Probabilistic Inference for Nucleosome Positioning with MNase-Based or Sonicated Short-Read Data

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dc.contributor.authorZhang, Xuekui
dc.contributor.authorRobertson, G.
dc.contributor.authorWoo, S.
dc.contributor.authorHoffman, B.G.
dc.contributor.authorGottardo, R.
dc.date.accessioned2021-08-18T18:32:34Z
dc.date.available2021-08-18T18:32:34Z
dc.date.copyright2012en_US
dc.date.issued2012
dc.description.abstractWe describe a model-based method, PING, for predicting nucleosome positions in MNase-Seq and MNase- or sonicated- ChIP-Seq data. PING compares favorably to NPS and TemplateFilter in scalability, accuracy and robustness to low read density. To demonstrate that PING predictions from widely available sonicated data can have sufficient spatial resolution to be to be useful for biological inference, we use Illumina H3K4me1 ChIP-seq data to detect changes in nucleosome positioning around transcription factor binding sites due to tamoxifen stimulation, to discriminate functional and nonfunctional transcription factor binding sites more effectively than with enrichment profiles, and to confirm that the pioneer transcription factor Foxa2 associates with the accessible major groove of nucleosomal DNA.en_US
dc.description.reviewstatusRevieweden_US
dc.description.scholarlevelFacultyen_US
dc.description.sponsorshipRG was supported by National Insititutes of Health HG005692. XZ was supported by Natural Sciences and Engineering Research Council of Canada via the Alexander Graham Bell Canada Graduate Scholarships.en_US
dc.identifier.citationZhang, X., Robertson, G., Woo, S., Hoffman, B.G., Gottardo, R. (2012). Probabilistic Inference for Nucleosome Positioning with MNase-Based or Sonicated Short-Read Data. PLoS ONE, 7(2). https://doi.org/10.1371/journal.pone.0032095en_US
dc.identifier.urihttps://doi.org/10.1371/journal.pone.0032095
dc.identifier.urihttp://hdl.handle.net/1828/13278
dc.language.isoenen_US
dc.publisherPLoS ONEen_US
dc.subject.departmentDepartment of Mathematics and Statistics
dc.titleProbabilistic Inference for Nucleosome Positioning with MNase-Based or Sonicated Short-Read Dataen_US
dc.typeArticleen_US

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