The use of microarray data has become quite commonplace in medical and scientific experiments. We focus here on microarray data generated from cancer studies. It is potentially important for the discovery of biomarkers to identify genes whose expression levels correlate with tumor progression....

In many scientific and medical settings, large-scale experiments are generating large quantities of data that lead to inferential problems involving multiple hypotheses. This has led to recent tremendous interest in statistical methods regarding the false discovery rate (FDR). Several authors...

We present a new instance of Laplace's second Law of Errors and show how it can be used in the analysis of data from microarray experiments. This error distribution is shown to fit microarray expression data much better than a normal distribution. The use of this distribution in a parametric...

This is a summary of the author’s Ph.D. thesis supervised by Fioravante Patrone and Stefano Bonassi and defended on 25 May 2006 at the Università degli Studi di Genova. The thesis in written in English and a copy is available from the author upon request. This work deals with the discussion...

Several mathematical models have been proposed to predict the activation state of a transcription factor (TF) from the expression levels of its target genes. This inference problem is complicated however due to the fact that different genes may be regulated by different activation schemes...

In breast cancer research, it is of great interest to identify genomic markers associated with prognosis. Multiple gene profiling studies have been conducted for such a purpose. Genomic markers identified from the analysis of single datasets often do not have satisfactory reproducibility. Among...

High-gain nonlinear observers occur in the nonlinear automatic control theory and are in standard usage in chemical engineering processes. We apply such a type of analysis in the context of a very simple one-gene regulation circuit. In general, an observer combines an analytical...

In this paper, we focus on the estimation of a high-dimensional precision matrix. We propose a simple improvement of the graphical lasso framework (glasso) that is able to attain better statistical performance without sacrificing too much the computational cost. The proposed improvement is based...

To identify molecular mechanisms by which early life social conditions might influence adult risk of disease in rhesus macaques (Macaca mulatta), we analyze changes in basal leukocyte gene expression profiles in 4-month-old animals reared under adverse social conditions. Compared to the basal...

We present the Ontocancro Database (www.ontocancro.org) illustrated with applications to network modeling and pathway functional analysis. The database compiles information on gene pathways involved in Human Genome Maintenance Mechanisms (GMM) whose dysfunction accounts for cancer and several...