H. Craig Mak

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Failure of cells to respond to DNA damage is a primary event associated with mutagenesis and environmental toxicity. To map the transcriptional network controlling the damage response, we measured genomewide binding locations for 30 damage-related transcription factors (TFs) after exposure of yeast to methyl-methanesulfonate (MMS). The resulting 5272(More)
Transcription factors are most commonly thought of as proteins that regulate expression of specific genes, independently of the order of those genes along the chromosome. By screening genome-wide chromatin immunoprecipitation (ChIP) profiles in yeast, we find that more than 10% of DNA-binding transcription factors concentrate at the subtelomeric regions(More)
As genome-scale measurements lead to increasingly complex models of gene regulation, systematic approaches are needed to validate and refine these models. Towards this goal, we describe an automated procedure for prioritizing genetic perturbations in order to discriminate optimally between alternative models of a gene-regulatory network. Using this(More)
CellCircuits (http://www.cellcircuits.org) is an open-access database of molecular network models, designed to bridge the gap between databases of individual pairwise molecular interactions and databases of validated pathways. CellCircuits captures the output from an increasing number of approaches that screen molecular interaction networks to identify(More)
  • T Wucherpfennig, M Wilsch-Brauninger, +34 authors Trey Ideker
  • 2006
to a decrease in the density of presynaptic Ca 2þ channel clusters. It is conceivable that BRP tightly surrounds but is not part of the T-bar structure, contained within the unlabeled center of donuts. BRP may establish a matrix, required for both T-bar assembly as well as the appropriate localization of active zone components including Ca 2þ channels,(More)
The concept of multi-plane ad hoc networks is introduced for two emerging applications, namely, multi-plane three-dimensional indoor topologies and virtual multi-plane routing in dense networks. The connectivity between different planes is established with the use of distributed gateways consisting of a prescribed number of interconnected nodes on each(More)
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