Related papers: Lethality and centrality in protein networks
Protein interaction networks aim to summarize the complex interplay of proteins in an organism. Early studies suggested that the position of a protein in the network determines its evolutionary rate but there has been considerable…
Genetic interactions have been widely used to define functional relationships between proteins and pathways. In this study, we demonstrated that yeast synthetic lethal genetic interactions can be explained by the genetic interactions…
We present a method that compares the protein interaction networks of two species to detect functionally similar (conserved) protein modules between them. The method is based on an algorithm we developed to identify matching subgraphs…
We introduce a stochastic model of growing networks where both, the number of new nodes which joins the network and the number of connections, vary stochastically. We provide an exact mapping between this model and zero range process, and…
Starting from linear chains of amino acids, the spontaneous folding of proteins into their elaborate three-dimensional structures is one of the remarkable examples of biological self-organization. We investigated native state structures of…
Many complex systems--from social and communication networks to biological networks and the Internet--are thought to exhibit scale-free structure. However, prevailing explanations rely on the constant addition of new nodes, an assumption…
Genetic interactions confer robustness on cells in response to genetic perturbations. This often occurs through molecular buffering mechanisms that can be predicted using, among other features, the degree of coexpression between genes,…
We present a comparative analysis of large-scale topological and evolutionary properties of transcription networks in three species, the two distant bacteria E. coli and B. subtilis, and the yeast S. cerevisiae. The study focuses on the…
Active centres and hot spots of proteins have a paramount importance in enzyme action, protein complex formation and drug design. Recently a number of publications successfully applied the analysis of residue networks to predict active…
Temporal gene expression data (Wen, et. al.) was analyzed using the recently introduced inverse modeling technique of Embedded Complex Logistic Maps (ECLM). Preliminary results indicate scale-free structure in the gene regulatory network…
Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease. Comparison and alignment of biological networks will likely have a similar impact. Existing network alignments use…
Scale invariance profoundly influences the dynamics and structure of complex systems, spanning from critical phenomena to network architecture. Here, we propose a precise definition of scale-invariant networks by leveraging the concept of a…
In a cell or microorganism the processes that generate mass, energy, information transfer, and cell fate specification are seamlessly integrated through a complex network of various cellular constituents and reactions. However, despite the…
The structure of complex networks in previous research has been widely described as scale-free networks generated by the preferential attachment model. However, the preferential attachment model does not take into account the detailed…
We present a sequence-based probabilistic formalism that directly addresses co-operative effects in networks of interacting positions in proteins, providing significantly improved contact prediction, as well as accurate quantitative…
BACKGROUND. Signal recognition and information processing is a fundamental cellular function, which in part involves comprehensive transcriptional regulatory (TR) mechanisms carried out in response to complex environmental signals in the…
A number of recent works have concentrated on a few statistical properties of complex networks, such as the clustering, the right-skewed degree distribution and the community, which are common to many real world networks. In this paper, we…
We explore the interplay between the protein-protein interactions network and the expression of the interacting proteins. It is shown that interacting proteins are expressed in significantly more similar cellular concentrations. This is…
The capacity to resist attacks from the environment is crucial to the survival of all organisms. We quantitatively analyze the susceptibility of protein interaction networks of numerous organisms to random and malicious attacks. We find for…
Tolerance against failures and errors is an important feature of many complex networked systems [1,2]. It has been shown that a class of inhomogeneously wired networks called scale-free[1,3] networks can be surprisingly robust to failures,…