J's Open Publishing index

This post is an index with a one-line description of the projects I've published. Read how this blog works for more general information.

2) Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata
Description: Microarray compendia for E. coli, Shewanella, and yeast (currently 524, 530, and 14 arrays for each of these species respectively). The arrays are normalized together to allow all arrays for each species to be analyzed as a single group.
Blog post on this publication: When will gene expression data become collective knowledge?
Date work was published: Sept 18, 2007

1) Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles
Description: How well can we computationally infer regulatory interactions between transcription factors and their targets using microarray data? Predictions from several algorithms were validated using the 3500 experimentally determined interactions in RegulonDB plus and additional 300 interactions were tested with ChIP. Most importantly, once we've reliably inferred this networks, what can we do with them?
Useful resources: The microarray data used in this paper is available at M3D. In addition, we have supplemental site containing links to the algorithms and the RegulonDB known interactions we used in the publication.
Date work was published: January 9, 2007