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Research Article

RNA-Seq Mapping and Detection of Gene Fusions with a Suffix Array Algorithm

  • Onur Sakarya mail,

    osakarya@yahoo.com (OS); fiona.hyland@lifetech.com (FCH); asim.siddiqui@lifetech.com (ASS)

    Affiliation: Life Technologies, Foster City, California, United States of America

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  • Heinz Breu,

    Affiliation: Life Technologies, Foster City, California, United States of America

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  • Milan Radovich,

    Affiliation: Indiana University School of Medicine, Indianapolis, Indiana, United States of America

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  • Yongzhi Chen,

    Affiliation: Life Technologies, Foster City, California, United States of America

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  • Yulei N. Wang,

    Affiliation: Life Technologies, Foster City, California, United States of America

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  • Catalin Barbacioru,

    Affiliation: Life Technologies, Foster City, California, United States of America

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  • Sowmi Utiramerur,

    Affiliation: Life Technologies, Foster City, California, United States of America

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  • Penn P. Whitley,

    Affiliation: Life Technologies (Ambion), Austin, Texas, United States of America

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  • Joel P. Brockman,

    Affiliation: Life Technologies (Ambion), Austin, Texas, United States of America

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  • Paolo Vatta,

    Affiliation: Life Technologies, Foster City, California, United States of America

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  • Zheng Zhang,

    Affiliation: Life Technologies, Foster City, California, United States of America

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  • Liviu Popescu,

    Affiliation: Life Technologies, Foster City, California, United States of America

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  • Matthew W. Muller,

    Affiliation: Life Technologies, Foster City, California, United States of America

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  • Vidya Kudlingar,

    Affiliation: Life Technologies, Foster City, California, United States of America

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  • Nriti Garg,

    Affiliation: Life Technologies, Foster City, California, United States of America

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  • Chieh-Yuan Li,

    Affiliation: Life Technologies, Foster City, California, United States of America

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  • Benjamin S. Kong,

    Affiliation: Life Technologies, Foster City, California, United States of America

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  • John P. Bodeau,

    Affiliation: Life Technologies, Foster City, California, United States of America

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  • Robert C. Nutter,

    Affiliation: Life Technologies, Foster City, California, United States of America

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  • Jian Gu,

    Affiliation: Life Technologies (Ambion), Austin, Texas, United States of America

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  • Kelli S. Bramlett,

    Affiliation: Life Technologies (Ambion), Austin, Texas, United States of America

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  • Jeffrey K. Ichikawa,

    Affiliation: Life Technologies, Foster City, California, United States of America

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  • Fiona C. Hyland mail,

    osakarya@yahoo.com (OS); fiona.hyland@lifetech.com (FCH); asim.siddiqui@lifetech.com (ASS)

    Affiliation: Life Technologies, Foster City, California, United States of America

    X
  • Asim S. Siddiqui mail

    osakarya@yahoo.com (OS); fiona.hyland@lifetech.com (FCH); asim.siddiqui@lifetech.com (ASS)

    Affiliation: Life Technologies, Foster City, California, United States of America

    X
  • Published: April 05, 2012
  • DOI: 10.1371/journal.pcbi.1002464

About the Authors

Onur Sakarya, Heinz Breu, Yongzhi Chen, Yulei N. Wang, Catalin Barbacioru, Sowmi Utiramerur, Paolo Vatta, Zheng Zhang, Liviu Popescu, Matthew W. Muller, Vidya Kudlingar, Nriti Garg, Chieh-Yuan Li, Benjamin S. Kong, John P. Bodeau, Robert C. Nutter, Jeffrey K. Ichikawa, Fiona C. Hyland, Asim S. Siddiqui
Life Technologies, Foster City, California, United States of America
Milan Radovich
Indiana University School of Medicine, Indianapolis, Indiana, United States of America
Penn P. Whitley, Joel P. Brockman, Jian Gu, Kelli S. Bramlett
Life Technologies (Ambion), Austin, Texas, United States of America

Corresponding Authors

Competing Interests

I have read the journal's policy and have the following conflicts. Some of the authors are employees of Life Technologies Corporation.

Author Contributions

Conceived and designed the experiments: OS PV HBB MR JG KSB FCH ASS. Performed the experiments: OS HBB YC YNW CB SU ZZ LP MWM VK NG C-YL BSK JPB JG. Analyzed the data: OS MR YNW PPW PV FCH. Contributed reagents/materials/analysis tools: YNW JPB RCN KSB JKI FCH ASS. Wrote the paper: OS FCH ASS.