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 next step in the understanding of the genome organization, after the determination of complete sequences, involves proteomics. The proteome includes the whole set of protein-protein interactions, and two recent independent studies have shown that its topology displays a number of surprising...

Andreas Wagner <p> <p> The transcription of many eukaryotic genes is regulated via cooperative interactions among transcription factors (TFs). Cooperativity may be homotypic, involving binding of only one transcription factor to multiple sites in a genes' regulatory region. It may also be heterotypic,...</p></p>

Large scale gene perturbation experiments generate information about the number of genes whose activity is directly or indirectly affected by a gene perturbation. From this information, one can numerically estimate coarse structural network features such as the total number of direct regulatory...

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...

The topology of the proteome map revealed by recent large-scale hybridization methods has shown that the distribution of protein-protein interactions is highly heterogeneous, with many proteins having few links while a few of them are heavily connected. This particular topology is shared by...