Related papers: Modeling Interactome: Scale-Free or Geometric?
We study a recent model of random networks based on the presence of an intrinsic character of the vertices called fitness. The vertices fitnesses are drawn from a given probability distribution density. The edges between pair of vertices…
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…
The behavior of complex networks under failure or attack depends strongly on the specific scenario. Of special interest are scale-free networks, which are usually seen as robust under random failure but appear to be especially vulnerable to…
The problem of learning the structure of a high dimensional graphical model from data has received considerable attention in recent years. In many applications such as sensor networks and proteomics it is often expensive to obtain samples…
Cellular function is widely believed to be organized in a modular fashion. On all scales and at all levels of complexity, relatively independent sub-units perform relatively independent sub-tasks of biological function. This functional…
We report on parallel observations in two seemingly unrelated areas of dynamical network research. The one is the so-called small world phenomenon and/or the observation of scale freeness in certain types of large (empirical) networks and…
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…
Link prediction is one of the fundamental problems in network analysis. In many applications, notably in genetics, a partially observed network may not contain any negative examples of absent edges, which creates a difficulty for many…
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…
Scale-free (SF) networks and small world networks have been found to occur in very diverse contexts. It is this striking universality which makes one look for widely applicable mechanisms which lead to the formation of such networks. In…
Genome-wide protein-protein interaction (PPI) data are readily available thanks to recent breakthroughs in biotechnology. However, PPI networks of extant organisms are only snapshots of the network evolution. How to infer the whole…
Computational protein-protein interaction (PPI) prediction techniques can contribute greatly in reducing time, cost and false-positive interactions compared to experimental approaches. Sequence is one of the key and primary information of…
The topology of interactions in network dynamical systems fundamentally underlies their function. Accelerating technological progress creates massively available data about collective nonlinear dynamics in physical, biological, and…
Various approaches and measures from network analysis have been applied to granular and particulate networks to gain insights into their structural, transport, failure-propagation and other systems-level properties. In this article, we…
Networks are a powerful abstraction with applicability to a variety of scientific fields. Models explaining their morphology and growth processes permit a wide range of phenomena to be more systematically analysed and understood. At the…
The models of the Internet reported in the literature are mainly aimed at reproducing the scale-free structure, the high clustering coefficient and the small world effects found in the real Internet, while other important properties (e.g.…
Protein-protein interaction (PPI) networks consist of the physical and/or functional interactions between the proteins of an organism. Since the biophysical and high-throughput methods used to form PPI networks are expensive,…
Spatial phenomena are subject to scale effects, but there are rarely studies addressing such effects on spatially embedded contact networks. There are two types of structure in these networks, network structure and spatial structure. The…
The movement changes the underlying spatial representation of the participated mobile objects or nodes. In real world scenario, such mobile nodes can be part of any biological network, transportation network, social network, human…
Complex networks are characterized by several topological properties: degree distribution, clustering coefficient, average shortest path length, etc. Using a simple model to generate scale-free networks embedded on geographical space, we…