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Publications of Eduardo D. Sontag jointly with T. Riley
Articles in journal or book chapters
  1. T. Riley, X. Yu, E.D. Sontag, and A. Levine. The P53HMM algorithm: using novel profile Hidden Markov Models to detect p53-responsive genes. BMC Bioinformatics, 10:111, 2009. [PDF] [doi:10.1186/1471-2105-10-111] Keyword(s): Hidden Markov Models, p53, transcription factors.
    Abstract:
    A novel computational method (called p53HMM) is presented that utilizes Profile Hidden Markov Models (PHMM's) to estimate the relative binding affinities of putative p53 response elements (RE's), both p53 single-sites and cluster-sites. These models incorporate a novel ``Correlated Baum Welch'' training algorithm that provides increased predictive power by exploiting the redundancy of information found in the repeated, palindromic p53-binding motif. The predictive accuracy of these new models are compared against other predictive models, including position specic score matrices (PSSM's, or weight matrices). Finally, we provide experimental evidence that verifies a predicted p53-target site that regu- lates the CHMP4C gene. The P53HMM algorithm is available on-line from http://tools.csb.ias.edu.


  2. T. Riley, E.D. Sontag, P. Chen, and A. Levine. The transcriptional regulation of human p53-regulated genes. Nature Reviews Molecular Cell Biology, 9:402-412, 2008. [PDF] Keyword(s): Hidden Markov Models, p53, transcription.
    Abstract:
    The p53 protein regulates the transcription of many different genes in response to a wide variety of stress signals. Following DNA damage, p53 regulates key processes, including DNA repair, cell-cycle arrest, senescence and apoptosis, in order to suppress cancer. This Analysis article provides an overview of the current knowledge of p53-regulated genes in these pathways and others, and the mechanisms of their regulation. In addition, we present the most comprehensive list so far of human p53-regulated genes and their experimentally validated, functional binding sites that confer p53 regulation.



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Last modified: Thu Nov 23 10:40:56 2017
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