understanding of the molecular mechanisms underlying oncogenesis. In this review, we describe the recent advances in studying cancer-associated genes…
Numerous cellular functions rely on protein$\unicode{x2013}$protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep…
Graphs are a common model for complex relational data such as social networks and protein interactions, and such data can evolve over time (e.g., new friendships) and be noisy (e.g., unmeasured interactions). Link prediction aims to predict…
Biological information processing as implemented by regulatory and signaling networks in living cells requires sufficient specificity of molecular interaction to distinguish signals from one another, but much of regulation and signaling…
Motivation: Signaling pathways control a large variety of cellular processes. However, currently, even within the same database signaling pathways are often curated at different levels of detail. This makes comparative and cross-talk…
Complexes of physically interacting proteins are one of the fundamental functional units responsible for driving key biological mechanisms within the cell. Their identification is therefore necessary not only to understand complex formation…
The ability of a cell to communicate with its environment is essential for key cellular functions like replication, metabolism, or cell fate decisions. The involved molecular mechanisms are highly dynamic and difficult to capture…
Biological networks are pivotal in deciphering the complexity and functionality of biological systems. Causal inference, which focuses on determining the directionality and strength of interactions between variables rather than merely…
Motivation: In the last few years a growing interest in biology has been shifting towards the problem of optimal information extraction from the huge amount of data generated via large scale and high-throughput techniques. One of the most…
Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…
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…
System dynamics is a popular approach in many fields of science and technology, but it has not been investigated for cell signaling pathways yet. It is a well formulated methodology used to analyze the components of a system considering the…
The pathway is a biological term that refers to a series of interactions between molecules in a cell that causes a certain product or a change in the cell. Pathway analysis is a powerful method for gene expression analysis. Through pathway…
Network-based computational approaches to predict unknown genes associated with certain diseases are of considerable significance for uncovering the molecular basis of human diseases. In this paper, we proposed a kind of new…
Non-genetic heterogeneity is key to cellular decisions, as even genetically identical cells respond in very different ways to the same external stimulus, e.g., during cell differentiation or therapeutic treatment of disease. Strong…
Living systems rely on coordinated molecular interactions, especially those related to gene expression and protein activity. The Unfolded Protein Response is a crucial mechanism in eukaryotic cells, activated when unfolded proteins exceed a…
Uncovering causal relationships in data is a major objective of data analytics. Causal relationships are normally discovered with designed experiments, e.g. randomised controlled trials, which, however are expensive or infeasible to be…