Transient oscillatory dynamics of interferon beta signaling in macrophages.

Background: Interferon-beta (IFN-beta) activates the immune response through the type I IFN signaling pathway. IFN-beta is important in the response to pathogen infections and is used as a therapy for Multiple Sclerosis. The mechanisms of self-regulation and control of this pathway allow precise and environment-dependent response of the cells in different conditions.

Information routing driven by background chatter in a signaling network.

Living systems are capable of processing multiple sources of information simultaneously. This is true even at the cellular level, where not only coexisting signals stimulate the cell, but also the presence of fluctuating conditions is significant. When information is received by a cell signaling network via one specific input, the existence of other stimuli can provide a background activity -or chatter- that may affect signal transmission through the network and, therefore, the response of the cell.

Statistical model comparison applied to common network motifs.

Background: Network motifs are small modules that show interesting functional and dynamic properties, and are believed to be the building blocks of complex cellular processes. However, the mechanistic details of such modules are often unknown: there is uncertainty about the motif architecture as well as the functional form and parameter values when converted to ordinary differential equations (ODEs). This translates into a number of candidate models being compatible with the system under study.

Applying GIFT, a Gene Interactions Finder in Text, to fly literature.

Unlabelled: A number of freely available text mining tools have been put together to extract highly reliable Drosophila gene interaction data from text. The system has been tested with The Interactive Fly, showing low recall (27-34%), but very high precision (93-97%).

Availability: The extracted data and a web interface for submission of texts to GIFT analysis are available at http://gift.