[Bioinformatics] TODAY'S Bioinformatics Seminar: Richard A. Bonneau, Ph.D.
Bioinformatics IDP-Seminar Series
bioinformatics at lists.ucla.edu
Mon Dec 1 08:51:17 PST 2008
"Learning of Regulatory Modules and Predictive Models of Global Transcriptional Dynamics"
Richard A. Bonneau, Ph.D.
Department of Biology, Computer Science, New York University
TODAY, December 1, 2008
Our system for network inference and modeling consists of three major components: cMonkey (a method for learning co-regulated biclusters and pathways), the Inferelator (regulatory network inference, regulatory networks modeled as large systems of ODEs). We describe our application of these methods to Halobacterium and several other model organisms. This effort represents one of the first coordinated functional genomics effort in archaea and in particular, under hypersaline conditions. The Inferelator infers regulatory influences for genes and/or gene clusters from mRNA and/or protein expression levels. The procedure models transcriptional networks as large sets of coupled ODEs and can simultaneously model equilibrium and time-course expression levels, such that both kinetic and equilibrium expression levels may be predicted by the resulting models (or used to learn/parameterize regulatory network models). Through the explicit inclusion of time, and gene-knockout information, the method is capable of learning several causal relationships. It also includes a novel solution to the problem of encoding interactions between predictors. We discuss the results from an initial application of this method to the halophilic archaeon, Halobacterium NRC-1. We have found the network to be predictive of global regulatory dynamics over 150 newly collected microarray datasets and have also validated parts of the network using ChIP-chip. This network offers a means of deciphering how this intensely tough organism maintains homeostasis and responds to wide varieties of metabolic, genetic and environmental states.
Host: Matteo Pellegrini
*Refreshments will be served after the seminar at 5:00 pm*
IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the Bioinformatics