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A biological experiment is the most reliable way of assigning function to a protein. However, in the era of high-throughput sequencing, scientists are unable to carry out experiments to determine the function of every single gene product. Therefore, to gain insights into the activity of these molecules and guide experiments, we must rely on computational means to functionally annotate the majority of sequence data. To understand how well these algorithms perform, we have established a challenge involving a broad scientific community in which we evaluate different annotation methods according to their ability to predict the associations between previously unannotated protein sequences and Gene Ontology terms. Here we discuss the rationale, benefits and issues associated with evaluating computational methods in an ongoing community-wide challenge.
The canine lymphoma blood test detects the levels of two biomarkers, the acute phase proteins (C-Reactive Protein and Haptoglobin). This test can be used for diagnostics, for screening, and for remission monitoring as well. We analyze clinical data,
Cell type (e.g. pluripotent cell, fibroblast) is the end result of many complex processes that unfold due to evolutionary, developmental, and transformational stimuli. A cells phenotype and the discrete, a priori states that define various cell subty
In computational biology and other sciences, researchers are frequently faced with a choice between several computational methods for performing data analyses. Benchmarking studies aim to rigorously compare the performance of different methods using
Dynamic flux balance analysis uses a quasi-steady state assumption to calculate an organisms metabolic activity at each time-step of a dynamic simulation, using the well-known technique of flux balance analysis. For microbial communities, this calcul
Microbiome-based stratification of healthy individuals into compositional categories, referred to as community types, holds promise for drastically improving personalized medicine. Despite this potential, the existence of community types and the degr