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DC-ATLAS: a systems biology resource to dissect receptor specific signal transduction in dendritic cells

Background The advent of Systems Biology has been accompanied by the blooming of pathway databases. Currently pathways are defined generically with respect to the organ or cell type where a reaction takes place. The cell type specificity of the reactions is the foundation of immunological research, and capturing this specificity is of paramount importance when using pathway-based...

ONS: an ontology for a standardized description of interventions and observational studies in nutrition

BackgroundThe multidisciplinary nature of nutrition research is one of its main strengths. At the same time, however, it presents a major obstacle to integrate data analysis, especially for the terminological and semantic interpretations that specific research fields or communities are used to. To date, a proper ontology to structure and formalize the concepts used for the...

Plant microRNAs as novel immunomodulatory agents

Rizzetto in:Nature Research journals • PubMed • Google ScholarSearch for Noemi Tocci in:Nature Research journals • PubMed • Google ScholarSearch for Damariz Rivero in:Nature Research journals • PubMed

The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways

Motivation: Many models and analysis of signaling pathways have been proposed. However, neither of them takes into account that a biological pathway is not a fixed system, but instead it depends on the organism, tissue and cell type as well as on physiological, pathological and experimental conditions. Results: The Biological Connection Markup Language (BCML) is a format to...

The Micronutrient Genomics Project: a community-driven knowledge base for micronutrient research

Micronutrients influence multiple metabolic pathways including oxidative and inflammatory processes. Optimum micronutrient supply is important for the maintenance of homeostasis in metabolism and, ultimately, for maintaining good health. With advances in systems biology and genomics technologies, it is becoming feasible to assess the activity of single and multiple micronutrients...