• A new pipeline for PPI network detection and 3D structure construction. Detecting 35,125 confident PPIs in E coli that is 4.5-fold higher than HTE alone. Confident quaternary model was constructed 6771 E. coli. Essential proteins have distinct networks from non-essential ones Genome-wide protein–protein interaction (PPI) determination remains a significant unsolved problem structural biology....

We investigated the biological significance of path lengths in 12 protein-protein interaction (PPI) networks. We put forward three predictions, based on the idea that biological complexity influences path lengths. First, at the network level, path lengths are generally longer in PPIs than in random networks. Second, this pattern is more pronounced in more complex organisms. Third, within a PPI ...

Osteoarthritis is the most common form of arthritis among elderly adults. Herein, we performed protein-protein interaction (PPI) and miRNA network analysis to evaluate the global correlation between miRNA regulation and the PPI network in human osteoarthritis. Our results showed that desmoplakin (DSP), cystatin A (CSTA), calmodulin 1, tyrosine kinase endothelial, insulin-like growth factor 1 (I...

background alcoholic hepatitis (ah) is an acute manifestation of alcoholic liver disease with high mortality rates. objectives our aim was to study the molecular mechanisms of ah. materials and methods the differentially expressed genes (degs) in liver between ah and control cases were identified by analyzing the gse28619 microarray data using t-test. the kyoto encyclopedia of genes and genomes...

Small molecule nonpeptidic mimics of α-helices are widely recognised as protein-protein interaction (PPIs) inhibitors. Protein-protein interactions mediate virtually all important regulatory pathways in a cell, and the ability to control and modulate PPIs is therefore of great significance to basic biology, where controlled disruption of protein networks is key to understanding network connecti...

There has been much recent interest in the extraction of PPIs (protein-protein interactions) from biomedical texts, but in order to assist with curation efforts, the PPIs must be enriched with further information of biological interest. This paper describes the implementation of a system to extract and enrich PPIs, developed and tested using an annotated corpus of biomedical texts, and employin...

Background: Crohn's disease (CD) is a type of inflammatory bowel disease (IBD) which despite the unknown details is generally related to genetic, immune system, and environmental factors. In this study, we identify transcriptional signatures in patients with CD and then explain the potential molecular mechanisms in inflamed and non-inflamed intestinal mucosa in these patients. Materials and Me...

Protein-protein interactions (PPI) are a hallmark of cellular signaling. Such interactions occur abundantly within the cellular milieu and encompass interactions involved in vital cellular processes. Understanding the various types, mechanisms, and consequences of PPIs with respect to cellular signaling and function is vital for targeted drug therapy. Various types of small-molecule drugs and t...

MOTIVATION Infectious diseases such as malaria result in millions of deaths each year. An important aspect of any host-pathogen system is the mechanism by which a pathogen can infect its host. One method of infection is via protein-protein interactions (PPIs) where pathogen proteins target host proteins. Developing computational methods that identify which PPIs enable a pathogen to infect a hos...

MOTIVATION The identification of events such as protein-protein interactions (PPIs) from the scientific literature is a complex task. One of the reasons is that there is no formal syntax to denote such relations in the scientific literature. Nonetheless, it is important to understand such relational event representations to improve information extraction solutions (e.g., for gene regulatory eve...