Related papers: Yeast Protein Interactome Topology Provides Framew…
An approach that combines Self-Organizing maps, hierarchical clustering and network components is presented, aimed at comparing protein conformational ensembles obtained from multiple Molecular Dynamic simulations. As a first result the…
Cytoskeletal motors known as motor proteins are molecules that drive cellular transport along several parallel cytoskeletal filaments and support many biological processes. Experimental evidences suggest that they interact with the nearest…
Aligning protein-protein interaction (PPI) networks of different species has drawn a considerable interest recently. This problem is important to investigate evolutionary conserved pathways or protein complexes across species, and to help…
Brain connectomics is a developing field in neurosciences which strives to understand cognitive processes and psychiatric diseases through the analysis of interactions between brain regions. However, in the high-dimensional, low-sample, and…
Neural communication operates on both fast synaptic transmission and slower, diffusive extrasynaptic signaling, yet how these two modes jointly organize brain function remains unclear. Here, using the complete synaptic and neuropeptidergic…
Proteins are the workhorse molecules of the cell and perform their biological functions by binding to other molecules through physical contact. Protein function is then regulated through coupling of bindings on the protein (allosteric…
The human organism is an integrated network where complex physiologic systems, each with its own regulatory mechanisms, continuously interact, and where failure of one system can trigger a breakdown of the entire network. Identifying and…
Understanding the dynamical behavior of complex systems from their underlying network architectures is a long-standing question in complexity theory. Therefore, many metrics have been devised to extract network features like motifs,…
Cooperativity is a hallmark of proteins, many of which show a modular architecture comprising discrete structural domains. Detecting and describing dynamic couplings between structural regions is difficult in view of the many-body nature of…
The human structural connectome has a complex internal community organization, characterized by a high degree of overlap and related to functional and cognitive phenomena. We explored connectivity properties in connectome networks and…
Identifying and explaining the structure of complex networks at different scales has become an important problem across disciplines. At the mesoscale, modular architecture has attracted most of the attention. At the macroscale, other…
The network representation is becoming increasingly popular for the description of cardiovascular interactions based on the analysis of multiple simultaneously collected variables. However, the traditional methods to assess network links…
Recent evidence indicates that the abundance of recurring elementary interaction patterns in complex networks, often called subgraphs or motifs, carry significant information about their function and overall organization. Yet, the…
Gene/protein interactions provide critical information for a thorough understanding of cellular processes. Recently, considerable interest and effort has been focused on the construction and analysis of genome-wide gene networks. The large…
Biological networks are customarily described as structurally robust. This means that they often function extremely well under large forms of perturbations affecting both the concentrations and the kinetic parameters. In order to explain…
Complex networks provide us a new view for investigation of immune systems. In this paper we collect data through STRING database and present a model with cooperation network theory. The cytokine-protein network model we consider is…
Interaction networks are of central importance in post-genomic molecular biology, with increasing amounts of data becoming available by high-throughput methods. Examples are gene regulatory networks or protein interaction maps. The main…
Baker's yeast (Saccharomyces cerevisiae) is a model organism for studying the morphology that emerges at the scale of multi-cell colonies. To look at how morphology develops, we collect a dataset of time-lapse photographs of the growth of…
The biological processes that execute complex multiple functions, such as cell cycle, must ensure the order of sequential events and keep the dynamic robustness against various fluctuations. Here, we examine the dynamic mechanism and the…
High-throughput methods for yielding the set of connections in a neural system, the connectome, are now being developed. This tutorial describes ways to analyze the topological and spatial organization of the connectome at the macroscopic…