Molecular Inference of Wisdom

Measuring the wisdom of the crowds in network-based gene function inference

MOTIVATION Network-based gene function inference methods have proliferated in recent years, but measurable progress remains elusive. We wished to better explore performance trends by controlling data and algorithm implementation, with a particular focus on the performance of aggregate predictions. RESULTS Hypothesizing that popular methods would perform well without hand-tuning, we used well-...

Bayesian Inference in Molecular Phylogenetics

"o. ~ ,1:. 200<;. 1--. \\.B~~ ~ ,~ ~~c..("" ." V I P '7\rt~ . :r~ M~l(.$ 4 ~~oV\ "",cJ.f"-1'~~'/ (~~. O. Gaswd) . O'6~ ~"'\v. tp,~ss.,~ I (Jf. b~O~ [49] Swofford, D., Olsen, G.J., Waddell, P.J., and Hillis, D.M. (1996). Phylogenetic inference. In Molecular Systematics (2nd edn) (ed. D. Hillis, C. Moritz, and B. Mable), pp. 438-514. Sinauer, Sutherland, MA. [50] Thorne, J.L., Goldman, N., and Jo...

Ancestral Inference in Molecular Biology

Wisdom of Crowds or Wisdom of a Few?

The Web continues to grow and evolve very fast, changing our daily lives. This activity represents the collaborative work of the millions of institutions and people that contribute content to the Web as well as more than two billion people that use it. In this ocean of hyperlinked data there is explicit and implicit information and knowledge. But how is the Web? What are the activities of peopl...

Impact of Noise on Molecular Network Inference

Molecular entities work in concert as a system and mediate phenotypic outcomes and disease states. There has been recent interest in modelling the associations between molecular entities from their observed expression profiles as networks using a battery of algorithms. These networks have proven to be useful abstractions of the underlying pathways and signalling mechanisms. Noise is ubiquitous ...