Extending protein interaction networks using proteoforms and small molecules.

Motivation: Biological network analysis for high-throughput biomedical data interpretation relies heavily on topological characteristics. Networks are commonly composed of nodes representing genes or proteins that are connected by edges when interacting. In this study, we use the rich information available in the Reactome pathway database to build biological networks accounting for small molecules and proteoforms modeled using protein isoforms and post-translational modifications to study the topological changes induced by this refinement of the network representation.

Analyzing the Structure of Pathways and Its Influence on the Interpretation of Biomedical Proteomics Data Sets.

Biochemical pathways are commonly used as a reference to conduct functional analysis on biomedical omics data sets, where experimental results are mapped to knowledgebases comprising known molecular interactions collected from the literature. Due to their central role, the content of the functional knowledgebases directly influences the outcome of pathway analyses. In this study, we investigate the structure of the current pathway knowledge, as exemplified by Reactome, discuss the consequences for biological interpretation, and outline possible improvements in the use of pathway knowledgebases.

Fifteen-year trend in information on the World Wide Web for patients with rheumatoid arthritis: evolving, but opportunities for improvement remain.

The aim of this study was to assess the changes in the characteristics of rheumatoid arthritis information on the Internet over a 15-year period and the positioning of Web sites posted by universities, hospitals, and medical associations. We replicated the methods of a 2001 study assessing rheumatoid arthritis information on the Internet using WebCrawler. All Web sites and pages were critically assessed for relevance, scope, authorship, type of publication, and financial objectives.

Readability, relevance and quality of the information in Spanish on the Web for patients with rheumatoid arthritis.

Background: Education is a major health determinant and one of the main independent outcome predictors in rheumatoid arthritis (RA). The use of the Internet by patients has grown exponentially in the last decade.

Objective: To assess the characteristics, legibility and quality of the information available in Spanish in the Internet regarding to rheumatoid arthritis.

Systemic Analysis of Regulated Functional Networks.

In biological and medical sciences, high throughput analytical methods are now commonly used to investigate samples of different conditions, e.g., patients versus controls.