Marcel Dettling

TL;DR: Details of the aims and methods of Bioconductor, the collaborative creation of extensible software for computational biology and bioinformatics, and current challenges are described.

TL;DR: When bagging is used as a module in boosting, the resulting classifier consistently improves the predictive performance and the probability estimates of both bagging and boosting on real and simulated gene expression data.

TL;DR: The alveolar rhabdomyosarcoma signature was used to classify an additional alveolars case lacking any known PAX3 or PAX7 fusion as belonging to the translocation-positive group, leading to the identification of a novel translocation t(2;2)(q35;p23), which generates a fusion protein composed of PAX3 and the nuclear receptor coactivator NCOA1, having similar transactivation properties as PAX3/FKHR.

TL;DR: A new method for finding groups of genes by directly incorporating the response variables into the grouping process, yielding a supervised clustering algorithm for genes that identifies gene clusters with excellent predictive potential.

TL;DR: Pelora is presented, an algorithm based on penalized logistic regression analysis, that combines gene selection, gene grouping and sample classification in a supervised, simultaneous way and identifies gene groups whose expression centroids have very good predictive potential and yield results that can keep up with state-of-the-art classification methods based on single genes.