Related papers: Global Snapshot of Protein Interaction Network -- …
Identifying interactions between proteins is important to understand underlying biological processes. Extracting a protein-protein interaction (PPI) from the raw text is often very difficult. Previous supervised learning methods have used…
Gene and protein networks are very important to model complex large-scale systems in molecular biology. Inferring or reverseengineering such networks can be defined as the process of identifying gene/protein interactions from experimental…
It is not merely the position of residues that are of utmost importance in protein function and stability, but the interactions between them. We illustrate, by using a network construction on a set of 595 non-homologous proteins, that…
The principles underlying protein folding remains one of Nature's puzzles with important practical consequences for Life. An approach that has gathered momentum since the late 1990's, looks at protein hetero-polymers and their folding…
Aligning protein interaction networks (PPI) of two or more organisms consists of finding a mapping of the nodes (proteins) of the networks that captures important structural and functional associations (similarity). It is a well studied but…
We introduce a new centrality measure that characterizes the participation of each node in all subgraphs in a network. Smaller subgraphs are given more weight than larger ones, which makes this measure appropriate for characterizing network…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
We analyze gene expression time-series data of yeast S. cerevisiae measured along two full cell-cycles. We quantify these data by using q-exponentials, gene expression ranking and a temporal mean-variance analysis. We construct gene…
New advances in nano sciences open the door for scientists to study biological processes on a microscopic molecule-by-molecule basis. Recent single-molecule biophysical experiments on enzyme systems, in particular, reveal that enzyme…
The outcome of an epidemic is closely related to the network of interactions between the individuals. Likewise, protein functions depend on the 3D arrangement of their residues and on the underlying energetic interaction network. Borrowing…
We study how the dynamic equilibrium of the reversible protein-protein binding network in yeast Saccharomyces cerevisiae responds to large changes in abundances of individual proteins. The magnitude of shifts between free and bound…
We test the claim by Yu et al. -- presented in Science 322, 104 (2008) -- that the degree distribution of the yeast (Saccharomyces cerevisiae) protein-interaction network is best approximated by a power law. Yu et al. consider three…
Measuring and optimizing the influence of nodes in big-data online social networks are important for many practical applications, such as the viral marketing and the adoption of new products. As the viral spreading on social network is a…
Protein-DNA interactions are critical for the successful functioning of all natural systems. The key role in these interactions is played by processes of protein search for specific sites on DNA. Although it has been studied for many years,…
We participated in three of the protein-protein interaction subtasks of the Second BioCreative Challenge: classification of abstracts relevant for protein-protein interaction (IAS), discovery of protein pairs (IPS) and text passages…
Often questions arise about old or extinct networks. What proteins interacted in a long-extinct ancestor species of yeast? Who were the central players in the Last.fm social network 3 years ago? Our ability to answer such questions has been…
Motivated by the study of social insects, we introduce a stochastic model based on interacting particle systems in order to understand the effect of communication on the division of labor. Members of the colony are located on the vertex set…
Elastic network models, simple structure-based representations of biomolecules where atoms interact via short-range harmonic potentials, provide great insight into a molecule's internal dynamics and mechanical properties at extremely low…
Future wireless networks are expected to be a convergence of many diverse network technologies and architectures, such as cellular networks, wireless local area networks, sensor networks, and device to device communications. Through…
Topological network motifs represent functional relationships within and between regulatory and protein-protein interaction networks. Enriched motifs often aggregate into self-contained units forming functional modules. Theoretical models…