Related papers: Bacterial protein interaction networks: connectivi…
Molecular networks act as the backbone of cellular activities, providing an {excellent} opportunity to understand the developmental changes in an organism. While network data usually constitute only stationary network graphs, constructing…
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…
Infections depend on interactions between pathogen and host proteins, but comprehensively mapping these interactions is challenging and labor intensive. Many biological networks have hierarchical, scale-free structure, so we developed a…
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…
The widespread of Coronavirus has led to a worldwide pandemic with a high mortality rate. Currently, the knowledge accumulated from different studies about this virus is very limited. Leveraging a wide-range of biological knowledge, such as…
High-throughput protein interaction detection methods are strongly affected by false positive and false negative results. Focused experiments are needed to complement the large-scale methods by validating previously detected interactions…
The phenomenon of gene conservation is an interesting evolutionary problem related to speciation and adaptation. Conserved genes are acted upon in evolution in a way that preserves their function despite other structural and functional…
Protein structures are much more conserved than sequences during evolution. Based on this observation, we investigate the consequences of structural conservation on protein evolution. We study seven of the most studied protein folds,…
The system comprises of three interconnected power system networks based on thermal, wind and hydro power generation. The load variation in any one of the network results in frequency deviation in all the connected systems.The PI…
Recent advances in AI for science have highlighted the power of contrastive learning in bridging heterogeneous biological data modalities. Building on this paradigm, we propose HIPPO (HIerarchical Protein-Protein interaction prediction…
The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…
The alignment of protein-protein interaction (PPI) networks has many applications, such as the detection of conserved biological network motifs, the prediction of protein interactions, and the reconstruction of phylogenetic trees [1, 2, 3].…
The identification of essential proteins in protein-protein interaction networks (PINs) can help to discover drug targets and prevent disease. In order to improve the accuracy of the identification of essential proteins, researchers…
We construct a gene network based on expression data from DNA microarray experiments, by establishing a link between two genes whenever the Pearson's correlation coefficient between their expression profiles is higher than a certain cutoff.…
Retrieving the biological impacts of protein-protein interactions (PPIs) is essential for target identification (Target ID) in drug development. Given the vast number of proteins involved, this process remains time-consuming and…
We propose a general parametrizable model to capture the dynamic interaction among bacteria in the formation of micro-colonies. micro-colonies represent the first social step towards the formation of structured multicellular communities…
The evolution processes of complex systems carry key information in the systems' functional properties. Applying machine learning algorithms, we demonstrate that the historical formation process of various networked complex systems can be…
The identification of essential proteins can help in understanding the minimum requirements for cell survival and development. Network-based centrality approaches are commonly used to identify essential proteins from protein-protein…
While most studies emphasize on certain aspects of Pathogen-Host Interactions (PHI), such as the preferential attachment of bacteria or virus to its human receptor homolog, studies have attempted to methodically classify interactions among…
Genes are not located randomly along genomes. Synteny, the conservation of their relative positions in genomes of different species, reflects fundamental constraints on natural evolution. We present approaches to infer pairs of co-localized…