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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

About the Authors

Dongjun Chung, Kun Liang, Sündüz Keleş
Department of Statistics, University of Wisconsin, Madison, Wisconsin, United States of America
Dongjun Chung, Kun Liang, Colin Dewey, Sündüz Keleş
Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin, United States of America
Pei Fen Kuan
Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, United States of America
Bo Li, Colin Dewey
Department of Computer Sciences, University of Wisconsin, Madison, Wisconsin, United States of America
Rajendran Sanalkumar, Emery H. Bresnick
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

Corresponding Author

Email: keles@stat.wisc.edu.

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: DC SK. Performed the experiments: DC PFK BL RS KL SK. Analyzed the data: DC PFK BL KL. Contributed reagents/materials/analysis tools: BL RS EHB CD. Wrote the paper: DC CD SK.