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Research Article

Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data

  • Dongjun Chung,

    Affiliations: Department of Statistics, University of Wisconsin, Madison, Wisconsin, United States of America, Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin, United States of America

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  • Pei Fen Kuan,

    Affiliation: Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, United States of America

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  • Bo Li,

    Affiliation: Department of Computer Sciences, University of Wisconsin, Madison, Wisconsin, United States of America

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  • Rajendran Sanalkumar,

    Affiliation: Wisconsin Institutes for Medical Research, UW Carbone Cancer Center, Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America

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  • Kun Liang,

    Affiliations: Department of Statistics, University of Wisconsin, Madison, Wisconsin, United States of America, Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin, United States of America

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  • Emery H. Bresnick,

    Affiliation: Wisconsin Institutes for Medical Research, UW Carbone Cancer Center, Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America

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  • Colin Dewey,

    Affiliations: Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin, United States of America, Department of Computer Sciences, University of Wisconsin, Madison, Wisconsin, United States of America

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  • Sündüz Keleş mail

    keles@stat.wisc.edu.

    Affiliations: Department of Statistics, University of Wisconsin, Madison, Wisconsin, United States of America, Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin, United States of America

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  • Published: July 14, 2011
  • DOI: 10.1371/journal.pcbi.1002111

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