In this paper, we propose a novel method for sparse logistic regression with non-convex regularization Lp (p 1). Based on smooth approximation, we develop several fast algorithms for learning the classifier that is applicable to high dimensional dataset such as gene expression. To the best of...

The problem of finding periodically expressed genes from time course microarray experiments is at the center of numerous efforts to identify the molecular components of biological clocks. We present a new approach to this problem based on the cyclohedron test, which is a rank test inspired by...

We propose an original statistical method to estimate how the occurrences of a given process along a genome, genes or motifs for instance, may be influenced by the occurrences of a second process. More precisely, the aim is to detect avoided and/or favored distances between two motifs, for...

As a powerful tool for analyzing full conditional (in-)dependencies between random variables, graphical models have become increasingly popular to infer genetic networks based on gene expression data. However, full (unconstrained) conditional relationships between random variables can be only...

Visualisation methods for exploring microarray data are particularly important for gaining insight into data from gene expression experiments, such as those concerned with the development of an understanding of gene function and interactions. Further, good visualisation techniques are useful for...

The evolution of drug resistance in HIV is characterized by the accumulation of resistance-associated mutations in the HIV genome. Mutagenetic trees, a family of restricted Bayesian tree models, have been applied to infer the order and rate of occurrence of these mutations. Understanding and...

A combined score test for association and linkage analysis is introduced, based on a biologically plausible model with association between markers and causal genes and penetrance between phenotypes and the causal gene. The test is based on a retrospective likelihood of marker data given...

We propose an approximate distribution for the gapped local score of a two sequence comparison. Our method stands on combining an adapted scoring scheme that includes the gaps and an approximate distribution of the ungapped local score of two independent sequences of i.i.d. random variables. The...

We outline a method of sample size calculation in microarray experiments on the basis of pilot data and illustrate its practical application with both simulated and real data. The method was shown to be consistent (as the number of `probed genes' tends to infinity) under general conditions in an...

The detection of remote homologies is of major importance for molecular biology applications like drug discovery. The problem is still very challenging even for state-of-the-art probabilistic models of protein families, namely Profile HMMs. In order to improve remote homology detection we...