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Understanding the dependence and interplay between architecture and function in biological networks has great relevance to disease progression, biological fabrication and biological systems in general. We propose methods to assess the…
With the completion of human genome mapping, the focus of scientists seeking to explain the biological complexity of living systems is shifting from analyzing the individual components (such as a particular gene or biochemical reaction) to…
Transcriptomic data is a treasure-trove in modern molecular biology, as it offers a comprehensive viewpoint into the intricate nuances of gene expression dynamics underlying biological systems. This genetic information must be utilised to…
Understanding the structure and dynamics of biological networks is one of the important challenges in system biology. In addition, increasing amount of experimental data in biological networks necessitate the use of efficient methods to…
This paper presents the foundation for a decomposition theory for Boolean networks, a type of discrete dynamical system that has found a wide range of applications in the life sciences, engineering, and physics. Given a Boolean network…
Metagenomics has lowered the barrier to microbial discovery--enabling the identification of novel microbes without isolation--but cultures remain imperative for the deep study of microbes. Cultivation and isolation of non-model microbes…
Complex networks provide a powerful mathematical representation of complex systems in nature and society. To understand complex networks, it is crucial to explore their internal structures, also called structural regularities. The task of…
Chemical reaction networks underpin biological and physical phenomena across scales, from microbial interactions to planetary atmosphere dynamics. Bacterial communities exhibit complex competitive interactions for resources, human organs…
The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from…
Different network models have been suggested for the topology underlying complex interactions in natural systems. These models are aimed at replicating specific statistical features encountered in real-world networks. However, it is rarely…
Link prediction in complex networks has attracted increasing attention from both physical and computer science communities. The algorithms can be used to extract missing information, identify spurious interactions, evaluate network evolving…
Using a large database (~ 215 000 records) of relevant articles, we empirically study the "complex systems" field and its claims to find universal principles applying to systems in general. The study of references shared by the papers…
During the past two decades, percolation has long served as a basic paradigm for network resilience, community formation and so on in complex systems. While the percolation transition is known as one of the most robust continuous…
In the past years, network theory has successfully characterized the interaction among the constituents of a variety of complex systems, ranging from biological to technological, and social systems. However, up until recently, attention was…
The last decade has witnessed a surge of theoretical and computational models to describe the dynamics of complex gene regulatory networks, and how these interactions can give rise to multistable and heterogeneous cell populations. As the…
Real networks exhibit heterogeneous nature with nodes playing far different roles in structure and function. To identify vital nodes is thus very significant, allowing us to control the outbreak of epidemics, to conduct advertisements for…
Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales. Although the field…
The topology of many real complex networks has been conjectured to be embedded in hidden metric spaces, where distances between nodes encode their likelihood of being connected. Besides of providing a natural geometrical interpretation of…
This review was written for the Encyclopedia of Complexity and System Science (Springer-Verlag, Berlin, 2008), and is intended as a guide to the growing literature which approaches the phenomena of cell biology from a more theoretical point…
Networks have attracted a burst of attention in the last decade, with applications to natural, social, and technological systems. While networks provide a powerful abstraction for investigating relationships and interactions, the…