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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)
1. CC-BY-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not. Abstract Polygenic scores (PGS) summarize the genetic contribution of a person's genotype to a disease or phenotype. They are useful in a wide variety of analyses of genetic data. Many possible ways(More)
45 Seq), but mapping and assembling the resulting reads are challenging owing to the complexities introduced by RNA splicing. The two methods are the first that robustly assemble full-length transcripts, including alternative splicing iso-forms. In contrast to previous approaches, these two methods first map reads to the genome using software that takes(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)
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