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>

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...

In this work, we modify the superparamagnetic clustering algorithm (SPC) by adding an extra weight to the interaction formula that considers which genes are regulated by the same transcription factor. With this modified algorithm which we call SPCTF, we analyze the Spellman et al. microarray...

Microarray studies often need to simultaneously examine thousands of genes to determine which are differentially expressed. One main challenge in those studies is to find suitable multiple testing procedures that provide accurate control of the error rates of interest and meanwhile are most...

Gene co-expression networks are increasingly used to explore the system-level functionality of genes. The network construction is conceptually straightforward: nodes represent genes and nodes are connected if the corresponding genes are significantly co-expressed across appropriately chosen...