Jörg Rahnenführer

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Gene Ontology (GO) is a standard vocabulary of functional terms and allows for coherent annotation of gene products. These annotations provide a basis for new methods that compare gene products regarding their molecular function and biological role. We present a new method for comparing sets of GO terms and for assessing the functional similarity of gene(More)
MOTIVATION The result of a typical microarray experiment is a long list of genes with corresponding expression measurements. This list is only the starting point for a meaningful biological interpretation. Modern methods identify relevant biological processes or functions from gene expression data by scoring the statistical significance of predefined(More)
MOTIVATION Microarray images challenge existing analytical methods in many ways given that gene spots are often comprised of characteristic imperfections. Irregular contours, donut shapes, artifacts, and low or heterogeneous expression impair corresponding values for red and green intensities as well as their ratio R/G. New approaches are needed to ensure(More)
The development of multicellular organisms is controlled by differential gene expression whereby cells adopt distinct fates. A spatially resolved view of gene expression allows the elucidation of transcriptional networks that are linked to cellular identity and function. The haploid female gametophyte of flowering plants is a highly reduced organism: at(More)
We introduce a mixture model of trees to describe evolutionary processes that are characterized by the accumulation of permanent genetic changes. The basic building block of the model is a directed weighted tree that generates a probability distribution on the set of all patterns of genetic events. We present an EM-like algorithm for learning a mixture(More)
Predicting subcellular localization has become a valuable alternative to time-consuming experimental methods. Major drawbacks of many of these predictors is their lack of interpretability and the fact that they do not provide an estimate of the confidence of an individual prediction. We present YLoc, an interpretable web server for predicting subcellular(More)
PURPOSE Global gene expression profiling has been widely used in lung cancer research to identify clinically relevant molecular subtypes as well as to predict prognosis and therapy response. So far, the value of these multigene signatures in clinical practice is unclear, and the biologic importance of individual genes is difficult to assess, as the(More)
MOTIVATION Protein subcellular localization is pivotal in understanding a protein's function. Computational prediction of subcellular localization has become a viable alternative to experimental approaches. While current machine learning-based methods yield good prediction accuracy, most of them suffer from two key problems: lack of interpretability and(More)
PURPOSE The prognostic and predictive relevance of epidermal growth factor receptor 2 (ERBB2) and topoisomerase II alpha (TOP2A) have long been a matter of debate. However, the correlation of DNA amplification, RNA levels, and protein expression and their prognostic role and association with anthracycline responses in node-negative breast cancer have not(More)
The ciliary epithelium (CE) in the adult mammalian eye harbors a mitotic quiescent population of neural stem cells. Here we have compared the cellular and molecular properties of CE stem cells and populations of retinal progenitors that define the early and late stages of histogenesis. The CE stem cells and retinal progenitors proliferate in the presence of(More)