Identifying differentially expressed genes in the absence of replication.

In microarray data analysis, the comparison of gene expression levels in different conditions and selection of biologically relevant genes are essential tasks. In this study, we propose a novel statistical procedure based on standardised conditional residuals from a linear mixed-effects model which allows comparison of conditions, even if only one replicate per experimental condition is available. We illustrate this method by using three publicly available datasets.

The influence of mixing methods and disinfectant on the physical properties of alginate impression materials.

The aims of this in vitro study were to quantify the effect of manual versus automatic mixing and of using a disinfectant on mechanical properties of three different alginate impression materials. Two of the three alginates tested were especially developed for orthodontic use: Orthotrace® and Orthofine® while the third was a conventional alginate CA37FS®. Alginates were mixed by hand or automatically using a Cavex alginate mixer II®.

The use of semiparametric mixed models to analyze PamChip(R) peptide array data: an application to an oncology experiment.

Motivation: Phosphorylation by protein kinases is a central theme in biological systems. Aberrant protein kinase activity has been implicated in a variety of human diseases (e.g.

Modeling the asymmetric evolution of a mouse and rat-specific microRNA gene cluster intron 10 of the Sfmbt2 gene.

Background: The total number of miRNA genes in a genome, expression of which is responsible for the miRNA repertoire of an organism, is not precisely known. Moreover, the question of how new miRNA genes arise during evolution is incompletely understood. Recent data in humans and opossum indicate that retrotranspons of the class of short interspersed nuclear elements have contributed to the growth of microRNA gene clusters.

A nonlinear mixed-effects model for estimating calibration intervals for unknown concentrations in two-color microarray data with spike-ins.

In this study, we propose a calibration method for preprocessing spiked-in microarray experiments based on nonlinear mixed-effects models. This method uses a spike-in calibration curve to estimate normalized absolute expression values. Moreover, using the asymptotic properties of the calibration estimate, 100(1-alpha)% confidence intervals for the estimated expression values can be constructed.

Evidence for co-evolution between human microRNAs and Alu-repeats.

This paper connects Alu repeats, the most abundant repetitive elements in the human genome and microRNAs, small RNAs that alter gene expression at the post-transcriptional level. Base-pair complementarity could be demonstrated between the seed sequence of a subset of human microRNAs and Alu repeats that are integrated parallel (sense) in mRNAs. The most common target site coincides with the evolutionary most conserved part of Alu.