I present an algorithm that determines the longest path between every gene pair in an arbitrarily large genetic network from large scale gene perturbation data. As a by-product, the algorithm reconstructs all direct regulatory gene interactions in the network. The algorithm is recursive, and is...

n Gene Perturbations in Fewer than n2 Easy Steps <p> [gzipped postscript] [postscript] [pdf] <p> Andreas Wagner <p>I present an algorithm to reconstruct direct regulatory interactions in gene networks from the effects of genetic perturbations on gene activity. Genomic technology has made feasible...</p></p></p>

The neutralist perspective on molecular evolution maintains that the vast majority of mutations effecting gene function are neutral or deleterious. Following a gene duplication where both genes are retained, it predicts that original and duplicate genes diverge at clock-like rates. This...

For many organisms, and especially for the model organisms of molecular and cell biology, the primary locus of study is the laboratory, and not their natural habitat. Thus, a huge body of knowledge accumulated through a century of laboratory studies contrasts with the limited amount of...

We derive and validate an estimator for the parameters of a transformation for the joint calibration (normalization) and variance stabilization of microarray intensity data. With this, the variances of the transformed intensities become approximately independent of their expected values. The...

Motivated in part by applications in model selection in statistical genetics and sequential monitoring of financial data, we study an empirical process framework for a class of stopping rules which rely on kernel-weighted averages of past data. We are interested in the asymptotic distribution...

One application of gene expression arrays is to derive molecular profiles, i.e., sets of genes, which discriminate well between two classes of samples, for example between tumour types. Users are confronted with a multitude of classification methods of varying complexity that can be applied to...