Related papers: Asymptotic Evolution of Protein-Protein Interactio…
Protein complexes conserved across species indicate processes that are core to cellular machinery (e.g. cell-cycle or DNA damage-repair complexes conserved across human and yeast). While numerous computational methods have been devised to…
Protein domains are found on genomes with notable statistical distributions, which bear a high degree of similarity. Previous work has shown how these distributions can be accounted for by simple models, where the main ingredients are…
Network growth as described by the Duplication-Divergence model proposes a simple general idea for the evolution dynamics of natural networks. In particular it is an alternative to the well known Barab\'asi-Albert model when applied to…
We observe an undirected graph $G$ without multiple edges and self-loops, which is to represent a protein-protein interaction (PPI) network. We assume that $G$ evolved under the duplication-mutation with complementarity (DMC) model from a…
The study of multi-type Protein-Protein Interaction (PPI) is fundamental for understanding biological processes from a systematic perspective and revealing disease mechanisms. Existing methods suffer from significant performance degradation…
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 protein-protein interaction (PPI) network is crucial for cellular information processing and decision-making. With suitable inputs, PPI networks drive the cells to diverse functional outcomes such as cell proliferation or cell death.…
The next step in the understanding of the genome organization, after the determination of complete sequences, involves proteomics. The proteome includes the whole set of protein-protein interactions, and two recent independent studies have…
We employed the random graph theory approach to analyze the protein-protein interaction database DIP (Feb. 2004), for seven species (S. cerevisiae, H. pylori, E. coli, C. elegans, H. sapiens, M. musculus and D. melanogaster). Several global…
Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted…
From the spectral plot of the (normalized) graph Laplacian, the essential qualitative properties of a network can be simultaneously deduced. Given a class of empirical networks, reconstruction schemes for elucidating the evolutionary…
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…
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,…
Research shows that gene duplication followed by either repurposing or removal of duplicated genes is an important contributor to evolution of gene and protein interaction networks. We aim to identify which characteristics of a network can…
Background. Human aging is linked to many prevalent diseases. The aging process is highly influenced by genetic factors. Hence, it is important to identify human aging-related genes. We focus on supervised prediction of such genes. Gene…
Gene duplication is a fundamental evolutionary mechanism that contributes to biological complexity and diversity (Fortna et al., 2004). Traditionally, research has focused on the duplication of gene sequences (Zhang, 1914). However,…
The function of a protein is defined by its interaction partners. Thus, topology-driven network alignment of the protein-protein interaction (PPI) networks of two species should uncover similar interaction patterns and allow identification…
Protein-protein interactions (PPIs) are crucial in various biological processes and their study has significant implications for drug development and disease diagnosis. Existing deep learning methods suffer from significant performance…
Identifying protein-protein interactions (PPI) is crucial for gaining in-depth insights into numerous biological processes within cells and holds significant guiding value in areas such as drug development and disease treatment. Currently,…
We investigate a model protein interaction network whose links represent interactions between individual proteins. This network evolves by the functional duplication of proteins, supplemented by random link addition to account for…